Starting phenix.real_space_refine on Wed Aug 5 01:15:40 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9pdv_71545/08_2026/9pdv_71545.cif Found real_map, /net/cci-nas-00/data/ceres_data/9pdv_71545/08_2026/9pdv_71545.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9pdv_71545/08_2026/9pdv_71545.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9pdv_71545/08_2026/9pdv_71545.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9pdv_71545/08_2026/9pdv_71545.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9pdv_71545/08_2026/9pdv_71545.map" } resolution = 3.1 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= 0.004 sd= 0.032 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 5700 2.51 5 N 1100 2.21 5 O 1100 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 51 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 7900 Number of models: 1 Model: "" Number of chains: 200 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: "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: "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: "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: "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: "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: "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: "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: "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: "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: "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: "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: "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: "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: "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: "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: "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: "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: "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: "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: "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: "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: "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: "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: "a" 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: "a" 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: "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: "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: "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: "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: "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: "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: "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: "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: "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: "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: "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: "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: "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: "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: "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: "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: "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: "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: "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: "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: "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: "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: "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: "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: "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: "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: "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: "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: "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: "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: "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: "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: "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: "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: "AZ" 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: "AZ" 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: "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: "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: "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: "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: "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: "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: "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: "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: "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: "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: "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: "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: "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: "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: "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: "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: "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: "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: "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: "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: "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: "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: "Az" 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: "Az" 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: "A1" 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: "A1" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "A2" 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: "A2" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "A4" 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: "A4" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "A3" 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: "A3" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "A5" 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: "A5" 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: 2.16, per 1000 atoms: 0.27 Number of scatterers: 7900 At special positions: 0 Unit cell: (100.43, 100.43, 63.91, 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 1100 8.00 N 1100 7.00 C 5700 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=100, symmetry=0 Number of additional bonds: simple=100, symmetry=0 Coordination: Other bonds: Time building additional restraints: 0.64 Conformation dependent library (CDL) restraints added in 277.0 milliseconds 1200 Ramachandran restraints generated. 600 Oldfield, 0 Emsley, 600 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1400 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 20 sheets defined 0.0% alpha, 35.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.23 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'T' and resid 5 through 6 removed outlier: 3.829A pdb=" N PHE T 5 " --> pdb=" O PHE n 3 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N PHE n 3 " --> pdb=" O PHE T 5 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'p' and resid 2 through 7 removed outlier: 6.080A pdb=" N LYS i 2 " --> pdb=" O PHE q 3 " (cutoff:3.500A) removed outlier: 7.645A pdb=" N PHE q 5 " --> pdb=" O LYS i 2 " (cutoff:3.500A) removed outlier: 6.011A pdb=" N GLY i 4 " --> pdb=" O PHE q 5 " (cutoff:3.500A) removed outlier: 7.550A pdb=" N PHE q 7 " --> pdb=" O GLY i 4 " (cutoff:3.500A) removed outlier: 6.602A pdb=" N LYS i 6 " --> pdb=" O PHE q 7 " (cutoff:3.500A) removed outlier: 6.065A pdb=" N LYS j 2 " --> pdb=" O PHE s 3 " (cutoff:3.500A) removed outlier: 7.636A pdb=" N PHE s 5 " --> pdb=" O LYS j 2 " (cutoff:3.500A) removed outlier: 5.993A pdb=" N GLY j 4 " --> pdb=" O PHE s 5 " (cutoff:3.500A) removed outlier: 7.542A pdb=" N PHE s 7 " --> pdb=" O GLY j 4 " (cutoff:3.500A) removed outlier: 6.570A pdb=" N LYS j 6 " --> pdb=" O PHE s 7 " (cutoff:3.500A) removed outlier: 6.158A pdb=" N LYS k 2 " --> pdb=" O PHE u 3 " (cutoff:3.500A) removed outlier: 7.706A pdb=" N PHE u 5 " --> pdb=" O LYS k 2 " (cutoff:3.500A) removed outlier: 6.040A pdb=" N GLY k 4 " --> pdb=" O PHE u 5 " (cutoff:3.500A) removed outlier: 7.520A pdb=" N PHE u 7 " --> pdb=" O GLY k 4 " (cutoff:3.500A) removed outlier: 6.522A pdb=" N LYS k 6 " --> pdb=" O PHE u 7 " (cutoff:3.500A) removed outlier: 6.137A pdb=" N LYS l 2 " --> pdb=" O PHE w 3 " (cutoff:3.500A) removed outlier: 7.676A pdb=" N PHE w 5 " --> pdb=" O LYS l 2 " (cutoff:3.500A) removed outlier: 6.013A pdb=" N GLY l 4 " --> pdb=" O PHE w 5 " (cutoff:3.500A) removed outlier: 7.554A pdb=" N PHE w 7 " --> pdb=" O GLY l 4 " (cutoff:3.500A) removed outlier: 6.650A pdb=" N LYS l 6 " --> pdb=" O PHE w 7 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'U' and resid 5 through 6 removed outlier: 3.709A pdb=" N PHE U 5 " --> pdb=" O PHE o 3 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N PHE o 3 " --> pdb=" O PHE U 5 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'V' and resid 5 through 6 removed outlier: 3.704A pdb=" N PHE V 5 " --> pdb=" O PHE r 3 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N PHE r 3 " --> pdb=" O PHE V 5 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'Y' and resid 5 through 6 removed outlier: 3.840A pdb=" N PHE Y 5 " --> pdb=" O PHE y 3 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N PHE y 3 " --> pdb=" O PHE Y 5 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'z' and resid 2 through 7 removed outlier: 6.081A pdb=" N LYS x 2 " --> pdb=" O PHE 3 3 " (cutoff:3.500A) removed outlier: 7.646A pdb=" N PHE 3 5 " --> pdb=" O LYS x 2 " (cutoff:3.500A) removed outlier: 6.013A pdb=" N GLY x 4 " --> pdb=" O PHE 3 5 " (cutoff:3.500A) removed outlier: 7.552A pdb=" N PHE 3 7 " --> pdb=" O GLY x 4 " (cutoff:3.500A) removed outlier: 6.608A pdb=" N LYS x 6 " --> pdb=" O PHE 3 7 " (cutoff:3.500A) removed outlier: 6.063A pdb=" N LYS 1 2 " --> pdb=" O PHE 6 3 " (cutoff:3.500A) removed outlier: 7.637A pdb=" N PHE 6 5 " --> pdb=" O LYS 1 2 " (cutoff:3.500A) removed outlier: 6.001A pdb=" N GLY 1 4 " --> pdb=" O PHE 6 5 " (cutoff:3.500A) removed outlier: 7.540A pdb=" N PHE 6 7 " --> pdb=" O GLY 1 4 " (cutoff:3.500A) removed outlier: 6.605A pdb=" N LYS 1 6 " --> pdb=" O PHE 6 7 " (cutoff:3.500A) removed outlier: 6.152A pdb=" N LYS 4 2 " --> pdb=" O PHE 9 3 " (cutoff:3.500A) removed outlier: 7.691A pdb=" N PHE 9 5 " --> pdb=" O LYS 4 2 " (cutoff:3.500A) removed outlier: 6.002A pdb=" N GLY 4 4 " --> pdb=" O PHE 9 5 " (cutoff:3.500A) removed outlier: 7.545A pdb=" N PHE 9 7 " --> pdb=" O GLY 4 4 " (cutoff:3.500A) removed outlier: 6.608A pdb=" N LYS 4 6 " --> pdb=" O PHE 9 7 " (cutoff:3.500A) removed outlier: 6.132A pdb=" N LYS 7 2 " --> pdb=" O PHEAB 3 " (cutoff:3.500A) removed outlier: 7.676A pdb=" N PHEAB 5 " --> pdb=" O LYS 7 2 " (cutoff:3.500A) removed outlier: 6.012A pdb=" N GLY 7 4 " --> pdb=" O PHEAB 5 " (cutoff:3.500A) removed outlier: 7.547A pdb=" N PHEAB 7 " --> pdb=" O GLY 7 4 " (cutoff:3.500A) removed outlier: 6.648A pdb=" N LYS 7 6 " --> pdb=" O PHEAB 7 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'Z' and resid 5 through 6 removed outlier: 3.657A pdb=" N PHE Z 5 " --> pdb=" O PHE 2 3 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N PHE 2 3 " --> pdb=" O PHE Z 5 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'a' and resid 5 through 6 removed outlier: 3.699A pdb=" N PHE a 5 " --> pdb=" O PHE 5 3 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N PHE 5 3 " --> pdb=" O PHE a 5 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'd' and resid 5 through 6 removed outlier: 3.836A pdb=" N PHE d 5 " --> pdb=" O PHEAD 3 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N PHEAD 3 " --> pdb=" O PHE d 5 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'AE' and resid 2 through 7 removed outlier: 6.077A pdb=" N LYSAC 2 " --> pdb=" O PHEAH 3 " (cutoff:3.500A) removed outlier: 7.647A pdb=" N PHEAH 5 " --> pdb=" O LYSAC 2 " (cutoff:3.500A) removed outlier: 6.021A pdb=" N GLYAC 4 " --> pdb=" O PHEAH 5 " (cutoff:3.500A) removed outlier: 7.560A pdb=" N PHEAH 7 " --> pdb=" O GLYAC 4 " (cutoff:3.500A) removed outlier: 6.602A pdb=" N LYSAC 6 " --> pdb=" O PHEAH 7 " (cutoff:3.500A) removed outlier: 6.082A pdb=" N LYSAF 2 " --> pdb=" O PHEAK 3 " (cutoff:3.500A) removed outlier: 7.647A pdb=" N PHEAK 5 " --> pdb=" O LYSAF 2 " (cutoff:3.500A) removed outlier: 6.002A pdb=" N GLYAF 4 " --> pdb=" O PHEAK 5 " (cutoff:3.500A) removed outlier: 7.549A pdb=" N PHEAK 7 " --> pdb=" O GLYAF 4 " (cutoff:3.500A) removed outlier: 6.591A pdb=" N LYSAF 6 " --> pdb=" O PHEAK 7 " (cutoff:3.500A) removed outlier: 6.155A pdb=" N LYSAI 2 " --> pdb=" O PHEAN 3 " (cutoff:3.500A) removed outlier: 7.686A pdb=" N PHEAN 5 " --> pdb=" O LYSAI 2 " (cutoff:3.500A) removed outlier: 6.003A pdb=" N GLYAI 4 " --> pdb=" O PHEAN 5 " (cutoff:3.500A) removed outlier: 7.541A pdb=" N PHEAN 7 " --> pdb=" O GLYAI 4 " (cutoff:3.500A) removed outlier: 6.605A pdb=" N LYSAI 6 " --> pdb=" O PHEAN 7 " (cutoff:3.500A) removed outlier: 6.103A pdb=" N LYSAL 2 " --> pdb=" O PHEAQ 3 " (cutoff:3.500A) removed outlier: 7.648A pdb=" N PHEAQ 5 " --> pdb=" O LYSAL 2 " (cutoff:3.500A) removed outlier: 6.004A pdb=" N GLYAL 4 " --> pdb=" O PHEAQ 5 " (cutoff:3.500A) removed outlier: 7.535A pdb=" N PHEAQ 7 " --> pdb=" O GLYAL 4 " (cutoff:3.500A) removed outlier: 6.638A pdb=" N LYSAL 6 " --> pdb=" O PHEAQ 7 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'e' and resid 5 through 6 removed outlier: 3.717A pdb=" N PHE e 5 " --> pdb=" O PHEAG 3 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N PHEAG 3 " --> pdb=" O PHE e 5 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'f' and resid 5 through 6 removed outlier: 3.686A pdb=" N PHE f 5 " --> pdb=" O PHEAJ 3 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N PHEAJ 3 " --> pdb=" O PHE f 5 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 Processing sheet with id=AB4, first strand: chain 'AR' and resid 5 through 6 removed outlier: 3.838A pdb=" N PHEAR 5 " --> pdb=" O PHEAT 3 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N PHEAT 3 " --> pdb=" O PHEAR 5 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB4 Processing sheet with id=AB5, first strand: chain 'AU' and resid 2 through 7 removed outlier: 6.077A pdb=" N LYSAS 2 " --> pdb=" O PHEAY 3 " (cutoff:3.500A) removed outlier: 7.642A pdb=" N PHEAY 5 " --> pdb=" O LYSAS 2 " (cutoff:3.500A) removed outlier: 6.019A pdb=" N GLYAS 4 " --> pdb=" O PHEAY 5 " (cutoff:3.500A) removed outlier: 7.559A pdb=" N PHEAY 7 " --> pdb=" O GLYAS 4 " (cutoff:3.500A) removed outlier: 6.605A pdb=" N LYSAS 6 " --> pdb=" O PHEAY 7 " (cutoff:3.500A) removed outlier: 6.072A pdb=" N LYSAW 2 " --> pdb=" O PHEAc 3 " (cutoff:3.500A) removed outlier: 7.641A pdb=" N PHEAc 5 " --> pdb=" O LYSAW 2 " (cutoff:3.500A) removed outlier: 5.996A pdb=" N GLYAW 4 " --> pdb=" O PHEAc 5 " (cutoff:3.500A) removed outlier: 7.543A pdb=" N PHEAc 7 " --> pdb=" O GLYAW 4 " (cutoff:3.500A) removed outlier: 6.576A pdb=" N LYSAW 6 " --> pdb=" O PHEAc 7 " (cutoff:3.500A) removed outlier: 6.151A pdb=" N LYSAa 2 " --> pdb=" O PHEAg 3 " (cutoff:3.500A) removed outlier: 7.689A pdb=" N PHEAg 5 " --> pdb=" O LYSAa 2 " (cutoff:3.500A) removed outlier: 6.010A pdb=" N GLYAa 4 " --> pdb=" O PHEAg 5 " (cutoff:3.500A) removed outlier: 7.526A pdb=" N PHEAg 7 " --> pdb=" O GLYAa 4 " (cutoff:3.500A) removed outlier: 6.530A pdb=" N LYSAa 6 " --> pdb=" O PHEAg 7 " (cutoff:3.500A) removed outlier: 6.129A pdb=" N LYSAe 2 " --> pdb=" O PHEAk 3 " (cutoff:3.500A) removed outlier: 7.677A pdb=" N PHEAk 5 " --> pdb=" O LYSAe 2 " (cutoff:3.500A) removed outlier: 6.014A pdb=" N GLYAe 4 " --> pdb=" O PHEAk 5 " (cutoff:3.500A) removed outlier: 7.552A pdb=" N PHEAk 7 " --> pdb=" O GLYAe 4 " (cutoff:3.500A) removed outlier: 6.656A pdb=" N LYSAe 6 " --> pdb=" O PHEAk 7 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'AV' and resid 5 through 6 removed outlier: 3.716A pdb=" N PHEAV 5 " --> pdb=" O PHEAX 3 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N PHEAX 3 " --> pdb=" O PHEAV 5 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB6 Processing sheet with id=AB7, first strand: chain 'AZ' and resid 5 through 6 removed outlier: 3.683A pdb=" N PHEAZ 5 " --> pdb=" O PHEAb 3 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N PHEAb 3 " --> pdb=" O PHEAZ 5 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB7 Processing sheet with id=AB8, first strand: chain 'Al' and resid 5 through 6 removed outlier: 3.837A pdb=" N PHEAl 5 " --> pdb=" O PHEAn 3 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N PHEAn 3 " --> pdb=" O PHEAl 5 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB8 Processing sheet with id=AB9, first strand: chain 'Ao' and resid 2 through 7 removed outlier: 6.061A pdb=" N LYSAm 2 " --> pdb=" O PHEAs 3 " (cutoff:3.500A) removed outlier: 7.626A pdb=" N PHEAs 5 " --> pdb=" O LYSAm 2 " (cutoff:3.500A) removed outlier: 6.011A pdb=" N GLYAm 4 " --> pdb=" O PHEAs 5 " (cutoff:3.500A) removed outlier: 7.544A pdb=" N PHEAs 7 " --> pdb=" O GLYAm 4 " (cutoff:3.500A) removed outlier: 6.619A pdb=" N LYSAm 6 " --> pdb=" O PHEAs 7 " (cutoff:3.500A) removed outlier: 6.083A pdb=" N LYSAq 2 " --> pdb=" O PHEAw 3 " (cutoff:3.500A) removed outlier: 7.658A pdb=" N PHEAw 5 " --> pdb=" O LYSAq 2 " (cutoff:3.500A) removed outlier: 6.000A pdb=" N GLYAq 4 " --> pdb=" O PHEAw 5 " (cutoff:3.500A) removed outlier: 7.539A pdb=" N PHEAw 7 " --> pdb=" O GLYAq 4 " (cutoff:3.500A) removed outlier: 6.529A pdb=" N LYSAq 6 " --> pdb=" O PHEAw 7 " (cutoff:3.500A) removed outlier: 6.154A pdb=" N LYSAu 2 " --> pdb=" O PHEA1 3 " (cutoff:3.500A) removed outlier: 7.688A pdb=" N PHEA1 5 " --> pdb=" O LYSAu 2 " (cutoff:3.500A) removed outlier: 6.001A pdb=" N GLYAu 4 " --> pdb=" O PHEA1 5 " (cutoff:3.500A) removed outlier: 7.525A pdb=" N PHEA1 7 " --> pdb=" O GLYAu 4 " (cutoff:3.500A) removed outlier: 6.545A pdb=" N LYSAu 6 " --> pdb=" O PHEA1 7 " (cutoff:3.500A) removed outlier: 6.133A pdb=" N LYSAy 2 " --> pdb=" O PHEA5 3 " (cutoff:3.500A) removed outlier: 7.675A pdb=" N PHEA5 5 " --> pdb=" O LYSAy 2 " (cutoff:3.500A) removed outlier: 6.011A pdb=" N GLYAy 4 " --> pdb=" O PHEA5 5 " (cutoff:3.500A) removed outlier: 7.546A pdb=" N PHEA5 7 " --> pdb=" O GLYAy 4 " (cutoff:3.500A) removed outlier: 6.653A pdb=" N LYSAy 6 " --> pdb=" O PHEA5 7 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'Ap' and resid 5 through 6 removed outlier: 3.719A pdb=" N PHEAp 5 " --> pdb=" O PHEAr 3 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N PHEAr 3 " --> pdb=" O PHEAp 5 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC1 Processing sheet with id=AC2, first strand: chain 'At' and resid 5 through 6 removed outlier: 3.687A pdb=" N PHEAt 5 " --> pdb=" O PHEAv 3 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N PHEAv 3 " --> pdb=" O PHEAt 5 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC2 125 hydrogen bonds defined for protein. 375 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: 0.99 Time building geometry restraints manager: 0.81 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: 846 1.26 - 1.33: 953 1.33 - 1.41: 2401 1.41 - 1.48: 900 1.48 - 1.56: 3000 Bond restraints: 8100 Sorted by residual: bond pdb=" C ACE 9 0 " pdb=" N PHE 9 1 " ideal model delta sigma weight residual 1.329 1.455 -0.126 2.00e-02 2.50e+03 4.00e+01 bond pdb=" C ACE T 0 " pdb=" N PHE T 1 " ideal model delta sigma weight residual 1.329 1.455 -0.126 2.00e-02 2.50e+03 3.99e+01 bond pdb=" C ACEA1 0 " pdb=" N PHEA1 1 " ideal model delta sigma weight residual 1.329 1.455 -0.126 2.00e-02 2.50e+03 3.98e+01 bond pdb=" C ACEAZ 0 " pdb=" N PHEAZ 1 " ideal model delta sigma weight residual 1.329 1.455 -0.126 2.00e-02 2.50e+03 3.97e+01 bond pdb=" C ACE d 0 " pdb=" N PHE d 1 " ideal model delta sigma weight residual 1.329 1.455 -0.126 2.00e-02 2.50e+03 3.96e+01 ... (remaining 8095 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.63: 9184 1.63 - 3.26: 772 3.26 - 4.89: 392 4.89 - 6.52: 16 6.52 - 8.15: 36 Bond angle restraints: 10400 Sorted by residual: angle pdb=" CA PHE y 7 " pdb=" C PHE y 7 " pdb=" N GLU y 8 " ideal model delta sigma weight residual 119.46 116.01 3.45 6.10e-01 2.69e+00 3.20e+01 angle pdb=" CA PHE n 7 " pdb=" C PHE n 7 " pdb=" N GLU n 8 " ideal model delta sigma weight residual 119.46 116.04 3.42 6.10e-01 2.69e+00 3.15e+01 angle pdb=" CA PHEAn 7 " pdb=" C PHEAn 7 " pdb=" N GLUAn 8 " ideal model delta sigma weight residual 119.46 116.05 3.41 6.10e-01 2.69e+00 3.12e+01 angle pdb=" CA PHEAT 7 " pdb=" C PHEAT 7 " pdb=" N GLUAT 8 " ideal model delta sigma weight residual 119.46 116.07 3.39 6.10e-01 2.69e+00 3.10e+01 angle pdb=" CA PHEAD 7 " pdb=" C PHEAD 7 " pdb=" N GLUAD 8 " ideal model delta sigma weight residual 119.46 116.08 3.38 6.10e-01 2.69e+00 3.08e+01 ... (remaining 10395 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.99: 3784 35.99 - 71.99: 336 71.99 - 107.98: 5 107.98 - 143.98: 0 143.98 - 179.97: 75 Dihedral angle restraints: 4200 sinusoidal: 2100 harmonic: 2100 Sorted by residual: dihedral pdb=" CH3 ACE p 0 " pdb=" C ACE p 0 " pdb=" N PHE p 1 " pdb=" CA PHE p 1 " ideal model delta sinusoidal sigma weight residual -180.00 -0.03 -179.97 1 5.00e+00 4.00e-02 7.68e+02 dihedral pdb=" CH3 ACE z 0 " pdb=" C ACE z 0 " pdb=" N PHE z 1 " pdb=" CA PHE z 1 " ideal model delta sinusoidal sigma weight residual -180.00 -0.04 -179.96 1 5.00e+00 4.00e-02 7.68e+02 dihedral pdb=" CH3 ACE m 0 " pdb=" C ACE m 0 " pdb=" N PHE m 1 " pdb=" CA PHE m 1 " ideal model delta sinusoidal sigma weight residual 180.00 0.04 179.96 1 5.00e+00 4.00e-02 7.68e+02 ... (remaining 4197 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.045: 598 0.045 - 0.090: 52 0.090 - 0.136: 25 0.136 - 0.181: 0 0.181 - 0.226: 25 Chirality restraints: 700 Sorted by residual: chirality pdb=" CA GLUAM 8 " pdb=" N GLUAM 8 " pdb=" C GLUAM 8 " pdb=" CB GLUAM 8 " both_signs ideal model delta sigma weight residual False 2.51 2.28 0.23 2.00e-01 2.50e+01 1.28e+00 chirality pdb=" CA GLU t 8 " pdb=" N GLU t 8 " pdb=" C GLU t 8 " pdb=" CB GLU t 8 " both_signs ideal model delta sigma weight residual False 2.51 2.29 0.22 2.00e-01 2.50e+01 1.24e+00 chirality pdb=" CA GLUAf 8 " pdb=" N GLUAf 8 " pdb=" C GLUAf 8 " pdb=" CB GLUAf 8 " both_signs ideal model delta sigma weight residual False 2.51 2.29 0.22 2.00e-01 2.50e+01 1.24e+00 ... (remaining 697 not shown) Planarity restraints: 1300 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLY Y 4 " 0.003 2.00e-02 2.50e+03 6.26e-03 3.92e-01 pdb=" C GLY Y 4 " -0.011 2.00e-02 2.50e+03 pdb=" O GLY Y 4 " 0.004 2.00e-02 2.50e+03 pdb=" N PHE Y 5 " 0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLY W 4 " 0.003 2.00e-02 2.50e+03 5.73e-03 3.28e-01 pdb=" C GLY W 4 " -0.010 2.00e-02 2.50e+03 pdb=" O GLY W 4 " 0.004 2.00e-02 2.50e+03 pdb=" N PHE W 5 " 0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLYAd 4 " 0.003 2.00e-02 2.50e+03 5.60e-03 3.14e-01 pdb=" C GLYAd 4 " -0.010 2.00e-02 2.50e+03 pdb=" O GLYAd 4 " 0.004 2.00e-02 2.50e+03 pdb=" N PHEAd 5 " 0.003 2.00e-02 2.50e+03 ... (remaining 1297 not shown) Histogram of nonbonded interaction distances: 2.35 - 2.86: 2898 2.86 - 3.37: 5173 3.37 - 3.88: 13771 3.88 - 4.39: 16143 4.39 - 4.90: 27850 Nonbonded interactions: 65835 Sorted by model distance: nonbonded pdb=" NZ LYSA1 6 " pdb=" OE1 GLUA1 8 " model vdw 2.352 3.120 nonbonded pdb=" NZ LYSAg 6 " pdb=" OE1 GLUAg 8 " model vdw 2.379 3.120 nonbonded pdb=" NZ LYSAU 6 " pdb=" OE1 GLUAU 8 " model vdw 2.380 3.120 nonbonded pdb=" NZ LYS u 6 " pdb=" OE1 GLU u 8 " model vdw 2.384 3.120 nonbonded pdb=" NZ LYSAE 6 " pdb=" OE1 GLUAE 8 " model vdw 2.385 3.120 ... (remaining 65830 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 'A1' selection = chain 'A2' selection = chain 'A3' selection = chain 'A4' selection = chain 'A5' 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 'AZ' 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 'Az' selection = chain 'T' selection = chain 'U' selection = chain 'V' selection = chain 'W' selection = chain 'X' selection = chain 'Y' selection = chain 'Z' selection = chain 'a' selection = chain 'b' selection = chain 'c' selection = chain 'd' selection = chain 'e' selection = chain 'f' selection = chain 'g' selection = chain 'h' selection = chain 'i' selection = chain 'j' selection = chain 'k' selection = chain 'l' selection = chain 'm' selection = chain 'n' selection = chain 'o' selection = chain 'p' selection = chain 'q' selection = chain 'r' selection = chain 's' selection = chain 't' selection = chain 'u' selection = chain 'v' selection = chain 'w' selection = chain 'x' selection = chain 'y' selection = chain 'z' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.230 Set stop_for_unknowns flag: 0.010 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: 0.170 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 8.460 Find NCS groups from input model: 0.300 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.060 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 11.340 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7881 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 0.126 8200 Z= 0.970 Angle : 1.239 8.146 10400 Z= 0.658 Chirality : 0.052 0.226 700 Planarity : 0.001 0.006 1300 Dihedral : 36.373 179.974 2800 Min Nonbonded Distance : 2.352 Molprobity Statistics. All-atom Clashscore : 5.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.50 % Favored : 87.50 % Rotamer: Outliers : 7.14 % Allowed : 26.14 % Favored : 66.71 % 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: -3.58 (0.29), residues: 600 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.72 (0.22), residues: 600 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.009 0.001 PHE 2 7 Details of bonding type rmsd/Z covalent geometry : bond 0.01592 / 0.79 ( 8100) covalent geometry : angle 1.23946 / 0.66 (10400) hydrogen bonds : bond 0.11705 / 6.86 ( 125) hydrogen bonds : angle 7.96090 / 5.07 ( 375) Misc. bond : bond 0.05173 / 2.87 ( 100) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1200 Ramachandran restraints generated. 600 Oldfield, 0 Emsley, 600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1200 Ramachandran restraints generated. 600 Oldfield, 0 Emsley, 600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 218 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 168 time to evaluate : 0.312 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: T 2 LYS cc_start: 0.7312 (tmtt) cc_final: 0.7010 (tmtt) REVERT: n 1 PHE cc_start: 0.6142 (OUTLIER) cc_final: 0.5510 (m-10) REVERT: o 1 PHE cc_start: 0.6164 (OUTLIER) cc_final: 0.5744 (m-80) REVERT: r 1 PHE cc_start: 0.6254 (OUTLIER) cc_final: 0.5922 (m-80) REVERT: t 1 PHE cc_start: 0.6371 (OUTLIER) cc_final: 0.6097 (m-80) REVERT: v 1 PHE cc_start: 0.6310 (OUTLIER) cc_final: 0.5826 (m-80) REVERT: y 1 PHE cc_start: 0.6171 (OUTLIER) cc_final: 0.5549 (m-10) REVERT: 2 1 PHE cc_start: 0.6135 (OUTLIER) cc_final: 0.5604 (m-80) REVERT: a 2 LYS cc_start: 0.7176 (tmtt) cc_final: 0.6632 (tmtt) REVERT: 5 1 PHE cc_start: 0.5974 (OUTLIER) cc_final: 0.5659 (m-80) REVERT: 8 1 PHE cc_start: 0.6236 (OUTLIER) cc_final: 0.5887 (m-80) REVERT: AA 1 PHE cc_start: 0.6088 (OUTLIER) cc_final: 0.5583 (m-80) REVERT: AD 1 PHE cc_start: 0.6262 (OUTLIER) cc_final: 0.5901 (m-80) REVERT: AG 1 PHE cc_start: 0.6061 (OUTLIER) cc_final: 0.5728 (m-80) REVERT: AJ 1 PHE cc_start: 0.6101 (OUTLIER) cc_final: 0.5838 (m-80) REVERT: AM 1 PHE cc_start: 0.6054 (OUTLIER) cc_final: 0.5759 (m-80) REVERT: AP 1 PHE cc_start: 0.6099 (OUTLIER) cc_final: 0.5563 (m-80) REVERT: AR 2 LYS cc_start: 0.7373 (tmtt) cc_final: 0.7079 (tmtt) REVERT: AT 1 PHE cc_start: 0.6318 (OUTLIER) cc_final: 0.5575 (m-10) REVERT: AX 1 PHE cc_start: 0.6181 (OUTLIER) cc_final: 0.5758 (m-80) REVERT: Ab 1 PHE cc_start: 0.6189 (OUTLIER) cc_final: 0.5911 (m-80) REVERT: Af 1 PHE cc_start: 0.6162 (OUTLIER) cc_final: 0.5949 (m-80) REVERT: Aj 1 PHE cc_start: 0.6359 (OUTLIER) cc_final: 0.5915 (m-80) REVERT: An 1 PHE cc_start: 0.6091 (OUTLIER) cc_final: 0.5375 (m-10) REVERT: Ar 1 PHE cc_start: 0.6187 (OUTLIER) cc_final: 0.5607 (m-80) REVERT: Av 1 PHE cc_start: 0.6152 (OUTLIER) cc_final: 0.5811 (m-80) REVERT: Az 1 PHE cc_start: 0.6052 (OUTLIER) cc_final: 0.5830 (m-80) REVERT: A4 1 PHE cc_start: 0.6259 (OUTLIER) cc_final: 0.5802 (m-80) outliers start: 50 outliers final: 0 residues processed: 218 average time/residue: 0.1234 time to fit residues: 33.9808 Evaluate side-chains 164 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 139 time to evaluate : 0.297 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain n residue 1 PHE Chi-restraints excluded: chain o residue 1 PHE Chi-restraints excluded: chain r residue 1 PHE Chi-restraints excluded: chain t residue 1 PHE Chi-restraints excluded: chain v residue 1 PHE Chi-restraints excluded: chain y residue 1 PHE Chi-restraints excluded: chain 2 residue 1 PHE Chi-restraints excluded: chain 5 residue 1 PHE Chi-restraints excluded: chain 8 residue 1 PHE Chi-restraints excluded: chain AA residue 1 PHE Chi-restraints excluded: chain AD residue 1 PHE Chi-restraints excluded: chain AG residue 1 PHE Chi-restraints excluded: chain AJ residue 1 PHE Chi-restraints excluded: chain AM residue 1 PHE Chi-restraints excluded: chain AP residue 1 PHE Chi-restraints excluded: chain AT residue 1 PHE Chi-restraints excluded: chain AX residue 1 PHE Chi-restraints excluded: chain Ab residue 1 PHE Chi-restraints excluded: chain Af residue 1 PHE Chi-restraints excluded: chain Aj residue 1 PHE Chi-restraints excluded: chain An residue 1 PHE Chi-restraints excluded: chain Ar residue 1 PHE Chi-restraints excluded: chain Av residue 1 PHE Chi-restraints excluded: chain Az residue 1 PHE Chi-restraints excluded: chain A4 residue 1 PHE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1 random chunks: chunk 0 optimal weight: 0.9980 overall best weight: 50.0000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3656 r_free = 0.3656 target = 0.113506 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3281 r_free = 0.3281 target = 0.086772 restraints weight = 13386.719| |-----------------------------------------------------------------------------| r_work (start): 0.3211 rms_B_bonded: 1.63 r_work: 0.3083 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.2961 rms_B_bonded: 4.18 restraints_weight: 0.2500 r_work (final): 0.2961 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8859 moved from start: 0.6965 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.060 0.195 8200 Z= 2.557 Angle : 2.521 26.614 10400 Z= 1.240 Chirality : 0.165 0.483 700 Planarity : 0.021 0.133 1300 Dihedral : 47.417 178.227 950 Min Nonbonded Distance : 1.720 Molprobity Statistics. All-atom Clashscore : 59.70 Ramachandran Plot: Outliers : 0.33 % Allowed : 32.50 % Favored : 67.17 % Rotamer: Outliers : 10.29 % Allowed : 23.57 % Favored : 66.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 1.14 % 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: -5.66 (0.22), residues: 600 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.31 (0.16), residues: 600 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.064 0.010 PHE o 1 Details of bonding type rmsd/Z covalent geometry : bond 0.06028 / 2.57 ( 8100) covalent geometry : angle 2.52142 / 1.24 (10400) hydrogen bonds : bond 0.08644 / 5.07 ( 125) hydrogen bonds : angle 7.98507 / 4.98 ( 375) Misc. bond : bond 0.00913 / 0.48 ( 100) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1200 Ramachandran restraints generated. 600 Oldfield, 0 Emsley, 600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1200 Ramachandran restraints generated. 600 Oldfield, 0 Emsley, 600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 262 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 190 time to evaluate : 0.342 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: U 2 LYS cc_start: 0.8228 (tmtt) cc_final: 0.7546 (tmtt) REVERT: t 5 PHE cc_start: 0.8574 (OUTLIER) cc_final: 0.7807 (p90) REVERT: X 2 LYS cc_start: 0.8687 (ttpp) cc_final: 0.7990 (mptt) REVERT: Y 6 LYS cc_start: 0.8758 (mmtt) cc_final: 0.8548 (mmtm) REVERT: y 1 PHE cc_start: 0.7726 (OUTLIER) cc_final: 0.7245 (t80) REVERT: 2 1 PHE cc_start: 0.7448 (OUTLIER) cc_final: 0.7146 (m-80) REVERT: b 6 LYS cc_start: 0.8634 (mmtt) cc_final: 0.8421 (mmtt) REVERT: c 2 LYS cc_start: 0.8683 (ttpp) cc_final: 0.7925 (mptt) REVERT: AD 1 PHE cc_start: 0.7618 (m-80) cc_final: 0.7412 (m-80) REVERT: e 2 LYS cc_start: 0.8020 (tmtt) cc_final: 0.7312 (tmtt) REVERT: f 2 LYS cc_start: 0.8281 (tmtt) cc_final: 0.8063 (tttp) REVERT: AM 1 PHE cc_start: 0.7502 (OUTLIER) cc_final: 0.7213 (t80) REVERT: Ab 1 PHE cc_start: 0.7470 (OUTLIER) cc_final: 0.7251 (m-80) REVERT: Ad 6 LYS cc_start: 0.8660 (mmtt) cc_final: 0.8453 (mmtt) REVERT: Ah 2 LYS cc_start: 0.8816 (ttpp) cc_final: 0.8372 (tmtt) REVERT: Al 2 LYS cc_start: 0.7981 (tmtt) cc_final: 0.7760 (tmtt) REVERT: Ap 2 LYS cc_start: 0.8307 (tmtt) cc_final: 0.7597 (tmtt) REVERT: Az 1 PHE cc_start: 0.7506 (OUTLIER) cc_final: 0.7221 (t80) REVERT: A2 2 LYS cc_start: 0.8691 (ttpp) cc_final: 0.7950 (mptt) outliers start: 72 outliers final: 43 residues processed: 231 average time/residue: 0.1850 time to fit residues: 50.2893 Evaluate side-chains 235 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 186 time to evaluate : 0.334 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain n residue 1 PHE Chi-restraints excluded: chain p residue 8 GLU Chi-restraints excluded: chain U residue 8 GLU Chi-restraints excluded: chain o residue 1 PHE Chi-restraints excluded: chain o residue 5 PHE Chi-restraints excluded: chain r residue 1 PHE Chi-restraints excluded: chain t residue 1 PHE Chi-restraints excluded: chain t residue 5 PHE Chi-restraints excluded: chain X residue 8 GLU Chi-restraints excluded: chain v residue 1 PHE Chi-restraints excluded: chain v residue 5 PHE Chi-restraints excluded: chain Y residue 8 GLU Chi-restraints excluded: chain y residue 1 PHE Chi-restraints excluded: chain Z residue 8 GLU Chi-restraints excluded: chain 2 residue 1 PHE Chi-restraints excluded: chain 5 residue 1 PHE Chi-restraints excluded: chain 5 residue 5 PHE Chi-restraints excluded: chain b residue 8 GLU Chi-restraints excluded: chain 8 residue 1 PHE Chi-restraints excluded: chain c residue 8 GLU Chi-restraints excluded: chain AA residue 5 PHE Chi-restraints excluded: chain AE residue 8 GLU Chi-restraints excluded: chain e residue 8 GLU Chi-restraints excluded: chain AG residue 5 PHE Chi-restraints excluded: chain AJ residue 1 PHE Chi-restraints excluded: chain AM residue 1 PHE Chi-restraints excluded: chain h residue 8 GLU Chi-restraints excluded: chain AP residue 5 PHE Chi-restraints excluded: chain AT residue 1 PHE Chi-restraints excluded: chain AU residue 8 GLU Chi-restraints excluded: chain AV residue 8 GLU Chi-restraints excluded: chain AX residue 5 PHE Chi-restraints excluded: chain AZ residue 8 GLU Chi-restraints excluded: chain Ab residue 1 PHE Chi-restraints excluded: chain Ad residue 8 GLU Chi-restraints excluded: chain Af residue 1 PHE Chi-restraints excluded: chain Ah residue 8 GLU Chi-restraints excluded: chain Aj residue 1 PHE Chi-restraints excluded: chain Aj residue 5 PHE Chi-restraints excluded: chain Ao residue 6 LYS Chi-restraints excluded: chain Ap residue 8 GLU Chi-restraints excluded: chain Ar residue 1 PHE Chi-restraints excluded: chain Ar residue 5 PHE Chi-restraints excluded: chain At residue 8 GLU Chi-restraints excluded: chain Ax residue 8 GLU Chi-restraints excluded: chain Az residue 1 PHE Chi-restraints excluded: chain A2 residue 8 GLU Chi-restraints excluded: chain A4 residue 1 PHE Chi-restraints excluded: chain A4 residue 5 PHE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1 random chunks: chunk 0 optimal weight: 5.9990 overall best weight: 50.0000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3624 r_free = 0.3624 target = 0.110758 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3244 r_free = 0.3244 target = 0.083882 restraints weight = 15016.240| |-----------------------------------------------------------------------------| r_work (start): 0.3181 rms_B_bonded: 1.72 r_work: 0.3045 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.2923 rms_B_bonded: 4.29 restraints_weight: 0.2500 r_work (final): 0.2923 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8904 moved from start: 0.8059 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.060 0.207 8200 Z= 2.545 Angle : 2.592 25.445 10400 Z= 1.302 Chirality : 0.169 0.680 700 Planarity : 0.016 0.065 1300 Dihedral : 43.160 175.093 936 Min Nonbonded Distance : 1.806 Molprobity Statistics. All-atom Clashscore : 72.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 35.50 % Favored : 64.50 % Rotamer: Outliers : 10.00 % Allowed : 30.71 % Favored : 59.29 % Cbeta Deviations : 0.14 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 3.29 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -6.51 (0.19), residues: 600 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.96 (0.15), residues: 600 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.080 0.009 PHEAJ 5 Details of bonding type rmsd/Z covalent geometry : bond 0.06029 / 2.56 ( 8100) covalent geometry : angle 2.59236 / 1.30 (10400) hydrogen bonds : bond 0.09445 / 5.52 ( 125) hydrogen bonds : angle 8.19996 / 5.05 ( 375) Misc. bond : bond 0.00930 / 0.50 ( 100) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1200 Ramachandran restraints generated. 600 Oldfield, 0 Emsley, 600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1200 Ramachandran restraints generated. 600 Oldfield, 0 Emsley, 600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 256 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 186 time to evaluate : 0.341 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: X 2 LYS cc_start: 0.8777 (ttpp) cc_final: 0.8049 (mptt) REVERT: Y 2 LYS cc_start: 0.8246 (tmtt) cc_final: 0.8018 (tmtt) REVERT: c 2 LYS cc_start: 0.8822 (ttpp) cc_final: 0.8078 (mptt) REVERT: d 6 LYS cc_start: 0.8596 (mttm) cc_final: 0.8360 (mmtm) REVERT: AR 6 LYS cc_start: 0.8774 (mttm) cc_final: 0.8567 (mmtm) REVERT: AX 6 LYS cc_start: 0.8273 (mmtm) cc_final: 0.8006 (mmtm) REVERT: Ah 2 LYS cc_start: 0.8950 (ttpp) cc_final: 0.8491 (tmtt) REVERT: Aj 6 LYS cc_start: 0.8205 (OUTLIER) cc_final: 0.7955 (mmtt) REVERT: A2 2 LYS cc_start: 0.8829 (ttpp) cc_final: 0.8101 (mptt) REVERT: A4 1 PHE cc_start: 0.7962 (OUTLIER) cc_final: 0.7152 (m-10) outliers start: 70 outliers final: 49 residues processed: 217 average time/residue: 0.1826 time to fit residues: 46.9161 Evaluate side-chains 232 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 181 time to evaluate : 0.264 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain n residue 1 PHE Chi-restraints excluded: chain n residue 6 LYS Chi-restraints excluded: chain i residue 5 PHE Chi-restraints excluded: chain p residue 7 PHE Chi-restraints excluded: chain o residue 1 PHE Chi-restraints excluded: chain j residue 6 LYS Chi-restraints excluded: chain r residue 1 PHE Chi-restraints excluded: chain k residue 8 GLU Chi-restraints excluded: chain t residue 6 LYS Chi-restraints excluded: chain l residue 5 PHE Chi-restraints excluded: chain v residue 1 PHE Chi-restraints excluded: chain m residue 6 LYS Chi-restraints excluded: chain Y residue 8 GLU Chi-restraints excluded: chain y residue 1 PHE Chi-restraints excluded: chain y residue 6 LYS Chi-restraints excluded: chain x residue 5 PHE Chi-restraints excluded: chain z residue 7 PHE Chi-restraints excluded: chain 2 residue 1 PHE Chi-restraints excluded: chain 5 residue 1 PHE Chi-restraints excluded: chain b residue 8 GLU Chi-restraints excluded: chain 8 residue 1 PHE Chi-restraints excluded: chain c residue 8 GLU Chi-restraints excluded: chain AD residue 6 LYS Chi-restraints excluded: chain AC residue 5 PHE Chi-restraints excluded: chain AE residue 7 PHE Chi-restraints excluded: chain AE residue 8 GLU Chi-restraints excluded: chain AF residue 6 LYS Chi-restraints excluded: chain AM residue 1 PHE Chi-restraints excluded: chain AM residue 6 LYS Chi-restraints excluded: chain AT residue 1 PHE Chi-restraints excluded: chain AT residue 6 LYS Chi-restraints excluded: chain AS residue 5 PHE Chi-restraints excluded: chain AU residue 7 PHE Chi-restraints excluded: chain AU residue 8 GLU Chi-restraints excluded: chain Ad residue 8 GLU Chi-restraints excluded: chain Af residue 1 PHE Chi-restraints excluded: chain Af residue 6 LYS Chi-restraints excluded: chain Ah residue 8 GLU Chi-restraints excluded: chain Aj residue 1 PHE Chi-restraints excluded: chain Aj residue 6 LYS Chi-restraints excluded: chain Ai residue 6 LYS Chi-restraints excluded: chain An residue 6 LYS Chi-restraints excluded: chain Am residue 5 PHE Chi-restraints excluded: chain Ar residue 1 PHE Chi-restraints excluded: chain Ax residue 8 GLU Chi-restraints excluded: chain Az residue 1 PHE Chi-restraints excluded: chain Az residue 6 LYS Chi-restraints excluded: chain Ay residue 5 PHE Chi-restraints excluded: chain A2 residue 8 GLU Chi-restraints excluded: chain A4 residue 1 PHE Chi-restraints excluded: chain A3 residue 6 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1 random chunks: chunk 0 optimal weight: 5.9990 overall best weight: 50.0000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3604 r_free = 0.3604 target = 0.109241 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3226 r_free = 0.3226 target = 0.082609 restraints weight = 16185.503| |-----------------------------------------------------------------------------| r_work (start): 0.3053 rms_B_bonded: 1.83 r_work: 0.2928 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.2807 rms_B_bonded: 4.38 restraints_weight: 0.2500 r_work (final): 0.2807 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8850 moved from start: 0.8526 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.059 0.221 8200 Z= 2.515 Angle : 2.500 17.936 10400 Z= 1.257 Chirality : 0.165 0.426 700 Planarity : 0.015 0.039 1300 Dihedral : 42.832 174.895 930 Min Nonbonded Distance : 1.816 Molprobity Statistics. All-atom Clashscore : 77.45 Ramachandran Plot: Outliers : 0.50 % Allowed : 38.67 % Favored : 60.83 % Rotamer: Outliers : 11.14 % Allowed : 33.57 % Favored : 55.29 % Cbeta Deviations : 0.29 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 3.86 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -6.89 (0.18), residues: 600 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -5.25 (0.14), residues: 600 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.075 0.009 PHE 5 1 Details of bonding type rmsd/Z covalent geometry : bond 0.05960 / 2.53 ( 8100) covalent geometry : angle 2.49989 / 1.26 (10400) hydrogen bonds : bond 0.09762 / 5.69 ( 125) hydrogen bonds : angle 8.38969 / 5.17 ( 375) Misc. bond : bond 0.00929 / 0.49 ( 100) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1200 Ramachandran restraints generated. 600 Oldfield, 0 Emsley, 600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1200 Ramachandran restraints generated. 600 Oldfield, 0 Emsley, 600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 251 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 173 time to evaluate : 0.304 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: X 2 LYS cc_start: 0.8714 (ttpp) cc_final: 0.7925 (mptt) REVERT: c 2 LYS cc_start: 0.8722 (ttpp) cc_final: 0.7902 (mptt) REVERT: AG 1 PHE cc_start: 0.8178 (OUTLIER) cc_final: 0.7915 (m-10) REVERT: AJ 1 PHE cc_start: 0.8226 (OUTLIER) cc_final: 0.7982 (m-10) REVERT: AR 6 LYS cc_start: 0.8753 (mttm) cc_final: 0.8477 (mmtm) REVERT: AX 6 LYS cc_start: 0.8194 (mmtm) cc_final: 0.7914 (mmtm) REVERT: Ad 6 LYS cc_start: 0.8565 (mmtt) cc_final: 0.8208 (mmtt) REVERT: Aj 6 LYS cc_start: 0.8138 (OUTLIER) cc_final: 0.7884 (mmtt) REVERT: A2 2 LYS cc_start: 0.8787 (ttpp) cc_final: 0.7977 (mptt) REVERT: A4 6 LYS cc_start: 0.8261 (mmtm) cc_final: 0.7971 (mmtm) outliers start: 78 outliers final: 66 residues processed: 217 average time/residue: 0.1608 time to fit residues: 41.4319 Evaluate side-chains 236 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 167 time to evaluate : 0.311 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain n residue 1 PHE Chi-restraints excluded: chain n residue 6 LYS Chi-restraints excluded: chain i residue 5 PHE Chi-restraints excluded: chain p residue 7 PHE Chi-restraints excluded: chain o residue 1 PHE Chi-restraints excluded: chain j residue 6 LYS Chi-restraints excluded: chain r residue 1 PHE Chi-restraints excluded: chain k residue 5 PHE Chi-restraints excluded: chain k residue 8 GLU Chi-restraints excluded: chain t residue 1 PHE Chi-restraints excluded: chain t residue 6 LYS Chi-restraints excluded: chain l residue 5 PHE Chi-restraints excluded: chain v residue 1 PHE Chi-restraints excluded: chain m residue 6 LYS Chi-restraints excluded: chain Y residue 8 GLU Chi-restraints excluded: chain y residue 1 PHE Chi-restraints excluded: chain y residue 6 LYS Chi-restraints excluded: chain x residue 5 PHE Chi-restraints excluded: chain x residue 6 LYS Chi-restraints excluded: chain z residue 7 PHE Chi-restraints excluded: chain 2 residue 1 PHE Chi-restraints excluded: chain 1 residue 7 PHE Chi-restraints excluded: chain b residue 8 GLU Chi-restraints excluded: chain 8 residue 1 PHE Chi-restraints excluded: chain 7 residue 6 LYS Chi-restraints excluded: chain c residue 8 GLU Chi-restraints excluded: chain AD residue 6 LYS Chi-restraints excluded: chain AC residue 5 PHE Chi-restraints excluded: chain AE residue 8 GLU Chi-restraints excluded: chain AG residue 1 PHE Chi-restraints excluded: chain AF residue 6 LYS Chi-restraints excluded: chain AJ residue 1 PHE Chi-restraints excluded: chain AJ residue 5 PHE Chi-restraints excluded: chain AI residue 5 PHE Chi-restraints excluded: chain AM residue 1 PHE Chi-restraints excluded: chain AM residue 5 PHE Chi-restraints excluded: chain AM residue 6 LYS Chi-restraints excluded: chain AL residue 5 PHE Chi-restraints excluded: chain AO residue 6 LYS Chi-restraints excluded: chain AO residue 7 PHE Chi-restraints excluded: chain AT residue 1 PHE Chi-restraints excluded: chain AT residue 6 LYS Chi-restraints excluded: chain AS residue 5 PHE Chi-restraints excluded: chain AU residue 7 PHE Chi-restraints excluded: chain AU residue 8 GLU Chi-restraints excluded: chain Ad residue 8 GLU Chi-restraints excluded: chain Af residue 1 PHE Chi-restraints excluded: chain Af residue 5 PHE Chi-restraints excluded: chain Af residue 6 LYS Chi-restraints excluded: chain Ah residue 8 GLU Chi-restraints excluded: chain Aj residue 1 PHE Chi-restraints excluded: chain Aj residue 6 LYS Chi-restraints excluded: chain Ai residue 6 LYS Chi-restraints excluded: chain An residue 6 LYS Chi-restraints excluded: chain Am residue 5 PHE Chi-restraints excluded: chain Ao residue 7 PHE Chi-restraints excluded: chain Ar residue 1 PHE Chi-restraints excluded: chain As residue 8 GLU Chi-restraints excluded: chain Av residue 1 PHE Chi-restraints excluded: chain Av residue 5 PHE Chi-restraints excluded: chain Au residue 5 PHE Chi-restraints excluded: chain Ax residue 8 GLU Chi-restraints excluded: chain Az residue 1 PHE Chi-restraints excluded: chain Az residue 6 LYS Chi-restraints excluded: chain Ay residue 5 PHE Chi-restraints excluded: chain A2 residue 8 GLU Chi-restraints excluded: chain A4 residue 1 PHE Chi-restraints excluded: chain A3 residue 6 LYS Chi-restraints excluded: chain A3 residue 7 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1 random chunks: chunk 0 optimal weight: 5.9990 overall best weight: 50.0000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3580 r_free = 0.3580 target = 0.108179 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3214 r_free = 0.3214 target = 0.082001 restraints weight = 16674.612| |-----------------------------------------------------------------------------| r_work (start): 0.3143 rms_B_bonded: 1.82 r_work: 0.3012 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.2892 rms_B_bonded: 4.29 restraints_weight: 0.2500 r_work (final): 0.2892 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8920 moved from start: 0.8763 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.059 0.224 8200 Z= 2.508 Angle : 2.511 18.682 10400 Z= 1.258 Chirality : 0.164 0.411 700 Planarity : 0.015 0.039 1300 Dihedral : 42.996 174.551 928 Min Nonbonded Distance : 1.813 Molprobity Statistics. All-atom Clashscore : 80.46 Ramachandran Plot: Outliers : 0.67 % Allowed : 38.83 % Favored : 60.50 % Rotamer: Outliers : 15.29 % Allowed : 31.71 % Favored : 53.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 3.14 % 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: -7.00 (0.18), residues: 600 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -5.33 (0.14), residues: 600 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.074 0.009 PHEAP 1 Details of bonding type rmsd/Z covalent geometry : bond 0.05943 / 2.52 ( 8100) covalent geometry : angle 2.51128 / 1.26 (10400) hydrogen bonds : bond 0.09833 / 5.74 ( 125) hydrogen bonds : angle 8.43060 / 5.19 ( 375) Misc. bond : bond 0.00920 / 0.49 ( 100) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1200 Ramachandran restraints generated. 600 Oldfield, 0 Emsley, 600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1200 Ramachandran restraints generated. 600 Oldfield, 0 Emsley, 600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 263 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 107 poor density : 156 time to evaluate : 0.340 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: o 6 LYS cc_start: 0.8498 (OUTLIER) cc_final: 0.8194 (mmtt) REVERT: c 2 LYS cc_start: 0.8785 (ttpp) cc_final: 0.8534 (tmtt) REVERT: AG 1 PHE cc_start: 0.8244 (OUTLIER) cc_final: 0.7964 (m-80) REVERT: AG 6 LYS cc_start: 0.8340 (OUTLIER) cc_final: 0.8098 (mmtt) REVERT: AJ 1 PHE cc_start: 0.8303 (OUTLIER) cc_final: 0.7953 (m-10) REVERT: AR 6 LYS cc_start: 0.8940 (mttm) cc_final: 0.8721 (mmtm) REVERT: AX 1 PHE cc_start: 0.8292 (OUTLIER) cc_final: 0.7929 (m-10) REVERT: AX 6 LYS cc_start: 0.8441 (OUTLIER) cc_final: 0.8197 (mmtm) REVERT: Ab 6 LYS cc_start: 0.8325 (OUTLIER) cc_final: 0.7146 (mmtt) REVERT: Aj 6 LYS cc_start: 0.8378 (OUTLIER) cc_final: 0.8101 (mmtt) REVERT: Av 6 LYS cc_start: 0.8393 (OUTLIER) cc_final: 0.7259 (mmtt) REVERT: Ax 2 LYS cc_start: 0.8208 (tmtt) cc_final: 0.7401 (tmtt) REVERT: A2 2 LYS cc_start: 0.8822 (ttpp) cc_final: 0.8069 (mptt) REVERT: A4 6 LYS cc_start: 0.8440 (mmtm) cc_final: 0.8058 (mmtm) outliers start: 107 outliers final: 87 residues processed: 227 average time/residue: 0.1729 time to fit residues: 46.6319 Evaluate side-chains 249 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 153 time to evaluate : 0.322 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain n residue 1 PHE Chi-restraints excluded: chain n residue 5 PHE Chi-restraints excluded: chain n residue 6 LYS Chi-restraints excluded: chain i residue 5 PHE Chi-restraints excluded: chain p residue 7 PHE Chi-restraints excluded: chain o residue 1 PHE Chi-restraints excluded: chain o residue 6 LYS Chi-restraints excluded: chain j residue 6 LYS Chi-restraints excluded: chain r residue 1 PHE Chi-restraints excluded: chain k residue 5 PHE Chi-restraints excluded: chain k residue 8 GLU Chi-restraints excluded: chain t residue 1 PHE Chi-restraints excluded: chain t residue 5 PHE Chi-restraints excluded: chain t residue 6 LYS Chi-restraints excluded: chain l residue 5 PHE Chi-restraints excluded: chain u residue 6 LYS Chi-restraints excluded: chain v residue 1 PHE Chi-restraints excluded: chain m residue 6 LYS Chi-restraints excluded: chain m residue 7 PHE Chi-restraints excluded: chain Y residue 8 GLU Chi-restraints excluded: chain y residue 1 PHE Chi-restraints excluded: chain y residue 6 LYS Chi-restraints excluded: chain x residue 5 PHE Chi-restraints excluded: chain x residue 6 LYS Chi-restraints excluded: chain z residue 7 PHE Chi-restraints excluded: chain 2 residue 1 PHE Chi-restraints excluded: chain 1 residue 6 LYS Chi-restraints excluded: chain 1 residue 7 PHE Chi-restraints excluded: chain 5 residue 1 PHE Chi-restraints excluded: chain 4 residue 5 PHE Chi-restraints excluded: chain b residue 8 GLU Chi-restraints excluded: chain 8 residue 1 PHE Chi-restraints excluded: chain 7 residue 6 LYS Chi-restraints excluded: chain c residue 8 GLU Chi-restraints excluded: chain AA residue 1 PHE Chi-restraints excluded: chain 0 residue 7 PHE Chi-restraints excluded: chain AD residue 1 PHE Chi-restraints excluded: chain AD residue 6 LYS Chi-restraints excluded: chain AC residue 5 PHE Chi-restraints excluded: chain AE residue 7 PHE Chi-restraints excluded: chain AE residue 8 GLU Chi-restraints excluded: chain AG residue 1 PHE Chi-restraints excluded: chain AG residue 6 LYS Chi-restraints excluded: chain AF residue 6 LYS Chi-restraints excluded: chain AF residue 7 PHE Chi-restraints excluded: chain AJ residue 1 PHE Chi-restraints excluded: chain AJ residue 5 PHE Chi-restraints excluded: chain AI residue 5 PHE Chi-restraints excluded: chain AM residue 1 PHE Chi-restraints excluded: chain AM residue 5 PHE Chi-restraints excluded: chain AM residue 6 LYS Chi-restraints excluded: chain AL residue 5 PHE Chi-restraints excluded: chain AP residue 1 PHE Chi-restraints excluded: chain AP residue 5 PHE Chi-restraints excluded: chain AO residue 6 LYS Chi-restraints excluded: chain AO residue 7 PHE Chi-restraints excluded: chain AT residue 1 PHE Chi-restraints excluded: chain AT residue 5 PHE Chi-restraints excluded: chain AT residue 6 LYS Chi-restraints excluded: chain AS residue 5 PHE Chi-restraints excluded: chain AU residue 7 PHE Chi-restraints excluded: chain AU residue 8 GLU Chi-restraints excluded: chain AX residue 1 PHE Chi-restraints excluded: chain AX residue 6 LYS Chi-restraints excluded: chain AW residue 6 LYS Chi-restraints excluded: chain Ab residue 1 PHE Chi-restraints excluded: chain Ab residue 6 LYS Chi-restraints excluded: chain Ad residue 8 GLU Chi-restraints excluded: chain Af residue 1 PHE Chi-restraints excluded: chain Af residue 6 LYS Chi-restraints excluded: chain Ag residue 6 LYS Chi-restraints excluded: chain Ah residue 8 GLU Chi-restraints excluded: chain Aj residue 1 PHE Chi-restraints excluded: chain Aj residue 6 LYS Chi-restraints excluded: chain Ai residue 6 LYS Chi-restraints excluded: chain Ai residue 7 PHE Chi-restraints excluded: chain An residue 1 PHE Chi-restraints excluded: chain An residue 5 PHE Chi-restraints excluded: chain An residue 6 LYS Chi-restraints excluded: chain Am residue 5 PHE Chi-restraints excluded: chain Ao residue 7 PHE Chi-restraints excluded: chain Ar residue 1 PHE Chi-restraints excluded: chain Av residue 1 PHE Chi-restraints excluded: chain Av residue 5 PHE Chi-restraints excluded: chain Av residue 6 LYS Chi-restraints excluded: chain Au residue 5 PHE Chi-restraints excluded: chain Ax residue 8 GLU Chi-restraints excluded: chain Az residue 1 PHE Chi-restraints excluded: chain Az residue 6 LYS Chi-restraints excluded: chain Ay residue 5 PHE Chi-restraints excluded: chain Ay residue 7 PHE Chi-restraints excluded: chain A2 residue 8 GLU Chi-restraints excluded: chain A4 residue 1 PHE Chi-restraints excluded: chain A4 residue 5 PHE Chi-restraints excluded: chain A3 residue 6 LYS Chi-restraints excluded: chain A3 residue 7 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1 random chunks: chunk 0 optimal weight: 5.9990 overall best weight: 50.0000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3612 r_free = 0.3612 target = 0.109706 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3232 r_free = 0.3232 target = 0.082929 restraints weight = 16169.007| |-----------------------------------------------------------------------------| r_work (start): 0.3052 rms_B_bonded: 1.84 r_work: 0.2928 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.2808 rms_B_bonded: 4.37 restraints_weight: 0.2500 r_work (final): 0.2808 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8863 moved from start: 0.8809 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.059 0.225 8200 Z= 2.505 Angle : 2.519 18.497 10400 Z= 1.262 Chirality : 0.165 0.415 700 Planarity : 0.015 0.039 1300 Dihedral : 43.014 174.537 928 Min Nonbonded Distance : 1.811 Molprobity Statistics. All-atom Clashscore : 80.65 Ramachandran Plot: Outliers : 0.50 % Allowed : 39.67 % Favored : 59.83 % Rotamer: Outliers : 17.14 % Allowed : 30.71 % Favored : 52.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 3.14 % 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: -7.05 (0.18), residues: 600 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -5.37 (0.14), residues: 600 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.072 0.009 PHEAJ 5 Details of bonding type rmsd/Z covalent geometry : bond 0.05940 / 2.52 ( 8100) covalent geometry : angle 2.51869 / 1.26 (10400) hydrogen bonds : bond 0.09842 / 5.72 ( 125) hydrogen bonds : angle 8.45814 / 5.21 ( 375) Misc. bond : bond 0.00919 / 0.49 ( 100) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1200 Ramachandran restraints generated. 600 Oldfield, 0 Emsley, 600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1200 Ramachandran restraints generated. 600 Oldfield, 0 Emsley, 600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 272 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 120 poor density : 152 time to evaluate : 0.329 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: o 6 LYS cc_start: 0.8374 (OUTLIER) cc_final: 0.8013 (mmtt) REVERT: r 6 LYS cc_start: 0.8240 (OUTLIER) cc_final: 0.7233 (mmtt) REVERT: X 2 LYS cc_start: 0.8743 (ttpp) cc_final: 0.8464 (tmtt) REVERT: v 6 LYS cc_start: 0.8241 (OUTLIER) cc_final: 0.8034 (mmtm) REVERT: 2 6 LYS cc_start: 0.8244 (OUTLIER) cc_final: 0.7798 (mmtt) REVERT: 5 5 PHE cc_start: 0.8931 (OUTLIER) cc_final: 0.8301 (p90) REVERT: 5 6 LYS cc_start: 0.8159 (OUTLIER) cc_final: 0.7027 (mmtt) REVERT: c 2 LYS cc_start: 0.8760 (ttpp) cc_final: 0.8483 (tmtt) REVERT: AA 6 LYS cc_start: 0.8390 (OUTLIER) cc_final: 0.8166 (mmtm) REVERT: AG 1 PHE cc_start: 0.8246 (OUTLIER) cc_final: 0.7971 (m-10) REVERT: AG 6 LYS cc_start: 0.8244 (OUTLIER) cc_final: 0.7937 (mmtt) REVERT: AJ 1 PHE cc_start: 0.8305 (OUTLIER) cc_final: 0.7940 (m-10) REVERT: AJ 6 LYS cc_start: 0.8065 (OUTLIER) cc_final: 0.7053 (mmtt) REVERT: g 6 LYS cc_start: 0.8489 (OUTLIER) cc_final: 0.8137 (mttm) REVERT: AX 1 PHE cc_start: 0.8300 (OUTLIER) cc_final: 0.7955 (m-10) REVERT: AX 6 LYS cc_start: 0.8386 (OUTLIER) cc_final: 0.8151 (mmtm) REVERT: Ab 6 LYS cc_start: 0.8186 (OUTLIER) cc_final: 0.6969 (mmtt) REVERT: Aj 6 LYS cc_start: 0.8239 (OUTLIER) cc_final: 0.7975 (mmtt) REVERT: Ap 2 LYS cc_start: 0.8227 (tmtt) cc_final: 0.7366 (tmtt) REVERT: Av 6 LYS cc_start: 0.8239 (OUTLIER) cc_final: 0.6994 (mmtt) REVERT: Ax 2 LYS cc_start: 0.8091 (tmtt) cc_final: 0.7326 (tmtt) REVERT: A2 2 LYS cc_start: 0.8786 (ttpp) cc_final: 0.7963 (mptt) REVERT: A4 6 LYS cc_start: 0.8318 (mmtm) cc_final: 0.7925 (mmtm) outliers start: 120 outliers final: 90 residues processed: 229 average time/residue: 0.1631 time to fit residues: 44.6684 Evaluate side-chains 258 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 107 poor density : 151 time to evaluate : 0.310 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain n residue 1 PHE Chi-restraints excluded: chain n residue 5 PHE Chi-restraints excluded: chain n residue 6 LYS Chi-restraints excluded: chain i residue 5 PHE Chi-restraints excluded: chain p residue 7 PHE Chi-restraints excluded: chain o residue 1 PHE Chi-restraints excluded: chain o residue 6 LYS Chi-restraints excluded: chain j residue 6 LYS Chi-restraints excluded: chain r residue 1 PHE Chi-restraints excluded: chain r residue 6 LYS Chi-restraints excluded: chain k residue 5 PHE Chi-restraints excluded: chain k residue 8 GLU Chi-restraints excluded: chain t residue 1 PHE Chi-restraints excluded: chain t residue 5 PHE Chi-restraints excluded: chain t residue 6 LYS Chi-restraints excluded: chain l residue 5 PHE Chi-restraints excluded: chain u residue 6 LYS Chi-restraints excluded: chain v residue 1 PHE Chi-restraints excluded: chain v residue 6 LYS Chi-restraints excluded: chain m residue 6 LYS Chi-restraints excluded: chain m residue 7 PHE Chi-restraints excluded: chain Y residue 8 GLU Chi-restraints excluded: chain y residue 1 PHE Chi-restraints excluded: chain y residue 6 LYS Chi-restraints excluded: chain x residue 5 PHE Chi-restraints excluded: chain x residue 6 LYS Chi-restraints excluded: chain z residue 7 PHE Chi-restraints excluded: chain 2 residue 1 PHE Chi-restraints excluded: chain 2 residue 6 LYS Chi-restraints excluded: chain 1 residue 6 LYS Chi-restraints excluded: chain 1 residue 7 PHE Chi-restraints excluded: chain 5 residue 1 PHE Chi-restraints excluded: chain 5 residue 5 PHE Chi-restraints excluded: chain 5 residue 6 LYS Chi-restraints excluded: chain 4 residue 5 PHE Chi-restraints excluded: chain 8 residue 1 PHE Chi-restraints excluded: chain 7 residue 5 PHE Chi-restraints excluded: chain 7 residue 6 LYS Chi-restraints excluded: chain c residue 8 GLU Chi-restraints excluded: chain AA residue 1 PHE Chi-restraints excluded: chain AA residue 6 LYS Chi-restraints excluded: chain 0 residue 7 PHE Chi-restraints excluded: chain AD residue 1 PHE Chi-restraints excluded: chain AD residue 6 LYS Chi-restraints excluded: chain AC residue 5 PHE Chi-restraints excluded: chain AE residue 7 PHE Chi-restraints excluded: chain AE residue 8 GLU Chi-restraints excluded: chain AG residue 1 PHE Chi-restraints excluded: chain AG residue 6 LYS Chi-restraints excluded: chain AF residue 6 LYS Chi-restraints excluded: chain AF residue 7 PHE Chi-restraints excluded: chain AJ residue 1 PHE Chi-restraints excluded: chain AJ residue 5 PHE Chi-restraints excluded: chain AJ residue 6 LYS Chi-restraints excluded: chain AI residue 5 PHE Chi-restraints excluded: chain g residue 6 LYS Chi-restraints excluded: chain AM residue 1 PHE Chi-restraints excluded: chain AM residue 5 PHE Chi-restraints excluded: chain AM residue 6 LYS Chi-restraints excluded: chain AL residue 5 PHE Chi-restraints excluded: chain AP residue 3 PHE Chi-restraints excluded: chain AP residue 5 PHE Chi-restraints excluded: chain AO residue 6 LYS Chi-restraints excluded: chain AO residue 7 PHE Chi-restraints excluded: chain AT residue 1 PHE Chi-restraints excluded: chain AT residue 5 PHE Chi-restraints excluded: chain AT residue 6 LYS Chi-restraints excluded: chain AS residue 5 PHE Chi-restraints excluded: chain AU residue 7 PHE Chi-restraints excluded: chain AU residue 8 GLU Chi-restraints excluded: chain AX residue 1 PHE Chi-restraints excluded: chain AX residue 6 LYS Chi-restraints excluded: chain AW residue 6 LYS Chi-restraints excluded: chain Ab residue 1 PHE Chi-restraints excluded: chain Ab residue 5 PHE Chi-restraints excluded: chain Ab residue 6 LYS Chi-restraints excluded: chain Aa residue 5 PHE Chi-restraints excluded: chain Ad residue 8 GLU Chi-restraints excluded: chain Af residue 1 PHE Chi-restraints excluded: chain Af residue 5 PHE Chi-restraints excluded: chain Af residue 6 LYS Chi-restraints excluded: chain Ag residue 6 LYS Chi-restraints excluded: chain Ah residue 8 GLU Chi-restraints excluded: chain Aj residue 1 PHE Chi-restraints excluded: chain Aj residue 6 LYS Chi-restraints excluded: chain Ai residue 6 LYS Chi-restraints excluded: chain Ai residue 7 PHE Chi-restraints excluded: chain An residue 1 PHE Chi-restraints excluded: chain An residue 5 PHE Chi-restraints excluded: chain An residue 6 LYS Chi-restraints excluded: chain Am residue 5 PHE Chi-restraints excluded: chain Ao residue 7 PHE Chi-restraints excluded: chain Ar residue 1 PHE Chi-restraints excluded: chain Av residue 1 PHE Chi-restraints excluded: chain Av residue 5 PHE Chi-restraints excluded: chain Av residue 6 LYS Chi-restraints excluded: chain Au residue 5 PHE Chi-restraints excluded: chain Ax residue 8 GLU Chi-restraints excluded: chain Az residue 1 PHE Chi-restraints excluded: chain Az residue 6 LYS Chi-restraints excluded: chain Ay residue 5 PHE Chi-restraints excluded: chain Ay residue 7 PHE Chi-restraints excluded: chain A2 residue 8 GLU Chi-restraints excluded: chain A4 residue 1 PHE Chi-restraints excluded: chain A4 residue 5 PHE Chi-restraints excluded: chain A3 residue 6 LYS Chi-restraints excluded: chain A3 residue 7 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1 random chunks: chunk 0 optimal weight: 5.9990 overall best weight: 50.0000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.107828 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3157 r_free = 0.3157 target = 0.082079 restraints weight = 16919.680| |-----------------------------------------------------------------------------| r_work (start): 0.3045 rms_B_bonded: 1.82 r_work: 0.2932 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.2814 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.2814 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8841 moved from start: 0.8847 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.059 0.224 8200 Z= 2.502 Angle : 2.519 18.541 10400 Z= 1.263 Chirality : 0.166 0.418 700 Planarity : 0.015 0.039 1300 Dihedral : 42.980 174.643 928 Min Nonbonded Distance : 1.813 Molprobity Statistics. All-atom Clashscore : 80.13 Ramachandran Plot: Outliers : 0.33 % Allowed : 40.17 % Favored : 59.50 % Rotamer: Outliers : 17.57 % Allowed : 30.86 % Favored : 51.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 3.00 % 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: -7.06 (0.18), residues: 600 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -5.38 (0.14), residues: 600 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.073 0.009 PHEAJ 5 Details of bonding type rmsd/Z covalent geometry : bond 0.05936 / 2.52 ( 8100) covalent geometry : angle 2.51909 / 1.26 (10400) hydrogen bonds : bond 0.09831 / 5.71 ( 125) hydrogen bonds : angle 8.46440 / 5.21 ( 375) Misc. bond : bond 0.00917 / 0.49 ( 100) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1200 Ramachandran restraints generated. 600 Oldfield, 0 Emsley, 600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1200 Ramachandran restraints generated. 600 Oldfield, 0 Emsley, 600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 275 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 123 poor density : 152 time to evaluate : 0.252 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: o 6 LYS cc_start: 0.8330 (OUTLIER) cc_final: 0.8019 (mmtt) REVERT: r 6 LYS cc_start: 0.8285 (OUTLIER) cc_final: 0.7250 (mmtt) REVERT: X 2 LYS cc_start: 0.8746 (ttpp) cc_final: 0.8480 (tmtt) REVERT: v 6 LYS cc_start: 0.8271 (OUTLIER) cc_final: 0.8067 (mmtm) REVERT: Y 7 PHE cc_start: 0.8966 (OUTLIER) cc_final: 0.8622 (t80) REVERT: 2 6 LYS cc_start: 0.8266 (OUTLIER) cc_final: 0.7833 (mmtt) REVERT: 5 5 PHE cc_start: 0.8916 (OUTLIER) cc_final: 0.8242 (p90) REVERT: 5 6 LYS cc_start: 0.8161 (OUTLIER) cc_final: 0.6906 (mmtt) REVERT: c 2 LYS cc_start: 0.8770 (ttpp) cc_final: 0.8497 (tmtt) REVERT: AG 1 PHE cc_start: 0.8251 (OUTLIER) cc_final: 0.7978 (m-10) REVERT: AG 6 LYS cc_start: 0.8284 (OUTLIER) cc_final: 0.8009 (mmtt) REVERT: AJ 1 PHE cc_start: 0.8298 (OUTLIER) cc_final: 0.7938 (m-10) REVERT: AJ 6 LYS cc_start: 0.8040 (OUTLIER) cc_final: 0.7043 (mmtt) REVERT: g 6 LYS cc_start: 0.8477 (OUTLIER) cc_final: 0.8137 (mttm) REVERT: AP 6 LYS cc_start: 0.8356 (OUTLIER) cc_final: 0.8134 (mmtm) REVERT: AX 1 PHE cc_start: 0.8285 (OUTLIER) cc_final: 0.7959 (m-10) REVERT: AX 6 LYS cc_start: 0.8416 (OUTLIER) cc_final: 0.8174 (mmtm) REVERT: Ab 6 LYS cc_start: 0.8127 (OUTLIER) cc_final: 0.6884 (mmtt) REVERT: Ah 2 LYS cc_start: 0.8938 (ttpp) cc_final: 0.8453 (tmtt) REVERT: Aj 6 LYS cc_start: 0.8211 (OUTLIER) cc_final: 0.7960 (mmtt) REVERT: Ar 6 LYS cc_start: 0.8275 (OUTLIER) cc_final: 0.7980 (mmtt) REVERT: Av 6 LYS cc_start: 0.8238 (OUTLIER) cc_final: 0.7024 (mmtt) REVERT: Ax 2 LYS cc_start: 0.8122 (tmtt) cc_final: 0.7317 (tmtt) REVERT: A2 2 LYS cc_start: 0.8776 (ttpp) cc_final: 0.7935 (mptt) REVERT: A4 6 LYS cc_start: 0.8341 (mmtm) cc_final: 0.7980 (mmtm) outliers start: 123 outliers final: 94 residues processed: 232 average time/residue: 0.1539 time to fit residues: 42.7772 Evaluate side-chains 263 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 113 poor density : 150 time to evaluate : 0.330 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain n residue 1 PHE Chi-restraints excluded: chain n residue 5 PHE Chi-restraints excluded: chain n residue 6 LYS Chi-restraints excluded: chain i residue 5 PHE Chi-restraints excluded: chain p residue 7 PHE Chi-restraints excluded: chain o residue 1 PHE Chi-restraints excluded: chain o residue 6 LYS Chi-restraints excluded: chain j residue 6 LYS Chi-restraints excluded: chain r residue 1 PHE Chi-restraints excluded: chain r residue 6 LYS Chi-restraints excluded: chain k residue 5 PHE Chi-restraints excluded: chain k residue 8 GLU Chi-restraints excluded: chain t residue 1 PHE Chi-restraints excluded: chain t residue 5 PHE Chi-restraints excluded: chain t residue 6 LYS Chi-restraints excluded: chain l residue 5 PHE Chi-restraints excluded: chain u residue 6 LYS Chi-restraints excluded: chain v residue 1 PHE Chi-restraints excluded: chain v residue 6 LYS Chi-restraints excluded: chain m residue 6 LYS Chi-restraints excluded: chain m residue 7 PHE Chi-restraints excluded: chain Y residue 7 PHE Chi-restraints excluded: chain Y residue 8 GLU Chi-restraints excluded: chain y residue 1 PHE Chi-restraints excluded: chain y residue 5 PHE Chi-restraints excluded: chain y residue 6 LYS Chi-restraints excluded: chain x residue 5 PHE Chi-restraints excluded: chain x residue 6 LYS Chi-restraints excluded: chain z residue 7 PHE Chi-restraints excluded: chain 2 residue 1 PHE Chi-restraints excluded: chain 2 residue 6 LYS Chi-restraints excluded: chain 1 residue 6 LYS Chi-restraints excluded: chain 1 residue 7 PHE Chi-restraints excluded: chain 5 residue 1 PHE Chi-restraints excluded: chain 5 residue 5 PHE Chi-restraints excluded: chain 5 residue 6 LYS Chi-restraints excluded: chain 4 residue 5 PHE Chi-restraints excluded: chain 8 residue 1 PHE Chi-restraints excluded: chain 7 residue 5 PHE Chi-restraints excluded: chain 7 residue 6 LYS Chi-restraints excluded: chain c residue 8 GLU Chi-restraints excluded: chain AA residue 1 PHE Chi-restraints excluded: chain AA residue 5 PHE Chi-restraints excluded: chain 0 residue 7 PHE Chi-restraints excluded: chain AD residue 1 PHE Chi-restraints excluded: chain AD residue 6 LYS Chi-restraints excluded: chain AC residue 5 PHE Chi-restraints excluded: chain AC residue 6 LYS Chi-restraints excluded: chain AE residue 7 PHE Chi-restraints excluded: chain AE residue 8 GLU Chi-restraints excluded: chain AG residue 1 PHE Chi-restraints excluded: chain AG residue 6 LYS Chi-restraints excluded: chain AF residue 6 LYS Chi-restraints excluded: chain AF residue 7 PHE Chi-restraints excluded: chain AJ residue 1 PHE Chi-restraints excluded: chain AJ residue 5 PHE Chi-restraints excluded: chain AJ residue 6 LYS Chi-restraints excluded: chain AI residue 5 PHE Chi-restraints excluded: chain g residue 6 LYS Chi-restraints excluded: chain AM residue 1 PHE Chi-restraints excluded: chain AM residue 5 PHE Chi-restraints excluded: chain AM residue 6 LYS Chi-restraints excluded: chain AL residue 5 PHE Chi-restraints excluded: chain AP residue 3 PHE Chi-restraints excluded: chain AP residue 5 PHE Chi-restraints excluded: chain AP residue 6 LYS Chi-restraints excluded: chain AO residue 6 LYS Chi-restraints excluded: chain AO residue 7 PHE Chi-restraints excluded: chain AT residue 1 PHE Chi-restraints excluded: chain AT residue 5 PHE Chi-restraints excluded: chain AT residue 6 LYS Chi-restraints excluded: chain AS residue 5 PHE Chi-restraints excluded: chain AU residue 7 PHE Chi-restraints excluded: chain AU residue 8 GLU Chi-restraints excluded: chain AX residue 1 PHE Chi-restraints excluded: chain AX residue 6 LYS Chi-restraints excluded: chain AW residue 6 LYS Chi-restraints excluded: chain Ab residue 1 PHE Chi-restraints excluded: chain Ab residue 3 PHE Chi-restraints excluded: chain Ab residue 5 PHE Chi-restraints excluded: chain Ab residue 6 LYS Chi-restraints excluded: chain Aa residue 5 PHE Chi-restraints excluded: chain Ad residue 8 GLU Chi-restraints excluded: chain Af residue 1 PHE Chi-restraints excluded: chain Af residue 5 PHE Chi-restraints excluded: chain Af residue 6 LYS Chi-restraints excluded: chain Ag residue 6 LYS Chi-restraints excluded: chain Ah residue 8 GLU Chi-restraints excluded: chain Aj residue 1 PHE Chi-restraints excluded: chain Aj residue 6 LYS Chi-restraints excluded: chain Ai residue 6 LYS Chi-restraints excluded: chain Ai residue 7 PHE Chi-restraints excluded: chain An residue 1 PHE Chi-restraints excluded: chain An residue 5 PHE Chi-restraints excluded: chain An residue 6 LYS Chi-restraints excluded: chain Am residue 5 PHE Chi-restraints excluded: chain Ao residue 7 PHE Chi-restraints excluded: chain Ar residue 1 PHE Chi-restraints excluded: chain Ar residue 6 LYS Chi-restraints excluded: chain Av residue 1 PHE Chi-restraints excluded: chain Av residue 5 PHE Chi-restraints excluded: chain Av residue 6 LYS Chi-restraints excluded: chain Au residue 5 PHE Chi-restraints excluded: chain Ax residue 8 GLU Chi-restraints excluded: chain Az residue 1 PHE Chi-restraints excluded: chain Az residue 6 LYS Chi-restraints excluded: chain Ay residue 5 PHE Chi-restraints excluded: chain Ay residue 7 PHE Chi-restraints excluded: chain A2 residue 8 GLU Chi-restraints excluded: chain A4 residue 1 PHE Chi-restraints excluded: chain A4 residue 5 PHE Chi-restraints excluded: chain A3 residue 6 LYS Chi-restraints excluded: chain A3 residue 7 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1 random chunks: chunk 0 optimal weight: 5.9990 overall best weight: 50.0000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.106742 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3139 r_free = 0.3139 target = 0.080894 restraints weight = 18771.583| |-----------------------------------------------------------------------------| r_work (start): 0.3047 rms_B_bonded: 1.92 r_work: 0.2933 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.2814 rms_B_bonded: 4.44 restraints_weight: 0.2500 r_work (final): 0.2814 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8845 moved from start: 0.8861 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.059 0.225 8200 Z= 2.503 Angle : 2.522 18.524 10400 Z= 1.264 Chirality : 0.166 0.419 700 Planarity : 0.015 0.039 1300 Dihedral : 42.985 174.661 928 Min Nonbonded Distance : 1.811 Molprobity Statistics. All-atom Clashscore : 79.80 Ramachandran Plot: Outliers : 0.50 % Allowed : 40.17 % Favored : 59.33 % Rotamer: Outliers : 17.14 % Allowed : 31.29 % Favored : 51.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 3.14 % 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: -7.07 (0.18), residues: 600 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -5.39 (0.14), residues: 600 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.073 0.009 PHEAJ 5 Details of bonding type rmsd/Z covalent geometry : bond 0.05939 / 2.52 ( 8100) covalent geometry : angle 2.52165 / 1.26 (10400) hydrogen bonds : bond 0.09824 / 5.71 ( 125) hydrogen bonds : angle 8.49699 / 5.23 ( 375) Misc. bond : bond 0.00917 / 0.49 ( 100) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1200 Ramachandran restraints generated. 600 Oldfield, 0 Emsley, 600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1200 Ramachandran restraints generated. 600 Oldfield, 0 Emsley, 600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 270 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 120 poor density : 150 time to evaluate : 0.274 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: o 6 LYS cc_start: 0.8320 (OUTLIER) cc_final: 0.7951 (mmtt) REVERT: r 6 LYS cc_start: 0.8294 (OUTLIER) cc_final: 0.7259 (mmtt) REVERT: X 2 LYS cc_start: 0.8733 (ttpp) cc_final: 0.8468 (tmtt) REVERT: v 6 LYS cc_start: 0.8303 (OUTLIER) cc_final: 0.8087 (mmtm) REVERT: Y 7 PHE cc_start: 0.8969 (OUTLIER) cc_final: 0.8625 (t80) REVERT: 2 6 LYS cc_start: 0.8305 (OUTLIER) cc_final: 0.7849 (mmtt) REVERT: 5 5 PHE cc_start: 0.8902 (OUTLIER) cc_final: 0.8276 (p90) REVERT: 5 6 LYS cc_start: 0.8115 (OUTLIER) cc_final: 0.6856 (mmtt) REVERT: c 2 LYS cc_start: 0.8766 (ttpp) cc_final: 0.8507 (tmtt) REVERT: AA 6 LYS cc_start: 0.8314 (OUTLIER) cc_final: 0.8102 (mmtm) REVERT: AG 1 PHE cc_start: 0.8256 (OUTLIER) cc_final: 0.7981 (m-10) REVERT: AG 6 LYS cc_start: 0.8262 (OUTLIER) cc_final: 0.7964 (mmtt) REVERT: AF 5 PHE cc_start: 0.9166 (OUTLIER) cc_final: 0.8665 (m-80) REVERT: AJ 1 PHE cc_start: 0.8318 (OUTLIER) cc_final: 0.7953 (m-10) REVERT: AJ 6 LYS cc_start: 0.8034 (OUTLIER) cc_final: 0.7029 (mmtt) REVERT: g 6 LYS cc_start: 0.8466 (OUTLIER) cc_final: 0.8124 (mttm) REVERT: AX 1 PHE cc_start: 0.8293 (OUTLIER) cc_final: 0.7974 (m-10) REVERT: AX 6 LYS cc_start: 0.8419 (OUTLIER) cc_final: 0.8182 (mmtm) REVERT: Ab 6 LYS cc_start: 0.8146 (OUTLIER) cc_final: 0.6941 (mmtt) REVERT: Aj 6 LYS cc_start: 0.8203 (OUTLIER) cc_final: 0.7942 (mmtt) REVERT: Ar 6 LYS cc_start: 0.8295 (OUTLIER) cc_final: 0.8007 (mmtt) REVERT: Av 6 LYS cc_start: 0.8269 (OUTLIER) cc_final: 0.7051 (mmtt) REVERT: A2 2 LYS cc_start: 0.8767 (ttpp) cc_final: 0.7926 (mptt) REVERT: A4 6 LYS cc_start: 0.8359 (mmtm) cc_final: 0.8081 (mmtm) outliers start: 120 outliers final: 93 residues processed: 231 average time/residue: 0.1585 time to fit residues: 43.7572 Evaluate side-chains 264 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 113 poor density : 151 time to evaluate : 0.248 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain n residue 1 PHE Chi-restraints excluded: chain n residue 5 PHE Chi-restraints excluded: chain n residue 6 LYS Chi-restraints excluded: chain i residue 5 PHE Chi-restraints excluded: chain p residue 7 PHE Chi-restraints excluded: chain o residue 1 PHE Chi-restraints excluded: chain o residue 6 LYS Chi-restraints excluded: chain j residue 6 LYS Chi-restraints excluded: chain r residue 1 PHE Chi-restraints excluded: chain r residue 6 LYS Chi-restraints excluded: chain k residue 5 PHE Chi-restraints excluded: chain k residue 8 GLU Chi-restraints excluded: chain t residue 1 PHE Chi-restraints excluded: chain t residue 5 PHE Chi-restraints excluded: chain t residue 6 LYS Chi-restraints excluded: chain l residue 5 PHE Chi-restraints excluded: chain u residue 6 LYS Chi-restraints excluded: chain v residue 1 PHE Chi-restraints excluded: chain v residue 6 LYS Chi-restraints excluded: chain m residue 6 LYS Chi-restraints excluded: chain m residue 7 PHE Chi-restraints excluded: chain Y residue 7 PHE Chi-restraints excluded: chain Y residue 8 GLU Chi-restraints excluded: chain y residue 1 PHE Chi-restraints excluded: chain y residue 5 PHE Chi-restraints excluded: chain y residue 6 LYS Chi-restraints excluded: chain x residue 5 PHE Chi-restraints excluded: chain z residue 7 PHE Chi-restraints excluded: chain 2 residue 1 PHE Chi-restraints excluded: chain 2 residue 6 LYS Chi-restraints excluded: chain 1 residue 6 LYS Chi-restraints excluded: chain 1 residue 7 PHE Chi-restraints excluded: chain 5 residue 1 PHE Chi-restraints excluded: chain 5 residue 5 PHE Chi-restraints excluded: chain 5 residue 6 LYS Chi-restraints excluded: chain 4 residue 5 PHE Chi-restraints excluded: chain 8 residue 1 PHE Chi-restraints excluded: chain 7 residue 5 PHE Chi-restraints excluded: chain 7 residue 6 LYS Chi-restraints excluded: chain c residue 8 GLU Chi-restraints excluded: chain AA residue 1 PHE Chi-restraints excluded: chain AA residue 5 PHE Chi-restraints excluded: chain AA residue 6 LYS Chi-restraints excluded: chain 0 residue 7 PHE Chi-restraints excluded: chain AD residue 1 PHE Chi-restraints excluded: chain AD residue 6 LYS Chi-restraints excluded: chain AC residue 5 PHE Chi-restraints excluded: chain AC residue 6 LYS Chi-restraints excluded: chain AE residue 7 PHE Chi-restraints excluded: chain AE residue 8 GLU Chi-restraints excluded: chain AG residue 1 PHE Chi-restraints excluded: chain AG residue 6 LYS Chi-restraints excluded: chain AF residue 5 PHE Chi-restraints excluded: chain AF residue 6 LYS Chi-restraints excluded: chain AF residue 7 PHE Chi-restraints excluded: chain AJ residue 1 PHE Chi-restraints excluded: chain AJ residue 5 PHE Chi-restraints excluded: chain AJ residue 6 LYS Chi-restraints excluded: chain AI residue 5 PHE Chi-restraints excluded: chain g residue 6 LYS Chi-restraints excluded: chain AM residue 1 PHE Chi-restraints excluded: chain AM residue 5 PHE Chi-restraints excluded: chain AM residue 6 LYS Chi-restraints excluded: chain AL residue 5 PHE Chi-restraints excluded: chain AP residue 3 PHE Chi-restraints excluded: chain AP residue 5 PHE Chi-restraints excluded: chain AO residue 6 LYS Chi-restraints excluded: chain AO residue 7 PHE Chi-restraints excluded: chain AT residue 1 PHE Chi-restraints excluded: chain AT residue 5 PHE Chi-restraints excluded: chain AT residue 6 LYS Chi-restraints excluded: chain AS residue 5 PHE Chi-restraints excluded: chain AU residue 7 PHE Chi-restraints excluded: chain AU residue 8 GLU Chi-restraints excluded: chain AX residue 1 PHE Chi-restraints excluded: chain AX residue 5 PHE Chi-restraints excluded: chain AX residue 6 LYS Chi-restraints excluded: chain AW residue 6 LYS Chi-restraints excluded: chain Ab residue 1 PHE Chi-restraints excluded: chain Ab residue 5 PHE Chi-restraints excluded: chain Ab residue 6 LYS Chi-restraints excluded: chain Aa residue 5 PHE Chi-restraints excluded: chain Ad residue 8 GLU Chi-restraints excluded: chain Af residue 1 PHE Chi-restraints excluded: chain Af residue 6 LYS Chi-restraints excluded: chain Ag residue 6 LYS Chi-restraints excluded: chain Ah residue 8 GLU Chi-restraints excluded: chain Aj residue 1 PHE Chi-restraints excluded: chain Aj residue 6 LYS Chi-restraints excluded: chain Ai residue 6 LYS Chi-restraints excluded: chain Ai residue 7 PHE Chi-restraints excluded: chain An residue 1 PHE Chi-restraints excluded: chain An residue 5 PHE Chi-restraints excluded: chain An residue 6 LYS Chi-restraints excluded: chain Am residue 5 PHE Chi-restraints excluded: chain Ao residue 7 PHE Chi-restraints excluded: chain Ar residue 1 PHE Chi-restraints excluded: chain Ar residue 6 LYS Chi-restraints excluded: chain Av residue 1 PHE Chi-restraints excluded: chain Av residue 5 PHE Chi-restraints excluded: chain Av residue 6 LYS Chi-restraints excluded: chain Au residue 5 PHE Chi-restraints excluded: chain Ax residue 8 GLU Chi-restraints excluded: chain Az residue 1 PHE Chi-restraints excluded: chain Az residue 6 LYS Chi-restraints excluded: chain Ay residue 5 PHE Chi-restraints excluded: chain Ay residue 7 PHE Chi-restraints excluded: chain A2 residue 8 GLU Chi-restraints excluded: chain A4 residue 1 PHE Chi-restraints excluded: chain A4 residue 5 PHE Chi-restraints excluded: chain A3 residue 5 PHE Chi-restraints excluded: chain A3 residue 6 LYS Chi-restraints excluded: chain A3 residue 7 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1 random chunks: chunk 0 optimal weight: 5.9990 overall best weight: 50.0000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.106729 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3138 r_free = 0.3138 target = 0.080904 restraints weight = 18290.765| |-----------------------------------------------------------------------------| r_work (start): 0.3043 rms_B_bonded: 1.91 r_work: 0.2930 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.2811 rms_B_bonded: 4.41 restraints_weight: 0.2500 r_work (final): 0.2811 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8840 moved from start: 0.8872 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.059 0.225 8200 Z= 2.503 Angle : 2.525 18.671 10400 Z= 1.266 Chirality : 0.166 0.429 700 Planarity : 0.015 0.039 1300 Dihedral : 42.992 174.712 928 Min Nonbonded Distance : 1.813 Molprobity Statistics. All-atom Clashscore : 79.93 Ramachandran Plot: Outliers : 0.33 % Allowed : 40.67 % Favored : 59.00 % Rotamer: Outliers : 16.86 % Allowed : 32.14 % Favored : 51.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 3.14 % 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: -7.07 (0.18), residues: 600 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -5.39 (0.14), residues: 600 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.073 0.009 PHEAJ 5 Details of bonding type rmsd/Z covalent geometry : bond 0.05937 / 2.52 ( 8100) covalent geometry : angle 2.52470 / 1.27 (10400) hydrogen bonds : bond 0.09828 / 5.71 ( 125) hydrogen bonds : angle 8.49616 / 5.23 ( 375) Misc. bond : bond 0.00913 / 0.49 ( 100) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1200 Ramachandran restraints generated. 600 Oldfield, 0 Emsley, 600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1200 Ramachandran restraints generated. 600 Oldfield, 0 Emsley, 600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 268 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 118 poor density : 150 time to evaluate : 0.329 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: o 6 LYS cc_start: 0.8315 (OUTLIER) cc_final: 0.8003 (mmtt) REVERT: r 6 LYS cc_start: 0.8292 (OUTLIER) cc_final: 0.7260 (mmtt) REVERT: X 2 LYS cc_start: 0.8718 (ttpp) cc_final: 0.8453 (tmtt) REVERT: v 6 LYS cc_start: 0.8315 (OUTLIER) cc_final: 0.8097 (mmtm) REVERT: Y 7 PHE cc_start: 0.8969 (OUTLIER) cc_final: 0.8668 (t80) REVERT: 2 6 LYS cc_start: 0.8301 (OUTLIER) cc_final: 0.7845 (mmtt) REVERT: 5 5 PHE cc_start: 0.8902 (OUTLIER) cc_final: 0.8315 (p90) REVERT: 5 6 LYS cc_start: 0.8099 (OUTLIER) cc_final: 0.6997 (mmtt) REVERT: b 7 PHE cc_start: 0.8998 (OUTLIER) cc_final: 0.8525 (t80) REVERT: c 2 LYS cc_start: 0.8766 (ttpp) cc_final: 0.8509 (tmtt) REVERT: AG 1 PHE cc_start: 0.8242 (OUTLIER) cc_final: 0.7964 (m-10) REVERT: AG 6 LYS cc_start: 0.8280 (OUTLIER) cc_final: 0.8008 (mmtt) REVERT: AF 5 PHE cc_start: 0.9162 (OUTLIER) cc_final: 0.8660 (m-80) REVERT: AJ 1 PHE cc_start: 0.8332 (OUTLIER) cc_final: 0.7974 (m-10) REVERT: AJ 6 LYS cc_start: 0.8032 (OUTLIER) cc_final: 0.7027 (mmtt) REVERT: g 6 LYS cc_start: 0.8457 (OUTLIER) cc_final: 0.8118 (mttm) REVERT: AX 1 PHE cc_start: 0.8269 (OUTLIER) cc_final: 0.7955 (m-10) REVERT: AX 6 LYS cc_start: 0.8420 (OUTLIER) cc_final: 0.8211 (mmtm) REVERT: Ab 6 LYS cc_start: 0.8135 (OUTLIER) cc_final: 0.6949 (mmtt) REVERT: Aj 6 LYS cc_start: 0.8183 (OUTLIER) cc_final: 0.7924 (mmtt) REVERT: Ar 6 LYS cc_start: 0.8301 (OUTLIER) cc_final: 0.7990 (mmtt) REVERT: Av 6 LYS cc_start: 0.8271 (OUTLIER) cc_final: 0.7059 (mmtt) REVERT: Ax 2 LYS cc_start: 0.8130 (tmtt) cc_final: 0.7895 (tttm) REVERT: A2 2 LYS cc_start: 0.8760 (ttpp) cc_final: 0.7910 (mptt) REVERT: A4 6 LYS cc_start: 0.8375 (mmtm) cc_final: 0.8105 (mmtm) outliers start: 118 outliers final: 94 residues processed: 231 average time/residue: 0.1568 time to fit residues: 43.6510 Evaluate side-chains 264 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 114 poor density : 150 time to evaluate : 0.330 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain n residue 1 PHE Chi-restraints excluded: chain n residue 5 PHE Chi-restraints excluded: chain n residue 6 LYS Chi-restraints excluded: chain i residue 5 PHE Chi-restraints excluded: chain p residue 7 PHE Chi-restraints excluded: chain o residue 1 PHE Chi-restraints excluded: chain o residue 6 LYS Chi-restraints excluded: chain j residue 6 LYS Chi-restraints excluded: chain r residue 1 PHE Chi-restraints excluded: chain r residue 6 LYS Chi-restraints excluded: chain k residue 5 PHE Chi-restraints excluded: chain k residue 8 GLU Chi-restraints excluded: chain t residue 1 PHE Chi-restraints excluded: chain t residue 5 PHE Chi-restraints excluded: chain t residue 6 LYS Chi-restraints excluded: chain l residue 5 PHE Chi-restraints excluded: chain u residue 6 LYS Chi-restraints excluded: chain v residue 1 PHE Chi-restraints excluded: chain v residue 6 LYS Chi-restraints excluded: chain m residue 6 LYS Chi-restraints excluded: chain m residue 7 PHE Chi-restraints excluded: chain Y residue 7 PHE Chi-restraints excluded: chain Y residue 8 GLU Chi-restraints excluded: chain y residue 1 PHE Chi-restraints excluded: chain y residue 5 PHE Chi-restraints excluded: chain y residue 6 LYS Chi-restraints excluded: chain x residue 5 PHE Chi-restraints excluded: chain z residue 7 PHE Chi-restraints excluded: chain 2 residue 1 PHE Chi-restraints excluded: chain 2 residue 6 LYS Chi-restraints excluded: chain 1 residue 6 LYS Chi-restraints excluded: chain 1 residue 7 PHE Chi-restraints excluded: chain 5 residue 1 PHE Chi-restraints excluded: chain 5 residue 5 PHE Chi-restraints excluded: chain 5 residue 6 LYS Chi-restraints excluded: chain 4 residue 5 PHE Chi-restraints excluded: chain b residue 7 PHE Chi-restraints excluded: chain 8 residue 1 PHE Chi-restraints excluded: chain 8 residue 6 LYS Chi-restraints excluded: chain 7 residue 5 PHE Chi-restraints excluded: chain 7 residue 6 LYS Chi-restraints excluded: chain c residue 8 GLU Chi-restraints excluded: chain AA residue 1 PHE Chi-restraints excluded: chain AA residue 5 PHE Chi-restraints excluded: chain 0 residue 7 PHE Chi-restraints excluded: chain AD residue 1 PHE Chi-restraints excluded: chain AD residue 6 LYS Chi-restraints excluded: chain AC residue 5 PHE Chi-restraints excluded: chain AC residue 6 LYS Chi-restraints excluded: chain AE residue 7 PHE Chi-restraints excluded: chain AE residue 8 GLU Chi-restraints excluded: chain AG residue 1 PHE Chi-restraints excluded: chain AG residue 6 LYS Chi-restraints excluded: chain AF residue 5 PHE Chi-restraints excluded: chain AF residue 6 LYS Chi-restraints excluded: chain AF residue 7 PHE Chi-restraints excluded: chain AJ residue 1 PHE Chi-restraints excluded: chain AJ residue 5 PHE Chi-restraints excluded: chain AJ residue 6 LYS Chi-restraints excluded: chain AI residue 5 PHE Chi-restraints excluded: chain g residue 6 LYS Chi-restraints excluded: chain AM residue 1 PHE Chi-restraints excluded: chain AM residue 5 PHE Chi-restraints excluded: chain AM residue 6 LYS Chi-restraints excluded: chain AL residue 5 PHE Chi-restraints excluded: chain AP residue 3 PHE Chi-restraints excluded: chain AP residue 5 PHE Chi-restraints excluded: chain AO residue 6 LYS Chi-restraints excluded: chain AO residue 7 PHE Chi-restraints excluded: chain AT residue 1 PHE Chi-restraints excluded: chain AT residue 5 PHE Chi-restraints excluded: chain AT residue 6 LYS Chi-restraints excluded: chain AS residue 5 PHE Chi-restraints excluded: chain AU residue 7 PHE Chi-restraints excluded: chain AU residue 8 GLU Chi-restraints excluded: chain AX residue 1 PHE Chi-restraints excluded: chain AX residue 5 PHE Chi-restraints excluded: chain AX residue 6 LYS Chi-restraints excluded: chain AW residue 6 LYS Chi-restraints excluded: chain Ab residue 1 PHE Chi-restraints excluded: chain Ab residue 5 PHE Chi-restraints excluded: chain Ab residue 6 LYS Chi-restraints excluded: chain Aa residue 5 PHE Chi-restraints excluded: chain Ad residue 8 GLU Chi-restraints excluded: chain Af residue 1 PHE Chi-restraints excluded: chain Af residue 6 LYS Chi-restraints excluded: chain Ag residue 6 LYS Chi-restraints excluded: chain Ah residue 8 GLU Chi-restraints excluded: chain Aj residue 1 PHE Chi-restraints excluded: chain Aj residue 6 LYS Chi-restraints excluded: chain Ai residue 6 LYS Chi-restraints excluded: chain Ai residue 7 PHE Chi-restraints excluded: chain An residue 1 PHE Chi-restraints excluded: chain An residue 5 PHE Chi-restraints excluded: chain An residue 6 LYS Chi-restraints excluded: chain Am residue 5 PHE Chi-restraints excluded: chain Ao residue 7 PHE Chi-restraints excluded: chain Ar residue 1 PHE Chi-restraints excluded: chain Ar residue 6 LYS Chi-restraints excluded: chain Av residue 1 PHE Chi-restraints excluded: chain Av residue 5 PHE Chi-restraints excluded: chain Av residue 6 LYS Chi-restraints excluded: chain Au residue 5 PHE Chi-restraints excluded: chain Ax residue 8 GLU Chi-restraints excluded: chain Az residue 1 PHE Chi-restraints excluded: chain Az residue 6 LYS Chi-restraints excluded: chain Ay residue 5 PHE Chi-restraints excluded: chain Ay residue 7 PHE Chi-restraints excluded: chain A2 residue 8 GLU Chi-restraints excluded: chain A4 residue 1 PHE Chi-restraints excluded: chain A4 residue 5 PHE Chi-restraints excluded: chain A3 residue 5 PHE Chi-restraints excluded: chain A3 residue 6 LYS Chi-restraints excluded: chain A3 residue 7 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1 random chunks: chunk 0 optimal weight: 5.9990 overall best weight: 50.0000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.106634 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3139 r_free = 0.3139 target = 0.080927 restraints weight = 17766.473| |-----------------------------------------------------------------------------| r_work (start): 0.3049 rms_B_bonded: 1.87 r_work: 0.2936 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.2818 rms_B_bonded: 4.37 restraints_weight: 0.2500 r_work (final): 0.2818 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8843 moved from start: 0.8878 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.059 0.226 8200 Z= 2.503 Angle : 2.530 18.690 10400 Z= 1.267 Chirality : 0.167 0.446 700 Planarity : 0.015 0.039 1300 Dihedral : 42.992 174.623 928 Min Nonbonded Distance : 1.812 Molprobity Statistics. All-atom Clashscore : 79.61 Ramachandran Plot: Outliers : 0.33 % Allowed : 40.50 % Favored : 59.17 % Rotamer: Outliers : 17.29 % Allowed : 32.14 % Favored : 50.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 3.14 % 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: -7.08 (0.18), residues: 600 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -5.39 (0.14), residues: 600 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.074 0.009 PHEAJ 5 Details of bonding type rmsd/Z covalent geometry : bond 0.05938 / 2.52 ( 8100) covalent geometry : angle 2.52980 / 1.27 (10400) hydrogen bonds : bond 0.09807 / 5.70 ( 125) hydrogen bonds : angle 8.48792 / 5.23 ( 375) Misc. bond : bond 0.00914 / 0.49 ( 100) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1200 Ramachandran restraints generated. 600 Oldfield, 0 Emsley, 600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1200 Ramachandran restraints generated. 600 Oldfield, 0 Emsley, 600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 271 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 121 poor density : 150 time to evaluate : 0.195 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: o 6 LYS cc_start: 0.8322 (OUTLIER) cc_final: 0.8009 (mmtt) REVERT: V 2 LYS cc_start: 0.8048 (tmtt) cc_final: 0.7720 (tttm) REVERT: r 6 LYS cc_start: 0.8273 (OUTLIER) cc_final: 0.7226 (mmtt) REVERT: X 2 LYS cc_start: 0.8725 (ttpp) cc_final: 0.8471 (tmtt) REVERT: v 6 LYS cc_start: 0.8325 (OUTLIER) cc_final: 0.8102 (mmtm) REVERT: Y 7 PHE cc_start: 0.8972 (OUTLIER) cc_final: 0.8669 (t80) REVERT: 2 6 LYS cc_start: 0.8288 (OUTLIER) cc_final: 0.7840 (mmtt) REVERT: 5 5 PHE cc_start: 0.8906 (OUTLIER) cc_final: 0.8322 (p90) REVERT: 5 6 LYS cc_start: 0.8128 (OUTLIER) cc_final: 0.7024 (mmtt) REVERT: b 7 PHE cc_start: 0.8996 (OUTLIER) cc_final: 0.8522 (t80) REVERT: c 2 LYS cc_start: 0.8766 (ttpp) cc_final: 0.8531 (tmtt) REVERT: AG 1 PHE cc_start: 0.8209 (OUTLIER) cc_final: 0.7932 (m-10) REVERT: AG 6 LYS cc_start: 0.8299 (OUTLIER) cc_final: 0.7972 (mmtt) REVERT: AF 5 PHE cc_start: 0.9160 (OUTLIER) cc_final: 0.8657 (m-80) REVERT: AJ 1 PHE cc_start: 0.8299 (OUTLIER) cc_final: 0.7934 (m-10) REVERT: AJ 6 LYS cc_start: 0.8038 (OUTLIER) cc_final: 0.7032 (mmtt) REVERT: g 6 LYS cc_start: 0.8464 (OUTLIER) cc_final: 0.8131 (mttm) REVERT: AX 1 PHE cc_start: 0.8258 (OUTLIER) cc_final: 0.7942 (m-10) REVERT: AX 6 LYS cc_start: 0.8428 (OUTLIER) cc_final: 0.8219 (mmtm) REVERT: AZ 2 LYS cc_start: 0.8419 (tttm) cc_final: 0.8160 (tttm) REVERT: Ab 6 LYS cc_start: 0.8143 (OUTLIER) cc_final: 0.6956 (mmtt) REVERT: Aj 6 LYS cc_start: 0.8189 (OUTLIER) cc_final: 0.7927 (mmtt) REVERT: Ar 6 LYS cc_start: 0.8308 (OUTLIER) cc_final: 0.8022 (mmtt) REVERT: Av 6 LYS cc_start: 0.8280 (OUTLIER) cc_final: 0.7065 (mmtt) REVERT: Ax 2 LYS cc_start: 0.8148 (tmtt) cc_final: 0.7918 (tttm) REVERT: A2 2 LYS cc_start: 0.8763 (ttpp) cc_final: 0.7920 (mptt) REVERT: A4 6 LYS cc_start: 0.8333 (mmtm) cc_final: 0.8063 (mmtm) outliers start: 121 outliers final: 95 residues processed: 232 average time/residue: 0.1469 time to fit residues: 40.9522 Evaluate side-chains 266 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 115 poor density : 151 time to evaluate : 0.316 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain n residue 1 PHE Chi-restraints excluded: chain n residue 5 PHE Chi-restraints excluded: chain n residue 6 LYS Chi-restraints excluded: chain i residue 5 PHE Chi-restraints excluded: chain p residue 7 PHE Chi-restraints excluded: chain o residue 1 PHE Chi-restraints excluded: chain o residue 6 LYS Chi-restraints excluded: chain j residue 6 LYS Chi-restraints excluded: chain r residue 1 PHE Chi-restraints excluded: chain r residue 6 LYS Chi-restraints excluded: chain k residue 5 PHE Chi-restraints excluded: chain k residue 8 GLU Chi-restraints excluded: chain t residue 1 PHE Chi-restraints excluded: chain t residue 5 PHE Chi-restraints excluded: chain t residue 6 LYS Chi-restraints excluded: chain l residue 5 PHE Chi-restraints excluded: chain u residue 6 LYS Chi-restraints excluded: chain v residue 1 PHE Chi-restraints excluded: chain v residue 6 LYS Chi-restraints excluded: chain m residue 6 LYS Chi-restraints excluded: chain m residue 7 PHE Chi-restraints excluded: chain Y residue 7 PHE Chi-restraints excluded: chain Y residue 8 GLU Chi-restraints excluded: chain y residue 1 PHE Chi-restraints excluded: chain y residue 5 PHE Chi-restraints excluded: chain y residue 6 LYS Chi-restraints excluded: chain x residue 5 PHE Chi-restraints excluded: chain z residue 7 PHE Chi-restraints excluded: chain 2 residue 1 PHE Chi-restraints excluded: chain 2 residue 6 LYS Chi-restraints excluded: chain 1 residue 6 LYS Chi-restraints excluded: chain 1 residue 7 PHE Chi-restraints excluded: chain 5 residue 1 PHE Chi-restraints excluded: chain 5 residue 5 PHE Chi-restraints excluded: chain 5 residue 6 LYS Chi-restraints excluded: chain 4 residue 5 PHE Chi-restraints excluded: chain b residue 7 PHE Chi-restraints excluded: chain 8 residue 1 PHE Chi-restraints excluded: chain 8 residue 6 LYS Chi-restraints excluded: chain 7 residue 5 PHE Chi-restraints excluded: chain 7 residue 6 LYS Chi-restraints excluded: chain 7 residue 7 PHE Chi-restraints excluded: chain c residue 8 GLU Chi-restraints excluded: chain AA residue 1 PHE Chi-restraints excluded: chain AA residue 5 PHE Chi-restraints excluded: chain 0 residue 7 PHE Chi-restraints excluded: chain AD residue 1 PHE Chi-restraints excluded: chain AD residue 6 LYS Chi-restraints excluded: chain AC residue 5 PHE Chi-restraints excluded: chain AC residue 6 LYS Chi-restraints excluded: chain AE residue 7 PHE Chi-restraints excluded: chain AE residue 8 GLU Chi-restraints excluded: chain AG residue 1 PHE Chi-restraints excluded: chain AG residue 6 LYS Chi-restraints excluded: chain AF residue 5 PHE Chi-restraints excluded: chain AF residue 6 LYS Chi-restraints excluded: chain AF residue 7 PHE Chi-restraints excluded: chain AJ residue 1 PHE Chi-restraints excluded: chain AJ residue 5 PHE Chi-restraints excluded: chain AJ residue 6 LYS Chi-restraints excluded: chain AI residue 5 PHE Chi-restraints excluded: chain g residue 6 LYS Chi-restraints excluded: chain AM residue 1 PHE Chi-restraints excluded: chain AM residue 5 PHE Chi-restraints excluded: chain AM residue 6 LYS Chi-restraints excluded: chain AL residue 5 PHE Chi-restraints excluded: chain AP residue 3 PHE Chi-restraints excluded: chain AP residue 5 PHE Chi-restraints excluded: chain AO residue 6 LYS Chi-restraints excluded: chain AO residue 7 PHE Chi-restraints excluded: chain AT residue 1 PHE Chi-restraints excluded: chain AT residue 5 PHE Chi-restraints excluded: chain AT residue 6 LYS Chi-restraints excluded: chain AS residue 5 PHE Chi-restraints excluded: chain AU residue 7 PHE Chi-restraints excluded: chain AU residue 8 GLU Chi-restraints excluded: chain AX residue 1 PHE Chi-restraints excluded: chain AX residue 5 PHE Chi-restraints excluded: chain AX residue 6 LYS Chi-restraints excluded: chain AW residue 6 LYS Chi-restraints excluded: chain Ab residue 1 PHE Chi-restraints excluded: chain Ab residue 5 PHE Chi-restraints excluded: chain Ab residue 6 LYS Chi-restraints excluded: chain Aa residue 5 PHE Chi-restraints excluded: chain Ad residue 8 GLU Chi-restraints excluded: chain Af residue 1 PHE Chi-restraints excluded: chain Af residue 5 PHE Chi-restraints excluded: chain Af residue 6 LYS Chi-restraints excluded: chain Ag residue 6 LYS Chi-restraints excluded: chain Aj residue 1 PHE Chi-restraints excluded: chain Aj residue 6 LYS Chi-restraints excluded: chain Ai residue 6 LYS Chi-restraints excluded: chain Ai residue 7 PHE Chi-restraints excluded: chain An residue 1 PHE Chi-restraints excluded: chain An residue 5 PHE Chi-restraints excluded: chain An residue 6 LYS Chi-restraints excluded: chain Am residue 5 PHE Chi-restraints excluded: chain Ao residue 7 PHE Chi-restraints excluded: chain Ar residue 1 PHE Chi-restraints excluded: chain Ar residue 6 LYS Chi-restraints excluded: chain Av residue 1 PHE Chi-restraints excluded: chain Av residue 5 PHE Chi-restraints excluded: chain Av residue 6 LYS Chi-restraints excluded: chain Au residue 5 PHE Chi-restraints excluded: chain Ax residue 8 GLU Chi-restraints excluded: chain Az residue 1 PHE Chi-restraints excluded: chain Az residue 6 LYS Chi-restraints excluded: chain Ay residue 5 PHE Chi-restraints excluded: chain Ay residue 7 PHE Chi-restraints excluded: chain A2 residue 8 GLU Chi-restraints excluded: chain A4 residue 1 PHE Chi-restraints excluded: chain A4 residue 5 PHE Chi-restraints excluded: chain A3 residue 5 PHE Chi-restraints excluded: chain A3 residue 6 LYS Chi-restraints excluded: chain A3 residue 7 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1 random chunks: chunk 0 optimal weight: 5.9990 overall best weight: 50.0000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.106670 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3141 r_free = 0.3141 target = 0.081046 restraints weight = 17379.910| |-----------------------------------------------------------------------------| r_work (start): 0.3050 rms_B_bonded: 1.84 r_work: 0.2937 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.2820 rms_B_bonded: 4.33 restraints_weight: 0.2500 r_work (final): 0.2820 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8839 moved from start: 0.8886 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.059 0.225 8200 Z= 2.503 Angle : 2.534 19.045 10400 Z= 1.269 Chirality : 0.167 0.439 700 Planarity : 0.015 0.039 1300 Dihedral : 43.002 174.680 928 Min Nonbonded Distance : 1.811 Molprobity Statistics. All-atom Clashscore : 79.61 Ramachandran Plot: Outliers : 0.50 % Allowed : 40.50 % Favored : 59.00 % Rotamer: Outliers : 16.86 % Allowed : 32.57 % Favored : 50.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 3.14 % 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: -7.09 (0.18), residues: 600 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -5.40 (0.14), residues: 600 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.074 0.009 PHEAJ 5 Details of bonding type rmsd/Z covalent geometry : bond 0.05937 / 2.52 ( 8100) covalent geometry : angle 2.53396 / 1.27 (10400) hydrogen bonds : bond 0.09812 / 5.70 ( 125) hydrogen bonds : angle 8.50501 / 5.24 ( 375) Misc. bond : bond 0.00915 / 0.49 ( 100) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1833.63 seconds wall clock time: 32 minutes 18.59 seconds (1938.59 seconds total)