Starting phenix.real_space_refine on Fri Oct 23 02:22:05 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9pdv_71545/10_2026/9pdv_71545.cif Found real_map, /net/cci-nas-00/data/ceres_data/9pdv_71545/10_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_71545/10_2026/9pdv_71545.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9pdv_71545/10_2026/9pdv_71545.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9pdv_71545/10_2026/9pdv_71545.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9pdv_71545/10_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-2.3rc1-6221/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: 2.08, per 1000 atoms: 0.26 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: 0.68 Conformation dependent library (CDL) restraints added in 287.1 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: 0.21 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: 1.11 Time building geometry restraints manager: 0.90 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: 0.550 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.140 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 8.360 Find NCS groups from input model: 0.280 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.260 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 10.700 ------------------------------------------------------------------------------- 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 : 0.289 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: 0.1193 time to fit residues: 32.8624 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 : 0.305 ------------------------------------------------------------------------------- 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: [0] chunk 0 optimal weight: 0.9980 overall best weight: 0.9980 ------------------------------------------------------------------------------- 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 = 0.4210 r_free = 0.4210 target = 0.153783 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 23)----------------| | r_work = 0.3866 r_free = 0.3866 target = 0.127947 restraints weight = 10985.421| |-----------------------------------------------------------------------------| r_work (start): 0.3854 rms_B_bonded: 1.99 r_work: 0.3728 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work (final): 0.3728 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7906 moved from start: 0.2316 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 8200 Z= 0.118 Angle : 0.661 5.504 10400 Z= 0.321 Chirality : 0.030 0.070 700 Planarity : 0.003 0.009 1300 Dihedral : 52.355 179.995 950 Min Nonbonded Distance : 2.599 Molprobity Statistics. All-atom Clashscore : 3.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.50 % Favored : 91.50 % Rotamer: Outliers : 5.00 % Allowed : 27.71 % Favored : 67.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.93 (0.31), residues: 600 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.23 (0.24), residues: 600 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.016 0.001 PHE m 1 Details of bonding type rmsd/Z covalent geometry : bond 0.00277 / 0.12 ( 8100) covalent geometry : angle 0.66145 / 0.32 (10400) hydrogen bonds : bond 0.02393 / 1.40 ( 125) hydrogen bonds : angle 3.63393 / 2.37 ( 375) Misc. bond : bond 0.00028 / 0.01 ( 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 180 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 145 time to evaluate : 0.263 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: T 6 LYS cc_start: 0.7808 (mttm) cc_final: 0.7556 (mmtm) REVERT: n 1 PHE cc_start: 0.5896 (OUTLIER) cc_final: 0.5443 (m-10) REVERT: o 1 PHE cc_start: 0.6106 (OUTLIER) cc_final: 0.5625 (m-80) REVERT: V 6 LYS cc_start: 0.7719 (mttp) cc_final: 0.7278 (mptt) REVERT: r 1 PHE cc_start: 0.5845 (OUTLIER) cc_final: 0.5372 (m-80) REVERT: t 1 PHE cc_start: 0.6199 (OUTLIER) cc_final: 0.5861 (m-80) REVERT: v 1 PHE cc_start: 0.6076 (OUTLIER) cc_final: 0.5590 (m-80) REVERT: y 1 PHE cc_start: 0.6011 (OUTLIER) cc_final: 0.5423 (m-10) REVERT: 2 1 PHE cc_start: 0.5961 (OUTLIER) cc_final: 0.5405 (m-80) REVERT: a 6 LYS cc_start: 0.7647 (mttp) cc_final: 0.7233 (mptt) REVERT: 5 1 PHE cc_start: 0.5752 (OUTLIER) cc_final: 0.5265 (m-80) REVERT: 8 1 PHE cc_start: 0.5891 (OUTLIER) cc_final: 0.5409 (m-80) REVERT: AA 1 PHE cc_start: 0.5965 (OUTLIER) cc_final: 0.5358 (m-80) REVERT: d 6 LYS cc_start: 0.7559 (mttp) cc_final: 0.7254 (mmtm) REVERT: AD 1 PHE cc_start: 0.6098 (OUTLIER) cc_final: 0.5421 (m-10) REVERT: e 6 LYS cc_start: 0.7677 (mttm) cc_final: 0.7304 (mptt) REVERT: AG 1 PHE cc_start: 0.5746 (OUTLIER) cc_final: 0.5248 (m-80) REVERT: f 6 LYS cc_start: 0.7699 (mttp) cc_final: 0.7287 (mptt) REVERT: AJ 1 PHE cc_start: 0.5956 (OUTLIER) cc_final: 0.5467 (m-80) REVERT: AM 1 PHE cc_start: 0.5930 (OUTLIER) cc_final: 0.5455 (m-80) REVERT: AP 1 PHE cc_start: 0.6072 (OUTLIER) cc_final: 0.5487 (m-80) REVERT: AR 6 LYS cc_start: 0.7624 (mttm) cc_final: 0.7357 (mmtm) REVERT: AT 1 PHE cc_start: 0.6206 (OUTLIER) cc_final: 0.5581 (m-10) REVERT: AX 1 PHE cc_start: 0.5948 (OUTLIER) cc_final: 0.5534 (m-80) REVERT: Ab 1 PHE cc_start: 0.6109 (OUTLIER) cc_final: 0.5844 (m-80) REVERT: Af 1 PHE cc_start: 0.5957 (OUTLIER) cc_final: 0.5541 (m-80) REVERT: Aj 1 PHE cc_start: 0.6120 (OUTLIER) cc_final: 0.5634 (m-80) REVERT: Al 6 LYS cc_start: 0.7654 (mttm) cc_final: 0.7403 (mmtm) REVERT: An 1 PHE cc_start: 0.5959 (OUTLIER) cc_final: 0.5383 (m-10) REVERT: Am 8 GLU cc_start: 0.8627 (tt0) cc_final: 0.8426 (tt0) REVERT: Ar 1 PHE cc_start: 0.5962 (OUTLIER) cc_final: 0.5382 (m-80) REVERT: At 6 LYS cc_start: 0.7783 (mttp) cc_final: 0.7309 (mptt) REVERT: Av 1 PHE cc_start: 0.6033 (OUTLIER) cc_final: 0.5530 (m-80) REVERT: Az 1 PHE cc_start: 0.5864 (OUTLIER) cc_final: 0.5595 (m-80) REVERT: A4 1 PHE cc_start: 0.6233 (OUTLIER) cc_final: 0.5716 (m-80) outliers start: 35 outliers final: 0 residues processed: 180 average time/residue: 0.1265 time to fit residues: 28.4690 Evaluate side-chains 135 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 110 time to evaluate : 0.205 ------------------------------------------------------------------------------- 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=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1 random chunks: [0] chunk 0 optimal weight: 10.0000 overall best weight: 10.0000 ------------------------------------------------------------------------------- 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 = 0.3919 r_free = 0.3919 target = 0.134193 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.106673 restraints weight = 12190.229| |-----------------------------------------------------------------------------| r_work (start): 0.3503 rms_B_bonded: 2.01 r_work: 0.3374 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work: 0.3230 rms_B_bonded: 5.00 restraints_weight: 0.2500 r_work (final): 0.3230 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8464 moved from start: 0.4510 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.013 0.040 8200 Z= 0.563 Angle : 0.989 7.822 10400 Z= 0.475 Chirality : 0.044 0.120 700 Planarity : 0.006 0.017 1300 Dihedral : 51.842 179.954 950 Min Nonbonded Distance : 2.175 Molprobity Statistics. All-atom Clashscore : 15.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 22.50 % Favored : 77.50 % Rotamer: Outliers : 5.00 % Allowed : 31.43 % Favored : 63.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.00 (0.24), residues: 600 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.04 (0.18), residues: 600 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.026 0.004 PHE Z 1 Details of bonding type rmsd/Z covalent geometry : bond 0.01318 / 0.57 ( 8100) covalent geometry : angle 0.98877 / 0.47 (10400) hydrogen bonds : bond 0.02318 / 1.35 ( 125) hydrogen bonds : angle 4.03241 / 2.50 ( 375) Misc. bond : bond 0.00189 / 0.10 ( 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 163 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 128 time to evaluate : 0.344 Fit side-chains revert: symmetry clash REVERT: T 2 LYS cc_start: 0.7406 (tmtt) cc_final: 0.7033 (tmtt) REVERT: T 6 LYS cc_start: 0.8418 (mttm) cc_final: 0.7964 (mmtt) REVERT: p 8 GLU cc_start: 0.5813 (tp30) cc_final: 0.3802 (tp30) REVERT: U 6 LYS cc_start: 0.8289 (mttm) cc_final: 0.7962 (mptt) REVERT: o 1 PHE cc_start: 0.6618 (OUTLIER) cc_final: 0.6297 (m-80) REVERT: V 2 LYS cc_start: 0.7324 (tmtt) cc_final: 0.6654 (tmtt) REVERT: r 1 PHE cc_start: 0.6575 (OUTLIER) cc_final: 0.6161 (m-80) REVERT: W 2 LYS cc_start: 0.7300 (tmtt) cc_final: 0.6975 (tmtt) REVERT: t 6 LYS cc_start: 0.7847 (mmtt) cc_final: 0.7584 (mmtm) REVERT: X 2 LYS cc_start: 0.8472 (ttpp) cc_final: 0.7972 (tmtt) REVERT: v 1 PHE cc_start: 0.6633 (OUTLIER) cc_final: 0.6111 (m-80) REVERT: Y 2 LYS cc_start: 0.7216 (tmtt) cc_final: 0.6918 (tmtt) REVERT: Y 6 LYS cc_start: 0.8521 (mmtt) cc_final: 0.8301 (mmtt) REVERT: y 1 PHE cc_start: 0.6876 (OUTLIER) cc_final: 0.6540 (m-80) REVERT: z 8 GLU cc_start: 0.5729 (tp30) cc_final: 0.3812 (tp30) REVERT: Z 6 LYS cc_start: 0.8249 (mttm) cc_final: 0.7928 (mptt) REVERT: 2 1 PHE cc_start: 0.6638 (OUTLIER) cc_final: 0.6115 (m-80) REVERT: a 2 LYS cc_start: 0.7304 (tmtt) cc_final: 0.6672 (tmtt) REVERT: a 6 LYS cc_start: 0.8150 (mttp) cc_final: 0.7851 (mptt) REVERT: 5 1 PHE cc_start: 0.6697 (OUTLIER) cc_final: 0.6303 (m-80) REVERT: b 2 LYS cc_start: 0.7211 (tmtt) cc_final: 0.6948 (tmtt) REVERT: c 2 LYS cc_start: 0.8452 (ttpp) cc_final: 0.7884 (tmtt) REVERT: AA 1 PHE cc_start: 0.6521 (OUTLIER) cc_final: 0.5990 (m-80) REVERT: d 2 LYS cc_start: 0.7301 (tmtt) cc_final: 0.6976 (tmtt) REVERT: AD 1 PHE cc_start: 0.6873 (OUTLIER) cc_final: 0.6405 (m-80) REVERT: AE 8 GLU cc_start: 0.5869 (tp30) cc_final: 0.4929 (tp30) REVERT: e 2 LYS cc_start: 0.6949 (tmtt) cc_final: 0.6244 (tmtt) REVERT: AG 1 PHE cc_start: 0.6453 (OUTLIER) cc_final: 0.6149 (m-80) REVERT: f 2 LYS cc_start: 0.7401 (tmtt) cc_final: 0.6889 (tmtt) REVERT: f 6 LYS cc_start: 0.8238 (mttp) cc_final: 0.7954 (mptt) REVERT: AJ 1 PHE cc_start: 0.6602 (OUTLIER) cc_final: 0.6165 (m-80) REVERT: g 2 LYS cc_start: 0.7285 (tmtt) cc_final: 0.6969 (tmtt) REVERT: AM 1 PHE cc_start: 0.6797 (OUTLIER) cc_final: 0.6407 (m-80) REVERT: AM 6 LYS cc_start: 0.7724 (mmtt) cc_final: 0.7469 (mmtm) REVERT: AP 1 PHE cc_start: 0.6605 (OUTLIER) cc_final: 0.6003 (m-80) REVERT: AR 2 LYS cc_start: 0.7474 (tmtt) cc_final: 0.7116 (tmtt) REVERT: AR 6 LYS cc_start: 0.8255 (mttm) cc_final: 0.7800 (mmtt) REVERT: AU 8 GLU cc_start: 0.5410 (tp30) cc_final: 0.4518 (tp30) REVERT: AV 6 LYS cc_start: 0.8210 (mttm) cc_final: 0.7873 (mptt) REVERT: AX 1 PHE cc_start: 0.6593 (OUTLIER) cc_final: 0.6241 (m-80) REVERT: AZ 2 LYS cc_start: 0.7217 (tmtt) cc_final: 0.6625 (tmtt) REVERT: AZ 6 LYS cc_start: 0.8279 (mttp) cc_final: 0.7915 (mptt) REVERT: Ab 1 PHE cc_start: 0.6685 (OUTLIER) cc_final: 0.6032 (m-80) REVERT: Ad 2 LYS cc_start: 0.7230 (tmtt) cc_final: 0.7024 (tmtt) REVERT: Ad 6 LYS cc_start: 0.8285 (mmtt) cc_final: 0.7908 (mptt) REVERT: Af 6 LYS cc_start: 0.7792 (mmtt) cc_final: 0.7548 (mmtm) REVERT: Ah 2 LYS cc_start: 0.8559 (ttpp) cc_final: 0.7960 (tmtt) REVERT: Ai 8 GLU cc_start: 0.8645 (tt0) cc_final: 0.7470 (pm20) REVERT: Al 6 LYS cc_start: 0.8384 (mttm) cc_final: 0.7964 (mmtt) REVERT: Ap 6 LYS cc_start: 0.8324 (mttm) cc_final: 0.7973 (mptt) REVERT: Ar 1 PHE cc_start: 0.6565 (OUTLIER) cc_final: 0.6099 (m-80) REVERT: At 2 LYS cc_start: 0.7312 (tmtt) cc_final: 0.6725 (tmtt) REVERT: At 6 LYS cc_start: 0.8213 (mttp) cc_final: 0.7884 (mptt) REVERT: Av 1 PHE cc_start: 0.6695 (OUTLIER) cc_final: 0.6306 (m-80) REVERT: Ax 2 LYS cc_start: 0.7147 (tmtt) cc_final: 0.6878 (tmtt) REVERT: Az 6 LYS cc_start: 0.7778 (mmtt) cc_final: 0.7526 (mmtm) REVERT: A2 2 LYS cc_start: 0.8471 (ttpp) cc_final: 0.7917 (tmtt) REVERT: A4 1 PHE cc_start: 0.6556 (OUTLIER) cc_final: 0.6000 (m-80) REVERT: A3 8 GLU cc_start: 0.8878 (tt0) cc_final: 0.7069 (pm20) outliers start: 35 outliers final: 13 residues processed: 163 average time/residue: 0.1579 time to fit residues: 31.0489 Evaluate side-chains 142 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 112 time to evaluate : 0.316 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain T residue 8 GLU 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 8 GLU 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 d residue 8 GLU 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 AR residue 8 GLU 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 Al residue 8 GLU 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1 random chunks: [0] chunk 0 optimal weight: 0.8980 overall best weight: 0.8980 ------------------------------------------------------------------------------- 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 = 0.4046 r_free = 0.4046 target = 0.143730 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3681 r_free = 0.3681 target = 0.116722 restraints weight = 11885.909| |-----------------------------------------------------------------------------| r_work (start): 0.3672 rms_B_bonded: 2.13 r_work: 0.3536 rms_B_bonded: 3.32 restraints_weight: 0.5000 r_work (final): 0.3536 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8247 moved from start: 0.4352 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.020 8200 Z= 0.111 Angle : 0.611 6.263 10400 Z= 0.296 Chirality : 0.029 0.076 700 Planarity : 0.002 0.011 1300 Dihedral : 52.346 179.990 950 Min Nonbonded Distance : 2.347 Molprobity Statistics. All-atom Clashscore : 8.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.33 % Favored : 93.67 % Rotamer: Outliers : 4.00 % Allowed : 30.86 % Favored : 65.14 % 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: -3.23 (0.27), residues: 600 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.45 (0.21), residues: 600 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.025 0.002 PHE X 1 Details of bonding type rmsd/Z covalent geometry : bond 0.00250 / 0.11 ( 8100) covalent geometry : angle 0.61105 / 0.30 (10400) hydrogen bonds : bond 0.01968 / 1.16 ( 125) hydrogen bonds : angle 3.38446 / 2.13 ( 375) Misc. bond : bond 0.00022 / 0.01 ( 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 170 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 142 time to evaluate : 0.246 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: T 2 LYS cc_start: 0.7368 (tmtt) cc_final: 0.7000 (tmtt) REVERT: T 6 LYS cc_start: 0.7876 (mttm) cc_final: 0.7449 (mmtt) REVERT: p 8 GLU cc_start: 0.5258 (tp30) cc_final: 0.3220 (tm-30) REVERT: U 6 LYS cc_start: 0.8020 (mttm) cc_final: 0.7584 (mptt) REVERT: o 1 PHE cc_start: 0.6045 (OUTLIER) cc_final: 0.5247 (m-80) REVERT: V 2 LYS cc_start: 0.7131 (tmtt) cc_final: 0.6590 (tmtt) REVERT: r 1 PHE cc_start: 0.6017 (OUTLIER) cc_final: 0.5348 (m-80) REVERT: W 2 LYS cc_start: 0.7256 (tmtt) cc_final: 0.6915 (tmtt) REVERT: W 6 LYS cc_start: 0.7877 (mmtt) cc_final: 0.7578 (mptt) REVERT: t 6 LYS cc_start: 0.7784 (mmtt) cc_final: 0.7421 (mmtm) REVERT: y 1 PHE cc_start: 0.6233 (OUTLIER) cc_final: 0.5648 (m-80) REVERT: z 8 GLU cc_start: 0.5227 (tp30) cc_final: 0.3586 (tm-30) REVERT: Z 6 LYS cc_start: 0.7911 (mttm) cc_final: 0.7550 (mmtm) REVERT: 2 1 PHE cc_start: 0.6034 (OUTLIER) cc_final: 0.5400 (m-80) REVERT: a 2 LYS cc_start: 0.7218 (tmtt) cc_final: 0.6682 (tmtt) REVERT: a 6 LYS cc_start: 0.7884 (mttp) cc_final: 0.7497 (mptt) REVERT: 5 1 PHE cc_start: 0.6250 (OUTLIER) cc_final: 0.5518 (m-80) REVERT: b 2 LYS cc_start: 0.7219 (tmtt) cc_final: 0.6875 (tmtt) REVERT: b 6 LYS cc_start: 0.7910 (mmtt) cc_final: 0.7599 (mptt) REVERT: AA 1 PHE cc_start: 0.6052 (OUTLIER) cc_final: 0.5071 (m-80) REVERT: AE 8 GLU cc_start: 0.5223 (tp30) cc_final: 0.3869 (tm-30) REVERT: e 6 LYS cc_start: 0.7804 (mttm) cc_final: 0.7548 (mptt) REVERT: AG 1 PHE cc_start: 0.5909 (OUTLIER) cc_final: 0.5208 (m-80) REVERT: f 2 LYS cc_start: 0.7192 (tmtt) cc_final: 0.6621 (tmtt) REVERT: f 6 LYS cc_start: 0.7919 (mttp) cc_final: 0.7572 (mptt) REVERT: AJ 1 PHE cc_start: 0.5912 (OUTLIER) cc_final: 0.5074 (m-80) REVERT: g 2 LYS cc_start: 0.7191 (tmtt) cc_final: 0.6926 (tmtt) REVERT: g 6 LYS cc_start: 0.7844 (mmtt) cc_final: 0.7535 (mptt) REVERT: AM 1 PHE cc_start: 0.6407 (OUTLIER) cc_final: 0.5730 (m-80) REVERT: AM 6 LYS cc_start: 0.7749 (mmtt) cc_final: 0.7502 (mmtm) REVERT: AP 1 PHE cc_start: 0.6134 (OUTLIER) cc_final: 0.4987 (m-80) REVERT: AQ 1 PHE cc_start: 0.8970 (m-80) cc_final: 0.8748 (m-80) REVERT: AR 2 LYS cc_start: 0.7314 (tmtt) cc_final: 0.6844 (tmtt) REVERT: AR 6 LYS cc_start: 0.7783 (mttm) cc_final: 0.7371 (mmtt) REVERT: AU 8 GLU cc_start: 0.4963 (tp30) cc_final: 0.3925 (tm-30) REVERT: AV 6 LYS cc_start: 0.7791 (mttm) cc_final: 0.7393 (mptt) REVERT: AX 1 PHE cc_start: 0.5974 (OUTLIER) cc_final: 0.5178 (m-80) REVERT: AZ 2 LYS cc_start: 0.7108 (tmtt) cc_final: 0.6597 (tmtt) REVERT: Ab 1 PHE cc_start: 0.6076 (OUTLIER) cc_final: 0.5366 (m-80) REVERT: Ad 6 LYS cc_start: 0.7964 (mmtt) cc_final: 0.7475 (mptt) REVERT: Af 1 PHE cc_start: 0.6345 (OUTLIER) cc_final: 0.5577 (m-80) REVERT: Af 6 LYS cc_start: 0.7776 (mmtt) cc_final: 0.7543 (mmtm) REVERT: Al 6 LYS cc_start: 0.7939 (mttm) cc_final: 0.7555 (mmtt) REVERT: Am 6 LYS cc_start: 0.8509 (tttt) cc_final: 0.8288 (tttp) REVERT: Ap 6 LYS cc_start: 0.7944 (mttm) cc_final: 0.7502 (mptt) REVERT: Ar 1 PHE cc_start: 0.6096 (OUTLIER) cc_final: 0.5323 (m-80) REVERT: At 2 LYS cc_start: 0.7133 (tmtt) cc_final: 0.6539 (tmtt) REVERT: At 6 LYS cc_start: 0.7977 (mttp) cc_final: 0.7520 (mptt) REVERT: Av 1 PHE cc_start: 0.6145 (OUTLIER) cc_final: 0.5278 (m-80) REVERT: Ax 2 LYS cc_start: 0.7145 (tmtt) cc_final: 0.6907 (tmtt) REVERT: Ax 6 LYS cc_start: 0.7930 (mmtt) cc_final: 0.7663 (mptt) REVERT: Az 6 LYS cc_start: 0.7834 (mmtt) cc_final: 0.7489 (mmtm) REVERT: A4 1 PHE cc_start: 0.6202 (OUTLIER) cc_final: 0.5104 (m-80) outliers start: 28 outliers final: 4 residues processed: 169 average time/residue: 0.1395 time to fit residues: 28.9956 Evaluate side-chains 131 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 111 time to evaluate : 0.208 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 AX residue 1 PHE Chi-restraints excluded: chain Ab residue 1 PHE Chi-restraints excluded: chain Af 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1 random chunks: [0] chunk 0 optimal weight: 10.0000 overall best weight: 10.0000 ------------------------------------------------------------------------------- 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 = 0.3873 r_free = 0.3873 target = 0.130059 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3509 r_free = 0.3509 target = 0.103402 restraints weight = 11791.970| |-----------------------------------------------------------------------------| r_work (start): 0.3444 rms_B_bonded: 1.93 r_work: 0.3307 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work: 0.3164 rms_B_bonded: 4.81 restraints_weight: 0.2500 r_work (final): 0.3164 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8550 moved from start: 0.5348 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.014 0.042 8200 Z= 0.574 Angle : 0.966 6.838 10400 Z= 0.461 Chirality : 0.044 0.126 700 Planarity : 0.005 0.016 1300 Dihedral : 51.713 179.994 940 Min Nonbonded Distance : 2.132 Molprobity Statistics. All-atom Clashscore : 16.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 29.00 % Favored : 71.00 % Rotamer: Outliers : 5.57 % Allowed : 26.29 % Favored : 68.14 % 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: -3.75 (0.25), residues: 600 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.85 (0.19), residues: 600 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.034 0.004 PHEAV 1 Details of bonding type rmsd/Z covalent geometry : bond 0.01359 / 0.58 ( 8100) covalent geometry : angle 0.96558 / 0.46 (10400) hydrogen bonds : bond 0.02492 / 1.44 ( 125) hydrogen bonds : angle 3.92063 / 2.42 ( 375) Misc. bond : bond 0.00210 / 0.11 ( 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 157 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 118 time to evaluate : 0.276 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: T 2 LYS cc_start: 0.7559 (tmtt) cc_final: 0.7071 (tmtt) REVERT: T 6 LYS cc_start: 0.8357 (mttm) cc_final: 0.7897 (mmtt) REVERT: U 6 LYS cc_start: 0.8294 (mttm) cc_final: 0.7974 (mptt) REVERT: o 1 PHE cc_start: 0.6717 (OUTLIER) cc_final: 0.5901 (m-80) REVERT: r 5 PHE cc_start: 0.8098 (OUTLIER) cc_final: 0.7682 (p90) REVERT: W 2 LYS cc_start: 0.7338 (tmtt) cc_final: 0.6974 (tmtt) REVERT: X 2 LYS cc_start: 0.8443 (ttpp) cc_final: 0.7860 (tmtt) REVERT: Y 2 LYS cc_start: 0.7213 (tmtt) cc_final: 0.6835 (tmtt) REVERT: Z 2 LYS cc_start: 0.7346 (tmtt) cc_final: 0.6836 (tmtt) REVERT: a 6 LYS cc_start: 0.8209 (mttp) cc_final: 0.7921 (mptt) REVERT: b 2 LYS cc_start: 0.7408 (tmtt) cc_final: 0.7075 (tmtt) REVERT: c 2 LYS cc_start: 0.8450 (ttpp) cc_final: 0.7854 (tmtt) REVERT: d 2 LYS cc_start: 0.7261 (tmtt) cc_final: 0.6874 (tmtt) REVERT: e 2 LYS cc_start: 0.6979 (tmtt) cc_final: 0.6193 (tmtt) REVERT: AF 6 LYS cc_start: 0.8640 (tttt) cc_final: 0.8439 (tttp) REVERT: f 6 LYS cc_start: 0.8327 (mttp) cc_final: 0.8045 (mptt) REVERT: AJ 1 PHE cc_start: 0.6789 (OUTLIER) cc_final: 0.5787 (m-80) REVERT: g 2 LYS cc_start: 0.7227 (tmtt) cc_final: 0.6828 (tmtt) REVERT: AR 2 LYS cc_start: 0.7582 (tmtt) cc_final: 0.7076 (tmtt) REVERT: AR 6 LYS cc_start: 0.8238 (mttm) cc_final: 0.7830 (mmtt) REVERT: AV 2 LYS cc_start: 0.7136 (tmtt) cc_final: 0.6338 (tmtt) REVERT: AV 6 LYS cc_start: 0.8221 (mttm) cc_final: 0.7871 (mptt) REVERT: AZ 6 LYS cc_start: 0.8295 (mttp) cc_final: 0.7962 (mptt) REVERT: Ab 5 PHE cc_start: 0.8021 (OUTLIER) cc_final: 0.7633 (p90) REVERT: Ad 2 LYS cc_start: 0.7311 (tmtt) cc_final: 0.6920 (tmtt) REVERT: Ad 6 LYS cc_start: 0.8295 (mmtt) cc_final: 0.8012 (mmtt) REVERT: Ah 2 LYS cc_start: 0.8546 (ttpp) cc_final: 0.7896 (tmtt) REVERT: Al 2 LYS cc_start: 0.7435 (tmtt) cc_final: 0.7063 (tmtt) REVERT: Al 6 LYS cc_start: 0.8352 (mttm) cc_final: 0.7945 (mmtt) REVERT: Ap 6 LYS cc_start: 0.8318 (mttm) cc_final: 0.7966 (mptt) REVERT: Ar 1 PHE cc_start: 0.6674 (OUTLIER) cc_final: 0.5822 (m-80) REVERT: At 6 LYS cc_start: 0.8307 (mttp) cc_final: 0.7969 (mptt) REVERT: Ax 2 LYS cc_start: 0.7288 (tmtt) cc_final: 0.6914 (tmtt) REVERT: A2 2 LYS cc_start: 0.8402 (ttpp) cc_final: 0.7774 (tmtt) outliers start: 39 outliers final: 27 residues processed: 156 average time/residue: 0.1676 time to fit residues: 31.1190 Evaluate side-chains 145 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 113 time to evaluate : 0.362 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain n residue 5 PHE Chi-restraints excluded: chain o residue 1 PHE Chi-restraints excluded: chain o residue 5 PHE Chi-restraints excluded: chain r residue 5 PHE Chi-restraints excluded: chain t residue 1 PHE Chi-restraints excluded: chain t residue 5 PHE Chi-restraints excluded: chain v residue 5 PHE Chi-restraints excluded: chain y residue 1 PHE Chi-restraints excluded: chain y residue 5 PHE Chi-restraints excluded: chain 2 residue 1 PHE Chi-restraints excluded: chain 2 residue 5 PHE Chi-restraints excluded: chain 8 residue 1 PHE Chi-restraints excluded: chain 8 residue 5 PHE Chi-restraints excluded: chain AA residue 5 PHE Chi-restraints excluded: chain AD residue 5 PHE Chi-restraints excluded: chain AG residue 1 PHE 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 AM residue 5 PHE Chi-restraints excluded: chain AP residue 5 PHE Chi-restraints excluded: chain AT residue 1 PHE Chi-restraints excluded: chain AT residue 5 PHE Chi-restraints excluded: chain AX residue 1 PHE Chi-restraints excluded: chain AX residue 5 PHE Chi-restraints excluded: chain Ab residue 5 PHE Chi-restraints excluded: chain Af residue 5 PHE Chi-restraints excluded: chain An residue 1 PHE Chi-restraints excluded: chain Ar residue 1 PHE Chi-restraints excluded: chain Ar residue 5 PHE Chi-restraints excluded: chain Az residue 5 PHE Chi-restraints excluded: chain A4 residue 5 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1 random chunks: [0] chunk 0 optimal weight: 0.9980 overall best weight: 0.9980 ------------------------------------------------------------------------------- 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 = 0.3999 r_free = 0.3999 target = 0.140833 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3641 r_free = 0.3641 target = 0.113861 restraints weight = 11122.932| |-----------------------------------------------------------------------------| r_work (start): 0.3620 rms_B_bonded: 2.04 r_work: 0.3482 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work (final): 0.3482 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8328 moved from start: 0.5161 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 8200 Z= 0.112 Angle : 0.641 6.237 10400 Z= 0.310 Chirality : 0.029 0.064 700 Planarity : 0.003 0.012 1300 Dihedral : 52.489 179.994 920 Min Nonbonded Distance : 2.351 Molprobity Statistics. All-atom Clashscore : 7.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.00 % Favored : 89.00 % Rotamer: Outliers : 1.57 % Allowed : 30.00 % Favored : 68.43 % 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: -3.59 (0.25), residues: 600 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.73 (0.19), residues: 600 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.027 0.002 PHEAV 1 Details of bonding type rmsd/Z covalent geometry : bond 0.00263 / 0.11 ( 8100) covalent geometry : angle 0.64069 / 0.31 (10400) hydrogen bonds : bond 0.02097 / 1.23 ( 125) hydrogen bonds : angle 3.11605 / 1.97 ( 375) Misc. bond : bond 0.00028 / 0.02 ( 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 135 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 124 time to evaluate : 0.296 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: T 2 LYS cc_start: 0.7463 (tmtt) cc_final: 0.7051 (tmtt) REVERT: U 6 LYS cc_start: 0.8083 (mttm) cc_final: 0.7716 (mmtm) REVERT: V 6 LYS cc_start: 0.7885 (mttp) cc_final: 0.7656 (mptt) REVERT: W 2 LYS cc_start: 0.7009 (tmtt) cc_final: 0.6647 (tmtt) REVERT: Y 6 LYS cc_start: 0.8067 (mmtt) cc_final: 0.7840 (mptt) REVERT: Z 2 LYS cc_start: 0.7161 (tmtt) cc_final: 0.6677 (tmtt) REVERT: Z 6 LYS cc_start: 0.7995 (mttm) cc_final: 0.7620 (mmtm) REVERT: b 2 LYS cc_start: 0.7239 (tmtt) cc_final: 0.6866 (tmtt) REVERT: d 6 LYS cc_start: 0.7972 (mttm) cc_final: 0.7588 (mmtm) REVERT: e 6 LYS cc_start: 0.7913 (mttm) cc_final: 0.7685 (mptt) REVERT: AF 6 LYS cc_start: 0.8416 (tttt) cc_final: 0.8208 (tptm) REVERT: g 2 LYS cc_start: 0.7084 (tmtt) cc_final: 0.6726 (tmtt) REVERT: AR 2 LYS cc_start: 0.7420 (tmtt) cc_final: 0.6955 (tmtt) REVERT: AR 6 LYS cc_start: 0.7989 (mttm) cc_final: 0.7508 (mmtt) REVERT: AV 6 LYS cc_start: 0.7885 (mttm) cc_final: 0.7099 (mmtm) REVERT: Ad 2 LYS cc_start: 0.7044 (tmtt) cc_final: 0.6480 (tmtt) REVERT: Aj 8 GLU cc_start: 0.7587 (mp0) cc_final: 0.7369 (mp0) REVERT: Al 2 LYS cc_start: 0.7329 (tmtt) cc_final: 0.6964 (tmtt) REVERT: Am 6 LYS cc_start: 0.8546 (tttt) cc_final: 0.8323 (tttp) REVERT: At 2 LYS cc_start: 0.7309 (tmtt) cc_final: 0.6679 (tmtt) REVERT: Av 5 PHE cc_start: 0.8043 (OUTLIER) cc_final: 0.7374 (p90) REVERT: Ax 2 LYS cc_start: 0.7092 (tmtt) cc_final: 0.6734 (tmtt) REVERT: Ax 6 LYS cc_start: 0.8033 (mmtt) cc_final: 0.7775 (mmtt) outliers start: 11 outliers final: 2 residues processed: 135 average time/residue: 0.1710 time to fit residues: 27.3602 Evaluate side-chains 120 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 117 time to evaluate : 0.302 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 8 residue 5 PHE Chi-restraints excluded: chain An residue 1 PHE Chi-restraints excluded: chain Av residue 5 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1 random chunks: [0] chunk 0 optimal weight: 10.0000 overall best weight: 10.0000 ------------------------------------------------------------------------------- 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 = 0.3835 r_free = 0.3835 target = 0.128514 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.102603 restraints weight = 11663.228| |-----------------------------------------------------------------------------| r_work (start): 0.3426 rms_B_bonded: 1.82 r_work: 0.3291 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.3150 rms_B_bonded: 4.73 restraints_weight: 0.2500 r_work (final): 0.3150 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8567 moved from start: 0.5914 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.013 0.041 8200 Z= 0.570 Angle : 1.018 7.528 10400 Z= 0.482 Chirality : 0.045 0.124 700 Planarity : 0.005 0.014 1300 Dihedral : 52.440 179.989 900 Min Nonbonded Distance : 2.096 Molprobity Statistics. All-atom Clashscore : 14.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 29.33 % Favored : 70.67 % Rotamer: Outliers : 5.14 % Allowed : 24.00 % Favored : 70.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.56 (0.28), residues: 600 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.71 (0.21), residues: 600 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.031 0.004 PHEAV 1 Details of bonding type rmsd/Z covalent geometry : bond 0.01345 / 0.57 ( 8100) covalent geometry : angle 1.01778 / 0.48 (10400) hydrogen bonds : bond 0.02529 / 1.48 ( 125) hydrogen bonds : angle 3.96275 / 2.42 ( 375) Misc. bond : bond 0.00209 / 0.11 ( 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 148 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 112 time to evaluate : 0.256 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: 0.7504 (tmtt) cc_final: 0.7045 (tmtt) REVERT: T 6 LYS cc_start: 0.8344 (mttm) cc_final: 0.7890 (mmtt) REVERT: r 5 PHE cc_start: 0.8240 (OUTLIER) cc_final: 0.7777 (p90) REVERT: W 2 LYS cc_start: 0.7317 (tmtt) cc_final: 0.6932 (tmtt) REVERT: X 2 LYS cc_start: 0.8445 (ttpp) cc_final: 0.7853 (tmtt) REVERT: Y 2 LYS cc_start: 0.7246 (tmtt) cc_final: 0.6843 (tmtt) REVERT: Y 6 LYS cc_start: 0.8419 (mmtt) cc_final: 0.8199 (mptt) REVERT: Z 2 LYS cc_start: 0.7326 (tmtt) cc_final: 0.6807 (tmtt) REVERT: b 2 LYS cc_start: 0.7483 (tmtt) cc_final: 0.7117 (tmtt) REVERT: c 2 LYS cc_start: 0.8433 (ttpp) cc_final: 0.7806 (tmtt) REVERT: d 2 LYS cc_start: 0.7189 (tmtt) cc_final: 0.6802 (tmtt) REVERT: e 2 LYS cc_start: 0.7188 (tmtt) cc_final: 0.6693 (tmtt) REVERT: AF 6 LYS cc_start: 0.8678 (tttt) cc_final: 0.8474 (tttp) REVERT: f 6 LYS cc_start: 0.8400 (mttp) cc_final: 0.8118 (mptt) REVERT: g 2 LYS cc_start: 0.7197 (tmtt) cc_final: 0.6841 (tmtt) REVERT: AR 6 LYS cc_start: 0.8291 (mttm) cc_final: 0.7936 (mmtt) REVERT: AV 2 LYS cc_start: 0.7056 (tmtt) cc_final: 0.6559 (tmtt) REVERT: AZ 6 LYS cc_start: 0.8329 (mttp) cc_final: 0.7989 (mptt) REVERT: Ab 5 PHE cc_start: 0.8158 (OUTLIER) cc_final: 0.7822 (p90) REVERT: Ad 2 LYS cc_start: 0.7222 (tmtt) cc_final: 0.6855 (tmtt) REVERT: Ad 6 LYS cc_start: 0.8311 (mmtt) cc_final: 0.8026 (mmtt) REVERT: Al 2 LYS cc_start: 0.7385 (tmtt) cc_final: 0.6973 (tmtt) REVERT: Al 6 LYS cc_start: 0.8357 (mttm) cc_final: 0.7948 (mmtt) REVERT: Ap 2 LYS cc_start: 0.7118 (tmtt) cc_final: 0.6673 (tmtt) REVERT: Ap 6 LYS cc_start: 0.8330 (mttm) cc_final: 0.7943 (mptt) REVERT: At 6 LYS cc_start: 0.8279 (mttp) cc_final: 0.7938 (mptt) REVERT: Ax 2 LYS cc_start: 0.7253 (tmtt) cc_final: 0.6875 (tmtt) REVERT: A2 2 LYS cc_start: 0.8409 (ttpp) cc_final: 0.7796 (tmtt) outliers start: 36 outliers final: 20 residues processed: 147 average time/residue: 0.1595 time to fit residues: 28.0559 Evaluate side-chains 131 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 109 time to evaluate : 0.281 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain n residue 5 PHE Chi-restraints excluded: chain o residue 5 PHE Chi-restraints excluded: chain r residue 5 PHE Chi-restraints excluded: chain v residue 5 PHE Chi-restraints excluded: chain y residue 5 PHE Chi-restraints excluded: chain 8 residue 5 PHE Chi-restraints excluded: chain AA residue 5 PHE Chi-restraints excluded: chain AD residue 5 PHE Chi-restraints excluded: chain AG residue 5 PHE Chi-restraints excluded: chain AM residue 5 PHE Chi-restraints excluded: chain AP residue 5 PHE Chi-restraints excluded: chain AT residue 1 PHE Chi-restraints excluded: chain AT residue 5 PHE Chi-restraints excluded: chain AX residue 5 PHE Chi-restraints excluded: chain Ab residue 5 PHE Chi-restraints excluded: chain Af residue 5 PHE Chi-restraints excluded: chain Aj residue 5 PHE Chi-restraints excluded: chain An residue 1 PHE Chi-restraints excluded: chain An residue 5 PHE Chi-restraints excluded: chain Ar residue 5 PHE Chi-restraints excluded: chain Az residue 5 PHE Chi-restraints excluded: chain A4 residue 5 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1 random chunks: [0] chunk 0 optimal weight: 0.9990 overall best weight: 0.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3940 r_free = 0.3940 target = 0.135479 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3596 r_free = 0.3596 target = 0.109366 restraints weight = 11225.047| |-----------------------------------------------------------------------------| r_work (start): 0.3593 rms_B_bonded: 2.01 r_work: 0.3451 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work (final): 0.3451 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8361 moved from start: 0.5708 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 8200 Z= 0.113 Angle : 0.649 6.710 10400 Z= 0.314 Chirality : 0.027 0.068 700 Planarity : 0.002 0.011 1300 Dihedral : 52.790 179.996 900 Min Nonbonded Distance : 2.344 Molprobity Statistics. All-atom Clashscore : 6.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 15.00 % Favored : 85.00 % Rotamer: Outliers : 0.00 % Allowed : 28.00 % Favored : 72.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.63 (0.25), residues: 600 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.76 (0.19), residues: 600 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.026 0.002 PHEAh 1 Details of bonding type rmsd/Z covalent geometry : bond 0.00260 / 0.11 ( 8100) covalent geometry : angle 0.64877 / 0.31 (10400) hydrogen bonds : bond 0.02022 / 1.18 ( 125) hydrogen bonds : angle 3.14193 / 1.96 ( 375) Misc. bond : bond 0.00028 / 0.02 ( 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 122 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 122 time to evaluate : 0.301 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: T 2 LYS cc_start: 0.7398 (tmtt) cc_final: 0.6954 (tmtt) REVERT: U 6 LYS cc_start: 0.8015 (mttm) cc_final: 0.7606 (mmtm) REVERT: V 6 LYS cc_start: 0.7907 (mttp) cc_final: 0.7628 (mptt) REVERT: W 2 LYS cc_start: 0.7005 (tmtt) cc_final: 0.6630 (tmtt) REVERT: Y 2 LYS cc_start: 0.7107 (tmtt) cc_final: 0.6663 (tmtt) REVERT: Z 6 LYS cc_start: 0.7912 (mttm) cc_final: 0.7605 (mptt) REVERT: a 2 LYS cc_start: 0.7171 (tttm) cc_final: 0.6556 (tmtt) REVERT: b 2 LYS cc_start: 0.7153 (tmtt) cc_final: 0.6836 (tmtt) REVERT: d 6 LYS cc_start: 0.8063 (mttm) cc_final: 0.7669 (mmtm) REVERT: e 2 LYS cc_start: 0.7018 (tmtt) cc_final: 0.6548 (tmtt) REVERT: e 6 LYS cc_start: 0.7965 (mttm) cc_final: 0.7700 (mptt) REVERT: g 2 LYS cc_start: 0.7031 (tmtt) cc_final: 0.6673 (tmtt) REVERT: AR 6 LYS cc_start: 0.8057 (mttm) cc_final: 0.7608 (mmtt) REVERT: AV 6 LYS cc_start: 0.7761 (mttp) cc_final: 0.7316 (mmtm) REVERT: AZ 2 LYS cc_start: 0.7300 (tttm) cc_final: 0.6565 (tmtt) REVERT: Ad 2 LYS cc_start: 0.6973 (tmtt) cc_final: 0.6647 (tmtt) REVERT: Ad 6 LYS cc_start: 0.8170 (mmtt) cc_final: 0.7659 (mptt) REVERT: Al 2 LYS cc_start: 0.7296 (tmtt) cc_final: 0.6873 (tmtt) REVERT: Am 6 LYS cc_start: 0.8571 (tttt) cc_final: 0.8339 (tttp) REVERT: Ap 6 LYS cc_start: 0.8055 (mttm) cc_final: 0.7602 (mmtm) REVERT: Ax 2 LYS cc_start: 0.7068 (tmtt) cc_final: 0.6680 (tmtt) outliers start: 0 outliers final: 0 residues processed: 122 average time/residue: 0.1825 time to fit residues: 25.9305 Evaluate side-chains 116 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 116 time to evaluate : 0.301 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1 random chunks: [0] chunk 0 optimal weight: 10.0000 overall best weight: 10.0000 ------------------------------------------------------------------------------- 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 = 0.3824 r_free = 0.3824 target = 0.127949 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.101896 restraints weight = 11933.622| |-----------------------------------------------------------------------------| r_work (start): 0.3386 rms_B_bonded: 1.89 r_work: 0.3249 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work: 0.3109 rms_B_bonded: 4.87 restraints_weight: 0.2500 r_work (final): 0.3109 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8549 moved from start: 0.6160 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.013 0.046 8200 Z= 0.560 Angle : 0.987 7.270 10400 Z= 0.467 Chirality : 0.044 0.118 700 Planarity : 0.005 0.015 1300 Dihedral : 52.406 179.922 900 Min Nonbonded Distance : 2.090 Molprobity Statistics. All-atom Clashscore : 11.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 29.00 % Favored : 71.00 % Rotamer: Outliers : 1.57 % Allowed : 25.71 % Favored : 72.71 % 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: -3.66 (0.27), residues: 600 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.78 (0.21), residues: 600 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.035 0.004 PHE 5 5 Details of bonding type rmsd/Z covalent geometry : bond 0.01328 / 0.56 ( 8100) covalent geometry : angle 0.98721 / 0.47 (10400) hydrogen bonds : bond 0.02336 / 1.36 ( 125) hydrogen bonds : angle 3.97928 / 2.44 ( 375) Misc. bond : bond 0.00212 / 0.11 ( 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 123 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 112 time to evaluate : 0.224 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: 0.7485 (tmtt) cc_final: 0.7021 (tmtt) REVERT: T 6 LYS cc_start: 0.8324 (mttm) cc_final: 0.7880 (mmtt) REVERT: U 2 LYS cc_start: 0.6962 (tmtt) cc_final: 0.6469 (tmtt) REVERT: W 2 LYS cc_start: 0.7300 (tmtt) cc_final: 0.6831 (tmtt) REVERT: X 2 LYS cc_start: 0.8416 (ttpp) cc_final: 0.7823 (tmtt) REVERT: Y 2 LYS cc_start: 0.7249 (tmtt) cc_final: 0.6842 (tmtt) REVERT: a 6 LYS cc_start: 0.8220 (mttp) cc_final: 0.7891 (mptt) REVERT: b 2 LYS cc_start: 0.7380 (tmtt) cc_final: 0.7029 (tmtt) REVERT: c 2 LYS cc_start: 0.8440 (ttpp) cc_final: 0.7804 (tmtt) REVERT: 0 6 LYS cc_start: 0.8851 (tttt) cc_final: 0.8640 (tttp) REVERT: e 2 LYS cc_start: 0.7030 (tmtt) cc_final: 0.6510 (tmtt) REVERT: f 6 LYS cc_start: 0.8344 (mttp) cc_final: 0.8053 (mptt) REVERT: AJ 5 PHE cc_start: 0.8267 (OUTLIER) cc_final: 0.7814 (p90) REVERT: g 2 LYS cc_start: 0.7210 (tmtt) cc_final: 0.6804 (tmtt) REVERT: AO 8 GLU cc_start: 0.8744 (tt0) cc_final: 0.7318 (pm20) REVERT: AR 6 LYS cc_start: 0.8284 (mttm) cc_final: 0.7863 (mmtt) REVERT: AV 2 LYS cc_start: 0.7000 (tmtt) cc_final: 0.6776 (tmtt) REVERT: AV 6 LYS cc_start: 0.8098 (mttp) cc_final: 0.7719 (mptt) REVERT: AZ 6 LYS cc_start: 0.8306 (mttp) cc_final: 0.7927 (mptt) REVERT: Ad 2 LYS cc_start: 0.7141 (tmtt) cc_final: 0.6782 (tmtt) REVERT: Ad 6 LYS cc_start: 0.8246 (mmtt) cc_final: 0.7972 (mmtt) REVERT: Al 2 LYS cc_start: 0.7419 (tmtt) cc_final: 0.7009 (tmtt) REVERT: Al 6 LYS cc_start: 0.8332 (mttm) cc_final: 0.7910 (mmtt) REVERT: Ap 2 LYS cc_start: 0.7212 (tmtt) cc_final: 0.6997 (tmtt) REVERT: Ap 6 LYS cc_start: 0.8288 (mttm) cc_final: 0.7892 (mptt) REVERT: At 6 LYS cc_start: 0.8250 (mttp) cc_final: 0.7871 (mptt) REVERT: Ax 2 LYS cc_start: 0.7177 (tmtt) cc_final: 0.6780 (tmtt) REVERT: A2 2 LYS cc_start: 0.8368 (ttpp) cc_final: 0.7797 (tmtt) outliers start: 11 outliers final: 5 residues processed: 123 average time/residue: 0.1708 time to fit residues: 24.7789 Evaluate side-chains 115 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 109 time to evaluate : 0.314 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 5 PHE Chi-restraints excluded: chain 8 residue 5 PHE Chi-restraints excluded: chain AJ residue 5 PHE Chi-restraints excluded: chain AX residue 5 PHE Chi-restraints excluded: chain An residue 5 PHE Chi-restraints excluded: chain Ar residue 5 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1 random chunks: [0] chunk 0 optimal weight: 0.9990 overall best weight: 0.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3951 r_free = 0.3951 target = 0.136310 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3607 r_free = 0.3607 target = 0.110167 restraints weight = 11214.861| |-----------------------------------------------------------------------------| r_work (start): 0.3598 rms_B_bonded: 2.04 r_work: 0.3454 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.3454 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8363 moved from start: 0.5991 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 8200 Z= 0.116 Angle : 0.680 7.102 10400 Z= 0.330 Chirality : 0.026 0.065 700 Planarity : 0.002 0.011 1300 Dihedral : 52.788 179.981 900 Min Nonbonded Distance : 2.336 Molprobity Statistics. All-atom Clashscore : 7.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.83 % Favored : 86.17 % Rotamer: Outliers : 0.00 % Allowed : 27.71 % Favored : 72.29 % 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: -3.62 (0.26), residues: 600 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.75 (0.20), residues: 600 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.026 0.002 PHEAh 1 Details of bonding type rmsd/Z covalent geometry : bond 0.00274 / 0.12 ( 8100) covalent geometry : angle 0.67952 / 0.33 (10400) hydrogen bonds : bond 0.01731 / 1.01 ( 125) hydrogen bonds : angle 3.19018 / 2.00 ( 375) Misc. bond : bond 0.00028 / 0.01 ( 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 110 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 110 time to evaluate : 0.310 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: T 2 LYS cc_start: 0.7368 (tmtt) cc_final: 0.6899 (tmtt) REVERT: U 6 LYS cc_start: 0.7998 (mttm) cc_final: 0.7590 (mmtm) REVERT: W 2 LYS cc_start: 0.7055 (tmtt) cc_final: 0.6615 (tmtt) REVERT: Y 2 LYS cc_start: 0.7068 (tmtt) cc_final: 0.6687 (tmtt) REVERT: Z 6 LYS cc_start: 0.7910 (mttm) cc_final: 0.7622 (mptt) REVERT: b 2 LYS cc_start: 0.6969 (tmtt) cc_final: 0.6614 (tmtt) REVERT: d 6 LYS cc_start: 0.8068 (mttm) cc_final: 0.7680 (mmtm) REVERT: e 2 LYS cc_start: 0.6985 (tmtt) cc_final: 0.6474 (tmtt) REVERT: e 6 LYS cc_start: 0.7969 (mttm) cc_final: 0.7706 (mptt) REVERT: f 2 LYS cc_start: 0.7327 (tttp) cc_final: 0.6667 (tmtt) REVERT: g 2 LYS cc_start: 0.7043 (tmtt) cc_final: 0.6664 (tmtt) REVERT: AR 2 LYS cc_start: 0.7090 (tttm) cc_final: 0.6567 (tmtt) REVERT: AR 6 LYS cc_start: 0.8038 (mttm) cc_final: 0.7607 (mmtt) REVERT: AV 6 LYS cc_start: 0.7816 (mttp) cc_final: 0.7360 (mmtm) REVERT: Ad 2 LYS cc_start: 0.7016 (tmtt) cc_final: 0.6624 (tmtt) REVERT: Al 2 LYS cc_start: 0.7158 (tmtt) cc_final: 0.6782 (tmtt) REVERT: Am 6 LYS cc_start: 0.8583 (tttt) cc_final: 0.8358 (tttp) REVERT: Ap 6 LYS cc_start: 0.7980 (mttm) cc_final: 0.7523 (mmtm) REVERT: Ax 2 LYS cc_start: 0.7036 (tmtt) cc_final: 0.6606 (tmtt) outliers start: 0 outliers final: 0 residues processed: 110 average time/residue: 0.1892 time to fit residues: 24.4593 Evaluate side-chains 108 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 108 time to evaluate : 0.355 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1 random chunks: [0] chunk 0 optimal weight: 10.0000 overall best weight: 10.0000 ------------------------------------------------------------------------------- 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 = 0.3826 r_free = 0.3826 target = 0.127952 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.101699 restraints weight = 11740.710| |-----------------------------------------------------------------------------| r_work (start): 0.3389 rms_B_bonded: 1.88 r_work: 0.3252 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work: 0.3111 rms_B_bonded: 4.87 restraints_weight: 0.2500 r_work (final): 0.3111 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8558 moved from start: 0.6377 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.013 0.048 8200 Z= 0.566 Angle : 0.983 7.046 10400 Z= 0.468 Chirality : 0.043 0.123 700 Planarity : 0.005 0.017 1300 Dihedral : 52.388 179.985 900 Min Nonbonded Distance : 2.086 Molprobity Statistics. All-atom Clashscore : 11.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 31.33 % Favored : 68.67 % Rotamer: Outliers : 0.57 % Allowed : 26.14 % Favored : 73.29 % 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: -3.75 (0.27), residues: 600 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.85 (0.21), residues: 600 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.040 0.004 PHEAv 5 Details of bonding type rmsd/Z covalent geometry : bond 0.01344 / 0.57 ( 8100) covalent geometry : angle 0.98345 / 0.47 (10400) hydrogen bonds : bond 0.02332 / 1.35 ( 125) hydrogen bonds : angle 4.06884 / 2.50 ( 375) Misc. bond : bond 0.00213 / 0.11 ( 100) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1492.41 seconds wall clock time: 26 minutes 45.55 seconds (1605.55 seconds total)