Starting phenix.real_space_refine on Thu Aug 6 20:39:14 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9pjc_71686/08_2026/9pjc_71686_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/9pjc_71686/08_2026/9pjc_71686.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9pjc_71686/08_2026/9pjc_71686_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9pjc_71686/08_2026/9pjc_71686_trim.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9pjc_71686/08_2026/9pjc_71686.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9pjc_71686/08_2026/9pjc_71686.map" } resolution = 3.8 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 ------------------------------------------------------------------------------- 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= 0.002 sd= 0.028 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: 4 Type Number sf(0) Gaussians C 5400 2.51 5 N 1350 2.21 5 O 1550 1.98 5 H 8900 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 17200 Number of models: 1 Model: "" Number of chains: 100 Chain: "D" Number of atoms: 343 Number of conformers: 1 Conformer: "" Number of residues, atoms: 22, 343 Unusual residues: {'ACE': 1} Classifications: {'peptide': 21, 'undetermined': 1} Link IDs: {'ACE_C-N': 1, 'TRANS': 20} 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: "C" Number of atoms: 343 Number of conformers: 1 Conformer: "" Number of residues, atoms: 22, 343 Unusual residues: {'ACE': 1} Classifications: {'peptide': 21, 'undetermined': 1} Link IDs: {'ACE_C-N': 1, 'TRANS': 20} 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: "F" Number of atoms: 343 Number of conformers: 1 Conformer: "" Number of residues, atoms: 22, 343 Unusual residues: {'ACE': 1} Classifications: {'peptide': 21, 'undetermined': 1} Link IDs: {'ACE_C-N': 1, 'TRANS': 20} 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: "E" Number of atoms: 343 Number of conformers: 1 Conformer: "" Number of residues, atoms: 22, 343 Unusual residues: {'ACE': 1} Classifications: {'peptide': 21, 'undetermined': 1} Link IDs: {'ACE_C-N': 1, 'TRANS': 20} 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: "H" Number of atoms: 343 Number of conformers: 1 Conformer: "" Number of residues, atoms: 22, 343 Unusual residues: {'ACE': 1} Classifications: {'peptide': 21, 'undetermined': 1} Link IDs: {'ACE_C-N': 1, 'TRANS': 20} 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: "G" Number of atoms: 343 Number of conformers: 1 Conformer: "" Number of residues, atoms: 22, 343 Unusual residues: {'ACE': 1} Classifications: {'peptide': 21, 'undetermined': 1} Link IDs: {'ACE_C-N': 1, 'TRANS': 20} 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: "J" Number of atoms: 343 Number of conformers: 1 Conformer: "" Number of residues, atoms: 22, 343 Unusual residues: {'ACE': 1} Classifications: {'peptide': 21, 'undetermined': 1} Link IDs: {'ACE_C-N': 1, 'TRANS': 20} Chain: "J" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "I" Number of atoms: 343 Number of conformers: 1 Conformer: "" Number of residues, atoms: 22, 343 Unusual residues: {'ACE': 1} Classifications: {'peptide': 21, 'undetermined': 1} Link IDs: {'ACE_C-N': 1, 'TRANS': 20} 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: "L" Number of atoms: 343 Number of conformers: 1 Conformer: "" Number of residues, atoms: 22, 343 Unusual residues: {'ACE': 1} Classifications: {'peptide': 21, 'undetermined': 1} Link IDs: {'ACE_C-N': 1, 'TRANS': 20} 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: "K" Number of atoms: 343 Number of conformers: 1 Conformer: "" Number of residues, atoms: 22, 343 Unusual residues: {'ACE': 1} Classifications: {'peptide': 21, 'undetermined': 1} Link IDs: {'ACE_C-N': 1, 'TRANS': 20} 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: "N" Number of atoms: 343 Number of conformers: 1 Conformer: "" Number of residues, atoms: 22, 343 Unusual residues: {'ACE': 1} Classifications: {'peptide': 21, 'undetermined': 1} Link IDs: {'ACE_C-N': 1, 'TRANS': 20} 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: "M" Number of atoms: 343 Number of conformers: 1 Conformer: "" Number of residues, atoms: 22, 343 Unusual residues: {'ACE': 1} Classifications: {'peptide': 21, 'undetermined': 1} Link IDs: {'ACE_C-N': 1, 'TRANS': 20} 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: "P" Number of atoms: 343 Number of conformers: 1 Conformer: "" Number of residues, atoms: 22, 343 Unusual residues: {'ACE': 1} Classifications: {'peptide': 21, 'undetermined': 1} Link IDs: {'ACE_C-N': 1, 'TRANS': 20} 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: "O" Number of atoms: 343 Number of conformers: 1 Conformer: "" Number of residues, atoms: 22, 343 Unusual residues: {'ACE': 1} Classifications: {'peptide': 21, 'undetermined': 1} Link IDs: {'ACE_C-N': 1, 'TRANS': 20} 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: "R" Number of atoms: 343 Number of conformers: 1 Conformer: "" Number of residues, atoms: 22, 343 Unusual residues: {'ACE': 1} Classifications: {'peptide': 21, 'undetermined': 1} Link IDs: {'ACE_C-N': 1, 'TRANS': 20} 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: "Q" Number of atoms: 343 Number of conformers: 1 Conformer: "" Number of residues, atoms: 22, 343 Unusual residues: {'ACE': 1} Classifications: {'peptide': 21, 'undetermined': 1} Link IDs: {'ACE_C-N': 1, 'TRANS': 20} 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: "T" Number of atoms: 343 Number of conformers: 1 Conformer: "" Number of residues, atoms: 22, 343 Unusual residues: {'ACE': 1} Classifications: {'peptide': 21, 'undetermined': 1} Link IDs: {'ACE_C-N': 1, 'TRANS': 20} 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: "S" Number of atoms: 343 Number of conformers: 1 Conformer: "" Number of residues, atoms: 22, 343 Unusual residues: {'ACE': 1} Classifications: {'peptide': 21, 'undetermined': 1} Link IDs: {'ACE_C-N': 1, 'TRANS': 20} 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: "V" Number of atoms: 343 Number of conformers: 1 Conformer: "" Number of residues, atoms: 22, 343 Unusual residues: {'ACE': 1} Classifications: {'peptide': 21, 'undetermined': 1} Link IDs: {'ACE_C-N': 1, 'TRANS': 20} 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: "U" Number of atoms: 343 Number of conformers: 1 Conformer: "" Number of residues, atoms: 22, 343 Unusual residues: {'ACE': 1} Classifications: {'peptide': 21, 'undetermined': 1} Link IDs: {'ACE_C-N': 1, 'TRANS': 20} 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: 343 Number of conformers: 1 Conformer: "" Number of residues, atoms: 22, 343 Unusual residues: {'ACE': 1} Classifications: {'peptide': 21, 'undetermined': 1} Link IDs: {'ACE_C-N': 1, 'TRANS': 20} Chain: "X" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "W" Number of atoms: 343 Number of conformers: 1 Conformer: "" Number of residues, atoms: 22, 343 Unusual residues: {'ACE': 1} Classifications: {'peptide': 21, 'undetermined': 1} Link IDs: {'ACE_C-N': 1, 'TRANS': 20} 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: "Z" Number of atoms: 343 Number of conformers: 1 Conformer: "" Number of residues, atoms: 22, 343 Unusual residues: {'ACE': 1} Classifications: {'peptide': 21, 'undetermined': 1} Link IDs: {'ACE_C-N': 1, 'TRANS': 20} 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: "Y" Number of atoms: 343 Number of conformers: 1 Conformer: "" Number of residues, atoms: 22, 343 Unusual residues: {'ACE': 1} Classifications: {'peptide': 21, 'undetermined': 1} Link IDs: {'ACE_C-N': 1, 'TRANS': 20} 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: "b" Number of atoms: 343 Number of conformers: 1 Conformer: "" Number of residues, atoms: 22, 343 Unusual residues: {'ACE': 1} Classifications: {'peptide': 21, 'undetermined': 1} Link IDs: {'ACE_C-N': 1, 'TRANS': 20} 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: "a" Number of atoms: 343 Number of conformers: 1 Conformer: "" Number of residues, atoms: 22, 343 Unusual residues: {'ACE': 1} Classifications: {'peptide': 21, 'undetermined': 1} Link IDs: {'ACE_C-N': 1, 'TRANS': 20} 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: "d" Number of atoms: 343 Number of conformers: 1 Conformer: "" Number of residues, atoms: 22, 343 Unusual residues: {'ACE': 1} Classifications: {'peptide': 21, 'undetermined': 1} Link IDs: {'ACE_C-N': 1, 'TRANS': 20} 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: "c" Number of atoms: 343 Number of conformers: 1 Conformer: "" Number of residues, atoms: 22, 343 Unusual residues: {'ACE': 1} Classifications: {'peptide': 21, 'undetermined': 1} Link IDs: {'ACE_C-N': 1, 'TRANS': 20} 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: "f" Number of atoms: 343 Number of conformers: 1 Conformer: "" Number of residues, atoms: 22, 343 Unusual residues: {'ACE': 1} Classifications: {'peptide': 21, 'undetermined': 1} Link IDs: {'ACE_C-N': 1, 'TRANS': 20} 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: "e" Number of atoms: 343 Number of conformers: 1 Conformer: "" Number of residues, atoms: 22, 343 Unusual residues: {'ACE': 1} Classifications: {'peptide': 21, 'undetermined': 1} Link IDs: {'ACE_C-N': 1, 'TRANS': 20} 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: "h" Number of atoms: 343 Number of conformers: 1 Conformer: "" Number of residues, atoms: 22, 343 Unusual residues: {'ACE': 1} Classifications: {'peptide': 21, 'undetermined': 1} Link IDs: {'ACE_C-N': 1, 'TRANS': 20} 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: "g" Number of atoms: 343 Number of conformers: 1 Conformer: "" Number of residues, atoms: 22, 343 Unusual residues: {'ACE': 1} Classifications: {'peptide': 21, 'undetermined': 1} Link IDs: {'ACE_C-N': 1, 'TRANS': 20} 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: "j" Number of atoms: 343 Number of conformers: 1 Conformer: "" Number of residues, atoms: 22, 343 Unusual residues: {'ACE': 1} Classifications: {'peptide': 21, 'undetermined': 1} Link IDs: {'ACE_C-N': 1, 'TRANS': 20} Chain: "j" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "i" Number of atoms: 343 Number of conformers: 1 Conformer: "" Number of residues, atoms: 22, 343 Unusual residues: {'ACE': 1} Classifications: {'peptide': 21, 'undetermined': 1} Link IDs: {'ACE_C-N': 1, 'TRANS': 20} 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: "l" Number of atoms: 343 Number of conformers: 1 Conformer: "" Number of residues, atoms: 22, 343 Unusual residues: {'ACE': 1} Classifications: {'peptide': 21, 'undetermined': 1} Link IDs: {'ACE_C-N': 1, 'TRANS': 20} 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: "k" Number of atoms: 343 Number of conformers: 1 Conformer: "" Number of residues, atoms: 22, 343 Unusual residues: {'ACE': 1} Classifications: {'peptide': 21, 'undetermined': 1} Link IDs: {'ACE_C-N': 1, 'TRANS': 20} 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: "n" Number of atoms: 343 Number of conformers: 1 Conformer: "" Number of residues, atoms: 22, 343 Unusual residues: {'ACE': 1} Classifications: {'peptide': 21, 'undetermined': 1} Link IDs: {'ACE_C-N': 1, 'TRANS': 20} 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: "m" Number of atoms: 343 Number of conformers: 1 Conformer: "" Number of residues, atoms: 22, 343 Unusual residues: {'ACE': 1} Classifications: {'peptide': 21, 'undetermined': 1} Link IDs: {'ACE_C-N': 1, 'TRANS': 20} 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: "p" Number of atoms: 343 Number of conformers: 1 Conformer: "" Number of residues, atoms: 22, 343 Unusual residues: {'ACE': 1} Classifications: {'peptide': 21, 'undetermined': 1} Link IDs: {'ACE_C-N': 1, 'TRANS': 20} 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: "o" Number of atoms: 343 Number of conformers: 1 Conformer: "" Number of residues, atoms: 22, 343 Unusual residues: {'ACE': 1} Classifications: {'peptide': 21, 'undetermined': 1} Link IDs: {'ACE_C-N': 1, 'TRANS': 20} 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: "r" Number of atoms: 343 Number of conformers: 1 Conformer: "" Number of residues, atoms: 22, 343 Unusual residues: {'ACE': 1} Classifications: {'peptide': 21, 'undetermined': 1} Link IDs: {'ACE_C-N': 1, 'TRANS': 20} 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: "q" Number of atoms: 343 Number of conformers: 1 Conformer: "" Number of residues, atoms: 22, 343 Unusual residues: {'ACE': 1} Classifications: {'peptide': 21, 'undetermined': 1} Link IDs: {'ACE_C-N': 1, 'TRANS': 20} 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: "t" Number of atoms: 343 Number of conformers: 1 Conformer: "" Number of residues, atoms: 22, 343 Unusual residues: {'ACE': 1} Classifications: {'peptide': 21, 'undetermined': 1} Link IDs: {'ACE_C-N': 1, 'TRANS': 20} 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: "s" Number of atoms: 343 Number of conformers: 1 Conformer: "" Number of residues, atoms: 22, 343 Unusual residues: {'ACE': 1} Classifications: {'peptide': 21, 'undetermined': 1} Link IDs: {'ACE_C-N': 1, 'TRANS': 20} 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: "v" Number of atoms: 343 Number of conformers: 1 Conformer: "" Number of residues, atoms: 22, 343 Unusual residues: {'ACE': 1} Classifications: {'peptide': 21, 'undetermined': 1} Link IDs: {'ACE_C-N': 1, 'TRANS': 20} 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: "u" Number of atoms: 343 Number of conformers: 1 Conformer: "" Number of residues, atoms: 22, 343 Unusual residues: {'ACE': 1} Classifications: {'peptide': 21, 'undetermined': 1} Link IDs: {'ACE_C-N': 1, 'TRANS': 20} 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: 343 Number of conformers: 1 Conformer: "" Number of residues, atoms: 22, 343 Unusual residues: {'ACE': 1} Classifications: {'peptide': 21, 'undetermined': 1} Link IDs: {'ACE_C-N': 1, 'TRANS': 20} Chain: "x" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "w" Number of atoms: 343 Number of conformers: 1 Conformer: "" Number of residues, atoms: 22, 343 Unusual residues: {'ACE': 1} Classifications: {'peptide': 21, 'undetermined': 1} Link IDs: {'ACE_C-N': 1, 'TRANS': 20} 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: "B" Number of atoms: 343 Number of conformers: 1 Conformer: "" Number of residues, atoms: 22, 343 Unusual residues: {'ACE': 1} Classifications: {'peptide': 21, 'undetermined': 1} Link IDs: {'ACE_C-N': 1, 'TRANS': 20} 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: "A" Number of atoms: 343 Number of conformers: 1 Conformer: "" Number of residues, atoms: 22, 343 Unusual residues: {'ACE': 1} Classifications: {'peptide': 21, 'undetermined': 1} Link IDs: {'ACE_C-N': 1, 'TRANS': 20} Chain: "A" 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: 3.04, per 1000 atoms: 0.18 Number of scatterers: 17200 At special positions: 0 Unit cell: (65.88, 64.8, 153.36, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) O 1550 8.00 N 1350 7.00 C 5400 6.00 H 8900 1.00 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=50, symmetry=0 Number of additional bonds: simple=50, symmetry=0 Coordination: Other bonds: Time building additional restraints: 1.55 Conformation dependent library (CDL) restraints added in 524.4 milliseconds 1900 Ramachandran restraints generated. 950 Oldfield, 0 Emsley, 950 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2100 Finding SS restraints... Secondary structure from input PDB file: 50 helices and 0 sheets defined 97.2% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.34 Creating SS restraints... Processing helix chain 'D' and resid 2 through 21 removed outlier: 4.190A pdb=" N GLN D 19 " --> pdb=" O GLU D 15 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N LEU D 20 " --> pdb=" O LYS D 16 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N ALA D 21 " --> pdb=" O ALA D 17 " (cutoff:3.500A) Processing helix chain 'C' and resid 2 through 22 Processing helix chain 'F' and resid 2 through 22 removed outlier: 3.682A pdb=" N LEU F 20 " --> pdb=" O LYS F 16 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N ALA F 21 " --> pdb=" O ALA F 17 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N LYS F 22 " --> pdb=" O LEU F 18 " (cutoff:3.500A) Processing helix chain 'E' and resid 2 through 22 Processing helix chain 'H' and resid 2 through 21 removed outlier: 4.097A pdb=" N GLN H 19 " --> pdb=" O GLU H 15 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N LEU H 20 " --> pdb=" O LYS H 16 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N ALA H 21 " --> pdb=" O ALA H 17 " (cutoff:3.500A) Processing helix chain 'G' and resid 2 through 22 Processing helix chain 'J' and resid 2 through 21 removed outlier: 4.307A pdb=" N GLN J 19 " --> pdb=" O GLU J 15 " (cutoff:3.500A) removed outlier: 4.092A pdb=" N LEU J 20 " --> pdb=" O LYS J 16 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N ALA J 21 " --> pdb=" O ALA J 17 " (cutoff:3.500A) Processing helix chain 'I' and resid 2 through 22 Processing helix chain 'L' and resid 2 through 21 removed outlier: 4.427A pdb=" N GLN L 19 " --> pdb=" O GLU L 15 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N LEU L 20 " --> pdb=" O LYS L 16 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N ALA L 21 " --> pdb=" O ALA L 17 " (cutoff:3.500A) Processing helix chain 'K' and resid 2 through 22 Processing helix chain 'N' and resid 2 through 21 removed outlier: 4.251A pdb=" N GLN N 19 " --> pdb=" O GLU N 15 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N LEU N 20 " --> pdb=" O LYS N 16 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N ALA N 21 " --> pdb=" O ALA N 17 " (cutoff:3.500A) Processing helix chain 'M' and resid 2 through 22 removed outlier: 3.570A pdb=" N GLN M 19 " --> pdb=" O GLU M 15 " (cutoff:3.500A) Processing helix chain 'P' and resid 2 through 21 removed outlier: 3.769A pdb=" N GLN P 19 " --> pdb=" O GLU P 15 " (cutoff:3.500A) removed outlier: 4.067A pdb=" N LEU P 20 " --> pdb=" O LYS P 16 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N ALA P 21 " --> pdb=" O ALA P 17 " (cutoff:3.500A) Processing helix chain 'O' and resid 2 through 22 Processing helix chain 'R' and resid 2 through 18 Processing helix chain 'Q' and resid 2 through 22 Processing helix chain 'T' and resid 2 through 21 removed outlier: 3.573A pdb=" N LYS T 16 " --> pdb=" O TYR T 12 " (cutoff:3.500A) removed outlier: 4.192A pdb=" N GLN T 19 " --> pdb=" O GLU T 15 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N LEU T 20 " --> pdb=" O LYS T 16 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N ALA T 21 " --> pdb=" O ALA T 17 " (cutoff:3.500A) Processing helix chain 'S' and resid 2 through 22 Processing helix chain 'V' and resid 2 through 21 removed outlier: 3.558A pdb=" N LYS V 16 " --> pdb=" O TYR V 12 " (cutoff:3.500A) removed outlier: 4.676A pdb=" N GLN V 19 " --> pdb=" O GLU V 15 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N LEU V 20 " --> pdb=" O LYS V 16 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N ALA V 21 " --> pdb=" O ALA V 17 " (cutoff:3.500A) Processing helix chain 'U' and resid 2 through 22 Processing helix chain 'X' and resid 2 through 21 removed outlier: 4.297A pdb=" N GLN X 19 " --> pdb=" O GLU X 15 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N LEU X 20 " --> pdb=" O LYS X 16 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N ALA X 21 " --> pdb=" O ALA X 17 " (cutoff:3.500A) Processing helix chain 'W' and resid 2 through 22 Processing helix chain 'Z' and resid 2 through 22 removed outlier: 4.258A pdb=" N LEU Z 20 " --> pdb=" O LYS Z 16 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N ALA Z 21 " --> pdb=" O ALA Z 17 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N LYS Z 22 " --> pdb=" O LEU Z 18 " (cutoff:3.500A) Processing helix chain 'Y' and resid 2 through 22 Processing helix chain 'b' and resid 2 through 21 removed outlier: 4.462A pdb=" N GLN b 19 " --> pdb=" O GLU b 15 " (cutoff:3.500A) removed outlier: 4.164A pdb=" N LEU b 20 " --> pdb=" O LYS b 16 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N ALA b 21 " --> pdb=" O ALA b 17 " (cutoff:3.500A) Processing helix chain 'a' and resid 2 through 22 Processing helix chain 'd' and resid 2 through 20 removed outlier: 4.171A pdb=" N LEU d 20 " --> pdb=" O LYS d 16 " (cutoff:3.500A) Processing helix chain 'c' and resid 2 through 22 Processing helix chain 'f' and resid 2 through 21 removed outlier: 3.952A pdb=" N GLN f 19 " --> pdb=" O GLU f 15 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N LEU f 20 " --> pdb=" O LYS f 16 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N ALA f 21 " --> pdb=" O ALA f 17 " (cutoff:3.500A) Processing helix chain 'e' and resid 2 through 22 Processing helix chain 'h' and resid 2 through 21 removed outlier: 4.033A pdb=" N GLN h 19 " --> pdb=" O GLU h 15 " (cutoff:3.500A) Processing helix chain 'g' and resid 2 through 22 Processing helix chain 'j' and resid 2 through 21 removed outlier: 4.177A pdb=" N GLN j 19 " --> pdb=" O GLU j 15 " (cutoff:3.500A) removed outlier: 4.235A pdb=" N LEU j 20 " --> pdb=" O LYS j 16 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N ALA j 21 " --> pdb=" O ALA j 17 " (cutoff:3.500A) Processing helix chain 'i' and resid 2 through 22 Processing helix chain 'l' and resid 2 through 21 removed outlier: 3.814A pdb=" N GLN l 19 " --> pdb=" O GLU l 15 " (cutoff:3.500A) removed outlier: 4.091A pdb=" N LEU l 20 " --> pdb=" O LYS l 16 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N ALA l 21 " --> pdb=" O ALA l 17 " (cutoff:3.500A) Processing helix chain 'k' and resid 2 through 22 Processing helix chain 'n' and resid 2 through 21 removed outlier: 3.578A pdb=" N GLN n 19 " --> pdb=" O GLU n 15 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N LEU n 20 " --> pdb=" O LYS n 16 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N ALA n 21 " --> pdb=" O ALA n 17 " (cutoff:3.500A) Processing helix chain 'm' and resid 2 through 22 Processing helix chain 'p' and resid 2 through 22 removed outlier: 3.590A pdb=" N LEU p 20 " --> pdb=" O LYS p 16 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N ALA p 21 " --> pdb=" O ALA p 17 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N LYS p 22 " --> pdb=" O LEU p 18 " (cutoff:3.500A) Processing helix chain 'o' and resid 2 through 22 Processing helix chain 'r' and resid 2 through 22 removed outlier: 4.373A pdb=" N GLN r 19 " --> pdb=" O GLU r 15 " (cutoff:3.500A) removed outlier: 4.151A pdb=" N LEU r 20 " --> pdb=" O LYS r 16 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N ALA r 21 " --> pdb=" O ALA r 17 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N LYS r 22 " --> pdb=" O LEU r 18 " (cutoff:3.500A) Processing helix chain 'q' and resid 2 through 22 Processing helix chain 't' and resid 2 through 18 Processing helix chain 's' and resid 2 through 22 Processing helix chain 'v' and resid 2 through 20 removed outlier: 3.560A pdb=" N ALA v 7 " --> pdb=" O ALA v 3 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N LEU v 20 " --> pdb=" O LYS v 16 " (cutoff:3.500A) Processing helix chain 'u' and resid 2 through 22 removed outlier: 3.577A pdb=" N GLN u 19 " --> pdb=" O GLU u 15 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N LEU u 20 " --> pdb=" O LYS u 16 " (cutoff:3.500A) Processing helix chain 'x' and resid 2 through 21 removed outlier: 3.891A pdb=" N LEU x 6 " --> pdb=" O GLU x 2 " (cutoff:3.500A) Processing helix chain 'w' and resid 2 through 22 Processing helix chain 'B' and resid 2 through 21 removed outlier: 3.889A pdb=" N GLN B 19 " --> pdb=" O GLU B 15 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N LEU B 20 " --> pdb=" O LYS B 16 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N ALA B 21 " --> pdb=" O ALA B 17 " (cutoff:3.500A) Processing helix chain 'A' and resid 2 through 22 removed outlier: 3.574A pdb=" N LYS A 22 " --> pdb=" O LEU A 18 " (cutoff:3.500A) 752 hydrogen bonds defined for protein. 2256 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: 3.89 Time building geometry restraints manager: 2.20 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.95 - 1.07: 1822 1.07 - 1.19: 7078 1.19 - 1.31: 1500 1.31 - 1.43: 1500 1.43 - 1.55: 5250 Bond restraints: 17150 Sorted by residual: bond pdb=" NE2 GLN t 19 " pdb="HE22 GLN t 19 " ideal model delta sigma weight residual 0.860 1.004 -0.144 2.00e-02 2.50e+03 5.20e+01 bond pdb=" NE2 GLN V 19 " pdb="HE22 GLN V 19 " ideal model delta sigma weight residual 0.860 1.004 -0.144 2.00e-02 2.50e+03 5.15e+01 bond pdb=" NE2 GLN L 19 " pdb="HE22 GLN L 19 " ideal model delta sigma weight residual 0.860 1.003 -0.143 2.00e-02 2.50e+03 5.14e+01 bond pdb=" NE2 GLN r 19 " pdb="HE22 GLN r 19 " ideal model delta sigma weight residual 0.860 1.003 -0.143 2.00e-02 2.50e+03 5.11e+01 bond pdb=" NE2 GLN P 19 " pdb="HE22 GLN P 19 " ideal model delta sigma weight residual 0.860 1.003 -0.143 2.00e-02 2.50e+03 5.11e+01 ... (remaining 17145 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.52: 22310 1.52 - 3.05: 6183 3.05 - 4.57: 1771 4.57 - 6.09: 1026 6.09 - 7.62: 160 Bond angle restraints: 31450 Sorted by residual: angle pdb=" CB GLU p 9 " pdb=" CG GLU p 9 " pdb=" CD GLU p 9 " ideal model delta sigma weight residual 112.60 104.98 7.62 1.70e+00 3.46e-01 2.01e+01 angle pdb=" OE1 GLN N 19 " pdb=" CD GLN N 19 " pdb=" NE2 GLN N 19 " ideal model delta sigma weight residual 122.60 118.44 4.16 1.00e+00 1.00e+00 1.73e+01 angle pdb=" OE1 GLN d 19 " pdb=" CD GLN d 19 " pdb=" NE2 GLN d 19 " ideal model delta sigma weight residual 122.60 118.59 4.01 1.00e+00 1.00e+00 1.61e+01 angle pdb=" OE1 GLN v 19 " pdb=" CD GLN v 19 " pdb=" NE2 GLN v 19 " ideal model delta sigma weight residual 122.60 118.65 3.95 1.00e+00 1.00e+00 1.56e+01 angle pdb=" OE1 GLN n 19 " pdb=" CD GLN n 19 " pdb=" NE2 GLN n 19 " ideal model delta sigma weight residual 122.60 118.68 3.92 1.00e+00 1.00e+00 1.53e+01 ... (remaining 31445 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.11: 7422 18.11 - 36.23: 213 36.23 - 54.34: 79 54.34 - 72.45: 25 72.45 - 90.56: 11 Dihedral angle restraints: 7750 sinusoidal: 4400 harmonic: 3350 Sorted by residual: dihedral pdb=" CB GLU v 2 " pdb=" CG GLU v 2 " pdb=" CD GLU v 2 " pdb=" OE1 GLU v 2 " ideal model delta sinusoidal sigma weight residual 0.00 90.56 -90.56 1 3.00e+01 1.11e-03 1.08e+01 dihedral pdb=" CB GLU l 2 " pdb=" CG GLU l 2 " pdb=" CD GLU l 2 " pdb=" OE1 GLU l 2 " ideal model delta sinusoidal sigma weight residual 0.00 86.61 -86.61 1 3.00e+01 1.11e-03 1.00e+01 dihedral pdb=" CB GLU Q 9 " pdb=" CG GLU Q 9 " pdb=" CD GLU Q 9 " pdb=" OE1 GLU Q 9 " ideal model delta sinusoidal sigma weight residual 0.00 85.17 -85.17 1 3.00e+01 1.11e-03 9.77e+00 ... (remaining 7747 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.040: 647 0.040 - 0.080: 336 0.080 - 0.120: 103 0.120 - 0.160: 192 0.160 - 0.200: 72 Chirality restraints: 1350 Sorted by residual: chirality pdb=" CG LEU d 18 " pdb=" CB LEU d 18 " pdb=" CD1 LEU d 18 " pdb=" CD2 LEU d 18 " both_signs ideal model delta sigma weight residual False -2.59 -2.79 0.20 2.00e-01 2.50e+01 9.96e-01 chirality pdb=" CG LEU X 11 " pdb=" CB LEU X 11 " pdb=" CD1 LEU X 11 " pdb=" CD2 LEU X 11 " both_signs ideal model delta sigma weight residual False -2.59 -2.78 0.19 2.00e-01 2.50e+01 9.13e-01 chirality pdb=" CG LEU t 18 " pdb=" CB LEU t 18 " pdb=" CD1 LEU t 18 " pdb=" CD2 LEU t 18 " both_signs ideal model delta sigma weight residual False -2.59 -2.78 0.19 2.00e-01 2.50e+01 8.80e-01 ... (remaining 1347 not shown) Planarity restraints: 2350 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR n 12 " 0.116 2.00e-02 2.50e+03 5.09e-02 7.76e+01 pdb=" CG TYR n 12 " -0.031 2.00e-02 2.50e+03 pdb=" CD1 TYR n 12 " -0.032 2.00e-02 2.50e+03 pdb=" CD2 TYR n 12 " -0.039 2.00e-02 2.50e+03 pdb=" CE1 TYR n 12 " -0.024 2.00e-02 2.50e+03 pdb=" CE2 TYR n 12 " -0.035 2.00e-02 2.50e+03 pdb=" CZ TYR n 12 " -0.006 2.00e-02 2.50e+03 pdb=" OH TYR n 12 " 0.107 2.00e-02 2.50e+03 pdb=" HD1 TYR n 12 " -0.019 2.00e-02 2.50e+03 pdb=" HD2 TYR n 12 " -0.010 2.00e-02 2.50e+03 pdb=" HE1 TYR n 12 " -0.013 2.00e-02 2.50e+03 pdb=" HE2 TYR n 12 " -0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR t 12 " -0.087 2.00e-02 2.50e+03 3.70e-02 4.11e+01 pdb=" CG TYR t 12 " 0.036 2.00e-02 2.50e+03 pdb=" CD1 TYR t 12 " 0.023 2.00e-02 2.50e+03 pdb=" CD2 TYR t 12 " 0.032 2.00e-02 2.50e+03 pdb=" CE1 TYR t 12 " 0.013 2.00e-02 2.50e+03 pdb=" CE2 TYR t 12 " 0.022 2.00e-02 2.50e+03 pdb=" CZ TYR t 12 " 0.013 2.00e-02 2.50e+03 pdb=" OH TYR t 12 " -0.070 2.00e-02 2.50e+03 pdb=" HD1 TYR t 12 " 0.005 2.00e-02 2.50e+03 pdb=" HD2 TYR t 12 " 0.011 2.00e-02 2.50e+03 pdb=" HE1 TYR t 12 " 0.009 2.00e-02 2.50e+03 pdb=" HE2 TYR t 12 " -0.005 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLN l 5 " -0.053 2.00e-02 2.50e+03 4.99e-02 3.74e+01 pdb=" CD GLN l 5 " 0.014 2.00e-02 2.50e+03 pdb=" OE1 GLN l 5 " 0.046 2.00e-02 2.50e+03 pdb=" NE2 GLN l 5 " 0.005 2.00e-02 2.50e+03 pdb="HE21 GLN l 5 " 0.064 2.00e-02 2.50e+03 pdb="HE22 GLN l 5 " -0.076 2.00e-02 2.50e+03 ... (remaining 2347 not shown) Histogram of nonbonded interaction distances: 1.63 - 2.21: 589 2.21 - 2.78: 33550 2.78 - 3.35: 47975 3.35 - 3.93: 61106 3.93 - 4.50: 83201 Nonbonded interactions: 226421 Sorted by model distance: nonbonded pdb=" OE2 GLU X 9 " pdb=" HH TYR b 12 " model vdw 1.632 2.450 nonbonded pdb=" OE2 GLU h 9 " pdb=" HH TYR l 12 " model vdw 1.639 2.450 nonbonded pdb=" OE2 GLU R 9 " pdb=" HH TYR V 12 " model vdw 1.641 2.450 nonbonded pdb=" OE2 GLU r 9 " pdb=" HH TYR v 12 " model vdw 1.646 2.450 nonbonded pdb=" OE2 GLU J 9 " pdb=" HH TYR N 12 " model vdw 1.647 2.450 ... (remaining 226416 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 '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' 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' } 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 group one per residue 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: 2.130 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: 0.140 Extract box with map and model: 0.260 Check model and map are aligned: 0.050 Set scattering table: 0.050 Process input model: 17.390 Find NCS groups from input model: 0.290 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.220 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.600 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8342 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 : 0.014 0.102 8300 Z= 1.018 Angle : 1.603 7.616 11000 Z= 0.968 Chirality : 0.079 0.200 1350 Planarity : 0.010 0.061 1350 Dihedral : 13.325 90.563 3200 Min Nonbonded Distance : 2.581 Molprobity Statistics. All-atom Clashscore : 0.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % 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: 1.92 (0.27), residues: 950 helix: 0.45 (0.15), residues: 800 sheet: None (None), residues: 0 loop : 7.24 (0.68), residues: 150 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.109 0.016 TYR n 12 Details of bonding type rmsd/Z covalent geometry : bond 0.01171 / 0.66 ( 8250) covalent geometry : angle 1.60253 / 0.97 (11000) hydrogen bonds : bond 0.16073 / 10.39 ( 752) hydrogen bonds : angle 6.25253 / 4.35 ( 2256) Misc. bond : bond 0.10055 / 6.56 ( 50) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1900 Ramachandran restraints generated. 950 Oldfield, 0 Emsley, 950 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1900 Ramachandran restraints generated. 950 Oldfield, 0 Emsley, 950 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 161 time to evaluate : 0.460 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: g 9 GLU cc_start: 0.8536 (tp30) cc_final: 0.8289 (tp30) REVERT: o 6 LEU cc_start: 0.8615 (tp) cc_final: 0.8299 (tp) outliers start: 0 outliers final: 0 residues processed: 161 average time/residue: 0.2210 time to fit residues: 49.2350 Evaluate side-chains 100 residues out of total 750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 100 time to evaluate : 0.454 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 49 optimal weight: 0.6980 chunk 97 optimal weight: 0.6980 chunk 53 optimal weight: 0.7980 chunk 5 optimal weight: 0.8980 chunk 33 optimal weight: 0.7980 chunk 65 optimal weight: 0.6980 chunk 62 optimal weight: 0.7980 chunk 51 optimal weight: 0.6980 chunk 38 optimal weight: 0.7980 chunk 61 optimal weight: 0.6980 chunk 45 optimal weight: 0.6980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... m 19 GLN s 19 GLN x 19 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.115230 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.108110 restraints weight = 29784.359| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.111025 restraints weight = 16572.155| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.112717 restraints weight = 9584.354| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.113728 restraints weight = 5689.882| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.114320 restraints weight = 3422.409| |-----------------------------------------------------------------------------| r_work (final): 0.3347 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8391 moved from start: 0.2846 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 8300 Z= 0.126 Angle : 0.492 3.615 11000 Z= 0.250 Chirality : 0.019 0.075 1350 Planarity : 0.002 0.007 1350 Dihedral : 4.080 26.394 1150 Min Nonbonded Distance : 2.564 Molprobity Statistics. All-atom Clashscore : 0.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 0.27 % Allowed : 4.40 % Favored : 95.33 % 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: 5.16 (0.22), residues: 950 helix: 3.07 (0.15), residues: 800 sheet: None (None), residues: 0 loop : 5.68 (0.49), residues: 150 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.015 0.002 TYR i 12 Details of bonding type rmsd/Z covalent geometry : bond 0.00281 / 0.13 ( 8250) covalent geometry : angle 0.49155 / 0.25 (11000) hydrogen bonds : bond 0.03107 / 1.98 ( 752) hydrogen bonds : angle 3.53505 / 2.44 ( 2256) Misc. bond : bond 0.00019 / 0.01 ( 50) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1900 Ramachandran restraints generated. 950 Oldfield, 0 Emsley, 950 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1900 Ramachandran restraints generated. 950 Oldfield, 0 Emsley, 950 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 110 time to evaluate : 0.578 Fit side-chains revert: symmetry clash REVERT: G 12 TYR cc_start: 0.7728 (t80) cc_final: 0.7306 (m-10) REVERT: Q 12 TYR cc_start: 0.7488 (m-80) cc_final: 0.7285 (m-10) REVERT: S 15 GLU cc_start: 0.8098 (tt0) cc_final: 0.7809 (tt0) REVERT: f 19 GLN cc_start: 0.8060 (OUTLIER) cc_final: 0.7785 (mt0) REVERT: g 15 GLU cc_start: 0.8254 (tt0) cc_final: 0.8022 (tt0) REVERT: o 6 LEU cc_start: 0.8547 (tp) cc_final: 0.8266 (tp) outliers start: 2 outliers final: 1 residues processed: 111 average time/residue: 0.1840 time to fit residues: 29.6319 Evaluate side-chains 96 residues out of total 750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 94 time to evaluate : 0.465 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain f residue 19 GLN Chi-restraints excluded: chain k residue 16 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 36 optimal weight: 1.9990 chunk 53 optimal weight: 1.9990 chunk 25 optimal weight: 1.9990 chunk 65 optimal weight: 1.9990 chunk 57 optimal weight: 0.9980 chunk 13 optimal weight: 1.9990 chunk 11 optimal weight: 1.9990 chunk 82 optimal weight: 1.9990 chunk 68 optimal weight: 0.9980 chunk 20 optimal weight: 1.9990 chunk 14 optimal weight: 0.9980 overall best weight: 1.3984 ------------------------------------------------------------------------------- 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 = 0.3211 r_free = 0.3211 target = 0.104908 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3069 r_free = 0.3069 target = 0.095259 restraints weight = 31055.362| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3120 r_free = 0.3120 target = 0.098719 restraints weight = 17280.605| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3156 r_free = 0.3156 target = 0.101061 restraints weight = 10310.282| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3175 r_free = 0.3175 target = 0.102399 restraints weight = 6297.854| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3188 r_free = 0.3188 target = 0.103325 restraints weight = 3983.659| |-----------------------------------------------------------------------------| r_work (final): 0.3268 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8464 moved from start: 0.3510 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.028 8300 Z= 0.197 Angle : 0.532 4.691 11000 Z= 0.264 Chirality : 0.020 0.085 1350 Planarity : 0.001 0.006 1350 Dihedral : 4.795 42.138 1150 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 0.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 0.27 % Allowed : 4.53 % Favored : 95.20 % 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: 6.10 (0.21), residues: 950 helix: 3.88 (0.14), residues: 800 sheet: None (None), residues: 0 loop : 4.92 (0.43), residues: 150 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.013 0.002 TYR U 12 Details of bonding type rmsd/Z covalent geometry : bond 0.00465 / 0.20 ( 8250) covalent geometry : angle 0.53153 / 0.26 (11000) hydrogen bonds : bond 0.03359 / 2.15 ( 752) hydrogen bonds : angle 3.63700 / 2.49 ( 2256) Misc. bond : bond 0.00033 / 0.02 ( 50) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1900 Ramachandran restraints generated. 950 Oldfield, 0 Emsley, 950 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1900 Ramachandran restraints generated. 950 Oldfield, 0 Emsley, 950 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 101 time to evaluate : 0.470 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 12 TYR cc_start: 0.7759 (t80) cc_final: 0.7370 (m-10) REVERT: K 6 LEU cc_start: 0.8715 (tp) cc_final: 0.8504 (tp) REVERT: S 15 GLU cc_start: 0.8232 (tt0) cc_final: 0.7964 (tt0) REVERT: o 6 LEU cc_start: 0.8540 (tp) cc_final: 0.8327 (tp) REVERT: A 22 LYS cc_start: 0.8165 (mttp) cc_final: 0.7586 (mmtt) outliers start: 2 outliers final: 1 residues processed: 102 average time/residue: 0.1929 time to fit residues: 28.3624 Evaluate side-chains 91 residues out of total 750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 90 time to evaluate : 0.550 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain k residue 16 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 66 optimal weight: 1.9990 chunk 22 optimal weight: 0.9990 chunk 61 optimal weight: 1.9990 chunk 48 optimal weight: 1.9990 chunk 63 optimal weight: 0.6980 chunk 65 optimal weight: 0.9990 chunk 89 optimal weight: 1.9990 chunk 92 optimal weight: 1.9990 chunk 12 optimal weight: 0.9990 chunk 44 optimal weight: 0.9990 chunk 41 optimal weight: 0.9990 overall best weight: 0.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... b 19 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3243 r_free = 0.3243 target = 0.107352 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3100 r_free = 0.3100 target = 0.097406 restraints weight = 30737.125| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3155 r_free = 0.3155 target = 0.101152 restraints weight = 16836.543| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3188 r_free = 0.3188 target = 0.103463 restraints weight = 9846.566| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 54)----------------| | r_work = 0.3209 r_free = 0.3209 target = 0.104900 restraints weight = 5988.350| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3221 r_free = 0.3221 target = 0.105772 restraints weight = 3709.164| |-----------------------------------------------------------------------------| r_work (final): 0.3300 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8431 moved from start: 0.3732 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.020 8300 Z= 0.137 Angle : 0.432 4.159 11000 Z= 0.213 Chirality : 0.016 0.071 1350 Planarity : 0.001 0.006 1350 Dihedral : 4.905 42.075 1150 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 1.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 0.13 % Allowed : 5.60 % Favored : 94.27 % 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: 6.80 (0.20), residues: 950 helix: 4.44 (0.13), residues: 800 sheet: None (None), residues: 0 loop : 4.61 (0.44), residues: 150 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.013 0.001 TYR i 12 Details of bonding type rmsd/Z covalent geometry : bond 0.00324 / 0.14 ( 8250) covalent geometry : angle 0.43172 / 0.21 (11000) hydrogen bonds : bond 0.02480 / 1.58 ( 752) hydrogen bonds : angle 3.20642 / 2.20 ( 2256) Misc. bond : bond 0.00018 / 0.01 ( 50) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1900 Ramachandran restraints generated. 950 Oldfield, 0 Emsley, 950 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1900 Ramachandran restraints generated. 950 Oldfield, 0 Emsley, 950 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 99 time to evaluate : 0.456 Fit side-chains REVERT: G 12 TYR cc_start: 0.7718 (t80) cc_final: 0.7345 (m-10) REVERT: S 15 GLU cc_start: 0.8176 (tt0) cc_final: 0.7951 (tt0) REVERT: x 2 GLU cc_start: 0.7818 (tm-30) cc_final: 0.7617 (tt0) REVERT: A 22 LYS cc_start: 0.8099 (mttp) cc_final: 0.7502 (mmtt) outliers start: 1 outliers final: 1 residues processed: 99 average time/residue: 0.1953 time to fit residues: 27.7556 Evaluate side-chains 96 residues out of total 750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 95 time to evaluate : 0.466 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain k residue 16 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 71 optimal weight: 0.9990 chunk 31 optimal weight: 0.9990 chunk 90 optimal weight: 0.9980 chunk 27 optimal weight: 1.9990 chunk 42 optimal weight: 1.9990 chunk 13 optimal weight: 1.9990 chunk 30 optimal weight: 0.8980 chunk 97 optimal weight: 1.9990 chunk 91 optimal weight: 0.9980 chunk 73 optimal weight: 0.7980 chunk 53 optimal weight: 1.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... p 19 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3217 r_free = 0.3217 target = 0.105382 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3067 r_free = 0.3067 target = 0.095166 restraints weight = 30748.195| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3122 r_free = 0.3122 target = 0.098947 restraints weight = 16849.771| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3159 r_free = 0.3159 target = 0.101368 restraints weight = 9808.752| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3180 r_free = 0.3180 target = 0.102843 restraints weight = 5932.790| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3194 r_free = 0.3194 target = 0.103780 restraints weight = 3663.631| |-----------------------------------------------------------------------------| r_work (final): 0.3283 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8427 moved from start: 0.3980 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.018 8300 Z= 0.139 Angle : 0.438 4.044 11000 Z= 0.216 Chirality : 0.016 0.071 1350 Planarity : 0.001 0.005 1350 Dihedral : 4.947 42.220 1150 Min Nonbonded Distance : 2.395 Molprobity Statistics. All-atom Clashscore : 1.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 0.27 % Allowed : 6.80 % Favored : 92.93 % 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: 7.21 (0.20), residues: 950 helix: 4.74 (0.13), residues: 800 sheet: None (None), residues: 0 loop : 4.58 (0.44), residues: 150 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.012 0.001 TYR k 12 Details of bonding type rmsd/Z covalent geometry : bond 0.00329 / 0.14 ( 8250) covalent geometry : angle 0.43794 / 0.22 (11000) hydrogen bonds : bond 0.02452 / 1.56 ( 752) hydrogen bonds : angle 3.15698 / 2.16 ( 2256) Misc. bond : bond 0.00016 / 0.01 ( 50) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1900 Ramachandran restraints generated. 950 Oldfield, 0 Emsley, 950 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1900 Ramachandran restraints generated. 950 Oldfield, 0 Emsley, 950 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 95 time to evaluate : 0.375 Fit side-chains revert: symmetry clash REVERT: G 12 TYR cc_start: 0.7777 (t80) cc_final: 0.7338 (m-10) REVERT: K 19 GLN cc_start: 0.8131 (tm-30) cc_final: 0.7876 (tm-30) REVERT: S 15 GLU cc_start: 0.8207 (tt0) cc_final: 0.7929 (tt0) REVERT: A 22 LYS cc_start: 0.8173 (mttp) cc_final: 0.7544 (mmtt) outliers start: 2 outliers final: 1 residues processed: 95 average time/residue: 0.1940 time to fit residues: 26.6633 Evaluate side-chains 90 residues out of total 750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 89 time to evaluate : 0.435 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain h residue 19 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 7 optimal weight: 0.9990 chunk 25 optimal weight: 1.9990 chunk 75 optimal weight: 0.9990 chunk 2 optimal weight: 0.9980 chunk 23 optimal weight: 0.9990 chunk 98 optimal weight: 0.9980 chunk 87 optimal weight: 0.9980 chunk 28 optimal weight: 1.9990 chunk 32 optimal weight: 1.9990 chunk 39 optimal weight: 0.9990 chunk 34 optimal weight: 1.9990 overall best weight: 0.9984 ------------------------------------------------------------------------------- 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 = 0.3203 r_free = 0.3203 target = 0.104809 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3064 r_free = 0.3064 target = 0.094963 restraints weight = 31074.582| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3117 r_free = 0.3117 target = 0.098692 restraints weight = 16990.212| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3150 r_free = 0.3150 target = 0.101027 restraints weight = 9785.572| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.3170 r_free = 0.3170 target = 0.102469 restraints weight = 5858.102| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3183 r_free = 0.3183 target = 0.103365 restraints weight = 3561.005| |-----------------------------------------------------------------------------| r_work (final): 0.3262 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8443 moved from start: 0.4092 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.019 8300 Z= 0.145 Angle : 0.438 4.056 11000 Z= 0.216 Chirality : 0.016 0.074 1350 Planarity : 0.001 0.006 1350 Dihedral : 5.075 42.876 1150 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 1.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 0.27 % Allowed : 6.67 % Favored : 93.07 % 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: 7.39 (0.19), residues: 950 helix: 4.88 (0.12), residues: 800 sheet: None (None), residues: 0 loop : 4.52 (0.42), residues: 150 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.014 0.001 TYR i 12 Details of bonding type rmsd/Z covalent geometry : bond 0.00344 / 0.15 ( 8250) covalent geometry : angle 0.43773 / 0.22 (11000) hydrogen bonds : bond 0.02404 / 1.53 ( 752) hydrogen bonds : angle 3.17653 / 2.17 ( 2256) Misc. bond : bond 0.00019 / 0.01 ( 50) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1900 Ramachandran restraints generated. 950 Oldfield, 0 Emsley, 950 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1900 Ramachandran restraints generated. 950 Oldfield, 0 Emsley, 950 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 92 time to evaluate : 0.371 Fit side-chains revert: symmetry clash REVERT: G 12 TYR cc_start: 0.7769 (t80) cc_final: 0.7375 (m-10) REVERT: K 19 GLN cc_start: 0.8292 (tm-30) cc_final: 0.7947 (tm-30) REVERT: S 15 GLU cc_start: 0.8196 (tt0) cc_final: 0.7931 (tt0) REVERT: A 22 LYS cc_start: 0.8001 (mttp) cc_final: 0.7397 (mmtt) outliers start: 2 outliers final: 2 residues processed: 92 average time/residue: 0.2053 time to fit residues: 27.2386 Evaluate side-chains 91 residues out of total 750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 89 time to evaluate : 0.479 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain h residue 19 GLN Chi-restraints excluded: chain k residue 16 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 6 optimal weight: 0.9990 chunk 18 optimal weight: 1.9990 chunk 36 optimal weight: 1.9990 chunk 61 optimal weight: 0.6980 chunk 41 optimal weight: 1.9990 chunk 33 optimal weight: 0.5980 chunk 27 optimal weight: 0.9980 chunk 70 optimal weight: 0.8980 chunk 9 optimal weight: 1.9990 chunk 52 optimal weight: 1.9990 chunk 89 optimal weight: 1.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- 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 = 0.3198 r_free = 0.3198 target = 0.104570 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3053 r_free = 0.3053 target = 0.094331 restraints weight = 30817.239| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3109 r_free = 0.3109 target = 0.098214 restraints weight = 16571.489| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3143 r_free = 0.3143 target = 0.100647 restraints weight = 9535.845| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 46)----------------| | r_work = 0.3165 r_free = 0.3165 target = 0.102157 restraints weight = 5667.664| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3177 r_free = 0.3177 target = 0.103051 restraints weight = 3434.084| |-----------------------------------------------------------------------------| r_work (final): 0.3190 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8398 moved from start: 0.4215 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 8300 Z= 0.127 Angle : 0.419 4.358 11000 Z= 0.208 Chirality : 0.015 0.070 1350 Planarity : 0.001 0.005 1350 Dihedral : 5.014 42.122 1150 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 2.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 0.27 % Allowed : 7.33 % Favored : 92.40 % 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: 7.62 (0.19), residues: 950 helix: 5.06 (0.12), residues: 800 sheet: None (None), residues: 0 loop : 4.45 (0.43), residues: 150 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.012 0.001 TYR k 12 Details of bonding type rmsd/Z covalent geometry : bond 0.00301 / 0.13 ( 8250) covalent geometry : angle 0.41922 / 0.21 (11000) hydrogen bonds : bond 0.02181 / 1.39 ( 752) hydrogen bonds : angle 3.02141 / 2.07 ( 2256) Misc. bond : bond 0.00016 / 0.01 ( 50) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1900 Ramachandran restraints generated. 950 Oldfield, 0 Emsley, 950 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1900 Ramachandran restraints generated. 950 Oldfield, 0 Emsley, 950 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 94 time to evaluate : 0.510 Fit side-chains revert: symmetry clash REVERT: G 12 TYR cc_start: 0.7795 (t80) cc_final: 0.7360 (m-10) REVERT: K 19 GLN cc_start: 0.8250 (tm-30) cc_final: 0.7859 (tm-30) REVERT: S 15 GLU cc_start: 0.8192 (tt0) cc_final: 0.7924 (tt0) REVERT: A 22 LYS cc_start: 0.8123 (mttp) cc_final: 0.7396 (mmtt) outliers start: 2 outliers final: 1 residues processed: 94 average time/residue: 0.1980 time to fit residues: 27.0065 Evaluate side-chains 87 residues out of total 750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 86 time to evaluate : 0.395 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain k residue 16 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 41 optimal weight: 1.9990 chunk 91 optimal weight: 0.9990 chunk 81 optimal weight: 0.5980 chunk 51 optimal weight: 0.0980 chunk 90 optimal weight: 0.9990 chunk 86 optimal weight: 0.9990 chunk 87 optimal weight: 0.9980 chunk 19 optimal weight: 0.9980 chunk 49 optimal weight: 0.5980 chunk 38 optimal weight: 1.9990 chunk 60 optimal weight: 0.9980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... f 19 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3212 r_free = 0.3212 target = 0.105582 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3068 r_free = 0.3068 target = 0.095252 restraints weight = 30755.097| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3123 r_free = 0.3123 target = 0.099185 restraints weight = 16646.557| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3157 r_free = 0.3157 target = 0.101639 restraints weight = 9549.906| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3179 r_free = 0.3179 target = 0.103152 restraints weight = 5676.767| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3191 r_free = 0.3191 target = 0.104040 restraints weight = 3441.239| |-----------------------------------------------------------------------------| r_work (final): 0.3204 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8386 moved from start: 0.4275 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 8300 Z= 0.105 Angle : 0.399 4.687 11000 Z= 0.199 Chirality : 0.014 0.066 1350 Planarity : 0.001 0.005 1350 Dihedral : 4.815 40.306 1150 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 2.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 0.13 % Allowed : 7.33 % Favored : 92.53 % 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: 7.89 (0.19), residues: 950 helix: 5.26 (0.12), residues: 800 sheet: None (None), residues: 0 loop : 4.43 (0.45), residues: 150 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.013 0.001 TYR i 12 Details of bonding type rmsd/Z covalent geometry : bond 0.00250 / 0.11 ( 8250) covalent geometry : angle 0.39896 / 0.20 (11000) hydrogen bonds : bond 0.01978 / 1.26 ( 752) hydrogen bonds : angle 2.88129 / 1.97 ( 2256) Misc. bond : bond 0.00014 / 0.01 ( 50) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1900 Ramachandran restraints generated. 950 Oldfield, 0 Emsley, 950 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1900 Ramachandran restraints generated. 950 Oldfield, 0 Emsley, 950 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 95 time to evaluate : 0.471 Fit side-chains revert: symmetry clash REVERT: G 12 TYR cc_start: 0.7764 (t80) cc_final: 0.7333 (m-10) REVERT: K 19 GLN cc_start: 0.8267 (tm-30) cc_final: 0.7885 (tm-30) REVERT: S 15 GLU cc_start: 0.8164 (tt0) cc_final: 0.7940 (tt0) REVERT: A 22 LYS cc_start: 0.8098 (mttp) cc_final: 0.7396 (mmtt) outliers start: 1 outliers final: 1 residues processed: 95 average time/residue: 0.2100 time to fit residues: 28.5174 Evaluate side-chains 89 residues out of total 750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 88 time to evaluate : 0.470 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain k residue 16 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 87 optimal weight: 0.9980 chunk 73 optimal weight: 0.9990 chunk 98 optimal weight: 0.9980 chunk 12 optimal weight: 1.9990 chunk 41 optimal weight: 1.9990 chunk 62 optimal weight: 0.9990 chunk 48 optimal weight: 0.9990 chunk 51 optimal weight: 0.6980 chunk 71 optimal weight: 1.9990 chunk 78 optimal weight: 0.9980 chunk 4 optimal weight: 0.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... h 19 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3186 r_free = 0.3186 target = 0.103749 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3037 r_free = 0.3037 target = 0.093284 restraints weight = 31204.978| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3092 r_free = 0.3092 target = 0.097205 restraints weight = 17155.295| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3129 r_free = 0.3129 target = 0.099728 restraints weight = 9886.424| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3150 r_free = 0.3150 target = 0.101276 restraints weight = 5887.029| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3163 r_free = 0.3163 target = 0.102232 restraints weight = 3565.868| |-----------------------------------------------------------------------------| r_work (final): 0.3257 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8442 moved from start: 0.4319 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 8300 Z= 0.137 Angle : 0.442 5.109 11000 Z= 0.218 Chirality : 0.016 0.075 1350 Planarity : 0.001 0.005 1350 Dihedral : 4.965 41.685 1150 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 2.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 0.27 % Allowed : 7.73 % Favored : 92.00 % 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: 7.73 (0.19), residues: 950 helix: 5.15 (0.12), residues: 800 sheet: None (None), residues: 0 loop : 4.40 (0.43), residues: 150 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.013 0.001 TYR k 12 Details of bonding type rmsd/Z covalent geometry : bond 0.00324 / 0.14 ( 8250) covalent geometry : angle 0.44234 / 0.22 (11000) hydrogen bonds : bond 0.02281 / 1.46 ( 752) hydrogen bonds : angle 3.10830 / 2.12 ( 2256) Misc. bond : bond 0.00019 / 0.01 ( 50) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1900 Ramachandran restraints generated. 950 Oldfield, 0 Emsley, 950 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1900 Ramachandran restraints generated. 950 Oldfield, 0 Emsley, 950 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 87 time to evaluate : 0.506 Fit side-chains revert: symmetry clash REVERT: G 12 TYR cc_start: 0.7842 (t80) cc_final: 0.7413 (m-10) REVERT: K 19 GLN cc_start: 0.8209 (tm-30) cc_final: 0.7816 (tm-30) REVERT: S 15 GLU cc_start: 0.8198 (tt0) cc_final: 0.7949 (tt0) REVERT: A 22 LYS cc_start: 0.8052 (mttp) cc_final: 0.7363 (mmtt) outliers start: 2 outliers final: 1 residues processed: 88 average time/residue: 0.2039 time to fit residues: 26.0320 Evaluate side-chains 87 residues out of total 750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 86 time to evaluate : 0.453 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain o residue 19 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 82 optimal weight: 0.9980 chunk 36 optimal weight: 1.9990 chunk 1 optimal weight: 0.9990 chunk 16 optimal weight: 1.9990 chunk 58 optimal weight: 0.8980 chunk 84 optimal weight: 0.9980 chunk 32 optimal weight: 0.9980 chunk 22 optimal weight: 0.9990 chunk 73 optimal weight: 0.9990 chunk 59 optimal weight: 0.6980 chunk 17 optimal weight: 0.9990 overall best weight: 0.9180 ------------------------------------------------------------------------------- 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 = 0.3192 r_free = 0.3192 target = 0.104111 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3043 r_free = 0.3043 target = 0.093720 restraints weight = 30969.535| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3097 r_free = 0.3097 target = 0.097545 restraints weight = 16811.923| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3134 r_free = 0.3134 target = 0.100070 restraints weight = 9783.483| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3155 r_free = 0.3155 target = 0.101549 restraints weight = 5862.569| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3169 r_free = 0.3169 target = 0.102534 restraints weight = 3631.325| |-----------------------------------------------------------------------------| r_work (final): 0.3182 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8403 moved from start: 0.4311 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 8300 Z= 0.136 Angle : 0.438 5.452 11000 Z= 0.217 Chirality : 0.016 0.074 1350 Planarity : 0.001 0.005 1350 Dihedral : 5.026 42.259 1150 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 2.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 0.00 % Allowed : 8.13 % Favored : 91.87 % 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: 7.74 (0.19), residues: 950 helix: 5.17 (0.12), residues: 800 sheet: None (None), residues: 0 loop : 4.29 (0.43), residues: 150 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.013 0.001 TYR e 12 Details of bonding type rmsd/Z covalent geometry : bond 0.00323 / 0.14 ( 8250) covalent geometry : angle 0.43828 / 0.22 (11000) hydrogen bonds : bond 0.02188 / 1.40 ( 752) hydrogen bonds : angle 3.06164 / 2.09 ( 2256) Misc. bond : bond 0.00018 / 0.01 ( 50) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1900 Ramachandran restraints generated. 950 Oldfield, 0 Emsley, 950 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1900 Ramachandran restraints generated. 950 Oldfield, 0 Emsley, 950 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 87 time to evaluate : 0.411 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: G 12 TYR cc_start: 0.7869 (t80) cc_final: 0.7340 (m-10) REVERT: K 19 GLN cc_start: 0.8203 (tm-30) cc_final: 0.7794 (tm-30) REVERT: S 15 GLU cc_start: 0.8195 (tt0) cc_final: 0.7928 (tt0) REVERT: A 22 LYS cc_start: 0.8105 (mttp) cc_final: 0.7354 (mmtt) outliers start: 0 outliers final: 0 residues processed: 87 average time/residue: 0.2074 time to fit residues: 26.1649 Evaluate side-chains 86 residues out of total 750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 86 time to evaluate : 0.482 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 76 optimal weight: 0.9980 chunk 62 optimal weight: 1.9990 chunk 66 optimal weight: 0.9990 chunk 54 optimal weight: 0.6980 chunk 69 optimal weight: 0.9990 chunk 93 optimal weight: 0.9980 chunk 28 optimal weight: 0.9980 chunk 95 optimal weight: 0.5980 chunk 98 optimal weight: 0.9990 chunk 60 optimal weight: 0.5980 chunk 63 optimal weight: 0.6980 overall best weight: 0.7180 ------------------------------------------------------------------------------- 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 = 0.3206 r_free = 0.3206 target = 0.105150 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3059 r_free = 0.3059 target = 0.094687 restraints weight = 30911.581| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3115 r_free = 0.3115 target = 0.098660 restraints weight = 16581.599| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3151 r_free = 0.3151 target = 0.101151 restraints weight = 9482.703| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3171 r_free = 0.3171 target = 0.102624 restraints weight = 5646.934| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3184 r_free = 0.3184 target = 0.103601 restraints weight = 3483.168| |-----------------------------------------------------------------------------| r_work (final): 0.3185 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8387 moved from start: 0.4382 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 8300 Z= 0.112 Angle : 0.414 5.512 11000 Z= 0.206 Chirality : 0.015 0.068 1350 Planarity : 0.001 0.005 1350 Dihedral : 4.898 41.097 1150 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 2.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 0.13 % Allowed : 8.13 % Favored : 91.73 % 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: 7.92 (0.19), residues: 950 helix: 5.31 (0.12), residues: 800 sheet: None (None), residues: 0 loop : 4.24 (0.43), residues: 150 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.012 0.001 TYR k 12 Details of bonding type rmsd/Z covalent geometry : bond 0.00265 / 0.11 ( 8250) covalent geometry : angle 0.41356 / 0.21 (11000) hydrogen bonds : bond 0.01993 / 1.27 ( 752) hydrogen bonds : angle 2.91655 / 1.99 ( 2256) Misc. bond : bond 0.00014 / 0.01 ( 50) =============================================================================== Job complete usr+sys time: 2327.46 seconds wall clock time: 40 minutes 40.03 seconds (2440.03 seconds total)