Starting phenix.real_space_refine on Sun Aug 24 11:26:07 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/5w7v_8781/08_2025/5w7v_8781.cif Found real_map, /net/cci-nas-00/data/ceres_data/5w7v_8781/08_2025/5w7v_8781.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 { real_map_files = "/net/cci-nas-00/data/ceres_data/5w7v_8781/08_2025/5w7v_8781.map" default_real_map = "/net/cci-nas-00/data/ceres_data/5w7v_8781/08_2025/5w7v_8781.map" model { file = "/net/cci-nas-00/data/ceres_data/5w7v_8781/08_2025/5w7v_8781.cif" } default_model = "/net/cci-nas-00/data/ceres_data/5w7v_8781/08_2025/5w7v_8781.cif" } 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= 0.001 sd= 0.007 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 3 Type Number sf(0) Gaussians C 13500 2.51 5 N 3330 2.21 5 O 3600 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 20430 Number of models: 1 Model: "" Number of chains: 270 Chain: "A" Number of atoms: 85 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 85 Classifications: {'peptide': 11} Modifications used: {'COO': 1} Link IDs: {'TRANS': 10} Chain: "B" Number of atoms: 85 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 85 Classifications: {'peptide': 11} Modifications used: {'COO': 1} Link IDs: {'TRANS': 10} Chain: "C" Number of atoms: 85 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 85 Classifications: {'peptide': 11} Modifications used: {'COO': 1} Link IDs: {'TRANS': 10} Chain: "D" Number of atoms: 85 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 85 Classifications: {'peptide': 11} Modifications used: {'COO': 1} Link IDs: {'TRANS': 10} Chain: "E" Number of atoms: 85 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 85 Classifications: {'peptide': 11} Modifications used: {'COO': 1} Link IDs: {'TRANS': 10} Chain: "F" Number of atoms: 85 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 85 Classifications: {'peptide': 11} Modifications used: {'COO': 1} Link IDs: {'TRANS': 10} Chain: "G" Number of atoms: 85 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 85 Classifications: {'peptide': 11} Modifications used: {'COO': 1} Link IDs: {'TRANS': 10} Chain: "H" Number of atoms: 45 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 45 Classifications: {'peptide': 6} Link IDs: {'TRANS': 5} Chain: "I" Number of atoms: 41 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 41 Classifications: {'peptide': 5} Link IDs: {'TRANS': 4} Chain: "J" Number of atoms: 85 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 85 Classifications: {'peptide': 11} Modifications used: {'COO': 1} Link IDs: {'TRANS': 10} Chain: "K" Number of atoms: 85 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 85 Classifications: {'peptide': 11} Modifications used: {'COO': 1} Link IDs: {'TRANS': 10} Chain: "L" Number of atoms: 85 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 85 Classifications: {'peptide': 11} Modifications used: {'COO': 1} Link IDs: {'TRANS': 10} Chain: "M" Number of atoms: 85 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 85 Classifications: {'peptide': 11} Modifications used: {'COO': 1} Link IDs: {'TRANS': 10} Chain: "N" Number of atoms: 85 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 85 Classifications: {'peptide': 11} Modifications used: {'COO': 1} Link IDs: {'TRANS': 10} Chain: "O" Number of atoms: 85 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 85 Classifications: {'peptide': 11} Modifications used: {'COO': 1} Link IDs: {'TRANS': 10} Chain: "P" Number of atoms: 85 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 85 Classifications: {'peptide': 11} Modifications used: {'COO': 1} Link IDs: {'TRANS': 10} Chain: "Q" Number of atoms: 45 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 45 Classifications: {'peptide': 6} Link IDs: {'TRANS': 5} Chain: "R" Number of atoms: 41 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 41 Classifications: {'peptide': 5} Link IDs: {'TRANS': 4} Chain: "S" Number of atoms: 85 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 85 Classifications: {'peptide': 11} Modifications used: {'COO': 1} Link IDs: {'TRANS': 10} Chain: "T" Number of atoms: 85 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 85 Classifications: {'peptide': 11} Modifications used: {'COO': 1} Link IDs: {'TRANS': 10} Chain: "U" Number of atoms: 85 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 85 Classifications: {'peptide': 11} Modifications used: {'COO': 1} Link IDs: {'TRANS': 10} Chain: "V" Number of atoms: 85 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 85 Classifications: {'peptide': 11} Modifications used: {'COO': 1} Link IDs: {'TRANS': 10} Chain: "W" Number of atoms: 85 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 85 Classifications: {'peptide': 11} Modifications used: {'COO': 1} Link IDs: {'TRANS': 10} Chain: "X" Number of atoms: 85 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 85 Classifications: {'peptide': 11} Modifications used: {'COO': 1} Link IDs: {'TRANS': 10} Chain: "Y" Number of atoms: 85 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 85 Classifications: {'peptide': 11} Modifications used: {'COO': 1} Link IDs: {'TRANS': 10} Chain: "Z" Number of atoms: 45 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 45 Classifications: {'peptide': 6} Link IDs: {'TRANS': 5} Chain: "9" Number of atoms: 41 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 41 Classifications: {'peptide': 5} Link IDs: {'TRANS': 4} Chain: "a" Number of atoms: 85 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 85 Classifications: {'peptide': 11} Modifications used: {'COO': 1} Link IDs: {'TRANS': 10} Chain: "b" Number of atoms: 85 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 85 Classifications: {'peptide': 11} Modifications used: {'COO': 1} Link IDs: {'TRANS': 10} Chain: "c" Number of atoms: 85 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 85 Classifications: {'peptide': 11} Modifications used: {'COO': 1} Link IDs: {'TRANS': 10} Chain: "d" Number of atoms: 85 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 85 Classifications: {'peptide': 11} Modifications used: {'COO': 1} Link IDs: {'TRANS': 10} Chain: "e" Number of atoms: 85 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 85 Classifications: {'peptide': 11} Modifications used: {'COO': 1} Link IDs: {'TRANS': 10} Chain: "f" Number of atoms: 85 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 85 Classifications: {'peptide': 11} Modifications used: {'COO': 1} Link IDs: {'TRANS': 10} Chain: "g" Number of atoms: 85 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 85 Classifications: {'peptide': 11} Modifications used: {'COO': 1} Link IDs: {'TRANS': 10} Chain: "h" Number of atoms: 45 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 45 Classifications: {'peptide': 6} Link IDs: {'TRANS': 5} Chain: "i" Number of atoms: 41 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 41 Classifications: {'peptide': 5} Link IDs: {'TRANS': 4} Chain: "j" Number of atoms: 85 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 85 Classifications: {'peptide': 11} Modifications used: {'COO': 1} Link IDs: {'TRANS': 10} Chain: "k" Number of atoms: 85 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 85 Classifications: {'peptide': 11} Modifications used: {'COO': 1} Link IDs: {'TRANS': 10} Chain: "l" Number of atoms: 85 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 85 Classifications: {'peptide': 11} Modifications used: {'COO': 1} Link IDs: {'TRANS': 10} Chain: "m" Number of atoms: 85 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 85 Classifications: {'peptide': 11} Modifications used: {'COO': 1} Link IDs: {'TRANS': 10} Chain: "n" Number of atoms: 85 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 85 Classifications: {'peptide': 11} Modifications used: {'COO': 1} Link IDs: {'TRANS': 10} Chain: "o" Number of atoms: 85 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 85 Classifications: {'peptide': 11} Modifications used: {'COO': 1} Link IDs: {'TRANS': 10} Chain: "p" Number of atoms: 85 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 85 Classifications: {'peptide': 11} Modifications used: {'COO': 1} Link IDs: {'TRANS': 10} Chain: "q" Number of atoms: 45 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 45 Classifications: {'peptide': 6} Link IDs: {'TRANS': 5} Chain: "r" Number of atoms: 41 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 41 Classifications: {'peptide': 5} Link IDs: {'TRANS': 4} Chain: "s" Number of atoms: 85 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 85 Classifications: {'peptide': 11} Modifications used: {'COO': 1} Link IDs: {'TRANS': 10} Chain: "t" Number of atoms: 85 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 85 Classifications: {'peptide': 11} Modifications used: {'COO': 1} Link IDs: {'TRANS': 10} Chain: "u" Number of atoms: 85 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 85 Classifications: {'peptide': 11} Modifications used: {'COO': 1} Link IDs: {'TRANS': 10} Chain: "v" Number of atoms: 85 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 85 Classifications: {'peptide': 11} Modifications used: {'COO': 1} Link IDs: {'TRANS': 10} Chain: "w" Number of atoms: 85 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 85 Classifications: {'peptide': 11} Modifications used: {'COO': 1} Link IDs: {'TRANS': 10} Chain: "x" Number of atoms: 85 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 85 Classifications: {'peptide': 11} Modifications used: {'COO': 1} Link IDs: {'TRANS': 10} Chain: "y" Number of atoms: 85 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 85 Classifications: {'peptide': 11} Modifications used: {'COO': 1} Link IDs: {'TRANS': 10} Chain: "z" Number of atoms: 45 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 45 Classifications: {'peptide': 6} Link IDs: {'TRANS': 5} Chain: "AA" Number of atoms: 41 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 41 Classifications: {'peptide': 5} Link IDs: {'TRANS': 4} Chain: "AB" Number of atoms: 85 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 85 Classifications: {'peptide': 11} Modifications used: {'COO': 1} Link IDs: {'TRANS': 10} Chain: "AC" Number of atoms: 85 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 85 Classifications: {'peptide': 11} Modifications used: {'COO': 1} Link IDs: {'TRANS': 10} Chain: "AD" Number of atoms: 85 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 85 Classifications: {'peptide': 11} Modifications used: {'COO': 1} Link IDs: {'TRANS': 10} Chain: "AE" Number of atoms: 85 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 85 Classifications: {'peptide': 11} Modifications used: {'COO': 1} Link IDs: {'TRANS': 10} Chain: "AF" Number of atoms: 85 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 85 Classifications: {'peptide': 11} Modifications used: {'COO': 1} Link IDs: {'TRANS': 10} Chain: "AG" Number of atoms: 85 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 85 Classifications: {'peptide': 11} Modifications used: {'COO': 1} Link IDs: {'TRANS': 10} Chain: "AH" Number of atoms: 85 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 85 Classifications: {'peptide': 11} Modifications used: {'COO': 1} Link IDs: {'TRANS': 10} Chain: "AI" Number of atoms: 45 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 45 Classifications: {'peptide': 6} Link IDs: {'TRANS': 5} Chain: "AJ" Number of atoms: 41 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 41 Classifications: {'peptide': 5} Link IDs: {'TRANS': 4} Chain: "AK" Number of atoms: 85 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 85 Classifications: {'peptide': 11} Modifications used: {'COO': 1} Link IDs: {'TRANS': 10} Chain: "AL" Number of atoms: 85 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 85 Classifications: {'peptide': 11} Modifications used: {'COO': 1} Link IDs: {'TRANS': 10} Chain: "AM" Number of atoms: 85 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 85 Classifications: {'peptide': 11} Modifications used: {'COO': 1} Link IDs: {'TRANS': 10} Chain: "AN" Number of atoms: 85 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 85 Classifications: {'peptide': 11} Modifications used: {'COO': 1} Link IDs: {'TRANS': 10} Chain: "AO" Number of atoms: 85 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 85 Classifications: {'peptide': 11} Modifications used: {'COO': 1} Link IDs: {'TRANS': 10} Chain: "AP" Number of atoms: 85 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 85 Classifications: {'peptide': 11} Modifications used: {'COO': 1} Link IDs: {'TRANS': 10} Chain: "AQ" Number of atoms: 85 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 85 Classifications: {'peptide': 11} Modifications used: {'COO': 1} Link IDs: {'TRANS': 10} Chain: "AR" Number of atoms: 45 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 45 Classifications: {'peptide': 6} Link IDs: {'TRANS': 5} Chain: "AS" Number of atoms: 41 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 41 Classifications: {'peptide': 5} Link IDs: {'TRANS': 4} Chain: "AT" Number of atoms: 85 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 85 Classifications: {'peptide': 11} Modifications used: {'COO': 1} Link IDs: {'TRANS': 10} Chain: "AU" Number of atoms: 85 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 85 Classifications: {'peptide': 11} Modifications used: {'COO': 1} Link IDs: {'TRANS': 10} Chain: "AV" Number of atoms: 85 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 85 Classifications: {'peptide': 11} Modifications used: {'COO': 1} Link IDs: {'TRANS': 10} Chain: "AW" Number of atoms: 85 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 85 Classifications: {'peptide': 11} Modifications used: {'COO': 1} Link IDs: {'TRANS': 10} Chain: "AX" Number of atoms: 85 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 85 Classifications: {'peptide': 11} Modifications used: {'COO': 1} Link IDs: {'TRANS': 10} Chain: "AY" Number of atoms: 85 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 85 Classifications: {'peptide': 11} Modifications used: {'COO': 1} Link IDs: {'TRANS': 10} Chain: "AZ" Number of atoms: 85 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 85 Classifications: {'peptide': 11} Modifications used: {'COO': 1} Link IDs: {'TRANS': 10} Chain: "A0" Number of atoms: 45 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 45 Classifications: {'peptide': 6} Link IDs: {'TRANS': 5} Chain: "A1" Number of atoms: 41 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 41 Classifications: {'peptide': 5} Link IDs: {'TRANS': 4} Chain: "A2" Number of atoms: 85 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 85 Classifications: {'peptide': 11} Modifications used: {'COO': 1} Link IDs: {'TRANS': 10} Chain: "A3" Number of atoms: 85 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 85 Classifications: {'peptide': 11} Modifications used: {'COO': 1} Link IDs: {'TRANS': 10} Chain: "A4" Number of atoms: 85 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 85 Classifications: {'peptide': 11} Modifications used: {'COO': 1} Link IDs: {'TRANS': 10} Chain: "A5" Number of atoms: 85 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 85 Classifications: {'peptide': 11} Modifications used: {'COO': 1} Link IDs: {'TRANS': 10} Chain: "A6" Number of atoms: 85 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 85 Classifications: {'peptide': 11} Modifications used: {'COO': 1} Link IDs: {'TRANS': 10} Chain: "A7" Number of atoms: 85 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 85 Classifications: {'peptide': 11} Modifications used: {'COO': 1} Link IDs: {'TRANS': 10} Chain: "A8" Number of atoms: 85 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 85 Classifications: {'peptide': 11} Modifications used: {'COO': 1} Link IDs: {'TRANS': 10} Chain: "A9" Number of atoms: 45 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 45 Classifications: {'peptide': 6} Link IDs: {'TRANS': 5} Chain: "BA" Number of atoms: 41 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 41 Classifications: {'peptide': 5} Link IDs: {'TRANS': 4} Chain: "BB" Number of atoms: 85 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 85 Classifications: {'peptide': 11} Modifications used: {'COO': 1} Link IDs: {'TRANS': 10} Chain: "BC" Number of atoms: 85 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 85 Classifications: {'peptide': 11} Modifications used: {'COO': 1} Link IDs: {'TRANS': 10} Chain: "BD" Number of atoms: 85 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 85 Classifications: {'peptide': 11} Modifications used: {'COO': 1} Link IDs: {'TRANS': 10} Chain: "BE" Number of atoms: 85 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 85 Classifications: {'peptide': 11} Modifications used: {'COO': 1} Link IDs: {'TRANS': 10} Chain: "BF" Number of atoms: 85 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 85 Classifications: {'peptide': 11} Modifications used: {'COO': 1} Link IDs: {'TRANS': 10} Chain: "BG" Number of atoms: 85 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 85 Classifications: {'peptide': 11} Modifications used: {'COO': 1} Link IDs: {'TRANS': 10} Chain: "BH" Number of atoms: 85 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 85 Classifications: {'peptide': 11} Modifications used: {'COO': 1} Link IDs: {'TRANS': 10} Chain: "BI" Number of atoms: 45 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 45 Classifications: {'peptide': 6} Link IDs: {'TRANS': 5} Chain: "BJ" Number of atoms: 41 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 41 Classifications: {'peptide': 5} Link IDs: {'TRANS': 4} Chain: "BK" Number of atoms: 85 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 85 Classifications: {'peptide': 11} Modifications used: {'COO': 1} Link IDs: {'TRANS': 10} Chain: "BL" Number of atoms: 85 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 85 Classifications: {'peptide': 11} Modifications used: {'COO': 1} Link IDs: {'TRANS': 10} Chain: "BM" Number of atoms: 85 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 85 Classifications: {'peptide': 11} Modifications used: {'COO': 1} Link IDs: {'TRANS': 10} Chain: "BN" Number of atoms: 85 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 85 Classifications: {'peptide': 11} Modifications used: {'COO': 1} Link IDs: {'TRANS': 10} Chain: "BO" Number of atoms: 85 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 85 Classifications: {'peptide': 11} Modifications used: {'COO': 1} Link IDs: {'TRANS': 10} Chain: "BP" Number of atoms: 85 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 85 Classifications: {'peptide': 11} Modifications used: {'COO': 1} Link IDs: {'TRANS': 10} Chain: "BQ" Number of atoms: 85 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 85 Classifications: {'peptide': 11} Modifications used: {'COO': 1} Link IDs: {'TRANS': 10} Chain: "BR" Number of atoms: 45 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 45 Classifications: {'peptide': 6} Link IDs: {'TRANS': 5} Chain: "BS" Number of atoms: 41 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 41 Classifications: {'peptide': 5} Link IDs: {'TRANS': 4} Chain: "BT" Number of atoms: 85 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 85 Classifications: {'peptide': 11} Modifications used: {'COO': 1} Link IDs: {'TRANS': 10} Chain: "BU" Number of atoms: 85 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 85 Classifications: {'peptide': 11} Modifications used: {'COO': 1} Link IDs: {'TRANS': 10} Chain: "BV" Number of atoms: 85 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 85 Classifications: {'peptide': 11} Modifications used: {'COO': 1} Link IDs: {'TRANS': 10} Chain: "BW" Number of atoms: 85 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 85 Classifications: {'peptide': 11} Modifications used: {'COO': 1} Link IDs: {'TRANS': 10} Chain: "BX" Number of atoms: 85 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 85 Classifications: {'peptide': 11} Modifications used: {'COO': 1} Link IDs: {'TRANS': 10} Chain: "BY" Number of atoms: 85 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 85 Classifications: {'peptide': 11} Modifications used: {'COO': 1} Link IDs: {'TRANS': 10} Chain: "BZ" Number of atoms: 85 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 85 Classifications: {'peptide': 11} Modifications used: {'COO': 1} Link IDs: {'TRANS': 10} Chain: "B0" Number of atoms: 45 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 45 Classifications: {'peptide': 6} Link IDs: {'TRANS': 5} Chain: "B1" Number of atoms: 41 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 41 Classifications: {'peptide': 5} Link IDs: {'TRANS': 4} Chain: "B2" Number of atoms: 85 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 85 Classifications: {'peptide': 11} Modifications used: {'COO': 1} Link IDs: {'TRANS': 10} Chain: "B3" Number of atoms: 85 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 85 Classifications: {'peptide': 11} Modifications used: {'COO': 1} Link IDs: {'TRANS': 10} Chain: "B4" Number of atoms: 85 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 85 Classifications: {'peptide': 11} Modifications used: {'COO': 1} Link IDs: {'TRANS': 10} Chain: "B5" Number of atoms: 85 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 85 Classifications: {'peptide': 11} Modifications used: {'COO': 1} Link IDs: {'TRANS': 10} Chain: "B6" Number of atoms: 85 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 85 Classifications: {'peptide': 11} Modifications used: {'COO': 1} Link IDs: {'TRANS': 10} Chain: "B7" Number of atoms: 85 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 85 Classifications: {'peptide': 11} Modifications used: {'COO': 1} Link IDs: {'TRANS': 10} Chain: "B8" Number of atoms: 85 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 85 Classifications: {'peptide': 11} Modifications used: {'COO': 1} Link IDs: {'TRANS': 10} Chain: "B9" Number of atoms: 45 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 45 Classifications: {'peptide': 6} Link IDs: {'TRANS': 5} Chain: "CA" Number of atoms: 41 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 41 Classifications: {'peptide': 5} Link IDs: {'TRANS': 4} Chain: "CB" Number of atoms: 85 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 85 Classifications: {'peptide': 11} Modifications used: {'COO': 1} Link IDs: {'TRANS': 10} Chain: "CC" Number of atoms: 85 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 85 Classifications: {'peptide': 11} Modifications used: {'COO': 1} Link IDs: {'TRANS': 10} Chain: "CD" Number of atoms: 85 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 85 Classifications: {'peptide': 11} Modifications used: {'COO': 1} Link IDs: {'TRANS': 10} Chain: "CE" Number of atoms: 85 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 85 Classifications: {'peptide': 11} Modifications used: {'COO': 1} Link IDs: {'TRANS': 10} Chain: "CF" Number of atoms: 85 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 85 Classifications: {'peptide': 11} Modifications used: {'COO': 1} Link IDs: {'TRANS': 10} Chain: "CG" Number of atoms: 85 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 85 Classifications: {'peptide': 11} Modifications used: {'COO': 1} Link IDs: {'TRANS': 10} Chain: "CH" Number of atoms: 85 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 85 Classifications: {'peptide': 11} Modifications used: {'COO': 1} Link IDs: {'TRANS': 10} Chain: "CI" Number of atoms: 45 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 45 Classifications: {'peptide': 6} Link IDs: {'TRANS': 5} Chain: "CJ" Number of atoms: 41 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 41 Classifications: {'peptide': 5} Link IDs: {'TRANS': 4} Chain: "1" Number of atoms: 85 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 85 Classifications: {'peptide': 11} Modifications used: {'COO': 1} Link IDs: {'TRANS': 10} Chain: "3" Number of atoms: 85 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 85 Classifications: {'peptide': 11} Modifications used: {'COO': 1} Link IDs: {'TRANS': 10} Chain: "2" Number of atoms: 85 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 85 Classifications: {'peptide': 11} Modifications used: {'COO': 1} Link IDs: {'TRANS': 10} Chain: "6" Number of atoms: 85 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 85 Classifications: {'peptide': 11} Modifications used: {'COO': 1} Link IDs: {'TRANS': 10} Chain: "5" Number of atoms: 85 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 85 Classifications: {'peptide': 11} Modifications used: {'COO': 1} Link IDs: {'TRANS': 10} Chain: "4" Number of atoms: 85 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 85 Classifications: {'peptide': 11} Modifications used: {'COO': 1} Link IDs: {'TRANS': 10} Chain: "7" Number of atoms: 85 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 85 Classifications: {'peptide': 11} Modifications used: {'COO': 1} Link IDs: {'TRANS': 10} Chain: "0" Number of atoms: 45 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 45 Classifications: {'peptide': 6} Link IDs: {'TRANS': 5} Chain: "8" Number of atoms: 41 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 41 Classifications: {'peptide': 5} Link IDs: {'TRANS': 4} Chain: "CK" Number of atoms: 85 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 85 Classifications: {'peptide': 11} Modifications used: {'COO': 1} Link IDs: {'TRANS': 10} Chain: "CL" Number of atoms: 85 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 85 Classifications: {'peptide': 11} Modifications used: {'COO': 1} Link IDs: {'TRANS': 10} Chain: "CM" Number of atoms: 85 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 85 Classifications: {'peptide': 11} Modifications used: {'COO': 1} Link IDs: {'TRANS': 10} Chain: "CN" Number of atoms: 85 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 85 Classifications: {'peptide': 11} Modifications used: {'COO': 1} Link IDs: {'TRANS': 10} Chain: "CO" Number of atoms: 85 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 85 Classifications: {'peptide': 11} Modifications used: {'COO': 1} Link IDs: {'TRANS': 10} Chain: "CP" Number of atoms: 85 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 85 Classifications: {'peptide': 11} Modifications used: {'COO': 1} Link IDs: {'TRANS': 10} Chain: "CQ" Number of atoms: 85 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 85 Classifications: {'peptide': 11} Modifications used: {'COO': 1} Link IDs: {'TRANS': 10} Chain: "CR" Number of atoms: 45 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 45 Classifications: {'peptide': 6} Link IDs: {'TRANS': 5} Chain: "CS" Number of atoms: 41 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 41 Classifications: {'peptide': 5} Link IDs: {'TRANS': 4} Chain: "CT" Number of atoms: 85 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 85 Classifications: {'peptide': 11} Modifications used: {'COO': 1} Link IDs: {'TRANS': 10} Chain: "CU" Number of atoms: 85 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 85 Classifications: {'peptide': 11} Modifications used: {'COO': 1} Link IDs: {'TRANS': 10} Chain: "CV" Number of atoms: 85 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 85 Classifications: {'peptide': 11} Modifications used: {'COO': 1} Link IDs: {'TRANS': 10} Chain: "CW" Number of atoms: 85 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 85 Classifications: {'peptide': 11} Modifications used: {'COO': 1} Link IDs: {'TRANS': 10} Chain: "CX" Number of atoms: 85 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 85 Classifications: {'peptide': 11} Modifications used: {'COO': 1} Link IDs: {'TRANS': 10} Chain: "CY" Number of atoms: 85 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 85 Classifications: {'peptide': 11} Modifications used: {'COO': 1} Link IDs: {'TRANS': 10} Chain: "CZ" Number of atoms: 85 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 85 Classifications: {'peptide': 11} Modifications used: {'COO': 1} Link IDs: {'TRANS': 10} Chain: "C0" Number of atoms: 45 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 45 Classifications: {'peptide': 6} Link IDs: {'TRANS': 5} Chain: "C1" Number of atoms: 41 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 41 Classifications: {'peptide': 5} Link IDs: {'TRANS': 4} Chain: "C2" Number of atoms: 85 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 85 Classifications: {'peptide': 11} Modifications used: {'COO': 1} Link IDs: {'TRANS': 10} Chain: "C3" Number of atoms: 85 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 85 Classifications: {'peptide': 11} Modifications used: {'COO': 1} Link IDs: {'TRANS': 10} Chain: "C4" Number of atoms: 85 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 85 Classifications: {'peptide': 11} Modifications used: {'COO': 1} Link IDs: {'TRANS': 10} Chain: "C5" Number of atoms: 85 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 85 Classifications: {'peptide': 11} Modifications used: {'COO': 1} Link IDs: {'TRANS': 10} Chain: "C6" Number of atoms: 85 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 85 Classifications: {'peptide': 11} Modifications used: {'COO': 1} Link IDs: {'TRANS': 10} Chain: "C7" Number of atoms: 85 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 85 Classifications: {'peptide': 11} Modifications used: {'COO': 1} Link IDs: {'TRANS': 10} Chain: "C8" Number of atoms: 85 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 85 Classifications: {'peptide': 11} Modifications used: {'COO': 1} Link IDs: {'TRANS': 10} Chain: "C9" Number of atoms: 45 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 45 Classifications: {'peptide': 6} Link IDs: {'TRANS': 5} Chain: "DA" Number of atoms: 41 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 41 Classifications: {'peptide': 5} Link IDs: {'TRANS': 4} Chain: "DB" Number of atoms: 85 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 85 Classifications: {'peptide': 11} Modifications used: {'COO': 1} Link IDs: {'TRANS': 10} Chain: "DC" Number of atoms: 85 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 85 Classifications: {'peptide': 11} Modifications used: {'COO': 1} Link IDs: {'TRANS': 10} Chain: "DD" Number of atoms: 85 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 85 Classifications: {'peptide': 11} Modifications used: {'COO': 1} Link IDs: {'TRANS': 10} Chain: "DE" Number of atoms: 85 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 85 Classifications: {'peptide': 11} Modifications used: {'COO': 1} Link IDs: {'TRANS': 10} Chain: "DF" Number of atoms: 85 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 85 Classifications: {'peptide': 11} Modifications used: {'COO': 1} Link IDs: {'TRANS': 10} Chain: "DG" Number of atoms: 85 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 85 Classifications: {'peptide': 11} Modifications used: {'COO': 1} Link IDs: {'TRANS': 10} Chain: "DH" Number of atoms: 85 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 85 Classifications: {'peptide': 11} Modifications used: {'COO': 1} Link IDs: {'TRANS': 10} Chain: "DI" Number of atoms: 45 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 45 Classifications: {'peptide': 6} Link IDs: {'TRANS': 5} Chain: "DJ" Number of atoms: 41 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 41 Classifications: {'peptide': 5} Link IDs: {'TRANS': 4} Chain: "DK" Number of atoms: 85 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 85 Classifications: {'peptide': 11} Modifications used: {'COO': 1} Link IDs: {'TRANS': 10} Chain: "DL" Number of atoms: 85 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 85 Classifications: {'peptide': 11} Modifications used: {'COO': 1} Link IDs: {'TRANS': 10} Chain: "DM" Number of atoms: 85 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 85 Classifications: {'peptide': 11} Modifications used: {'COO': 1} Link IDs: {'TRANS': 10} Chain: "DN" Number of atoms: 85 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 85 Classifications: {'peptide': 11} Modifications used: {'COO': 1} Link IDs: {'TRANS': 10} Chain: "DO" Number of atoms: 85 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 85 Classifications: {'peptide': 11} Modifications used: {'COO': 1} Link IDs: {'TRANS': 10} Chain: "DP" Number of atoms: 85 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 85 Classifications: {'peptide': 11} Modifications used: {'COO': 1} Link IDs: {'TRANS': 10} Chain: "DQ" Number of atoms: 85 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 85 Classifications: {'peptide': 11} Modifications used: {'COO': 1} Link IDs: {'TRANS': 10} Chain: "DR" Number of atoms: 45 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 45 Classifications: {'peptide': 6} Link IDs: {'TRANS': 5} Chain: "DS" Number of atoms: 41 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 41 Classifications: {'peptide': 5} Link IDs: {'TRANS': 4} Chain: "DT" Number of atoms: 85 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 85 Classifications: {'peptide': 11} Modifications used: {'COO': 1} Link IDs: {'TRANS': 10} Chain: "DU" Number of atoms: 85 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 85 Classifications: {'peptide': 11} Modifications used: {'COO': 1} Link IDs: {'TRANS': 10} Chain: "DV" Number of atoms: 85 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 85 Classifications: {'peptide': 11} Modifications used: {'COO': 1} Link IDs: {'TRANS': 10} Chain: "DW" Number of atoms: 85 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 85 Classifications: {'peptide': 11} Modifications used: {'COO': 1} Link IDs: {'TRANS': 10} Chain: "DX" Number of atoms: 85 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 85 Classifications: {'peptide': 11} Modifications used: {'COO': 1} Link IDs: {'TRANS': 10} Chain: "DY" Number of atoms: 85 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 85 Classifications: {'peptide': 11} Modifications used: {'COO': 1} Link IDs: {'TRANS': 10} Chain: "DZ" Number of atoms: 85 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 85 Classifications: {'peptide': 11} Modifications used: {'COO': 1} Link IDs: {'TRANS': 10} Chain: "D0" Number of atoms: 45 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 45 Classifications: {'peptide': 6} Link IDs: {'TRANS': 5} Chain: "D1" Number of atoms: 41 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 41 Classifications: {'peptide': 5} Link IDs: {'TRANS': 4} Chain: "D2" Number of atoms: 85 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 85 Classifications: {'peptide': 11} Modifications used: {'COO': 1} Link IDs: {'TRANS': 10} Chain: "D3" Number of atoms: 85 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 85 Classifications: {'peptide': 11} Modifications used: {'COO': 1} Link IDs: {'TRANS': 10} Chain: "D4" Number of atoms: 85 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 85 Classifications: {'peptide': 11} Modifications used: {'COO': 1} Link IDs: {'TRANS': 10} Chain: "D5" Number of atoms: 85 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 85 Classifications: {'peptide': 11} Modifications used: {'COO': 1} Link IDs: {'TRANS': 10} Chain: "D6" Number of atoms: 85 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 85 Classifications: {'peptide': 11} Modifications used: {'COO': 1} Link IDs: {'TRANS': 10} Chain: "D7" Number of atoms: 85 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 85 Classifications: {'peptide': 11} Modifications used: {'COO': 1} Link IDs: {'TRANS': 10} Chain: "D8" Number of atoms: 85 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 85 Classifications: {'peptide': 11} Modifications used: {'COO': 1} Link IDs: {'TRANS': 10} Chain: "D9" Number of atoms: 45 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 45 Classifications: {'peptide': 6} Link IDs: {'TRANS': 5} Chain: "EA" Number of atoms: 41 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 41 Classifications: {'peptide': 5} Link IDs: {'TRANS': 4} Chain: "EB" Number of atoms: 85 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 85 Classifications: {'peptide': 11} Modifications used: {'COO': 1} Link IDs: {'TRANS': 10} Chain: "EC" Number of atoms: 85 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 85 Classifications: {'peptide': 11} Modifications used: {'COO': 1} Link IDs: {'TRANS': 10} Chain: "ED" Number of atoms: 85 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 85 Classifications: {'peptide': 11} Modifications used: {'COO': 1} Link IDs: {'TRANS': 10} Chain: "EE" Number of atoms: 85 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 85 Classifications: {'peptide': 11} Modifications used: {'COO': 1} Link IDs: {'TRANS': 10} Chain: "EF" Number of atoms: 85 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 85 Classifications: {'peptide': 11} Modifications used: {'COO': 1} Link IDs: {'TRANS': 10} Chain: "EG" Number of atoms: 85 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 85 Classifications: {'peptide': 11} Modifications used: {'COO': 1} Link IDs: {'TRANS': 10} Chain: "EH" Number of atoms: 85 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 85 Classifications: {'peptide': 11} Modifications used: {'COO': 1} Link IDs: {'TRANS': 10} Chain: "EI" Number of atoms: 45 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 45 Classifications: {'peptide': 6} Link IDs: {'TRANS': 5} Chain: "EJ" Number of atoms: 41 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 41 Classifications: {'peptide': 5} Link IDs: {'TRANS': 4} Chain: "EK" Number of atoms: 85 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 85 Classifications: {'peptide': 11} Modifications used: {'COO': 1} Link IDs: {'TRANS': 10} Chain: "EL" Number of atoms: 85 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 85 Classifications: {'peptide': 11} Modifications used: {'COO': 1} Link IDs: {'TRANS': 10} Chain: "EM" Number of atoms: 85 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 85 Classifications: {'peptide': 11} Modifications used: {'COO': 1} Link IDs: {'TRANS': 10} Chain: "EN" Number of atoms: 85 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 85 Classifications: {'peptide': 11} Modifications used: {'COO': 1} Link IDs: {'TRANS': 10} Chain: "EO" Number of atoms: 85 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 85 Classifications: {'peptide': 11} Modifications used: {'COO': 1} Link IDs: {'TRANS': 10} Chain: "EP" Number of atoms: 85 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 85 Classifications: {'peptide': 11} Modifications used: {'COO': 1} Link IDs: {'TRANS': 10} Chain: "EQ" Number of atoms: 85 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 85 Classifications: {'peptide': 11} Modifications used: {'COO': 1} Link IDs: {'TRANS': 10} Chain: "ER" Number of atoms: 45 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 45 Classifications: {'peptide': 6} Link IDs: {'TRANS': 5} Chain: "ES" Number of atoms: 41 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 41 Classifications: {'peptide': 5} Link IDs: {'TRANS': 4} Chain: "ET" Number of atoms: 85 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 85 Classifications: {'peptide': 11} Modifications used: {'COO': 1} Link IDs: {'TRANS': 10} Chain: "EU" Number of atoms: 85 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 85 Classifications: {'peptide': 11} Modifications used: {'COO': 1} Link IDs: {'TRANS': 10} Chain: "EV" Number of atoms: 85 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 85 Classifications: {'peptide': 11} Modifications used: {'COO': 1} Link IDs: {'TRANS': 10} Chain: "EW" Number of atoms: 85 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 85 Classifications: {'peptide': 11} Modifications used: {'COO': 1} Link IDs: {'TRANS': 10} Chain: "EX" Number of atoms: 85 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 85 Classifications: {'peptide': 11} Modifications used: {'COO': 1} Link IDs: {'TRANS': 10} Chain: "EY" Number of atoms: 85 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 85 Classifications: {'peptide': 11} Modifications used: {'COO': 1} Link IDs: {'TRANS': 10} Chain: "EZ" Number of atoms: 85 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 85 Classifications: {'peptide': 11} Modifications used: {'COO': 1} Link IDs: {'TRANS': 10} Chain: "E0" Number of atoms: 45 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 45 Classifications: {'peptide': 6} Link IDs: {'TRANS': 5} Chain: "E1" Number of atoms: 41 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 41 Classifications: {'peptide': 5} Link IDs: {'TRANS': 4} Chain: "E2" Number of atoms: 85 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 85 Classifications: {'peptide': 11} Modifications used: {'COO': 1} Link IDs: {'TRANS': 10} Chain: "E3" Number of atoms: 85 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 85 Classifications: {'peptide': 11} Modifications used: {'COO': 1} Link IDs: {'TRANS': 10} Chain: "E4" Number of atoms: 85 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 85 Classifications: {'peptide': 11} Modifications used: {'COO': 1} Link IDs: {'TRANS': 10} Chain: "E5" Number of atoms: 85 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 85 Classifications: {'peptide': 11} Modifications used: {'COO': 1} Link IDs: {'TRANS': 10} Chain: "E6" Number of atoms: 85 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 85 Classifications: {'peptide': 11} Modifications used: {'COO': 1} Link IDs: {'TRANS': 10} Chain: "E7" Number of atoms: 85 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 85 Classifications: {'peptide': 11} Modifications used: {'COO': 1} Link IDs: {'TRANS': 10} Chain: "E8" Number of atoms: 85 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 85 Classifications: {'peptide': 11} Modifications used: {'COO': 1} Link IDs: {'TRANS': 10} Chain: "E9" Number of atoms: 45 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 45 Classifications: {'peptide': 6} Link IDs: {'TRANS': 5} Chain: "FA" Number of atoms: 41 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 41 Classifications: {'peptide': 5} Link IDs: {'TRANS': 4} Chain: "FB" Number of atoms: 85 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 85 Classifications: {'peptide': 11} Modifications used: {'COO': 1} Link IDs: {'TRANS': 10} Chain: "FC" Number of atoms: 85 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 85 Classifications: {'peptide': 11} Modifications used: {'COO': 1} Link IDs: {'TRANS': 10} Chain: "FD" Number of atoms: 85 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 85 Classifications: {'peptide': 11} Modifications used: {'COO': 1} Link IDs: {'TRANS': 10} Chain: "FE" Number of atoms: 85 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 85 Classifications: {'peptide': 11} Modifications used: {'COO': 1} Link IDs: {'TRANS': 10} Chain: "FF" Number of atoms: 85 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 85 Classifications: {'peptide': 11} Modifications used: {'COO': 1} Link IDs: {'TRANS': 10} Chain: "FG" Number of atoms: 85 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 85 Classifications: {'peptide': 11} Modifications used: {'COO': 1} Link IDs: {'TRANS': 10} Chain: "FH" Number of atoms: 85 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 85 Classifications: {'peptide': 11} Modifications used: {'COO': 1} Link IDs: {'TRANS': 10} Chain: "FI" Number of atoms: 45 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 45 Classifications: {'peptide': 6} Link IDs: {'TRANS': 5} Chain: "FJ" Number of atoms: 41 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 41 Classifications: {'peptide': 5} Link IDs: {'TRANS': 4} Chain: "FK" Number of atoms: 85 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 85 Classifications: {'peptide': 11} Modifications used: {'COO': 1} Link IDs: {'TRANS': 10} Chain: "FL" Number of atoms: 85 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 85 Classifications: {'peptide': 11} Modifications used: {'COO': 1} Link IDs: {'TRANS': 10} Chain: "FM" Number of atoms: 85 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 85 Classifications: {'peptide': 11} Modifications used: {'COO': 1} Link IDs: {'TRANS': 10} Chain: "FN" Number of atoms: 85 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 85 Classifications: {'peptide': 11} Modifications used: {'COO': 1} Link IDs: {'TRANS': 10} Chain: "FO" Number of atoms: 85 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 85 Classifications: {'peptide': 11} Modifications used: {'COO': 1} Link IDs: {'TRANS': 10} Chain: "FP" Number of atoms: 85 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 85 Classifications: {'peptide': 11} Modifications used: {'COO': 1} Link IDs: {'TRANS': 10} Chain: "FQ" Number of atoms: 85 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 85 Classifications: {'peptide': 11} Modifications used: {'COO': 1} Link IDs: {'TRANS': 10} Chain: "FR" Number of atoms: 45 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 45 Classifications: {'peptide': 6} Link IDs: {'TRANS': 5} Chain: "FS" Number of atoms: 41 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 41 Classifications: {'peptide': 5} Link IDs: {'TRANS': 4} Chain: "FT" Number of atoms: 85 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 85 Classifications: {'peptide': 11} Modifications used: {'COO': 1} Link IDs: {'TRANS': 10} Chain: "FU" Number of atoms: 85 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 85 Classifications: {'peptide': 11} Modifications used: {'COO': 1} Link IDs: {'TRANS': 10} Chain: "FV" Number of atoms: 85 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 85 Classifications: {'peptide': 11} Modifications used: {'COO': 1} Link IDs: {'TRANS': 10} Chain: "FW" Number of atoms: 85 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 85 Classifications: {'peptide': 11} Modifications used: {'COO': 1} Link IDs: {'TRANS': 10} Chain: "FX" Number of atoms: 85 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 85 Classifications: {'peptide': 11} Modifications used: {'COO': 1} Link IDs: {'TRANS': 10} Chain: "FY" Number of atoms: 85 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 85 Classifications: {'peptide': 11} Modifications used: {'COO': 1} Link IDs: {'TRANS': 10} Chain: "FZ" Number of atoms: 85 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 85 Classifications: {'peptide': 11} Modifications used: {'COO': 1} Link IDs: {'TRANS': 10} Chain: "F0" Number of atoms: 45 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 45 Classifications: {'peptide': 6} Link IDs: {'TRANS': 5} Chain: "F1" Number of atoms: 41 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 41 Classifications: {'peptide': 5} Link IDs: {'TRANS': 4} Time building chain proxies: 6.84, per 1000 atoms: 0.33 Number of scatterers: 20430 At special positions: 0 Unit cell: (133.75, 131.61, 71.69, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 3 Type Number sf(0) O 3600 8.00 N 3330 7.00 C 13500 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.55 Conformation dependent library (CDL) restraints added in 788.5 milliseconds Enol-peptide restraints added in 1.4 microseconds 4200 Ramachandran restraints generated. 2100 Oldfield, 0 Emsley, 2100 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4800 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 0 helices and 0 sheets defined 0.0% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.91 Creating SS restraints... No hydrogen bonds defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 0.01 Time building geometry restraints manager: 2.13 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.29: 3390 1.29 - 1.35: 2853 1.35 - 1.42: 777 1.42 - 1.48: 2704 1.48 - 1.55: 10646 Bond restraints: 20370 Sorted by residual: bond pdb=" CB VALEB 9 " pdb=" CG2 VALEB 9 " ideal model delta sigma weight residual 1.521 1.485 0.036 3.30e-02 9.18e+02 1.20e+00 bond pdb=" CB VALDK 9 " pdb=" CG2 VALDK 9 " ideal model delta sigma weight residual 1.521 1.485 0.036 3.30e-02 9.18e+02 1.20e+00 bond pdb=" CB VAL J 9 " pdb=" CG2 VAL J 9 " ideal model delta sigma weight residual 1.521 1.485 0.036 3.30e-02 9.18e+02 1.20e+00 bond pdb=" CB VALEK 9 " pdb=" CG2 VALEK 9 " ideal model delta sigma weight residual 1.521 1.485 0.036 3.30e-02 9.18e+02 1.20e+00 bond pdb=" CB VALFK 9 " pdb=" CG2 VALFK 9 " ideal model delta sigma weight residual 1.521 1.485 0.036 3.30e-02 9.18e+02 1.20e+00 ... (remaining 20365 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.43: 26028 1.43 - 2.86: 1032 2.86 - 4.29: 0 4.29 - 5.73: 30 5.73 - 7.16: 120 Bond angle restraints: 27210 Sorted by residual: angle pdb=" CA LEUC2 2 " pdb=" CB LEUC2 2 " pdb=" CG LEUC2 2 " ideal model delta sigma weight residual 116.30 123.46 -7.16 3.50e+00 8.16e-02 4.18e+00 angle pdb=" CA LEUCT 2 " pdb=" CB LEUCT 2 " pdb=" CG LEUCT 2 " ideal model delta sigma weight residual 116.30 123.45 -7.15 3.50e+00 8.16e-02 4.17e+00 angle pdb=" CA LEUB2 2 " pdb=" CB LEUB2 2 " pdb=" CG LEUB2 2 " ideal model delta sigma weight residual 116.30 123.44 -7.14 3.50e+00 8.16e-02 4.17e+00 angle pdb=" CA LEUFK 2 " pdb=" CB LEUFK 2 " pdb=" CG LEUFK 2 " ideal model delta sigma weight residual 116.30 123.44 -7.14 3.50e+00 8.16e-02 4.17e+00 angle pdb=" CA LEUBK 2 " pdb=" CB LEUBK 2 " pdb=" CG LEUBK 2 " ideal model delta sigma weight residual 116.30 123.44 -7.14 3.50e+00 8.16e-02 4.17e+00 ... (remaining 27205 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 11.46: 11130 11.46 - 22.93: 513 22.93 - 34.39: 267 34.39 - 45.85: 330 45.85 - 57.31: 60 Dihedral angle restraints: 12300 sinusoidal: 5130 harmonic: 7170 Sorted by residual: dihedral pdb=" CA ILEAX 4 " pdb=" CB ILEAX 4 " pdb=" CG1 ILEAX 4 " pdb=" CD1 ILEAX 4 " ideal model delta sinusoidal sigma weight residual 60.00 107.08 -47.08 3 1.50e+01 4.44e-03 8.44e+00 dihedral pdb=" CA ILEDF 4 " pdb=" CB ILEDF 4 " pdb=" CG1 ILEDF 4 " pdb=" CD1 ILEDF 4 " ideal model delta sinusoidal sigma weight residual 60.00 107.07 -47.07 3 1.50e+01 4.44e-03 8.44e+00 dihedral pdb=" CA ILEA6 4 " pdb=" CB ILEA6 4 " pdb=" CG1 ILEA6 4 " pdb=" CD1 ILEA6 4 " ideal model delta sinusoidal sigma weight residual 60.00 107.07 -47.07 3 1.50e+01 4.44e-03 8.44e+00 ... (remaining 12297 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.034: 1833 0.034 - 0.067: 1051 0.067 - 0.101: 297 0.101 - 0.134: 569 0.134 - 0.168: 90 Chirality restraints: 3840 Sorted by residual: chirality pdb=" CB VAL S 9 " pdb=" CA VAL S 9 " pdb=" CG1 VAL S 9 " pdb=" CG2 VAL S 9 " both_signs ideal model delta sigma weight residual False -2.63 -2.46 -0.17 2.00e-01 2.50e+01 7.06e-01 chirality pdb=" CB VALFB 9 " pdb=" CA VALFB 9 " pdb=" CG1 VALFB 9 " pdb=" CG2 VALFB 9 " both_signs ideal model delta sigma weight residual False -2.63 -2.46 -0.17 2.00e-01 2.50e+01 7.05e-01 chirality pdb=" CB VALFT 9 " pdb=" CA VALFT 9 " pdb=" CG1 VALFT 9 " pdb=" CG2 VALFT 9 " both_signs ideal model delta sigma weight residual False -2.63 -2.46 -0.17 2.00e-01 2.50e+01 7.02e-01 ... (remaining 3837 not shown) Planarity restraints: 3060 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA VALCF 9 " -0.006 2.00e-02 2.50e+03 1.13e-02 1.27e+00 pdb=" C VALCF 9 " 0.020 2.00e-02 2.50e+03 pdb=" O VALCF 9 " -0.007 2.00e-02 2.50e+03 pdb=" N HISCF 10 " -0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VALAX 9 " -0.006 2.00e-02 2.50e+03 1.11e-02 1.24e+00 pdb=" C VALAX 9 " 0.019 2.00e-02 2.50e+03 pdb=" O VALAX 9 " -0.007 2.00e-02 2.50e+03 pdb=" N HISAX 10 " -0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VALFF 9 " 0.006 2.00e-02 2.50e+03 1.11e-02 1.24e+00 pdb=" C VALFF 9 " -0.019 2.00e-02 2.50e+03 pdb=" O VALFF 9 " 0.007 2.00e-02 2.50e+03 pdb=" N HISFF 10 " 0.006 2.00e-02 2.50e+03 ... (remaining 3057 not shown) Histogram of nonbonded interaction distances: 2.37 - 2.87: 5559 2.87 - 3.38: 18710 3.38 - 3.89: 35853 3.89 - 4.39: 35544 4.39 - 4.90: 71101 Nonbonded interactions: 166767 Sorted by model distance: nonbonded pdb=" OXT ILEFF 11 " pdb=" N ASPFG 1 " model vdw 2.365 3.120 nonbonded pdb=" OXT ILECO 11 " pdb=" N ASPCP 1 " model vdw 2.365 3.120 nonbonded pdb=" OXT ILEFO 11 " pdb=" N ASPFP 1 " model vdw 2.365 3.120 nonbonded pdb=" OXT ILE e 11 " pdb=" N ASP f 1 " model vdw 2.365 3.120 nonbonded pdb=" OXT ILEA6 11 " pdb=" N ASPA7 1 " model vdw 2.365 3.120 ... (remaining 166762 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain '0' selection = chain 'A0' selection = chain 'A9' selection = chain 'AI' selection = chain 'AR' selection = chain 'B0' selection = chain 'B9' selection = chain 'BI' selection = chain 'BR' selection = chain 'C0' selection = chain 'C9' selection = chain 'CI' selection = chain 'CR' selection = chain 'D0' selection = chain 'D9' selection = chain 'DI' selection = chain 'DR' selection = chain 'E0' selection = chain 'E9' selection = chain 'EI' selection = chain 'ER' selection = chain 'F0' selection = chain 'FI' selection = chain 'FR' selection = chain 'H' selection = chain 'Q' selection = chain 'Z' selection = chain 'h' selection = chain 'q' selection = chain 'z' } ncs_group { reference = chain '1' selection = chain '2' selection = chain '3' selection = chain '4' selection = chain '5' selection = chain '6' selection = chain '7' selection = chain 'A' selection = chain 'A2' selection = chain 'A3' selection = chain 'A4' selection = chain 'A5' selection = chain 'A6' selection = chain 'A7' selection = chain 'A8' selection = chain 'AB' selection = chain 'AC' selection = chain 'AD' selection = chain 'AE' selection = chain 'AF' selection = chain 'AG' selection = chain 'AH' selection = chain 'AK' selection = chain 'AL' selection = chain 'AM' selection = chain 'AN' selection = chain 'AO' selection = chain 'AP' selection = chain 'AQ' selection = chain 'AT' selection = chain 'AU' selection = chain 'AV' selection = chain 'AW' selection = chain 'AX' selection = chain 'AY' selection = chain 'AZ' selection = chain 'B' selection = chain 'B2' selection = chain 'B3' selection = chain 'B4' selection = chain 'B5' selection = chain 'B6' selection = chain 'B7' selection = chain 'B8' selection = chain 'BB' selection = chain 'BC' selection = chain 'BD' selection = chain 'BE' selection = chain 'BF' selection = chain 'BG' selection = chain 'BH' selection = chain 'BK' selection = chain 'BL' selection = chain 'BM' selection = chain 'BN' selection = chain 'BO' selection = chain 'BP' selection = chain 'BQ' selection = chain 'BT' selection = chain 'BU' selection = chain 'BV' selection = chain 'BW' selection = chain 'BX' selection = chain 'BY' selection = chain 'BZ' selection = chain 'C' selection = chain 'C2' selection = chain 'C3' selection = chain 'C4' selection = chain 'C5' selection = chain 'C6' selection = chain 'C7' selection = chain 'C8' selection = chain 'CB' selection = chain 'CC' selection = chain 'CD' selection = chain 'CE' selection = chain 'CF' selection = chain 'CG' selection = chain 'CH' selection = chain 'CK' selection = chain 'CL' selection = chain 'CM' selection = chain 'CN' selection = chain 'CO' selection = chain 'CP' selection = chain 'CQ' selection = chain 'CT' selection = chain 'CU' selection = chain 'CV' selection = chain 'CW' selection = chain 'CX' selection = chain 'CY' selection = chain 'CZ' selection = chain 'D' selection = chain 'D2' selection = chain 'D3' selection = chain 'D4' selection = chain 'D5' selection = chain 'D6' selection = chain 'D7' selection = chain 'D8' selection = chain 'DB' selection = chain 'DC' selection = chain 'DD' selection = chain 'DE' selection = chain 'DF' selection = chain 'DG' selection = chain 'DH' selection = chain 'DK' selection = chain 'DL' selection = chain 'DM' selection = chain 'DN' selection = chain 'DO' selection = chain 'DP' selection = chain 'DQ' selection = chain 'DT' selection = chain 'DU' selection = chain 'DV' selection = chain 'DW' selection = chain 'DX' selection = chain 'DY' selection = chain 'DZ' selection = chain 'E' selection = chain 'E2' selection = chain 'E3' selection = chain 'E4' selection = chain 'E5' selection = chain 'E6' selection = chain 'E7' selection = chain 'E8' selection = chain 'EB' selection = chain 'EC' selection = chain 'ED' selection = chain 'EE' selection = chain 'EF' selection = chain 'EG' selection = chain 'EH' selection = chain 'EK' selection = chain 'EL' selection = chain 'EM' selection = chain 'EN' selection = chain 'EO' selection = chain 'EP' selection = chain 'EQ' selection = chain 'ET' selection = chain 'EU' selection = chain 'EV' selection = chain 'EW' selection = chain 'EX' selection = chain 'EY' selection = chain 'EZ' selection = chain 'F' selection = chain 'FB' selection = chain 'FC' selection = chain 'FD' selection = chain 'FE' selection = chain 'FF' selection = chain 'FG' selection = chain 'FH' selection = chain 'FK' selection = chain 'FL' selection = chain 'FM' selection = chain 'FN' selection = chain 'FO' selection = chain 'FP' selection = chain 'FQ' selection = chain 'FT' selection = chain 'FU' selection = chain 'FV' selection = chain 'FW' selection = chain 'FX' selection = chain 'FY' selection = chain 'FZ' selection = chain 'G' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'S' selection = chain 'T' selection = chain 'U' selection = chain 'V' selection = chain 'W' selection = chain 'X' selection = chain 'Y' selection = chain 'a' selection = chain 'b' selection = chain 'c' selection = chain 'd' selection = chain 'e' selection = chain 'f' selection = chain 'g' selection = chain 'j' selection = chain 'k' selection = chain 'l' selection = chain 'm' selection = chain 'n' selection = chain 'o' selection = chain 'p' selection = chain 's' selection = chain 't' selection = chain 'u' selection = chain 'v' selection = chain 'w' selection = chain 'x' selection = chain 'y' } ncs_group { reference = chain '8' selection = chain '9' selection = chain 'A1' selection = chain 'AA' selection = chain 'AJ' selection = chain 'AS' selection = chain 'B1' selection = chain 'BA' selection = chain 'BJ' selection = chain 'BS' selection = chain 'C1' selection = chain 'CA' selection = chain 'CJ' selection = chain 'CS' selection = chain 'D1' selection = chain 'DA' selection = chain 'DJ' selection = chain 'DS' selection = chain 'E1' selection = chain 'EA' selection = chain 'EJ' selection = chain 'ES' selection = chain 'F1' selection = chain 'FA' selection = chain 'FJ' selection = chain 'FS' selection = chain 'I' selection = chain 'R' selection = chain 'i' selection = chain 'r' } 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=0.00 max=1.00 mean=0.94 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: 0.180 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.310 Check model and map are aligned: 0.050 Set scattering table: 0.060 Process input model: 17.700 Find NCS groups from input model: 1.100 Set up NCS constraints: 0.370 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:1.340 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.120 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7241 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 : 0.007 0.039 20370 Z= 0.263 Angle : 0.770 7.158 27210 Z= 0.346 Chirality : 0.063 0.168 3840 Planarity : 0.002 0.011 3060 Dihedral : 12.788 57.314 7500 Min Nonbonded Distance : 2.365 Molprobity Statistics. All-atom Clashscore : 15.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.43 % Favored : 98.57 % Rotamer: Outliers : 0.00 % Allowed : 8.75 % Favored : 91.25 % 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 aren not related in a simple way. whole: -2.52 (0.13), residues: 2100 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.91 (0.10), residues: 2100 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.008 0.002 HISCM 10 Details of bonding type rmsd covalent geometry : bond 0.00670 (20370) covalent geometry : angle 0.77042 (27210) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4200 Ramachandran restraints generated. 2100 Oldfield, 0 Emsley, 2100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4200 Ramachandran restraints generated. 2100 Oldfield, 0 Emsley, 2100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 641 residues out of total 2400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 641 time to evaluate : 0.900 Fit side-chains REVERT: C 5 LYS cc_start: 0.8198 (ptmt) cc_final: 0.7994 (ptpt) REVERT: D 5 LYS cc_start: 0.8014 (mttt) cc_final: 0.7734 (mttm) REVERT: M 5 LYS cc_start: 0.7685 (mttt) cc_final: 0.7382 (mttm) REVERT: U 3 ILE cc_start: 0.8003 (mp) cc_final: 0.7802 (mm) REVERT: m 5 LYS cc_start: 0.7814 (mttt) cc_final: 0.7610 (mttm) REVERT: v 5 LYS cc_start: 0.7390 (mttt) cc_final: 0.7047 (mttm) REVERT: AD 3 ILE cc_start: 0.7868 (mp) cc_final: 0.7624 (mm) REVERT: AE 5 LYS cc_start: 0.7680 (mttt) cc_final: 0.7338 (mttm) REVERT: AN 5 LYS cc_start: 0.7509 (mttt) cc_final: 0.7192 (mttm) REVERT: AV 3 ILE cc_start: 0.7940 (mp) cc_final: 0.7724 (mm) REVERT: A5 5 LYS cc_start: 0.7415 (mttt) cc_final: 0.7212 (mttm) REVERT: BE 5 LYS cc_start: 0.7520 (mttt) cc_final: 0.7226 (mttm) REVERT: BN 3 ILE cc_start: 0.8452 (mt) cc_final: 0.8115 (mp) REVERT: BP 4 ILE cc_start: 0.8399 (mt) cc_final: 0.8192 (mt) REVERT: BW 5 LYS cc_start: 0.7629 (mttt) cc_final: 0.7390 (mttm) REVERT: B5 5 LYS cc_start: 0.7597 (mttt) cc_final: 0.7182 (mttm) REVERT: CD 3 ILE cc_start: 0.7895 (mp) cc_final: 0.7651 (mm) REVERT: 6 5 LYS cc_start: 0.7421 (mttt) cc_final: 0.7019 (mttp) REVERT: CM 3 ILE cc_start: 0.7791 (mp) cc_final: 0.7468 (mm) REVERT: CW 3 ILE cc_start: 0.8430 (mt) cc_final: 0.8165 (mp) REVERT: CW 5 LYS cc_start: 0.7598 (mttt) cc_final: 0.7211 (mttm) REVERT: C4 3 ILE cc_start: 0.8010 (mp) cc_final: 0.7708 (mm) REVERT: C5 5 LYS cc_start: 0.7277 (mttt) cc_final: 0.6988 (mttm) REVERT: DD 3 ILE cc_start: 0.7613 (mp) cc_final: 0.7380 (mp) REVERT: DE 5 LYS cc_start: 0.7239 (mttt) cc_final: 0.6877 (mttm) REVERT: DM 3 ILE cc_start: 0.7933 (mp) cc_final: 0.7665 (mm) REVERT: DW 3 ILE cc_start: 0.8576 (mt) cc_final: 0.8319 (mp) REVERT: D4 3 ILE cc_start: 0.7888 (mp) cc_final: 0.7579 (mm) REVERT: EE 3 ILE cc_start: 0.8511 (mt) cc_final: 0.8278 (mp) REVERT: EE 5 LYS cc_start: 0.7238 (mttt) cc_final: 0.6947 (mttm) REVERT: EW 3 ILE cc_start: 0.8433 (mt) cc_final: 0.8137 (mp) REVERT: E4 3 ILE cc_start: 0.7981 (mp) cc_final: 0.7742 (mm) REVERT: E5 5 LYS cc_start: 0.7441 (mttt) cc_final: 0.7240 (mttp) REVERT: FE 3 ILE cc_start: 0.8837 (mt) cc_final: 0.8539 (mp) REVERT: FE 5 LYS cc_start: 0.8212 (mttt) cc_final: 0.7945 (mttm) outliers start: 0 outliers final: 0 residues processed: 641 average time/residue: 0.1228 time to fit residues: 123.1517 Evaluate side-chains 449 residues out of total 2400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 449 time to evaluate : 0.531 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 98 optimal weight: 6.9990 chunk 194 optimal weight: 30.0000 chunk 107 optimal weight: 4.9990 chunk 10 optimal weight: 20.0000 chunk 66 optimal weight: 30.0000 chunk 130 optimal weight: 20.0000 chunk 124 optimal weight: 30.0000 chunk 103 optimal weight: 9.9990 chunk 200 optimal weight: 7.9990 chunk 77 optimal weight: 1.9990 chunk 122 optimal weight: 6.9990 overall best weight: 5.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 10 HIS B 10 HIS C 10 HIS K 10 HIS T 10 HIS U 10 HIS b 10 HIS ** g 10 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** k 10 HIS ** p 10 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** s 10 HIS t 10 HIS ** y 10 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** AB 10 HIS AC 10 HIS ** AH 10 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** AL 10 HIS ** AM 10 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** AQ 10 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** AT 10 HIS AU 10 HIS ** AZ 10 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A3 10 HIS A4 10 HIS ** A8 10 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** BC 10 HIS ** BD 10 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** BH 10 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** BL 10 HIS ** BQ 10 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** BU 10 HIS BV 10 HIS ** BZ 10 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B3 10 HIS ** B8 10 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** CC 10 HIS CD 10 HIS ** CH 10 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 3 10 HIS ** 7 10 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** CL 10 HIS ** CQ 10 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** CU 10 HIS ** CZ 10 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C2 10 HIS C3 10 HIS C4 10 HIS ** C8 10 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** DC 10 HIS ** DH 10 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** DL 10 HIS DM 10 HIS ** DQ 10 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** DU 10 HIS ** DZ 10 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D2 10 HIS D3 10 HIS ** D8 10 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** EC 10 HIS ED 10 HIS ** EH 10 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** EL 10 HIS ** EQ 10 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** EU 10 HIS ** EV 10 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** EW 10 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** EZ 10 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E3 10 HIS E4 10 HIS ** E5 10 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E8 10 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** FE 10 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** FH 10 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** FN 10 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** FQ 10 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** FT 10 HIS ** FW 10 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** FZ 10 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 43 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3540 r_free = 0.3540 target = 0.119766 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.101427 restraints weight = 29220.393| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.104816 restraints weight = 14994.221| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.107136 restraints weight = 9403.500| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.108811 restraints weight = 6681.346| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.110028 restraints weight = 5138.691| |-----------------------------------------------------------------------------| r_work (final): 0.3425 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7720 moved from start: 0.1887 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.024 20370 Z= 0.154 Angle : 0.691 10.109 27210 Z= 0.291 Chirality : 0.058 0.142 3840 Planarity : 0.002 0.007 3060 Dihedral : 11.585 60.191 2580 Min Nonbonded Distance : 2.587 Molprobity Statistics. All-atom Clashscore : 5.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 6.08 % Allowed : 17.00 % Favored : 76.92 % 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 aren not related in a simple way. whole: -1.88 (0.15), residues: 2100 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.42 (0.11), residues: 2100 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.002 HISAT 10 Details of bonding type rmsd covalent geometry : bond 0.00388 (20370) covalent geometry : angle 0.69053 (27210) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4200 Ramachandran restraints generated. 2100 Oldfield, 0 Emsley, 2100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4200 Ramachandran restraints generated. 2100 Oldfield, 0 Emsley, 2100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 660 residues out of total 2400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 146 poor density : 514 time to evaluate : 0.716 Fit side-chains REVERT: J 4 ILE cc_start: 0.8580 (OUTLIER) cc_final: 0.8276 (mp) REVERT: M 5 LYS cc_start: 0.8430 (mttt) cc_final: 0.8180 (mttm) REVERT: U 3 ILE cc_start: 0.8282 (mp) cc_final: 0.8075 (mm) REVERT: a 4 ILE cc_start: 0.8655 (OUTLIER) cc_final: 0.8413 (mp) REVERT: d 3 ILE cc_start: 0.9164 (mt) cc_final: 0.8913 (mp) REVERT: s 4 ILE cc_start: 0.8672 (OUTLIER) cc_final: 0.8419 (mp) REVERT: v 5 LYS cc_start: 0.8212 (mttt) cc_final: 0.7824 (mttm) REVERT: AD 3 ILE cc_start: 0.8141 (mp) cc_final: 0.7907 (mm) REVERT: AE 5 LYS cc_start: 0.8362 (mttt) cc_final: 0.8157 (mttm) REVERT: AK 4 ILE cc_start: 0.8703 (OUTLIER) cc_final: 0.8341 (mp) REVERT: AN 5 LYS cc_start: 0.8185 (mttt) cc_final: 0.7838 (mttm) REVERT: A2 4 ILE cc_start: 0.8688 (OUTLIER) cc_final: 0.8323 (mp) REVERT: A5 5 LYS cc_start: 0.8080 (mttt) cc_final: 0.7852 (mttm) REVERT: BK 4 ILE cc_start: 0.8655 (OUTLIER) cc_final: 0.8350 (mp) REVERT: BN 3 ILE cc_start: 0.8983 (mt) cc_final: 0.8780 (mp) REVERT: BV 5 LYS cc_start: 0.8253 (ptmt) cc_final: 0.8024 (ptpt) REVERT: B2 4 ILE cc_start: 0.8745 (OUTLIER) cc_final: 0.8479 (mp) REVERT: 1 4 ILE cc_start: 0.8768 (OUTLIER) cc_final: 0.8459 (mp) REVERT: 6 2 LEU cc_start: 0.8278 (pt) cc_final: 0.7974 (pp) REVERT: 6 5 LYS cc_start: 0.8084 (mttt) cc_final: 0.7771 (mttp) REVERT: CN 2 LEU cc_start: 0.7910 (pt) cc_final: 0.7688 (pp) REVERT: CT 4 ILE cc_start: 0.8663 (OUTLIER) cc_final: 0.8446 (mp) REVERT: CW 5 LYS cc_start: 0.8187 (mttt) cc_final: 0.7747 (mttm) REVERT: C4 3 ILE cc_start: 0.8291 (mp) cc_final: 0.8028 (mm) REVERT: C5 5 LYS cc_start: 0.8119 (mttt) cc_final: 0.7765 (mttm) REVERT: DB 4 ILE cc_start: 0.8641 (OUTLIER) cc_final: 0.8398 (mp) REVERT: DE 5 LYS cc_start: 0.7891 (mttt) cc_final: 0.7545 (mttm) REVERT: DT 4 ILE cc_start: 0.8793 (OUTLIER) cc_final: 0.8563 (mp) REVERT: D4 3 ILE cc_start: 0.8125 (mp) cc_final: 0.7877 (mm) REVERT: EB 4 ILE cc_start: 0.8650 (OUTLIER) cc_final: 0.8411 (mp) REVERT: EE 5 LYS cc_start: 0.7820 (mttt) cc_final: 0.7520 (mttm) REVERT: EN 5 LYS cc_start: 0.8289 (mttm) cc_final: 0.8032 (mttm) REVERT: ET 4 ILE cc_start: 0.8760 (OUTLIER) cc_final: 0.8555 (mp) REVERT: E5 5 LYS cc_start: 0.8087 (mttt) cc_final: 0.7806 (mttp) REVERT: FE 5 LYS cc_start: 0.8470 (mttt) cc_final: 0.8213 (mttm) REVERT: FN 2 LEU cc_start: 0.8248 (pt) cc_final: 0.6897 (mm) REVERT: FT 4 ILE cc_start: 0.8630 (OUTLIER) cc_final: 0.8412 (mp) outliers start: 146 outliers final: 68 residues processed: 560 average time/residue: 0.1311 time to fit residues: 115.0928 Evaluate side-chains 503 residues out of total 2400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 421 time to evaluate : 0.982 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 9 VAL Chi-restraints excluded: chain E residue 9 VAL Chi-restraints excluded: chain G residue 2 LEU Chi-restraints excluded: chain J residue 4 ILE Chi-restraints excluded: chain S residue 8 SER Chi-restraints excluded: chain T residue 9 VAL Chi-restraints excluded: chain W residue 9 VAL Chi-restraints excluded: chain Y residue 2 LEU Chi-restraints excluded: chain a residue 4 ILE Chi-restraints excluded: chain b residue 9 VAL Chi-restraints excluded: chain e residue 9 VAL Chi-restraints excluded: chain k residue 9 VAL Chi-restraints excluded: chain n residue 9 VAL Chi-restraints excluded: chain o residue 8 SER Chi-restraints excluded: chain s residue 4 ILE Chi-restraints excluded: chain t residue 9 VAL Chi-restraints excluded: chain y residue 2 LEU Chi-restraints excluded: chain AC residue 9 VAL Chi-restraints excluded: chain AF residue 9 VAL Chi-restraints excluded: chain AH residue 7 ILE Chi-restraints excluded: chain AK residue 4 ILE Chi-restraints excluded: chain AL residue 9 VAL Chi-restraints excluded: chain AO residue 9 VAL Chi-restraints excluded: chain AU residue 9 VAL Chi-restraints excluded: chain AZ residue 2 LEU Chi-restraints excluded: chain A0 residue 5 LYS Chi-restraints excluded: chain A2 residue 4 ILE Chi-restraints excluded: chain A3 residue 9 VAL Chi-restraints excluded: chain A6 residue 9 VAL Chi-restraints excluded: chain A8 residue 2 LEU Chi-restraints excluded: chain BC residue 9 VAL Chi-restraints excluded: chain BK residue 4 ILE Chi-restraints excluded: chain BL residue 9 VAL Chi-restraints excluded: chain BO residue 9 VAL Chi-restraints excluded: chain BQ residue 2 LEU Chi-restraints excluded: chain BU residue 9 VAL Chi-restraints excluded: chain B2 residue 4 ILE Chi-restraints excluded: chain B3 residue 9 VAL Chi-restraints excluded: chain B7 residue 8 SER Chi-restraints excluded: chain B8 residue 2 LEU Chi-restraints excluded: chain CB residue 8 SER Chi-restraints excluded: chain CC residue 9 VAL Chi-restraints excluded: chain CH residue 2 LEU Chi-restraints excluded: chain CI residue 5 LYS Chi-restraints excluded: chain 1 residue 4 ILE Chi-restraints excluded: chain 3 residue 9 VAL Chi-restraints excluded: chain 7 residue 2 LEU Chi-restraints excluded: chain CL residue 9 VAL Chi-restraints excluded: chain CR residue 5 LYS Chi-restraints excluded: chain CT residue 4 ILE Chi-restraints excluded: chain CU residue 9 VAL Chi-restraints excluded: chain CZ residue 2 LEU Chi-restraints excluded: chain C3 residue 9 VAL Chi-restraints excluded: chain DB residue 4 ILE Chi-restraints excluded: chain DC residue 9 VAL Chi-restraints excluded: chain DH residue 2 LEU Chi-restraints excluded: chain DL residue 9 VAL Chi-restraints excluded: chain DT residue 4 ILE Chi-restraints excluded: chain DU residue 9 VAL Chi-restraints excluded: chain DZ residue 2 LEU Chi-restraints excluded: chain D3 residue 9 VAL Chi-restraints excluded: chain D7 residue 8 SER Chi-restraints excluded: chain EB residue 4 ILE Chi-restraints excluded: chain EB residue 8 SER Chi-restraints excluded: chain EC residue 9 VAL Chi-restraints excluded: chain EH residue 2 LEU Chi-restraints excluded: chain EL residue 9 VAL Chi-restraints excluded: chain EO residue 9 VAL Chi-restraints excluded: chain EP residue 8 SER Chi-restraints excluded: chain ET residue 4 ILE Chi-restraints excluded: chain EU residue 9 VAL Chi-restraints excluded: chain E3 residue 9 VAL Chi-restraints excluded: chain E6 residue 9 VAL Chi-restraints excluded: chain E8 residue 7 ILE Chi-restraints excluded: chain FB residue 8 SER Chi-restraints excluded: chain FC residue 9 VAL Chi-restraints excluded: chain FH residue 2 LEU Chi-restraints excluded: chain FL residue 9 VAL Chi-restraints excluded: chain FO residue 9 VAL Chi-restraints excluded: chain FT residue 4 ILE Chi-restraints excluded: chain FT residue 8 SER Chi-restraints excluded: chain FU residue 9 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 128 optimal weight: 30.0000 chunk 199 optimal weight: 5.9990 chunk 145 optimal weight: 30.0000 chunk 55 optimal weight: 2.9990 chunk 117 optimal weight: 9.9990 chunk 112 optimal weight: 20.0000 chunk 140 optimal weight: 4.9990 chunk 143 optimal weight: 40.0000 chunk 33 optimal weight: 30.0000 chunk 6 optimal weight: 0.9980 chunk 135 optimal weight: 20.0000 overall best weight: 4.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: a 10 HIS c 10 HIS l 10 HIS ** p 10 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** AB 10 HIS AD 10 HIS ** AH 10 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** AQ 10 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** AT 10 HIS ** AZ 10 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A4 10 HIS ** A8 10 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** BD 10 HIS ** BH 10 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** BQ 10 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** BZ 10 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B8 10 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** CH 10 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 10 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** CQ 10 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** CZ 10 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C2 10 HIS ** C8 10 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** DH 10 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** DQ 10 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** DZ 10 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D4 10 HIS ** D8 10 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** EB 10 HIS ** EH 10 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** EQ 10 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** EW 10 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** EZ 10 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E8 10 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** FE 10 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** FH 10 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** FM 10 HIS ** FN 10 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** FQ 10 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** FT 10 HIS ** FW 10 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** FZ 10 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3546 r_free = 0.3546 target = 0.117254 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.098320 restraints weight = 30314.518| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.101648 restraints weight = 15789.403| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.103976 restraints weight = 10039.623| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.105626 restraints weight = 7217.402| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.106764 restraints weight = 5618.218| |-----------------------------------------------------------------------------| r_work (final): 0.3420 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7698 moved from start: 0.2464 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 20370 Z= 0.136 Angle : 0.657 9.188 27210 Z= 0.276 Chirality : 0.057 0.164 3840 Planarity : 0.001 0.008 3060 Dihedral : 11.156 60.773 2580 Min Nonbonded Distance : 2.580 Molprobity Statistics. All-atom Clashscore : 5.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.10 % Favored : 99.90 % Rotamer: Outliers : 7.38 % Allowed : 18.79 % Favored : 73.83 % 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 aren not related in a simple way. whole: -1.38 (0.16), residues: 2100 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.04 (0.12), residues: 2100 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HISAB 10 Details of bonding type rmsd covalent geometry : bond 0.00341 (20370) covalent geometry : angle 0.65657 (27210) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4200 Ramachandran restraints generated. 2100 Oldfield, 0 Emsley, 2100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4200 Ramachandran restraints generated. 2100 Oldfield, 0 Emsley, 2100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 621 residues out of total 2400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 177 poor density : 444 time to evaluate : 0.571 Fit side-chains REVERT: D 2 LEU cc_start: 0.8417 (pt) cc_final: 0.8085 (tt) REVERT: M 5 LYS cc_start: 0.8423 (mttt) cc_final: 0.8204 (mttm) REVERT: U 3 ILE cc_start: 0.8285 (mp) cc_final: 0.7890 (mp) REVERT: V 2 LEU cc_start: 0.8347 (pt) cc_final: 0.8082 (tt) REVERT: a 4 ILE cc_start: 0.8678 (OUTLIER) cc_final: 0.8390 (mp) REVERT: s 4 ILE cc_start: 0.8539 (OUTLIER) cc_final: 0.8264 (mp) REVERT: v 5 LYS cc_start: 0.8197 (mttt) cc_final: 0.7884 (mttm) REVERT: AD 3 ILE cc_start: 0.8013 (mp) cc_final: 0.7510 (mp) REVERT: AK 4 ILE cc_start: 0.8683 (OUTLIER) cc_final: 0.8320 (mp) REVERT: AN 5 LYS cc_start: 0.8127 (mttt) cc_final: 0.7791 (mttm) REVERT: A2 4 ILE cc_start: 0.8617 (OUTLIER) cc_final: 0.8244 (mp) REVERT: BK 4 ILE cc_start: 0.8531 (OUTLIER) cc_final: 0.8174 (mp) REVERT: BN 3 ILE cc_start: 0.8891 (mt) cc_final: 0.8690 (mp) REVERT: BV 5 LYS cc_start: 0.8275 (ptmt) cc_final: 0.8000 (ptpt) REVERT: B2 4 ILE cc_start: 0.8650 (OUTLIER) cc_final: 0.8362 (mp) REVERT: B5 5 LYS cc_start: 0.8382 (mttm) cc_final: 0.8154 (mttp) REVERT: 1 4 ILE cc_start: 0.8691 (OUTLIER) cc_final: 0.8363 (mp) REVERT: 6 2 LEU cc_start: 0.8315 (pt) cc_final: 0.8042 (pp) REVERT: 6 5 LYS cc_start: 0.8049 (mttt) cc_final: 0.7655 (mttm) REVERT: CT 4 ILE cc_start: 0.8629 (OUTLIER) cc_final: 0.8387 (mp) REVERT: DB 4 ILE cc_start: 0.8533 (OUTLIER) cc_final: 0.8280 (mp) REVERT: DE 5 LYS cc_start: 0.7907 (mttt) cc_final: 0.7550 (mttm) REVERT: DT 4 ILE cc_start: 0.8662 (OUTLIER) cc_final: 0.8397 (mp) REVERT: DW 2 LEU cc_start: 0.8440 (pp) cc_final: 0.8197 (pt) REVERT: DW 3 ILE cc_start: 0.9052 (mt) cc_final: 0.8803 (mp) REVERT: EB 4 ILE cc_start: 0.8565 (OUTLIER) cc_final: 0.8321 (mp) REVERT: EE 5 LYS cc_start: 0.7916 (mttt) cc_final: 0.7569 (mttm) REVERT: EN 5 LYS cc_start: 0.8113 (mttm) cc_final: 0.7827 (mttm) REVERT: ET 4 ILE cc_start: 0.8664 (OUTLIER) cc_final: 0.8451 (mp) REVERT: EW 2 LEU cc_start: 0.8266 (pt) cc_final: 0.7996 (pp) REVERT: E5 5 LYS cc_start: 0.7977 (mttt) cc_final: 0.7731 (mttp) REVERT: FE 2 LEU cc_start: 0.8316 (pp) cc_final: 0.6739 (mm) REVERT: FE 5 LYS cc_start: 0.8477 (mttt) cc_final: 0.8207 (mttm) REVERT: FN 2 LEU cc_start: 0.8180 (pt) cc_final: 0.6692 (mm) REVERT: FT 4 ILE cc_start: 0.8606 (OUTLIER) cc_final: 0.8390 (mp) outliers start: 177 outliers final: 91 residues processed: 510 average time/residue: 0.1207 time to fit residues: 98.4510 Evaluate side-chains 516 residues out of total 2400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 104 poor density : 412 time to evaluate : 0.882 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 VAL Chi-restraints excluded: chain E residue 9 VAL Chi-restraints excluded: chain G residue 2 LEU Chi-restraints excluded: chain G residue 4 ILE Chi-restraints excluded: chain P residue 9 VAL Chi-restraints excluded: chain S residue 8 SER Chi-restraints excluded: chain T residue 9 VAL Chi-restraints excluded: chain W residue 9 VAL Chi-restraints excluded: chain Y residue 2 LEU Chi-restraints excluded: chain a residue 4 ILE Chi-restraints excluded: chain a residue 8 SER Chi-restraints excluded: chain b residue 9 VAL Chi-restraints excluded: chain d residue 8 SER Chi-restraints excluded: chain g residue 2 LEU Chi-restraints excluded: chain j residue 8 SER Chi-restraints excluded: chain k residue 9 VAL Chi-restraints excluded: chain n residue 9 VAL Chi-restraints excluded: chain o residue 8 SER Chi-restraints excluded: chain p residue 2 LEU Chi-restraints excluded: chain p residue 7 ILE Chi-restraints excluded: chain q residue 5 LYS Chi-restraints excluded: chain s residue 4 ILE Chi-restraints excluded: chain t residue 9 VAL Chi-restraints excluded: chain y residue 2 LEU Chi-restraints excluded: chain AC residue 9 VAL Chi-restraints excluded: chain AF residue 9 VAL Chi-restraints excluded: chain AH residue 2 LEU Chi-restraints excluded: chain AH residue 7 ILE Chi-restraints excluded: chain AK residue 4 ILE Chi-restraints excluded: chain AL residue 9 VAL Chi-restraints excluded: chain AN residue 8 SER Chi-restraints excluded: chain AO residue 9 VAL Chi-restraints excluded: chain AQ residue 2 LEU Chi-restraints excluded: chain AQ residue 7 ILE Chi-restraints excluded: chain AU residue 9 VAL Chi-restraints excluded: chain AW residue 8 SER Chi-restraints excluded: chain AZ residue 2 LEU Chi-restraints excluded: chain A0 residue 5 LYS Chi-restraints excluded: chain A2 residue 4 ILE Chi-restraints excluded: chain A3 residue 9 VAL Chi-restraints excluded: chain A8 residue 2 LEU Chi-restraints excluded: chain BC residue 9 VAL Chi-restraints excluded: chain BE residue 8 SER Chi-restraints excluded: chain BF residue 9 VAL Chi-restraints excluded: chain BK residue 4 ILE Chi-restraints excluded: chain BL residue 9 VAL Chi-restraints excluded: chain BQ residue 2 LEU Chi-restraints excluded: chain BU residue 9 VAL Chi-restraints excluded: chain B2 residue 4 ILE Chi-restraints excluded: chain B3 residue 9 VAL Chi-restraints excluded: chain B7 residue 8 SER Chi-restraints excluded: chain B8 residue 2 LEU Chi-restraints excluded: chain CB residue 8 SER Chi-restraints excluded: chain CC residue 9 VAL Chi-restraints excluded: chain CH residue 2 LEU Chi-restraints excluded: chain CI residue 5 LYS Chi-restraints excluded: chain 1 residue 4 ILE Chi-restraints excluded: chain 3 residue 9 VAL Chi-restraints excluded: chain 7 residue 2 LEU Chi-restraints excluded: chain 7 residue 7 ILE Chi-restraints excluded: chain CL residue 9 VAL Chi-restraints excluded: chain CR residue 3 ILE Chi-restraints excluded: chain CR residue 5 LYS Chi-restraints excluded: chain CT residue 4 ILE Chi-restraints excluded: chain CU residue 9 VAL Chi-restraints excluded: chain CZ residue 2 LEU Chi-restraints excluded: chain CZ residue 7 ILE Chi-restraints excluded: chain C3 residue 9 VAL Chi-restraints excluded: chain DB residue 4 ILE Chi-restraints excluded: chain DC residue 9 VAL Chi-restraints excluded: chain DH residue 2 LEU Chi-restraints excluded: chain DH residue 7 ILE Chi-restraints excluded: chain DK residue 9 VAL Chi-restraints excluded: chain DL residue 9 VAL Chi-restraints excluded: chain DN residue 8 SER Chi-restraints excluded: chain DQ residue 2 LEU Chi-restraints excluded: chain DT residue 4 ILE Chi-restraints excluded: chain DU residue 9 VAL Chi-restraints excluded: chain DZ residue 2 LEU Chi-restraints excluded: chain DZ residue 7 ILE Chi-restraints excluded: chain D3 residue 9 VAL Chi-restraints excluded: chain D7 residue 8 SER Chi-restraints excluded: chain EB residue 4 ILE Chi-restraints excluded: chain EB residue 8 SER Chi-restraints excluded: chain EC residue 9 VAL Chi-restraints excluded: chain EH residue 2 LEU Chi-restraints excluded: chain EL residue 9 VAL Chi-restraints excluded: chain ET residue 4 ILE Chi-restraints excluded: chain EU residue 9 VAL Chi-restraints excluded: chain EZ residue 2 LEU Chi-restraints excluded: chain E3 residue 9 VAL Chi-restraints excluded: chain E5 residue 8 SER Chi-restraints excluded: chain E6 residue 9 VAL Chi-restraints excluded: chain E8 residue 7 ILE Chi-restraints excluded: chain E9 residue 3 ILE Chi-restraints excluded: chain FB residue 8 SER Chi-restraints excluded: chain FC residue 9 VAL Chi-restraints excluded: chain FH residue 2 LEU Chi-restraints excluded: chain FL residue 9 VAL Chi-restraints excluded: chain FO residue 9 VAL Chi-restraints excluded: chain FT residue 4 ILE Chi-restraints excluded: chain FT residue 8 SER Chi-restraints excluded: chain FU residue 9 VAL Chi-restraints excluded: chain FZ residue 7 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 51 optimal weight: 30.0000 chunk 73 optimal weight: 40.0000 chunk 41 optimal weight: 30.0000 chunk 108 optimal weight: 30.0000 chunk 141 optimal weight: 2.9990 chunk 96 optimal weight: 30.0000 chunk 72 optimal weight: 10.0000 chunk 165 optimal weight: 40.0000 chunk 125 optimal weight: 50.0000 chunk 172 optimal weight: 20.0000 chunk 85 optimal weight: 10.0000 overall best weight: 14.5998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: a 10 HIS j 10 HIS AB 10 HIS BB 10 HIS ** BH 10 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** BZ 10 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B8 10 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** CB 10 HIS ** 7 10 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** CK 10 HIS CM 10 HIS ** CQ 10 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C8 10 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** DH 10 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** DZ 10 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D2 10 HIS ** D8 10 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** EB 10 HIS ** EN 10 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** EQ 10 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** EW 10 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** EZ 10 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E2 10 HIS ** E8 10 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** FE 10 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** FH 10 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** FN 10 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** FQ 10 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** FV 10 HIS ** FW 10 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** FZ 10 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.114173 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.094292 restraints weight = 30307.594| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.097543 restraints weight = 16169.360| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.099834 restraints weight = 10483.850| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.101477 restraints weight = 7650.505| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.102687 restraints weight = 6031.024| |-----------------------------------------------------------------------------| r_work (final): 0.3344 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7780 moved from start: 0.2963 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.048 20370 Z= 0.310 Angle : 0.820 10.657 27210 Z= 0.359 Chirality : 0.060 0.179 3840 Planarity : 0.002 0.008 3060 Dihedral : 12.040 58.579 2580 Min Nonbonded Distance : 2.593 Molprobity Statistics. All-atom Clashscore : 8.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 9.67 % Allowed : 19.00 % Favored : 71.33 % 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 aren not related in a simple way. whole: -1.76 (0.16), residues: 2100 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.33 (0.12), residues: 2100 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.008 0.002 HISEO 10 Details of bonding type rmsd covalent geometry : bond 0.00777 (20370) covalent geometry : angle 0.82034 (27210) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4200 Ramachandran restraints generated. 2100 Oldfield, 0 Emsley, 2100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4200 Ramachandran restraints generated. 2100 Oldfield, 0 Emsley, 2100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 757 residues out of total 2400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 232 poor density : 525 time to evaluate : 0.660 Fit side-chains REVERT: A 5 LYS cc_start: 0.8501 (mttt) cc_final: 0.8066 (mttp) REVERT: J 4 ILE cc_start: 0.8498 (OUTLIER) cc_final: 0.8251 (mp) REVERT: M 5 LYS cc_start: 0.8499 (mttt) cc_final: 0.8191 (mttm) REVERT: S 5 LYS cc_start: 0.8443 (mttt) cc_final: 0.8168 (mttp) REVERT: V 2 LEU cc_start: 0.8320 (pt) cc_final: 0.8042 (tt) REVERT: a 4 ILE cc_start: 0.8589 (OUTLIER) cc_final: 0.8310 (mp) REVERT: f 3 ILE cc_start: 0.8474 (mt) cc_final: 0.8214 (mt) REVERT: j 5 LYS cc_start: 0.8675 (mttt) cc_final: 0.8290 (mttp) REVERT: q 5 LYS cc_start: 0.8508 (OUTLIER) cc_final: 0.8272 (mtmm) REVERT: s 4 ILE cc_start: 0.8546 (OUTLIER) cc_final: 0.8263 (mp) REVERT: v 5 LYS cc_start: 0.8200 (mttt) cc_final: 0.7977 (mttm) REVERT: x 3 ILE cc_start: 0.8504 (mt) cc_final: 0.8218 (mt) REVERT: AB 5 LYS cc_start: 0.8495 (mttt) cc_final: 0.7921 (mttp) REVERT: AK 4 ILE cc_start: 0.8689 (OUTLIER) cc_final: 0.8286 (mp) REVERT: AN 5 LYS cc_start: 0.8044 (mttt) cc_final: 0.7680 (mttm) REVERT: AT 5 LYS cc_start: 0.8532 (mttt) cc_final: 0.8081 (mttp) REVERT: A2 4 ILE cc_start: 0.8582 (OUTLIER) cc_final: 0.8225 (mp) REVERT: A5 5 LYS cc_start: 0.8072 (mttm) cc_final: 0.7790 (mttm) REVERT: A7 3 ILE cc_start: 0.8503 (mt) cc_final: 0.8248 (mt) REVERT: BB 5 LYS cc_start: 0.8563 (mttt) cc_final: 0.8090 (mttp) REVERT: BK 4 ILE cc_start: 0.8521 (OUTLIER) cc_final: 0.8157 (mp) REVERT: BT 5 LYS cc_start: 0.8327 (mttt) cc_final: 0.8018 (mttp) REVERT: BW 2 LEU cc_start: 0.8405 (pt) cc_final: 0.8183 (pp) REVERT: B2 4 ILE cc_start: 0.8667 (OUTLIER) cc_final: 0.8358 (mp) REVERT: B5 2 LEU cc_start: 0.8502 (pp) cc_final: 0.8231 (pt) REVERT: 1 4 ILE cc_start: 0.8680 (OUTLIER) cc_final: 0.8341 (mp) REVERT: 6 5 LYS cc_start: 0.8023 (mttt) cc_final: 0.7522 (mttm) REVERT: CR 5 LYS cc_start: 0.8605 (OUTLIER) cc_final: 0.8217 (mtmm) REVERT: CT 4 ILE cc_start: 0.8613 (OUTLIER) cc_final: 0.8358 (mp) REVERT: DB 4 ILE cc_start: 0.8532 (OUTLIER) cc_final: 0.8254 (mp) REVERT: DE 5 LYS cc_start: 0.8173 (mttt) cc_final: 0.7750 (mttm) REVERT: DT 4 ILE cc_start: 0.8690 (OUTLIER) cc_final: 0.8446 (mp) REVERT: DW 2 LEU cc_start: 0.8631 (pp) cc_final: 0.8268 (pt) REVERT: EB 4 ILE cc_start: 0.8647 (OUTLIER) cc_final: 0.8406 (mp) REVERT: EE 5 LYS cc_start: 0.8024 (mttt) cc_final: 0.7643 (mttm) REVERT: EK 5 LYS cc_start: 0.8353 (mttt) cc_final: 0.8047 (mttp) REVERT: ET 4 ILE cc_start: 0.8715 (OUTLIER) cc_final: 0.8451 (mp) REVERT: E5 5 LYS cc_start: 0.8180 (mttt) cc_final: 0.7824 (mttp) REVERT: FE 5 LYS cc_start: 0.8417 (mttt) cc_final: 0.7985 (mttm) REVERT: FT 4 ILE cc_start: 0.8653 (OUTLIER) cc_final: 0.8426 (mp) outliers start: 232 outliers final: 146 residues processed: 619 average time/residue: 0.1233 time to fit residues: 118.9487 Evaluate side-chains 619 residues out of total 2400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 162 poor density : 457 time to evaluate : 0.690 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 9 VAL Chi-restraints excluded: chain E residue 9 VAL Chi-restraints excluded: chain G residue 2 LEU Chi-restraints excluded: chain J residue 4 ILE Chi-restraints excluded: chain K residue 9 VAL Chi-restraints excluded: chain M residue 8 SER Chi-restraints excluded: chain P residue 2 LEU Chi-restraints excluded: chain P residue 7 ILE Chi-restraints excluded: chain S residue 8 SER Chi-restraints excluded: chain T residue 9 VAL Chi-restraints excluded: chain V residue 5 LYS Chi-restraints excluded: chain V residue 8 SER Chi-restraints excluded: chain W residue 9 VAL Chi-restraints excluded: chain Y residue 2 LEU Chi-restraints excluded: chain a residue 4 ILE Chi-restraints excluded: chain a residue 8 SER Chi-restraints excluded: chain a residue 10 HIS Chi-restraints excluded: chain b residue 9 VAL Chi-restraints excluded: chain d residue 8 SER Chi-restraints excluded: chain e residue 9 VAL Chi-restraints excluded: chain g residue 2 LEU Chi-restraints excluded: chain g residue 7 ILE Chi-restraints excluded: chain j residue 8 SER Chi-restraints excluded: chain k residue 9 VAL Chi-restraints excluded: chain m residue 8 SER Chi-restraints excluded: chain n residue 9 VAL Chi-restraints excluded: chain o residue 8 SER Chi-restraints excluded: chain p residue 2 LEU Chi-restraints excluded: chain q residue 3 ILE Chi-restraints excluded: chain q residue 5 LYS Chi-restraints excluded: chain s residue 4 ILE Chi-restraints excluded: chain t residue 9 VAL Chi-restraints excluded: chain v residue 8 SER Chi-restraints excluded: chain y residue 2 LEU Chi-restraints excluded: chain y residue 7 ILE Chi-restraints excluded: chain z residue 3 ILE Chi-restraints excluded: chain AC residue 9 VAL Chi-restraints excluded: chain AE residue 8 SER Chi-restraints excluded: chain AF residue 9 VAL Chi-restraints excluded: chain AH residue 2 LEU Chi-restraints excluded: chain AI residue 3 ILE Chi-restraints excluded: chain AK residue 4 ILE Chi-restraints excluded: chain AL residue 9 VAL Chi-restraints excluded: chain AN residue 8 SER Chi-restraints excluded: chain AO residue 9 VAL Chi-restraints excluded: chain AQ residue 2 LEU Chi-restraints excluded: chain AQ residue 7 ILE Chi-restraints excluded: chain AT residue 8 SER Chi-restraints excluded: chain AU residue 9 VAL Chi-restraints excluded: chain AW residue 8 SER Chi-restraints excluded: chain AX residue 9 VAL Chi-restraints excluded: chain AZ residue 2 LEU Chi-restraints excluded: chain AZ residue 7 ILE Chi-restraints excluded: chain A0 residue 3 ILE Chi-restraints excluded: chain A0 residue 5 LYS Chi-restraints excluded: chain A2 residue 4 ILE Chi-restraints excluded: chain A3 residue 9 VAL Chi-restraints excluded: chain A8 residue 2 LEU Chi-restraints excluded: chain A8 residue 7 ILE Chi-restraints excluded: chain BC residue 9 VAL Chi-restraints excluded: chain BE residue 8 SER Chi-restraints excluded: chain BF residue 9 VAL Chi-restraints excluded: chain BH residue 2 LEU Chi-restraints excluded: chain BH residue 4 ILE Chi-restraints excluded: chain BI residue 3 ILE Chi-restraints excluded: chain BK residue 4 ILE Chi-restraints excluded: chain BL residue 9 VAL Chi-restraints excluded: chain BO residue 9 VAL Chi-restraints excluded: chain BQ residue 2 LEU Chi-restraints excluded: chain BQ residue 7 ILE Chi-restraints excluded: chain BU residue 9 VAL Chi-restraints excluded: chain BW residue 8 SER Chi-restraints excluded: chain BX residue 9 VAL Chi-restraints excluded: chain B0 residue 3 ILE Chi-restraints excluded: chain B0 residue 5 LYS Chi-restraints excluded: chain B2 residue 4 ILE Chi-restraints excluded: chain B3 residue 9 VAL Chi-restraints excluded: chain B7 residue 8 SER Chi-restraints excluded: chain B8 residue 2 LEU Chi-restraints excluded: chain B8 residue 7 ILE Chi-restraints excluded: chain CB residue 8 SER Chi-restraints excluded: chain CC residue 9 VAL Chi-restraints excluded: chain CE residue 8 SER Chi-restraints excluded: chain CH residue 2 LEU Chi-restraints excluded: chain CH residue 7 ILE Chi-restraints excluded: chain CI residue 5 LYS Chi-restraints excluded: chain 1 residue 4 ILE Chi-restraints excluded: chain 3 residue 9 VAL Chi-restraints excluded: chain 4 residue 8 SER Chi-restraints excluded: chain 7 residue 2 LEU Chi-restraints excluded: chain 7 residue 7 ILE Chi-restraints excluded: chain CK residue 8 SER Chi-restraints excluded: chain CL residue 9 VAL Chi-restraints excluded: chain CN residue 8 SER Chi-restraints excluded: chain CO residue 9 VAL Chi-restraints excluded: chain CR residue 3 ILE Chi-restraints excluded: chain CR residue 5 LYS Chi-restraints excluded: chain CT residue 4 ILE Chi-restraints excluded: chain CU residue 9 VAL Chi-restraints excluded: chain CZ residue 2 LEU Chi-restraints excluded: chain CZ residue 7 ILE Chi-restraints excluded: chain C2 residue 9 VAL Chi-restraints excluded: chain C3 residue 9 VAL Chi-restraints excluded: chain C5 residue 8 SER Chi-restraints excluded: chain C6 residue 9 VAL Chi-restraints excluded: chain DB residue 4 ILE Chi-restraints excluded: chain DC residue 9 VAL Chi-restraints excluded: chain DH residue 2 LEU Chi-restraints excluded: chain DH residue 7 ILE Chi-restraints excluded: chain DL residue 9 VAL Chi-restraints excluded: chain DN residue 8 SER Chi-restraints excluded: chain DO residue 9 VAL Chi-restraints excluded: chain DQ residue 2 LEU Chi-restraints excluded: chain DQ residue 7 ILE Chi-restraints excluded: chain DR residue 3 ILE Chi-restraints excluded: chain DT residue 4 ILE Chi-restraints excluded: chain DU residue 9 VAL Chi-restraints excluded: chain DU residue 11 ILE Chi-restraints excluded: chain DZ residue 2 LEU Chi-restraints excluded: chain DZ residue 7 ILE Chi-restraints excluded: chain D3 residue 9 VAL Chi-restraints excluded: chain D5 residue 8 SER Chi-restraints excluded: chain D6 residue 9 VAL Chi-restraints excluded: chain D7 residue 8 SER Chi-restraints excluded: chain D8 residue 2 LEU Chi-restraints excluded: chain D8 residue 7 ILE Chi-restraints excluded: chain D9 residue 2 LEU Chi-restraints excluded: chain D9 residue 3 ILE Chi-restraints excluded: chain EB residue 4 ILE Chi-restraints excluded: chain EB residue 8 SER Chi-restraints excluded: chain EB residue 10 HIS Chi-restraints excluded: chain EC residue 9 VAL Chi-restraints excluded: chain EG residue 11 ILE Chi-restraints excluded: chain EH residue 2 LEU Chi-restraints excluded: chain EH residue 7 ILE Chi-restraints excluded: chain EK residue 4 ILE Chi-restraints excluded: chain EL residue 9 VAL Chi-restraints excluded: chain EO residue 9 VAL Chi-restraints excluded: chain EQ residue 7 ILE Chi-restraints excluded: chain ER residue 3 ILE Chi-restraints excluded: chain ET residue 4 ILE Chi-restraints excluded: chain EU residue 9 VAL Chi-restraints excluded: chain EZ residue 2 LEU Chi-restraints excluded: chain EZ residue 7 ILE Chi-restraints excluded: chain E3 residue 9 VAL Chi-restraints excluded: chain E5 residue 8 SER Chi-restraints excluded: chain E8 residue 2 LEU Chi-restraints excluded: chain E9 residue 3 ILE Chi-restraints excluded: chain FB residue 8 SER Chi-restraints excluded: chain FC residue 9 VAL Chi-restraints excluded: chain FH residue 2 LEU Chi-restraints excluded: chain FH residue 7 ILE Chi-restraints excluded: chain FK residue 4 ILE Chi-restraints excluded: chain FL residue 9 VAL Chi-restraints excluded: chain FN residue 8 SER Chi-restraints excluded: chain FQ residue 2 LEU Chi-restraints excluded: chain FQ residue 7 ILE Chi-restraints excluded: chain FT residue 4 ILE Chi-restraints excluded: chain FT residue 8 SER Chi-restraints excluded: chain FU residue 9 VAL Chi-restraints excluded: chain FZ residue 2 LEU Chi-restraints excluded: chain FZ residue 7 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 150 optimal weight: 30.0000 chunk 126 optimal weight: 20.0000 chunk 154 optimal weight: 8.9990 chunk 96 optimal weight: 8.9990 chunk 100 optimal weight: 6.9990 chunk 66 optimal weight: 6.9990 chunk 103 optimal weight: 0.8980 chunk 196 optimal weight: 9.9990 chunk 67 optimal weight: 6.9990 chunk 20 optimal weight: 10.0000 chunk 136 optimal weight: 6.9990 overall best weight: 5.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 10 HIS ** M 10 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** a 10 HIS d 10 HIS v 10 HIS AW 10 HIS A5 10 HIS ** BE 10 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** BN 10 HIS BT 10 HIS ** B5 10 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** CB 10 HIS 6 10 HIS EB 10 HIS EM 10 HIS EN 10 HIS ** EW 10 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E5 10 HIS FE 10 HIS ** FH 10 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** FN 10 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** FQ 10 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** FW 10 HIS ** FZ 10 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.117097 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.097567 restraints weight = 30179.540| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.100872 restraints weight = 16091.857| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.103213 restraints weight = 10402.594| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.104750 restraints weight = 7552.200| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.105981 restraints weight = 5981.028| |-----------------------------------------------------------------------------| r_work (final): 0.3406 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7741 moved from start: 0.3250 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 20370 Z= 0.149 Angle : 0.685 9.908 27210 Z= 0.286 Chirality : 0.058 0.175 3840 Planarity : 0.002 0.012 3060 Dihedral : 11.469 58.765 2580 Min Nonbonded Distance : 2.564 Molprobity Statistics. All-atom Clashscore : 7.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 8.71 % Allowed : 21.42 % Favored : 69.88 % 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 aren not related in a simple way. whole: -1.26 (0.17), residues: 2100 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.95 (0.13), residues: 2100 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.013 0.001 HIS a 10 Details of bonding type rmsd covalent geometry : bond 0.00375 (20370) covalent geometry : angle 0.68539 (27210) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4200 Ramachandran restraints generated. 2100 Oldfield, 0 Emsley, 2100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4200 Ramachandran restraints generated. 2100 Oldfield, 0 Emsley, 2100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 652 residues out of total 2400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 209 poor density : 443 time to evaluate : 0.841 Fit side-chains REVERT: A 5 LYS cc_start: 0.8444 (mttt) cc_final: 0.7993 (mttp) REVERT: J 4 ILE cc_start: 0.8537 (OUTLIER) cc_final: 0.8323 (mp) REVERT: M 5 LYS cc_start: 0.8344 (mttt) cc_final: 0.8134 (mttm) REVERT: S 5 LYS cc_start: 0.8435 (mttt) cc_final: 0.7926 (mttp) REVERT: U 3 ILE cc_start: 0.8250 (OUTLIER) cc_final: 0.7809 (mp) REVERT: V 2 LEU cc_start: 0.8290 (pt) cc_final: 0.8046 (tt) REVERT: a 4 ILE cc_start: 0.8654 (OUTLIER) cc_final: 0.8384 (mp) REVERT: f 3 ILE cc_start: 0.8452 (mt) cc_final: 0.8232 (mt) REVERT: j 5 LYS cc_start: 0.8578 (mttt) cc_final: 0.8061 (mttp) REVERT: s 4 ILE cc_start: 0.8538 (OUTLIER) cc_final: 0.8246 (mp) REVERT: v 5 LYS cc_start: 0.8168 (mttt) cc_final: 0.7809 (mttm) REVERT: AB 5 LYS cc_start: 0.8425 (mttt) cc_final: 0.7879 (mttp) REVERT: AE 5 LYS cc_start: 0.8283 (mttt) cc_final: 0.7882 (mttm) REVERT: AK 4 ILE cc_start: 0.8660 (OUTLIER) cc_final: 0.8265 (mp) REVERT: A2 4 ILE cc_start: 0.8626 (OUTLIER) cc_final: 0.8268 (mp) REVERT: A5 5 LYS cc_start: 0.8125 (mttm) cc_final: 0.7846 (mttm) REVERT: A7 3 ILE cc_start: 0.8428 (mt) cc_final: 0.8167 (mt) REVERT: BB 5 LYS cc_start: 0.8479 (mttt) cc_final: 0.8020 (mttp) REVERT: BK 4 ILE cc_start: 0.8494 (OUTLIER) cc_final: 0.8135 (mp) REVERT: BT 5 LYS cc_start: 0.8225 (mttt) cc_final: 0.7939 (mttp) REVERT: B2 4 ILE cc_start: 0.8625 (OUTLIER) cc_final: 0.8311 (mp) REVERT: B5 2 LEU cc_start: 0.8322 (pp) cc_final: 0.8097 (pt) REVERT: B5 5 LYS cc_start: 0.8421 (mttm) cc_final: 0.8197 (mttp) REVERT: 1 4 ILE cc_start: 0.8659 (OUTLIER) cc_final: 0.8353 (mp) REVERT: 6 5 LYS cc_start: 0.7927 (mttt) cc_final: 0.7478 (mttm) REVERT: CN 2 LEU cc_start: 0.7889 (pt) cc_final: 0.7609 (pp) REVERT: CR 5 LYS cc_start: 0.8613 (OUTLIER) cc_final: 0.8339 (mtmm) REVERT: CT 4 ILE cc_start: 0.8596 (OUTLIER) cc_final: 0.8356 (mp) REVERT: CW 5 LYS cc_start: 0.8246 (mttm) cc_final: 0.7916 (mttm) REVERT: DB 4 ILE cc_start: 0.8493 (OUTLIER) cc_final: 0.8232 (mp) REVERT: DE 5 LYS cc_start: 0.8029 (mttt) cc_final: 0.7626 (mttm) REVERT: DT 4 ILE cc_start: 0.8699 (OUTLIER) cc_final: 0.8450 (mp) REVERT: D4 3 ILE cc_start: 0.8030 (OUTLIER) cc_final: 0.7527 (mp) REVERT: D5 2 LEU cc_start: 0.8078 (pt) cc_final: 0.7587 (tt) REVERT: EB 4 ILE cc_start: 0.8630 (OUTLIER) cc_final: 0.8392 (mp) REVERT: EE 5 LYS cc_start: 0.7941 (mttt) cc_final: 0.7575 (mttm) REVERT: ET 4 ILE cc_start: 0.8671 (OUTLIER) cc_final: 0.8430 (mp) REVERT: E5 5 LYS cc_start: 0.8027 (mttt) cc_final: 0.7734 (mttp) REVERT: FE 2 LEU cc_start: 0.8206 (pt) cc_final: 0.6726 (mm) REVERT: FE 5 LYS cc_start: 0.8370 (mttt) cc_final: 0.8002 (mttm) REVERT: FN 2 LEU cc_start: 0.8380 (pt) cc_final: 0.8046 (pp) REVERT: FT 4 ILE cc_start: 0.8623 (OUTLIER) cc_final: 0.8400 (mp) outliers start: 209 outliers final: 132 residues processed: 522 average time/residue: 0.1182 time to fit residues: 98.1722 Evaluate side-chains 567 residues out of total 2400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 149 poor density : 418 time to evaluate : 0.845 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 SER Chi-restraints excluded: chain B residue 9 VAL Chi-restraints excluded: chain D residue 2 LEU Chi-restraints excluded: chain E residue 9 VAL Chi-restraints excluded: chain G residue 2 LEU Chi-restraints excluded: chain J residue 4 ILE Chi-restraints excluded: chain J residue 8 SER Chi-restraints excluded: chain P residue 2 LEU Chi-restraints excluded: chain S residue 8 SER Chi-restraints excluded: chain U residue 3 ILE Chi-restraints excluded: chain V residue 8 SER Chi-restraints excluded: chain W residue 9 VAL Chi-restraints excluded: chain Y residue 2 LEU Chi-restraints excluded: chain Z residue 3 ILE Chi-restraints excluded: chain a residue 4 ILE Chi-restraints excluded: chain b residue 9 VAL Chi-restraints excluded: chain d residue 8 SER Chi-restraints excluded: chain f residue 8 SER Chi-restraints excluded: chain g residue 9 VAL Chi-restraints excluded: chain j residue 8 SER Chi-restraints excluded: chain k residue 9 VAL Chi-restraints excluded: chain m residue 8 SER Chi-restraints excluded: chain n residue 9 VAL Chi-restraints excluded: chain o residue 8 SER Chi-restraints excluded: chain p residue 2 LEU Chi-restraints excluded: chain p residue 9 VAL Chi-restraints excluded: chain q residue 3 ILE Chi-restraints excluded: chain s residue 4 ILE Chi-restraints excluded: chain t residue 9 VAL Chi-restraints excluded: chain y residue 2 LEU Chi-restraints excluded: chain y residue 7 ILE Chi-restraints excluded: chain y residue 9 VAL Chi-restraints excluded: chain z residue 3 ILE Chi-restraints excluded: chain AC residue 9 VAL Chi-restraints excluded: chain AE residue 8 SER Chi-restraints excluded: chain AF residue 9 VAL Chi-restraints excluded: chain AH residue 2 LEU Chi-restraints excluded: chain AH residue 9 VAL Chi-restraints excluded: chain AI residue 3 ILE Chi-restraints excluded: chain AK residue 4 ILE Chi-restraints excluded: chain AL residue 9 VAL Chi-restraints excluded: chain AN residue 8 SER Chi-restraints excluded: chain AQ residue 2 LEU Chi-restraints excluded: chain AT residue 8 SER Chi-restraints excluded: chain AU residue 9 VAL Chi-restraints excluded: chain AW residue 8 SER Chi-restraints excluded: chain AX residue 9 VAL Chi-restraints excluded: chain AZ residue 2 LEU Chi-restraints excluded: chain AZ residue 7 ILE Chi-restraints excluded: chain AZ residue 9 VAL Chi-restraints excluded: chain A0 residue 3 ILE Chi-restraints excluded: chain A0 residue 5 LYS Chi-restraints excluded: chain A2 residue 4 ILE Chi-restraints excluded: chain A3 residue 9 VAL Chi-restraints excluded: chain A8 residue 2 LEU Chi-restraints excluded: chain A8 residue 7 ILE Chi-restraints excluded: chain BC residue 9 VAL Chi-restraints excluded: chain BF residue 9 VAL Chi-restraints excluded: chain BH residue 2 LEU Chi-restraints excluded: chain BH residue 7 ILE Chi-restraints excluded: chain BH residue 9 VAL Chi-restraints excluded: chain BI residue 3 ILE Chi-restraints excluded: chain BK residue 4 ILE Chi-restraints excluded: chain BL residue 9 VAL Chi-restraints excluded: chain BQ residue 2 LEU Chi-restraints excluded: chain BQ residue 7 ILE Chi-restraints excluded: chain BQ residue 9 VAL Chi-restraints excluded: chain BU residue 9 VAL Chi-restraints excluded: chain BW residue 8 SER Chi-restraints excluded: chain BX residue 9 VAL Chi-restraints excluded: chain BZ residue 5 LYS Chi-restraints excluded: chain BZ residue 9 VAL Chi-restraints excluded: chain B0 residue 3 ILE Chi-restraints excluded: chain B0 residue 5 LYS Chi-restraints excluded: chain B2 residue 4 ILE Chi-restraints excluded: chain B3 residue 9 VAL Chi-restraints excluded: chain B7 residue 8 SER Chi-restraints excluded: chain B8 residue 2 LEU Chi-restraints excluded: chain B8 residue 7 ILE Chi-restraints excluded: chain B8 residue 9 VAL Chi-restraints excluded: chain CB residue 8 SER Chi-restraints excluded: chain CC residue 9 VAL Chi-restraints excluded: chain CE residue 8 SER Chi-restraints excluded: chain CH residue 2 LEU Chi-restraints excluded: chain CH residue 7 ILE Chi-restraints excluded: chain CH residue 9 VAL Chi-restraints excluded: chain CI residue 5 LYS Chi-restraints excluded: chain 1 residue 4 ILE Chi-restraints excluded: chain 3 residue 9 VAL Chi-restraints excluded: chain 7 residue 2 LEU Chi-restraints excluded: chain CK residue 8 SER Chi-restraints excluded: chain CL residue 9 VAL Chi-restraints excluded: chain CN residue 8 SER Chi-restraints excluded: chain CO residue 9 VAL Chi-restraints excluded: chain CQ residue 2 LEU Chi-restraints excluded: chain CQ residue 9 VAL Chi-restraints excluded: chain CR residue 3 ILE Chi-restraints excluded: chain CR residue 5 LYS Chi-restraints excluded: chain CT residue 4 ILE Chi-restraints excluded: chain CU residue 9 VAL Chi-restraints excluded: chain CZ residue 2 LEU Chi-restraints excluded: chain CZ residue 7 ILE Chi-restraints excluded: chain CZ residue 9 VAL Chi-restraints excluded: chain C3 residue 9 VAL Chi-restraints excluded: chain C5 residue 8 SER Chi-restraints excluded: chain C6 residue 9 VAL Chi-restraints excluded: chain DB residue 4 ILE Chi-restraints excluded: chain DC residue 9 VAL Chi-restraints excluded: chain DH residue 2 LEU Chi-restraints excluded: chain DL residue 9 VAL Chi-restraints excluded: chain DO residue 9 VAL Chi-restraints excluded: chain DQ residue 2 LEU Chi-restraints excluded: chain DQ residue 7 ILE Chi-restraints excluded: chain DQ residue 9 VAL Chi-restraints excluded: chain DT residue 4 ILE Chi-restraints excluded: chain DU residue 9 VAL Chi-restraints excluded: chain DZ residue 2 LEU Chi-restraints excluded: chain DZ residue 7 ILE Chi-restraints excluded: chain D3 residue 9 VAL Chi-restraints excluded: chain D4 residue 3 ILE Chi-restraints excluded: chain D5 residue 8 SER Chi-restraints excluded: chain D6 residue 9 VAL Chi-restraints excluded: chain D7 residue 8 SER Chi-restraints excluded: chain D8 residue 2 LEU Chi-restraints excluded: chain EB residue 4 ILE Chi-restraints excluded: chain EB residue 8 SER Chi-restraints excluded: chain EC residue 9 VAL Chi-restraints excluded: chain EH residue 2 LEU Chi-restraints excluded: chain EH residue 7 ILE Chi-restraints excluded: chain EL residue 9 VAL Chi-restraints excluded: chain EQ residue 2 LEU Chi-restraints excluded: chain EQ residue 7 ILE Chi-restraints excluded: chain ET residue 4 ILE Chi-restraints excluded: chain EU residue 9 VAL Chi-restraints excluded: chain EZ residue 2 LEU Chi-restraints excluded: chain EZ residue 7 ILE Chi-restraints excluded: chain E3 residue 9 VAL Chi-restraints excluded: chain E5 residue 8 SER Chi-restraints excluded: chain E8 residue 2 LEU Chi-restraints excluded: chain E8 residue 7 ILE Chi-restraints excluded: chain FC residue 9 VAL Chi-restraints excluded: chain FH residue 2 LEU Chi-restraints excluded: chain FK residue 4 ILE Chi-restraints excluded: chain FL residue 9 VAL Chi-restraints excluded: chain FN residue 8 SER Chi-restraints excluded: chain FT residue 4 ILE Chi-restraints excluded: chain FT residue 8 SER Chi-restraints excluded: chain FU residue 9 VAL Chi-restraints excluded: chain FZ residue 7 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 109 optimal weight: 30.0000 chunk 126 optimal weight: 8.9990 chunk 54 optimal weight: 20.0000 chunk 46 optimal weight: 30.0000 chunk 133 optimal weight: 20.0000 chunk 43 optimal weight: 0.3980 chunk 134 optimal weight: 7.9990 chunk 108 optimal weight: 20.0000 chunk 121 optimal weight: 30.0000 chunk 139 optimal weight: 20.0000 chunk 114 optimal weight: 30.0000 overall best weight: 11.4792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: M 10 HIS v 10 HIS BE 10 HIS BN 10 HIS B5 10 HIS DE 10 HIS DK 10 HIS ED 10 HIS ** EW 10 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** FH 10 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** FN 10 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** FQ 10 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** FZ 10 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3506 r_free = 0.3506 target = 0.115406 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.095877 restraints weight = 30379.899| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.098959 restraints weight = 16847.305| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.101234 restraints weight = 11226.906| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.102784 restraints weight = 8303.506| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.103921 restraints weight = 6620.071| |-----------------------------------------------------------------------------| r_work (final): 0.3370 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7764 moved from start: 0.3486 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.043 20370 Z= 0.249 Angle : 0.782 11.103 27210 Z= 0.333 Chirality : 0.058 0.192 3840 Planarity : 0.002 0.009 3060 Dihedral : 11.743 57.982 2580 Min Nonbonded Distance : 2.569 Molprobity Statistics. All-atom Clashscore : 8.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 9.21 % Allowed : 21.92 % Favored : 68.88 % 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 aren not related in a simple way. whole: -1.39 (0.17), residues: 2100 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.05 (0.13), residues: 2100 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.007 0.002 HISDK 10 Details of bonding type rmsd covalent geometry : bond 0.00629 (20370) covalent geometry : angle 0.78243 (27210) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4200 Ramachandran restraints generated. 2100 Oldfield, 0 Emsley, 2100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4200 Ramachandran restraints generated. 2100 Oldfield, 0 Emsley, 2100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 663 residues out of total 2400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 221 poor density : 442 time to evaluate : 0.787 Fit side-chains REVERT: A 5 LYS cc_start: 0.8503 (mttt) cc_final: 0.8073 (mttp) REVERT: D 2 LEU cc_start: 0.8791 (OUTLIER) cc_final: 0.8465 (pt) REVERT: J 4 ILE cc_start: 0.8564 (OUTLIER) cc_final: 0.8342 (mp) REVERT: M 5 LYS cc_start: 0.8311 (mttt) cc_final: 0.8034 (mttm) REVERT: S 5 LYS cc_start: 0.8446 (mttt) cc_final: 0.8173 (mttp) REVERT: U 3 ILE cc_start: 0.8241 (OUTLIER) cc_final: 0.7817 (mp) REVERT: a 4 ILE cc_start: 0.8548 (OUTLIER) cc_final: 0.8252 (mp) REVERT: f 3 ILE cc_start: 0.8472 (mt) cc_final: 0.8269 (mt) REVERT: j 4 ILE cc_start: 0.8601 (OUTLIER) cc_final: 0.8397 (mt) REVERT: j 5 LYS cc_start: 0.8698 (mttt) cc_final: 0.8355 (mttp) REVERT: s 4 ILE cc_start: 0.8540 (OUTLIER) cc_final: 0.8261 (mp) REVERT: v 5 LYS cc_start: 0.8085 (mttt) cc_final: 0.7872 (mttm) REVERT: x 3 ILE cc_start: 0.8583 (mt) cc_final: 0.8291 (mt) REVERT: AB 5 LYS cc_start: 0.8497 (mttt) cc_final: 0.7923 (mttp) REVERT: AD 3 ILE cc_start: 0.7944 (OUTLIER) cc_final: 0.7389 (mp) REVERT: AE 5 LYS cc_start: 0.8300 (mttt) cc_final: 0.7888 (mttm) REVERT: AK 4 ILE cc_start: 0.8658 (OUTLIER) cc_final: 0.8240 (mp) REVERT: AV 3 ILE cc_start: 0.7826 (OUTLIER) cc_final: 0.7293 (mp) REVERT: A2 4 ILE cc_start: 0.8549 (OUTLIER) cc_final: 0.8186 (mp) REVERT: A5 5 LYS cc_start: 0.8185 (mttm) cc_final: 0.7873 (mttm) REVERT: BB 5 LYS cc_start: 0.8534 (mttt) cc_final: 0.8069 (mttp) REVERT: BK 4 ILE cc_start: 0.8436 (OUTLIER) cc_final: 0.8076 (mp) REVERT: BT 5 LYS cc_start: 0.8278 (mttt) cc_final: 0.7998 (mttp) REVERT: BV 3 ILE cc_start: 0.8034 (OUTLIER) cc_final: 0.7551 (mp) REVERT: B2 4 ILE cc_start: 0.8616 (OUTLIER) cc_final: 0.8347 (mp) REVERT: B5 2 LEU cc_start: 0.8384 (pp) cc_final: 0.8129 (pt) REVERT: B5 5 LYS cc_start: 0.8455 (mttm) cc_final: 0.8162 (mttm) REVERT: CD 1 ASP cc_start: 0.7410 (m-30) cc_final: 0.7088 (m-30) REVERT: CD 3 ILE cc_start: 0.8048 (OUTLIER) cc_final: 0.7536 (mp) REVERT: 1 4 ILE cc_start: 0.8616 (OUTLIER) cc_final: 0.8294 (mp) REVERT: 6 5 LYS cc_start: 0.7945 (mttt) cc_final: 0.7499 (mttm) REVERT: CK 5 LYS cc_start: 0.8472 (mttt) cc_final: 0.8083 (mttp) REVERT: CN 2 LEU cc_start: 0.8021 (pt) cc_final: 0.7756 (pp) REVERT: CR 5 LYS cc_start: 0.8722 (OUTLIER) cc_final: 0.8366 (mtmm) REVERT: CT 4 ILE cc_start: 0.8571 (OUTLIER) cc_final: 0.8330 (mp) REVERT: DB 4 ILE cc_start: 0.8477 (OUTLIER) cc_final: 0.8185 (mp) REVERT: DE 5 LYS cc_start: 0.8083 (mttt) cc_final: 0.7639 (mttm) REVERT: DM 3 ILE cc_start: 0.7987 (OUTLIER) cc_final: 0.7428 (mp) REVERT: DT 4 ILE cc_start: 0.8669 (OUTLIER) cc_final: 0.8420 (mp) REVERT: D4 3 ILE cc_start: 0.8013 (OUTLIER) cc_final: 0.7487 (mp) REVERT: EB 4 ILE cc_start: 0.8585 (OUTLIER) cc_final: 0.8337 (mp) REVERT: EE 5 LYS cc_start: 0.7975 (mttt) cc_final: 0.7630 (mttm) REVERT: EK 5 LYS cc_start: 0.8393 (mttt) cc_final: 0.8040 (mttp) REVERT: ET 4 ILE cc_start: 0.8649 (OUTLIER) cc_final: 0.8390 (mp) REVERT: E4 3 ILE cc_start: 0.8165 (OUTLIER) cc_final: 0.7947 (mm) REVERT: E5 5 LYS cc_start: 0.8132 (mttt) cc_final: 0.7789 (mttp) REVERT: FE 5 LYS cc_start: 0.8342 (mttt) cc_final: 0.8006 (mttm) REVERT: FM 3 ILE cc_start: 0.8326 (OUTLIER) cc_final: 0.7774 (mp) REVERT: FT 4 ILE cc_start: 0.8622 (OUTLIER) cc_final: 0.8380 (mp) outliers start: 221 outliers final: 165 residues processed: 524 average time/residue: 0.1193 time to fit residues: 100.7407 Evaluate side-chains 621 residues out of total 2400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 191 poor density : 430 time to evaluate : 0.635 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 SER Chi-restraints excluded: chain B residue 9 VAL Chi-restraints excluded: chain D residue 2 LEU Chi-restraints excluded: chain E residue 9 VAL Chi-restraints excluded: chain G residue 2 LEU Chi-restraints excluded: chain H residue 2 LEU Chi-restraints excluded: chain J residue 4 ILE Chi-restraints excluded: chain J residue 8 SER Chi-restraints excluded: chain M residue 8 SER Chi-restraints excluded: chain P residue 2 LEU Chi-restraints excluded: chain P residue 7 ILE Chi-restraints excluded: chain S residue 8 SER Chi-restraints excluded: chain T residue 9 VAL Chi-restraints excluded: chain U residue 3 ILE Chi-restraints excluded: chain V residue 8 SER Chi-restraints excluded: chain W residue 9 VAL Chi-restraints excluded: chain Y residue 2 LEU Chi-restraints excluded: chain Y residue 4 ILE Chi-restraints excluded: chain a residue 4 ILE Chi-restraints excluded: chain a residue 8 SER Chi-restraints excluded: chain b residue 9 VAL Chi-restraints excluded: chain d residue 8 SER Chi-restraints excluded: chain e residue 9 VAL Chi-restraints excluded: chain f residue 8 SER Chi-restraints excluded: chain g residue 2 LEU Chi-restraints excluded: chain g residue 7 ILE Chi-restraints excluded: chain g residue 9 VAL Chi-restraints excluded: chain h residue 3 ILE Chi-restraints excluded: chain j residue 4 ILE Chi-restraints excluded: chain j residue 8 SER Chi-restraints excluded: chain k residue 9 VAL Chi-restraints excluded: chain m residue 8 SER Chi-restraints excluded: chain n residue 9 VAL Chi-restraints excluded: chain o residue 8 SER Chi-restraints excluded: chain p residue 2 LEU Chi-restraints excluded: chain p residue 9 VAL Chi-restraints excluded: chain q residue 3 ILE Chi-restraints excluded: chain s residue 4 ILE Chi-restraints excluded: chain t residue 9 VAL Chi-restraints excluded: chain v residue 8 SER Chi-restraints excluded: chain w residue 9 VAL Chi-restraints excluded: chain y residue 2 LEU Chi-restraints excluded: chain y residue 7 ILE Chi-restraints excluded: chain y residue 9 VAL Chi-restraints excluded: chain z residue 3 ILE Chi-restraints excluded: chain AC residue 9 VAL Chi-restraints excluded: chain AD residue 3 ILE Chi-restraints excluded: chain AE residue 8 SER Chi-restraints excluded: chain AF residue 9 VAL Chi-restraints excluded: chain AH residue 2 LEU Chi-restraints excluded: chain AH residue 9 VAL Chi-restraints excluded: chain AI residue 3 ILE Chi-restraints excluded: chain AK residue 4 ILE Chi-restraints excluded: chain AL residue 9 VAL Chi-restraints excluded: chain AN residue 8 SER Chi-restraints excluded: chain AO residue 9 VAL Chi-restraints excluded: chain AQ residue 2 LEU Chi-restraints excluded: chain AQ residue 7 ILE Chi-restraints excluded: chain AT residue 8 SER Chi-restraints excluded: chain AU residue 9 VAL Chi-restraints excluded: chain AV residue 3 ILE Chi-restraints excluded: chain AW residue 8 SER Chi-restraints excluded: chain AX residue 9 VAL Chi-restraints excluded: chain AZ residue 2 LEU Chi-restraints excluded: chain AZ residue 7 ILE Chi-restraints excluded: chain AZ residue 9 VAL Chi-restraints excluded: chain A0 residue 3 ILE Chi-restraints excluded: chain A0 residue 5 LYS Chi-restraints excluded: chain A2 residue 4 ILE Chi-restraints excluded: chain A3 residue 9 VAL Chi-restraints excluded: chain A5 residue 8 SER Chi-restraints excluded: chain A8 residue 2 LEU Chi-restraints excluded: chain A8 residue 7 ILE Chi-restraints excluded: chain BC residue 9 VAL Chi-restraints excluded: chain BE residue 8 SER Chi-restraints excluded: chain BF residue 9 VAL Chi-restraints excluded: chain BH residue 2 LEU Chi-restraints excluded: chain BH residue 7 ILE Chi-restraints excluded: chain BH residue 9 VAL Chi-restraints excluded: chain BI residue 3 ILE Chi-restraints excluded: chain BK residue 4 ILE Chi-restraints excluded: chain BL residue 9 VAL Chi-restraints excluded: chain BO residue 9 VAL Chi-restraints excluded: chain BQ residue 2 LEU Chi-restraints excluded: chain BQ residue 7 ILE Chi-restraints excluded: chain BQ residue 9 VAL Chi-restraints excluded: chain BU residue 9 VAL Chi-restraints excluded: chain BV residue 3 ILE Chi-restraints excluded: chain BW residue 8 SER Chi-restraints excluded: chain BX residue 9 VAL Chi-restraints excluded: chain BZ residue 2 LEU Chi-restraints excluded: chain BZ residue 5 LYS Chi-restraints excluded: chain BZ residue 9 VAL Chi-restraints excluded: chain B0 residue 3 ILE Chi-restraints excluded: chain B0 residue 5 LYS Chi-restraints excluded: chain B2 residue 4 ILE Chi-restraints excluded: chain B3 residue 9 VAL Chi-restraints excluded: chain B5 residue 8 SER Chi-restraints excluded: chain B7 residue 8 SER Chi-restraints excluded: chain B8 residue 2 LEU Chi-restraints excluded: chain B8 residue 7 ILE Chi-restraints excluded: chain B8 residue 9 VAL Chi-restraints excluded: chain CB residue 8 SER Chi-restraints excluded: chain CC residue 9 VAL Chi-restraints excluded: chain CD residue 3 ILE Chi-restraints excluded: chain CE residue 8 SER Chi-restraints excluded: chain CH residue 2 LEU Chi-restraints excluded: chain CH residue 7 ILE Chi-restraints excluded: chain CH residue 9 VAL Chi-restraints excluded: chain CI residue 5 LYS Chi-restraints excluded: chain 1 residue 4 ILE Chi-restraints excluded: chain 3 residue 9 VAL Chi-restraints excluded: chain 4 residue 8 SER Chi-restraints excluded: chain 7 residue 2 LEU Chi-restraints excluded: chain 7 residue 7 ILE Chi-restraints excluded: chain 7 residue 9 VAL Chi-restraints excluded: chain CK residue 8 SER Chi-restraints excluded: chain CL residue 9 VAL Chi-restraints excluded: chain CN residue 8 SER Chi-restraints excluded: chain CO residue 9 VAL Chi-restraints excluded: chain CQ residue 2 LEU Chi-restraints excluded: chain CQ residue 9 VAL Chi-restraints excluded: chain CR residue 3 ILE Chi-restraints excluded: chain CR residue 5 LYS Chi-restraints excluded: chain CT residue 4 ILE Chi-restraints excluded: chain CU residue 9 VAL Chi-restraints excluded: chain CZ residue 2 LEU Chi-restraints excluded: chain CZ residue 7 ILE Chi-restraints excluded: chain CZ residue 9 VAL Chi-restraints excluded: chain C3 residue 9 VAL Chi-restraints excluded: chain C5 residue 8 SER Chi-restraints excluded: chain C6 residue 9 VAL Chi-restraints excluded: chain DB residue 4 ILE Chi-restraints excluded: chain DC residue 9 VAL Chi-restraints excluded: chain DH residue 2 LEU Chi-restraints excluded: chain DH residue 7 ILE Chi-restraints excluded: chain DL residue 9 VAL Chi-restraints excluded: chain DM residue 3 ILE Chi-restraints excluded: chain DN residue 8 SER Chi-restraints excluded: chain DO residue 9 VAL Chi-restraints excluded: chain DQ residue 2 LEU Chi-restraints excluded: chain DQ residue 7 ILE Chi-restraints excluded: chain DQ residue 9 VAL Chi-restraints excluded: chain DR residue 3 ILE Chi-restraints excluded: chain DT residue 4 ILE Chi-restraints excluded: chain DU residue 9 VAL Chi-restraints excluded: chain DU residue 11 ILE Chi-restraints excluded: chain DZ residue 2 LEU Chi-restraints excluded: chain DZ residue 7 ILE Chi-restraints excluded: chain D3 residue 9 VAL Chi-restraints excluded: chain D4 residue 3 ILE Chi-restraints excluded: chain D5 residue 8 SER Chi-restraints excluded: chain D6 residue 9 VAL Chi-restraints excluded: chain D7 residue 8 SER Chi-restraints excluded: chain D8 residue 2 LEU Chi-restraints excluded: chain D8 residue 7 ILE Chi-restraints excluded: chain D8 residue 9 VAL Chi-restraints excluded: chain D9 residue 3 ILE Chi-restraints excluded: chain EB residue 4 ILE Chi-restraints excluded: chain EC residue 9 VAL Chi-restraints excluded: chain EG residue 11 ILE Chi-restraints excluded: chain EH residue 2 LEU Chi-restraints excluded: chain EH residue 7 ILE Chi-restraints excluded: chain EK residue 4 ILE Chi-restraints excluded: chain EL residue 9 VAL Chi-restraints excluded: chain EQ residue 2 LEU Chi-restraints excluded: chain EQ residue 7 ILE Chi-restraints excluded: chain EQ residue 9 VAL Chi-restraints excluded: chain ER residue 3 ILE Chi-restraints excluded: chain ET residue 4 ILE Chi-restraints excluded: chain EU residue 9 VAL Chi-restraints excluded: chain EZ residue 2 LEU Chi-restraints excluded: chain EZ residue 7 ILE Chi-restraints excluded: chain E3 residue 9 VAL Chi-restraints excluded: chain E4 residue 3 ILE Chi-restraints excluded: chain E5 residue 8 SER Chi-restraints excluded: chain E8 residue 2 LEU Chi-restraints excluded: chain E8 residue 7 ILE Chi-restraints excluded: chain E9 residue 3 ILE Chi-restraints excluded: chain FC residue 9 VAL Chi-restraints excluded: chain FH residue 2 LEU Chi-restraints excluded: chain FK residue 4 ILE Chi-restraints excluded: chain FL residue 9 VAL Chi-restraints excluded: chain FM residue 3 ILE Chi-restraints excluded: chain FN residue 8 SER Chi-restraints excluded: chain FQ residue 2 LEU Chi-restraints excluded: chain FQ residue 7 ILE Chi-restraints excluded: chain FT residue 4 ILE Chi-restraints excluded: chain FT residue 8 SER Chi-restraints excluded: chain FU residue 9 VAL Chi-restraints excluded: chain FZ residue 7 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 104 optimal weight: 30.0000 chunk 38 optimal weight: 9.9990 chunk 141 optimal weight: 1.9990 chunk 149 optimal weight: 20.0000 chunk 173 optimal weight: 5.9990 chunk 189 optimal weight: 6.9990 chunk 148 optimal weight: 2.9990 chunk 181 optimal weight: 30.0000 chunk 130 optimal weight: 9.9990 chunk 164 optimal weight: 6.9990 chunk 195 optimal weight: 10.0000 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: BD 10 HIS BN 10 HIS ** EW 10 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E5 10 HIS ** FH 10 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** FM 10 HIS ** FN 10 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** FQ 10 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** FV 10 HIS ** FZ 10 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3557 r_free = 0.3557 target = 0.117197 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.097608 restraints weight = 30052.172| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.100990 restraints weight = 15949.074| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.103388 restraints weight = 10213.878| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.105064 restraints weight = 7357.247| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.106157 restraints weight = 5757.551| |-----------------------------------------------------------------------------| r_work (final): 0.3432 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7748 moved from start: 0.3556 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 20370 Z= 0.134 Angle : 0.674 9.977 27210 Z= 0.278 Chirality : 0.057 0.194 3840 Planarity : 0.001 0.017 3060 Dihedral : 11.055 57.817 2580 Min Nonbonded Distance : 2.575 Molprobity Statistics. All-atom Clashscore : 7.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.24 % Favored : 97.76 % Rotamer: Outliers : 8.62 % Allowed : 22.21 % Favored : 69.17 % 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 aren not related in a simple way. whole: -0.92 (0.18), residues: 2100 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.69 (0.14), residues: 2100 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.001 HISBN 10 Details of bonding type rmsd covalent geometry : bond 0.00334 (20370) covalent geometry : angle 0.67391 (27210) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4200 Ramachandran restraints generated. 2100 Oldfield, 0 Emsley, 2100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4200 Ramachandran restraints generated. 2100 Oldfield, 0 Emsley, 2100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 632 residues out of total 2400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 207 poor density : 425 time to evaluate : 0.912 Fit side-chains REVERT: A 5 LYS cc_start: 0.8437 (mttt) cc_final: 0.8030 (mttp) REVERT: J 5 LYS cc_start: 0.8558 (mttt) cc_final: 0.8089 (mttp) REVERT: M 2 LEU cc_start: 0.8116 (pt) cc_final: 0.7864 (pp) REVERT: S 5 LYS cc_start: 0.8422 (mttt) cc_final: 0.7930 (mttp) REVERT: U 3 ILE cc_start: 0.8268 (OUTLIER) cc_final: 0.7811 (mp) REVERT: a 4 ILE cc_start: 0.8670 (OUTLIER) cc_final: 0.8389 (mp) REVERT: j 5 LYS cc_start: 0.8555 (mttt) cc_final: 0.8042 (mttp) REVERT: m 2 LEU cc_start: 0.8047 (pt) cc_final: 0.7669 (tt) REVERT: s 4 ILE cc_start: 0.8597 (OUTLIER) cc_final: 0.8311 (mp) REVERT: AB 5 LYS cc_start: 0.8426 (mttt) cc_final: 0.7902 (mttp) REVERT: AD 3 ILE cc_start: 0.7903 (OUTLIER) cc_final: 0.7368 (mp) REVERT: AE 5 LYS cc_start: 0.8183 (mttt) cc_final: 0.7912 (mttm) REVERT: AK 4 ILE cc_start: 0.8701 (OUTLIER) cc_final: 0.8330 (mp) REVERT: AV 3 ILE cc_start: 0.7931 (OUTLIER) cc_final: 0.7400 (mp) REVERT: A2 4 ILE cc_start: 0.8591 (OUTLIER) cc_final: 0.8230 (mp) REVERT: BB 5 LYS cc_start: 0.8423 (mttt) cc_final: 0.8039 (mttp) REVERT: BK 4 ILE cc_start: 0.8500 (OUTLIER) cc_final: 0.8152 (mp) REVERT: BT 5 LYS cc_start: 0.8255 (mttt) cc_final: 0.7792 (mttp) REVERT: BV 3 ILE cc_start: 0.8084 (OUTLIER) cc_final: 0.7620 (mp) REVERT: B2 4 ILE cc_start: 0.8650 (OUTLIER) cc_final: 0.8381 (mp) REVERT: CD 1 ASP cc_start: 0.7450 (m-30) cc_final: 0.7146 (m-30) REVERT: CD 3 ILE cc_start: 0.8090 (OUTLIER) cc_final: 0.7579 (mp) REVERT: CE 3 ILE cc_start: 0.8978 (mt) cc_final: 0.8722 (mp) REVERT: 1 4 ILE cc_start: 0.8647 (OUTLIER) cc_final: 0.8334 (mp) REVERT: 6 5 LYS cc_start: 0.7909 (mttt) cc_final: 0.7543 (mttm) REVERT: CK 5 LYS cc_start: 0.8474 (mttt) cc_final: 0.7913 (mttp) REVERT: CN 2 LEU cc_start: 0.8027 (pt) cc_final: 0.7762 (pp) REVERT: CR 5 LYS cc_start: 0.8648 (OUTLIER) cc_final: 0.8393 (mtmm) REVERT: CT 4 ILE cc_start: 0.8622 (OUTLIER) cc_final: 0.8382 (mp) REVERT: CW 5 LYS cc_start: 0.8079 (mttm) cc_final: 0.7827 (mttm) REVERT: DB 4 ILE cc_start: 0.8525 (OUTLIER) cc_final: 0.8244 (mp) REVERT: DE 5 LYS cc_start: 0.8147 (mttt) cc_final: 0.7771 (mttm) REVERT: DM 3 ILE cc_start: 0.8055 (OUTLIER) cc_final: 0.7497 (mp) REVERT: DN 2 LEU cc_start: 0.7966 (pt) cc_final: 0.7725 (pp) REVERT: DT 4 ILE cc_start: 0.8709 (OUTLIER) cc_final: 0.8466 (mp) REVERT: D4 3 ILE cc_start: 0.8066 (OUTLIER) cc_final: 0.7547 (mp) REVERT: D5 2 LEU cc_start: 0.8090 (pt) cc_final: 0.7722 (tt) REVERT: EB 4 ILE cc_start: 0.8641 (OUTLIER) cc_final: 0.8410 (mp) REVERT: EE 5 LYS cc_start: 0.7929 (mttt) cc_final: 0.7591 (mttm) REVERT: EK 5 LYS cc_start: 0.8444 (mttt) cc_final: 0.8063 (mttp) REVERT: EM 3 ILE cc_start: 0.8153 (OUTLIER) cc_final: 0.7726 (mp) REVERT: EN 2 LEU cc_start: 0.8131 (pt) cc_final: 0.7812 (pp) REVERT: ET 4 ILE cc_start: 0.8694 (OUTLIER) cc_final: 0.8457 (mp) REVERT: E4 3 ILE cc_start: 0.8231 (OUTLIER) cc_final: 0.8021 (mm) REVERT: E5 5 LYS cc_start: 0.7915 (mttt) cc_final: 0.7633 (mttp) REVERT: FE 2 LEU cc_start: 0.8304 (pp) cc_final: 0.6808 (mm) REVERT: FE 5 LYS cc_start: 0.8328 (mttt) cc_final: 0.8002 (mttm) REVERT: FM 3 ILE cc_start: 0.8352 (OUTLIER) cc_final: 0.7803 (mp) REVERT: FN 2 LEU cc_start: 0.8265 (pt) cc_final: 0.6795 (mm) outliers start: 207 outliers final: 139 residues processed: 502 average time/residue: 0.1172 time to fit residues: 95.1516 Evaluate side-chains 567 residues out of total 2400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 162 poor density : 405 time to evaluate : 0.569 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 SER Chi-restraints excluded: chain D residue 8 SER Chi-restraints excluded: chain E residue 9 VAL Chi-restraints excluded: chain G residue 2 LEU Chi-restraints excluded: chain G residue 9 VAL Chi-restraints excluded: chain J residue 8 SER Chi-restraints excluded: chain M residue 8 SER Chi-restraints excluded: chain P residue 2 LEU Chi-restraints excluded: chain S residue 8 SER Chi-restraints excluded: chain T residue 9 VAL Chi-restraints excluded: chain U residue 3 ILE Chi-restraints excluded: chain V residue 8 SER Chi-restraints excluded: chain W residue 9 VAL Chi-restraints excluded: chain X residue 8 SER Chi-restraints excluded: chain Y residue 2 LEU Chi-restraints excluded: chain Z residue 3 ILE Chi-restraints excluded: chain a residue 4 ILE Chi-restraints excluded: chain b residue 9 VAL Chi-restraints excluded: chain d residue 8 SER Chi-restraints excluded: chain g residue 2 LEU Chi-restraints excluded: chain g residue 9 VAL Chi-restraints excluded: chain j residue 8 SER Chi-restraints excluded: chain k residue 9 VAL Chi-restraints excluded: chain m residue 8 SER Chi-restraints excluded: chain n residue 9 VAL Chi-restraints excluded: chain o residue 8 SER Chi-restraints excluded: chain p residue 2 LEU Chi-restraints excluded: chain p residue 9 VAL Chi-restraints excluded: chain q residue 3 ILE Chi-restraints excluded: chain s residue 4 ILE Chi-restraints excluded: chain t residue 9 VAL Chi-restraints excluded: chain y residue 2 LEU Chi-restraints excluded: chain y residue 7 ILE Chi-restraints excluded: chain y residue 9 VAL Chi-restraints excluded: chain z residue 3 ILE Chi-restraints excluded: chain AC residue 9 VAL Chi-restraints excluded: chain AD residue 3 ILE Chi-restraints excluded: chain AE residue 8 SER Chi-restraints excluded: chain AF residue 9 VAL Chi-restraints excluded: chain AH residue 2 LEU Chi-restraints excluded: chain AH residue 9 VAL Chi-restraints excluded: chain AK residue 4 ILE Chi-restraints excluded: chain AL residue 9 VAL Chi-restraints excluded: chain AN residue 8 SER Chi-restraints excluded: chain AO residue 9 VAL Chi-restraints excluded: chain AQ residue 2 LEU Chi-restraints excluded: chain AT residue 8 SER Chi-restraints excluded: chain AU residue 9 VAL Chi-restraints excluded: chain AV residue 3 ILE Chi-restraints excluded: chain AW residue 8 SER Chi-restraints excluded: chain AX residue 9 VAL Chi-restraints excluded: chain AZ residue 2 LEU Chi-restraints excluded: chain AZ residue 7 ILE Chi-restraints excluded: chain AZ residue 9 VAL Chi-restraints excluded: chain A0 residue 3 ILE Chi-restraints excluded: chain A0 residue 5 LYS Chi-restraints excluded: chain A2 residue 4 ILE Chi-restraints excluded: chain A3 residue 9 VAL Chi-restraints excluded: chain A8 residue 2 LEU Chi-restraints excluded: chain A8 residue 7 ILE Chi-restraints excluded: chain BC residue 9 VAL Chi-restraints excluded: chain BF residue 9 VAL Chi-restraints excluded: chain BH residue 2 LEU Chi-restraints excluded: chain BH residue 7 ILE Chi-restraints excluded: chain BH residue 9 VAL Chi-restraints excluded: chain BI residue 3 ILE Chi-restraints excluded: chain BK residue 4 ILE Chi-restraints excluded: chain BL residue 9 VAL Chi-restraints excluded: chain BN residue 8 SER Chi-restraints excluded: chain BQ residue 2 LEU Chi-restraints excluded: chain BQ residue 7 ILE Chi-restraints excluded: chain BQ residue 9 VAL Chi-restraints excluded: chain BU residue 9 VAL Chi-restraints excluded: chain BV residue 3 ILE Chi-restraints excluded: chain BW residue 8 SER Chi-restraints excluded: chain BX residue 9 VAL Chi-restraints excluded: chain BZ residue 2 LEU Chi-restraints excluded: chain BZ residue 9 VAL Chi-restraints excluded: chain B0 residue 3 ILE Chi-restraints excluded: chain B0 residue 5 LYS Chi-restraints excluded: chain B2 residue 4 ILE Chi-restraints excluded: chain B3 residue 9 VAL Chi-restraints excluded: chain B7 residue 8 SER Chi-restraints excluded: chain B8 residue 2 LEU Chi-restraints excluded: chain B8 residue 7 ILE Chi-restraints excluded: chain B8 residue 9 VAL Chi-restraints excluded: chain CB residue 8 SER Chi-restraints excluded: chain CC residue 9 VAL Chi-restraints excluded: chain CD residue 3 ILE Chi-restraints excluded: chain CE residue 8 SER Chi-restraints excluded: chain CH residue 2 LEU Chi-restraints excluded: chain CH residue 7 ILE Chi-restraints excluded: chain CH residue 9 VAL Chi-restraints excluded: chain CI residue 5 LYS Chi-restraints excluded: chain 1 residue 4 ILE Chi-restraints excluded: chain 3 residue 9 VAL Chi-restraints excluded: chain 7 residue 2 LEU Chi-restraints excluded: chain 7 residue 7 ILE Chi-restraints excluded: chain CK residue 8 SER Chi-restraints excluded: chain CL residue 9 VAL Chi-restraints excluded: chain CN residue 8 SER Chi-restraints excluded: chain CO residue 9 VAL Chi-restraints excluded: chain CQ residue 2 LEU Chi-restraints excluded: chain CQ residue 9 VAL Chi-restraints excluded: chain CR residue 3 ILE Chi-restraints excluded: chain CR residue 5 LYS Chi-restraints excluded: chain CT residue 4 ILE Chi-restraints excluded: chain CU residue 9 VAL Chi-restraints excluded: chain CZ residue 2 LEU Chi-restraints excluded: chain CZ residue 7 ILE Chi-restraints excluded: chain CZ residue 9 VAL Chi-restraints excluded: chain C3 residue 9 VAL Chi-restraints excluded: chain C5 residue 8 SER Chi-restraints excluded: chain C6 residue 9 VAL Chi-restraints excluded: chain C8 residue 9 VAL Chi-restraints excluded: chain DB residue 4 ILE Chi-restraints excluded: chain DC residue 9 VAL Chi-restraints excluded: chain DH residue 2 LEU Chi-restraints excluded: chain DL residue 9 VAL Chi-restraints excluded: chain DM residue 3 ILE Chi-restraints excluded: chain DN residue 8 SER Chi-restraints excluded: chain DO residue 9 VAL Chi-restraints excluded: chain DQ residue 2 LEU Chi-restraints excluded: chain DQ residue 7 ILE Chi-restraints excluded: chain DQ residue 9 VAL Chi-restraints excluded: chain DT residue 4 ILE Chi-restraints excluded: chain DU residue 9 VAL Chi-restraints excluded: chain DZ residue 2 LEU Chi-restraints excluded: chain DZ residue 7 ILE Chi-restraints excluded: chain D3 residue 9 VAL Chi-restraints excluded: chain D4 residue 3 ILE Chi-restraints excluded: chain D5 residue 8 SER Chi-restraints excluded: chain D7 residue 8 SER Chi-restraints excluded: chain D8 residue 2 LEU Chi-restraints excluded: chain D8 residue 9 VAL Chi-restraints excluded: chain EB residue 4 ILE Chi-restraints excluded: chain EC residue 9 VAL Chi-restraints excluded: chain EH residue 2 LEU Chi-restraints excluded: chain EH residue 7 ILE Chi-restraints excluded: chain EL residue 9 VAL Chi-restraints excluded: chain EM residue 3 ILE Chi-restraints excluded: chain EQ residue 2 LEU Chi-restraints excluded: chain EQ residue 7 ILE Chi-restraints excluded: chain EQ residue 9 VAL Chi-restraints excluded: chain ET residue 4 ILE Chi-restraints excluded: chain EU residue 9 VAL Chi-restraints excluded: chain EZ residue 2 LEU Chi-restraints excluded: chain EZ residue 7 ILE Chi-restraints excluded: chain E3 residue 9 VAL Chi-restraints excluded: chain E4 residue 3 ILE Chi-restraints excluded: chain E5 residue 8 SER Chi-restraints excluded: chain E8 residue 2 LEU Chi-restraints excluded: chain E8 residue 7 ILE Chi-restraints excluded: chain FC residue 9 VAL Chi-restraints excluded: chain FH residue 2 LEU Chi-restraints excluded: chain FK residue 4 ILE Chi-restraints excluded: chain FL residue 9 VAL Chi-restraints excluded: chain FM residue 3 ILE Chi-restraints excluded: chain FN residue 8 SER Chi-restraints excluded: chain FO residue 9 VAL Chi-restraints excluded: chain FQ residue 2 LEU Chi-restraints excluded: chain FU residue 9 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 186 optimal weight: 40.0000 chunk 97 optimal weight: 50.0000 chunk 179 optimal weight: 20.0000 chunk 40 optimal weight: 20.0000 chunk 188 optimal weight: 40.0000 chunk 64 optimal weight: 20.0000 chunk 203 optimal weight: 1.9990 chunk 107 optimal weight: 10.0000 chunk 162 optimal weight: 0.0970 chunk 79 optimal weight: 9.9990 chunk 65 optimal weight: 30.0000 overall best weight: 8.4190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: BN 10 HIS BT 10 HIS ** EW 10 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** FH 10 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** FN 10 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** FQ 10 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** FZ 10 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.116024 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3299 r_free = 0.3299 target = 0.096312 restraints weight = 30337.686| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.099606 restraints weight = 16181.934| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.101964 restraints weight = 10459.432| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.103599 restraints weight = 7602.975| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.104785 restraints weight = 5979.426| |-----------------------------------------------------------------------------| r_work (final): 0.3406 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7767 moved from start: 0.3663 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 20370 Z= 0.193 Angle : 0.731 11.523 27210 Z= 0.307 Chirality : 0.058 0.214 3840 Planarity : 0.002 0.020 3060 Dihedral : 11.217 57.620 2580 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 7.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 8.83 % Allowed : 22.12 % Favored : 69.04 % 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 aren not related in a simple way. whole: -0.91 (0.18), residues: 2100 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.69 (0.14), residues: 2100 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.001 HISBN 10 Details of bonding type rmsd covalent geometry : bond 0.00487 (20370) covalent geometry : angle 0.73079 (27210) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4200 Ramachandran restraints generated. 2100 Oldfield, 0 Emsley, 2100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4200 Ramachandran restraints generated. 2100 Oldfield, 0 Emsley, 2100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 639 residues out of total 2400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 212 poor density : 427 time to evaluate : 1.333 Fit side-chains REVERT: A 5 LYS cc_start: 0.8494 (mttt) cc_final: 0.8066 (mttp) REVERT: D 2 LEU cc_start: 0.8768 (OUTLIER) cc_final: 0.8456 (pt) REVERT: J 5 LYS cc_start: 0.8573 (mttt) cc_final: 0.8094 (mttp) REVERT: S 5 LYS cc_start: 0.8446 (mttt) cc_final: 0.8184 (mttp) REVERT: U 3 ILE cc_start: 0.8253 (OUTLIER) cc_final: 0.7799 (mp) REVERT: a 4 ILE cc_start: 0.8643 (OUTLIER) cc_final: 0.8351 (mp) REVERT: j 5 LYS cc_start: 0.8610 (mttt) cc_final: 0.8111 (mttp) REVERT: s 4 ILE cc_start: 0.8566 (OUTLIER) cc_final: 0.8283 (mp) REVERT: x 3 ILE cc_start: 0.8499 (mt) cc_final: 0.8213 (mt) REVERT: AB 5 LYS cc_start: 0.8456 (mttt) cc_final: 0.7933 (mttp) REVERT: AD 3 ILE cc_start: 0.7958 (OUTLIER) cc_final: 0.7415 (mp) REVERT: AE 5 LYS cc_start: 0.8240 (mttt) cc_final: 0.7953 (mttm) REVERT: AK 4 ILE cc_start: 0.8687 (OUTLIER) cc_final: 0.8315 (mp) REVERT: AV 3 ILE cc_start: 0.7938 (OUTLIER) cc_final: 0.7405 (mp) REVERT: A2 4 ILE cc_start: 0.8545 (OUTLIER) cc_final: 0.8178 (mp) REVERT: BB 5 LYS cc_start: 0.8472 (mttt) cc_final: 0.8069 (mttp) REVERT: BK 4 ILE cc_start: 0.8438 (OUTLIER) cc_final: 0.8072 (mp) REVERT: BT 5 LYS cc_start: 0.8295 (mttt) cc_final: 0.7823 (mttp) REVERT: BV 3 ILE cc_start: 0.8078 (OUTLIER) cc_final: 0.7608 (mp) REVERT: B2 4 ILE cc_start: 0.8656 (OUTLIER) cc_final: 0.8375 (mp) REVERT: CD 1 ASP cc_start: 0.7433 (m-30) cc_final: 0.7120 (m-30) REVERT: CD 3 ILE cc_start: 0.8088 (OUTLIER) cc_final: 0.7570 (mp) REVERT: 1 4 ILE cc_start: 0.8649 (OUTLIER) cc_final: 0.8329 (mp) REVERT: 6 5 LYS cc_start: 0.7916 (mttt) cc_final: 0.7534 (mttm) REVERT: CK 5 LYS cc_start: 0.8476 (mttt) cc_final: 0.8056 (mttp) REVERT: CR 5 LYS cc_start: 0.8672 (OUTLIER) cc_final: 0.8383 (mtmm) REVERT: CT 4 ILE cc_start: 0.8596 (OUTLIER) cc_final: 0.8342 (mp) REVERT: C4 2 LEU cc_start: 0.8580 (tt) cc_final: 0.8345 (tp) REVERT: C4 3 ILE cc_start: 0.8232 (OUTLIER) cc_final: 0.7953 (mm) REVERT: C5 2 LEU cc_start: 0.8449 (pp) cc_final: 0.8223 (pt) REVERT: DB 4 ILE cc_start: 0.8511 (OUTLIER) cc_final: 0.8222 (mp) REVERT: DE 5 LYS cc_start: 0.8013 (mttt) cc_final: 0.7633 (mttm) REVERT: DM 3 ILE cc_start: 0.8024 (OUTLIER) cc_final: 0.7469 (mp) REVERT: DT 4 ILE cc_start: 0.8705 (OUTLIER) cc_final: 0.8467 (mp) REVERT: DW 2 LEU cc_start: 0.8272 (pt) cc_final: 0.8026 (pp) REVERT: D4 3 ILE cc_start: 0.8020 (OUTLIER) cc_final: 0.7493 (mp) REVERT: EB 4 ILE cc_start: 0.8652 (OUTLIER) cc_final: 0.8403 (mp) REVERT: EE 5 LYS cc_start: 0.7939 (mttt) cc_final: 0.7593 (mttm) REVERT: EK 5 LYS cc_start: 0.8449 (mttt) cc_final: 0.8100 (mttp) REVERT: EM 3 ILE cc_start: 0.8149 (OUTLIER) cc_final: 0.7715 (mp) REVERT: ET 4 ILE cc_start: 0.8687 (OUTLIER) cc_final: 0.8450 (mp) REVERT: E4 3 ILE cc_start: 0.8195 (OUTLIER) cc_final: 0.7982 (mm) REVERT: E5 5 LYS cc_start: 0.7933 (mttt) cc_final: 0.7617 (mttp) REVERT: FE 2 LEU cc_start: 0.8324 (pp) cc_final: 0.6803 (mm) REVERT: FE 5 LYS cc_start: 0.8352 (mttt) cc_final: 0.8028 (mttm) REVERT: FM 3 ILE cc_start: 0.8355 (OUTLIER) cc_final: 0.7809 (mp) REVERT: FN 2 LEU cc_start: 0.8343 (pt) cc_final: 0.8041 (pp) REVERT: FT 4 ILE cc_start: 0.8662 (OUTLIER) cc_final: 0.8423 (mp) outliers start: 212 outliers final: 158 residues processed: 510 average time/residue: 0.1168 time to fit residues: 96.0178 Evaluate side-chains 604 residues out of total 2400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 184 poor density : 420 time to evaluate : 0.797 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 SER Chi-restraints excluded: chain B residue 9 VAL Chi-restraints excluded: chain D residue 2 LEU Chi-restraints excluded: chain D residue 8 SER Chi-restraints excluded: chain E residue 9 VAL Chi-restraints excluded: chain G residue 2 LEU Chi-restraints excluded: chain G residue 9 VAL Chi-restraints excluded: chain H residue 3 ILE Chi-restraints excluded: chain J residue 8 SER Chi-restraints excluded: chain M residue 8 SER Chi-restraints excluded: chain P residue 2 LEU Chi-restraints excluded: chain S residue 8 SER Chi-restraints excluded: chain T residue 9 VAL Chi-restraints excluded: chain U residue 3 ILE Chi-restraints excluded: chain V residue 8 SER Chi-restraints excluded: chain W residue 9 VAL Chi-restraints excluded: chain X residue 8 SER Chi-restraints excluded: chain Y residue 2 LEU Chi-restraints excluded: chain Z residue 3 ILE Chi-restraints excluded: chain a residue 4 ILE Chi-restraints excluded: chain b residue 9 VAL Chi-restraints excluded: chain d residue 8 SER Chi-restraints excluded: chain f residue 8 SER Chi-restraints excluded: chain g residue 2 LEU Chi-restraints excluded: chain g residue 9 VAL Chi-restraints excluded: chain h residue 3 ILE Chi-restraints excluded: chain j residue 8 SER Chi-restraints excluded: chain k residue 9 VAL Chi-restraints excluded: chain m residue 8 SER Chi-restraints excluded: chain n residue 9 VAL Chi-restraints excluded: chain o residue 8 SER Chi-restraints excluded: chain p residue 2 LEU Chi-restraints excluded: chain p residue 9 VAL Chi-restraints excluded: chain q residue 3 ILE Chi-restraints excluded: chain s residue 4 ILE Chi-restraints excluded: chain t residue 9 VAL Chi-restraints excluded: chain v residue 8 SER Chi-restraints excluded: chain y residue 2 LEU Chi-restraints excluded: chain y residue 4 ILE Chi-restraints excluded: chain y residue 7 ILE Chi-restraints excluded: chain y residue 9 VAL Chi-restraints excluded: chain z residue 3 ILE Chi-restraints excluded: chain AC residue 9 VAL Chi-restraints excluded: chain AD residue 3 ILE Chi-restraints excluded: chain AE residue 8 SER Chi-restraints excluded: chain AF residue 9 VAL Chi-restraints excluded: chain AH residue 2 LEU Chi-restraints excluded: chain AH residue 9 VAL Chi-restraints excluded: chain AI residue 3 ILE Chi-restraints excluded: chain AK residue 4 ILE Chi-restraints excluded: chain AL residue 9 VAL Chi-restraints excluded: chain AN residue 8 SER Chi-restraints excluded: chain AO residue 9 VAL Chi-restraints excluded: chain AQ residue 2 LEU Chi-restraints excluded: chain AQ residue 7 ILE Chi-restraints excluded: chain AT residue 8 SER Chi-restraints excluded: chain AU residue 9 VAL Chi-restraints excluded: chain AV residue 3 ILE Chi-restraints excluded: chain AW residue 8 SER Chi-restraints excluded: chain AX residue 9 VAL Chi-restraints excluded: chain AZ residue 2 LEU Chi-restraints excluded: chain AZ residue 7 ILE Chi-restraints excluded: chain AZ residue 9 VAL Chi-restraints excluded: chain A0 residue 3 ILE Chi-restraints excluded: chain A0 residue 5 LYS Chi-restraints excluded: chain A2 residue 4 ILE Chi-restraints excluded: chain A3 residue 9 VAL Chi-restraints excluded: chain A8 residue 2 LEU Chi-restraints excluded: chain A8 residue 7 ILE Chi-restraints excluded: chain BC residue 9 VAL Chi-restraints excluded: chain BF residue 9 VAL Chi-restraints excluded: chain BH residue 2 LEU Chi-restraints excluded: chain BH residue 7 ILE Chi-restraints excluded: chain BH residue 9 VAL Chi-restraints excluded: chain BI residue 3 ILE Chi-restraints excluded: chain BK residue 4 ILE Chi-restraints excluded: chain BL residue 9 VAL Chi-restraints excluded: chain BN residue 8 SER Chi-restraints excluded: chain BO residue 9 VAL Chi-restraints excluded: chain BQ residue 2 LEU Chi-restraints excluded: chain BQ residue 7 ILE Chi-restraints excluded: chain BQ residue 9 VAL Chi-restraints excluded: chain BU residue 9 VAL Chi-restraints excluded: chain BV residue 3 ILE Chi-restraints excluded: chain BW residue 8 SER Chi-restraints excluded: chain BX residue 9 VAL Chi-restraints excluded: chain BZ residue 2 LEU Chi-restraints excluded: chain BZ residue 5 LYS Chi-restraints excluded: chain BZ residue 9 VAL Chi-restraints excluded: chain B0 residue 2 LEU Chi-restraints excluded: chain B0 residue 3 ILE Chi-restraints excluded: chain B0 residue 5 LYS Chi-restraints excluded: chain B2 residue 4 ILE Chi-restraints excluded: chain B3 residue 9 VAL Chi-restraints excluded: chain B5 residue 8 SER Chi-restraints excluded: chain B7 residue 8 SER Chi-restraints excluded: chain B8 residue 2 LEU Chi-restraints excluded: chain B8 residue 7 ILE Chi-restraints excluded: chain B8 residue 9 VAL Chi-restraints excluded: chain CB residue 8 SER Chi-restraints excluded: chain CC residue 9 VAL Chi-restraints excluded: chain CD residue 3 ILE Chi-restraints excluded: chain CE residue 8 SER Chi-restraints excluded: chain CH residue 2 LEU Chi-restraints excluded: chain CH residue 7 ILE Chi-restraints excluded: chain CH residue 9 VAL Chi-restraints excluded: chain CI residue 5 LYS Chi-restraints excluded: chain 1 residue 4 ILE Chi-restraints excluded: chain 3 residue 9 VAL Chi-restraints excluded: chain 6 residue 8 SER Chi-restraints excluded: chain 7 residue 2 LEU Chi-restraints excluded: chain 7 residue 7 ILE Chi-restraints excluded: chain CK residue 8 SER Chi-restraints excluded: chain CL residue 9 VAL Chi-restraints excluded: chain CN residue 8 SER Chi-restraints excluded: chain CO residue 9 VAL Chi-restraints excluded: chain CQ residue 2 LEU Chi-restraints excluded: chain CQ residue 9 VAL Chi-restraints excluded: chain CR residue 3 ILE Chi-restraints excluded: chain CR residue 5 LYS Chi-restraints excluded: chain CT residue 4 ILE Chi-restraints excluded: chain CU residue 9 VAL Chi-restraints excluded: chain CZ residue 2 LEU Chi-restraints excluded: chain CZ residue 7 ILE Chi-restraints excluded: chain CZ residue 9 VAL Chi-restraints excluded: chain C3 residue 9 VAL Chi-restraints excluded: chain C4 residue 3 ILE Chi-restraints excluded: chain C5 residue 8 SER Chi-restraints excluded: chain C6 residue 9 VAL Chi-restraints excluded: chain C7 residue 4 ILE Chi-restraints excluded: chain C8 residue 9 VAL Chi-restraints excluded: chain DB residue 4 ILE Chi-restraints excluded: chain DC residue 9 VAL Chi-restraints excluded: chain DH residue 2 LEU Chi-restraints excluded: chain DL residue 9 VAL Chi-restraints excluded: chain DM residue 3 ILE Chi-restraints excluded: chain DN residue 8 SER Chi-restraints excluded: chain DO residue 9 VAL Chi-restraints excluded: chain DQ residue 2 LEU Chi-restraints excluded: chain DQ residue 7 ILE Chi-restraints excluded: chain DQ residue 9 VAL Chi-restraints excluded: chain DR residue 2 LEU Chi-restraints excluded: chain DT residue 4 ILE Chi-restraints excluded: chain DU residue 9 VAL Chi-restraints excluded: chain DZ residue 2 LEU Chi-restraints excluded: chain DZ residue 7 ILE Chi-restraints excluded: chain D3 residue 9 VAL Chi-restraints excluded: chain D4 residue 3 ILE Chi-restraints excluded: chain D5 residue 8 SER Chi-restraints excluded: chain D7 residue 8 SER Chi-restraints excluded: chain D8 residue 2 LEU Chi-restraints excluded: chain D8 residue 9 VAL Chi-restraints excluded: chain EB residue 4 ILE Chi-restraints excluded: chain EC residue 9 VAL Chi-restraints excluded: chain EG residue 11 ILE Chi-restraints excluded: chain EH residue 2 LEU Chi-restraints excluded: chain EH residue 7 ILE Chi-restraints excluded: chain EL residue 9 VAL Chi-restraints excluded: chain EM residue 3 ILE Chi-restraints excluded: chain EQ residue 2 LEU Chi-restraints excluded: chain EQ residue 7 ILE Chi-restraints excluded: chain EQ residue 9 VAL Chi-restraints excluded: chain ER residue 3 ILE Chi-restraints excluded: chain ET residue 4 ILE Chi-restraints excluded: chain EU residue 9 VAL Chi-restraints excluded: chain EZ residue 2 LEU Chi-restraints excluded: chain EZ residue 7 ILE Chi-restraints excluded: chain E3 residue 9 VAL Chi-restraints excluded: chain E4 residue 3 ILE Chi-restraints excluded: chain E5 residue 8 SER Chi-restraints excluded: chain E8 residue 2 LEU Chi-restraints excluded: chain E8 residue 7 ILE Chi-restraints excluded: chain E9 residue 3 ILE Chi-restraints excluded: chain FC residue 9 VAL Chi-restraints excluded: chain FH residue 2 LEU Chi-restraints excluded: chain FK residue 4 ILE Chi-restraints excluded: chain FL residue 9 VAL Chi-restraints excluded: chain FM residue 3 ILE Chi-restraints excluded: chain FN residue 8 SER Chi-restraints excluded: chain FO residue 2 LEU Chi-restraints excluded: chain FQ residue 2 LEU Chi-restraints excluded: chain FT residue 4 ILE Chi-restraints excluded: chain FU residue 9 VAL Chi-restraints excluded: chain FZ residue 7 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 132 optimal weight: 30.0000 chunk 9 optimal weight: 5.9990 chunk 15 optimal weight: 6.9990 chunk 32 optimal weight: 4.9990 chunk 67 optimal weight: 20.0000 chunk 8 optimal weight: 0.6980 chunk 94 optimal weight: 10.0000 chunk 3 optimal weight: 20.0000 chunk 39 optimal weight: 20.0000 chunk 43 optimal weight: 0.0570 chunk 55 optimal weight: 0.8980 overall best weight: 2.5302 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: c 10 HIS BN 10 HIS BT 10 HIS ** EW 10 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** FH 10 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** FN 10 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** FQ 10 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** FZ 10 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3612 r_free = 0.3612 target = 0.119816 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.100322 restraints weight = 29475.477| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.103745 restraints weight = 15579.078| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.106190 restraints weight = 9934.265| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.107867 restraints weight = 7103.554| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.109119 restraints weight = 5506.759| |-----------------------------------------------------------------------------| r_work (final): 0.3489 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7685 moved from start: 0.3808 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 20370 Z= 0.097 Angle : 0.652 10.097 27210 Z= 0.267 Chirality : 0.057 0.203 3840 Planarity : 0.001 0.018 3060 Dihedral : 10.422 57.673 2580 Min Nonbonded Distance : 2.562 Molprobity Statistics. All-atom Clashscore : 5.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.52 % Favored : 99.48 % Rotamer: Outliers : 7.42 % Allowed : 23.62 % Favored : 68.96 % 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 aren not related in a simple way. whole: -0.49 (0.19), residues: 2100 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.36 (0.14), residues: 2100 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.000 HISBN 10 Details of bonding type rmsd covalent geometry : bond 0.00239 (20370) covalent geometry : angle 0.65248 (27210) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4200 Ramachandran restraints generated. 2100 Oldfield, 0 Emsley, 2100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4200 Ramachandran restraints generated. 2100 Oldfield, 0 Emsley, 2100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 592 residues out of total 2400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 178 poor density : 414 time to evaluate : 0.812 Fit side-chains REVERT: A 5 LYS cc_start: 0.8421 (mttt) cc_final: 0.8029 (mttp) REVERT: D 2 LEU cc_start: 0.8628 (OUTLIER) cc_final: 0.8359 (tt) REVERT: J 5 LYS cc_start: 0.8532 (mttt) cc_final: 0.8077 (mttp) REVERT: S 5 LYS cc_start: 0.8420 (mttt) cc_final: 0.7958 (mttp) REVERT: U 3 ILE cc_start: 0.8191 (OUTLIER) cc_final: 0.7719 (mp) REVERT: m 3 ILE cc_start: 0.9135 (mt) cc_final: 0.8869 (mp) REVERT: AD 3 ILE cc_start: 0.7886 (OUTLIER) cc_final: 0.7358 (mp) REVERT: AE 5 LYS cc_start: 0.8092 (mttt) cc_final: 0.7872 (mttm) REVERT: AV 3 ILE cc_start: 0.7855 (OUTLIER) cc_final: 0.7338 (mp) REVERT: AZ 4 ILE cc_start: 0.5592 (pt) cc_final: 0.5333 (tp) REVERT: BK 4 ILE cc_start: 0.8433 (OUTLIER) cc_final: 0.8106 (mp) REVERT: BT 5 LYS cc_start: 0.8230 (mttt) cc_final: 0.7722 (mttp) REVERT: BT 10 HIS cc_start: 0.7707 (OUTLIER) cc_final: 0.7158 (t-90) REVERT: BV 3 ILE cc_start: 0.8062 (OUTLIER) cc_final: 0.7589 (mp) REVERT: B2 4 ILE cc_start: 0.8585 (OUTLIER) cc_final: 0.8352 (mp) REVERT: CD 1 ASP cc_start: 0.7416 (m-30) cc_final: 0.7131 (m-30) REVERT: CD 3 ILE cc_start: 0.8023 (OUTLIER) cc_final: 0.7472 (mp) REVERT: 1 4 ILE cc_start: 0.8574 (OUTLIER) cc_final: 0.8325 (mp) REVERT: 6 5 LYS cc_start: 0.7879 (mttt) cc_final: 0.7567 (mttm) REVERT: CN 2 LEU cc_start: 0.7887 (pt) cc_final: 0.7679 (pp) REVERT: CT 4 ILE cc_start: 0.8552 (OUTLIER) cc_final: 0.8309 (mp) REVERT: C5 3 ILE cc_start: 0.8846 (mt) cc_final: 0.8583 (mp) REVERT: DB 4 ILE cc_start: 0.8444 (OUTLIER) cc_final: 0.8188 (mp) REVERT: DE 5 LYS cc_start: 0.7773 (mttt) cc_final: 0.7544 (mttm) REVERT: DM 3 ILE cc_start: 0.8027 (OUTLIER) cc_final: 0.7500 (mp) REVERT: DN 2 LEU cc_start: 0.8029 (pt) cc_final: 0.7732 (pp) REVERT: DT 4 ILE cc_start: 0.8621 (OUTLIER) cc_final: 0.8366 (mp) REVERT: DW 2 LEU cc_start: 0.8235 (pt) cc_final: 0.7952 (pp) REVERT: D4 3 ILE cc_start: 0.8005 (OUTLIER) cc_final: 0.7494 (mp) REVERT: D5 2 LEU cc_start: 0.8023 (pt) cc_final: 0.7626 (tt) REVERT: EB 4 ILE cc_start: 0.8567 (OUTLIER) cc_final: 0.8347 (mp) REVERT: EE 2 LEU cc_start: 0.8023 (pt) cc_final: 0.7759 (pp) REVERT: EE 5 LYS cc_start: 0.7668 (mttt) cc_final: 0.7410 (mttm) REVERT: EM 3 ILE cc_start: 0.8127 (OUTLIER) cc_final: 0.7711 (mp) REVERT: EN 2 LEU cc_start: 0.7965 (pt) cc_final: 0.7692 (pp) REVERT: ET 4 ILE cc_start: 0.8626 (OUTLIER) cc_final: 0.8407 (mp) REVERT: E4 3 ILE cc_start: 0.8232 (OUTLIER) cc_final: 0.8001 (mm) REVERT: FE 2 LEU cc_start: 0.8092 (pp) cc_final: 0.6554 (mm) REVERT: FE 5 LYS cc_start: 0.8298 (mttt) cc_final: 0.8001 (mttm) REVERT: FM 3 ILE cc_start: 0.8319 (OUTLIER) cc_final: 0.7763 (mp) REVERT: FN 2 LEU cc_start: 0.8073 (pt) cc_final: 0.6578 (mm) outliers start: 178 outliers final: 125 residues processed: 485 average time/residue: 0.1209 time to fit residues: 95.1393 Evaluate side-chains 534 residues out of total 2400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 145 poor density : 389 time to evaluate : 0.908 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 SER Chi-restraints excluded: chain D residue 2 LEU Chi-restraints excluded: chain D residue 8 SER Chi-restraints excluded: chain E residue 9 VAL Chi-restraints excluded: chain G residue 2 LEU Chi-restraints excluded: chain G residue 9 VAL Chi-restraints excluded: chain M residue 8 SER Chi-restraints excluded: chain S residue 8 SER Chi-restraints excluded: chain U residue 3 ILE Chi-restraints excluded: chain V residue 8 SER Chi-restraints excluded: chain W residue 9 VAL Chi-restraints excluded: chain X residue 8 SER Chi-restraints excluded: chain b residue 9 VAL Chi-restraints excluded: chain d residue 8 SER Chi-restraints excluded: chain f residue 8 SER Chi-restraints excluded: chain g residue 9 VAL Chi-restraints excluded: chain j residue 8 SER Chi-restraints excluded: chain k residue 9 VAL Chi-restraints excluded: chain m residue 8 SER Chi-restraints excluded: chain n residue 9 VAL Chi-restraints excluded: chain o residue 8 SER Chi-restraints excluded: chain p residue 2 LEU Chi-restraints excluded: chain p residue 9 VAL Chi-restraints excluded: chain t residue 9 VAL Chi-restraints excluded: chain y residue 2 LEU Chi-restraints excluded: chain y residue 7 ILE Chi-restraints excluded: chain y residue 9 VAL Chi-restraints excluded: chain z residue 3 ILE Chi-restraints excluded: chain AC residue 9 VAL Chi-restraints excluded: chain AD residue 3 ILE Chi-restraints excluded: chain AE residue 8 SER Chi-restraints excluded: chain AF residue 9 VAL Chi-restraints excluded: chain AH residue 2 LEU Chi-restraints excluded: chain AH residue 9 VAL Chi-restraints excluded: chain AL residue 9 VAL Chi-restraints excluded: chain AN residue 8 SER Chi-restraints excluded: chain AQ residue 2 LEU Chi-restraints excluded: chain AT residue 8 SER Chi-restraints excluded: chain AU residue 9 VAL Chi-restraints excluded: chain AV residue 3 ILE Chi-restraints excluded: chain AW residue 8 SER Chi-restraints excluded: chain AX residue 9 VAL Chi-restraints excluded: chain AZ residue 2 LEU Chi-restraints excluded: chain AZ residue 7 ILE Chi-restraints excluded: chain AZ residue 9 VAL Chi-restraints excluded: chain A0 residue 3 ILE Chi-restraints excluded: chain A0 residue 5 LYS Chi-restraints excluded: chain A3 residue 9 VAL Chi-restraints excluded: chain A8 residue 2 LEU Chi-restraints excluded: chain A8 residue 7 ILE Chi-restraints excluded: chain BC residue 9 VAL Chi-restraints excluded: chain BF residue 9 VAL Chi-restraints excluded: chain BH residue 2 LEU Chi-restraints excluded: chain BH residue 7 ILE Chi-restraints excluded: chain BH residue 9 VAL Chi-restraints excluded: chain BI residue 3 ILE Chi-restraints excluded: chain BK residue 4 ILE Chi-restraints excluded: chain BL residue 9 VAL Chi-restraints excluded: chain BN residue 8 SER Chi-restraints excluded: chain BQ residue 2 LEU Chi-restraints excluded: chain BQ residue 7 ILE Chi-restraints excluded: chain BQ residue 9 VAL Chi-restraints excluded: chain BT residue 10 HIS Chi-restraints excluded: chain BU residue 9 VAL Chi-restraints excluded: chain BV residue 3 ILE Chi-restraints excluded: chain BW residue 8 SER Chi-restraints excluded: chain BX residue 9 VAL Chi-restraints excluded: chain BZ residue 2 LEU Chi-restraints excluded: chain BZ residue 9 VAL Chi-restraints excluded: chain B0 residue 2 LEU Chi-restraints excluded: chain B0 residue 5 LYS Chi-restraints excluded: chain B2 residue 4 ILE Chi-restraints excluded: chain B3 residue 9 VAL Chi-restraints excluded: chain B5 residue 8 SER Chi-restraints excluded: chain B6 residue 9 VAL Chi-restraints excluded: chain B7 residue 8 SER Chi-restraints excluded: chain B8 residue 2 LEU Chi-restraints excluded: chain B8 residue 7 ILE Chi-restraints excluded: chain B8 residue 9 VAL Chi-restraints excluded: chain CB residue 8 SER Chi-restraints excluded: chain CC residue 9 VAL Chi-restraints excluded: chain CD residue 3 ILE Chi-restraints excluded: chain CE residue 8 SER Chi-restraints excluded: chain CH residue 2 LEU Chi-restraints excluded: chain CH residue 7 ILE Chi-restraints excluded: chain CH residue 9 VAL Chi-restraints excluded: chain CI residue 5 LYS Chi-restraints excluded: chain 1 residue 4 ILE Chi-restraints excluded: chain 3 residue 9 VAL Chi-restraints excluded: chain 7 residue 2 LEU Chi-restraints excluded: chain CK residue 8 SER Chi-restraints excluded: chain CL residue 9 VAL Chi-restraints excluded: chain CN residue 8 SER Chi-restraints excluded: chain CO residue 9 VAL Chi-restraints excluded: chain CQ residue 2 LEU Chi-restraints excluded: chain CQ residue 9 VAL Chi-restraints excluded: chain CT residue 4 ILE Chi-restraints excluded: chain CU residue 9 VAL Chi-restraints excluded: chain CZ residue 7 ILE Chi-restraints excluded: chain CZ residue 9 VAL Chi-restraints excluded: chain C3 residue 9 VAL Chi-restraints excluded: chain C5 residue 8 SER Chi-restraints excluded: chain C8 residue 9 VAL Chi-restraints excluded: chain DB residue 4 ILE Chi-restraints excluded: chain DC residue 9 VAL Chi-restraints excluded: chain DH residue 2 LEU Chi-restraints excluded: chain DH residue 9 VAL Chi-restraints excluded: chain DL residue 9 VAL Chi-restraints excluded: chain DM residue 3 ILE Chi-restraints excluded: chain DN residue 8 SER Chi-restraints excluded: chain DQ residue 2 LEU Chi-restraints excluded: chain DQ residue 7 ILE Chi-restraints excluded: chain DQ residue 9 VAL Chi-restraints excluded: chain DR residue 2 LEU Chi-restraints excluded: chain DT residue 4 ILE Chi-restraints excluded: chain DU residue 9 VAL Chi-restraints excluded: chain DZ residue 2 LEU Chi-restraints excluded: chain D3 residue 9 VAL Chi-restraints excluded: chain D4 residue 3 ILE Chi-restraints excluded: chain D8 residue 9 VAL Chi-restraints excluded: chain EB residue 4 ILE Chi-restraints excluded: chain EC residue 9 VAL Chi-restraints excluded: chain EG residue 11 ILE Chi-restraints excluded: chain EH residue 2 LEU Chi-restraints excluded: chain EH residue 7 ILE Chi-restraints excluded: chain EL residue 9 VAL Chi-restraints excluded: chain EM residue 3 ILE Chi-restraints excluded: chain EQ residue 2 LEU Chi-restraints excluded: chain EQ residue 7 ILE Chi-restraints excluded: chain EQ residue 9 VAL Chi-restraints excluded: chain ET residue 4 ILE Chi-restraints excluded: chain EU residue 9 VAL Chi-restraints excluded: chain EZ residue 2 LEU Chi-restraints excluded: chain EZ residue 7 ILE Chi-restraints excluded: chain E3 residue 9 VAL Chi-restraints excluded: chain E4 residue 3 ILE Chi-restraints excluded: chain E5 residue 8 SER Chi-restraints excluded: chain E6 residue 9 VAL Chi-restraints excluded: chain E8 residue 2 LEU Chi-restraints excluded: chain E8 residue 7 ILE Chi-restraints excluded: chain FC residue 9 VAL Chi-restraints excluded: chain FL residue 9 VAL Chi-restraints excluded: chain FM residue 3 ILE Chi-restraints excluded: chain FN residue 8 SER Chi-restraints excluded: chain FU residue 9 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 89 optimal weight: 30.0000 chunk 7 optimal weight: 20.0000 chunk 91 optimal weight: 20.0000 chunk 124 optimal weight: 20.0000 chunk 98 optimal weight: 10.0000 chunk 112 optimal weight: 10.0000 chunk 155 optimal weight: 20.0000 chunk 107 optimal weight: 8.9990 chunk 145 optimal weight: 7.9990 chunk 127 optimal weight: 40.0000 chunk 24 optimal weight: 20.0000 overall best weight: 11.3996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: O 10 HIS A7 10 HIS BP 10 HIS BT 10 HIS ** C7 10 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** DG 10 HIS DK 10 HIS EG 10 HIS EK 10 HIS ** EW 10 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** FH 10 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** FN 10 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** FQ 10 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** FZ 10 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.115810 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.096041 restraints weight = 30400.268| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.099147 restraints weight = 16883.696| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.101420 restraints weight = 11210.778| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.102957 restraints weight = 8285.272| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.104095 restraints weight = 6627.740| |-----------------------------------------------------------------------------| r_work (final): 0.3394 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7764 moved from start: 0.3812 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.059 20370 Z= 0.249 Angle : 0.794 10.167 27210 Z= 0.338 Chirality : 0.058 0.171 3840 Planarity : 0.002 0.019 3060 Dihedral : 11.433 57.425 2580 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 8.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.38 % Favored : 95.62 % Rotamer: Outliers : 7.79 % Allowed : 23.92 % Favored : 68.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.85 (0.19), residues: 2100 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.63 (0.14), residues: 2100 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.022 0.002 HISBT 10 Details of bonding type rmsd covalent geometry : bond 0.00632 (20370) covalent geometry : angle 0.79416 (27210) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4200 Ramachandran restraints generated. 2100 Oldfield, 0 Emsley, 2100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4200 Ramachandran restraints generated. 2100 Oldfield, 0 Emsley, 2100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 632 residues out of total 2400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 187 poor density : 445 time to evaluate : 0.805 Fit side-chains REVERT: A 5 LYS cc_start: 0.8512 (mttt) cc_final: 0.8091 (mttp) REVERT: D 2 LEU cc_start: 0.8781 (OUTLIER) cc_final: 0.8440 (pt) REVERT: J 5 LYS cc_start: 0.8596 (mttt) cc_final: 0.8192 (mttp) REVERT: S 5 LYS cc_start: 0.8416 (mttt) cc_final: 0.8188 (mttp) REVERT: U 3 ILE cc_start: 0.8208 (OUTLIER) cc_final: 0.7738 (mp) REVERT: j 5 LYS cc_start: 0.8594 (mttt) cc_final: 0.8091 (mttp) REVERT: x 3 ILE cc_start: 0.8438 (mt) cc_final: 0.8147 (mt) REVERT: AB 5 LYS cc_start: 0.8505 (mttt) cc_final: 0.7971 (mttp) REVERT: AD 3 ILE cc_start: 0.7958 (OUTLIER) cc_final: 0.7411 (mp) REVERT: AE 5 LYS cc_start: 0.8242 (mttt) cc_final: 0.7979 (mttm) REVERT: AK 4 ILE cc_start: 0.8633 (OUTLIER) cc_final: 0.8259 (mp) REVERT: AV 3 ILE cc_start: 0.7906 (OUTLIER) cc_final: 0.7374 (mp) REVERT: A2 4 ILE cc_start: 0.8498 (OUTLIER) cc_final: 0.8135 (mp) REVERT: BB 5 LYS cc_start: 0.8487 (mttt) cc_final: 0.8071 (mttp) REVERT: BK 4 ILE cc_start: 0.8364 (OUTLIER) cc_final: 0.8029 (mp) REVERT: BT 5 LYS cc_start: 0.8325 (mttt) cc_final: 0.8043 (mttp) REVERT: BV 3 ILE cc_start: 0.8108 (OUTLIER) cc_final: 0.7631 (mp) REVERT: B2 4 ILE cc_start: 0.8560 (OUTLIER) cc_final: 0.8257 (mp) REVERT: CD 1 ASP cc_start: 0.7366 (m-30) cc_final: 0.7048 (m-30) REVERT: CD 3 ILE cc_start: 0.8027 (OUTLIER) cc_final: 0.7493 (mp) REVERT: CE 3 ILE cc_start: 0.9055 (mt) cc_final: 0.8834 (mp) REVERT: 1 4 ILE cc_start: 0.8613 (OUTLIER) cc_final: 0.8287 (mp) REVERT: 6 5 LYS cc_start: 0.7785 (mttt) cc_final: 0.7461 (mttm) REVERT: CK 5 LYS cc_start: 0.8505 (mttt) cc_final: 0.8086 (mttp) REVERT: CN 2 LEU cc_start: 0.8095 (pt) cc_final: 0.7851 (pp) REVERT: CT 4 ILE cc_start: 0.8518 (OUTLIER) cc_final: 0.8264 (mp) REVERT: C5 5 LYS cc_start: 0.8212 (mttt) cc_final: 0.7795 (mttm) REVERT: DB 4 ILE cc_start: 0.8471 (OUTLIER) cc_final: 0.8178 (mp) REVERT: DE 5 LYS cc_start: 0.7845 (mttt) cc_final: 0.7546 (mttm) REVERT: DM 3 ILE cc_start: 0.8130 (OUTLIER) cc_final: 0.7614 (mp) REVERT: DN 2 LEU cc_start: 0.8111 (pt) cc_final: 0.7864 (pp) REVERT: DT 4 ILE cc_start: 0.8654 (OUTLIER) cc_final: 0.8406 (mp) REVERT: D4 3 ILE cc_start: 0.7997 (OUTLIER) cc_final: 0.7466 (mp) REVERT: D5 2 LEU cc_start: 0.8320 (pt) cc_final: 0.7822 (tt) REVERT: EB 4 ILE cc_start: 0.8602 (OUTLIER) cc_final: 0.8355 (mp) REVERT: EE 5 LYS cc_start: 0.7819 (mttt) cc_final: 0.7437 (mttm) REVERT: EK 5 LYS cc_start: 0.8474 (mttt) cc_final: 0.8130 (mttp) REVERT: EM 3 ILE cc_start: 0.8108 (OUTLIER) cc_final: 0.7658 (mp) REVERT: ET 4 ILE cc_start: 0.8664 (OUTLIER) cc_final: 0.8418 (mp) REVERT: E4 3 ILE cc_start: 0.8244 (OUTLIER) cc_final: 0.8016 (mm) REVERT: FE 2 LEU cc_start: 0.8490 (pp) cc_final: 0.6895 (mm) REVERT: FE 5 LYS cc_start: 0.8332 (mttt) cc_final: 0.7984 (mttm) REVERT: FM 3 ILE cc_start: 0.8327 (OUTLIER) cc_final: 0.7775 (mp) REVERT: FT 4 ILE cc_start: 0.8644 (OUTLIER) cc_final: 0.8412 (mp) outliers start: 187 outliers final: 141 residues processed: 516 average time/residue: 0.1259 time to fit residues: 104.9103 Evaluate side-chains 595 residues out of total 2400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 163 poor density : 432 time to evaluate : 1.480 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 SER Chi-restraints excluded: chain D residue 2 LEU Chi-restraints excluded: chain D residue 8 SER Chi-restraints excluded: chain E residue 9 VAL Chi-restraints excluded: chain G residue 2 LEU Chi-restraints excluded: chain G residue 9 VAL Chi-restraints excluded: chain H residue 2 LEU Chi-restraints excluded: chain J residue 8 SER Chi-restraints excluded: chain M residue 8 SER Chi-restraints excluded: chain S residue 8 SER Chi-restraints excluded: chain U residue 3 ILE Chi-restraints excluded: chain V residue 8 SER Chi-restraints excluded: chain W residue 9 VAL Chi-restraints excluded: chain X residue 8 SER Chi-restraints excluded: chain b residue 9 VAL Chi-restraints excluded: chain d residue 8 SER Chi-restraints excluded: chain e residue 9 VAL Chi-restraints excluded: chain f residue 8 SER Chi-restraints excluded: chain g residue 2 LEU Chi-restraints excluded: chain g residue 9 VAL Chi-restraints excluded: chain h residue 3 ILE Chi-restraints excluded: chain j residue 8 SER Chi-restraints excluded: chain k residue 9 VAL Chi-restraints excluded: chain m residue 8 SER Chi-restraints excluded: chain n residue 9 VAL Chi-restraints excluded: chain o residue 8 SER Chi-restraints excluded: chain p residue 2 LEU Chi-restraints excluded: chain p residue 9 VAL Chi-restraints excluded: chain t residue 9 VAL Chi-restraints excluded: chain y residue 2 LEU Chi-restraints excluded: chain y residue 7 ILE Chi-restraints excluded: chain y residue 9 VAL Chi-restraints excluded: chain z residue 3 ILE Chi-restraints excluded: chain AC residue 9 VAL Chi-restraints excluded: chain AD residue 3 ILE Chi-restraints excluded: chain AE residue 8 SER Chi-restraints excluded: chain AF residue 9 VAL Chi-restraints excluded: chain AH residue 2 LEU Chi-restraints excluded: chain AH residue 9 VAL Chi-restraints excluded: chain AK residue 4 ILE Chi-restraints excluded: chain AL residue 9 VAL Chi-restraints excluded: chain AN residue 8 SER Chi-restraints excluded: chain AQ residue 2 LEU Chi-restraints excluded: chain AQ residue 7 ILE Chi-restraints excluded: chain AT residue 8 SER Chi-restraints excluded: chain AU residue 9 VAL Chi-restraints excluded: chain AV residue 3 ILE Chi-restraints excluded: chain AW residue 8 SER Chi-restraints excluded: chain AX residue 9 VAL Chi-restraints excluded: chain AZ residue 2 LEU Chi-restraints excluded: chain AZ residue 7 ILE Chi-restraints excluded: chain AZ residue 9 VAL Chi-restraints excluded: chain A0 residue 3 ILE Chi-restraints excluded: chain A0 residue 5 LYS Chi-restraints excluded: chain A2 residue 4 ILE Chi-restraints excluded: chain A3 residue 9 VAL Chi-restraints excluded: chain A5 residue 8 SER Chi-restraints excluded: chain A8 residue 2 LEU Chi-restraints excluded: chain A8 residue 7 ILE Chi-restraints excluded: chain BC residue 9 VAL Chi-restraints excluded: chain BE residue 8 SER Chi-restraints excluded: chain BF residue 9 VAL Chi-restraints excluded: chain BH residue 2 LEU Chi-restraints excluded: chain BH residue 7 ILE Chi-restraints excluded: chain BH residue 9 VAL Chi-restraints excluded: chain BI residue 3 ILE Chi-restraints excluded: chain BK residue 4 ILE Chi-restraints excluded: chain BL residue 9 VAL Chi-restraints excluded: chain BN residue 8 SER Chi-restraints excluded: chain BP residue 4 ILE Chi-restraints excluded: chain BQ residue 2 LEU Chi-restraints excluded: chain BQ residue 7 ILE Chi-restraints excluded: chain BQ residue 9 VAL Chi-restraints excluded: chain BU residue 9 VAL Chi-restraints excluded: chain BV residue 3 ILE Chi-restraints excluded: chain BW residue 8 SER Chi-restraints excluded: chain BX residue 9 VAL Chi-restraints excluded: chain BZ residue 2 LEU Chi-restraints excluded: chain BZ residue 5 LYS Chi-restraints excluded: chain BZ residue 9 VAL Chi-restraints excluded: chain B0 residue 2 LEU Chi-restraints excluded: chain B0 residue 5 LYS Chi-restraints excluded: chain B2 residue 4 ILE Chi-restraints excluded: chain B3 residue 9 VAL Chi-restraints excluded: chain B5 residue 8 SER Chi-restraints excluded: chain B6 residue 9 VAL Chi-restraints excluded: chain B7 residue 8 SER Chi-restraints excluded: chain B8 residue 2 LEU Chi-restraints excluded: chain B8 residue 7 ILE Chi-restraints excluded: chain B8 residue 9 VAL Chi-restraints excluded: chain CB residue 8 SER Chi-restraints excluded: chain CC residue 9 VAL Chi-restraints excluded: chain CD residue 3 ILE Chi-restraints excluded: chain CE residue 8 SER Chi-restraints excluded: chain CH residue 2 LEU Chi-restraints excluded: chain CH residue 7 ILE Chi-restraints excluded: chain CH residue 9 VAL Chi-restraints excluded: chain CI residue 5 LYS Chi-restraints excluded: chain 1 residue 4 ILE Chi-restraints excluded: chain 3 residue 9 VAL Chi-restraints excluded: chain 7 residue 2 LEU Chi-restraints excluded: chain 7 residue 9 VAL Chi-restraints excluded: chain CK residue 8 SER Chi-restraints excluded: chain CL residue 9 VAL Chi-restraints excluded: chain CN residue 8 SER Chi-restraints excluded: chain CO residue 9 VAL Chi-restraints excluded: chain CQ residue 2 LEU Chi-restraints excluded: chain CQ residue 9 VAL Chi-restraints excluded: chain CR residue 3 ILE Chi-restraints excluded: chain CT residue 4 ILE Chi-restraints excluded: chain CU residue 9 VAL Chi-restraints excluded: chain CZ residue 7 ILE Chi-restraints excluded: chain CZ residue 9 VAL Chi-restraints excluded: chain C3 residue 9 VAL Chi-restraints excluded: chain C5 residue 8 SER Chi-restraints excluded: chain C8 residue 9 VAL Chi-restraints excluded: chain DB residue 4 ILE Chi-restraints excluded: chain DC residue 9 VAL Chi-restraints excluded: chain DH residue 2 LEU Chi-restraints excluded: chain DH residue 9 VAL Chi-restraints excluded: chain DL residue 9 VAL Chi-restraints excluded: chain DM residue 3 ILE Chi-restraints excluded: chain DN residue 8 SER Chi-restraints excluded: chain DQ residue 2 LEU Chi-restraints excluded: chain DQ residue 7 ILE Chi-restraints excluded: chain DQ residue 9 VAL Chi-restraints excluded: chain DR residue 2 LEU Chi-restraints excluded: chain DT residue 4 ILE Chi-restraints excluded: chain DU residue 9 VAL Chi-restraints excluded: chain DZ residue 2 LEU Chi-restraints excluded: chain DZ residue 7 ILE Chi-restraints excluded: chain D3 residue 9 VAL Chi-restraints excluded: chain D4 residue 3 ILE Chi-restraints excluded: chain D8 residue 9 VAL Chi-restraints excluded: chain D9 residue 3 ILE Chi-restraints excluded: chain EB residue 4 ILE Chi-restraints excluded: chain EC residue 9 VAL Chi-restraints excluded: chain EH residue 2 LEU Chi-restraints excluded: chain EH residue 7 ILE Chi-restraints excluded: chain EL residue 9 VAL Chi-restraints excluded: chain EM residue 3 ILE Chi-restraints excluded: chain EQ residue 2 LEU Chi-restraints excluded: chain EQ residue 7 ILE Chi-restraints excluded: chain EQ residue 9 VAL Chi-restraints excluded: chain ER residue 3 ILE Chi-restraints excluded: chain ET residue 4 ILE Chi-restraints excluded: chain EU residue 9 VAL Chi-restraints excluded: chain EZ residue 2 LEU Chi-restraints excluded: chain EZ residue 7 ILE Chi-restraints excluded: chain E3 residue 9 VAL Chi-restraints excluded: chain E4 residue 3 ILE Chi-restraints excluded: chain E5 residue 8 SER Chi-restraints excluded: chain E8 residue 2 LEU Chi-restraints excluded: chain E8 residue 7 ILE Chi-restraints excluded: chain E9 residue 3 ILE Chi-restraints excluded: chain FC residue 9 VAL Chi-restraints excluded: chain FH residue 2 LEU Chi-restraints excluded: chain FL residue 9 VAL Chi-restraints excluded: chain FM residue 3 ILE Chi-restraints excluded: chain FN residue 8 SER Chi-restraints excluded: chain FQ residue 2 LEU Chi-restraints excluded: chain FT residue 4 ILE Chi-restraints excluded: chain FU residue 9 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 129 optimal weight: 20.0000 chunk 145 optimal weight: 20.0000 chunk 169 optimal weight: 30.0000 chunk 96 optimal weight: 9.9990 chunk 14 optimal weight: 20.0000 chunk 3 optimal weight: 20.0000 chunk 177 optimal weight: 20.0000 chunk 38 optimal weight: 7.9990 chunk 112 optimal weight: 20.0000 chunk 199 optimal weight: 9.9990 chunk 71 optimal weight: 20.0000 overall best weight: 13.5994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: O 10 HIS A7 10 HIS BP 10 HIS BT 10 HIS ** C7 10 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** DG 10 HIS DK 10 HIS EG 10 HIS ** EW 10 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** FH 10 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** FN 10 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** FQ 10 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** FZ 10 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.115081 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.094991 restraints weight = 30533.779| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.098144 restraints weight = 16779.093| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.100424 restraints weight = 11066.441| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.102040 restraints weight = 8173.053| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.103156 restraints weight = 6513.691| |-----------------------------------------------------------------------------| r_work (final): 0.3377 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7786 moved from start: 0.3890 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.053 20370 Z= 0.288 Angle : 0.836 10.135 27210 Z= 0.359 Chirality : 0.059 0.172 3840 Planarity : 0.002 0.018 3060 Dihedral : 11.821 61.716 2580 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 9.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.71 % Favored : 96.29 % Rotamer: Outliers : 8.50 % Allowed : 23.58 % Favored : 67.92 % 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 aren not related in a simple way. whole: -1.15 (0.18), residues: 2100 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.87 (0.14), residues: 2100 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.007 0.002 HIS n 10 Details of bonding type rmsd covalent geometry : bond 0.00731 (20370) covalent geometry : angle 0.83572 (27210) =============================================================================== Job complete usr+sys time: 2710.44 seconds wall clock time: 48 minutes 34.20 seconds (2914.20 seconds total)