Starting phenix.real_space_refine on Sat Sep 28 14:11:05 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5w7v_8781/09_2024/5w7v_8781.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5w7v_8781/09_2024/5w7v_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5w7v_8781/09_2024/5w7v_8781.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5w7v_8781/09_2024/5w7v_8781.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5w7v_8781/09_2024/5w7v_8781.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5w7v_8781/09_2024/5w7v_8781.cif" } resolution = 3.8 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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-filer2/raid1/xp/phenix/phenix-dev-5461/modules/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: 15.14, per 1000 atoms: 0.74 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: 4.36 Conformation dependent library (CDL) restraints added in 2.3 seconds 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: 2.59 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: 5.13 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: 0.130 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.790 Check model and map are aligned: 0.160 Set scattering table: 0.180 Process input model: 40.270 Find NCS groups from input model: 2.250 Set up NCS constraints: 0.890 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: 0.020 Load rotamer database and sin/cos tables:2.670 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 47.370 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 *********************** 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 fitting. rotamer outliers: 0 poor density : 641 time to evaluate : 2.668 Fit side-chains REVERT: C 5 LYS cc_start: 0.8198 (ptmt) cc_final: 0.7993 (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: 0.8191 (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: 0.8164 (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: 0.7709 (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: 0.6948 (mttm) REVERT: EW 3 ILE cc_start: 0.8433 (mt) cc_final: 0.8138 (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: 0.3037 time to fit residues: 299.7513 Evaluate side-chains 449 residues out of total 2400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 449 time to evaluate : 2.506 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 177 optimal weight: 10.0000 chunk 159 optimal weight: 30.0000 chunk 88 optimal weight: 8.9990 chunk 54 optimal weight: 30.0000 chunk 107 optimal weight: 4.9990 chunk 85 optimal weight: 7.9990 chunk 164 optimal weight: 30.0000 chunk 63 optimal weight: 10.0000 chunk 100 optimal weight: 30.0000 chunk 122 optimal weight: 6.9990 chunk 190 optimal weight: 0.4980 overall best weight: 5.8988 ------------------------------------------------------------------------------- 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 ** 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7231 moved from start: 0.1893 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.025 20370 Z= 0.156 Angle : 0.692 10.025 27210 Z= 0.292 Chirality : 0.058 0.140 3840 Planarity : 0.002 0.007 3060 Dihedral : 11.602 60.636 2580 Min Nonbonded Distance : 2.585 Molprobity Statistics. All-atom Clashscore : 5.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 6.00 % Allowed : 17.50 % Favored : 76.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.87 (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 HISDD 10 *********************** 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 655 residues out of total 2400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 144 poor density : 511 time to evaluate : 2.753 Fit side-chains REVERT: C 5 LYS cc_start: 0.8123 (ptmt) cc_final: 0.7911 (ptpt) REVERT: J 4 ILE cc_start: 0.8318 (OUTLIER) cc_final: 0.8113 (mp) REVERT: M 3 ILE cc_start: 0.8744 (mt) cc_final: 0.8477 (mp) REVERT: M 5 LYS cc_start: 0.7821 (mttt) cc_final: 0.7449 (mttm) REVERT: U 3 ILE cc_start: 0.7975 (mp) cc_final: 0.7744 (mm) REVERT: a 4 ILE cc_start: 0.7609 (OUTLIER) cc_final: 0.7366 (mp) REVERT: d 3 ILE cc_start: 0.8612 (mt) cc_final: 0.8255 (mp) REVERT: s 4 ILE cc_start: 0.7694 (OUTLIER) cc_final: 0.7454 (mp) REVERT: v 3 ILE cc_start: 0.8583 (mt) cc_final: 0.8306 (mp) REVERT: v 5 LYS cc_start: 0.7440 (mttt) cc_final: 0.6995 (mttm) REVERT: AD 3 ILE cc_start: 0.7895 (mp) cc_final: 0.7606 (mm) REVERT: AE 5 LYS cc_start: 0.7802 (mttt) cc_final: 0.7520 (mttm) REVERT: AK 4 ILE cc_start: 0.7521 (OUTLIER) cc_final: 0.7233 (mp) REVERT: AN 4 ILE cc_start: 0.8499 (mt) cc_final: 0.8297 (mt) REVERT: AN 5 LYS cc_start: 0.7671 (mttt) cc_final: 0.7276 (mttm) REVERT: AW 5 LYS cc_start: 0.7725 (mttm) cc_final: 0.7323 (mttm) REVERT: A2 4 ILE cc_start: 0.7576 (OUTLIER) cc_final: 0.7264 (mp) REVERT: BE 5 LYS cc_start: 0.7711 (mttt) cc_final: 0.7490 (mttm) REVERT: BK 4 ILE cc_start: 0.7538 (OUTLIER) cc_final: 0.7271 (mp) REVERT: BN 3 ILE cc_start: 0.8399 (mt) cc_final: 0.8096 (mp) REVERT: BV 5 LYS cc_start: 0.8046 (ptmt) cc_final: 0.7795 (ptpt) REVERT: BW 5 LYS cc_start: 0.7516 (mttt) cc_final: 0.7224 (mttm) REVERT: B5 5 LYS cc_start: 0.7772 (mttt) cc_final: 0.7549 (mttm) REVERT: 1 4 ILE cc_start: 0.7669 (OUTLIER) cc_final: 0.7430 (mp) REVERT: 6 2 LEU cc_start: 0.8199 (pt) cc_final: 0.7921 (pp) REVERT: 6 5 LYS cc_start: 0.7477 (mttt) cc_final: 0.7048 (mttp) REVERT: CN 2 LEU cc_start: 0.7863 (pt) cc_final: 0.7626 (pp) REVERT: CT 4 ILE cc_start: 0.7682 (OUTLIER) cc_final: 0.7462 (mp) REVERT: CW 5 LYS cc_start: 0.7558 (mttt) cc_final: 0.7053 (mttm) REVERT: C4 3 ILE cc_start: 0.8063 (mp) cc_final: 0.7767 (mm) REVERT: C5 5 LYS cc_start: 0.7551 (mttt) cc_final: 0.7139 (mttm) REVERT: DE 5 LYS cc_start: 0.7292 (mttt) cc_final: 0.6883 (mttm) REVERT: DT 4 ILE cc_start: 0.7834 (OUTLIER) cc_final: 0.7630 (mp) REVERT: D4 3 ILE cc_start: 0.7886 (mp) cc_final: 0.7600 (mm) REVERT: EB 4 ILE cc_start: 0.7568 (OUTLIER) cc_final: 0.7367 (mp) REVERT: EE 5 LYS cc_start: 0.7198 (mttt) cc_final: 0.6830 (mttm) REVERT: ET 4 ILE cc_start: 0.7673 (OUTLIER) cc_final: 0.7469 (mp) REVERT: EW 3 ILE cc_start: 0.8407 (mt) cc_final: 0.8148 (mp) REVERT: E5 5 LYS cc_start: 0.7580 (mttt) cc_final: 0.7234 (mttp) REVERT: FB 4 ILE cc_start: 0.7676 (OUTLIER) cc_final: 0.7473 (mp) REVERT: FE 3 ILE cc_start: 0.8773 (mt) cc_final: 0.8427 (mp) REVERT: FE 5 LYS cc_start: 0.8344 (mttt) cc_final: 0.7963 (mttm) REVERT: FN 2 LEU cc_start: 0.8320 (pt) cc_final: 0.6798 (mm) REVERT: FT 4 ILE cc_start: 0.7704 (OUTLIER) cc_final: 0.7485 (mp) outliers start: 144 outliers final: 69 residues processed: 557 average time/residue: 0.3006 time to fit residues: 259.1017 Evaluate side-chains 507 residues out of total 2400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 82 poor density : 425 time to evaluate : 2.703 ------------------------------------------------------------------------------- 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 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 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 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 4 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 105 optimal weight: 8.9990 chunk 59 optimal weight: 30.0000 chunk 158 optimal weight: 20.0000 chunk 129 optimal weight: 20.0000 chunk 52 optimal weight: 5.9990 chunk 191 optimal weight: 20.0000 chunk 206 optimal weight: 7.9990 chunk 170 optimal weight: 20.0000 chunk 189 optimal weight: 6.9990 chunk 65 optimal weight: 30.0000 chunk 153 optimal weight: 40.0000 overall best weight: 9.9992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 10 HIS a 10 HIS c 10 HIS l 10 HIS s 10 HIS AB 10 HIS AD 10 HIS ** AH 10 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** AQ 10 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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** BK 10 HIS ** 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** ** 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** DV 10 HIS ** 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** ** 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** ** E8 10 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** FD 10 HIS ** FE 10 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** FH 10 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** FK 10 HIS 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: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7259 moved from start: 0.2580 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.035 20370 Z= 0.226 Angle : 0.746 9.342 27210 Z= 0.321 Chirality : 0.058 0.172 3840 Planarity : 0.002 0.008 3060 Dihedral : 11.660 59.796 2580 Min Nonbonded Distance : 2.585 Molprobity Statistics. All-atom Clashscore : 7.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.48 % Favored : 99.52 % Rotamer: Outliers : 8.38 % Allowed : 18.54 % Favored : 73.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.81 (0.16), residues: 2100 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.37 (0.12), residues: 2100 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HISCF 10 *********************** 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 690 residues out of total 2400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 201 poor density : 489 time to evaluate : 2.725 Fit side-chains revert: symmetry clash REVERT: M 5 LYS cc_start: 0.7884 (mttt) cc_final: 0.7552 (mttm) REVERT: a 4 ILE cc_start: 0.7580 (OUTLIER) cc_final: 0.7345 (mp) REVERT: j 5 LYS cc_start: 0.7972 (mttt) cc_final: 0.7599 (mttp) REVERT: s 4 ILE cc_start: 0.7544 (OUTLIER) cc_final: 0.7298 (mp) REVERT: v 5 LYS cc_start: 0.7522 (mttt) cc_final: 0.7289 (mttm) REVERT: x 3 ILE cc_start: 0.7719 (mt) cc_final: 0.7515 (mt) REVERT: AK 4 ILE cc_start: 0.7537 (OUTLIER) cc_final: 0.7217 (mp) REVERT: AN 5 LYS cc_start: 0.7677 (mttt) cc_final: 0.7266 (mttm) REVERT: AT 5 LYS cc_start: 0.7895 (mttt) cc_final: 0.7482 (mttp) REVERT: A2 4 ILE cc_start: 0.7548 (OUTLIER) cc_final: 0.7248 (mp) REVERT: A5 5 LYS cc_start: 0.7730 (mttm) cc_final: 0.7429 (mttm) REVERT: BB 5 LYS cc_start: 0.7808 (mttt) cc_final: 0.7372 (mttp) REVERT: BK 4 ILE cc_start: 0.7431 (OUTLIER) cc_final: 0.7109 (mp) REVERT: BT 5 LYS cc_start: 0.7581 (mttt) cc_final: 0.7296 (mttp) REVERT: BW 5 LYS cc_start: 0.7550 (mttt) cc_final: 0.7330 (mttm) REVERT: B5 5 LYS cc_start: 0.7683 (mttt) cc_final: 0.7474 (mttm) REVERT: 1 4 ILE cc_start: 0.7628 (OUTLIER) cc_final: 0.7352 (mp) REVERT: 6 5 LYS cc_start: 0.7391 (mttt) cc_final: 0.6866 (mttm) REVERT: CK 5 LYS cc_start: 0.7829 (mttt) cc_final: 0.7412 (mttp) REVERT: CR 5 LYS cc_start: 0.8599 (OUTLIER) cc_final: 0.8251 (mtmm) REVERT: CT 4 ILE cc_start: 0.7651 (OUTLIER) cc_final: 0.7398 (mp) REVERT: CW 5 LYS cc_start: 0.7560 (mttt) cc_final: 0.7053 (mttm) REVERT: DE 5 LYS cc_start: 0.7392 (mttt) cc_final: 0.6956 (mttm) REVERT: DT 4 ILE cc_start: 0.7788 (OUTLIER) cc_final: 0.7564 (mp) REVERT: DW 2 LEU cc_start: 0.8310 (pp) cc_final: 0.7983 (pt) REVERT: DW 3 ILE cc_start: 0.8569 (mt) cc_final: 0.8271 (mp) REVERT: EE 5 LYS cc_start: 0.7337 (mttt) cc_final: 0.6899 (mttm) REVERT: EN 2 LEU cc_start: 0.8274 (pt) cc_final: 0.8049 (pp) REVERT: ET 4 ILE cc_start: 0.7658 (OUTLIER) cc_final: 0.7444 (mp) REVERT: EW 2 LEU cc_start: 0.8225 (pt) cc_final: 0.7985 (pp) REVERT: E5 5 LYS cc_start: 0.7551 (mttt) cc_final: 0.7203 (mttp) REVERT: FB 4 ILE cc_start: 0.7639 (OUTLIER) cc_final: 0.7409 (mp) REVERT: FE 3 ILE cc_start: 0.8792 (mt) cc_final: 0.8476 (mp) REVERT: FE 5 LYS cc_start: 0.8325 (mttt) cc_final: 0.7834 (mttm) REVERT: FT 4 ILE cc_start: 0.7773 (OUTLIER) cc_final: 0.7556 (mp) outliers start: 201 outliers final: 112 residues processed: 560 average time/residue: 0.2862 time to fit residues: 251.1960 Evaluate side-chains 564 residues out of total 2400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 124 poor density : 440 time to evaluate : 1.986 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 VAL 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 K residue 9 VAL 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 Y residue 7 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 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 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 y residue 7 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 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 AQ residue 2 LEU 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 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 BF residue 9 VAL Chi-restraints excluded: chain BH residue 2 LEU 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 BU residue 9 VAL Chi-restraints excluded: chain BW residue 8 SER Chi-restraints excluded: chain BX residue 9 VAL 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 CE residue 8 SER Chi-restraints excluded: chain CH residue 2 LEU Chi-restraints excluded: chain CI residue 3 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 7 residue 2 LEU 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 C3 residue 9 VAL Chi-restraints excluded: chain C6 residue 9 VAL Chi-restraints excluded: chain C8 residue 7 ILE Chi-restraints excluded: chain C9 residue 3 ILE Chi-restraints excluded: chain DC residue 9 VAL Chi-restraints excluded: chain DH residue 2 LEU 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 DO residue 9 VAL Chi-restraints excluded: chain DQ residue 2 LEU 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 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 D7 residue 8 SER Chi-restraints excluded: chain D9 residue 3 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 EP residue 8 SER 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 7 ILE Chi-restraints excluded: chain E9 residue 3 ILE Chi-restraints excluded: chain FB residue 4 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 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 4 ILE 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 188 optimal weight: 10.0000 chunk 143 optimal weight: 8.9990 chunk 99 optimal weight: 30.0000 chunk 21 optimal weight: 20.0000 chunk 91 optimal weight: 20.0000 chunk 128 optimal weight: 20.0000 chunk 191 optimal weight: 20.0000 chunk 202 optimal weight: 20.0000 chunk 100 optimal weight: 10.0000 chunk 181 optimal weight: 7.9990 chunk 54 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: ** M 10 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** a 10 HIS ** d 10 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** j 10 HIS s 10 HIS ** v 10 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** AE 10 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** AN 10 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** AV 10 HIS ** AW 10 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A5 10 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** BB 10 HIS ** BE 10 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** BH 10 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** BK 10 HIS ** BN 10 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** BT 10 HIS ** BW 10 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B8 10 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** CB 10 HIS ** CE 10 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** CK 10 HIS CM 10 HIS ** CN 10 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** CQ 10 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C5 10 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** DE 10 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** DH 10 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** DK 10 HIS DV 10 HIS ** D8 10 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** EN 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 ** 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** ** 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7263 moved from start: 0.3028 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.041 20370 Z= 0.247 Angle : 0.765 10.362 27210 Z= 0.328 Chirality : 0.059 0.169 3840 Planarity : 0.002 0.008 3060 Dihedral : 11.835 58.364 2580 Min Nonbonded Distance : 2.591 Molprobity Statistics. All-atom Clashscore : 7.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 9.67 % Allowed : 20.12 % Favored : 70.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.69 (0.17), residues: 2100 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.28 (0.13), residues: 2100 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.007 0.002 HISCB 10 *********************** 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 709 residues out of total 2400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 232 poor density : 477 time to evaluate : 2.497 Fit side-chains REVERT: A 5 LYS cc_start: 0.7992 (mttt) cc_final: 0.7571 (mttp) REVERT: M 5 LYS cc_start: 0.7876 (mttt) cc_final: 0.7496 (mttm) REVERT: S 5 LYS cc_start: 0.8022 (mttt) cc_final: 0.7794 (mttp) REVERT: U 3 ILE cc_start: 0.7983 (OUTLIER) cc_final: 0.7524 (mp) REVERT: V 2 LEU cc_start: 0.8410 (pt) cc_final: 0.7918 (tt) REVERT: V 10 HIS cc_start: 0.8182 (t70) cc_final: 0.7981 (t-90) REVERT: a 4 ILE cc_start: 0.7498 (OUTLIER) cc_final: 0.7238 (mp) REVERT: j 5 LYS cc_start: 0.8143 (mttt) cc_final: 0.7820 (mttp) REVERT: m 5 LYS cc_start: 0.7728 (mttm) cc_final: 0.7517 (mttm) REVERT: q 5 LYS cc_start: 0.8851 (OUTLIER) cc_final: 0.8635 (mtmm) REVERT: s 4 ILE cc_start: 0.7535 (OUTLIER) cc_final: 0.7298 (mp) REVERT: v 5 LYS cc_start: 0.7453 (mttt) cc_final: 0.7139 (mttm) REVERT: x 3 ILE cc_start: 0.7672 (mt) cc_final: 0.7438 (mt) REVERT: AB 5 LYS cc_start: 0.7939 (mttt) cc_final: 0.7405 (mttp) REVERT: AK 4 ILE cc_start: 0.7501 (OUTLIER) cc_final: 0.7189 (mp) REVERT: AN 5 LYS cc_start: 0.7488 (mttt) cc_final: 0.7086 (mttm) REVERT: AT 5 LYS cc_start: 0.7928 (mttt) cc_final: 0.7543 (mttp) REVERT: A2 4 ILE cc_start: 0.7465 (OUTLIER) cc_final: 0.7169 (mp) REVERT: A5 5 LYS cc_start: 0.7671 (mttm) cc_final: 0.7414 (mttm) REVERT: BB 5 LYS cc_start: 0.7822 (mttt) cc_final: 0.7426 (mttp) REVERT: BE 5 LYS cc_start: 0.7767 (mttt) cc_final: 0.7464 (mttm) REVERT: BK 4 ILE cc_start: 0.7450 (OUTLIER) cc_final: 0.7134 (mp) REVERT: BN 3 ILE cc_start: 0.8570 (mt) cc_final: 0.8349 (mp) REVERT: BT 5 LYS cc_start: 0.7626 (mttt) cc_final: 0.7359 (mttp) REVERT: BW 5 LYS cc_start: 0.7556 (mttt) cc_final: 0.7218 (mttm) REVERT: B5 5 LYS cc_start: 0.7735 (mttt) cc_final: 0.7491 (mttm) REVERT: CE 5 LYS cc_start: 0.7738 (mttm) cc_final: 0.7535 (mttm) REVERT: 1 4 ILE cc_start: 0.7570 (OUTLIER) cc_final: 0.7301 (mp) REVERT: 6 5 LYS cc_start: 0.7349 (mttt) cc_final: 0.6801 (mttm) REVERT: CN 2 LEU cc_start: 0.7855 (pt) cc_final: 0.7614 (pp) REVERT: CR 5 LYS cc_start: 0.8774 (OUTLIER) cc_final: 0.8342 (mtmm) REVERT: CW 5 LYS cc_start: 0.7563 (mttt) cc_final: 0.7048 (mttm) REVERT: DE 5 LYS cc_start: 0.7340 (mttt) cc_final: 0.6872 (mttm) REVERT: DT 4 ILE cc_start: 0.7755 (OUTLIER) cc_final: 0.7528 (mp) REVERT: DW 2 LEU cc_start: 0.8306 (pp) cc_final: 0.7964 (pt) REVERT: DW 3 ILE cc_start: 0.8592 (mt) cc_final: 0.8293 (mp) REVERT: EE 5 LYS cc_start: 0.7287 (mttt) cc_final: 0.6902 (mttm) REVERT: E5 5 LYS cc_start: 0.7512 (mttt) cc_final: 0.7150 (mttp) REVERT: FB 4 ILE cc_start: 0.7691 (OUTLIER) cc_final: 0.7458 (mp) REVERT: FE 3 ILE cc_start: 0.8790 (mt) cc_final: 0.8460 (mp) REVERT: FE 5 LYS cc_start: 0.8326 (mttt) cc_final: 0.7857 (mttm) REVERT: FT 4 ILE cc_start: 0.7738 (OUTLIER) cc_final: 0.7531 (mp) outliers start: 232 outliers final: 147 residues processed: 568 average time/residue: 0.2969 time to fit residues: 262.8207 Evaluate side-chains 600 residues out of total 2400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 159 poor density : 441 time to evaluate : 1.969 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 SER Chi-restraints excluded: chain A residue 9 VAL 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 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 P residue 2 LEU Chi-restraints excluded: chain P residue 7 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 U residue 3 ILE 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 Z residue 3 ILE Chi-restraints excluded: chain Z residue 5 LYS 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 f residue 8 SER 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 AK residue 4 ILE Chi-restraints excluded: chain AL residue 9 VAL 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 BG residue 4 ILE Chi-restraints excluded: chain BH residue 2 LEU Chi-restraints excluded: chain BH residue 7 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 BQ residue 2 LEU Chi-restraints excluded: chain BQ residue 7 ILE Chi-restraints excluded: chain BR residue 2 LEU 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 2 LEU Chi-restraints excluded: chain B0 residue 3 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 3 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 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 C5 residue 8 SER Chi-restraints excluded: chain C6 residue 9 VAL Chi-restraints excluded: chain C9 residue 3 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 DO residue 9 VAL Chi-restraints excluded: chain DQ residue 2 LEU Chi-restraints excluded: chain DQ residue 7 ILE 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 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 7 ILE Chi-restraints excluded: chain D9 residue 3 ILE Chi-restraints excluded: chain EB residue 8 SER 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 EK residue 4 ILE Chi-restraints excluded: chain EL residue 9 VAL Chi-restraints excluded: chain EP residue 8 SER Chi-restraints excluded: chain EQ residue 2 LEU Chi-restraints excluded: chain EQ residue 7 ILE Chi-restraints excluded: chain ER residue 3 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 E9 residue 3 ILE Chi-restraints excluded: chain FB residue 4 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 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 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 169 optimal weight: 20.0000 chunk 115 optimal weight: 20.0000 chunk 2 optimal weight: 30.0000 chunk 151 optimal weight: 30.0000 chunk 83 optimal weight: 30.0000 chunk 173 optimal weight: 20.0000 chunk 140 optimal weight: 20.0000 chunk 0 optimal weight: 20.0000 chunk 103 optimal weight: 20.0000 chunk 182 optimal weight: 7.9990 chunk 51 optimal weight: 10.0000 overall best weight: 15.5998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** M 10 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** a 10 HIS d 10 HIS s 10 HIS ** v 10 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** AN 10 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** AW 10 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A5 10 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** BE 10 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** BN 10 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** BW 10 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** CE 10 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** CN 10 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C5 10 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** DE 10 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** DN 10 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** EK 10 HIS EM 10 HIS ** EN 10 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** EW 10 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E5 10 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** FD 10 HIS ** 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** ** 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: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7277 moved from start: 0.3403 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.052 20370 Z= 0.323 Angle : 0.851 10.180 27210 Z= 0.370 Chirality : 0.060 0.163 3840 Planarity : 0.003 0.013 3060 Dihedral : 12.129 57.517 2580 Min Nonbonded Distance : 2.594 Molprobity Statistics. All-atom Clashscore : 10.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.90 % Favored : 96.10 % Rotamer: Outliers : 10.38 % Allowed : 21.12 % Favored : 68.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.93 (0.17), residues: 2100 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.46 (0.13), residues: 2100 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.018 0.002 HIS a 10 *********************** 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 724 residues out of total 2400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 249 poor density : 475 time to evaluate : 2.645 Fit side-chains REVERT: A 5 LYS cc_start: 0.8084 (mttt) cc_final: 0.7641 (mttp) REVERT: M 5 LYS cc_start: 0.7788 (mttt) cc_final: 0.7438 (mttm) REVERT: S 5 LYS cc_start: 0.8031 (mttt) cc_final: 0.7814 (mttp) REVERT: U 3 ILE cc_start: 0.7982 (OUTLIER) cc_final: 0.7509 (mp) REVERT: V 2 LEU cc_start: 0.8402 (pt) cc_final: 0.7920 (tt) REVERT: a 4 ILE cc_start: 0.7410 (OUTLIER) cc_final: 0.7129 (mp) REVERT: j 5 LYS cc_start: 0.8139 (mttt) cc_final: 0.7810 (mttp) REVERT: m 5 LYS cc_start: 0.7674 (mttm) cc_final: 0.7422 (mttm) REVERT: q 5 LYS cc_start: 0.8903 (OUTLIER) cc_final: 0.8507 (mtmm) REVERT: s 4 ILE cc_start: 0.7510 (OUTLIER) cc_final: 0.7257 (mp) REVERT: v 5 LYS cc_start: 0.7404 (mttt) cc_final: 0.7157 (mttm) REVERT: AB 5 LYS cc_start: 0.7964 (mttt) cc_final: 0.7427 (mttp) REVERT: AD 3 ILE cc_start: 0.7768 (OUTLIER) cc_final: 0.7203 (mp) REVERT: AE 5 LYS cc_start: 0.7765 (mttt) cc_final: 0.7283 (mttm) REVERT: AK 4 ILE cc_start: 0.7541 (OUTLIER) cc_final: 0.7245 (mp) REVERT: AN 5 LYS cc_start: 0.7486 (mttt) cc_final: 0.7190 (mttm) REVERT: AT 5 LYS cc_start: 0.8008 (mttt) cc_final: 0.7548 (mttp) REVERT: AV 3 ILE cc_start: 0.7620 (OUTLIER) cc_final: 0.7075 (mp) REVERT: AW 5 LYS cc_start: 0.7869 (mttm) cc_final: 0.7643 (mttm) REVERT: A2 4 ILE cc_start: 0.7451 (OUTLIER) cc_final: 0.7156 (mp) REVERT: A5 5 LYS cc_start: 0.7675 (mttm) cc_final: 0.7354 (mttm) REVERT: BB 5 LYS cc_start: 0.7846 (mttt) cc_final: 0.7439 (mttp) REVERT: BE 5 LYS cc_start: 0.7740 (mttt) cc_final: 0.7300 (mttp) REVERT: BK 4 ILE cc_start: 0.7383 (OUTLIER) cc_final: 0.7067 (mp) REVERT: BN 3 ILE cc_start: 0.8527 (mt) cc_final: 0.8306 (mp) REVERT: BT 5 LYS cc_start: 0.7710 (mttt) cc_final: 0.7449 (mttp) REVERT: BV 3 ILE cc_start: 0.7872 (OUTLIER) cc_final: 0.7366 (mp) REVERT: BW 5 LYS cc_start: 0.7707 (mttt) cc_final: 0.7316 (mttm) REVERT: B5 5 LYS cc_start: 0.7568 (mttt) cc_final: 0.7356 (mttm) REVERT: CD 3 ILE cc_start: 0.7840 (OUTLIER) cc_final: 0.7311 (mp) REVERT: 1 4 ILE cc_start: 0.7571 (OUTLIER) cc_final: 0.7323 (mp) REVERT: 6 5 LYS cc_start: 0.7323 (mttt) cc_final: 0.6787 (mttm) REVERT: CK 5 LYS cc_start: 0.7745 (mttt) cc_final: 0.7461 (mttp) REVERT: CR 5 LYS cc_start: 0.8861 (OUTLIER) cc_final: 0.8366 (mtmm) REVERT: CW 5 LYS cc_start: 0.7541 (mttt) cc_final: 0.7058 (mttm) REVERT: C5 5 LYS cc_start: 0.7524 (mttt) cc_final: 0.7059 (mttm) REVERT: DE 5 LYS cc_start: 0.7504 (mttt) cc_final: 0.7025 (mttm) REVERT: DM 3 ILE cc_start: 0.7792 (OUTLIER) cc_final: 0.7194 (mp) REVERT: DT 4 ILE cc_start: 0.7655 (OUTLIER) cc_final: 0.7400 (mp) REVERT: DW 3 ILE cc_start: 0.8638 (mt) cc_final: 0.8378 (mp) REVERT: D4 3 ILE cc_start: 0.7820 (OUTLIER) cc_final: 0.7262 (mp) REVERT: EE 5 LYS cc_start: 0.7257 (mttt) cc_final: 0.6814 (mttm) REVERT: E4 3 ILE cc_start: 0.7965 (OUTLIER) cc_final: 0.7430 (mp) REVERT: E5 5 LYS cc_start: 0.7670 (mttt) cc_final: 0.7255 (mttp) REVERT: FB 4 ILE cc_start: 0.7661 (OUTLIER) cc_final: 0.7426 (mp) REVERT: FE 5 LYS cc_start: 0.8251 (mttt) cc_final: 0.7822 (mttm) REVERT: FM 3 ILE cc_start: 0.8291 (OUTLIER) cc_final: 0.7730 (mp) REVERT: FT 4 ILE cc_start: 0.7751 (OUTLIER) cc_final: 0.7536 (mp) outliers start: 249 outliers final: 177 residues processed: 577 average time/residue: 0.2876 time to fit residues: 260.6319 Evaluate side-chains 656 residues out of total 2400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 197 poor density : 459 time to evaluate : 3.272 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 SER 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 H residue 2 LEU 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 P residue 2 LEU Chi-restraints excluded: chain P residue 7 ILE Chi-restraints excluded: chain P residue 9 VAL Chi-restraints excluded: chain Q 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 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 Y residue 9 VAL Chi-restraints excluded: chain Z residue 3 ILE Chi-restraints excluded: chain Z residue 5 LYS 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 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 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 q residue 5 LYS Chi-restraints excluded: chain s residue 4 ILE Chi-restraints excluded: chain t residue 9 VAL Chi-restraints excluded: chain u residue 5 LYS 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 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 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 AQ residue 9 VAL 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 A8 residue 9 VAL 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 BG residue 4 ILE 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 BR residue 2 LEU 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 B0 residue 2 LEU Chi-restraints excluded: chain B0 residue 3 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 CG residue 4 ILE 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 3 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 7 residue 9 VAL Chi-restraints excluded: chain CK residue 4 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 CU residue 9 VAL Chi-restraints excluded: chain CW residue 4 ILE 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 C9 residue 3 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 DH residue 9 VAL Chi-restraints excluded: chain DK 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 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 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 D9 residue 3 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 EK residue 4 ILE Chi-restraints excluded: chain EL residue 9 VAL Chi-restraints excluded: chain EP residue 8 SER 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 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 FB residue 4 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 FK residue 1 ASP 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 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 68 optimal weight: 0.9990 chunk 182 optimal weight: 8.9990 chunk 40 optimal weight: 8.9990 chunk 119 optimal weight: 9.9990 chunk 50 optimal weight: 0.9980 chunk 203 optimal weight: 4.9990 chunk 168 optimal weight: 5.9990 chunk 94 optimal weight: 20.0000 chunk 16 optimal weight: 20.0000 chunk 67 optimal weight: 8.9990 chunk 106 optimal weight: 4.9990 overall best weight: 3.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** M 10 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** a 10 HIS v 10 HIS ** AN 10 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** AW 10 HIS ** A5 10 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** BD 10 HIS ** BE 10 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** BN 10 HIS ** BW 10 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** CE 10 HIS ** CN 10 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C5 10 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** DE 10 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** DN 10 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** EW 10 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 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 Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7225 moved from start: 0.3505 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 20370 Z= 0.114 Angle : 0.653 9.728 27210 Z= 0.270 Chirality : 0.058 0.170 3840 Planarity : 0.001 0.012 3060 Dihedral : 11.056 58.753 2580 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 6.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.67 % Favored : 98.33 % Rotamer: Outliers : 8.33 % Allowed : 23.50 % Favored : 68.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.22 (0.18), residues: 2100 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.92 (0.13), residues: 2100 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.015 0.001 HIS a 10 *********************** 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 643 residues out of total 2400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 200 poor density : 443 time to evaluate : 2.646 Fit side-chains REVERT: A 5 LYS cc_start: 0.8003 (mttt) cc_final: 0.7572 (mttp) REVERT: D 2 LEU cc_start: 0.8448 (pt) cc_final: 0.8118 (tt) REVERT: M 2 LEU cc_start: 0.8278 (pt) cc_final: 0.7742 (tt) REVERT: M 5 LYS cc_start: 0.7741 (mttt) cc_final: 0.7504 (mttm) REVERT: S 5 LYS cc_start: 0.7912 (mttt) cc_final: 0.7502 (mttp) REVERT: V 2 LEU cc_start: 0.8472 (pt) cc_final: 0.8030 (tt) REVERT: a 4 ILE cc_start: 0.7521 (OUTLIER) cc_final: 0.7265 (mp) REVERT: s 4 ILE cc_start: 0.7471 (OUTLIER) cc_final: 0.7207 (mp) REVERT: v 5 LYS cc_start: 0.7422 (mttt) cc_final: 0.7139 (mttm) REVERT: AD 3 ILE cc_start: 0.7650 (OUTLIER) cc_final: 0.7102 (mp) REVERT: AE 5 LYS cc_start: 0.7670 (mttt) cc_final: 0.7338 (mttm) REVERT: AK 4 ILE cc_start: 0.7447 (OUTLIER) cc_final: 0.7149 (mp) REVERT: AN 5 LYS cc_start: 0.7263 (mttt) cc_final: 0.6931 (mttm) REVERT: AV 3 ILE cc_start: 0.7582 (OUTLIER) cc_final: 0.7045 (mp) REVERT: AW 5 LYS cc_start: 0.7736 (mttm) cc_final: 0.7529 (mttm) REVERT: A2 4 ILE cc_start: 0.7512 (OUTLIER) cc_final: 0.7219 (mp) REVERT: A5 5 LYS cc_start: 0.7691 (mttm) cc_final: 0.7438 (mttm) REVERT: BE 5 LYS cc_start: 0.7757 (mttt) cc_final: 0.7475 (mttm) REVERT: BK 4 ILE cc_start: 0.7336 (OUTLIER) cc_final: 0.7007 (mp) REVERT: BN 3 ILE cc_start: 0.8456 (mt) cc_final: 0.8222 (mp) REVERT: BT 5 LYS cc_start: 0.7593 (mttt) cc_final: 0.7340 (mttp) REVERT: BW 5 LYS cc_start: 0.7581 (mttt) cc_final: 0.7259 (mttm) REVERT: B5 5 LYS cc_start: 0.7637 (mttt) cc_final: 0.7403 (mttm) REVERT: CD 1 ASP cc_start: 0.7131 (m-30) cc_final: 0.6793 (m-30) REVERT: CD 3 ILE cc_start: 0.7855 (OUTLIER) cc_final: 0.7318 (mp) REVERT: CE 3 ILE cc_start: 0.8412 (mt) cc_final: 0.8078 (mp) REVERT: 1 4 ILE cc_start: 0.7570 (OUTLIER) cc_final: 0.7334 (mp) REVERT: 6 5 LYS cc_start: 0.7383 (mttt) cc_final: 0.6931 (mttm) REVERT: CN 2 LEU cc_start: 0.7763 (pt) cc_final: 0.7513 (pp) REVERT: CR 5 LYS cc_start: 0.8844 (OUTLIER) cc_final: 0.8616 (mtmm) REVERT: CW 5 LYS cc_start: 0.7421 (mttt) cc_final: 0.6981 (mttm) REVERT: C5 5 LYS cc_start: 0.7515 (mttt) cc_final: 0.7061 (mttm) REVERT: DE 5 LYS cc_start: 0.7365 (mttt) cc_final: 0.6956 (mttm) REVERT: DM 3 ILE cc_start: 0.7802 (OUTLIER) cc_final: 0.7259 (mp) REVERT: DM 5 LYS cc_start: 0.7958 (ptmt) cc_final: 0.7757 (ptpt) REVERT: DT 4 ILE cc_start: 0.7733 (OUTLIER) cc_final: 0.7486 (mp) REVERT: DW 2 LEU cc_start: 0.8069 (pp) cc_final: 0.7843 (pt) REVERT: DW 3 ILE cc_start: 0.8636 (mt) cc_final: 0.8405 (mp) REVERT: D4 3 ILE cc_start: 0.7860 (OUTLIER) cc_final: 0.7336 (mp) REVERT: EE 5 LYS cc_start: 0.7151 (mttt) cc_final: 0.6821 (mttm) REVERT: EM 3 ILE cc_start: 0.7935 (OUTLIER) cc_final: 0.7482 (mp) REVERT: E4 3 ILE cc_start: 0.7989 (OUTLIER) cc_final: 0.7724 (mm) REVERT: E5 3 ILE cc_start: 0.8389 (mt) cc_final: 0.8122 (mp) REVERT: E5 5 LYS cc_start: 0.7559 (mttt) cc_final: 0.7244 (mttp) REVERT: FE 2 LEU cc_start: 0.8323 (pp) cc_final: 0.6635 (mm) REVERT: FE 5 LYS cc_start: 0.8214 (mttt) cc_final: 0.7793 (mttm) REVERT: FN 2 LEU cc_start: 0.8349 (pt) cc_final: 0.6587 (mm) outliers start: 200 outliers final: 128 residues processed: 517 average time/residue: 0.2886 time to fit residues: 234.0001 Evaluate side-chains 559 residues out of total 2400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 143 poor density : 416 time to evaluate : 2.406 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A 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 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 9 VAL 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 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 AC residue 9 VAL Chi-restraints excluded: chain AD residue 3 ILE Chi-restraints excluded: chain AF residue 9 VAL Chi-restraints excluded: chain AH residue 2 LEU 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 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 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 2 LEU Chi-restraints excluded: chain BZ residue 9 VAL Chi-restraints excluded: chain B0 residue 2 LEU 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 3 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 6 residue 8 SER 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 CU residue 9 VAL Chi-restraints excluded: chain CW residue 4 ILE 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 DC residue 9 VAL Chi-restraints excluded: chain DH residue 2 LEU Chi-restraints excluded: chain DH residue 9 VAL Chi-restraints excluded: chain DK 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 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 D8 residue 2 LEU Chi-restraints excluded: chain D8 residue 9 VAL 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 EM residue 3 ILE Chi-restraints excluded: chain EQ residue 7 ILE Chi-restraints excluded: chain EQ residue 9 VAL 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 7 ILE Chi-restraints excluded: chain FC residue 9 VAL Chi-restraints excluded: chain FF 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 8 SER Chi-restraints excluded: chain FU residue 9 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 195 optimal weight: 20.0000 chunk 22 optimal weight: 10.0000 chunk 115 optimal weight: 30.0000 chunk 148 optimal weight: 3.9990 chunk 114 optimal weight: 30.0000 chunk 171 optimal weight: 10.0000 chunk 113 optimal weight: 20.0000 chunk 202 optimal weight: 20.0000 chunk 126 optimal weight: 5.9990 chunk 123 optimal weight: 10.0000 chunk 93 optimal weight: 7.9990 overall best weight: 7.5994 ------------------------------------------------------------------------------- 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 ** AN 10 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** AW 10 HIS ** A5 10 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** BE 10 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** BW 10 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C5 10 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** DN 10 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** EW 10 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E5 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** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7247 moved from start: 0.3603 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 20370 Z= 0.178 Angle : 0.715 10.843 27210 Z= 0.298 Chirality : 0.058 0.185 3840 Planarity : 0.002 0.016 3060 Dihedral : 11.190 59.836 2580 Min Nonbonded Distance : 2.571 Molprobity Statistics. All-atom Clashscore : 7.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 8.33 % Allowed : 24.25 % Favored : 67.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.13 (0.18), residues: 2100 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.85 (0.14), residues: 2100 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HISAF 10 *********************** 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 635 residues out of total 2400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 200 poor density : 435 time to evaluate : 2.432 Fit side-chains REVERT: A 5 LYS cc_start: 0.7985 (mttt) cc_final: 0.7582 (mttp) REVERT: D 2 LEU cc_start: 0.8430 (pt) cc_final: 0.8146 (tt) REVERT: M 2 LEU cc_start: 0.8281 (pt) cc_final: 0.7790 (tt) REVERT: M 5 LYS cc_start: 0.7670 (mttt) cc_final: 0.7440 (mttm) REVERT: S 5 LYS cc_start: 0.8025 (mttt) cc_final: 0.7600 (mttp) REVERT: V 2 LEU cc_start: 0.8440 (pt) cc_final: 0.8021 (tt) REVERT: a 4 ILE cc_start: 0.7481 (OUTLIER) cc_final: 0.7206 (mp) REVERT: j 5 LYS cc_start: 0.7960 (mttt) cc_final: 0.7491 (mttp) REVERT: s 4 ILE cc_start: 0.7439 (OUTLIER) cc_final: 0.7179 (mp) REVERT: v 5 LYS cc_start: 0.7462 (mttt) cc_final: 0.7185 (mttm) REVERT: AB 5 LYS cc_start: 0.7766 (mttt) cc_final: 0.7283 (mttp) REVERT: AD 3 ILE cc_start: 0.7723 (OUTLIER) cc_final: 0.7163 (mp) REVERT: AE 5 LYS cc_start: 0.7630 (mttt) cc_final: 0.7269 (mttm) REVERT: AK 4 ILE cc_start: 0.7428 (OUTLIER) cc_final: 0.7146 (mp) REVERT: AN 5 LYS cc_start: 0.7320 (mttt) cc_final: 0.7045 (mttm) REVERT: AV 3 ILE cc_start: 0.7608 (OUTLIER) cc_final: 0.7061 (mp) REVERT: AW 5 LYS cc_start: 0.7668 (mttm) cc_final: 0.7449 (mttm) REVERT: A2 4 ILE cc_start: 0.7406 (OUTLIER) cc_final: 0.7115 (mp) REVERT: A5 5 LYS cc_start: 0.7686 (mttm) cc_final: 0.7419 (mttm) REVERT: BB 5 LYS cc_start: 0.7670 (mttt) cc_final: 0.7305 (mttp) REVERT: BE 5 LYS cc_start: 0.7661 (mttt) cc_final: 0.7332 (mttp) REVERT: BK 4 ILE cc_start: 0.7282 (OUTLIER) cc_final: 0.6956 (mp) REVERT: BN 3 ILE cc_start: 0.8533 (mt) cc_final: 0.8298 (mp) REVERT: BT 5 LYS cc_start: 0.7608 (mttt) cc_final: 0.7364 (mttp) REVERT: BV 3 ILE cc_start: 0.7882 (OUTLIER) cc_final: 0.7379 (mp) REVERT: BW 5 LYS cc_start: 0.7576 (mttt) cc_final: 0.7286 (mttm) REVERT: B5 5 LYS cc_start: 0.7547 (mttt) cc_final: 0.7299 (mttm) REVERT: CD 1 ASP cc_start: 0.7133 (m-30) cc_final: 0.6789 (m-30) REVERT: CD 3 ILE cc_start: 0.7852 (OUTLIER) cc_final: 0.7325 (mp) REVERT: CE 3 ILE cc_start: 0.8549 (mt) cc_final: 0.8143 (mp) REVERT: 1 4 ILE cc_start: 0.7536 (OUTLIER) cc_final: 0.7297 (mp) REVERT: 6 2 LEU cc_start: 0.8260 (pt) cc_final: 0.8015 (pp) REVERT: 6 5 LYS cc_start: 0.7276 (mttt) cc_final: 0.6800 (mttm) REVERT: CK 5 LYS cc_start: 0.7762 (mttt) cc_final: 0.7223 (mttp) REVERT: CN 2 LEU cc_start: 0.7820 (pt) cc_final: 0.7581 (pp) REVERT: CR 5 LYS cc_start: 0.8857 (OUTLIER) cc_final: 0.8572 (mtmm) REVERT: CW 5 LYS cc_start: 0.7389 (mttt) cc_final: 0.6943 (mttm) REVERT: C5 5 LYS cc_start: 0.7532 (mttt) cc_final: 0.7098 (mttm) REVERT: DE 5 LYS cc_start: 0.7423 (mttt) cc_final: 0.6960 (mttm) REVERT: DM 3 ILE cc_start: 0.7802 (OUTLIER) cc_final: 0.7236 (mp) REVERT: DT 4 ILE cc_start: 0.7706 (OUTLIER) cc_final: 0.7463 (mp) REVERT: DW 3 ILE cc_start: 0.8698 (mt) cc_final: 0.8449 (mp) REVERT: D4 3 ILE cc_start: 0.7805 (OUTLIER) cc_final: 0.7241 (mp) REVERT: D5 2 LEU cc_start: 0.7924 (pt) cc_final: 0.7624 (pp) REVERT: EE 5 LYS cc_start: 0.7150 (mttt) cc_final: 0.6774 (mttm) REVERT: EK 5 LYS cc_start: 0.7797 (mttt) cc_final: 0.7438 (mttp) REVERT: E4 3 ILE cc_start: 0.7996 (OUTLIER) cc_final: 0.7742 (mm) REVERT: E5 5 LYS cc_start: 0.7401 (mttt) cc_final: 0.7037 (mttp) REVERT: FE 2 LEU cc_start: 0.8304 (pp) cc_final: 0.6662 (mm) REVERT: FE 5 LYS cc_start: 0.8231 (mttt) cc_final: 0.7791 (mttm) REVERT: FM 3 ILE cc_start: 0.8321 (OUTLIER) cc_final: 0.7767 (mp) REVERT: FT 4 ILE cc_start: 0.7740 (OUTLIER) cc_final: 0.7532 (mp) outliers start: 200 outliers final: 149 residues processed: 499 average time/residue: 0.2958 time to fit residues: 232.2138 Evaluate side-chains 596 residues out of total 2400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 166 poor density : 430 time to evaluate : 2.571 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A 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 P residue 2 LEU Chi-restraints excluded: chain S residue 8 SER 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 Y residue 9 VAL Chi-restraints excluded: chain Z residue 5 LYS 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 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 7 ILE Chi-restraints excluded: chain y residue 9 VAL 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 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 A8 residue 9 VAL 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 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 B3 residue 9 VAL Chi-restraints excluded: chain B5 residue 2 LEU 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 3 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 6 residue 8 SER 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 CU residue 9 VAL Chi-restraints excluded: chain CW residue 4 ILE 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 DC residue 9 VAL Chi-restraints excluded: chain DH residue 2 LEU Chi-restraints excluded: chain DH residue 9 VAL Chi-restraints excluded: chain DK 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 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 D8 residue 2 LEU Chi-restraints excluded: chain D8 residue 9 VAL 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 EQ residue 9 VAL 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 1 ASP 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 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 Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 125 optimal weight: 0.0000 chunk 80 optimal weight: 5.9990 chunk 120 optimal weight: 6.9990 chunk 60 optimal weight: 30.0000 chunk 39 optimal weight: 8.9990 chunk 128 optimal weight: 20.0000 chunk 137 optimal weight: 20.0000 chunk 100 optimal weight: 20.0000 chunk 18 optimal weight: 7.9990 chunk 159 optimal weight: 20.0000 chunk 184 optimal weight: 6.9990 overall best weight: 5.5992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: l 10 HIS ** AN 10 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A5 10 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** BE 10 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** BW 10 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C5 10 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** DN 10 HIS ** EW 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** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7233 moved from start: 0.3686 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 20370 Z= 0.142 Angle : 0.683 10.029 27210 Z= 0.283 Chirality : 0.057 0.193 3840 Planarity : 0.002 0.019 3060 Dihedral : 10.938 62.542 2580 Min Nonbonded Distance : 2.588 Molprobity Statistics. All-atom Clashscore : 7.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 8.42 % Allowed : 23.75 % Favored : 67.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.89 (0.18), residues: 2100 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.67 (0.14), residues: 2100 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HISAN 10 *********************** 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 628 residues out of total 2400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 202 poor density : 426 time to evaluate : 2.568 Fit side-chains REVERT: A 5 LYS cc_start: 0.8003 (mttt) cc_final: 0.7598 (mttp) REVERT: D 2 LEU cc_start: 0.8373 (pt) cc_final: 0.8148 (tt) REVERT: M 5 LYS cc_start: 0.7636 (mttt) cc_final: 0.7409 (mttm) REVERT: S 5 LYS cc_start: 0.8042 (mttt) cc_final: 0.7624 (mttp) REVERT: V 2 LEU cc_start: 0.8473 (pt) cc_final: 0.8132 (tt) REVERT: a 4 ILE cc_start: 0.7498 (OUTLIER) cc_final: 0.7223 (mp) REVERT: j 5 LYS cc_start: 0.7883 (mttt) cc_final: 0.7410 (mttp) REVERT: s 4 ILE cc_start: 0.7453 (OUTLIER) cc_final: 0.7189 (mp) REVERT: v 5 LYS cc_start: 0.7340 (mttt) cc_final: 0.7000 (mttm) REVERT: AD 3 ILE cc_start: 0.7720 (OUTLIER) cc_final: 0.7153 (mp) REVERT: AE 5 LYS cc_start: 0.7608 (mttt) cc_final: 0.7182 (mttm) REVERT: AK 4 ILE cc_start: 0.7423 (OUTLIER) cc_final: 0.7128 (mp) REVERT: AN 5 LYS cc_start: 0.7269 (mttt) cc_final: 0.6927 (mttm) REVERT: AV 3 ILE cc_start: 0.7593 (OUTLIER) cc_final: 0.7044 (mp) REVERT: AW 5 LYS cc_start: 0.7662 (mttm) cc_final: 0.7397 (mttm) REVERT: A2 4 ILE cc_start: 0.7296 (OUTLIER) cc_final: 0.7007 (mp) REVERT: A5 5 LYS cc_start: 0.7561 (mttm) cc_final: 0.7309 (mttm) REVERT: BB 5 LYS cc_start: 0.7672 (mttt) cc_final: 0.7325 (mttp) REVERT: BE 5 LYS cc_start: 0.7651 (mttt) cc_final: 0.7296 (mttp) REVERT: BK 4 ILE cc_start: 0.7271 (OUTLIER) cc_final: 0.6945 (mp) REVERT: BN 3 ILE cc_start: 0.8440 (mt) cc_final: 0.8216 (mp) REVERT: BT 5 LYS cc_start: 0.7612 (mttt) cc_final: 0.7186 (mttp) REVERT: BV 3 ILE cc_start: 0.7868 (OUTLIER) cc_final: 0.7382 (mp) REVERT: BW 5 LYS cc_start: 0.7524 (mttt) cc_final: 0.7219 (mttm) REVERT: B5 5 LYS cc_start: 0.7516 (mttt) cc_final: 0.7246 (mttm) REVERT: CD 1 ASP cc_start: 0.7079 (m-30) cc_final: 0.6756 (m-30) REVERT: CD 3 ILE cc_start: 0.7823 (OUTLIER) cc_final: 0.7293 (mp) REVERT: CE 3 ILE cc_start: 0.8554 (mt) cc_final: 0.8154 (mp) REVERT: 1 4 ILE cc_start: 0.7532 (OUTLIER) cc_final: 0.7296 (mp) REVERT: 6 2 LEU cc_start: 0.8178 (pt) cc_final: 0.7730 (pp) REVERT: 6 5 LYS cc_start: 0.7330 (mttt) cc_final: 0.6873 (mttm) REVERT: CK 5 LYS cc_start: 0.7808 (mttt) cc_final: 0.7261 (mttp) REVERT: CM 3 ILE cc_start: 0.7749 (OUTLIER) cc_final: 0.7193 (mp) REVERT: CN 2 LEU cc_start: 0.7771 (pt) cc_final: 0.7547 (pp) REVERT: CR 5 LYS cc_start: 0.8877 (OUTLIER) cc_final: 0.8643 (mtmm) REVERT: CW 5 LYS cc_start: 0.7378 (mttt) cc_final: 0.6957 (mttm) REVERT: C5 2 LEU cc_start: 0.7977 (pp) cc_final: 0.7673 (pt) REVERT: C5 5 LYS cc_start: 0.7570 (mttt) cc_final: 0.7145 (mttm) REVERT: DE 5 LYS cc_start: 0.7262 (mttt) cc_final: 0.6844 (mttm) REVERT: DM 3 ILE cc_start: 0.7813 (OUTLIER) cc_final: 0.7251 (mp) REVERT: DT 4 ILE cc_start: 0.7699 (OUTLIER) cc_final: 0.7452 (mp) REVERT: D4 3 ILE cc_start: 0.7803 (OUTLIER) cc_final: 0.7247 (mp) REVERT: D5 2 LEU cc_start: 0.7980 (pt) cc_final: 0.7688 (pp) REVERT: EE 5 LYS cc_start: 0.7149 (mttt) cc_final: 0.6779 (mttm) REVERT: EK 5 LYS cc_start: 0.7901 (mttt) cc_final: 0.7556 (mttp) REVERT: EM 3 ILE cc_start: 0.7959 (OUTLIER) cc_final: 0.7495 (mp) REVERT: EN 2 LEU cc_start: 0.7987 (pt) cc_final: 0.7666 (pp) REVERT: E4 3 ILE cc_start: 0.8025 (OUTLIER) cc_final: 0.7771 (mm) REVERT: E5 5 LYS cc_start: 0.7350 (mttt) cc_final: 0.7114 (mttp) REVERT: FE 2 LEU cc_start: 0.8300 (pp) cc_final: 0.6631 (mm) REVERT: FE 5 LYS cc_start: 0.8205 (mttt) cc_final: 0.7779 (mttm) REVERT: FM 3 ILE cc_start: 0.8326 (OUTLIER) cc_final: 0.7776 (mp) REVERT: FN 2 LEU cc_start: 0.8423 (pt) cc_final: 0.8093 (pp) REVERT: FT 4 ILE cc_start: 0.7750 (OUTLIER) cc_final: 0.7534 (mp) outliers start: 202 outliers final: 155 residues processed: 499 average time/residue: 0.2883 time to fit residues: 226.1413 Evaluate side-chains 592 residues out of total 2400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 174 poor density : 418 time to evaluate : 2.603 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A 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 P residue 2 LEU Chi-restraints excluded: chain S residue 8 SER 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 Y residue 9 VAL Chi-restraints excluded: chain Z residue 5 LYS 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 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 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 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 A8 residue 9 VAL 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 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 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 B3 residue 9 VAL Chi-restraints excluded: chain B5 residue 2 LEU 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 3 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 6 residue 8 SER 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 CM residue 3 ILE 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 CU residue 9 VAL Chi-restraints excluded: chain CW residue 4 ILE 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 C7 residue 4 ILE Chi-restraints excluded: chain C8 residue 9 VAL 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 DH residue 9 VAL Chi-restraints excluded: chain DK 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 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 D2 residue 8 SER 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 D8 residue 2 LEU Chi-restraints excluded: chain D8 residue 9 VAL 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 EM residue 3 ILE Chi-restraints excluded: chain EN residue 8 SER 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 EU residue 9 VAL Chi-restraints excluded: chain EZ residue 2 LEU 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 7 ILE Chi-restraints excluded: chain FC residue 9 VAL Chi-restraints excluded: chain FF 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 FO residue 2 LEU 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 FX residue 9 VAL Chi-restraints excluded: chain FZ residue 2 LEU 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 193 optimal weight: 10.0000 chunk 176 optimal weight: 30.0000 chunk 188 optimal weight: 5.9990 chunk 113 optimal weight: 9.9990 chunk 82 optimal weight: 20.0000 chunk 148 optimal weight: 2.9990 chunk 57 optimal weight: 6.9990 chunk 170 optimal weight: 10.0000 chunk 178 optimal weight: 8.9990 chunk 187 optimal weight: 20.0000 chunk 123 optimal weight: 0.9980 overall best weight: 5.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** AN 10 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A5 10 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** BE 10 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** BW 10 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C5 10 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7228 moved from start: 0.3771 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 20370 Z= 0.136 Angle : 0.677 9.860 27210 Z= 0.279 Chirality : 0.057 0.210 3840 Planarity : 0.001 0.018 3060 Dihedral : 10.759 62.310 2580 Min Nonbonded Distance : 2.594 Molprobity Statistics. All-atom Clashscore : 7.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer: Outliers : 8.21 % Allowed : 23.92 % Favored : 67.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.74 (0.19), residues: 2100 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.55 (0.14), residues: 2100 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HISAN 10 *********************** 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 621 residues out of total 2400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 197 poor density : 424 time to evaluate : 2.672 Fit side-chains REVERT: A 5 LYS cc_start: 0.8015 (mttt) cc_final: 0.7613 (mttp) REVERT: D 2 LEU cc_start: 0.8395 (pt) cc_final: 0.8175 (tt) REVERT: M 5 LYS cc_start: 0.7587 (mttt) cc_final: 0.7365 (mttm) REVERT: S 5 LYS cc_start: 0.7972 (mttt) cc_final: 0.7678 (mttp) REVERT: U 3 ILE cc_start: 0.7879 (OUTLIER) cc_final: 0.7359 (mp) REVERT: V 2 LEU cc_start: 0.8467 (pt) cc_final: 0.8220 (tt) REVERT: a 4 ILE cc_start: 0.7502 (OUTLIER) cc_final: 0.7226 (mp) REVERT: j 5 LYS cc_start: 0.7889 (mttt) cc_final: 0.7408 (mttp) REVERT: s 4 ILE cc_start: 0.7409 (OUTLIER) cc_final: 0.7147 (mp) REVERT: v 5 LYS cc_start: 0.7287 (mttt) cc_final: 0.6970 (mttm) REVERT: AD 3 ILE cc_start: 0.7649 (OUTLIER) cc_final: 0.7095 (mp) REVERT: AE 5 LYS cc_start: 0.7624 (mttt) cc_final: 0.7178 (mttm) REVERT: AK 4 ILE cc_start: 0.7417 (OUTLIER) cc_final: 0.7118 (mp) REVERT: AN 5 LYS cc_start: 0.7315 (mttt) cc_final: 0.6981 (mttm) REVERT: AV 3 ILE cc_start: 0.7608 (OUTLIER) cc_final: 0.7065 (mp) REVERT: AW 5 LYS cc_start: 0.7663 (mttm) cc_final: 0.7394 (mttm) REVERT: A2 4 ILE cc_start: 0.7396 (OUTLIER) cc_final: 0.7093 (mp) REVERT: A5 5 LYS cc_start: 0.7541 (mttm) cc_final: 0.7297 (mttm) REVERT: BB 5 LYS cc_start: 0.7709 (mttt) cc_final: 0.7367 (mttp) REVERT: BE 5 LYS cc_start: 0.7623 (mttt) cc_final: 0.7267 (mttp) REVERT: BK 4 ILE cc_start: 0.7208 (OUTLIER) cc_final: 0.6891 (mp) REVERT: BN 3 ILE cc_start: 0.8483 (mt) cc_final: 0.8267 (mp) REVERT: BQ 4 ILE cc_start: 0.6887 (pt) cc_final: 0.5990 (tp) REVERT: BT 5 LYS cc_start: 0.7637 (mttt) cc_final: 0.7199 (mttp) REVERT: BV 3 ILE cc_start: 0.7876 (OUTLIER) cc_final: 0.7388 (mp) REVERT: BW 5 LYS cc_start: 0.7516 (mttt) cc_final: 0.7211 (mttm) REVERT: B5 5 LYS cc_start: 0.7531 (mttt) cc_final: 0.7267 (mttm) REVERT: CD 1 ASP cc_start: 0.7082 (m-30) cc_final: 0.6752 (m-30) REVERT: CD 3 ILE cc_start: 0.7829 (OUTLIER) cc_final: 0.7295 (mp) REVERT: CE 3 ILE cc_start: 0.8523 (mt) cc_final: 0.8095 (mp) REVERT: 1 4 ILE cc_start: 0.7512 (OUTLIER) cc_final: 0.7276 (mp) REVERT: 6 2 LEU cc_start: 0.8157 (pt) cc_final: 0.7676 (pp) REVERT: 6 5 LYS cc_start: 0.7290 (mttt) cc_final: 0.6873 (mttm) REVERT: CK 5 LYS cc_start: 0.7809 (mttt) cc_final: 0.7267 (mttp) REVERT: CM 3 ILE cc_start: 0.7798 (OUTLIER) cc_final: 0.7249 (mp) REVERT: CN 2 LEU cc_start: 0.7655 (pt) cc_final: 0.7429 (pp) REVERT: CR 5 LYS cc_start: 0.8892 (OUTLIER) cc_final: 0.8675 (mtmm) REVERT: CW 5 LYS cc_start: 0.7422 (mttt) cc_final: 0.7005 (mttm) REVERT: C5 2 LEU cc_start: 0.7880 (pp) cc_final: 0.7608 (pt) REVERT: C5 5 LYS cc_start: 0.7566 (mttt) cc_final: 0.7187 (mttm) REVERT: DE 5 LYS cc_start: 0.7118 (mttt) cc_final: 0.6822 (mttm) REVERT: DM 3 ILE cc_start: 0.7887 (OUTLIER) cc_final: 0.7354 (mp) REVERT: DT 4 ILE cc_start: 0.7693 (OUTLIER) cc_final: 0.7449 (mp) REVERT: D4 3 ILE cc_start: 0.7814 (OUTLIER) cc_final: 0.7254 (mp) REVERT: D5 2 LEU cc_start: 0.7951 (pt) cc_final: 0.7654 (pp) REVERT: EE 5 LYS cc_start: 0.7121 (mttt) cc_final: 0.6754 (mttm) REVERT: EK 5 LYS cc_start: 0.7987 (mttt) cc_final: 0.7667 (mttp) REVERT: EM 3 ILE cc_start: 0.7864 (OUTLIER) cc_final: 0.7391 (mp) REVERT: EN 2 LEU cc_start: 0.8037 (pt) cc_final: 0.7808 (pp) REVERT: E4 3 ILE cc_start: 0.8031 (OUTLIER) cc_final: 0.7779 (mm) REVERT: E5 5 LYS cc_start: 0.7374 (mttt) cc_final: 0.7157 (mttp) REVERT: FE 2 LEU cc_start: 0.8232 (pp) cc_final: 0.6540 (mm) REVERT: FE 5 LYS cc_start: 0.8198 (mttt) cc_final: 0.7764 (mttm) REVERT: FM 3 ILE cc_start: 0.8333 (OUTLIER) cc_final: 0.7779 (mp) REVERT: FN 2 LEU cc_start: 0.8409 (pt) cc_final: 0.8071 (pp) REVERT: FT 4 ILE cc_start: 0.7750 (OUTLIER) cc_final: 0.7543 (mp) outliers start: 197 outliers final: 151 residues processed: 497 average time/residue: 0.3092 time to fit residues: 243.2526 Evaluate side-chains 587 residues out of total 2400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 171 poor density : 416 time to evaluate : 2.597 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A 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 2 LEU 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 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 9 VAL 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 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 7 ILE Chi-restraints excluded: chain y residue 9 VAL 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 A8 residue 9 VAL 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 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 B3 residue 9 VAL Chi-restraints excluded: chain B5 residue 2 LEU 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 3 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 6 residue 8 SER 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 CM residue 3 ILE 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 CU residue 9 VAL Chi-restraints excluded: chain CW residue 4 ILE 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 DC residue 9 VAL Chi-restraints excluded: chain DH residue 2 LEU Chi-restraints excluded: chain DH residue 9 VAL Chi-restraints excluded: chain DK 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 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 D2 residue 8 SER 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 D8 residue 2 LEU Chi-restraints excluded: chain D8 residue 9 VAL Chi-restraints excluded: chain D9 residue 3 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 EM residue 3 ILE Chi-restraints excluded: chain EN residue 8 SER Chi-restraints excluded: chain EO residue 9 VAL Chi-restraints excluded: chain EQ residue 7 ILE Chi-restraints excluded: chain EQ residue 9 VAL 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 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 FF 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 FO residue 2 LEU 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 FX residue 9 VAL Chi-restraints excluded: chain FZ residue 7 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 199 optimal weight: 20.0000 chunk 121 optimal weight: 10.0000 chunk 94 optimal weight: 6.9990 chunk 138 optimal weight: 7.9990 chunk 209 optimal weight: 6.9990 chunk 192 optimal weight: 0.0870 chunk 166 optimal weight: 0.9980 chunk 17 optimal weight: 20.0000 chunk 128 optimal weight: 20.0000 chunk 102 optimal weight: 20.0000 chunk 132 optimal weight: 20.0000 overall best weight: 4.6164 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: AN 10 HIS ** A5 10 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** BE 10 HIS ** BW 10 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** CB 10 HIS ** C5 10 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 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** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7222 moved from start: 0.3819 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 20370 Z= 0.126 Angle : 0.671 10.019 27210 Z= 0.276 Chirality : 0.057 0.208 3840 Planarity : 0.001 0.017 3060 Dihedral : 10.653 62.299 2580 Min Nonbonded Distance : 2.579 Molprobity Statistics. All-atom Clashscore : 6.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 7.42 % Allowed : 24.71 % Favored : 67.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.63 (0.19), residues: 2100 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.47 (0.14), residues: 2100 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HISCB 10 ********************** 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 604 residues out of total 2400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 178 poor density : 426 time to evaluate : 2.758 Fit side-chains REVERT: A 5 LYS cc_start: 0.8016 (mttt) cc_final: 0.7614 (mttp) REVERT: S 5 LYS cc_start: 0.7985 (mttt) cc_final: 0.7678 (mttp) REVERT: U 3 ILE cc_start: 0.7880 (OUTLIER) cc_final: 0.7360 (mp) REVERT: V 2 LEU cc_start: 0.8455 (pt) cc_final: 0.8213 (tt) REVERT: j 5 LYS cc_start: 0.7887 (mttt) cc_final: 0.7404 (mttp) REVERT: s 4 ILE cc_start: 0.7416 (OUTLIER) cc_final: 0.7153 (mp) REVERT: v 5 LYS cc_start: 0.7073 (mttt) cc_final: 0.6789 (mttm) REVERT: AD 3 ILE cc_start: 0.7658 (OUTLIER) cc_final: 0.7106 (mp) REVERT: AE 5 LYS cc_start: 0.7662 (mttt) cc_final: 0.7207 (mttm) REVERT: AK 4 ILE cc_start: 0.7435 (OUTLIER) cc_final: 0.7137 (mp) REVERT: AN 5 LYS cc_start: 0.7314 (mttt) cc_final: 0.6990 (mttm) REVERT: AV 3 ILE cc_start: 0.7566 (OUTLIER) cc_final: 0.7017 (mp) REVERT: AW 5 LYS cc_start: 0.7655 (mttm) cc_final: 0.7426 (mttm) REVERT: A2 4 ILE cc_start: 0.7398 (OUTLIER) cc_final: 0.7108 (mp) REVERT: A5 5 LYS cc_start: 0.7550 (mttm) cc_final: 0.7308 (mttm) REVERT: BB 5 LYS cc_start: 0.7691 (mttt) cc_final: 0.7360 (mttp) REVERT: BE 5 LYS cc_start: 0.7558 (mttt) cc_final: 0.7251 (mttp) REVERT: BK 4 ILE cc_start: 0.7205 (OUTLIER) cc_final: 0.6891 (mp) REVERT: BN 3 ILE cc_start: 0.8475 (mt) cc_final: 0.8253 (mp) REVERT: BT 5 LYS cc_start: 0.7634 (mttt) cc_final: 0.7193 (mttp) REVERT: BV 3 ILE cc_start: 0.7872 (OUTLIER) cc_final: 0.7376 (mp) REVERT: BW 5 LYS cc_start: 0.7521 (mttt) cc_final: 0.7225 (mttm) REVERT: B5 5 LYS cc_start: 0.7568 (mttt) cc_final: 0.7312 (mttm) REVERT: CD 1 ASP cc_start: 0.7069 (m-30) cc_final: 0.6742 (m-30) REVERT: CD 3 ILE cc_start: 0.7834 (OUTLIER) cc_final: 0.7301 (mp) REVERT: CE 3 ILE cc_start: 0.8512 (mt) cc_final: 0.8094 (mp) REVERT: 1 4 ILE cc_start: 0.7507 (OUTLIER) cc_final: 0.7298 (mp) REVERT: 6 2 LEU cc_start: 0.8166 (pt) cc_final: 0.7911 (pp) REVERT: 6 5 LYS cc_start: 0.7285 (mttt) cc_final: 0.6880 (mttm) REVERT: CK 5 LYS cc_start: 0.7857 (mttt) cc_final: 0.7276 (mttp) REVERT: CM 3 ILE cc_start: 0.7811 (OUTLIER) cc_final: 0.7259 (mp) REVERT: CR 5 LYS cc_start: 0.8891 (OUTLIER) cc_final: 0.8671 (mtmm) REVERT: CW 5 LYS cc_start: 0.7421 (mttt) cc_final: 0.7014 (mttm) REVERT: C5 5 LYS cc_start: 0.7706 (mttt) cc_final: 0.7343 (mttm) REVERT: DE 5 LYS cc_start: 0.7134 (mttt) cc_final: 0.6841 (mttm) REVERT: DM 3 ILE cc_start: 0.7895 (OUTLIER) cc_final: 0.7366 (mp) REVERT: DT 4 ILE cc_start: 0.7632 (OUTLIER) cc_final: 0.7377 (mp) REVERT: D4 3 ILE cc_start: 0.7832 (OUTLIER) cc_final: 0.7274 (mp) REVERT: D5 2 LEU cc_start: 0.7977 (pt) cc_final: 0.7661 (pp) REVERT: EE 5 LYS cc_start: 0.7016 (mttt) cc_final: 0.6687 (mttm) REVERT: EG 9 VAL cc_start: 0.8529 (t) cc_final: 0.8307 (p) REVERT: EK 5 LYS cc_start: 0.7982 (mttt) cc_final: 0.7665 (mttp) REVERT: EN 2 LEU cc_start: 0.7980 (pt) cc_final: 0.7732 (pp) REVERT: E4 3 ILE cc_start: 0.8042 (OUTLIER) cc_final: 0.7798 (mm) REVERT: FE 2 LEU cc_start: 0.8195 (pp) cc_final: 0.6473 (mm) REVERT: FE 5 LYS cc_start: 0.8198 (mttt) cc_final: 0.7766 (mttm) REVERT: FM 3 ILE cc_start: 0.8342 (OUTLIER) cc_final: 0.7786 (mp) REVERT: FN 2 LEU cc_start: 0.8397 (pt) cc_final: 0.8058 (pp) REVERT: FT 4 ILE cc_start: 0.7753 (OUTLIER) cc_final: 0.7552 (mp) outliers start: 178 outliers final: 147 residues processed: 498 average time/residue: 0.2920 time to fit residues: 229.6309 Evaluate side-chains 580 residues out of total 2400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 165 poor density : 415 time to evaluate : 2.598 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A 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 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 U residue 3 ILE Chi-restraints excluded: chain W residue 9 VAL Chi-restraints excluded: chain X residue 8 SER Chi-restraints excluded: chain Y residue 9 VAL 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 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 7 ILE Chi-restraints excluded: chain y residue 9 VAL 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 7 ILE 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 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 A8 residue 9 VAL 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 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 B3 residue 9 VAL Chi-restraints excluded: chain B5 residue 2 LEU 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 3 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 6 residue 8 SER 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 CM residue 3 ILE 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 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 DC residue 9 VAL Chi-restraints excluded: chain DH residue 2 LEU Chi-restraints excluded: chain DH residue 9 VAL Chi-restraints excluded: chain DK 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 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 D2 residue 8 SER 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 D8 residue 2 LEU Chi-restraints excluded: chain D8 residue 9 VAL 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 EN residue 8 SER Chi-restraints excluded: chain EO 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 EU residue 9 VAL Chi-restraints excluded: chain EZ residue 2 LEU 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 FF 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 FO residue 2 LEU 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 FX residue 9 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 177 optimal weight: 30.0000 chunk 51 optimal weight: 9.9990 chunk 153 optimal weight: 30.0000 chunk 24 optimal weight: 30.0000 chunk 46 optimal weight: 5.9990 chunk 166 optimal weight: 6.9990 chunk 69 optimal weight: 1.9990 chunk 171 optimal weight: 7.9990 chunk 21 optimal weight: 30.0000 chunk 30 optimal weight: 5.9990 chunk 146 optimal weight: 4.9990 overall best weight: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A5 10 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A7 10 HIS ** BW 10 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** CB 10 HIS ** C5 10 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D7 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** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3592 r_free = 0.3592 target = 0.118320 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.098616 restraints weight = 29780.597| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.101963 restraints weight = 15939.040| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.104339 restraints weight = 10280.251| |-----------------------------------------------------------------------------| r_work (final): 0.3425 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7731 moved from start: 0.3866 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 20370 Z= 0.136 Angle : 0.681 9.967 27210 Z= 0.281 Chirality : 0.057 0.178 3840 Planarity : 0.001 0.015 3060 Dihedral : 10.664 61.995 2580 Min Nonbonded Distance : 2.561 Molprobity Statistics. All-atom Clashscore : 7.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer: Outliers : 7.75 % Allowed : 24.58 % Favored : 67.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.63 (0.19), residues: 2100 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.47 (0.14), residues: 2100 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS n 10 =============================================================================== Job complete usr+sys time: 4355.82 seconds wall clock time: 84 minutes 10.87 seconds (5050.87 seconds total)