Starting phenix.real_space_refine on Sun Feb 18 00:34:02 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5w7v_8781/02_2024/5w7v_8781.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5w7v_8781/02_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_8781/02_2024/5w7v_8781.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5w7v_8781/02_2024/5w7v_8781.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5w7v_8781/02_2024/5w7v_8781.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5w7v_8781/02_2024/5w7v_8781.pdb" } 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 Symmetric amino acids flipped None Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/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: 11.56, per 1000 atoms: 0.57 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 - 3.50 Amino acid : False - 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: 8.08 Conformation dependent library (CDL) restraints added in 3.2 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: 2.64 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: 8.42 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: 2852 1.35 - 1.42: 778 1.42 - 1.48: 2703 1.48 - 1.55: 10647 Bond restraints: 20370 Sorted by residual: 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 1.21e+00 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 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: 106.02 - 111.07: 10173 111.07 - 116.11: 6087 116.11 - 121.16: 5326 121.16 - 126.21: 5414 126.21 - 131.25: 210 Bond angle restraints: 27210 Sorted by residual: 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 angle pdb=" CA LEUAB 2 " pdb=" CB LEUAB 2 " pdb=" CG LEUAB 2 " ideal model delta sigma weight residual 116.30 123.44 -7.14 3.50e+00 8.16e-02 4.16e+00 ... (remaining 27205 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 11.46: 11130 11.46 - 22.93: 514 22.93 - 34.39: 266 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: 1830 0.034 - 0.067: 1053 0.067 - 0.101: 299 0.101 - 0.134: 568 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: 5558 2.87 - 3.38: 18713 3.38 - 3.89: 35852 3.89 - 4.39: 35541 4.39 - 4.90: 71099 Nonbonded interactions: 166763 Sorted by model distance: nonbonded pdb=" OXT ILEFF 11 " pdb=" N ASPFG 1 " model vdw 2.365 2.520 nonbonded pdb=" OXT ILECO 11 " pdb=" N ASPCP 1 " model vdw 2.365 2.520 nonbonded pdb=" OXT ILEFO 11 " pdb=" N ASPFP 1 " model vdw 2.365 2.520 nonbonded pdb=" OXT ILE e 11 " pdb=" N ASP f 1 " model vdw 2.365 2.520 nonbonded pdb=" OXT ILEA6 11 " pdb=" N ASPA7 1 " model vdw 2.365 2.520 ... (remaining 166758 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model 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: 0.100 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: 0.020 Extract box with map and model: 1.950 Check model and map are aligned: 0.310 Set scattering table: 0.190 Process input model: 47.840 Find NCS groups from input model: 2.550 Set up NCS constraints: 1.220 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.640 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 56.820 ------------------------------------------------------------------------------- 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 7.151 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 0.007 0.002 HISA4 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 : 2.572 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: 0.7813 (mttt) cc_final: 0.7609 (mttm) REVERT: v 5 LYS cc_start: 0.7391 (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: 0.7792 (mp) cc_final: 0.7467 (mm) REVERT: CW 3 ILE cc_start: 0.8430 (mt) cc_final: 0.8165 (mp) REVERT: CW 5 LYS cc_start: 0.7598 (mttt) cc_final: 0.7211 (mttm) REVERT: C4 3 ILE cc_start: 0.8010 (mp) cc_final: 0.7709 (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: 0.6947 (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: 0.3011 time to fit residues: 298.5056 Evaluate side-chains 449 residues out of total 2400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 449 time to evaluate : 2.373 ------------------------------------------------------------------------------- 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: 9.9990 chunk 159 optimal weight: 30.0000 chunk 88 optimal weight: 20.0000 chunk 54 optimal weight: 30.0000 chunk 107 optimal weight: 2.9990 chunk 85 optimal weight: 8.9990 chunk 164 optimal weight: 30.0000 chunk 63 optimal weight: 4.9990 chunk 100 optimal weight: 30.0000 chunk 122 optimal weight: 7.9990 chunk 190 optimal weight: 20.0000 overall best weight: 6.9990 ------------------------------------------------------------------------------- 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 ** 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 ** 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 DD 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 ** 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: 47 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7236 moved from start: 0.1905 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.026 20370 Z= 0.171 Angle : 0.687 10.205 27210 Z= 0.287 Chirality : 0.057 0.139 3840 Planarity : 0.002 0.007 3060 Dihedral : 11.293 61.173 2580 Min Nonbonded Distance : 2.312 Molprobity Statistics. All-atom Clashscore : 5.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 7.00 % Allowed : 17.42 % Favored : 75.58 % 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 (0.15), residues: 2100 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.46 (0.11), residues: 2100 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.002 HISB4 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 670 residues out of total 2400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 168 poor density : 502 time to evaluate : 2.835 Fit side-chains REVERT: C 5 LYS cc_start: 0.8154 (ptmt) cc_final: 0.7942 (ptpt) REVERT: M 3 ILE cc_start: 0.8733 (mt) cc_final: 0.8478 (mp) REVERT: M 5 LYS cc_start: 0.7897 (mttt) cc_final: 0.7539 (mttm) REVERT: U 3 ILE cc_start: 0.8059 (mp) cc_final: 0.7642 (mp) REVERT: s 4 ILE cc_start: 0.7681 (OUTLIER) cc_final: 0.7453 (mp) REVERT: v 3 ILE cc_start: 0.8564 (mt) cc_final: 0.8293 (mp) REVERT: v 5 LYS cc_start: 0.7534 (mttt) cc_final: 0.7108 (mttm) REVERT: AD 3 ILE cc_start: 0.7866 (mp) cc_final: 0.7350 (mp) REVERT: AK 4 ILE cc_start: 0.7589 (OUTLIER) cc_final: 0.7313 (mp) REVERT: AN 5 LYS cc_start: 0.7678 (mttt) cc_final: 0.7277 (mttm) REVERT: AV 3 ILE cc_start: 0.7972 (mp) cc_final: 0.7449 (mp) REVERT: A2 4 ILE cc_start: 0.7593 (OUTLIER) cc_final: 0.7293 (mp) REVERT: A5 3 ILE cc_start: 0.8538 (mt) cc_final: 0.8328 (mp) REVERT: BK 4 ILE cc_start: 0.7539 (OUTLIER) cc_final: 0.7282 (mp) REVERT: BN 3 ILE cc_start: 0.8390 (mt) cc_final: 0.8086 (mp) REVERT: BV 5 LYS cc_start: 0.8072 (ptmt) cc_final: 0.7815 (ptpt) REVERT: BW 5 LYS cc_start: 0.7553 (mttt) cc_final: 0.7324 (mttm) REVERT: B2 4 ILE cc_start: 0.7714 (OUTLIER) cc_final: 0.7445 (mp) REVERT: CD 5 LYS cc_start: 0.7772 (ptmt) cc_final: 0.7571 (ptpt) REVERT: 1 4 ILE cc_start: 0.7680 (OUTLIER) cc_final: 0.7452 (mp) REVERT: 6 2 LEU cc_start: 0.8323 (pt) cc_final: 0.8060 (pp) REVERT: 6 5 LYS cc_start: 0.7477 (mttt) cc_final: 0.7013 (mttp) REVERT: CN 2 LEU cc_start: 0.7885 (pt) cc_final: 0.7584 (pp) REVERT: CT 4 ILE cc_start: 0.7710 (OUTLIER) cc_final: 0.7495 (mp) REVERT: CW 5 LYS cc_start: 0.7539 (mttt) cc_final: 0.7015 (mttm) REVERT: C4 3 ILE cc_start: 0.7999 (mp) cc_final: 0.7667 (mm) REVERT: DE 5 LYS cc_start: 0.7318 (mttt) cc_final: 0.6903 (mttm) REVERT: D4 3 ILE cc_start: 0.7862 (mp) cc_final: 0.7556 (mm) REVERT: EE 5 LYS cc_start: 0.7193 (mttt) cc_final: 0.6801 (mttm) REVERT: EW 3 ILE cc_start: 0.8417 (mt) cc_final: 0.8168 (mp) REVERT: E5 5 LYS cc_start: 0.7719 (mttt) cc_final: 0.7371 (mttp) REVERT: FE 3 ILE cc_start: 0.8788 (mt) cc_final: 0.8526 (mp) REVERT: FE 5 LYS cc_start: 0.8355 (mttt) cc_final: 0.7993 (mttm) REVERT: FN 2 LEU cc_start: 0.8332 (pt) cc_final: 0.6830 (mm) REVERT: FT 4 ILE cc_start: 0.7693 (OUTLIER) cc_final: 0.7471 (mp) outliers start: 168 outliers final: 88 residues processed: 566 average time/residue: 0.2964 time to fit residues: 262.1900 Evaluate side-chains 530 residues out of total 2400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 96 poor density : 434 time to evaluate : 2.438 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 9 VAL Chi-restraints excluded: chain D residue 1 ASP Chi-restraints excluded: chain E residue 9 VAL Chi-restraints excluded: chain G residue 2 LEU Chi-restraints excluded: chain S residue 8 SER Chi-restraints excluded: chain T residue 9 VAL Chi-restraints excluded: chain V residue 1 ASP Chi-restraints excluded: chain W residue 9 VAL Chi-restraints excluded: chain Y residue 2 LEU 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 m residue 1 ASP Chi-restraints excluded: chain m residue 8 SER Chi-restraints excluded: chain n residue 9 VAL 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 AE residue 1 ASP 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 AW residue 1 ASP Chi-restraints excluded: chain AW residue 8 SER Chi-restraints excluded: chain AZ residue 2 LEU Chi-restraints excluded: chain A0 residue 5 LYS Chi-restraints excluded: chain A2 residue 4 ILE Chi-restraints excluded: chain A3 residue 9 VAL Chi-restraints excluded: chain A8 residue 2 LEU Chi-restraints excluded: chain BC residue 9 VAL Chi-restraints excluded: chain BE residue 1 ASP Chi-restraints excluded: chain BF residue 9 VAL Chi-restraints excluded: chain BK residue 4 ILE Chi-restraints excluded: chain BL residue 9 VAL Chi-restraints excluded: chain BQ residue 2 LEU Chi-restraints excluded: chain BU residue 9 VAL Chi-restraints excluded: chain BW residue 1 ASP Chi-restraints excluded: chain BX residue 9 VAL Chi-restraints excluded: chain B2 residue 4 ILE Chi-restraints excluded: chain B3 residue 9 VAL 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 6 residue 1 ASP Chi-restraints excluded: chain 7 residue 2 LEU Chi-restraints excluded: chain CL residue 9 VAL Chi-restraints excluded: chain CN residue 1 ASP Chi-restraints excluded: chain CO 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 C5 residue 1 ASP 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 DN residue 1 ASP Chi-restraints excluded: chain DU residue 9 VAL Chi-restraints excluded: chain DW residue 1 ASP 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 8 SER Chi-restraints excluded: chain EC residue 9 VAL Chi-restraints excluded: chain EE residue 1 ASP Chi-restraints excluded: chain EH residue 2 LEU Chi-restraints excluded: chain EL residue 9 VAL Chi-restraints excluded: chain EN residue 1 ASP Chi-restraints excluded: chain EO residue 9 VAL Chi-restraints excluded: chain EP residue 8 SER Chi-restraints excluded: chain EU residue 9 VAL Chi-restraints excluded: chain EW residue 1 ASP Chi-restraints excluded: chain E3 residue 9 VAL Chi-restraints excluded: chain E5 residue 1 ASP Chi-restraints excluded: chain E6 residue 9 VAL Chi-restraints excluded: chain E8 residue 7 ILE Chi-restraints excluded: chain FB residue 8 SER Chi-restraints excluded: chain FC residue 9 VAL Chi-restraints excluded: chain FE residue 1 ASP Chi-restraints excluded: chain FH residue 2 LEU Chi-restraints excluded: chain FL residue 9 VAL Chi-restraints excluded: chain FN residue 1 ASP 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 FW residue 1 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 105 optimal weight: 5.9990 chunk 59 optimal weight: 20.0000 chunk 158 optimal weight: 20.0000 chunk 129 optimal weight: 0.4980 chunk 52 optimal weight: 30.0000 chunk 191 optimal weight: 20.0000 chunk 206 optimal weight: 20.0000 chunk 170 optimal weight: 10.0000 chunk 189 optimal weight: 8.9990 chunk 65 optimal weight: 30.0000 chunk 153 optimal weight: 40.0000 overall best weight: 9.0992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: c 10 HIS l 10 HIS u 10 HIS AD 10 HIS ** AH 10 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** AM 10 HIS ** AQ 10 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** AZ 10 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A4 10 HIS ** A5 10 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A8 10 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** BH 10 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** BQ 10 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** BZ 10 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B8 10 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** CH 10 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 10 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** CQ 10 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** CZ 10 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C8 10 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** DD 10 HIS ** DH 10 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** DQ 10 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** DZ 10 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D4 10 HIS ** D8 10 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** EH 10 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** EQ 10 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** EV 10 HIS ** EZ 10 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E2 10 HIS ** 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** FW 10 HIS ** FZ 10 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7254 moved from start: 0.2511 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.033 20370 Z= 0.206 Angle : 0.707 9.234 27210 Z= 0.299 Chirality : 0.057 0.165 3840 Planarity : 0.002 0.009 3060 Dihedral : 11.451 59.255 2580 Min Nonbonded Distance : 2.300 Molprobity Statistics. All-atom Clashscore : 7.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.62 % Favored : 99.38 % Rotamer: Outliers : 9.00 % Allowed : 19.79 % Favored : 71.21 % 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: -1.76 (0.16), residues: 2100 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.33 (0.12), residues: 2100 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HISC6 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 694 residues out of total 2400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 216 poor density : 478 time to evaluate : 2.664 Fit side-chains REVERT: M 3 ILE cc_start: 0.8667 (mt) cc_final: 0.8449 (mp) REVERT: M 5 LYS cc_start: 0.7900 (mttt) cc_final: 0.7557 (mttm) REVERT: P 5 LYS cc_start: 0.6200 (mmmt) cc_final: 0.4821 (pttm) REVERT: U 3 ILE cc_start: 0.7977 (mp) cc_final: 0.7533 (mp) REVERT: V 2 LEU cc_start: 0.8505 (pt) cc_final: 0.8292 (pp) REVERT: j 5 LYS cc_start: 0.8076 (mttt) cc_final: 0.7699 (mttp) REVERT: s 4 ILE cc_start: 0.7582 (OUTLIER) cc_final: 0.7348 (mp) REVERT: v 5 LYS cc_start: 0.7497 (mttt) cc_final: 0.7214 (mttm) REVERT: AK 4 ILE cc_start: 0.7556 (OUTLIER) cc_final: 0.7248 (mp) REVERT: AN 5 LYS cc_start: 0.7714 (mttt) cc_final: 0.7319 (mttm) REVERT: AW 5 LYS cc_start: 0.7824 (mttm) cc_final: 0.7532 (mttm) REVERT: A2 4 ILE cc_start: 0.7560 (OUTLIER) cc_final: 0.7275 (mp) REVERT: BB 5 LYS cc_start: 0.7792 (mttt) cc_final: 0.7344 (mttp) REVERT: BK 4 ILE cc_start: 0.7455 (OUTLIER) cc_final: 0.7137 (mp) REVERT: BT 5 LYS cc_start: 0.7639 (mttt) cc_final: 0.7379 (mttp) REVERT: BV 5 LYS cc_start: 0.7959 (ptmt) cc_final: 0.7736 (ptpt) REVERT: B2 4 ILE cc_start: 0.7684 (OUTLIER) cc_final: 0.7385 (mp) REVERT: B5 5 LYS cc_start: 0.7884 (mttm) cc_final: 0.7624 (mttm) REVERT: 1 4 ILE cc_start: 0.7640 (OUTLIER) cc_final: 0.7375 (mp) REVERT: 6 5 LYS cc_start: 0.7412 (mttt) cc_final: 0.6923 (mttm) REVERT: CT 4 ILE cc_start: 0.7659 (OUTLIER) cc_final: 0.7403 (mp) REVERT: CW 5 LYS cc_start: 0.7598 (mttt) cc_final: 0.7062 (mttm) REVERT: DE 5 LYS cc_start: 0.7393 (mttt) cc_final: 0.6935 (mttm) REVERT: DP 11 ILE cc_start: 0.8067 (OUTLIER) cc_final: 0.7861 (mt) REVERT: DW 3 ILE cc_start: 0.8579 (mt) cc_final: 0.8296 (mp) REVERT: EE 5 LYS cc_start: 0.7378 (mttt) cc_final: 0.6917 (mttm) REVERT: EN 2 LEU cc_start: 0.8256 (pt) cc_final: 0.8046 (pp) REVERT: EW 2 LEU cc_start: 0.8258 (pt) cc_final: 0.8011 (pp) REVERT: E5 5 LYS cc_start: 0.7550 (mttt) cc_final: 0.7198 (mttp) REVERT: FE 2 LEU cc_start: 0.8374 (pp) cc_final: 0.6798 (mm) REVERT: FE 3 ILE cc_start: 0.8763 (mt) cc_final: 0.8363 (mp) REVERT: FE 5 LYS cc_start: 0.8299 (mttt) cc_final: 0.7828 (mttm) REVERT: FT 4 ILE cc_start: 0.7783 (OUTLIER) cc_final: 0.7582 (mp) outliers start: 216 outliers final: 129 residues processed: 563 average time/residue: 0.2910 time to fit residues: 257.8096 Evaluate side-chains 571 residues out of total 2400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 138 poor density : 433 time to evaluate : 2.867 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 VAL Chi-restraints excluded: chain B residue 9 VAL Chi-restraints excluded: chain D residue 1 ASP Chi-restraints excluded: chain E residue 9 VAL Chi-restraints excluded: chain G residue 2 LEU Chi-restraints excluded: chain M residue 8 SER Chi-restraints excluded: chain S residue 8 SER Chi-restraints excluded: chain T residue 9 VAL Chi-restraints excluded: chain V residue 1 ASP 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 8 SER 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 1 ASP 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 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 AB residue 8 SER Chi-restraints excluded: chain AC residue 9 VAL Chi-restraints excluded: chain AE residue 1 ASP 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 1 ASP 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 BE residue 1 ASP 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 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 1 ASP Chi-restraints excluded: chain BW residue 8 SER Chi-restraints excluded: chain BX residue 9 VAL Chi-restraints excluded: chain B2 residue 4 ILE Chi-restraints excluded: chain B3 residue 9 VAL 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 6 residue 1 ASP Chi-restraints excluded: chain 7 residue 2 LEU Chi-restraints excluded: chain CL residue 9 VAL Chi-restraints excluded: chain CN residue 1 ASP 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 CW residue 1 ASP Chi-restraints excluded: chain CZ residue 2 LEU Chi-restraints excluded: chain C3 residue 9 VAL Chi-restraints excluded: chain C5 residue 1 ASP 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 1 ASP Chi-restraints excluded: chain DO residue 9 VAL Chi-restraints excluded: chain DP residue 11 ILE Chi-restraints excluded: chain DQ residue 2 LEU Chi-restraints excluded: chain DQ residue 7 ILE Chi-restraints excluded: chain DU residue 9 VAL Chi-restraints excluded: chain DW residue 1 ASP 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 7 ILE Chi-restraints excluded: chain EB residue 8 SER Chi-restraints excluded: chain EC residue 9 VAL Chi-restraints excluded: chain EE residue 1 ASP 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 EN residue 1 ASP Chi-restraints excluded: chain EP residue 8 SER Chi-restraints excluded: chain EU residue 9 VAL Chi-restraints excluded: chain EW residue 1 ASP 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 1 ASP 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 8 SER Chi-restraints excluded: chain FC residue 9 VAL Chi-restraints excluded: chain FE residue 1 ASP Chi-restraints excluded: chain FH residue 2 LEU Chi-restraints excluded: chain FL residue 9 VAL Chi-restraints excluded: chain FN residue 1 ASP 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 FW residue 1 ASP 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: 40.0000 chunk 143 optimal weight: 3.9990 chunk 99 optimal weight: 20.0000 chunk 21 optimal weight: 5.9990 chunk 91 optimal weight: 20.0000 chunk 128 optimal weight: 20.0000 chunk 191 optimal weight: 4.9990 chunk 202 optimal weight: 30.0000 chunk 100 optimal weight: 0.8980 chunk 181 optimal weight: 3.9990 chunk 54 optimal weight: 20.0000 overall best weight: 3.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: c 10 HIS j 10 HIS u 10 HIS AV 10 HIS BB 10 HIS ** BH 10 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B8 10 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** CB 10 HIS 2 10 HIS CM 10 HIS ** CQ 10 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** CW 10 HIS ** C8 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 ** DZ 10 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D8 10 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** EM 10 HIS ** EQ 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 ** 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** ** FZ 10 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7229 moved from start: 0.2809 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 20370 Z= 0.111 Angle : 0.611 10.100 27210 Z= 0.251 Chirality : 0.057 0.175 3840 Planarity : 0.001 0.008 3060 Dihedral : 10.602 55.772 2580 Min Nonbonded Distance : 2.317 Molprobity Statistics. All-atom Clashscore : 5.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.57 % Favored : 99.43 % Rotamer: Outliers : 8.58 % Allowed : 21.46 % Favored : 69.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -1.15 (0.17), residues: 2100 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.87 (0.13), residues: 2100 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.007 0.001 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 659 residues out of total 2400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 206 poor density : 453 time to evaluate : 2.506 Fit side-chains REVERT: D 2 LEU cc_start: 0.8542 (pt) cc_final: 0.8070 (tt) REVERT: M 5 LYS cc_start: 0.7909 (mttt) cc_final: 0.7600 (mttm) REVERT: P 5 LYS cc_start: 0.6207 (mmmt) cc_final: 0.4847 (pttm) REVERT: U 3 ILE cc_start: 0.7934 (mp) cc_final: 0.7451 (mp) REVERT: V 2 LEU cc_start: 0.8447 (pt) cc_final: 0.7964 (tt) REVERT: o 11 ILE cc_start: 0.8121 (OUTLIER) cc_final: 0.7909 (mt) REVERT: s 4 ILE cc_start: 0.7544 (OUTLIER) cc_final: 0.7323 (mp) REVERT: v 5 LYS cc_start: 0.7496 (mttt) cc_final: 0.7237 (mttm) REVERT: AK 4 ILE cc_start: 0.7565 (OUTLIER) cc_final: 0.7252 (mp) REVERT: AN 5 LYS cc_start: 0.7560 (mttt) cc_final: 0.7192 (mttm) REVERT: A2 4 ILE cc_start: 0.7575 (OUTLIER) cc_final: 0.7295 (mp) REVERT: A5 5 LYS cc_start: 0.7582 (mttm) cc_final: 0.7329 (mttp) REVERT: BB 5 LYS cc_start: 0.7662 (mttt) cc_final: 0.7242 (mttp) REVERT: BE 5 LYS cc_start: 0.7812 (mttt) cc_final: 0.7388 (mttp) REVERT: BG 11 ILE cc_start: 0.8017 (OUTLIER) cc_final: 0.7786 (mt) REVERT: BK 4 ILE cc_start: 0.7403 (OUTLIER) cc_final: 0.7090 (mp) REVERT: BN 3 ILE cc_start: 0.8523 (mt) cc_final: 0.8302 (mp) REVERT: BW 5 LYS cc_start: 0.7639 (mttt) cc_final: 0.7344 (mttp) REVERT: B2 4 ILE cc_start: 0.7705 (OUTLIER) cc_final: 0.7403 (mp) REVERT: B5 5 LYS cc_start: 0.7906 (mttm) cc_final: 0.7560 (mttm) REVERT: CE 3 ILE cc_start: 0.8457 (mt) cc_final: 0.8134 (mp) REVERT: CE 5 LYS cc_start: 0.7713 (mttm) cc_final: 0.7505 (mttm) REVERT: 1 4 ILE cc_start: 0.7686 (OUTLIER) cc_final: 0.7421 (mp) REVERT: 6 5 LYS cc_start: 0.7347 (mttt) cc_final: 0.6844 (mttm) REVERT: CN 2 LEU cc_start: 0.7760 (pt) cc_final: 0.7511 (pp) REVERT: CR 5 LYS cc_start: 0.8549 (OUTLIER) cc_final: 0.8314 (mtmm) REVERT: CW 5 LYS cc_start: 0.7478 (mttt) cc_final: 0.7018 (mttm) REVERT: DE 5 LYS cc_start: 0.7382 (mttt) cc_final: 0.6943 (mttm) REVERT: DW 3 ILE cc_start: 0.8623 (mt) cc_final: 0.8357 (mp) REVERT: EE 5 LYS cc_start: 0.7356 (mttt) cc_final: 0.6954 (mttm) REVERT: E5 5 LYS cc_start: 0.7473 (mttt) cc_final: 0.7157 (mttp) REVERT: FE 2 LEU cc_start: 0.8321 (pp) cc_final: 0.6649 (mm) REVERT: FE 3 ILE cc_start: 0.8711 (mt) cc_final: 0.8307 (mp) REVERT: FE 5 LYS cc_start: 0.8277 (mttt) cc_final: 0.7891 (mttm) REVERT: FN 2 LEU cc_start: 0.8294 (pt) cc_final: 0.6580 (mm) outliers start: 206 outliers final: 126 residues processed: 536 average time/residue: 0.2831 time to fit residues: 241.1466 Evaluate side-chains 555 residues out of total 2400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 135 poor density : 420 time to evaluate : 2.561 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 SER Chi-restraints excluded: chain D residue 1 ASP 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 P residue 7 ILE Chi-restraints excluded: chain S residue 8 SER Chi-restraints excluded: chain V residue 1 ASP Chi-restraints excluded: chain V residue 5 LYS Chi-restraints excluded: chain W residue 9 VAL Chi-restraints excluded: chain Y residue 2 LEU Chi-restraints excluded: chain b residue 9 VAL Chi-restraints excluded: chain d residue 8 SER Chi-restraints excluded: chain g residue 2 LEU Chi-restraints excluded: chain j residue 8 SER Chi-restraints excluded: chain k residue 9 VAL Chi-restraints excluded: chain m residue 1 ASP Chi-restraints excluded: chain m residue 8 SER Chi-restraints excluded: chain n residue 9 VAL Chi-restraints excluded: chain o residue 11 ILE Chi-restraints excluded: chain p residue 2 LEU 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 AB residue 8 SER Chi-restraints excluded: chain AC residue 9 VAL Chi-restraints excluded: chain AE residue 1 ASP 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 1 ASP 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 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 4 ILE Chi-restraints excluded: chain BC residue 9 VAL Chi-restraints excluded: chain BE residue 1 ASP Chi-restraints excluded: chain BE residue 8 SER Chi-restraints excluded: chain BF residue 9 VAL Chi-restraints excluded: chain BG residue 11 ILE Chi-restraints excluded: chain BH residue 8 SER Chi-restraints excluded: chain BK residue 4 ILE Chi-restraints excluded: chain BL residue 9 VAL Chi-restraints excluded: chain BQ residue 2 LEU Chi-restraints excluded: chain BU residue 9 VAL Chi-restraints excluded: chain BW residue 1 ASP 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 B0 residue 3 ILE Chi-restraints excluded: chain B2 residue 4 ILE Chi-restraints excluded: chain B3 residue 9 VAL Chi-restraints excluded: chain B5 residue 1 ASP Chi-restraints excluded: chain B8 residue 2 LEU 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 6 residue 1 ASP Chi-restraints excluded: chain 4 residue 11 ILE Chi-restraints excluded: chain 7 residue 2 LEU Chi-restraints excluded: chain 7 residue 7 ILE Chi-restraints excluded: chain CL residue 9 VAL Chi-restraints excluded: chain CN residue 1 ASP 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 1 ASP Chi-restraints excluded: chain C5 residue 8 SER 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 1 ASP 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 DU residue 9 VAL Chi-restraints excluded: chain DW residue 1 ASP Chi-restraints excluded: chain D3 residue 9 VAL Chi-restraints excluded: chain D5 residue 8 SER Chi-restraints excluded: chain D8 residue 7 ILE Chi-restraints excluded: chain EB residue 8 SER Chi-restraints excluded: chain EC residue 9 VAL Chi-restraints excluded: chain EE residue 1 ASP Chi-restraints excluded: chain EH residue 2 LEU Chi-restraints excluded: chain EL residue 9 VAL Chi-restraints excluded: chain EN residue 1 ASP Chi-restraints excluded: chain EQ residue 7 ILE Chi-restraints excluded: chain EQ residue 8 SER Chi-restraints excluded: chain EU residue 9 VAL Chi-restraints excluded: chain EW residue 1 ASP 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 1 ASP 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 FB residue 8 SER Chi-restraints excluded: chain FC residue 9 VAL Chi-restraints excluded: chain FE residue 1 ASP 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 FN residue 1 ASP Chi-restraints excluded: chain FN residue 8 SER Chi-restraints excluded: chain FO residue 9 VAL Chi-restraints excluded: chain FU residue 9 VAL Chi-restraints excluded: chain FW residue 1 ASP 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: 30.0000 chunk 115 optimal weight: 30.0000 chunk 2 optimal weight: 5.9990 chunk 151 optimal weight: 30.0000 chunk 83 optimal weight: 20.0000 chunk 173 optimal weight: 30.0000 chunk 140 optimal weight: 30.0000 chunk 0 optimal weight: 20.0000 chunk 103 optimal weight: 30.0000 chunk 182 optimal weight: 30.0000 chunk 51 optimal weight: 0.9980 overall best weight: 15.3994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: j 10 HIS ** B5 10 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** CE 10 HIS 2 10 HIS ** 6 10 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** DE 10 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** EE 10 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** EK 10 HIS ** E8 10 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** FH 10 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** FN 10 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** FQ 10 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** FZ 10 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7275 moved from start: 0.3200 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.059 20370 Z= 0.320 Angle : 0.813 11.011 27210 Z= 0.352 Chirality : 0.059 0.202 3840 Planarity : 0.002 0.008 3060 Dihedral : 11.962 58.100 2580 Min Nonbonded Distance : 2.281 Molprobity Statistics. All-atom Clashscore : 8.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 10.29 % Allowed : 21.92 % Favored : 67.79 % 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: -1.57 (0.17), residues: 2100 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.19 (0.13), residues: 2100 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.007 0.002 HISEO 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 728 residues out of total 2400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 247 poor density : 481 time to evaluate : 2.638 Fit side-chains REVERT: A 5 LYS cc_start: 0.8069 (mttt) cc_final: 0.7622 (mttp) REVERT: M 5 LYS cc_start: 0.7876 (mttt) cc_final: 0.7540 (mttm) REVERT: P 5 LYS cc_start: 0.6195 (mmmt) cc_final: 0.5036 (pttm) REVERT: S 5 LYS cc_start: 0.7952 (mttt) cc_final: 0.7726 (mttp) REVERT: V 2 LEU cc_start: 0.8501 (pt) cc_final: 0.8012 (tt) REVERT: j 5 LYS cc_start: 0.8119 (mttt) cc_final: 0.7782 (mttp) REVERT: s 4 ILE cc_start: 0.7509 (OUTLIER) cc_final: 0.7263 (mp) REVERT: v 5 LYS cc_start: 0.7475 (mttt) cc_final: 0.7205 (mttm) REVERT: x 3 ILE cc_start: 0.7602 (mt) cc_final: 0.7363 (mt) REVERT: AB 5 LYS cc_start: 0.8043 (mttt) cc_final: 0.7528 (mttp) REVERT: AE 5 LYS cc_start: 0.7811 (mttt) cc_final: 0.7325 (mttm) REVERT: AK 4 ILE cc_start: 0.7527 (OUTLIER) cc_final: 0.7217 (mp) REVERT: AN 5 LYS cc_start: 0.7558 (mttt) cc_final: 0.7176 (mttm) REVERT: AT 5 LYS cc_start: 0.7859 (mttt) cc_final: 0.7417 (mttp) REVERT: A2 4 ILE cc_start: 0.7539 (OUTLIER) cc_final: 0.7261 (mp) REVERT: A5 5 LYS cc_start: 0.7539 (mttm) cc_final: 0.7318 (mttp) REVERT: BB 5 LYS cc_start: 0.7855 (mttt) cc_final: 0.7423 (mttp) REVERT: BE 5 LYS cc_start: 0.7760 (mttt) cc_final: 0.7269 (mttp) REVERT: BK 4 ILE cc_start: 0.7273 (OUTLIER) cc_final: 0.6958 (mp) REVERT: BN 3 ILE cc_start: 0.8515 (mt) cc_final: 0.8306 (mp) REVERT: BW 5 LYS cc_start: 0.7709 (mttt) cc_final: 0.7313 (mttm) REVERT: B2 4 ILE cc_start: 0.7660 (OUTLIER) cc_final: 0.7393 (mp) REVERT: 1 4 ILE cc_start: 0.7571 (OUTLIER) cc_final: 0.7318 (mp) REVERT: 6 5 LYS cc_start: 0.7362 (mttt) cc_final: 0.6797 (mttm) REVERT: CR 5 LYS cc_start: 0.8786 (OUTLIER) cc_final: 0.8333 (mtmm) REVERT: CW 5 LYS cc_start: 0.7505 (mttt) cc_final: 0.7019 (mttm) REVERT: DE 5 LYS cc_start: 0.7485 (mttt) cc_final: 0.7007 (mttm) REVERT: EB 5 LYS cc_start: 0.8069 (mttt) cc_final: 0.7571 (mttp) REVERT: EE 5 LYS cc_start: 0.7306 (mttt) cc_final: 0.6880 (mttm) REVERT: EK 5 LYS cc_start: 0.7779 (mttt) cc_final: 0.7397 (mttp) REVERT: E5 5 LYS cc_start: 0.7669 (mttt) cc_final: 0.7294 (mttp) REVERT: FE 2 LEU cc_start: 0.8561 (pp) cc_final: 0.7041 (mm) REVERT: FE 3 ILE cc_start: 0.8837 (mt) cc_final: 0.8535 (mp) REVERT: FE 5 LYS cc_start: 0.8324 (mttt) cc_final: 0.7913 (mttm) REVERT: FT 4 ILE cc_start: 0.7747 (OUTLIER) cc_final: 0.7543 (mp) outliers start: 247 outliers final: 169 residues processed: 589 average time/residue: 0.2892 time to fit residues: 267.1535 Evaluate side-chains 632 residues out of total 2400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 177 poor density : 455 time to evaluate : 3.313 ------------------------------------------------------------------------------- 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 D residue 1 ASP 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 M residue 8 SER Chi-restraints excluded: chain P residue 2 LEU Chi-restraints excluded: chain P residue 7 ILE Chi-restraints excluded: chain S residue 8 SER Chi-restraints excluded: chain T residue 9 VAL Chi-restraints excluded: chain V residue 1 ASP 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 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 1 ASP 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 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 AB residue 8 SER Chi-restraints excluded: chain AC residue 9 VAL Chi-restraints excluded: chain AE residue 1 ASP 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 AT residue 8 SER Chi-restraints excluded: chain AU residue 9 VAL Chi-restraints excluded: chain AW residue 1 ASP 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 A5 residue 8 SER Chi-restraints excluded: chain A8 residue 2 LEU Chi-restraints excluded: chain A8 residue 7 ILE Chi-restraints excluded: chain BC residue 9 VAL Chi-restraints excluded: chain BE residue 1 ASP Chi-restraints excluded: chain BE residue 4 ILE Chi-restraints excluded: chain BE residue 8 SER Chi-restraints excluded: chain BF residue 9 VAL Chi-restraints excluded: chain BH residue 2 LEU Chi-restraints excluded: chain BH residue 7 ILE Chi-restraints excluded: chain BH residue 9 VAL Chi-restraints excluded: chain BI residue 3 ILE Chi-restraints excluded: chain BK residue 4 ILE Chi-restraints excluded: chain BL residue 9 VAL Chi-restraints excluded: chain BN residue 8 SER Chi-restraints excluded: chain 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 BT residue 4 ILE Chi-restraints excluded: chain BU residue 9 VAL Chi-restraints excluded: chain BW residue 1 ASP 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 B0 residue 3 ILE Chi-restraints excluded: chain B2 residue 4 ILE Chi-restraints excluded: chain B3 residue 9 VAL Chi-restraints excluded: chain B5 residue 1 ASP Chi-restraints excluded: chain B8 residue 2 LEU Chi-restraints excluded: chain B8 residue 7 ILE Chi-restraints excluded: chain B8 residue 9 VAL Chi-restraints excluded: chain CB residue 8 SER Chi-restraints excluded: chain CC residue 9 VAL Chi-restraints excluded: chain CE residue 8 SER Chi-restraints excluded: chain CG residue 4 ILE 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 6 residue 1 ASP 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 1 ASP 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 8 SER 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 1 ASP 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 1 ASP 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 7 ILE Chi-restraints excluded: chain DL residue 9 VAL Chi-restraints excluded: chain DN residue 1 ASP Chi-restraints excluded: chain DN residue 8 SER Chi-restraints excluded: chain DO residue 9 VAL Chi-restraints excluded: chain DQ residue 2 LEU Chi-restraints excluded: chain DQ residue 7 ILE Chi-restraints excluded: chain DR residue 3 ILE Chi-restraints excluded: chain DU residue 9 VAL Chi-restraints excluded: chain DW residue 1 ASP 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 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 EE residue 1 ASP Chi-restraints excluded: chain EG residue 11 ILE Chi-restraints excluded: chain EH residue 2 LEU Chi-restraints excluded: chain EH residue 7 ILE Chi-restraints excluded: chain EK residue 4 ILE Chi-restraints excluded: chain EL residue 9 VAL Chi-restraints excluded: chain EN residue 1 ASP 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 ET residue 1 ASP Chi-restraints excluded: chain EU residue 9 VAL Chi-restraints excluded: chain EW residue 1 ASP 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 1 ASP Chi-restraints excluded: chain E5 residue 8 SER Chi-restraints excluded: chain E8 residue 2 LEU Chi-restraints excluded: chain E9 residue 3 ILE Chi-restraints excluded: chain FB residue 8 SER Chi-restraints excluded: chain FC residue 9 VAL Chi-restraints excluded: chain FE residue 1 ASP Chi-restraints excluded: chain FH residue 2 LEU Chi-restraints excluded: chain FK residue 8 SER Chi-restraints excluded: chain FK residue 9 VAL Chi-restraints excluded: chain FL residue 9 VAL Chi-restraints excluded: chain FN residue 1 ASP Chi-restraints excluded: chain FN residue 8 SER Chi-restraints excluded: chain FQ residue 2 LEU Chi-restraints excluded: chain FT residue 4 ILE Chi-restraints excluded: chain FU residue 9 VAL Chi-restraints excluded: chain FW residue 1 ASP 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: 9.9990 chunk 182 optimal weight: 7.9990 chunk 40 optimal weight: 10.0000 chunk 119 optimal weight: 0.7980 chunk 50 optimal weight: 7.9990 chunk 203 optimal weight: 20.0000 chunk 168 optimal weight: 4.9990 chunk 94 optimal weight: 30.0000 chunk 16 optimal weight: 20.0000 chunk 67 optimal weight: 7.9990 chunk 106 optimal weight: 0.9990 overall best weight: 4.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B5 10 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 10 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** DE 10 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** EE 10 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** FH 10 HIS ** FN 10 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** FQ 10 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** FZ 10 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7233 moved from start: 0.3348 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 20370 Z= 0.119 Angle : 0.620 9.538 27210 Z= 0.256 Chirality : 0.057 0.166 3840 Planarity : 0.001 0.008 3060 Dihedral : 10.448 55.481 2580 Min Nonbonded Distance : 2.321 Molprobity Statistics. All-atom Clashscore : 6.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.81 % Favored : 99.19 % Rotamer: Outliers : 8.92 % Allowed : 23.88 % Favored : 67.21 % 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: -1.04 (0.18), residues: 2100 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.78 (0.14), residues: 2100 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HISB5 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 662 residues out of total 2400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 214 poor density : 448 time to evaluate : 2.434 Fit side-chains REVERT: D 2 LEU cc_start: 0.8472 (pt) cc_final: 0.8157 (tt) REVERT: M 2 LEU cc_start: 0.8362 (pt) cc_final: 0.7841 (tt) REVERT: M 5 LYS cc_start: 0.7774 (mttt) cc_final: 0.7524 (mttm) REVERT: P 5 LYS cc_start: 0.6035 (mmmt) cc_final: 0.4860 (pttm) REVERT: U 3 ILE cc_start: 0.7875 (OUTLIER) cc_final: 0.7343 (mp) REVERT: V 2 LEU cc_start: 0.8568 (pt) cc_final: 0.8097 (tt) REVERT: V 10 HIS cc_start: 0.8193 (t70) cc_final: 0.7982 (t-90) REVERT: v 5 LYS cc_start: 0.7390 (mttt) cc_final: 0.7139 (mttm) REVERT: x 3 ILE cc_start: 0.7659 (mt) cc_final: 0.7452 (mt) REVERT: AE 5 LYS cc_start: 0.7741 (mttt) cc_final: 0.7339 (mttm) REVERT: AK 4 ILE cc_start: 0.7525 (OUTLIER) cc_final: 0.7243 (mp) REVERT: AN 5 LYS cc_start: 0.7365 (mttt) cc_final: 0.7030 (mttm) REVERT: AV 3 ILE cc_start: 0.7607 (OUTLIER) cc_final: 0.7051 (mp) REVERT: A2 4 ILE cc_start: 0.7530 (OUTLIER) cc_final: 0.7253 (mp) REVERT: BB 5 LYS cc_start: 0.7611 (mttt) cc_final: 0.7245 (mttp) REVERT: BE 5 LYS cc_start: 0.7779 (mttt) cc_final: 0.7315 (mttm) REVERT: BK 4 ILE cc_start: 0.7373 (OUTLIER) cc_final: 0.7086 (mp) REVERT: BN 3 ILE cc_start: 0.8503 (mt) cc_final: 0.8268 (mp) REVERT: BW 5 LYS cc_start: 0.7650 (mttt) cc_final: 0.7290 (mttm) REVERT: B2 4 ILE cc_start: 0.7636 (OUTLIER) cc_final: 0.7340 (mp) REVERT: B5 5 LYS cc_start: 0.7777 (mttm) cc_final: 0.7457 (mttm) REVERT: CD 3 ILE cc_start: 0.7840 (OUTLIER) cc_final: 0.7301 (mp) REVERT: 1 4 ILE cc_start: 0.7583 (OUTLIER) cc_final: 0.7347 (mp) REVERT: 6 2 LEU cc_start: 0.8264 (pt) cc_final: 0.7990 (pp) REVERT: 6 5 LYS cc_start: 0.7329 (mttt) cc_final: 0.6831 (mttm) REVERT: CN 2 LEU cc_start: 0.7876 (pt) cc_final: 0.7612 (pp) REVERT: CR 5 LYS cc_start: 0.8744 (OUTLIER) cc_final: 0.8534 (mtmm) REVERT: CW 5 LYS cc_start: 0.7556 (mttt) cc_final: 0.7082 (mttm) REVERT: DE 5 LYS cc_start: 0.7307 (mttt) cc_final: 0.6837 (mttm) REVERT: DM 3 ILE cc_start: 0.7791 (OUTLIER) cc_final: 0.7213 (mp) REVERT: D4 3 ILE cc_start: 0.7845 (OUTLIER) cc_final: 0.7315 (mp) REVERT: EE 5 LYS cc_start: 0.7290 (mttt) cc_final: 0.6908 (mttm) REVERT: E5 5 LYS cc_start: 0.7507 (mttt) cc_final: 0.7154 (mttp) REVERT: FE 2 LEU cc_start: 0.8323 (pp) cc_final: 0.6659 (mm) REVERT: FE 3 ILE cc_start: 0.8705 (mt) cc_final: 0.8319 (mp) REVERT: FE 5 LYS cc_start: 0.8207 (mttt) cc_final: 0.7790 (mttm) REVERT: FN 2 LEU cc_start: 0.8429 (pt) cc_final: 0.6803 (mm) outliers start: 214 outliers final: 147 residues processed: 530 average time/residue: 0.2770 time to fit residues: 233.7779 Evaluate side-chains 579 residues out of total 2400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 158 poor density : 421 time to evaluate : 2.629 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 SER Chi-restraints excluded: chain D residue 1 ASP 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 7 ILE Chi-restraints excluded: chain S residue 8 SER Chi-restraints excluded: chain U residue 3 ILE Chi-restraints excluded: chain V residue 1 ASP 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 b residue 9 VAL Chi-restraints excluded: chain d residue 8 SER Chi-restraints excluded: chain g residue 2 LEU Chi-restraints excluded: chain g residue 9 VAL Chi-restraints excluded: chain j residue 8 SER Chi-restraints excluded: chain k residue 9 VAL Chi-restraints excluded: chain m residue 1 ASP 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 9 VAL Chi-restraints excluded: chain q residue 3 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 AB residue 8 SER Chi-restraints excluded: chain AC residue 9 VAL Chi-restraints excluded: chain AE residue 1 ASP Chi-restraints excluded: chain AE residue 8 SER Chi-restraints excluded: chain AF residue 9 VAL Chi-restraints excluded: chain AH residue 2 LEU Chi-restraints excluded: chain AI residue 3 ILE Chi-restraints excluded: chain AK residue 4 ILE Chi-restraints excluded: chain AL residue 9 VAL Chi-restraints excluded: chain 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 1 ASP 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 A5 residue 1 ASP 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 1 ASP 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 BW residue 1 ASP Chi-restraints excluded: chain BW residue 8 SER Chi-restraints excluded: chain BX residue 9 VAL Chi-restraints excluded: chain BZ residue 2 LEU Chi-restraints excluded: chain BZ residue 9 VAL Chi-restraints excluded: chain B0 residue 3 ILE Chi-restraints excluded: chain B2 residue 4 ILE Chi-restraints excluded: chain B3 residue 9 VAL Chi-restraints excluded: chain B5 residue 1 ASP 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 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 1 ASP Chi-restraints excluded: chain CK residue 8 SER Chi-restraints excluded: chain CL residue 9 VAL Chi-restraints excluded: chain CN residue 1 ASP 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 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 1 ASP 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 DL residue 9 VAL Chi-restraints excluded: chain DM residue 3 ILE Chi-restraints excluded: chain DN residue 1 ASP 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 DU residue 9 VAL Chi-restraints excluded: chain DW residue 1 ASP 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 7 ILE Chi-restraints excluded: chain EB residue 8 SER Chi-restraints excluded: chain EC residue 9 VAL Chi-restraints excluded: chain EE residue 1 ASP Chi-restraints excluded: chain EH residue 2 LEU Chi-restraints excluded: chain EH residue 9 VAL Chi-restraints excluded: chain EL residue 9 VAL Chi-restraints excluded: chain EN residue 1 ASP 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 EW residue 1 ASP 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 1 ASP 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 FE residue 1 ASP 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 FN residue 1 ASP Chi-restraints excluded: chain FN residue 8 SER Chi-restraints excluded: chain FU residue 9 VAL Chi-restraints excluded: chain FW residue 1 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 195 optimal weight: 0.6980 chunk 22 optimal weight: 30.0000 chunk 115 optimal weight: 7.9990 chunk 148 optimal weight: 2.9990 chunk 114 optimal weight: 30.0000 chunk 171 optimal weight: 20.0000 chunk 113 optimal weight: 7.9990 chunk 202 optimal weight: 0.5980 chunk 126 optimal weight: 1.9990 chunk 123 optimal weight: 30.0000 chunk 93 optimal weight: 5.9990 overall best weight: 2.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 10 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** BE 10 HIS B5 10 HIS ** 6 10 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ED 10 HIS ** EE 10 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E4 10 HIS FN 10 HIS ** FQ 10 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** FZ 10 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7208 moved from start: 0.3577 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 20370 Z= 0.086 Angle : 0.600 9.596 27210 Z= 0.241 Chirality : 0.057 0.174 3840 Planarity : 0.001 0.012 3060 Dihedral : 9.750 54.901 2580 Min Nonbonded Distance : 2.272 Molprobity Statistics. All-atom Clashscore : 5.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.71 % Favored : 98.29 % Rotamer: Outliers : 7.79 % Allowed : 24.54 % 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: -0.59 (0.18), residues: 2100 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.44 (0.14), residues: 2100 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.000 HISB5 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 623 residues out of total 2400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 187 poor density : 436 time to evaluate : 2.441 Fit side-chains REVERT: M 5 LYS cc_start: 0.7758 (mttt) cc_final: 0.7513 (mttm) REVERT: P 5 LYS cc_start: 0.6189 (mmmt) cc_final: 0.5041 (pttm) REVERT: U 3 ILE cc_start: 0.7905 (OUTLIER) cc_final: 0.7402 (mp) REVERT: V 2 LEU cc_start: 0.8595 (pt) cc_final: 0.8254 (tt) REVERT: m 3 ILE cc_start: 0.8589 (mt) cc_final: 0.8371 (mp) REVERT: s 4 ILE cc_start: 0.7527 (OUTLIER) cc_final: 0.7299 (mp) REVERT: v 5 LYS cc_start: 0.7391 (mttt) cc_final: 0.7073 (mttm) REVERT: AE 5 LYS cc_start: 0.7544 (mttt) cc_final: 0.7206 (mttm) REVERT: AN 5 LYS cc_start: 0.7369 (mttt) cc_final: 0.7020 (mttm) REVERT: BE 2 LEU cc_start: 0.8027 (pt) cc_final: 0.7819 (pp) REVERT: BE 5 LYS cc_start: 0.7671 (mttt) cc_final: 0.7361 (mttm) REVERT: BN 3 ILE cc_start: 0.8442 (mt) cc_final: 0.8224 (mp) REVERT: BW 5 LYS cc_start: 0.7744 (mttt) cc_final: 0.7415 (mttm) REVERT: B5 5 LYS cc_start: 0.7906 (mttm) cc_final: 0.7619 (mttm) REVERT: CD 3 ILE cc_start: 0.7864 (OUTLIER) cc_final: 0.7312 (mp) REVERT: CE 3 ILE cc_start: 0.8482 (mt) cc_final: 0.8069 (mp) REVERT: 6 2 LEU cc_start: 0.8284 (pt) cc_final: 0.8002 (pp) REVERT: 6 5 LYS cc_start: 0.7321 (mttt) cc_final: 0.6878 (mttm) REVERT: CW 5 LYS cc_start: 0.7530 (mttt) cc_final: 0.7073 (mttm) REVERT: C5 3 ILE cc_start: 0.8364 (mt) cc_final: 0.8092 (mp) REVERT: C5 5 LYS cc_start: 0.7517 (mttt) cc_final: 0.7128 (mttm) REVERT: DE 5 LYS cc_start: 0.7359 (mttt) cc_final: 0.6947 (mttm) REVERT: DM 3 ILE cc_start: 0.7916 (OUTLIER) cc_final: 0.7384 (mp) REVERT: D4 3 ILE cc_start: 0.7817 (OUTLIER) cc_final: 0.7294 (mp) REVERT: D5 3 ILE cc_start: 0.8375 (mt) cc_final: 0.8079 (mp) REVERT: EE 5 LYS cc_start: 0.7235 (mttt) cc_final: 0.6878 (mttm) REVERT: EW 3 ILE cc_start: 0.8334 (mt) cc_final: 0.8096 (mp) REVERT: E5 5 LYS cc_start: 0.7416 (mttt) cc_final: 0.7102 (mttp) REVERT: FE 2 LEU cc_start: 0.8305 (pp) cc_final: 0.6631 (mm) REVERT: FE 3 ILE cc_start: 0.8694 (mt) cc_final: 0.8287 (mp) REVERT: FE 5 LYS cc_start: 0.8194 (mttt) cc_final: 0.7813 (mttm) REVERT: FN 2 LEU cc_start: 0.8230 (pt) cc_final: 0.6529 (mm) outliers start: 187 outliers final: 136 residues processed: 515 average time/residue: 0.2724 time to fit residues: 225.2090 Evaluate side-chains 553 residues out of total 2400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 141 poor density : 412 time to evaluate : 2.611 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 SER Chi-restraints excluded: chain D residue 1 ASP Chi-restraints excluded: chain G residue 2 LEU Chi-restraints excluded: chain M residue 8 SER Chi-restraints excluded: chain P residue 7 ILE Chi-restraints excluded: chain S residue 8 SER Chi-restraints excluded: chain U residue 3 ILE Chi-restraints excluded: chain V residue 1 ASP Chi-restraints excluded: chain V residue 8 SER Chi-restraints excluded: chain W residue 9 VAL Chi-restraints excluded: chain b residue 9 VAL 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 1 ASP 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 9 VAL 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 7 ILE Chi-restraints excluded: chain y residue 9 VAL Chi-restraints excluded: chain AB residue 8 SER Chi-restraints excluded: chain AC residue 9 VAL Chi-restraints excluded: chain AE residue 1 ASP Chi-restraints excluded: chain AE residue 8 SER Chi-restraints excluded: chain AF residue 9 VAL Chi-restraints excluded: chain AH residue 2 LEU Chi-restraints excluded: chain AI residue 3 ILE Chi-restraints excluded: chain 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 7 ILE Chi-restraints excluded: chain AT residue 8 SER Chi-restraints excluded: chain AU residue 9 VAL Chi-restraints excluded: chain AW residue 1 ASP 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 5 LYS Chi-restraints excluded: chain A3 residue 9 VAL Chi-restraints excluded: chain A5 residue 1 ASP 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 1 ASP 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 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 1 ASP 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 B3 residue 9 VAL Chi-restraints excluded: chain B5 residue 2 LEU 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 CI residue 3 ILE Chi-restraints excluded: chain CI residue 5 LYS Chi-restraints excluded: chain 3 residue 9 VAL Chi-restraints excluded: chain 7 residue 2 LEU Chi-restraints excluded: chain CK residue 8 SER Chi-restraints excluded: chain CL residue 9 VAL Chi-restraints excluded: chain CN residue 1 ASP 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 CU residue 9 VAL Chi-restraints excluded: chain CW residue 1 ASP Chi-restraints excluded: chain CZ residue 7 ILE Chi-restraints excluded: chain C3 residue 9 VAL Chi-restraints excluded: chain C5 residue 1 ASP 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 DL residue 9 VAL Chi-restraints excluded: chain DM residue 3 ILE Chi-restraints excluded: chain DN residue 1 ASP 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 DU residue 9 VAL Chi-restraints excluded: chain DW residue 1 ASP Chi-restraints excluded: chain DX 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 D6 residue 9 VAL Chi-restraints excluded: chain D8 residue 2 LEU Chi-restraints excluded: chain D8 residue 7 ILE Chi-restraints excluded: chain D8 residue 9 VAL Chi-restraints excluded: chain EC residue 9 VAL Chi-restraints excluded: chain EE residue 1 ASP Chi-restraints excluded: chain EH residue 2 LEU Chi-restraints excluded: chain EH residue 7 ILE Chi-restraints excluded: chain EH residue 9 VAL Chi-restraints excluded: chain EL residue 9 VAL Chi-restraints excluded: chain EN residue 1 ASP 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 EW residue 1 ASP 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 1 ASP 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 E8 residue 8 SER Chi-restraints excluded: chain FC residue 9 VAL Chi-restraints excluded: chain FE residue 1 ASP 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 FN residue 1 ASP Chi-restraints excluded: chain FO residue 9 VAL Chi-restraints excluded: chain FU residue 9 VAL Chi-restraints excluded: chain FW residue 1 ASP Chi-restraints excluded: chain FX residue 9 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 125 optimal weight: 30.0000 chunk 80 optimal weight: 8.9990 chunk 120 optimal weight: 3.9990 chunk 60 optimal weight: 30.0000 chunk 39 optimal weight: 9.9990 chunk 128 optimal weight: 8.9990 chunk 137 optimal weight: 30.0000 chunk 100 optimal weight: 30.0000 chunk 18 optimal weight: 20.0000 chunk 159 optimal weight: 30.0000 chunk 184 optimal weight: 30.0000 overall best weight: 10.3992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 10 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 10 HIS l 10 HIS AP 10 HIS A7 10 HIS BT 10 HIS ** 6 10 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** DG 10 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** DY 10 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** EE 10 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** EG 10 HIS ** FQ 10 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7254 moved from start: 0.3616 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.044 20370 Z= 0.227 Angle : 0.744 10.433 27210 Z= 0.312 Chirality : 0.058 0.178 3840 Planarity : 0.002 0.014 3060 Dihedral : 11.019 55.417 2580 Min Nonbonded Distance : 2.286 Molprobity Statistics. All-atom Clashscore : 7.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.52 % Favored : 96.48 % Rotamer: Outliers : 8.96 % Allowed : 23.92 % Favored : 67.12 % 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: -0.79 (0.18), residues: 2100 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.59 (0.14), residues: 2100 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HISD6 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 675 residues out of total 2400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 215 poor density : 460 time to evaluate : 2.390 Fit side-chains REVERT: J 5 LYS cc_start: 0.7929 (mttt) cc_final: 0.7595 (mttp) REVERT: M 5 LYS cc_start: 0.7663 (mttt) cc_final: 0.7414 (mttm) REVERT: P 5 LYS cc_start: 0.6100 (mmmt) cc_final: 0.4953 (pttm) REVERT: S 5 LYS cc_start: 0.7956 (mttt) cc_final: 0.7739 (mttp) REVERT: U 3 ILE cc_start: 0.7822 (OUTLIER) cc_final: 0.7270 (mp) REVERT: V 2 LEU cc_start: 0.8603 (pt) cc_final: 0.8209 (tt) REVERT: V 10 HIS cc_start: 0.8260 (t70) cc_final: 0.8014 (t-90) REVERT: j 5 LYS cc_start: 0.8022 (mttt) cc_final: 0.7519 (mttp) REVERT: s 4 ILE cc_start: 0.7421 (OUTLIER) cc_final: 0.7163 (mp) REVERT: v 5 LYS cc_start: 0.7397 (mttt) cc_final: 0.6997 (mttm) REVERT: x 3 ILE cc_start: 0.7505 (mt) cc_final: 0.7289 (mt) REVERT: AB 5 LYS cc_start: 0.7814 (mttt) cc_final: 0.7296 (mttp) REVERT: AD 3 ILE cc_start: 0.7712 (OUTLIER) cc_final: 0.7163 (mp) REVERT: AE 5 LYS cc_start: 0.7599 (mttt) cc_final: 0.7254 (mttm) REVERT: AK 4 ILE cc_start: 0.7455 (OUTLIER) cc_final: 0.7137 (mp) REVERT: AN 5 LYS cc_start: 0.7328 (mttt) cc_final: 0.7031 (mttm) REVERT: AV 3 ILE cc_start: 0.7618 (OUTLIER) cc_final: 0.7059 (mp) REVERT: A2 4 ILE cc_start: 0.7396 (OUTLIER) cc_final: 0.7121 (mp) REVERT: BB 5 LYS cc_start: 0.7745 (mttt) cc_final: 0.7374 (mttp) REVERT: BE 5 LYS cc_start: 0.7650 (mttt) cc_final: 0.7287 (mtpp) REVERT: BK 4 ILE cc_start: 0.7230 (OUTLIER) cc_final: 0.6921 (mp) REVERT: BN 3 ILE cc_start: 0.8532 (mt) cc_final: 0.8305 (mp) REVERT: BW 5 LYS cc_start: 0.7582 (mttt) cc_final: 0.7304 (mttm) REVERT: B2 4 ILE cc_start: 0.7489 (OUTLIER) cc_final: 0.7256 (mp) REVERT: B5 5 LYS cc_start: 0.7594 (mttm) cc_final: 0.7310 (mttm) REVERT: CD 3 ILE cc_start: 0.7773 (OUTLIER) cc_final: 0.7219 (mp) REVERT: 1 4 ILE cc_start: 0.7494 (OUTLIER) cc_final: 0.7264 (mp) REVERT: 6 5 LYS cc_start: 0.7328 (mttt) cc_final: 0.6870 (mttm) REVERT: CK 5 LYS cc_start: 0.7842 (mttt) cc_final: 0.7389 (mttp) REVERT: CW 5 LYS cc_start: 0.7364 (mttt) cc_final: 0.6913 (mttm) REVERT: DE 5 LYS cc_start: 0.7348 (mttt) cc_final: 0.6881 (mttm) REVERT: DM 3 ILE cc_start: 0.7809 (OUTLIER) cc_final: 0.7242 (mp) REVERT: D4 3 ILE cc_start: 0.7821 (OUTLIER) cc_final: 0.7263 (mp) REVERT: EE 5 LYS cc_start: 0.7313 (mttt) cc_final: 0.6929 (mttm) REVERT: EK 5 LYS cc_start: 0.7876 (mttt) cc_final: 0.7508 (mttp) REVERT: E5 5 LYS cc_start: 0.7333 (mttt) cc_final: 0.6957 (mttp) REVERT: FE 2 LEU cc_start: 0.8531 (pp) cc_final: 0.6914 (mm) REVERT: FE 3 ILE cc_start: 0.8792 (mt) cc_final: 0.8485 (mp) REVERT: FE 5 LYS cc_start: 0.8247 (mttt) cc_final: 0.7852 (mttm) REVERT: FM 3 ILE cc_start: 0.8324 (OUTLIER) cc_final: 0.7781 (mp) REVERT: FT 5 LYS cc_start: 0.8623 (mttt) cc_final: 0.8122 (mttp) outliers start: 215 outliers final: 156 residues processed: 541 average time/residue: 0.2763 time to fit residues: 238.5062 Evaluate side-chains 613 residues out of total 2400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 169 poor density : 444 time to evaluate : 3.140 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 SER Chi-restraints excluded: chain D residue 1 ASP Chi-restraints excluded: chain G residue 2 LEU Chi-restraints excluded: chain G residue 9 VAL Chi-restraints excluded: chain M residue 2 LEU Chi-restraints excluded: chain M residue 8 SER Chi-restraints excluded: chain P residue 2 LEU Chi-restraints excluded: chain P residue 7 ILE Chi-restraints excluded: chain S residue 8 SER Chi-restraints excluded: chain U residue 3 ILE Chi-restraints excluded: chain V residue 1 ASP 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 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 9 VAL Chi-restraints excluded: chain k residue 9 VAL Chi-restraints excluded: chain m residue 1 ASP 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 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 AB residue 8 SER Chi-restraints excluded: chain AC residue 9 VAL Chi-restraints excluded: chain AD residue 3 ILE Chi-restraints excluded: chain AE residue 1 ASP Chi-restraints excluded: chain AE residue 8 SER Chi-restraints excluded: chain AF residue 9 VAL Chi-restraints excluded: chain AH residue 2 LEU Chi-restraints excluded: chain AI residue 3 ILE Chi-restraints excluded: chain AK residue 4 ILE Chi-restraints excluded: chain AL residue 9 VAL Chi-restraints excluded: chain AN residue 8 SER Chi-restraints excluded: chain 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 1 ASP 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 A5 residue 1 ASP Chi-restraints excluded: chain A5 residue 8 SER Chi-restraints excluded: chain A8 residue 2 LEU Chi-restraints excluded: chain A8 residue 7 ILE Chi-restraints excluded: chain BC residue 9 VAL Chi-restraints excluded: chain BE residue 1 ASP Chi-restraints excluded: chain BE residue 8 SER Chi-restraints excluded: chain BF residue 9 VAL Chi-restraints excluded: chain BH residue 2 LEU Chi-restraints excluded: chain BH residue 7 ILE Chi-restraints excluded: chain BH residue 9 VAL Chi-restraints excluded: chain BI residue 3 ILE Chi-restraints excluded: chain BK residue 4 ILE Chi-restraints excluded: chain BL residue 9 VAL Chi-restraints excluded: chain BO residue 9 VAL Chi-restraints excluded: chain BQ residue 2 LEU Chi-restraints excluded: chain BQ residue 7 ILE Chi-restraints excluded: chain BU residue 9 VAL Chi-restraints excluded: chain BW residue 1 ASP Chi-restraints excluded: chain BW residue 8 SER Chi-restraints excluded: chain BX residue 9 VAL Chi-restraints excluded: chain BZ residue 2 LEU Chi-restraints excluded: chain BZ residue 5 LYS Chi-restraints excluded: chain BZ residue 9 VAL Chi-restraints excluded: chain B0 residue 3 ILE Chi-restraints excluded: chain B2 residue 4 ILE Chi-restraints excluded: chain B3 residue 9 VAL Chi-restraints excluded: chain B5 residue 1 ASP Chi-restraints excluded: chain B5 residue 2 LEU Chi-restraints excluded: chain B5 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 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 1 ASP 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 1 ASP Chi-restraints excluded: chain CN residue 8 SER Chi-restraints excluded: chain CO residue 9 VAL Chi-restraints excluded: chain CQ residue 9 VAL Chi-restraints excluded: chain CU residue 9 VAL Chi-restraints excluded: chain CW residue 1 ASP Chi-restraints excluded: chain CZ residue 7 ILE Chi-restraints excluded: chain C3 residue 9 VAL Chi-restraints excluded: chain C5 residue 1 ASP 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 DL residue 9 VAL Chi-restraints excluded: chain DM residue 3 ILE Chi-restraints excluded: chain DN residue 1 ASP Chi-restraints excluded: chain DN residue 8 SER Chi-restraints excluded: chain DQ residue 2 LEU Chi-restraints excluded: chain DQ residue 7 ILE Chi-restraints excluded: chain DQ residue 9 VAL Chi-restraints excluded: chain DR residue 2 LEU Chi-restraints excluded: chain DU residue 9 VAL Chi-restraints excluded: chain DW residue 1 ASP 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 EC residue 9 VAL Chi-restraints excluded: chain EE residue 1 ASP Chi-restraints excluded: chain EH residue 2 LEU Chi-restraints excluded: chain EH residue 7 ILE Chi-restraints excluded: chain EH residue 9 VAL Chi-restraints excluded: chain EL residue 9 VAL Chi-restraints excluded: chain EN residue 1 ASP 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 EW residue 1 ASP 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 1 ASP Chi-restraints excluded: chain E5 residue 8 SER Chi-restraints excluded: chain E8 residue 2 LEU Chi-restraints excluded: chain E8 residue 8 SER Chi-restraints excluded: chain FB residue 1 ASP Chi-restraints excluded: chain FC residue 9 VAL Chi-restraints excluded: chain FE residue 1 ASP 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 1 ASP Chi-restraints excluded: chain FN residue 8 SER Chi-restraints excluded: chain FU residue 9 VAL Chi-restraints excluded: chain FW residue 1 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 193 optimal weight: 9.9990 chunk 176 optimal weight: 8.9990 chunk 188 optimal weight: 20.0000 chunk 113 optimal weight: 10.0000 chunk 82 optimal weight: 20.0000 chunk 148 optimal weight: 10.0000 chunk 57 optimal weight: 2.9990 chunk 170 optimal weight: 9.9990 chunk 178 optimal weight: 30.0000 chunk 187 optimal weight: 20.0000 chunk 123 optimal weight: 20.0000 overall best weight: 8.3992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 10 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 10 HIS A7 10 HIS ** 6 10 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** DG 10 HIS DY 10 HIS ** EE 10 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** EG 10 HIS ** FQ 10 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7244 moved from start: 0.3689 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 20370 Z= 0.188 Angle : 0.714 10.180 27210 Z= 0.294 Chirality : 0.057 0.197 3840 Planarity : 0.002 0.020 3060 Dihedral : 10.706 55.378 2580 Min Nonbonded Distance : 2.305 Molprobity Statistics. All-atom Clashscore : 7.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 8.58 % Allowed : 24.54 % Favored : 66.88 % 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: -0.75 (0.19), residues: 2100 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.56 (0.14), residues: 2100 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HISAF 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 650 residues out of total 2400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 206 poor density : 444 time to evaluate : 2.738 Fit side-chains REVERT: J 5 LYS cc_start: 0.7943 (mttt) cc_final: 0.7507 (mttp) REVERT: M 5 LYS cc_start: 0.7667 (mttt) cc_final: 0.7434 (mttm) REVERT: P 5 LYS cc_start: 0.6126 (mmmt) cc_final: 0.4909 (pttm) REVERT: S 5 LYS cc_start: 0.8009 (mttt) cc_final: 0.7701 (mttp) REVERT: U 3 ILE cc_start: 0.7896 (OUTLIER) cc_final: 0.7371 (mp) REVERT: V 2 LEU cc_start: 0.8596 (pt) cc_final: 0.8217 (tt) REVERT: V 10 HIS cc_start: 0.8267 (t70) cc_final: 0.8049 (t-90) REVERT: j 5 LYS cc_start: 0.8028 (mttt) cc_final: 0.7549 (mttp) REVERT: s 4 ILE cc_start: 0.7444 (OUTLIER) cc_final: 0.7193 (mp) REVERT: v 5 LYS cc_start: 0.7418 (mttt) cc_final: 0.7024 (mttm) REVERT: AB 5 LYS cc_start: 0.7942 (mttt) cc_final: 0.7431 (mttp) REVERT: AD 3 ILE cc_start: 0.7712 (OUTLIER) cc_final: 0.7180 (mp) REVERT: AE 5 LYS cc_start: 0.7665 (mttt) cc_final: 0.7155 (mttm) REVERT: AK 4 ILE cc_start: 0.7439 (OUTLIER) cc_final: 0.7123 (mp) REVERT: AN 5 LYS cc_start: 0.7379 (mttt) cc_final: 0.7094 (mttm) REVERT: AV 3 ILE cc_start: 0.7625 (OUTLIER) cc_final: 0.7060 (mp) REVERT: A2 4 ILE cc_start: 0.7427 (OUTLIER) cc_final: 0.7158 (mp) REVERT: BB 5 LYS cc_start: 0.7732 (mttt) cc_final: 0.7375 (mttp) REVERT: BE 5 LYS cc_start: 0.7645 (mttt) cc_final: 0.7296 (mtpp) REVERT: BK 4 ILE cc_start: 0.7257 (OUTLIER) cc_final: 0.6943 (mp) REVERT: BN 3 ILE cc_start: 0.8514 (mt) cc_final: 0.8289 (mp) REVERT: BW 5 LYS cc_start: 0.7552 (mttt) cc_final: 0.7293 (mttm) REVERT: B2 4 ILE cc_start: 0.7533 (OUTLIER) cc_final: 0.7306 (mp) REVERT: B5 5 LYS cc_start: 0.7699 (mttm) cc_final: 0.7383 (mttm) REVERT: CD 3 ILE cc_start: 0.7783 (OUTLIER) cc_final: 0.7237 (mp) REVERT: 1 4 ILE cc_start: 0.7486 (OUTLIER) cc_final: 0.7256 (mp) REVERT: 6 5 LYS cc_start: 0.7289 (mttt) cc_final: 0.6902 (mttm) REVERT: CK 5 LYS cc_start: 0.7875 (mttt) cc_final: 0.7404 (mttp) REVERT: CW 5 LYS cc_start: 0.7371 (mttt) cc_final: 0.6925 (mttm) REVERT: C5 5 LYS cc_start: 0.7618 (mttt) cc_final: 0.7174 (mttm) REVERT: DE 5 LYS cc_start: 0.7214 (mttt) cc_final: 0.6816 (mttm) REVERT: DM 3 ILE cc_start: 0.7812 (OUTLIER) cc_final: 0.7219 (mp) REVERT: D4 3 ILE cc_start: 0.7828 (OUTLIER) cc_final: 0.7290 (mp) REVERT: D5 2 LEU cc_start: 0.8028 (pt) cc_final: 0.7724 (pp) REVERT: EE 2 LEU cc_start: 0.8245 (pt) cc_final: 0.8037 (pp) REVERT: EE 5 LYS cc_start: 0.7314 (mttt) cc_final: 0.6944 (mttm) REVERT: E4 3 ILE cc_start: 0.8012 (OUTLIER) cc_final: 0.7495 (mp) REVERT: E5 5 LYS cc_start: 0.7339 (mttt) cc_final: 0.6960 (mttp) REVERT: FE 2 LEU cc_start: 0.8457 (pp) cc_final: 0.6845 (mm) REVERT: FE 3 ILE cc_start: 0.8757 (mt) cc_final: 0.8435 (mp) REVERT: FE 5 LYS cc_start: 0.8172 (mttt) cc_final: 0.7773 (mttm) REVERT: FN 2 LEU cc_start: 0.8505 (pt) cc_final: 0.8192 (pp) outliers start: 206 outliers final: 163 residues processed: 529 average time/residue: 0.2752 time to fit residues: 232.2923 Evaluate side-chains 608 residues out of total 2400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 176 poor density : 432 time to evaluate : 2.581 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 2 LEU Chi-restraints excluded: chain M residue 8 SER Chi-restraints excluded: chain P residue 2 LEU Chi-restraints excluded: chain P residue 7 ILE Chi-restraints excluded: chain S residue 8 SER Chi-restraints excluded: chain U residue 3 ILE Chi-restraints excluded: chain V residue 1 ASP 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 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 9 VAL Chi-restraints excluded: chain k residue 9 VAL Chi-restraints excluded: chain m residue 1 ASP 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 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 AB residue 8 SER Chi-restraints excluded: chain AC residue 9 VAL Chi-restraints excluded: chain AD residue 3 ILE Chi-restraints excluded: chain AE residue 1 ASP Chi-restraints excluded: chain AE residue 8 SER Chi-restraints excluded: chain AF residue 9 VAL Chi-restraints excluded: chain AH residue 2 LEU Chi-restraints excluded: chain AI residue 3 ILE Chi-restraints excluded: chain AK residue 4 ILE Chi-restraints excluded: chain AL residue 9 VAL Chi-restraints excluded: chain AN residue 8 SER Chi-restraints excluded: chain 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 1 ASP 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 A5 residue 1 ASP Chi-restraints excluded: chain A5 residue 8 SER Chi-restraints excluded: chain A8 residue 2 LEU Chi-restraints excluded: chain A8 residue 7 ILE Chi-restraints excluded: chain BC residue 9 VAL Chi-restraints excluded: chain BE residue 1 ASP 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 BT residue 8 SER Chi-restraints excluded: chain BU residue 9 VAL Chi-restraints excluded: chain BW residue 1 ASP Chi-restraints excluded: chain BW residue 8 SER Chi-restraints excluded: chain BX residue 9 VAL Chi-restraints excluded: chain BZ residue 2 LEU Chi-restraints excluded: chain BZ residue 5 LYS Chi-restraints excluded: chain BZ residue 9 VAL Chi-restraints excluded: chain B0 residue 3 ILE Chi-restraints excluded: chain B2 residue 4 ILE Chi-restraints excluded: chain B3 residue 9 VAL Chi-restraints excluded: chain B5 residue 1 ASP Chi-restraints excluded: chain B5 residue 2 LEU Chi-restraints excluded: chain B5 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 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 1 ASP 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 1 ASP Chi-restraints excluded: chain CN residue 8 SER Chi-restraints excluded: chain CO residue 9 VAL Chi-restraints excluded: chain CQ residue 9 VAL Chi-restraints excluded: chain CU residue 9 VAL Chi-restraints excluded: chain CW residue 1 ASP 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 1 ASP 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 DL residue 9 VAL Chi-restraints excluded: chain DM residue 3 ILE Chi-restraints excluded: chain DN residue 1 ASP 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 DU residue 9 VAL Chi-restraints excluded: chain DW residue 1 ASP 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 EC residue 9 VAL Chi-restraints excluded: chain EE residue 1 ASP Chi-restraints excluded: chain EH residue 2 LEU Chi-restraints excluded: chain EH residue 7 ILE Chi-restraints excluded: chain EH residue 9 VAL Chi-restraints excluded: chain EK residue 8 SER Chi-restraints excluded: chain EL residue 9 VAL Chi-restraints excluded: chain EN residue 1 ASP 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 ER residue 3 ILE Chi-restraints excluded: chain ET residue 1 ASP Chi-restraints excluded: chain EU residue 9 VAL Chi-restraints excluded: chain EW residue 1 ASP 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 1 ASP 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 E8 residue 8 SER Chi-restraints excluded: chain FC residue 9 VAL Chi-restraints excluded: chain FE residue 1 ASP Chi-restraints excluded: chain FH residue 2 LEU Chi-restraints excluded: chain FK residue 9 VAL Chi-restraints excluded: chain FL residue 9 VAL Chi-restraints excluded: chain FN residue 1 ASP Chi-restraints excluded: chain FN residue 8 SER Chi-restraints excluded: chain FO residue 2 LEU Chi-restraints excluded: chain FU residue 9 VAL Chi-restraints excluded: chain FW residue 1 ASP 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: 20.0000 chunk 94 optimal weight: 20.0000 chunk 138 optimal weight: 20.0000 chunk 209 optimal weight: 0.9990 chunk 192 optimal weight: 20.0000 chunk 166 optimal weight: 7.9990 chunk 17 optimal weight: 20.0000 chunk 128 optimal weight: 10.0000 chunk 102 optimal weight: 20.0000 chunk 132 optimal weight: 7.9990 overall best weight: 9.3994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 10 HIS ** D 10 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 10 HIS ** 6 10 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** DG 10 HIS ** DY 10 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** EE 10 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** EG 10 HIS ** 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: 0.7245 moved from start: 0.3786 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 20370 Z= 0.208 Angle : 0.748 10.282 27210 Z= 0.309 Chirality : 0.058 0.192 3840 Planarity : 0.002 0.017 3060 Dihedral : 10.877 54.929 2580 Min Nonbonded Distance : 2.285 Molprobity Statistics. All-atom Clashscore : 8.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.81 % Favored : 96.19 % Rotamer: Outliers : 8.17 % Allowed : 25.17 % Favored : 66.67 % 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: -0.85 (0.19), residues: 2100 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.64 (0.14), residues: 2100 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HISEO 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 641 residues out of total 2400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 196 poor density : 445 time to evaluate : 2.769 Fit side-chains REVERT: J 5 LYS cc_start: 0.7920 (mttt) cc_final: 0.7487 (mttp) REVERT: M 5 LYS cc_start: 0.7644 (mttt) cc_final: 0.7412 (mttm) REVERT: S 5 LYS cc_start: 0.7993 (mttt) cc_final: 0.7782 (mttp) REVERT: U 3 ILE cc_start: 0.7888 (OUTLIER) cc_final: 0.7383 (mp) REVERT: V 2 LEU cc_start: 0.8604 (pt) cc_final: 0.8205 (tt) REVERT: V 10 HIS cc_start: 0.8284 (t70) cc_final: 0.8057 (t-90) REVERT: j 5 LYS cc_start: 0.8031 (mttt) cc_final: 0.7560 (mttp) REVERT: s 4 ILE cc_start: 0.7450 (OUTLIER) cc_final: 0.7200 (mp) REVERT: v 5 LYS cc_start: 0.7326 (mttt) cc_final: 0.6961 (mttm) REVERT: x 3 ILE cc_start: 0.7533 (mt) cc_final: 0.7306 (mt) REVERT: AB 5 LYS cc_start: 0.7976 (mttt) cc_final: 0.7472 (mttp) REVERT: AD 3 ILE cc_start: 0.7726 (OUTLIER) cc_final: 0.7183 (mp) REVERT: AE 5 LYS cc_start: 0.7642 (mttt) cc_final: 0.7252 (mttm) REVERT: AK 4 ILE cc_start: 0.7452 (OUTLIER) cc_final: 0.7136 (mp) REVERT: AN 5 LYS cc_start: 0.7447 (mttt) cc_final: 0.7183 (mttm) REVERT: AV 3 ILE cc_start: 0.7581 (OUTLIER) cc_final: 0.7016 (mp) REVERT: A2 4 ILE cc_start: 0.7392 (OUTLIER) cc_final: 0.7119 (mp) REVERT: BB 5 LYS cc_start: 0.7749 (mttt) cc_final: 0.7382 (mttp) REVERT: BE 5 LYS cc_start: 0.7600 (mttt) cc_final: 0.7303 (mtpp) REVERT: BK 4 ILE cc_start: 0.7239 (OUTLIER) cc_final: 0.6921 (mp) REVERT: BN 3 ILE cc_start: 0.8516 (mt) cc_final: 0.8293 (mp) REVERT: BW 5 LYS cc_start: 0.7555 (mttt) cc_final: 0.7305 (mttm) REVERT: CD 3 ILE cc_start: 0.7774 (OUTLIER) cc_final: 0.7231 (mp) REVERT: 6 5 LYS cc_start: 0.7265 (mttt) cc_final: 0.6892 (mttm) REVERT: CK 5 LYS cc_start: 0.7839 (mttt) cc_final: 0.7332 (mttp) REVERT: CW 5 LYS cc_start: 0.7416 (mttt) cc_final: 0.6952 (mttm) REVERT: C5 5 LYS cc_start: 0.7576 (mttt) cc_final: 0.7137 (mttm) REVERT: DE 5 LYS cc_start: 0.7227 (mttt) cc_final: 0.6823 (mttm) REVERT: DM 3 ILE cc_start: 0.7809 (OUTLIER) cc_final: 0.7219 (mp) REVERT: D4 3 ILE cc_start: 0.7813 (OUTLIER) cc_final: 0.7273 (mp) REVERT: D5 2 LEU cc_start: 0.8037 (pt) cc_final: 0.7729 (pp) REVERT: EE 2 LEU cc_start: 0.8304 (pt) cc_final: 0.8099 (pp) REVERT: EE 5 LYS cc_start: 0.7218 (mttt) cc_final: 0.6878 (mttm) REVERT: EK 5 LYS cc_start: 0.7902 (mttt) cc_final: 0.7558 (mttp) REVERT: EM 3 ILE cc_start: 0.7817 (OUTLIER) cc_final: 0.7331 (mp) REVERT: E4 3 ILE cc_start: 0.7994 (OUTLIER) cc_final: 0.7472 (mp) REVERT: E5 5 LYS cc_start: 0.7410 (mttt) cc_final: 0.7013 (mttp) REVERT: FE 2 LEU cc_start: 0.8514 (pp) cc_final: 0.6880 (mm) REVERT: FE 3 ILE cc_start: 0.8766 (mt) cc_final: 0.8442 (mp) REVERT: FE 5 LYS cc_start: 0.8163 (mttt) cc_final: 0.7760 (mttm) REVERT: FN 2 LEU cc_start: 0.8526 (pt) cc_final: 0.8227 (pp) outliers start: 196 outliers final: 172 residues processed: 526 average time/residue: 0.2892 time to fit residues: 241.8231 Evaluate side-chains 622 residues out of total 2400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 184 poor density : 438 time to evaluate : 2.481 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 2 LEU Chi-restraints excluded: chain M residue 8 SER Chi-restraints excluded: chain P residue 2 LEU Chi-restraints excluded: chain P residue 7 ILE Chi-restraints excluded: chain S residue 8 SER Chi-restraints excluded: chain U residue 3 ILE Chi-restraints excluded: chain V residue 1 ASP 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 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 g residue 9 VAL Chi-restraints excluded: chain k residue 9 VAL Chi-restraints excluded: chain m residue 1 ASP 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 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 AB residue 8 SER Chi-restraints excluded: chain AC residue 9 VAL Chi-restraints excluded: chain AD residue 3 ILE Chi-restraints excluded: chain AE residue 1 ASP Chi-restraints excluded: chain AE residue 8 SER Chi-restraints excluded: chain AF residue 9 VAL Chi-restraints excluded: chain AH residue 2 LEU Chi-restraints excluded: chain AI residue 3 ILE Chi-restraints excluded: chain AK residue 4 ILE Chi-restraints excluded: chain AL residue 9 VAL Chi-restraints excluded: chain AN residue 8 SER Chi-restraints excluded: chain AO residue 9 VAL Chi-restraints excluded: chain AQ residue 2 LEU Chi-restraints excluded: chain AQ residue 7 ILE Chi-restraints excluded: chain AR residue 2 LEU Chi-restraints excluded: chain AT residue 8 SER Chi-restraints excluded: chain AU residue 9 VAL Chi-restraints excluded: chain AV residue 3 ILE Chi-restraints excluded: chain AW residue 1 ASP 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 A5 residue 1 ASP Chi-restraints excluded: chain A5 residue 8 SER Chi-restraints excluded: chain A8 residue 2 LEU Chi-restraints excluded: chain A8 residue 7 ILE Chi-restraints excluded: chain BC residue 9 VAL Chi-restraints excluded: chain BE residue 1 ASP 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 BT residue 8 SER Chi-restraints excluded: chain BU residue 9 VAL Chi-restraints excluded: chain BW residue 1 ASP Chi-restraints excluded: chain BW residue 8 SER Chi-restraints excluded: chain BX residue 9 VAL Chi-restraints excluded: chain BZ residue 2 LEU Chi-restraints excluded: chain BZ residue 5 LYS Chi-restraints excluded: chain BZ residue 9 VAL Chi-restraints excluded: chain B0 residue 3 ILE Chi-restraints excluded: chain B3 residue 9 VAL Chi-restraints excluded: chain B5 residue 1 ASP Chi-restraints excluded: chain B5 residue 2 LEU Chi-restraints excluded: chain B5 residue 8 SER Chi-restraints excluded: chain B6 residue 9 VAL 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 CI residue 3 ILE Chi-restraints excluded: chain CI residue 5 LYS 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 1 ASP Chi-restraints excluded: chain CN residue 8 SER Chi-restraints excluded: chain CO residue 9 VAL Chi-restraints excluded: chain CQ residue 9 VAL Chi-restraints excluded: chain CU residue 9 VAL Chi-restraints excluded: chain CW residue 1 ASP 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 1 ASP 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 DL residue 9 VAL Chi-restraints excluded: chain DM residue 3 ILE Chi-restraints excluded: chain DN residue 1 ASP 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 DU residue 9 VAL Chi-restraints excluded: chain DW residue 1 ASP 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 7 ILE Chi-restraints excluded: chain D8 residue 9 VAL Chi-restraints excluded: chain EC residue 9 VAL Chi-restraints excluded: chain EE residue 1 ASP Chi-restraints excluded: chain EH residue 2 LEU Chi-restraints excluded: chain EH residue 7 ILE Chi-restraints excluded: chain EH residue 9 VAL Chi-restraints excluded: chain EK residue 8 SER Chi-restraints excluded: chain EL residue 9 VAL Chi-restraints excluded: chain EM residue 3 ILE Chi-restraints excluded: chain EN residue 1 ASP 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 ER residue 3 ILE Chi-restraints excluded: chain ET residue 1 ASP Chi-restraints excluded: chain EU residue 9 VAL Chi-restraints excluded: chain EW residue 1 ASP 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 1 ASP 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 FB residue 1 ASP Chi-restraints excluded: chain FC residue 9 VAL Chi-restraints excluded: chain FE residue 1 ASP Chi-restraints excluded: chain FH residue 2 LEU Chi-restraints excluded: chain FK residue 9 VAL Chi-restraints excluded: chain FL residue 9 VAL Chi-restraints excluded: chain FN residue 1 ASP Chi-restraints excluded: chain FN residue 8 SER Chi-restraints excluded: chain FO residue 2 LEU Chi-restraints excluded: chain FU residue 9 VAL Chi-restraints excluded: chain FW residue 1 ASP Chi-restraints excluded: chain FZ residue 2 LEU 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 177 optimal weight: 30.0000 chunk 51 optimal weight: 30.0000 chunk 153 optimal weight: 2.9990 chunk 24 optimal weight: 40.0000 chunk 46 optimal weight: 2.9990 chunk 166 optimal weight: 0.8980 chunk 69 optimal weight: 20.0000 chunk 171 optimal weight: 20.0000 chunk 21 optimal weight: 7.9990 chunk 30 optimal weight: 6.9990 chunk 146 optimal weight: 20.0000 overall best weight: 4.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 10 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 10 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** DG 10 HIS DY 10 HIS ** EE 10 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** FQ 10 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3600 r_free = 0.3600 target = 0.118329 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.098230 restraints weight = 29531.916| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.101501 restraints weight = 15815.920| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.103926 restraints weight = 10277.449| |-----------------------------------------------------------------------------| r_work (final): 0.3430 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7710 moved from start: 0.3855 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 20370 Z= 0.117 Angle : 0.661 9.993 27210 Z= 0.265 Chirality : 0.057 0.177 3840 Planarity : 0.001 0.016 3060 Dihedral : 9.959 55.333 2580 Min Nonbonded Distance : 2.296 Molprobity Statistics. All-atom Clashscore : 6.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 7.75 % Allowed : 25.71 % Favored : 66.54 % 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: -0.54 (0.19), residues: 2100 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.40 (0.14), residues: 2100 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS 6 10 =============================================================================== Job complete usr+sys time: 4378.97 seconds wall clock time: 81 minutes 29.20 seconds (4889.20 seconds total)