Starting phenix.real_space_refine on Mon Jul 22 19:02:06 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5w7v_8781/07_2024/5w7v_8781.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5w7v_8781/07_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_8781/07_2024/5w7v_8781.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5w7v_8781/07_2024/5w7v_8781.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5w7v_8781/07_2024/5w7v_8781.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5w7v_8781/07_2024/5w7v_8781.cif" } resolution = 3.8 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.007 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 3 Type Number sf(0) Gaussians C 13500 2.51 5 N 3330 2.21 5 O 3600 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped None Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/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: 11.28, per 1000 atoms: 0.55 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: 6.59 Conformation dependent library (CDL) restraints added in 2.9 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: 2.32 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: 7.22 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.29: 3390 1.29 - 1.35: 2853 1.35 - 1.42: 777 1.42 - 1.48: 2704 1.48 - 1.55: 10646 Bond restraints: 20370 Sorted by residual: bond pdb=" CB VALEB 9 " pdb=" CG2 VALEB 9 " ideal model delta sigma weight residual 1.521 1.485 0.036 3.30e-02 9.18e+02 1.20e+00 bond pdb=" CB VALDK 9 " pdb=" CG2 VALDK 9 " ideal model delta sigma weight residual 1.521 1.485 0.036 3.30e-02 9.18e+02 1.20e+00 bond pdb=" CB VAL J 9 " pdb=" CG2 VAL J 9 " ideal model delta sigma weight residual 1.521 1.485 0.036 3.30e-02 9.18e+02 1.20e+00 bond pdb=" CB VALEK 9 " pdb=" CG2 VALEK 9 " ideal model delta sigma weight residual 1.521 1.485 0.036 3.30e-02 9.18e+02 1.20e+00 bond pdb=" CB VALFK 9 " pdb=" CG2 VALFK 9 " ideal model delta sigma weight residual 1.521 1.485 0.036 3.30e-02 9.18e+02 1.20e+00 ... (remaining 20365 not shown) Histogram of bond angle deviations from ideal: 106.02 - 111.07: 10172 111.07 - 116.11: 6088 116.11 - 121.16: 5329 121.16 - 126.21: 5411 126.21 - 131.25: 210 Bond angle restraints: 27210 Sorted by residual: angle pdb=" CA LEUC2 2 " pdb=" CB LEUC2 2 " pdb=" CG LEUC2 2 " ideal model delta sigma weight residual 116.30 123.46 -7.16 3.50e+00 8.16e-02 4.18e+00 angle pdb=" CA LEUCT 2 " pdb=" CB LEUCT 2 " pdb=" CG LEUCT 2 " ideal model delta sigma weight residual 116.30 123.45 -7.15 3.50e+00 8.16e-02 4.17e+00 angle pdb=" CA LEUB2 2 " pdb=" CB LEUB2 2 " pdb=" CG LEUB2 2 " ideal model delta sigma weight residual 116.30 123.44 -7.14 3.50e+00 8.16e-02 4.17e+00 angle pdb=" CA LEUFK 2 " pdb=" CB LEUFK 2 " pdb=" CG LEUFK 2 " ideal model delta sigma weight residual 116.30 123.44 -7.14 3.50e+00 8.16e-02 4.17e+00 angle pdb=" CA LEUBK 2 " pdb=" CB LEUBK 2 " pdb=" CG LEUBK 2 " ideal model delta sigma weight residual 116.30 123.44 -7.14 3.50e+00 8.16e-02 4.17e+00 ... (remaining 27205 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 11.46: 11130 11.46 - 22.93: 513 22.93 - 34.39: 267 34.39 - 45.85: 330 45.85 - 57.31: 60 Dihedral angle restraints: 12300 sinusoidal: 5130 harmonic: 7170 Sorted by residual: dihedral pdb=" CA ILEAX 4 " pdb=" CB ILEAX 4 " pdb=" CG1 ILEAX 4 " pdb=" CD1 ILEAX 4 " ideal model delta sinusoidal sigma weight residual 60.00 107.08 -47.08 3 1.50e+01 4.44e-03 8.44e+00 dihedral pdb=" CA ILEDF 4 " pdb=" CB ILEDF 4 " pdb=" CG1 ILEDF 4 " pdb=" CD1 ILEDF 4 " ideal model delta sinusoidal sigma weight residual 60.00 107.07 -47.07 3 1.50e+01 4.44e-03 8.44e+00 dihedral pdb=" CA ILEA6 4 " pdb=" CB ILEA6 4 " pdb=" CG1 ILEA6 4 " pdb=" CD1 ILEA6 4 " ideal model delta sinusoidal sigma weight residual 60.00 107.07 -47.07 3 1.50e+01 4.44e-03 8.44e+00 ... (remaining 12297 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.034: 1833 0.034 - 0.067: 1051 0.067 - 0.101: 297 0.101 - 0.134: 569 0.134 - 0.168: 90 Chirality restraints: 3840 Sorted by residual: chirality pdb=" CB VAL S 9 " pdb=" CA VAL S 9 " pdb=" CG1 VAL S 9 " pdb=" CG2 VAL S 9 " both_signs ideal model delta sigma weight residual False -2.63 -2.46 -0.17 2.00e-01 2.50e+01 7.06e-01 chirality pdb=" CB VALFB 9 " pdb=" CA VALFB 9 " pdb=" CG1 VALFB 9 " pdb=" CG2 VALFB 9 " both_signs ideal model delta sigma weight residual False -2.63 -2.46 -0.17 2.00e-01 2.50e+01 7.05e-01 chirality pdb=" CB VALFT 9 " pdb=" CA VALFT 9 " pdb=" CG1 VALFT 9 " pdb=" CG2 VALFT 9 " both_signs ideal model delta sigma weight residual False -2.63 -2.46 -0.17 2.00e-01 2.50e+01 7.02e-01 ... (remaining 3837 not shown) Planarity restraints: 3060 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA VALCF 9 " -0.006 2.00e-02 2.50e+03 1.13e-02 1.27e+00 pdb=" C VALCF 9 " 0.020 2.00e-02 2.50e+03 pdb=" O VALCF 9 " -0.007 2.00e-02 2.50e+03 pdb=" N HISCF 10 " -0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VALAX 9 " -0.006 2.00e-02 2.50e+03 1.11e-02 1.24e+00 pdb=" C VALAX 9 " 0.019 2.00e-02 2.50e+03 pdb=" O VALAX 9 " -0.007 2.00e-02 2.50e+03 pdb=" N HISAX 10 " -0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VALFF 9 " 0.006 2.00e-02 2.50e+03 1.11e-02 1.24e+00 pdb=" C VALFF 9 " -0.019 2.00e-02 2.50e+03 pdb=" O VALFF 9 " 0.007 2.00e-02 2.50e+03 pdb=" N HISFF 10 " 0.006 2.00e-02 2.50e+03 ... (remaining 3057 not shown) Histogram of nonbonded interaction distances: 2.37 - 2.87: 5559 2.87 - 3.38: 18710 3.38 - 3.89: 35853 3.89 - 4.39: 35544 4.39 - 4.90: 71101 Nonbonded interactions: 166767 Sorted by model distance: nonbonded pdb=" OXT ILEFF 11 " pdb=" N ASPFG 1 " model vdw 2.365 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 166762 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain '0' selection = chain 'A0' selection = chain 'A9' selection = chain 'AI' selection = chain 'AR' selection = chain 'B0' selection = chain 'B9' selection = chain 'BI' selection = chain 'BR' selection = chain 'C0' selection = chain 'C9' selection = chain 'CI' selection = chain 'CR' selection = chain 'D0' selection = chain 'D9' selection = chain 'DI' selection = chain 'DR' selection = chain 'E0' selection = chain 'E9' selection = chain 'EI' selection = chain 'ER' selection = chain 'F0' selection = chain 'FI' selection = chain 'FR' selection = chain 'H' selection = chain 'Q' selection = chain 'Z' selection = chain 'h' selection = chain 'q' selection = chain 'z' } ncs_group { reference = chain '1' selection = chain '2' selection = chain '3' selection = chain '4' selection = chain '5' selection = chain '6' selection = chain '7' selection = chain 'A' selection = chain 'A2' selection = chain 'A3' selection = chain 'A4' selection = chain 'A5' selection = chain 'A6' selection = chain 'A7' selection = chain 'A8' selection = chain 'AB' selection = chain 'AC' selection = chain 'AD' selection = chain 'AE' selection = chain 'AF' selection = chain 'AG' selection = chain 'AH' selection = chain 'AK' selection = chain 'AL' selection = chain 'AM' selection = chain 'AN' selection = chain 'AO' selection = chain 'AP' selection = chain 'AQ' selection = chain 'AT' selection = chain 'AU' selection = chain 'AV' selection = chain 'AW' selection = chain 'AX' selection = chain 'AY' selection = chain 'AZ' selection = chain 'B' selection = chain 'B2' selection = chain 'B3' selection = chain 'B4' selection = chain 'B5' selection = chain 'B6' selection = chain 'B7' selection = chain 'B8' selection = chain 'BB' selection = chain 'BC' selection = chain 'BD' selection = chain 'BE' selection = chain 'BF' selection = chain 'BG' selection = chain 'BH' selection = chain 'BK' selection = chain 'BL' selection = chain 'BM' selection = chain 'BN' selection = chain 'BO' selection = chain 'BP' selection = chain 'BQ' selection = chain 'BT' selection = chain 'BU' selection = chain 'BV' selection = chain 'BW' selection = chain 'BX' selection = chain 'BY' selection = chain 'BZ' selection = chain 'C' selection = chain 'C2' selection = chain 'C3' selection = chain 'C4' selection = chain 'C5' selection = chain 'C6' selection = chain 'C7' selection = chain 'C8' selection = chain 'CB' selection = chain 'CC' selection = chain 'CD' selection = chain 'CE' selection = chain 'CF' selection = chain 'CG' selection = chain 'CH' selection = chain 'CK' selection = chain 'CL' selection = chain 'CM' selection = chain 'CN' selection = chain 'CO' selection = chain 'CP' selection = chain 'CQ' selection = chain 'CT' selection = chain 'CU' selection = chain 'CV' selection = chain 'CW' selection = chain 'CX' selection = chain 'CY' selection = chain 'CZ' selection = chain 'D' selection = chain 'D2' selection = chain 'D3' selection = chain 'D4' selection = chain 'D5' selection = chain 'D6' selection = chain 'D7' selection = chain 'D8' selection = chain 'DB' selection = chain 'DC' selection = chain 'DD' selection = chain 'DE' selection = chain 'DF' selection = chain 'DG' selection = chain 'DH' selection = chain 'DK' selection = chain 'DL' selection = chain 'DM' selection = chain 'DN' selection = chain 'DO' selection = chain 'DP' selection = chain 'DQ' selection = chain 'DT' selection = chain 'DU' selection = chain 'DV' selection = chain 'DW' selection = chain 'DX' selection = chain 'DY' selection = chain 'DZ' selection = chain 'E' selection = chain 'E2' selection = chain 'E3' selection = chain 'E4' selection = chain 'E5' selection = chain 'E6' selection = chain 'E7' selection = chain 'E8' selection = chain 'EB' selection = chain 'EC' selection = chain 'ED' selection = chain 'EE' selection = chain 'EF' selection = chain 'EG' selection = chain 'EH' selection = chain 'EK' selection = chain 'EL' selection = chain 'EM' selection = chain 'EN' selection = chain 'EO' selection = chain 'EP' selection = chain 'EQ' selection = chain 'ET' selection = chain 'EU' selection = chain 'EV' selection = chain 'EW' selection = chain 'EX' selection = chain 'EY' selection = chain 'EZ' selection = chain 'F' selection = chain 'FB' selection = chain 'FC' selection = chain 'FD' selection = chain 'FE' selection = chain 'FF' selection = chain 'FG' selection = chain 'FH' selection = chain 'FK' selection = chain 'FL' selection = chain 'FM' selection = chain 'FN' selection = chain 'FO' selection = chain 'FP' selection = chain 'FQ' selection = chain 'FT' selection = chain 'FU' selection = chain 'FV' selection = chain 'FW' selection = chain 'FX' selection = chain 'FY' selection = chain 'FZ' selection = chain 'G' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'S' selection = chain 'T' selection = chain 'U' selection = chain 'V' selection = chain 'W' selection = chain 'X' selection = chain 'Y' selection = chain 'a' selection = chain 'b' selection = chain 'c' selection = chain 'd' selection = chain 'e' selection = chain 'f' selection = chain 'g' selection = chain 'j' selection = chain 'k' selection = chain 'l' selection = chain 'm' selection = chain 'n' selection = chain 'o' selection = chain 'p' selection = chain 's' selection = chain 't' selection = chain 'u' selection = chain 'v' selection = chain 'w' selection = chain 'x' selection = chain 'y' } ncs_group { reference = chain '8' selection = chain '9' selection = chain 'A1' selection = chain 'AA' selection = chain 'AJ' selection = chain 'AS' selection = chain 'B1' selection = chain 'BA' selection = chain 'BJ' selection = chain 'BS' selection = chain 'C1' selection = chain 'CA' selection = chain 'CJ' selection = chain 'CS' selection = chain 'D1' selection = chain 'DA' selection = chain 'DJ' selection = chain 'DS' selection = chain 'E1' selection = chain 'EA' selection = chain 'EJ' selection = chain 'ES' selection = chain 'F1' selection = chain 'FA' selection = chain 'FJ' selection = chain 'FS' selection = chain 'I' selection = chain 'R' selection = chain 'i' selection = chain 'r' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 max=1.00 mean=0.94 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.180 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.660 Check model and map are aligned: 0.130 Set scattering table: 0.160 Process input model: 43.760 Find NCS groups from input model: 2.420 Set up NCS constraints: 0.700 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:2.590 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 50.610 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7241 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.039 20370 Z= 0.263 Angle : 0.770 7.158 27210 Z= 0.346 Chirality : 0.063 0.168 3840 Planarity : 0.002 0.011 3060 Dihedral : 12.788 57.314 7500 Min Nonbonded Distance : 2.365 Molprobity Statistics. All-atom Clashscore : 15.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.43 % Favored : 98.57 % Rotamer: Outliers : 0.00 % Allowed : 8.75 % Favored : 91.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.52 (0.13), residues: 2100 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.91 (0.10), residues: 2100 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.008 0.002 HISCM 10 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4200 Ramachandran restraints generated. 2100 Oldfield, 0 Emsley, 2100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4200 Ramachandran restraints generated. 2100 Oldfield, 0 Emsley, 2100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 641 residues out of total 2400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 641 time to evaluate : 2.644 Fit side-chains REVERT: C 5 LYS cc_start: 0.8198 (ptmt) cc_final: 0.7993 (ptpt) REVERT: D 5 LYS cc_start: 0.8014 (mttt) cc_final: 0.7734 (mttm) REVERT: M 5 LYS cc_start: 0.7685 (mttt) cc_final: 0.7382 (mttm) REVERT: U 3 ILE cc_start: 0.8003 (mp) cc_final: 0.7802 (mm) REVERT: m 5 LYS cc_start: 0.7814 (mttt) cc_final: 0.7610 (mttm) REVERT: v 5 LYS cc_start: 0.7390 (mttt) cc_final: 0.7047 (mttm) REVERT: AD 3 ILE cc_start: 0.7868 (mp) cc_final: 0.7624 (mm) REVERT: AE 5 LYS cc_start: 0.7680 (mttt) cc_final: 0.7338 (mttm) REVERT: AN 5 LYS cc_start: 0.7509 (mttt) cc_final: 0.7192 (mttm) REVERT: AV 3 ILE cc_start: 0.7940 (mp) cc_final: 0.7724 (mm) REVERT: A5 5 LYS cc_start: 0.7415 (mttt) cc_final: 0.7212 (mttm) REVERT: BE 5 LYS cc_start: 0.7520 (mttt) cc_final: 0.7226 (mttm) REVERT: BN 3 ILE cc_start: 0.8452 (mt) cc_final: 0.8115 (mp) REVERT: BP 4 ILE cc_start: 0.8399 (mt) cc_final: 0.8191 (mt) REVERT: BW 5 LYS cc_start: 0.7629 (mttt) cc_final: 0.7390 (mttm) REVERT: B5 5 LYS cc_start: 0.7597 (mttt) cc_final: 0.7182 (mttm) REVERT: CD 3 ILE cc_start: 0.7895 (mp) cc_final: 0.7651 (mm) REVERT: 6 5 LYS cc_start: 0.7421 (mttt) cc_final: 0.7019 (mttp) REVERT: CM 3 ILE cc_start: 0.7791 (mp) cc_final: 0.7468 (mm) REVERT: CW 3 ILE cc_start: 0.8430 (mt) cc_final: 0.8164 (mp) REVERT: CW 5 LYS cc_start: 0.7598 (mttt) cc_final: 0.7211 (mttm) REVERT: C4 3 ILE cc_start: 0.8010 (mp) cc_final: 0.7709 (mm) REVERT: C5 5 LYS cc_start: 0.7277 (mttt) cc_final: 0.6988 (mttm) REVERT: DD 3 ILE cc_start: 0.7613 (mp) cc_final: 0.7380 (mp) REVERT: DE 5 LYS cc_start: 0.7239 (mttt) cc_final: 0.6877 (mttm) REVERT: DM 3 ILE cc_start: 0.7933 (mp) cc_final: 0.7665 (mm) REVERT: DW 3 ILE cc_start: 0.8576 (mt) cc_final: 0.8319 (mp) REVERT: D4 3 ILE cc_start: 0.7888 (mp) cc_final: 0.7579 (mm) REVERT: EE 3 ILE cc_start: 0.8511 (mt) cc_final: 0.8278 (mp) REVERT: EE 5 LYS cc_start: 0.7238 (mttt) cc_final: 0.6948 (mttm) REVERT: EW 3 ILE cc_start: 0.8433 (mt) cc_final: 0.8138 (mp) REVERT: E4 3 ILE cc_start: 0.7981 (mp) cc_final: 0.7742 (mm) REVERT: E5 5 LYS cc_start: 0.7441 (mttt) cc_final: 0.7240 (mttp) REVERT: FE 3 ILE cc_start: 0.8837 (mt) cc_final: 0.8539 (mp) REVERT: FE 5 LYS cc_start: 0.8212 (mttt) cc_final: 0.7945 (mttm) outliers start: 0 outliers final: 0 residues processed: 641 average time/residue: 0.2998 time to fit residues: 298.1545 Evaluate side-chains 449 residues out of total 2400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 449 time to evaluate : 2.940 ------------------------------------------------------------------------------- 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: 7.9990 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: 2.9990 chunk 100 optimal weight: 30.0000 chunk 122 optimal weight: 10.0000 chunk 190 optimal weight: 20.0000 overall best weight: 6.5990 ------------------------------------------------------------------------------- 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 ** 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: 46 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7234 moved from start: 0.1853 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.025 20370 Z= 0.163 Angle : 0.682 10.153 27210 Z= 0.284 Chirality : 0.057 0.139 3840 Planarity : 0.002 0.007 3060 Dihedral : 11.242 60.941 2580 Min Nonbonded Distance : 2.308 Molprobity Statistics. All-atom Clashscore : 5.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 6.83 % Allowed : 17.21 % Favored : 75.96 % 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: -1.90 (0.15), residues: 2100 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.44 (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 671 residues out of total 2400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 164 poor density : 507 time to evaluate : 2.702 Fit side-chains REVERT: C 5 LYS cc_start: 0.8145 (ptmt) cc_final: 0.7940 (ptpt) REVERT: M 3 ILE cc_start: 0.8729 (mt) cc_final: 0.8479 (mp) REVERT: M 5 LYS cc_start: 0.7838 (mttt) cc_final: 0.7462 (mttm) REVERT: U 3 ILE cc_start: 0.8060 (mp) cc_final: 0.7652 (mp) REVERT: d 3 ILE cc_start: 0.8572 (mt) cc_final: 0.8217 (mp) REVERT: s 4 ILE cc_start: 0.7687 (OUTLIER) cc_final: 0.7455 (mp) REVERT: v 3 ILE cc_start: 0.8552 (mt) cc_final: 0.8284 (mp) REVERT: v 5 LYS cc_start: 0.7537 (mttt) cc_final: 0.7106 (mttm) REVERT: AD 3 ILE cc_start: 0.7882 (mp) cc_final: 0.7369 (mp) REVERT: AK 4 ILE cc_start: 0.7590 (OUTLIER) cc_final: 0.7309 (mp) REVERT: AN 5 LYS cc_start: 0.7671 (mttt) cc_final: 0.7289 (mttm) REVERT: A2 4 ILE cc_start: 0.7595 (OUTLIER) cc_final: 0.7299 (mp) REVERT: A5 5 LYS cc_start: 0.7414 (mttt) cc_final: 0.7138 (mttm) REVERT: BE 5 LYS cc_start: 0.7717 (mttt) cc_final: 0.7433 (mttm) REVERT: BK 4 ILE cc_start: 0.7543 (OUTLIER) cc_final: 0.7285 (mp) REVERT: BN 3 ILE cc_start: 0.8388 (mt) cc_final: 0.8087 (mp) REVERT: BV 5 LYS cc_start: 0.8065 (ptmt) cc_final: 0.7806 (ptpt) REVERT: BW 5 LYS cc_start: 0.7545 (mttt) cc_final: 0.7226 (mttm) REVERT: B2 4 ILE cc_start: 0.7718 (OUTLIER) cc_final: 0.7443 (mp) REVERT: B5 5 LYS cc_start: 0.7817 (mttt) cc_final: 0.7587 (mttm) REVERT: 1 4 ILE cc_start: 0.7684 (OUTLIER) cc_final: 0.7450 (mp) REVERT: 6 2 LEU cc_start: 0.8314 (pt) cc_final: 0.8061 (pp) REVERT: 6 5 LYS cc_start: 0.7479 (mttt) cc_final: 0.7018 (mttp) REVERT: CN 2 LEU cc_start: 0.7866 (pt) cc_final: 0.7620 (pp) REVERT: CT 4 ILE cc_start: 0.7713 (OUTLIER) cc_final: 0.7494 (mp) REVERT: CW 5 LYS cc_start: 0.7514 (mttt) cc_final: 0.7009 (mttm) REVERT: C4 3 ILE cc_start: 0.8003 (mp) cc_final: 0.7672 (mm) REVERT: C5 5 LYS cc_start: 0.7565 (mttt) cc_final: 0.7113 (mttm) REVERT: DE 5 LYS cc_start: 0.7333 (mttt) cc_final: 0.6921 (mttm) REVERT: DT 4 ILE cc_start: 0.7834 (OUTLIER) cc_final: 0.7632 (mp) REVERT: D4 3 ILE cc_start: 0.7873 (mp) cc_final: 0.7566 (mm) REVERT: EE 5 LYS cc_start: 0.7173 (mttt) cc_final: 0.6800 (mttm) REVERT: EN 5 LYS cc_start: 0.7777 (mttm) cc_final: 0.7529 (mttm) REVERT: EW 3 ILE cc_start: 0.8416 (mt) cc_final: 0.8169 (mp) REVERT: E5 5 LYS cc_start: 0.7705 (mttt) cc_final: 0.7358 (mttp) REVERT: FB 4 ILE cc_start: 0.7675 (OUTLIER) cc_final: 0.7474 (mp) REVERT: FE 3 ILE cc_start: 0.8788 (mt) cc_final: 0.8442 (mp) REVERT: FE 5 LYS cc_start: 0.8352 (mttt) cc_final: 0.7973 (mttm) REVERT: FN 2 LEU cc_start: 0.8330 (pt) cc_final: 0.6829 (mm) REVERT: FT 4 ILE cc_start: 0.7694 (OUTLIER) cc_final: 0.7467 (mp) outliers start: 164 outliers final: 85 residues processed: 570 average time/residue: 0.2998 time to fit residues: 269.4773 Evaluate side-chains 536 residues out of total 2400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 95 poor density : 441 time to evaluate : 2.268 ------------------------------------------------------------------------------- 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 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 A6 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 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 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 DT residue 4 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 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 4 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: 6.9990 chunk 59 optimal weight: 20.0000 chunk 158 optimal weight: 20.0000 chunk 129 optimal weight: 6.9990 chunk 52 optimal weight: 30.0000 chunk 191 optimal weight: 7.9990 chunk 206 optimal weight: 20.0000 chunk 170 optimal weight: 20.0000 chunk 189 optimal weight: 9.9990 chunk 65 optimal weight: 30.0000 chunk 153 optimal weight: 50.0000 overall best weight: 10.3992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: c 10 HIS l 10 HIS s 10 HIS u 10 HIS ** y 10 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 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** ** 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** ** 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: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7259 moved from start: 0.2451 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.038 20370 Z= 0.231 Angle : 0.728 9.373 27210 Z= 0.310 Chirality : 0.057 0.169 3840 Planarity : 0.002 0.007 3060 Dihedral : 11.573 59.300 2580 Min Nonbonded Distance : 2.311 Molprobity Statistics. All-atom Clashscore : 7.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.62 % Favored : 99.38 % Rotamer: Outliers : 9.04 % Allowed : 19.46 % Favored : 71.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.83 (0.16), residues: 2100 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.38 (0.12), residues: 2100 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.002 HISCF 10 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4200 Ramachandran restraints generated. 2100 Oldfield, 0 Emsley, 2100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4200 Ramachandran restraints generated. 2100 Oldfield, 0 Emsley, 2100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 696 residues out of total 2400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 217 poor density : 479 time to evaluate : 2.479 Fit side-chains REVERT: M 3 ILE cc_start: 0.8667 (mt) cc_final: 0.8444 (mp) REVERT: M 5 LYS cc_start: 0.7895 (mttt) cc_final: 0.7544 (mttm) REVERT: P 5 LYS cc_start: 0.6197 (mmmt) cc_final: 0.4814 (pttm) REVERT: U 3 ILE cc_start: 0.7996 (mp) cc_final: 0.7547 (mp) REVERT: V 2 LEU cc_start: 0.8534 (pt) cc_final: 0.8318 (pp) REVERT: j 5 LYS cc_start: 0.8081 (mttt) cc_final: 0.7700 (mttp) REVERT: s 4 ILE cc_start: 0.7580 (OUTLIER) cc_final: 0.7348 (mp) REVERT: v 5 LYS cc_start: 0.7494 (mttt) cc_final: 0.7209 (mttm) REVERT: x 3 ILE cc_start: 0.7606 (mt) cc_final: 0.7380 (mt) REVERT: AK 4 ILE cc_start: 0.7569 (OUTLIER) cc_final: 0.7267 (mp) REVERT: AN 5 LYS cc_start: 0.7641 (mttt) cc_final: 0.7232 (mttm) REVERT: AW 5 LYS cc_start: 0.7811 (mttm) cc_final: 0.7510 (mttm) REVERT: A2 4 ILE cc_start: 0.7569 (OUTLIER) cc_final: 0.7275 (mp) REVERT: A5 5 LYS cc_start: 0.7449 (mttt) cc_final: 0.7101 (mttm) REVERT: BB 5 LYS cc_start: 0.7783 (mttt) cc_final: 0.7331 (mttp) REVERT: BK 4 ILE cc_start: 0.7464 (OUTLIER) cc_final: 0.7147 (mp) REVERT: BT 5 LYS cc_start: 0.7644 (mttt) cc_final: 0.7378 (mttp) REVERT: B2 4 ILE cc_start: 0.7687 (OUTLIER) cc_final: 0.7387 (mp) REVERT: B5 5 LYS cc_start: 0.7679 (mttt) cc_final: 0.7473 (mttm) REVERT: 1 4 ILE cc_start: 0.7648 (OUTLIER) cc_final: 0.7378 (mp) REVERT: 6 5 LYS cc_start: 0.7364 (mttt) cc_final: 0.6878 (mttm) REVERT: CT 4 ILE cc_start: 0.7671 (OUTLIER) cc_final: 0.7419 (mp) REVERT: CW 5 LYS cc_start: 0.7554 (mttt) cc_final: 0.7052 (mttm) REVERT: DE 5 LYS cc_start: 0.7384 (mttt) cc_final: 0.6948 (mttm) REVERT: DT 4 ILE cc_start: 0.7807 (OUTLIER) cc_final: 0.7585 (mp) REVERT: DW 3 ILE cc_start: 0.8608 (mt) cc_final: 0.8308 (mp) REVERT: EE 5 LYS cc_start: 0.7371 (mttt) cc_final: 0.6911 (mttm) REVERT: EW 2 LEU cc_start: 0.8270 (pt) cc_final: 0.8028 (pp) REVERT: E5 5 LYS cc_start: 0.7525 (mttt) cc_final: 0.7159 (mttp) REVERT: FB 4 ILE cc_start: 0.7682 (OUTLIER) cc_final: 0.7442 (mp) REVERT: FE 2 LEU cc_start: 0.8439 (pp) cc_final: 0.6834 (mm) REVERT: FE 3 ILE cc_start: 0.8804 (mt) cc_final: 0.8421 (mp) REVERT: FE 5 LYS cc_start: 0.8301 (mttt) cc_final: 0.7821 (mttm) REVERT: FT 4 ILE cc_start: 0.7757 (OUTLIER) cc_final: 0.7542 (mp) outliers start: 217 outliers final: 135 residues processed: 566 average time/residue: 0.2916 time to fit residues: 262.1069 Evaluate side-chains 586 residues out of total 2400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 145 poor density : 441 time to evaluate : 2.666 ------------------------------------------------------------------------------- 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 7 ILE 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 B5 residue 1 ASP 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 CZ residue 7 ILE 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 DQ residue 2 LEU Chi-restraints excluded: chain DQ residue 7 ILE Chi-restraints excluded: chain DR residue 3 ILE Chi-restraints excluded: chain DT residue 4 ILE Chi-restraints excluded: chain DU residue 9 VAL Chi-restraints excluded: chain 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 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 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 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 7 ILE Chi-restraints excluded: chain E9 residue 3 ILE Chi-restraints excluded: chain FB residue 4 ILE Chi-restraints excluded: chain FB residue 8 SER Chi-restraints excluded: chain FC residue 9 VAL Chi-restraints excluded: chain 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 4 ILE Chi-restraints excluded: chain FZ residue 7 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 188 optimal weight: 9.9990 chunk 143 optimal weight: 7.9990 chunk 99 optimal weight: 20.0000 chunk 21 optimal weight: 7.9990 chunk 91 optimal weight: 20.0000 chunk 128 optimal weight: 20.0000 chunk 191 optimal weight: 8.9990 chunk 202 optimal weight: 20.0000 chunk 100 optimal weight: 30.0000 chunk 181 optimal weight: 8.9990 chunk 54 optimal weight: 20.0000 overall best weight: 8.7990 ------------------------------------------------------------------------------- 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 ** BH 10 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B8 10 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** CB 10 HIS CM 10 HIS ** CQ 10 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** DH 10 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** DK 10 HIS ** 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** FH 10 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** FN 10 HIS ** FQ 10 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** FV 10 HIS ** FZ 10 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7255 moved from start: 0.2863 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.034 20370 Z= 0.196 Angle : 0.694 10.358 27210 Z= 0.291 Chirality : 0.057 0.181 3840 Planarity : 0.002 0.007 3060 Dihedral : 11.296 58.117 2580 Min Nonbonded Distance : 2.312 Molprobity Statistics. All-atom Clashscore : 6.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 10.21 % Allowed : 20.58 % Favored : 69.21 % 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: -1.52 (0.17), residues: 2100 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.15 (0.13), residues: 2100 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 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 724 residues out of total 2400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 245 poor density : 479 time to evaluate : 2.638 Fit side-chains REVERT: D 2 LEU cc_start: 0.8745 (OUTLIER) cc_final: 0.8520 (pt) REVERT: M 3 ILE cc_start: 0.8597 (mt) cc_final: 0.8390 (mp) REVERT: M 5 LYS cc_start: 0.7886 (mttt) cc_final: 0.7524 (mttm) REVERT: P 5 LYS cc_start: 0.6034 (mmmt) cc_final: 0.4824 (pttm) REVERT: V 2 LEU cc_start: 0.8419 (pt) cc_final: 0.7953 (tt) REVERT: j 5 LYS cc_start: 0.8094 (mttt) cc_final: 0.7771 (mttp) REVERT: s 4 ILE cc_start: 0.7512 (OUTLIER) cc_final: 0.7284 (mp) REVERT: v 5 LYS cc_start: 0.7496 (mttt) cc_final: 0.7205 (mttm) REVERT: x 3 ILE cc_start: 0.7548 (mt) cc_final: 0.7333 (mt) REVERT: AB 5 LYS cc_start: 0.7865 (mttt) cc_final: 0.7357 (mttp) REVERT: AK 4 ILE cc_start: 0.7539 (OUTLIER) cc_final: 0.7228 (mp) REVERT: AN 5 LYS cc_start: 0.7539 (mttt) cc_final: 0.7293 (mttm) REVERT: AT 5 LYS cc_start: 0.7850 (mttt) cc_final: 0.7470 (mttp) REVERT: AW 5 LYS cc_start: 0.7701 (mttm) cc_final: 0.7426 (mttm) REVERT: A2 4 ILE cc_start: 0.7575 (OUTLIER) cc_final: 0.7293 (mp) REVERT: A5 5 LYS cc_start: 0.7381 (mttt) cc_final: 0.6966 (mttm) REVERT: BB 5 LYS cc_start: 0.7772 (mttt) cc_final: 0.7360 (mttp) REVERT: BE 5 LYS cc_start: 0.7841 (mttt) cc_final: 0.7446 (mttp) REVERT: BG 11 ILE cc_start: 0.8062 (OUTLIER) cc_final: 0.7859 (mt) REVERT: BK 4 ILE cc_start: 0.7447 (OUTLIER) cc_final: 0.7136 (mp) REVERT: BN 3 ILE cc_start: 0.8569 (mt) cc_final: 0.8351 (mp) REVERT: BT 5 LYS cc_start: 0.7583 (mttt) cc_final: 0.7325 (mttp) REVERT: BW 2 LEU cc_start: 0.8175 (pt) cc_final: 0.7958 (pp) REVERT: BW 5 LYS cc_start: 0.7571 (mttt) cc_final: 0.7224 (mttm) REVERT: B2 4 ILE cc_start: 0.7646 (OUTLIER) cc_final: 0.7343 (mp) REVERT: B5 2 LEU cc_start: 0.8152 (pp) cc_final: 0.7920 (pt) REVERT: B5 5 LYS cc_start: 0.7725 (mttt) cc_final: 0.7458 (mttm) REVERT: 1 4 ILE cc_start: 0.7614 (OUTLIER) cc_final: 0.7343 (mp) REVERT: 6 5 LYS cc_start: 0.7348 (mttt) cc_final: 0.6827 (mttm) REVERT: CN 2 LEU cc_start: 0.7873 (pt) cc_final: 0.7631 (pp) REVERT: CR 5 LYS cc_start: 0.8592 (OUTLIER) cc_final: 0.8260 (mtmm) REVERT: CT 4 ILE cc_start: 0.7605 (OUTLIER) cc_final: 0.7357 (mp) REVERT: CW 5 LYS cc_start: 0.7576 (mttt) cc_final: 0.7051 (mttm) REVERT: DE 5 LYS cc_start: 0.7354 (mttt) cc_final: 0.6902 (mttm) REVERT: DT 4 ILE cc_start: 0.7802 (OUTLIER) cc_final: 0.7571 (mp) REVERT: DW 3 ILE cc_start: 0.8604 (mt) cc_final: 0.8313 (mp) REVERT: EE 5 LYS cc_start: 0.7334 (mttt) cc_final: 0.6905 (mttm) REVERT: E5 5 LYS cc_start: 0.7482 (mttt) cc_final: 0.7137 (mttp) REVERT: FB 4 ILE cc_start: 0.7649 (OUTLIER) cc_final: 0.7428 (mp) REVERT: FE 2 LEU cc_start: 0.8424 (pp) cc_final: 0.6814 (mm) REVERT: FE 3 ILE cc_start: 0.8760 (mt) cc_final: 0.8371 (mp) REVERT: FE 5 LYS cc_start: 0.8286 (mttt) cc_final: 0.7811 (mttm) outliers start: 245 outliers final: 141 residues processed: 582 average time/residue: 0.2953 time to fit residues: 272.5002 Evaluate side-chains 597 residues out of total 2400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 153 poor density : 444 time to evaluate : 2.661 ------------------------------------------------------------------------------- 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 D residue 2 LEU Chi-restraints excluded: chain E residue 9 VAL Chi-restraints excluded: chain G residue 2 LEU Chi-restraints excluded: chain J residue 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 5 LYS 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 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 z residue 3 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 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 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 BG residue 11 ILE Chi-restraints excluded: chain BH residue 2 LEU 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 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 CB residue 8 SER Chi-restraints excluded: chain CC residue 9 VAL Chi-restraints excluded: chain CE residue 8 SER Chi-restraints excluded: chain CH residue 2 LEU Chi-restraints excluded: chain CH residue 7 ILE Chi-restraints excluded: chain CI residue 3 ILE Chi-restraints excluded: chain CI residue 5 LYS Chi-restraints excluded: chain 1 residue 4 ILE Chi-restraints excluded: chain 3 residue 9 VAL Chi-restraints excluded: chain 6 residue 1 ASP Chi-restraints excluded: chain 4 residue 11 ILE 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 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 CZ residue 7 ILE Chi-restraints excluded: chain C3 residue 9 VAL Chi-restraints excluded: chain C5 residue 1 ASP 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 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 DT residue 4 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 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 EQ residue 7 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 E8 residue 7 ILE Chi-restraints excluded: chain FB residue 4 ILE Chi-restraints excluded: chain FB residue 8 SER Chi-restraints excluded: chain FC residue 9 VAL Chi-restraints excluded: chain 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 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 169 optimal weight: 20.0000 chunk 115 optimal weight: 9.9990 chunk 2 optimal weight: 30.0000 chunk 151 optimal weight: 8.9990 chunk 83 optimal weight: 3.9990 chunk 173 optimal weight: 30.0000 chunk 140 optimal weight: 7.9990 chunk 0 optimal weight: 20.0000 chunk 103 optimal weight: 20.0000 chunk 182 optimal weight: 20.0000 chunk 51 optimal weight: 30.0000 overall best weight: 10.1992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** V 10 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** BT 10 HIS ** B5 10 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** DE 10 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** DW 10 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** EE 10 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E4 10 HIS ** FE 10 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** FH 10 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** FM 10 HIS ** FQ 10 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** FZ 10 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7264 moved from start: 0.3192 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.047 20370 Z= 0.221 Angle : 0.719 9.893 27210 Z= 0.304 Chirality : 0.057 0.180 3840 Planarity : 0.002 0.008 3060 Dihedral : 11.362 57.600 2580 Min Nonbonded Distance : 2.267 Molprobity Statistics. All-atom Clashscore : 7.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 10.46 % Allowed : 21.42 % Favored : 68.12 % 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: -1.45 (0.17), residues: 2100 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.10 (0.13), residues: 2100 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HISC6 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 714 residues out of total 2400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 251 poor density : 463 time to evaluate : 2.251 Fit side-chains REVERT: D 2 LEU cc_start: 0.8726 (OUTLIER) cc_final: 0.8491 (pt) REVERT: M 5 LYS cc_start: 0.7878 (mttt) cc_final: 0.7507 (mttm) REVERT: P 5 LYS cc_start: 0.6004 (mmmt) cc_final: 0.4834 (pttm) REVERT: S 5 LYS cc_start: 0.7994 (mttt) cc_final: 0.7773 (mttp) REVERT: U 3 ILE cc_start: 0.7921 (OUTLIER) cc_final: 0.7433 (mp) REVERT: V 2 LEU cc_start: 0.8488 (pt) cc_final: 0.8016 (tt) REVERT: j 5 LYS cc_start: 0.8112 (mttt) cc_final: 0.7789 (mttp) REVERT: s 4 ILE cc_start: 0.7440 (OUTLIER) cc_final: 0.7193 (mp) REVERT: v 5 LYS cc_start: 0.7401 (mttt) cc_final: 0.7141 (mttm) REVERT: x 3 ILE cc_start: 0.7549 (mt) cc_final: 0.7308 (mt) REVERT: AB 5 LYS cc_start: 0.7904 (mttt) cc_final: 0.7395 (mttp) REVERT: AE 5 LYS cc_start: 0.7740 (mttt) cc_final: 0.7316 (mttm) REVERT: AK 4 ILE cc_start: 0.7526 (OUTLIER) cc_final: 0.7216 (mp) REVERT: AN 5 LYS cc_start: 0.7462 (mttt) cc_final: 0.7185 (mttm) REVERT: AT 5 LYS cc_start: 0.7816 (mttt) cc_final: 0.7436 (mttp) REVERT: A2 4 ILE cc_start: 0.7544 (OUTLIER) cc_final: 0.7264 (mp) REVERT: A5 5 LYS cc_start: 0.7490 (mttt) cc_final: 0.7049 (mttm) REVERT: A7 3 ILE cc_start: 0.7618 (mt) cc_final: 0.7397 (mt) REVERT: BB 5 LYS cc_start: 0.7790 (mttt) cc_final: 0.7381 (mttp) REVERT: BE 5 LYS cc_start: 0.7830 (mttt) cc_final: 0.7405 (mttp) REVERT: BK 4 ILE cc_start: 0.7393 (OUTLIER) cc_final: 0.7098 (mp) REVERT: BT 5 LYS cc_start: 0.7619 (mttt) cc_final: 0.7361 (mttp) REVERT: BW 2 LEU cc_start: 0.8224 (pt) cc_final: 0.8011 (pp) REVERT: BW 5 LYS cc_start: 0.7626 (mttt) cc_final: 0.7268 (mttm) REVERT: B2 4 ILE cc_start: 0.7639 (OUTLIER) cc_final: 0.7376 (mp) REVERT: B5 2 LEU cc_start: 0.8200 (pp) cc_final: 0.7941 (pt) REVERT: B5 5 LYS cc_start: 0.7737 (mttt) cc_final: 0.7453 (mttm) REVERT: CD 3 ILE cc_start: 0.7827 (OUTLIER) cc_final: 0.7286 (mp) REVERT: 1 4 ILE cc_start: 0.7579 (OUTLIER) cc_final: 0.7334 (mp) REVERT: 6 5 LYS cc_start: 0.7375 (mttt) cc_final: 0.6834 (mttm) REVERT: CN 5 LYS cc_start: 0.7621 (mttm) cc_final: 0.7411 (mttm) REVERT: CR 5 LYS cc_start: 0.8758 (OUTLIER) cc_final: 0.8389 (mtmm) REVERT: CT 4 ILE cc_start: 0.7541 (OUTLIER) cc_final: 0.7287 (mp) REVERT: CW 5 LYS cc_start: 0.7537 (mttt) cc_final: 0.7023 (mttm) REVERT: DE 5 LYS cc_start: 0.7298 (mttt) cc_final: 0.6833 (mttm) REVERT: DM 3 ILE cc_start: 0.7795 (OUTLIER) cc_final: 0.7220 (mp) REVERT: DT 4 ILE cc_start: 0.7795 (OUTLIER) cc_final: 0.7563 (mp) REVERT: DW 3 ILE cc_start: 0.8628 (mt) cc_final: 0.8373 (mp) REVERT: D4 3 ILE cc_start: 0.7826 (OUTLIER) cc_final: 0.7286 (mp) REVERT: EE 5 LYS cc_start: 0.7310 (mttt) cc_final: 0.6899 (mttm) REVERT: E5 5 LYS cc_start: 0.7493 (mttt) cc_final: 0.7137 (mttp) REVERT: FB 4 ILE cc_start: 0.7663 (OUTLIER) cc_final: 0.7437 (mp) REVERT: FE 2 LEU cc_start: 0.8474 (pp) cc_final: 0.6919 (mm) REVERT: FE 3 ILE cc_start: 0.8776 (mt) cc_final: 0.8414 (mp) REVERT: FE 5 LYS cc_start: 0.8291 (mttt) cc_final: 0.7835 (mttm) outliers start: 251 outliers final: 172 residues processed: 567 average time/residue: 0.3086 time to fit residues: 282.4829 Evaluate side-chains 637 residues out of total 2400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 187 poor density : 450 time to evaluate : 2.499 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 SER Chi-restraints excluded: chain B residue 9 VAL Chi-restraints excluded: chain D residue 1 ASP Chi-restraints excluded: chain D residue 2 LEU Chi-restraints excluded: chain E residue 9 VAL Chi-restraints excluded: chain G residue 2 LEU Chi-restraints excluded: chain J residue 8 SER Chi-restraints excluded: chain K residue 9 VAL Chi-restraints excluded: chain M residue 8 SER Chi-restraints excluded: chain N residue 9 VAL Chi-restraints excluded: chain P residue 2 LEU Chi-restraints excluded: chain P residue 7 ILE Chi-restraints excluded: chain S residue 8 SER Chi-restraints excluded: chain T residue 9 VAL Chi-restraints excluded: chain U residue 3 ILE Chi-restraints excluded: chain V residue 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 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 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 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 9 VAL 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 AZ residue 9 VAL Chi-restraints excluded: chain A0 residue 3 ILE Chi-restraints excluded: chain A0 residue 5 LYS Chi-restraints excluded: chain A2 residue 4 ILE Chi-restraints excluded: chain A3 residue 9 VAL Chi-restraints excluded: chain A5 residue 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 BG residue 4 ILE Chi-restraints excluded: chain BH residue 2 LEU Chi-restraints excluded: chain BH residue 9 VAL Chi-restraints excluded: chain BI residue 3 ILE Chi-restraints excluded: chain BK residue 4 ILE Chi-restraints excluded: chain BL residue 9 VAL Chi-restraints excluded: chain BN residue 8 SER Chi-restraints excluded: chain BQ residue 2 LEU Chi-restraints excluded: chain BQ residue 7 ILE Chi-restraints excluded: chain BQ residue 9 VAL Chi-restraints excluded: chain BU residue 9 VAL Chi-restraints excluded: chain 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 CD residue 3 ILE Chi-restraints excluded: chain CE residue 8 SER Chi-restraints excluded: chain CH residue 2 LEU Chi-restraints excluded: chain CH residue 7 ILE Chi-restraints excluded: chain CH residue 9 VAL Chi-restraints excluded: chain CI residue 3 ILE Chi-restraints excluded: chain CI residue 5 LYS Chi-restraints excluded: chain 1 residue 4 ILE Chi-restraints excluded: chain 3 residue 9 VAL Chi-restraints excluded: chain 6 residue 1 ASP Chi-restraints excluded: chain 4 residue 11 ILE 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 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 CZ residue 7 ILE Chi-restraints excluded: chain CZ residue 9 VAL Chi-restraints excluded: chain C3 residue 9 VAL Chi-restraints excluded: chain C5 residue 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 9 VAL Chi-restraints excluded: chain DK residue 9 VAL Chi-restraints excluded: chain DL residue 9 VAL Chi-restraints excluded: chain DM residue 3 ILE Chi-restraints excluded: chain DN residue 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 3 ILE Chi-restraints excluded: chain DT residue 4 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 D4 residue 3 ILE 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 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 EQ residue 2 LEU Chi-restraints excluded: chain EQ residue 7 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 E8 residue 7 ILE Chi-restraints excluded: chain E9 residue 3 ILE Chi-restraints excluded: chain FB residue 4 ILE 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 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 8 SER 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 68 optimal weight: 10.0000 chunk 182 optimal weight: 10.0000 chunk 40 optimal weight: 30.0000 chunk 119 optimal weight: 6.9990 chunk 50 optimal weight: 20.0000 chunk 203 optimal weight: 10.0000 chunk 168 optimal weight: 9.9990 chunk 94 optimal weight: 30.0000 chunk 16 optimal weight: 30.0000 chunk 67 optimal weight: 30.0000 chunk 106 optimal weight: 0.5980 overall best weight: 7.5192 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** V 10 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B5 10 HIS ** DW 10 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** EE 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** ** 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: 0.7250 moved from start: 0.3345 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 20370 Z= 0.172 Angle : 0.673 10.320 27210 Z= 0.279 Chirality : 0.057 0.185 3840 Planarity : 0.002 0.008 3060 Dihedral : 10.847 56.428 2580 Min Nonbonded Distance : 2.283 Molprobity Statistics. All-atom Clashscore : 6.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 10.12 % Allowed : 22.71 % Favored : 67.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.17 (0.18), residues: 2100 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.88 (0.13), residues: 2100 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HISD6 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 695 residues out of total 2400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 243 poor density : 452 time to evaluate : 2.399 Fit side-chains REVERT: D 2 LEU cc_start: 0.8740 (OUTLIER) cc_final: 0.8518 (pt) REVERT: M 2 LEU cc_start: 0.8355 (pt) cc_final: 0.7832 (tt) REVERT: M 5 LYS cc_start: 0.7806 (mttt) cc_final: 0.7523 (mttm) REVERT: P 5 LYS cc_start: 0.6019 (mmmt) cc_final: 0.4911 (pttm) REVERT: V 2 LEU cc_start: 0.8562 (pt) cc_final: 0.8105 (tt) REVERT: j 5 LYS cc_start: 0.8067 (mttt) cc_final: 0.7586 (mttp) REVERT: s 4 ILE cc_start: 0.7418 (OUTLIER) cc_final: 0.7170 (mp) REVERT: v 5 LYS cc_start: 0.7484 (mttt) cc_final: 0.7209 (mttm) REVERT: x 3 ILE cc_start: 0.7535 (mt) cc_final: 0.7300 (mt) REVERT: AB 5 LYS cc_start: 0.7879 (mttt) cc_final: 0.7377 (mttp) REVERT: AD 3 ILE cc_start: 0.7736 (OUTLIER) cc_final: 0.7191 (mp) REVERT: AE 5 LYS cc_start: 0.7724 (mttt) cc_final: 0.7410 (mttm) REVERT: AK 4 ILE cc_start: 0.7525 (OUTLIER) cc_final: 0.7212 (mp) REVERT: AN 5 LYS cc_start: 0.7395 (mttt) cc_final: 0.7127 (mttm) REVERT: AV 3 ILE cc_start: 0.7608 (OUTLIER) cc_final: 0.7076 (mp) REVERT: A2 4 ILE cc_start: 0.7537 (OUTLIER) cc_final: 0.7261 (mp) REVERT: A5 5 LYS cc_start: 0.7508 (mttt) cc_final: 0.7143 (mttm) REVERT: BB 5 LYS cc_start: 0.7635 (mttt) cc_final: 0.7274 (mttp) REVERT: BE 5 LYS cc_start: 0.7802 (mttt) cc_final: 0.7426 (mttp) REVERT: BK 4 ILE cc_start: 0.7284 (OUTLIER) cc_final: 0.6968 (mp) REVERT: BR 3 ILE cc_start: 0.8064 (OUTLIER) cc_final: 0.7863 (pt) REVERT: BW 5 LYS cc_start: 0.7650 (mttt) cc_final: 0.7260 (mttm) REVERT: B2 4 ILE cc_start: 0.7625 (OUTLIER) cc_final: 0.7328 (mp) REVERT: B5 5 LYS cc_start: 0.7819 (mttt) cc_final: 0.7570 (mttm) REVERT: 1 4 ILE cc_start: 0.7564 (OUTLIER) cc_final: 0.7326 (mp) REVERT: 6 5 LYS cc_start: 0.7279 (mttt) cc_final: 0.6793 (mttm) REVERT: CN 2 LEU cc_start: 0.7846 (pt) cc_final: 0.7557 (pp) REVERT: CN 5 LYS cc_start: 0.7617 (mttm) cc_final: 0.7367 (mttm) REVERT: CR 5 LYS cc_start: 0.8761 (OUTLIER) cc_final: 0.8471 (mtmm) REVERT: CW 5 LYS cc_start: 0.7526 (mttt) cc_final: 0.7039 (mttm) REVERT: DE 5 LYS cc_start: 0.7289 (mttt) cc_final: 0.6813 (mttm) REVERT: DM 3 ILE cc_start: 0.7786 (OUTLIER) cc_final: 0.7195 (mp) REVERT: DT 4 ILE cc_start: 0.7755 (OUTLIER) cc_final: 0.7508 (mp) REVERT: DW 3 ILE cc_start: 0.8631 (mt) cc_final: 0.8359 (mp) REVERT: D4 3 ILE cc_start: 0.7824 (OUTLIER) cc_final: 0.7264 (mp) REVERT: D5 2 LEU cc_start: 0.8063 (pt) cc_final: 0.7758 (pp) REVERT: EE 5 LYS cc_start: 0.7322 (mttt) cc_final: 0.6919 (mttm) REVERT: E4 3 ILE cc_start: 0.7985 (OUTLIER) cc_final: 0.7468 (mp) REVERT: E5 5 LYS cc_start: 0.7527 (mttt) cc_final: 0.7183 (mttp) REVERT: FB 4 ILE cc_start: 0.7681 (OUTLIER) cc_final: 0.7451 (mp) REVERT: FE 2 LEU cc_start: 0.8374 (pp) cc_final: 0.6749 (mm) REVERT: FE 3 ILE cc_start: 0.8752 (mt) cc_final: 0.8372 (mp) REVERT: FE 5 LYS cc_start: 0.8211 (mttt) cc_final: 0.7780 (mttm) REVERT: FM 3 ILE cc_start: 0.8306 (OUTLIER) cc_final: 0.7753 (mp) outliers start: 243 outliers final: 173 residues processed: 547 average time/residue: 0.2772 time to fit residues: 242.8262 Evaluate side-chains 633 residues out of total 2400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 190 poor density : 443 time to evaluate : 2.554 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 SER Chi-restraints excluded: chain B residue 9 VAL Chi-restraints excluded: chain D residue 1 ASP Chi-restraints excluded: chain D residue 2 LEU Chi-restraints excluded: chain E residue 9 VAL Chi-restraints excluded: chain G residue 2 LEU Chi-restraints excluded: chain G residue 9 VAL Chi-restraints excluded: chain J residue 8 SER Chi-restraints excluded: chain M residue 8 SER Chi-restraints excluded: chain P residue 2 LEU Chi-restraints excluded: chain 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 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 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 AC residue 11 ILE 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 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 AZ residue 9 VAL Chi-restraints excluded: chain A0 residue 3 ILE Chi-restraints excluded: chain A0 residue 5 LYS Chi-restraints excluded: chain A2 residue 4 ILE Chi-restraints excluded: chain A3 residue 9 VAL Chi-restraints excluded: chain A5 residue 1 ASP Chi-restraints excluded: chain A5 residue 8 SER 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 BG residue 4 ILE Chi-restraints excluded: chain BH residue 2 LEU Chi-restraints excluded: chain BH residue 7 ILE Chi-restraints excluded: chain BH residue 9 VAL Chi-restraints excluded: chain BI residue 3 ILE Chi-restraints excluded: chain BK residue 4 ILE Chi-restraints excluded: chain BL residue 9 VAL Chi-restraints excluded: chain BN residue 8 SER Chi-restraints excluded: chain BQ residue 2 LEU Chi-restraints excluded: chain BQ residue 7 ILE Chi-restraints excluded: chain BQ residue 9 VAL Chi-restraints excluded: chain BR residue 3 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 9 VAL Chi-restraints excluded: chain B2 residue 4 ILE Chi-restraints excluded: chain B3 residue 9 VAL Chi-restraints excluded: chain B4 residue 2 LEU 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 CH residue 2 LEU Chi-restraints excluded: chain CH residue 7 ILE Chi-restraints excluded: chain CH residue 9 VAL Chi-restraints excluded: chain CI residue 3 ILE Chi-restraints excluded: chain CI residue 5 LYS Chi-restraints excluded: chain 1 residue 4 ILE Chi-restraints excluded: chain 3 residue 9 VAL Chi-restraints excluded: chain 6 residue 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 2 LEU Chi-restraints excluded: chain CQ residue 9 VAL Chi-restraints excluded: chain CR residue 3 ILE Chi-restraints excluded: chain CR residue 5 LYS Chi-restraints excluded: chain CU residue 9 VAL Chi-restraints excluded: chain CW residue 1 ASP Chi-restraints excluded: chain CW residue 4 ILE Chi-restraints excluded: chain CZ residue 2 LEU Chi-restraints excluded: chain CZ residue 7 ILE Chi-restraints excluded: chain CZ residue 9 VAL Chi-restraints excluded: chain C3 residue 9 VAL Chi-restraints excluded: chain C5 residue 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 9 VAL Chi-restraints excluded: chain DK residue 9 VAL Chi-restraints excluded: chain DL residue 9 VAL Chi-restraints excluded: chain DL residue 11 ILE 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 DT residue 4 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 D2 residue 8 SER Chi-restraints excluded: chain D3 residue 9 VAL Chi-restraints excluded: chain D4 residue 3 ILE Chi-restraints excluded: chain D5 residue 8 SER Chi-restraints excluded: chain D8 residue 2 LEU Chi-restraints excluded: chain D8 residue 9 VAL Chi-restraints excluded: chain D9 residue 3 ILE Chi-restraints excluded: chain 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 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 E9 residue 3 ILE Chi-restraints excluded: chain FB residue 4 ILE 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 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 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 2 LEU Chi-restraints excluded: chain FZ residue 7 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 195 optimal weight: 0.0970 chunk 22 optimal weight: 20.0000 chunk 115 optimal weight: 7.9990 chunk 148 optimal weight: 0.9980 chunk 114 optimal weight: 5.9990 chunk 171 optimal weight: 9.9990 chunk 113 optimal weight: 0.8980 chunk 202 optimal weight: 8.9990 chunk 126 optimal weight: 3.9990 chunk 123 optimal weight: 30.0000 chunk 93 optimal weight: 7.9990 overall best weight: 2.3982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** V 10 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** l 10 HIS BD 10 HIS ** DW 10 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ED 10 HIS ** EE 10 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** FE 10 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** FH 10 HIS ** FQ 10 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** FZ 10 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7210 moved from start: 0.3535 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 20370 Z= 0.084 Angle : 0.595 9.726 27210 Z= 0.239 Chirality : 0.057 0.191 3840 Planarity : 0.001 0.017 3060 Dihedral : 9.692 54.656 2580 Min Nonbonded Distance : 2.279 Molprobity Statistics. All-atom Clashscore : 5.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.71 % Favored : 99.29 % Rotamer: Outliers : 7.96 % Allowed : 24.67 % Favored : 67.38 % 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: -0.62 (0.18), residues: 2100 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.46 (0.14), residues: 2100 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.000 HISCW 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 638 residues out of total 2400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 191 poor density : 447 time to evaluate : 2.379 Fit side-chains REVERT: M 2 LEU cc_start: 0.8201 (pt) cc_final: 0.7787 (tt) REVERT: M 5 LYS cc_start: 0.7732 (mttt) cc_final: 0.7469 (mttm) REVERT: U 3 ILE cc_start: 0.7932 (OUTLIER) cc_final: 0.7433 (mp) REVERT: V 2 LEU cc_start: 0.8554 (pt) cc_final: 0.8262 (tt) REVERT: m 3 ILE cc_start: 0.8449 (mt) cc_final: 0.8202 (mp) REVERT: v 5 LYS cc_start: 0.7415 (mttt) cc_final: 0.7148 (mttm) REVERT: AE 5 LYS cc_start: 0.7594 (mttt) cc_final: 0.7273 (mttm) REVERT: AN 5 LYS cc_start: 0.7329 (mttt) cc_final: 0.7024 (mttm) REVERT: AV 3 ILE cc_start: 0.7625 (OUTLIER) cc_final: 0.7078 (mp) REVERT: A5 5 LYS cc_start: 0.7463 (mttt) cc_final: 0.7076 (mttm) REVERT: BE 3 ILE cc_start: 0.8454 (mt) cc_final: 0.8153 (mp) REVERT: BE 5 LYS cc_start: 0.7716 (mttt) cc_final: 0.7450 (mttm) REVERT: BW 5 LYS cc_start: 0.7640 (mttt) cc_final: 0.7358 (mttm) REVERT: B5 2 LEU cc_start: 0.8062 (pt) cc_final: 0.7828 (pp) REVERT: B5 5 LYS cc_start: 0.7754 (mttt) cc_final: 0.7541 (mttm) REVERT: CD 3 ILE cc_start: 0.7862 (OUTLIER) cc_final: 0.7325 (mp) REVERT: CE 3 ILE cc_start: 0.8433 (mt) cc_final: 0.8023 (mp) REVERT: 6 5 LYS cc_start: 0.7327 (mttt) cc_final: 0.6838 (mttm) REVERT: CM 5 LYS cc_start: 0.7975 (ptmt) cc_final: 0.7749 (ptpt) REVERT: CN 2 LEU cc_start: 0.7625 (pt) cc_final: 0.7389 (pp) REVERT: CW 5 LYS cc_start: 0.7355 (mttt) cc_final: 0.6944 (mttm) REVERT: C5 5 LYS cc_start: 0.7515 (mttm) cc_final: 0.7104 (mttm) REVERT: DE 5 LYS cc_start: 0.7123 (mttt) cc_final: 0.6791 (mttm) REVERT: DM 5 LYS cc_start: 0.7924 (ptmt) cc_final: 0.7707 (ptpt) REVERT: DN 2 LEU cc_start: 0.7947 (pt) cc_final: 0.7726 (pp) REVERT: DT 4 ILE cc_start: 0.7732 (OUTLIER) cc_final: 0.7503 (mp) REVERT: DW 3 ILE cc_start: 0.8614 (mt) cc_final: 0.8299 (mp) REVERT: D5 2 LEU cc_start: 0.7923 (pt) cc_final: 0.7278 (tt) REVERT: D5 3 ILE cc_start: 0.8393 (mt) cc_final: 0.8104 (mp) REVERT: EE 5 LYS cc_start: 0.7219 (mttt) cc_final: 0.6866 (mttm) REVERT: EN 2 LEU cc_start: 0.7876 (pt) cc_final: 0.7590 (pp) REVERT: EW 3 ILE cc_start: 0.8359 (mt) cc_final: 0.8123 (mp) REVERT: E4 3 ILE cc_start: 0.8051 (OUTLIER) cc_final: 0.7525 (mp) REVERT: E5 5 LYS cc_start: 0.7404 (mttt) cc_final: 0.7094 (mttp) REVERT: FE 2 LEU cc_start: 0.8138 (pp) cc_final: 0.6435 (mm) REVERT: FE 3 ILE cc_start: 0.8668 (mt) cc_final: 0.8273 (mp) REVERT: FE 5 LYS cc_start: 0.8194 (mttt) cc_final: 0.7817 (mttm) REVERT: FN 2 LEU cc_start: 0.8221 (pt) cc_final: 0.6503 (mm) outliers start: 191 outliers final: 127 residues processed: 532 average time/residue: 0.2723 time to fit residues: 234.2523 Evaluate side-chains 547 residues out of total 2400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 132 poor density : 415 time to evaluate : 2.341 ------------------------------------------------------------------------------- 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 J 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 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 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 AL residue 9 VAL Chi-restraints excluded: chain AQ residue 2 LEU Chi-restraints excluded: chain AT residue 8 SER Chi-restraints excluded: chain AU residue 9 VAL Chi-restraints excluded: chain AV residue 3 ILE Chi-restraints excluded: chain AW residue 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 AZ residue 9 VAL Chi-restraints excluded: chain A0 residue 3 ILE Chi-restraints excluded: chain A0 residue 5 LYS Chi-restraints excluded: chain A3 residue 9 VAL Chi-restraints excluded: chain 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 B8 residue 7 ILE Chi-restraints excluded: chain B8 residue 9 VAL Chi-restraints excluded: chain CB residue 8 SER Chi-restraints excluded: chain CC residue 9 VAL Chi-restraints excluded: chain CD residue 3 ILE Chi-restraints excluded: chain CE residue 8 SER Chi-restraints excluded: chain CH residue 2 LEU Chi-restraints excluded: chain CH residue 7 ILE Chi-restraints excluded: chain CH residue 9 VAL Chi-restraints excluded: chain CI residue 3 ILE Chi-restraints excluded: chain CI residue 5 LYS Chi-restraints excluded: chain 3 residue 9 VAL 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 CZ residue 2 LEU Chi-restraints excluded: chain CZ residue 7 ILE Chi-restraints excluded: chain CZ residue 9 VAL Chi-restraints excluded: chain C3 residue 9 VAL Chi-restraints excluded: chain C5 residue 1 ASP Chi-restraints excluded: chain C5 residue 8 SER Chi-restraints excluded: chain C8 residue 9 VAL Chi-restraints excluded: chain DC residue 9 VAL Chi-restraints excluded: chain DH residue 2 LEU Chi-restraints excluded: chain DH residue 9 VAL Chi-restraints excluded: chain DL residue 9 VAL 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 DT residue 4 ILE Chi-restraints excluded: chain DU residue 9 VAL Chi-restraints excluded: chain DW residue 1 ASP Chi-restraints excluded: chain DZ residue 7 ILE Chi-restraints excluded: chain D3 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 EG residue 11 ILE 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 EQ residue 7 ILE Chi-restraints excluded: chain EQ residue 9 VAL Chi-restraints excluded: chain EU residue 9 VAL Chi-restraints excluded: chain EZ residue 2 LEU Chi-restraints excluded: chain E3 residue 9 VAL Chi-restraints excluded: chain E4 residue 3 ILE Chi-restraints excluded: chain E5 residue 8 SER Chi-restraints excluded: chain E6 residue 9 VAL Chi-restraints excluded: chain E8 residue 7 ILE Chi-restraints excluded: chain FC residue 9 VAL Chi-restraints excluded: chain FF residue 9 VAL Chi-restraints excluded: chain FH residue 2 LEU Chi-restraints excluded: chain FL residue 9 VAL Chi-restraints excluded: chain FO residue 9 VAL Chi-restraints excluded: chain FT residue 8 SER Chi-restraints excluded: chain FU residue 9 VAL Chi-restraints excluded: chain FZ residue 4 ILE Chi-restraints excluded: chain FZ residue 7 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 125 optimal weight: 10.0000 chunk 80 optimal weight: 0.9990 chunk 120 optimal weight: 7.9990 chunk 60 optimal weight: 30.0000 chunk 39 optimal weight: 8.9990 chunk 128 optimal weight: 20.0000 chunk 137 optimal weight: 30.0000 chunk 100 optimal weight: 30.0000 chunk 18 optimal weight: 10.0000 chunk 159 optimal weight: 30.0000 chunk 184 optimal weight: 30.0000 overall best weight: 7.5994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: M 10 HIS O 10 HIS ** V 10 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A7 10 HIS ** 6 10 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** DG 10 HIS ** DW 10 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D4 10 HIS D7 10 HIS ** EE 10 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** EG 10 HIS EK 10 HIS ** FE 10 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** FQ 10 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7245 moved from start: 0.3596 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 20370 Z= 0.174 Angle : 0.695 10.226 27210 Z= 0.285 Chirality : 0.057 0.192 3840 Planarity : 0.002 0.017 3060 Dihedral : 10.526 55.039 2580 Min Nonbonded Distance : 2.306 Molprobity Statistics. All-atom Clashscore : 7.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 8.54 % Allowed : 24.67 % Favored : 66.79 % 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: -0.65 (0.19), residues: 2100 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.48 (0.14), residues: 2100 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS 6 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 665 residues out of total 2400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 205 poor density : 460 time to evaluate : 2.684 Fit side-chains REVERT: D 2 LEU cc_start: 0.8493 (pt) cc_final: 0.7936 (tt) REVERT: J 5 LYS cc_start: 0.7941 (mttt) cc_final: 0.7476 (mttp) REVERT: M 2 LEU cc_start: 0.8192 (pt) cc_final: 0.7781 (tt) REVERT: M 5 LYS cc_start: 0.7763 (mttt) cc_final: 0.7477 (mttm) REVERT: P 5 LYS cc_start: 0.5978 (mmmt) cc_final: 0.4898 (pttm) REVERT: U 3 ILE cc_start: 0.7850 (OUTLIER) cc_final: 0.7313 (mp) REVERT: V 2 LEU cc_start: 0.8597 (pt) cc_final: 0.8210 (tt) REVERT: j 5 LYS cc_start: 0.7944 (mttt) cc_final: 0.7448 (mttp) REVERT: v 5 LYS cc_start: 0.7425 (mttt) cc_final: 0.7155 (mttm) REVERT: AB 5 LYS cc_start: 0.7871 (mttt) cc_final: 0.7368 (mttp) REVERT: AD 3 ILE cc_start: 0.7700 (OUTLIER) cc_final: 0.7134 (mp) REVERT: AE 5 LYS cc_start: 0.7684 (mttt) cc_final: 0.7342 (mttm) REVERT: AK 4 ILE cc_start: 0.7479 (OUTLIER) cc_final: 0.7160 (mp) REVERT: AN 5 LYS cc_start: 0.7368 (mttt) cc_final: 0.7020 (mttm) REVERT: AV 3 ILE cc_start: 0.7622 (OUTLIER) cc_final: 0.7057 (mp) REVERT: A2 4 ILE cc_start: 0.7409 (OUTLIER) cc_final: 0.7133 (mp) REVERT: A5 5 LYS cc_start: 0.7422 (mttt) cc_final: 0.7068 (mttp) REVERT: BB 5 LYS cc_start: 0.7740 (mttt) cc_final: 0.7391 (mttp) REVERT: BE 5 LYS cc_start: 0.7623 (mttt) cc_final: 0.7262 (mttp) REVERT: BK 4 ILE cc_start: 0.7253 (OUTLIER) cc_final: 0.6952 (mp) REVERT: BQ 4 ILE cc_start: 0.7131 (pt) cc_final: 0.6423 (tp) REVERT: BV 3 ILE cc_start: 0.7973 (OUTLIER) cc_final: 0.7489 (mp) REVERT: BW 5 LYS cc_start: 0.7584 (mttt) cc_final: 0.7223 (mttm) REVERT: B2 4 ILE cc_start: 0.7456 (OUTLIER) cc_final: 0.7229 (mp) REVERT: B5 2 LEU cc_start: 0.8107 (pt) cc_final: 0.7889 (pp) REVERT: B5 5 LYS cc_start: 0.7590 (mttt) cc_final: 0.7341 (mttm) REVERT: CD 3 ILE cc_start: 0.7833 (OUTLIER) cc_final: 0.7291 (mp) REVERT: CE 3 ILE cc_start: 0.8603 (mt) cc_final: 0.8181 (mp) REVERT: 1 4 ILE cc_start: 0.7484 (OUTLIER) cc_final: 0.7256 (mp) REVERT: 6 2 LEU cc_start: 0.8321 (pt) cc_final: 0.7909 (pp) REVERT: 6 5 LYS cc_start: 0.7253 (mttt) cc_final: 0.6746 (mttm) REVERT: CK 5 LYS cc_start: 0.7908 (mttt) cc_final: 0.7447 (mttp) REVERT: CN 2 LEU cc_start: 0.7791 (pt) cc_final: 0.7529 (pp) REVERT: CW 5 LYS cc_start: 0.7355 (mttt) cc_final: 0.6942 (mttm) REVERT: C5 2 LEU cc_start: 0.8049 (pp) cc_final: 0.7759 (pt) REVERT: DE 5 LYS cc_start: 0.7355 (mttt) cc_final: 0.6976 (mttm) REVERT: DM 3 ILE cc_start: 0.7809 (OUTLIER) cc_final: 0.7220 (mp) REVERT: DT 4 ILE cc_start: 0.7655 (OUTLIER) cc_final: 0.7396 (mp) REVERT: DW 3 ILE cc_start: 0.8632 (mt) cc_final: 0.8398 (mp) REVERT: D5 2 LEU cc_start: 0.8103 (pt) cc_final: 0.7586 (tt) REVERT: EE 5 LYS cc_start: 0.7205 (mttt) cc_final: 0.6838 (mttm) REVERT: EN 2 LEU cc_start: 0.8134 (pt) cc_final: 0.7919 (pp) REVERT: EW 2 LEU cc_start: 0.8280 (pt) cc_final: 0.7763 (pp) REVERT: E4 3 ILE cc_start: 0.8084 (OUTLIER) cc_final: 0.7575 (mp) REVERT: E5 5 LYS cc_start: 0.7347 (mttt) cc_final: 0.6983 (mttp) REVERT: FB 4 ILE cc_start: 0.7637 (OUTLIER) cc_final: 0.7406 (mp) REVERT: FE 2 LEU cc_start: 0.8321 (pp) cc_final: 0.6696 (mm) REVERT: FE 3 ILE cc_start: 0.8733 (mt) cc_final: 0.8380 (mp) REVERT: FE 5 LYS cc_start: 0.8242 (mttt) cc_final: 0.7803 (mttm) REVERT: FN 2 LEU cc_start: 0.8347 (pt) cc_final: 0.6671 (mm) outliers start: 205 outliers final: 145 residues processed: 542 average time/residue: 0.2773 time to fit residues: 240.0741 Evaluate side-chains 596 residues out of total 2400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 159 poor density : 437 time to evaluate : 2.504 ------------------------------------------------------------------------------- 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 H 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 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 d residue 8 SER Chi-restraints excluded: chain g residue 2 LEU Chi-restraints excluded: chain g residue 9 VAL Chi-restraints excluded: chain k residue 9 VAL Chi-restraints excluded: chain m residue 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 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 AH residue 9 VAL 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 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 2 LEU Chi-restraints excluded: chain AW residue 8 SER Chi-restraints excluded: chain AX residue 9 VAL Chi-restraints excluded: chain AZ residue 2 LEU Chi-restraints excluded: chain AZ residue 7 ILE Chi-restraints excluded: chain AZ residue 9 VAL Chi-restraints excluded: chain A0 residue 3 ILE Chi-restraints excluded: chain A0 residue 5 LYS Chi-restraints excluded: chain A2 residue 4 ILE Chi-restraints excluded: chain A3 residue 9 VAL Chi-restraints excluded: chain A5 residue 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 BU residue 9 VAL Chi-restraints excluded: chain BV residue 3 ILE 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 2 LEU 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 B8 residue 7 ILE Chi-restraints excluded: chain B8 residue 9 VAL Chi-restraints excluded: chain CB residue 8 SER Chi-restraints excluded: chain CC residue 9 VAL Chi-restraints excluded: chain CD residue 3 ILE Chi-restraints excluded: chain CE residue 8 SER Chi-restraints excluded: chain CH residue 2 LEU Chi-restraints excluded: chain CH residue 7 ILE Chi-restraints excluded: chain CH residue 9 VAL Chi-restraints excluded: chain CI residue 3 ILE Chi-restraints excluded: chain CI residue 5 LYS Chi-restraints excluded: chain 1 residue 4 ILE Chi-restraints excluded: chain 3 residue 9 VAL Chi-restraints excluded: chain 6 residue 8 SER Chi-restraints excluded: chain 7 residue 2 LEU Chi-restraints excluded: chain CK residue 8 SER Chi-restraints excluded: chain CL residue 9 VAL Chi-restraints excluded: chain CN residue 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 CZ residue 7 ILE Chi-restraints excluded: chain CZ residue 9 VAL Chi-restraints excluded: chain C3 residue 9 VAL Chi-restraints excluded: chain C5 residue 1 ASP Chi-restraints excluded: chain C5 residue 8 SER Chi-restraints excluded: chain C8 residue 9 VAL Chi-restraints excluded: chain DC residue 9 VAL Chi-restraints excluded: chain DH residue 2 LEU Chi-restraints excluded: chain DH residue 9 VAL Chi-restraints excluded: chain 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 DT residue 4 ILE Chi-restraints excluded: chain DU residue 9 VAL Chi-restraints excluded: chain DW residue 1 ASP Chi-restraints excluded: chain DZ residue 7 ILE Chi-restraints excluded: chain D3 residue 9 VAL Chi-restraints excluded: chain D5 residue 8 SER Chi-restraints excluded: chain D7 residue 8 SER Chi-restraints excluded: chain D8 residue 2 LEU Chi-restraints excluded: chain D8 residue 7 ILE Chi-restraints excluded: chain 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 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 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 E6 residue 9 VAL Chi-restraints excluded: chain E8 residue 7 ILE Chi-restraints excluded: chain FB residue 1 ASP Chi-restraints excluded: chain FB residue 4 ILE 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 FO residue 9 VAL Chi-restraints excluded: chain FQ 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 193 optimal weight: 30.0000 chunk 176 optimal weight: 0.2980 chunk 188 optimal weight: 30.0000 chunk 113 optimal weight: 9.9990 chunk 82 optimal weight: 0.8980 chunk 148 optimal weight: 0.0980 chunk 57 optimal weight: 0.2980 chunk 170 optimal weight: 30.0000 chunk 178 optimal weight: 3.9990 chunk 187 optimal weight: 20.0000 chunk 123 optimal weight: 30.0000 overall best weight: 1.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 10 HIS M 10 HIS O 10 HIS V 10 HIS A7 10 HIS ** 6 10 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** CW 10 HIS DG 10 HIS DW 10 HIS D7 10 HIS EE 10 HIS EG 10 HIS FE 10 HIS ** FQ 10 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7187 moved from start: 0.3845 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 20370 Z= 0.076 Angle : 0.625 10.081 27210 Z= 0.248 Chirality : 0.057 0.190 3840 Planarity : 0.001 0.021 3060 Dihedral : 9.320 53.595 2580 Min Nonbonded Distance : 2.246 Molprobity Statistics. All-atom Clashscore : 5.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.67 % Favored : 99.33 % Rotamer: Outliers : 5.83 % Allowed : 27.50 % 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: -0.24 (0.19), residues: 2100 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.17 (0.15), residues: 2100 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.000 HIS 6 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 565 residues out of total 2400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 140 poor density : 425 time to evaluate : 2.420 Fit side-chains REVERT: D 2 LEU cc_start: 0.8364 (pt) cc_final: 0.7963 (tt) REVERT: M 2 LEU cc_start: 0.8161 (pt) cc_final: 0.7824 (tt) REVERT: U 3 ILE cc_start: 0.7931 (OUTLIER) cc_final: 0.7431 (mp) REVERT: V 2 LEU cc_start: 0.8534 (pt) cc_final: 0.8217 (tt) REVERT: m 3 ILE cc_start: 0.8522 (mt) cc_final: 0.8309 (mp) REVERT: v 5 LYS cc_start: 0.7387 (mttt) cc_final: 0.7023 (mttm) REVERT: AD 3 ILE cc_start: 0.7652 (OUTLIER) cc_final: 0.7121 (mp) REVERT: AE 3 ILE cc_start: 0.8422 (mt) cc_final: 0.8179 (mp) REVERT: AE 5 LYS cc_start: 0.7600 (mttt) cc_final: 0.7219 (mttm) REVERT: AK 4 ILE cc_start: 0.7487 (OUTLIER) cc_final: 0.7200 (mp) REVERT: AN 5 LYS cc_start: 0.7328 (mttt) cc_final: 0.7024 (mttm) REVERT: AV 3 ILE cc_start: 0.7604 (OUTLIER) cc_final: 0.7049 (mp) REVERT: AW 2 LEU cc_start: 0.7998 (OUTLIER) cc_final: 0.7740 (pt) REVERT: A2 4 ILE cc_start: 0.7499 (OUTLIER) cc_final: 0.7247 (mp) REVERT: A5 5 LYS cc_start: 0.7355 (mttt) cc_final: 0.7022 (mttp) REVERT: BE 3 ILE cc_start: 0.8472 (mt) cc_final: 0.8172 (mp) REVERT: BE 5 LYS cc_start: 0.7562 (mttt) cc_final: 0.7349 (mttm) REVERT: BK 4 ILE cc_start: 0.7354 (OUTLIER) cc_final: 0.7085 (mp) REVERT: BV 3 ILE cc_start: 0.7914 (OUTLIER) cc_final: 0.7469 (mp) REVERT: BW 2 LEU cc_start: 0.7819 (pt) cc_final: 0.7107 (tt) REVERT: BW 3 ILE cc_start: 0.8373 (mt) cc_final: 0.8091 (mp) REVERT: BW 5 LYS cc_start: 0.7635 (mttt) cc_final: 0.7413 (mttm) REVERT: B5 2 LEU cc_start: 0.7988 (pt) cc_final: 0.7782 (pp) REVERT: B5 5 LYS cc_start: 0.7455 (mttt) cc_final: 0.7210 (mttm) REVERT: B7 9 VAL cc_start: 0.8629 (t) cc_final: 0.8350 (p) REVERT: CD 3 ILE cc_start: 0.7869 (OUTLIER) cc_final: 0.7328 (mp) REVERT: CE 3 ILE cc_start: 0.8470 (mt) cc_final: 0.8079 (mp) REVERT: 6 2 LEU cc_start: 0.8168 (pt) cc_final: 0.7740 (pp) REVERT: 6 5 LYS cc_start: 0.7265 (mttt) cc_final: 0.6828 (mttm) REVERT: CM 5 LYS cc_start: 0.7964 (ptmt) cc_final: 0.7740 (ptpt) REVERT: CN 2 LEU cc_start: 0.7741 (pt) cc_final: 0.7516 (pp) REVERT: CW 5 LYS cc_start: 0.7323 (mttt) cc_final: 0.6966 (mttm) REVERT: C5 3 ILE cc_start: 0.8415 (mt) cc_final: 0.8190 (mp) REVERT: C5 5 LYS cc_start: 0.7692 (mttm) cc_final: 0.7404 (mttm) REVERT: DE 5 LYS cc_start: 0.6968 (mttt) cc_final: 0.6717 (mttm) REVERT: DM 3 ILE cc_start: 0.7910 (OUTLIER) cc_final: 0.7354 (mp) REVERT: DM 5 LYS cc_start: 0.7918 (ptmt) cc_final: 0.7696 (ptpt) REVERT: DN 2 LEU cc_start: 0.7883 (pt) cc_final: 0.7662 (pp) REVERT: D5 2 LEU cc_start: 0.7978 (pt) cc_final: 0.7461 (tt) REVERT: EE 2 LEU cc_start: 0.7918 (pt) cc_final: 0.7623 (pp) REVERT: EE 5 LYS cc_start: 0.7153 (mttt) cc_final: 0.6830 (mttm) REVERT: EG 9 VAL cc_start: 0.8514 (t) cc_final: 0.8207 (p) REVERT: E4 3 ILE cc_start: 0.8151 (OUTLIER) cc_final: 0.7644 (mp) REVERT: E5 5 LYS cc_start: 0.7312 (mttt) cc_final: 0.7021 (mttp) REVERT: FE 2 LEU cc_start: 0.8017 (pp) cc_final: 0.6347 (mm) REVERT: FE 3 ILE cc_start: 0.8633 (mt) cc_final: 0.8261 (mp) REVERT: FE 5 LYS cc_start: 0.8186 (mttt) cc_final: 0.7816 (mttm) REVERT: FM 3 ILE cc_start: 0.8304 (OUTLIER) cc_final: 0.7795 (mp) REVERT: FN 2 LEU cc_start: 0.8142 (pt) cc_final: 0.6416 (mm) outliers start: 140 outliers final: 95 residues processed: 494 average time/residue: 0.2718 time to fit residues: 216.3501 Evaluate side-chains 511 residues out of total 2400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 107 poor density : 404 time to evaluate : 2.593 ------------------------------------------------------------------------------- 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 9 VAL Chi-restraints excluded: chain H residue 2 LEU Chi-restraints excluded: chain P residue 7 ILE Chi-restraints excluded: chain U residue 3 ILE Chi-restraints excluded: chain V residue 1 ASP Chi-restraints excluded: chain W residue 9 VAL Chi-restraints excluded: chain g residue 9 VAL Chi-restraints excluded: chain k residue 9 VAL Chi-restraints excluded: chain m residue 8 SER Chi-restraints excluded: chain n residue 9 VAL Chi-restraints excluded: chain p residue 9 VAL 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 AC residue 9 VAL Chi-restraints excluded: chain AD residue 3 ILE Chi-restraints excluded: chain AF residue 9 VAL Chi-restraints excluded: chain AH residue 9 VAL Chi-restraints excluded: chain AK residue 4 ILE Chi-restraints excluded: chain AL residue 9 VAL Chi-restraints excluded: chain AU residue 9 VAL Chi-restraints excluded: chain AV residue 3 ILE Chi-restraints excluded: chain AW residue 2 LEU Chi-restraints excluded: chain AW residue 8 SER Chi-restraints excluded: chain AX residue 9 VAL Chi-restraints excluded: chain AZ residue 2 LEU Chi-restraints excluded: chain AZ residue 7 ILE Chi-restraints excluded: chain AZ residue 9 VAL Chi-restraints excluded: chain A0 residue 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 BC residue 9 VAL Chi-restraints excluded: chain BE residue 8 SER Chi-restraints excluded: chain BF residue 9 VAL Chi-restraints excluded: chain BH residue 7 ILE Chi-restraints excluded: chain BH residue 9 VAL Chi-restraints excluded: chain BK residue 4 ILE Chi-restraints excluded: chain BL residue 9 VAL Chi-restraints excluded: chain BQ residue 2 LEU Chi-restraints excluded: chain BQ residue 9 VAL Chi-restraints excluded: chain BU residue 9 VAL Chi-restraints excluded: chain BV residue 3 ILE Chi-restraints excluded: chain BX residue 9 VAL Chi-restraints excluded: chain BZ residue 2 LEU Chi-restraints excluded: chain BZ residue 9 VAL Chi-restraints excluded: chain B0 residue 2 LEU Chi-restraints excluded: chain B3 residue 9 VAL Chi-restraints excluded: chain 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 CH residue 2 LEU Chi-restraints excluded: chain CH residue 7 ILE Chi-restraints excluded: chain CH residue 9 VAL Chi-restraints excluded: chain CI residue 3 ILE Chi-restraints excluded: chain CI residue 5 LYS Chi-restraints excluded: chain 3 residue 9 VAL Chi-restraints excluded: chain CL residue 9 VAL 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 CZ residue 7 ILE Chi-restraints excluded: chain CZ residue 9 VAL Chi-restraints excluded: chain C3 residue 9 VAL Chi-restraints excluded: chain C5 residue 8 SER Chi-restraints excluded: chain C8 residue 9 VAL Chi-restraints excluded: chain DC residue 9 VAL Chi-restraints excluded: chain DH residue 2 LEU Chi-restraints excluded: chain DH residue 9 VAL Chi-restraints excluded: chain DL residue 9 VAL Chi-restraints excluded: chain DM residue 3 ILE Chi-restraints excluded: chain 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 D3 residue 9 VAL 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 EH residue 2 LEU Chi-restraints excluded: chain EH residue 7 ILE Chi-restraints excluded: chain EL residue 9 VAL Chi-restraints excluded: chain EQ residue 7 ILE Chi-restraints excluded: chain EQ residue 9 VAL Chi-restraints excluded: chain EU residue 9 VAL Chi-restraints excluded: chain EZ residue 2 LEU Chi-restraints excluded: chain E3 residue 9 VAL Chi-restraints excluded: chain E4 residue 3 ILE Chi-restraints excluded: chain E6 residue 9 VAL Chi-restraints excluded: chain E8 residue 7 ILE Chi-restraints excluded: chain FC residue 9 VAL Chi-restraints excluded: chain FL residue 9 VAL Chi-restraints excluded: chain FM residue 3 ILE Chi-restraints excluded: chain FN residue 8 SER Chi-restraints excluded: chain FO residue 9 VAL Chi-restraints excluded: chain FQ residue 4 ILE Chi-restraints excluded: chain FU residue 9 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 199 optimal weight: 20.0000 chunk 121 optimal weight: 30.0000 chunk 94 optimal weight: 30.0000 chunk 138 optimal weight: 7.9990 chunk 209 optimal weight: 0.0670 chunk 192 optimal weight: 0.0980 chunk 166 optimal weight: 20.0000 chunk 17 optimal weight: 20.0000 chunk 128 optimal weight: 20.0000 chunk 102 optimal weight: 30.0000 chunk 132 optimal weight: 10.0000 overall best weight: 7.6328 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: M 10 HIS f 10 HIS x 10 HIS A7 10 HIS BB 10 HIS ** BY 10 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B7 10 HIS ** 6 10 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 4 10 HIS DG 10 HIS ** EE 10 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** EG 10 HIS EK 10 HIS EY 10 HIS FG 10 HIS ** FQ 10 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7235 moved from start: 0.3784 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 20370 Z= 0.175 Angle : 0.717 11.556 27210 Z= 0.291 Chirality : 0.057 0.198 3840 Planarity : 0.002 0.018 3060 Dihedral : 10.396 55.251 2580 Min Nonbonded Distance : 2.274 Molprobity Statistics. All-atom Clashscore : 7.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 6.12 % Allowed : 27.25 % Favored : 66.62 % 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: -0.38 (0.19), residues: 2100 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.28 (0.15), residues: 2100 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS 6 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 597 residues out of total 2400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 147 poor density : 450 time to evaluate : 2.313 Fit side-chains revert: symmetry clash REVERT: D 2 LEU cc_start: 0.8503 (pt) cc_final: 0.8084 (tt) REVERT: J 5 LYS cc_start: 0.7929 (mttt) cc_final: 0.7471 (mttp) REVERT: M 2 LEU cc_start: 0.8275 (pt) cc_final: 0.7918 (tt) REVERT: P 5 LYS cc_start: 0.6001 (mmmt) cc_final: 0.4950 (pttm) REVERT: U 3 ILE cc_start: 0.7889 (OUTLIER) cc_final: 0.7360 (mp) REVERT: V 2 LEU cc_start: 0.8591 (pt) cc_final: 0.8222 (tt) REVERT: j 5 LYS cc_start: 0.7928 (mttt) cc_final: 0.7491 (mttp) REVERT: v 5 LYS cc_start: 0.7404 (mttt) cc_final: 0.7119 (mttm) REVERT: AB 5 LYS cc_start: 0.7895 (mttt) cc_final: 0.7374 (mttp) REVERT: AD 3 ILE cc_start: 0.7711 (OUTLIER) cc_final: 0.7146 (mp) REVERT: AE 5 LYS cc_start: 0.7676 (mttt) cc_final: 0.7297 (mttm) REVERT: AK 4 ILE cc_start: 0.7432 (OUTLIER) cc_final: 0.7122 (mp) REVERT: AN 5 LYS cc_start: 0.7320 (mttt) cc_final: 0.7033 (mttm) REVERT: AV 3 ILE cc_start: 0.7628 (OUTLIER) cc_final: 0.7069 (mp) REVERT: A2 4 ILE cc_start: 0.7408 (OUTLIER) cc_final: 0.7133 (mp) REVERT: A5 5 LYS cc_start: 0.7397 (mttt) cc_final: 0.6993 (mttp) REVERT: BB 5 LYS cc_start: 0.7667 (mttt) cc_final: 0.7337 (mttp) REVERT: BE 5 LYS cc_start: 0.7602 (mttt) cc_final: 0.7275 (mttp) REVERT: BK 4 ILE cc_start: 0.7212 (OUTLIER) cc_final: 0.6914 (mp) REVERT: BV 3 ILE cc_start: 0.7785 (OUTLIER) cc_final: 0.7266 (mp) REVERT: B5 2 LEU cc_start: 0.8063 (pt) cc_final: 0.7852 (pp) REVERT: B5 5 LYS cc_start: 0.7561 (mttt) cc_final: 0.7353 (mttm) REVERT: CD 3 ILE cc_start: 0.7800 (OUTLIER) cc_final: 0.7253 (mp) REVERT: CE 3 ILE cc_start: 0.8543 (mt) cc_final: 0.8134 (mp) REVERT: 6 2 LEU cc_start: 0.8302 (pt) cc_final: 0.7893 (pp) REVERT: 6 5 LYS cc_start: 0.7170 (mttt) cc_final: 0.6756 (mttm) REVERT: CK 5 LYS cc_start: 0.7906 (mttt) cc_final: 0.7372 (mttp) REVERT: CN 2 LEU cc_start: 0.7892 (pt) cc_final: 0.7628 (pp) REVERT: CW 5 LYS cc_start: 0.7402 (mttt) cc_final: 0.6994 (mttm) REVERT: C2 5 LYS cc_start: 0.7902 (mttt) cc_final: 0.7427 (mttp) REVERT: C5 2 LEU cc_start: 0.8060 (pp) cc_final: 0.7852 (pt) REVERT: C5 5 LYS cc_start: 0.7779 (mttm) cc_final: 0.7418 (mttm) REVERT: DE 5 LYS cc_start: 0.7118 (mttt) cc_final: 0.6823 (mttm) REVERT: DM 3 ILE cc_start: 0.7846 (OUTLIER) cc_final: 0.7277 (mp) REVERT: DN 3 ILE cc_start: 0.8478 (mt) cc_final: 0.8144 (mp) REVERT: D5 2 LEU cc_start: 0.8090 (pt) cc_final: 0.7509 (tt) REVERT: EE 5 LYS cc_start: 0.7225 (mttt) cc_final: 0.6867 (mttm) REVERT: EK 5 LYS cc_start: 0.7900 (mttt) cc_final: 0.7553 (mttp) REVERT: EW 2 LEU cc_start: 0.8308 (pt) cc_final: 0.7789 (pp) REVERT: E4 3 ILE cc_start: 0.8075 (OUTLIER) cc_final: 0.7566 (mp) REVERT: E5 5 LYS cc_start: 0.7306 (mttt) cc_final: 0.6966 (mttp) REVERT: FE 2 LEU cc_start: 0.8282 (pp) cc_final: 0.6595 (mm) REVERT: FE 3 ILE cc_start: 0.8740 (mt) cc_final: 0.8425 (mp) REVERT: FE 5 LYS cc_start: 0.8248 (mttt) cc_final: 0.7859 (mttm) REVERT: FM 3 ILE cc_start: 0.8308 (OUTLIER) cc_final: 0.7792 (mp) REVERT: FN 2 LEU cc_start: 0.8334 (pt) cc_final: 0.6611 (mm) outliers start: 147 outliers final: 114 residues processed: 508 average time/residue: 0.2807 time to fit residues: 228.3998 Evaluate side-chains 561 residues out of total 2400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 125 poor density : 436 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 9 VAL Chi-restraints excluded: chain H residue 2 LEU Chi-restraints excluded: chain P residue 7 ILE 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 9 VAL Chi-restraints excluded: chain d residue 8 SER Chi-restraints excluded: chain g residue 9 VAL Chi-restraints excluded: chain k residue 9 VAL Chi-restraints excluded: chain m residue 8 SER Chi-restraints excluded: chain n residue 9 VAL Chi-restraints excluded: chain p residue 9 VAL 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 AC residue 9 VAL Chi-restraints excluded: chain AD residue 3 ILE Chi-restraints excluded: chain AE residue 8 SER Chi-restraints excluded: chain AF residue 9 VAL Chi-restraints excluded: chain AH residue 7 ILE Chi-restraints excluded: chain AH residue 9 VAL Chi-restraints excluded: chain AK residue 4 ILE Chi-restraints excluded: chain AL residue 9 VAL Chi-restraints excluded: chain AU residue 9 VAL Chi-restraints excluded: chain AV residue 3 ILE Chi-restraints excluded: chain AW residue 8 SER Chi-restraints excluded: chain AX residue 9 VAL Chi-restraints excluded: chain AZ residue 2 LEU Chi-restraints excluded: chain AZ residue 7 ILE Chi-restraints excluded: chain AZ residue 9 VAL Chi-restraints excluded: chain A0 residue 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 8 SER Chi-restraints excluded: chain BF residue 9 VAL Chi-restraints excluded: chain BH residue 7 ILE Chi-restraints excluded: chain BH residue 9 VAL Chi-restraints excluded: chain BK residue 4 ILE Chi-restraints excluded: chain BL residue 9 VAL Chi-restraints excluded: chain BN residue 8 SER Chi-restraints excluded: chain BQ residue 2 LEU Chi-restraints excluded: chain BQ residue 9 VAL Chi-restraints excluded: chain BU residue 9 VAL Chi-restraints excluded: chain BV residue 3 ILE Chi-restraints excluded: chain BW residue 8 SER Chi-restraints excluded: chain BX residue 9 VAL Chi-restraints excluded: chain BZ residue 2 LEU Chi-restraints excluded: chain BZ residue 9 VAL Chi-restraints excluded: chain B0 residue 2 LEU Chi-restraints excluded: chain B3 residue 9 VAL Chi-restraints excluded: chain 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 CH residue 2 LEU Chi-restraints excluded: chain CH residue 7 ILE Chi-restraints excluded: chain CH residue 9 VAL Chi-restraints excluded: chain CI residue 3 ILE Chi-restraints excluded: chain CI residue 5 LYS Chi-restraints excluded: chain 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 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 CZ residue 7 ILE Chi-restraints excluded: chain CZ residue 9 VAL Chi-restraints excluded: chain C3 residue 9 VAL Chi-restraints excluded: chain C5 residue 1 ASP Chi-restraints excluded: chain C5 residue 8 SER Chi-restraints excluded: chain C8 residue 9 VAL Chi-restraints excluded: chain DC residue 9 VAL Chi-restraints excluded: chain DH residue 2 LEU Chi-restraints excluded: chain DH residue 9 VAL Chi-restraints excluded: chain DL residue 9 VAL Chi-restraints excluded: chain DM residue 3 ILE 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 D3 residue 9 VAL 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 EK residue 9 VAL Chi-restraints excluded: chain EL 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 E3 residue 9 VAL Chi-restraints excluded: chain E4 residue 3 ILE Chi-restraints excluded: chain E6 residue 9 VAL 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 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 FO residue 9 VAL Chi-restraints excluded: chain FQ residue 4 ILE Chi-restraints excluded: chain FU residue 9 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 177 optimal weight: 30.0000 chunk 51 optimal weight: 30.0000 chunk 153 optimal weight: 40.0000 chunk 24 optimal weight: 20.0000 chunk 46 optimal weight: 0.9980 chunk 166 optimal weight: 30.0000 chunk 69 optimal weight: 30.0000 chunk 171 optimal weight: 5.9990 chunk 21 optimal weight: 30.0000 chunk 30 optimal weight: 6.9990 chunk 146 optimal weight: 10.0000 overall best weight: 8.7992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: M 10 HIS B7 10 HIS ** 6 10 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** DG 10 HIS D7 10 HIS ** EE 10 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** EG 10 HIS EY 10 HIS ** FQ 10 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.116154 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.096053 restraints weight = 29971.313| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.099274 restraints weight = 16159.772| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.101606 restraints weight = 10518.169| |-----------------------------------------------------------------------------| r_work (final): 0.3390 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7755 moved from start: 0.3825 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 20370 Z= 0.197 Angle : 0.746 11.741 27210 Z= 0.306 Chirality : 0.057 0.204 3840 Planarity : 0.002 0.020 3060 Dihedral : 10.700 55.101 2580 Min Nonbonded Distance : 2.289 Molprobity Statistics. All-atom Clashscore : 7.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 6.62 % Allowed : 27.00 % Favored : 66.38 % 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: -0.55 (0.19), residues: 2100 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.41 (0.14), residues: 2100 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HISEO 10 =============================================================================== Job complete usr+sys time: 4384.96 seconds wall clock time: 80 minutes 48.95 seconds (4848.95 seconds total)