Starting phenix.real_space_refine on Wed Mar 4 09:37:47 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6wkx_21812/03_2026/6wkx_21812.cif Found real_map, /net/cci-nas-00/data/ceres_data/6wkx_21812/03_2026/6wkx_21812.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/6wkx_21812/03_2026/6wkx_21812.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6wkx_21812/03_2026/6wkx_21812.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6wkx_21812/03_2026/6wkx_21812.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6wkx_21812/03_2026/6wkx_21812.map" } resolution = 4.2 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.000 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 8085 2.51 5 N 2415 2.21 5 O 2415 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 168 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 12915 Number of models: 1 Model: "" Number of chains: 105 Chain: "A" Number of atoms: 123 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 123 Classifications: {'peptide': 15} Modifications used: {'COO': 1} Link IDs: {'TRANS': 14} Chain: "V" Number of atoms: 123 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 123 Classifications: {'peptide': 15} Modifications used: {'COO': 1} Link IDs: {'TRANS': 14} Chain: "W" Number of atoms: 123 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 123 Classifications: {'peptide': 15} Modifications used: {'COO': 1} Link IDs: {'TRANS': 14} Chain: "X" Number of atoms: 123 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 123 Classifications: {'peptide': 15} Modifications used: {'COO': 1} Link IDs: {'TRANS': 14} Chain: "Y" Number of atoms: 123 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 123 Classifications: {'peptide': 15} Modifications used: {'COO': 1} Link IDs: {'TRANS': 14} Chain: "B" Number of atoms: 123 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 123 Classifications: {'peptide': 15} Modifications used: {'COO': 1} Link IDs: {'TRANS': 14} Chain: "Z" Number of atoms: 123 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 123 Classifications: {'peptide': 15} Modifications used: {'COO': 1} Link IDs: {'TRANS': 14} Chain: "a" Number of atoms: 123 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 123 Classifications: {'peptide': 15} Modifications used: {'COO': 1} Link IDs: {'TRANS': 14} Chain: "b" Number of atoms: 123 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 123 Classifications: {'peptide': 15} Modifications used: {'COO': 1} Link IDs: {'TRANS': 14} Chain: "c" Number of atoms: 123 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 123 Classifications: {'peptide': 15} Modifications used: {'COO': 1} Link IDs: {'TRANS': 14} Chain: "C" Number of atoms: 123 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 123 Classifications: {'peptide': 15} Modifications used: {'COO': 1} Link IDs: {'TRANS': 14} Chain: "d" Number of atoms: 123 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 123 Classifications: {'peptide': 15} Modifications used: {'COO': 1} Link IDs: {'TRANS': 14} Chain: "e" Number of atoms: 123 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 123 Classifications: {'peptide': 15} Modifications used: {'COO': 1} Link IDs: {'TRANS': 14} Chain: "f" Number of atoms: 123 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 123 Classifications: {'peptide': 15} Modifications used: {'COO': 1} Link IDs: {'TRANS': 14} Chain: "g" Number of atoms: 123 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 123 Classifications: {'peptide': 15} Modifications used: {'COO': 1} Link IDs: {'TRANS': 14} Chain: "D" Number of atoms: 123 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 123 Classifications: {'peptide': 15} Modifications used: {'COO': 1} Link IDs: {'TRANS': 14} Chain: "h" Number of atoms: 123 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 123 Classifications: {'peptide': 15} Modifications used: {'COO': 1} Link IDs: {'TRANS': 14} Chain: "i" Number of atoms: 123 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 123 Classifications: {'peptide': 15} Modifications used: {'COO': 1} Link IDs: {'TRANS': 14} Chain: "j" Number of atoms: 123 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 123 Classifications: {'peptide': 15} Modifications used: {'COO': 1} Link IDs: {'TRANS': 14} Chain: "k" Number of atoms: 123 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 123 Classifications: {'peptide': 15} Modifications used: {'COO': 1} Link IDs: {'TRANS': 14} Chain: "E" Number of atoms: 123 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 123 Classifications: {'peptide': 15} Modifications used: {'COO': 1} Link IDs: {'TRANS': 14} Chain: "l" Number of atoms: 123 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 123 Classifications: {'peptide': 15} Modifications used: {'COO': 1} Link IDs: {'TRANS': 14} Chain: "m" Number of atoms: 123 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 123 Classifications: {'peptide': 15} Modifications used: {'COO': 1} Link IDs: {'TRANS': 14} Chain: "n" Number of atoms: 123 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 123 Classifications: {'peptide': 15} Modifications used: {'COO': 1} Link IDs: {'TRANS': 14} Chain: "o" Number of atoms: 123 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 123 Classifications: {'peptide': 15} Modifications used: {'COO': 1} Link IDs: {'TRANS': 14} Chain: "F" Number of atoms: 123 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 123 Classifications: {'peptide': 15} Modifications used: {'COO': 1} Link IDs: {'TRANS': 14} Chain: "p" Number of atoms: 123 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 123 Classifications: {'peptide': 15} Modifications used: {'COO': 1} Link IDs: {'TRANS': 14} Chain: "q" Number of atoms: 123 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 123 Classifications: {'peptide': 15} Modifications used: {'COO': 1} Link IDs: {'TRANS': 14} Chain: "r" Number of atoms: 123 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 123 Classifications: {'peptide': 15} Modifications used: {'COO': 1} Link IDs: {'TRANS': 14} Chain: "s" Number of atoms: 123 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 123 Classifications: {'peptide': 15} Modifications used: {'COO': 1} Link IDs: {'TRANS': 14} Chain: "G" Number of atoms: 123 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 123 Classifications: {'peptide': 15} Modifications used: {'COO': 1} Link IDs: {'TRANS': 14} Chain: "t" Number of atoms: 123 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 123 Classifications: {'peptide': 15} Modifications used: {'COO': 1} Link IDs: {'TRANS': 14} Chain: "u" Number of atoms: 123 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 123 Classifications: {'peptide': 15} Modifications used: {'COO': 1} Link IDs: {'TRANS': 14} Chain: "v" Number of atoms: 123 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 123 Classifications: {'peptide': 15} Modifications used: {'COO': 1} Link IDs: {'TRANS': 14} Chain: "w" Number of atoms: 123 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 123 Classifications: {'peptide': 15} Modifications used: {'COO': 1} Link IDs: {'TRANS': 14} Chain: "H" Number of atoms: 123 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 123 Classifications: {'peptide': 15} Modifications used: {'COO': 1} Link IDs: {'TRANS': 14} Chain: "x" Number of atoms: 123 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 123 Classifications: {'peptide': 15} Modifications used: {'COO': 1} Link IDs: {'TRANS': 14} Chain: "y" Number of atoms: 123 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 123 Classifications: {'peptide': 15} Modifications used: {'COO': 1} Link IDs: {'TRANS': 14} Chain: "z" Number of atoms: 123 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 123 Classifications: {'peptide': 15} Modifications used: {'COO': 1} Link IDs: {'TRANS': 14} Chain: "0" Number of atoms: 123 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 123 Classifications: {'peptide': 15} Modifications used: {'COO': 1} Link IDs: {'TRANS': 14} Chain: "I" Number of atoms: 123 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 123 Classifications: {'peptide': 15} Modifications used: {'COO': 1} Link IDs: {'TRANS': 14} Chain: "1" Number of atoms: 123 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 123 Classifications: {'peptide': 15} Modifications used: {'COO': 1} Link IDs: {'TRANS': 14} Chain: "2" Number of atoms: 123 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 123 Classifications: {'peptide': 15} Modifications used: {'COO': 1} Link IDs: {'TRANS': 14} Chain: "3" Number of atoms: 123 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 123 Classifications: {'peptide': 15} Modifications used: {'COO': 1} Link IDs: {'TRANS': 14} Chain: "4" Number of atoms: 123 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 123 Classifications: {'peptide': 15} Modifications used: {'COO': 1} Link IDs: {'TRANS': 14} Chain: "J" Number of atoms: 123 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 123 Classifications: {'peptide': 15} Modifications used: {'COO': 1} Link IDs: {'TRANS': 14} Chain: "5" Number of atoms: 123 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 123 Classifications: {'peptide': 15} Modifications used: {'COO': 1} Link IDs: {'TRANS': 14} Chain: "6" Number of atoms: 123 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 123 Classifications: {'peptide': 15} Modifications used: {'COO': 1} Link IDs: {'TRANS': 14} Chain: "7" Number of atoms: 123 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 123 Classifications: {'peptide': 15} Modifications used: {'COO': 1} Link IDs: {'TRANS': 14} Chain: "8" Number of atoms: 123 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 123 Classifications: {'peptide': 15} Modifications used: {'COO': 1} Link IDs: {'TRANS': 14} Chain: "K" Number of atoms: 123 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 123 Classifications: {'peptide': 15} Modifications used: {'COO': 1} Link IDs: {'TRANS': 14} Chain: "9" Number of atoms: 123 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 123 Classifications: {'peptide': 15} Modifications used: {'COO': 1} Link IDs: {'TRANS': 14} Chain: "AA" Number of atoms: 123 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 123 Classifications: {'peptide': 15} Modifications used: {'COO': 1} Link IDs: {'TRANS': 14} Chain: "BA" Number of atoms: 123 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 123 Classifications: {'peptide': 15} Modifications used: {'COO': 1} Link IDs: {'TRANS': 14} Chain: "CA" Number of atoms: 123 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 123 Classifications: {'peptide': 15} Modifications used: {'COO': 1} Link IDs: {'TRANS': 14} Chain: "L" Number of atoms: 123 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 123 Classifications: {'peptide': 15} Modifications used: {'COO': 1} Link IDs: {'TRANS': 14} Chain: "DA" Number of atoms: 123 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 123 Classifications: {'peptide': 15} Modifications used: {'COO': 1} Link IDs: {'TRANS': 14} Chain: "EA" Number of atoms: 123 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 123 Classifications: {'peptide': 15} Modifications used: {'COO': 1} Link IDs: {'TRANS': 14} Chain: "FA" Number of atoms: 123 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 123 Classifications: {'peptide': 15} Modifications used: {'COO': 1} Link IDs: {'TRANS': 14} Chain: "GA" Number of atoms: 123 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 123 Classifications: {'peptide': 15} Modifications used: {'COO': 1} Link IDs: {'TRANS': 14} Chain: "M" Number of atoms: 123 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 123 Classifications: {'peptide': 15} Modifications used: {'COO': 1} Link IDs: {'TRANS': 14} Chain: "HA" Number of atoms: 123 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 123 Classifications: {'peptide': 15} Modifications used: {'COO': 1} Link IDs: {'TRANS': 14} Chain: "IA" Number of atoms: 123 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 123 Classifications: {'peptide': 15} Modifications used: {'COO': 1} Link IDs: {'TRANS': 14} Chain: "JA" Number of atoms: 123 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 123 Classifications: {'peptide': 15} Modifications used: {'COO': 1} Link IDs: {'TRANS': 14} Chain: "KA" Number of atoms: 123 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 123 Classifications: {'peptide': 15} Modifications used: {'COO': 1} Link IDs: {'TRANS': 14} Chain: "N" Number of atoms: 123 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 123 Classifications: {'peptide': 15} Modifications used: {'COO': 1} Link IDs: {'TRANS': 14} Chain: "LA" Number of atoms: 123 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 123 Classifications: {'peptide': 15} Modifications used: {'COO': 1} Link IDs: {'TRANS': 14} Chain: "MA" Number of atoms: 123 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 123 Classifications: {'peptide': 15} Modifications used: {'COO': 1} Link IDs: {'TRANS': 14} Chain: "NA" Number of atoms: 123 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 123 Classifications: {'peptide': 15} Modifications used: {'COO': 1} Link IDs: {'TRANS': 14} Chain: "OA" Number of atoms: 123 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 123 Classifications: {'peptide': 15} Modifications used: {'COO': 1} Link IDs: {'TRANS': 14} Chain: "O" Number of atoms: 123 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 123 Classifications: {'peptide': 15} Modifications used: {'COO': 1} Link IDs: {'TRANS': 14} Chain: "PA" Number of atoms: 123 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 123 Classifications: {'peptide': 15} Modifications used: {'COO': 1} Link IDs: {'TRANS': 14} Chain: "QA" Number of atoms: 123 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 123 Classifications: {'peptide': 15} Modifications used: {'COO': 1} Link IDs: {'TRANS': 14} Chain: "RA" Number of atoms: 123 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 123 Classifications: {'peptide': 15} Modifications used: {'COO': 1} Link IDs: {'TRANS': 14} Chain: "SA" Number of atoms: 123 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 123 Classifications: {'peptide': 15} Modifications used: {'COO': 1} Link IDs: {'TRANS': 14} Chain: "P" Number of atoms: 123 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 123 Classifications: {'peptide': 15} Modifications used: {'COO': 1} Link IDs: {'TRANS': 14} Chain: "TA" Number of atoms: 123 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 123 Classifications: {'peptide': 15} Modifications used: {'COO': 1} Link IDs: {'TRANS': 14} Chain: "UA" Number of atoms: 123 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 123 Classifications: {'peptide': 15} Modifications used: {'COO': 1} Link IDs: {'TRANS': 14} Chain: "VA" Number of atoms: 123 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 123 Classifications: {'peptide': 15} Modifications used: {'COO': 1} Link IDs: {'TRANS': 14} Chain: "WA" Number of atoms: 123 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 123 Classifications: {'peptide': 15} Modifications used: {'COO': 1} Link IDs: {'TRANS': 14} Chain: "Q" Number of atoms: 123 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 123 Classifications: {'peptide': 15} Modifications used: {'COO': 1} Link IDs: {'TRANS': 14} Chain: "XA" Number of atoms: 123 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 123 Classifications: {'peptide': 15} Modifications used: {'COO': 1} Link IDs: {'TRANS': 14} Chain: "YA" Number of atoms: 123 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 123 Classifications: {'peptide': 15} Modifications used: {'COO': 1} Link IDs: {'TRANS': 14} Chain: "ZA" Number of atoms: 123 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 123 Classifications: {'peptide': 15} Modifications used: {'COO': 1} Link IDs: {'TRANS': 14} Chain: "aA" Number of atoms: 123 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 123 Classifications: {'peptide': 15} Modifications used: {'COO': 1} Link IDs: {'TRANS': 14} Chain: "R" Number of atoms: 123 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 123 Classifications: {'peptide': 15} Modifications used: {'COO': 1} Link IDs: {'TRANS': 14} Chain: "bA" Number of atoms: 123 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 123 Classifications: {'peptide': 15} Modifications used: {'COO': 1} Link IDs: {'TRANS': 14} Chain: "cA" Number of atoms: 123 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 123 Classifications: {'peptide': 15} Modifications used: {'COO': 1} Link IDs: {'TRANS': 14} Chain: "dA" Number of atoms: 123 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 123 Classifications: {'peptide': 15} Modifications used: {'COO': 1} Link IDs: {'TRANS': 14} Chain: "eA" Number of atoms: 123 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 123 Classifications: {'peptide': 15} Modifications used: {'COO': 1} Link IDs: {'TRANS': 14} Chain: "S" Number of atoms: 123 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 123 Classifications: {'peptide': 15} Modifications used: {'COO': 1} Link IDs: {'TRANS': 14} Chain: "fA" Number of atoms: 123 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 123 Classifications: {'peptide': 15} Modifications used: {'COO': 1} Link IDs: {'TRANS': 14} Chain: "gA" Number of atoms: 123 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 123 Classifications: {'peptide': 15} Modifications used: {'COO': 1} Link IDs: {'TRANS': 14} Chain: "hA" Number of atoms: 123 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 123 Classifications: {'peptide': 15} Modifications used: {'COO': 1} Link IDs: {'TRANS': 14} Chain: "iA" Number of atoms: 123 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 123 Classifications: {'peptide': 15} Modifications used: {'COO': 1} Link IDs: {'TRANS': 14} Chain: "T" Number of atoms: 123 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 123 Classifications: {'peptide': 15} Modifications used: {'COO': 1} Link IDs: {'TRANS': 14} Chain: "jA" Number of atoms: 123 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 123 Classifications: {'peptide': 15} Modifications used: {'COO': 1} Link IDs: {'TRANS': 14} Chain: "kA" Number of atoms: 123 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 123 Classifications: {'peptide': 15} Modifications used: {'COO': 1} Link IDs: {'TRANS': 14} Chain: "lA" Number of atoms: 123 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 123 Classifications: {'peptide': 15} Modifications used: {'COO': 1} Link IDs: {'TRANS': 14} Chain: "mA" Number of atoms: 123 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 123 Classifications: {'peptide': 15} Modifications used: {'COO': 1} Link IDs: {'TRANS': 14} Chain: "U" Number of atoms: 123 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 123 Classifications: {'peptide': 15} Modifications used: {'COO': 1} Link IDs: {'TRANS': 14} Chain: "nA" Number of atoms: 123 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 123 Classifications: {'peptide': 15} Modifications used: {'COO': 1} Link IDs: {'TRANS': 14} Chain: "oA" Number of atoms: 123 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 123 Classifications: {'peptide': 15} Modifications used: {'COO': 1} Link IDs: {'TRANS': 14} Chain: "pA" Number of atoms: 123 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 123 Classifications: {'peptide': 15} Modifications used: {'COO': 1} Link IDs: {'TRANS': 14} Chain: "qA" Number of atoms: 123 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 123 Classifications: {'peptide': 15} Modifications used: {'COO': 1} Link IDs: {'TRANS': 14} Time building chain proxies: 3.10, per 1000 atoms: 0.24 Number of scatterers: 12915 At special positions: 0 Unit cell: (62.4, 63.44, 211.12, 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 2415 8.00 N 2415 7.00 C 8085 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.10 Conformation dependent library (CDL) restraints added in 610.9 milliseconds 2730 Ramachandran restraints generated. 1365 Oldfield, 0 Emsley, 1365 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3150 Finding SS restraints... Secondary structure from input PDB file: 105 helices and 0 sheets defined 93.4% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.35 Creating SS restraints... Processing helix chain 'A' and resid 1 through 15 removed outlier: 3.649A pdb=" N LEU A 5 " --> pdb=" O GLN A 1 " (cutoff:3.500A) Processing helix chain 'V' and resid 102 through 115 Processing helix chain 'W' and resid 202 through 215 Processing helix chain 'X' and resid 302 through 315 Processing helix chain 'Y' and resid 402 through 415 Processing helix chain 'B' and resid 2 through 15 Processing helix chain 'Z' and resid 102 through 115 Processing helix chain 'a' and resid 202 through 215 Processing helix chain 'b' and resid 302 through 315 Processing helix chain 'c' and resid 402 through 415 Processing helix chain 'C' and resid 2 through 15 Processing helix chain 'd' and resid 102 through 115 Processing helix chain 'e' and resid 202 through 215 Processing helix chain 'f' and resid 302 through 315 Processing helix chain 'g' and resid 402 through 415 Processing helix chain 'D' and resid 2 through 15 Processing helix chain 'h' and resid 102 through 115 Processing helix chain 'i' and resid 202 through 215 Processing helix chain 'j' and resid 302 through 315 Processing helix chain 'k' and resid 402 through 415 Processing helix chain 'E' and resid 2 through 15 Processing helix chain 'l' and resid 102 through 115 Processing helix chain 'm' and resid 202 through 215 Processing helix chain 'n' and resid 302 through 315 Processing helix chain 'o' and resid 402 through 415 Processing helix chain 'F' and resid 2 through 15 Processing helix chain 'p' and resid 102 through 115 Processing helix chain 'q' and resid 202 through 215 Processing helix chain 'r' and resid 302 through 315 Processing helix chain 's' and resid 402 through 415 Processing helix chain 'G' and resid 2 through 15 Processing helix chain 't' and resid 102 through 115 Processing helix chain 'u' and resid 202 through 215 Processing helix chain 'v' and resid 302 through 315 Processing helix chain 'w' and resid 402 through 415 Processing helix chain 'H' and resid 2 through 15 Processing helix chain 'x' and resid 102 through 115 Processing helix chain 'y' and resid 202 through 215 Processing helix chain 'z' and resid 302 through 315 Processing helix chain '0' and resid 402 through 415 Processing helix chain 'I' and resid 2 through 15 Processing helix chain '1' and resid 102 through 115 Processing helix chain '2' and resid 202 through 215 Processing helix chain '3' and resid 302 through 315 Processing helix chain '4' and resid 402 through 415 Processing helix chain 'J' and resid 2 through 15 Processing helix chain '5' and resid 102 through 115 Processing helix chain '6' and resid 202 through 215 Processing helix chain '7' and resid 302 through 315 Processing helix chain '8' and resid 402 through 415 Processing helix chain 'K' and resid 2 through 15 Processing helix chain '9' and resid 102 through 115 Processing helix chain 'AA' and resid 202 through 215 Processing helix chain 'BA' and resid 302 through 315 Processing helix chain 'CA' and resid 402 through 415 Processing helix chain 'L' and resid 2 through 15 Processing helix chain 'DA' and resid 102 through 115 Processing helix chain 'EA' and resid 202 through 215 Processing helix chain 'FA' and resid 302 through 315 Processing helix chain 'GA' and resid 402 through 415 Processing helix chain 'M' and resid 2 through 15 Processing helix chain 'HA' and resid 102 through 115 Processing helix chain 'IA' and resid 202 through 215 Processing helix chain 'JA' and resid 302 through 315 Processing helix chain 'KA' and resid 402 through 415 Processing helix chain 'N' and resid 2 through 15 Processing helix chain 'LA' and resid 102 through 115 Processing helix chain 'MA' and resid 202 through 215 Processing helix chain 'NA' and resid 302 through 315 Processing helix chain 'OA' and resid 402 through 415 Processing helix chain 'O' and resid 2 through 15 Processing helix chain 'PA' and resid 102 through 115 Processing helix chain 'QA' and resid 202 through 215 Processing helix chain 'RA' and resid 302 through 315 Processing helix chain 'SA' and resid 402 through 415 Processing helix chain 'P' and resid 2 through 15 Processing helix chain 'TA' and resid 102 through 115 Processing helix chain 'UA' and resid 202 through 215 Processing helix chain 'VA' and resid 302 through 315 Processing helix chain 'WA' and resid 402 through 415 Processing helix chain 'Q' and resid 2 through 15 Processing helix chain 'XA' and resid 102 through 115 Processing helix chain 'YA' and resid 202 through 215 Processing helix chain 'ZA' and resid 302 through 315 Processing helix chain 'aA' and resid 402 through 415 Processing helix chain 'R' and resid 2 through 15 Processing helix chain 'bA' and resid 102 through 115 Processing helix chain 'cA' and resid 202 through 215 Processing helix chain 'dA' and resid 302 through 315 Processing helix chain 'eA' and resid 402 through 415 Processing helix chain 'S' and resid 2 through 15 Processing helix chain 'fA' and resid 102 through 115 Processing helix chain 'gA' and resid 202 through 215 Processing helix chain 'hA' and resid 302 through 315 Processing helix chain 'iA' and resid 402 through 415 Processing helix chain 'T' and resid 2 through 15 Processing helix chain 'jA' and resid 102 through 115 Processing helix chain 'kA' and resid 202 through 215 Processing helix chain 'lA' and resid 302 through 315 Processing helix chain 'mA' and resid 402 through 415 Processing helix chain 'U' and resid 2 through 15 Processing helix chain 'nA' and resid 102 through 115 Processing helix chain 'oA' and resid 202 through 215 Processing helix chain 'pA' and resid 302 through 315 Processing helix chain 'qA' and resid 402 through 415 1050 hydrogen bonds defined for protein. 3150 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.06 Time building geometry restraints manager: 1.46 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: 2310 1.29 - 1.35: 2310 1.35 - 1.41: 735 1.41 - 1.47: 1785 1.47 - 1.54: 5775 Bond restraints: 12915 Sorted by residual: bond pdb=" CA ILEgA 211 " pdb=" C ILEgA 211 " ideal model delta sigma weight residual 1.524 1.516 0.008 1.18e-02 7.18e+03 4.90e-01 bond pdb=" CA GLUoA 213 " pdb=" C GLUoA 213 " ideal model delta sigma weight residual 1.527 1.518 0.008 1.21e-02 6.83e+03 4.73e-01 bond pdb=" CA ILEYA 211 " pdb=" C ILEYA 211 " ideal model delta sigma weight residual 1.524 1.516 0.008 1.18e-02 7.18e+03 4.69e-01 bond pdb=" CA ILE a 211 " pdb=" C ILE a 211 " ideal model delta sigma weight residual 1.524 1.516 0.008 1.18e-02 7.18e+03 4.58e-01 bond pdb=" CA GLU a 213 " pdb=" C GLU a 213 " ideal model delta sigma weight residual 1.527 1.519 0.008 1.21e-02 6.83e+03 4.57e-01 ... (remaining 12910 not shown) Histogram of bond angle deviations from ideal: 0.00 - 0.68: 14524 0.68 - 1.37: 2161 1.37 - 2.05: 452 2.05 - 2.73: 26 2.73 - 3.42: 162 Bond angle restraints: 17325 Sorted by residual: angle pdb=" NE ARGWA 406 " pdb=" CZ ARGWA 406 " pdb=" NH1 ARGWA 406 " ideal model delta sigma weight residual 121.50 119.78 1.72 1.00e+00 1.00e+00 2.96e+00 angle pdb=" NE ARG G 6 " pdb=" CZ ARG G 6 " pdb=" NH1 ARG G 6 " ideal model delta sigma weight residual 121.50 119.79 1.71 1.00e+00 1.00e+00 2.93e+00 angle pdb=" NE ARG R 6 " pdb=" CZ ARG R 6 " pdb=" NH1 ARG R 6 " ideal model delta sigma weight residual 121.50 119.79 1.71 1.00e+00 1.00e+00 2.91e+00 angle pdb=" NE ARG w 406 " pdb=" CZ ARG w 406 " pdb=" NH1 ARG w 406 " ideal model delta sigma weight residual 121.50 119.79 1.71 1.00e+00 1.00e+00 2.91e+00 angle pdb=" NE ARGOA 406 " pdb=" CZ ARGOA 406 " pdb=" NH1 ARGOA 406 " ideal model delta sigma weight residual 121.50 119.81 1.69 1.00e+00 1.00e+00 2.87e+00 ... (remaining 17320 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 8.02: 5691 8.02 - 16.05: 1232 16.05 - 24.07: 574 24.07 - 32.09: 399 32.09 - 40.11: 294 Dihedral angle restraints: 8190 sinusoidal: 3465 harmonic: 4725 Sorted by residual: dihedral pdb=" CA ILE 6 204 " pdb=" CB ILE 6 204 " pdb=" CG1 ILE 6 204 " pdb=" CD1 ILE 6 204 " ideal model delta sinusoidal sigma weight residual 60.00 100.11 -40.11 3 1.50e+01 4.44e-03 7.14e+00 dihedral pdb=" CA ILEgA 204 " pdb=" CB ILEgA 204 " pdb=" CG1 ILEgA 204 " pdb=" CD1 ILEgA 204 " ideal model delta sinusoidal sigma weight residual 60.00 100.11 -40.11 3 1.50e+01 4.44e-03 7.14e+00 dihedral pdb=" CA ILEIA 204 " pdb=" CB ILEIA 204 " pdb=" CG1 ILEIA 204 " pdb=" CD1 ILEIA 204 " ideal model delta sinusoidal sigma weight residual 60.00 100.11 -40.11 3 1.50e+01 4.44e-03 7.13e+00 ... (remaining 8187 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.017: 612 0.017 - 0.033: 449 0.033 - 0.050: 532 0.050 - 0.066: 205 0.066 - 0.083: 197 Chirality restraints: 1995 Sorted by residual: chirality pdb=" CA ILE 3 311 " pdb=" N ILE 3 311 " pdb=" C ILE 3 311 " pdb=" CB ILE 3 311 " both_signs ideal model delta sigma weight residual False 2.43 2.52 -0.08 2.00e-01 2.50e+01 1.71e-01 chirality pdb=" CA ILEBA 311 " pdb=" N ILEBA 311 " pdb=" C ILEBA 311 " pdb=" CB ILEBA 311 " both_signs ideal model delta sigma weight residual False 2.43 2.52 -0.08 2.00e-01 2.50e+01 1.69e-01 chirality pdb=" CA ILE j 311 " pdb=" N ILE j 311 " pdb=" C ILE j 311 " pdb=" CB ILE j 311 " both_signs ideal model delta sigma weight residual False 2.43 2.52 -0.08 2.00e-01 2.50e+01 1.68e-01 ... (remaining 1992 not shown) Planarity restraints: 2310 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR v 308 " -0.008 2.00e-02 2.50e+03 5.84e-03 6.83e-01 pdb=" CG TYR v 308 " 0.012 2.00e-02 2.50e+03 pdb=" CD1 TYR v 308 " -0.001 2.00e-02 2.50e+03 pdb=" CD2 TYR v 308 " 0.004 2.00e-02 2.50e+03 pdb=" CE1 TYR v 308 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 TYR v 308 " -0.006 2.00e-02 2.50e+03 pdb=" CZ TYR v 308 " -0.000 2.00e-02 2.50e+03 pdb=" OH TYR v 308 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYRdA 308 " -0.008 2.00e-02 2.50e+03 5.83e-03 6.80e-01 pdb=" CG TYRdA 308 " 0.012 2.00e-02 2.50e+03 pdb=" CD1 TYRdA 308 " -0.001 2.00e-02 2.50e+03 pdb=" CD2 TYRdA 308 " 0.004 2.00e-02 2.50e+03 pdb=" CE1 TYRdA 308 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 TYRdA 308 " -0.006 2.00e-02 2.50e+03 pdb=" CZ TYRdA 308 " 0.000 2.00e-02 2.50e+03 pdb=" OH TYRdA 308 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYRRA 308 " 0.008 2.00e-02 2.50e+03 5.79e-03 6.71e-01 pdb=" CG TYRRA 308 " -0.012 2.00e-02 2.50e+03 pdb=" CD1 TYRRA 308 " 0.001 2.00e-02 2.50e+03 pdb=" CD2 TYRRA 308 " -0.004 2.00e-02 2.50e+03 pdb=" CE1 TYRRA 308 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 TYRRA 308 " 0.007 2.00e-02 2.50e+03 pdb=" CZ TYRRA 308 " -0.001 2.00e-02 2.50e+03 pdb=" OH TYRRA 308 " -0.000 2.00e-02 2.50e+03 ... (remaining 2307 not shown) Histogram of nonbonded interaction distances: 2.30 - 2.82: 4158 2.82 - 3.34: 15647 3.34 - 3.86: 21033 3.86 - 4.38: 25256 4.38 - 4.90: 38427 Nonbonded interactions: 104521 Sorted by model distance: nonbonded pdb=" O GLU I 13 " pdb=" NH2 ARG 9 110 " model vdw 2.298 3.120 nonbonded pdb=" NH2 ARG 0 410 " pdb=" O GLU 7 313 " model vdw 2.311 3.120 nonbonded pdb=" O GLU M 13 " pdb=" NH2 ARGPA 110 " model vdw 2.329 3.120 nonbonded pdb=" O GLU C 13 " pdb=" NH2 ARG l 110 " model vdw 2.335 3.120 nonbonded pdb=" O GLU f 313 " pdb=" NH2 ARG o 410 " model vdw 2.341 3.120 ... (remaining 104516 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain '0' selection = chain '1' selection = chain '2' selection = chain '3' selection = chain '4' selection = chain '5' selection = chain '6' selection = chain '7' selection = chain '8' selection = chain '9' selection = chain 'A' selection = chain 'AA' selection = chain 'B' selection = chain 'BA' selection = chain 'C' selection = chain 'CA' selection = chain 'D' selection = chain 'DA' selection = chain 'E' selection = chain 'EA' selection = chain 'F' selection = chain 'FA' selection = chain 'G' selection = chain 'GA' selection = chain 'H' selection = chain 'HA' selection = chain 'I' selection = chain 'IA' selection = chain 'J' selection = chain 'JA' selection = chain 'K' selection = chain 'KA' selection = chain 'L' selection = chain 'LA' selection = chain 'M' selection = chain 'MA' selection = chain 'N' selection = chain 'NA' selection = chain 'O' selection = chain 'OA' selection = chain 'P' selection = chain 'PA' selection = chain 'Q' selection = chain 'QA' selection = chain 'R' selection = chain 'RA' selection = chain 'S' selection = chain 'SA' selection = chain 'T' selection = chain 'TA' selection = chain 'U' selection = chain 'UA' selection = chain 'V' selection = chain 'VA' selection = chain 'W' selection = chain 'WA' selection = chain 'X' selection = chain 'XA' selection = chain 'Y' selection = chain 'YA' selection = chain 'Z' selection = chain 'ZA' selection = chain 'a' selection = chain 'aA' selection = chain 'b' selection = chain 'bA' selection = chain 'c' selection = chain 'cA' selection = chain 'd' selection = chain 'dA' selection = chain 'e' selection = chain 'eA' selection = chain 'f' selection = chain 'fA' selection = chain 'g' selection = chain 'gA' selection = chain 'h' selection = chain 'hA' selection = chain 'i' selection = chain 'iA' selection = chain 'j' selection = chain 'jA' selection = chain 'k' selection = chain 'kA' selection = chain 'l' selection = chain 'lA' selection = chain 'm' selection = chain 'mA' selection = chain 'n' selection = chain 'nA' selection = chain 'o' selection = chain 'oA' selection = chain 'p' selection = chain 'pA' selection = chain 'q' selection = chain 'qA' selection = chain 'r' selection = chain 's' selection = chain 't' selection = chain 'u' selection = chain 'v' selection = chain 'w' selection = chain 'x' selection = chain 'y' selection = chain 'z' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.930 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: 0.150 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 12.710 Find NCS groups from input model: 0.250 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.530 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.760 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8965 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 : 0.006 0.018 12915 Z= 0.332 Angle : 0.595 3.415 17325 Z= 0.381 Chirality : 0.038 0.083 1995 Planarity : 0.002 0.006 2310 Dihedral : 15.107 40.115 5040 Min Nonbonded Distance : 2.298 Molprobity Statistics. All-atom Clashscore : 2.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 0.00 % Allowed : 9.09 % Favored : 90.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.67 (0.20), residues: 1365 helix: -2.12 (0.12), residues: 1365 sheet: None (None), residues: 0 loop : None (None), residues: 0 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARGHA 110 TYR 0.012 0.004 TYR X 308 Details of bonding type rmsd covalent geometry : bond 0.00637 (12915) covalent geometry : angle 0.59479 (17325) hydrogen bonds : bond 0.24973 ( 1050) hydrogen bonds : angle 7.62188 ( 3150) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2730 Ramachandran restraints generated. 1365 Oldfield, 0 Emsley, 1365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2730 Ramachandran restraints generated. 1365 Oldfield, 0 Emsley, 1365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 650 residues out of total 1155 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 650 time to evaluate : 0.500 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 8 TYR cc_start: 0.9301 (t80) cc_final: 0.8977 (t80) REVERT: A 15 GLN cc_start: 0.8855 (mt0) cc_final: 0.8508 (mt0) REVERT: V 108 TYR cc_start: 0.9316 (t80) cc_final: 0.8838 (t80) REVERT: V 112 LEU cc_start: 0.9478 (mm) cc_final: 0.9173 (mm) REVERT: V 115 GLN cc_start: 0.8958 (mt0) cc_final: 0.8521 (mt0) REVERT: W 208 TYR cc_start: 0.9317 (t80) cc_final: 0.8870 (t80) REVERT: W 212 LEU cc_start: 0.9437 (mm) cc_final: 0.9146 (mm) REVERT: W 215 GLN cc_start: 0.9125 (mt0) cc_final: 0.8751 (tt0) REVERT: X 308 TYR cc_start: 0.9317 (t80) cc_final: 0.8898 (t80) REVERT: X 315 GLN cc_start: 0.8967 (mt0) cc_final: 0.8416 (mt0) REVERT: Y 408 TYR cc_start: 0.9316 (t80) cc_final: 0.8688 (t80) REVERT: Y 412 LEU cc_start: 0.9460 (mm) cc_final: 0.9096 (mm) REVERT: Y 415 GLN cc_start: 0.8911 (mt0) cc_final: 0.8250 (mt0) REVERT: B 15 GLN cc_start: 0.8857 (mt0) cc_final: 0.8425 (mt0) REVERT: Z 112 LEU cc_start: 0.9439 (mm) cc_final: 0.9152 (mm) REVERT: a 215 GLN cc_start: 0.9140 (mt0) cc_final: 0.8883 (mt0) REVERT: b 315 GLN cc_start: 0.8833 (mt0) cc_final: 0.8454 (mt0) REVERT: C 8 TYR cc_start: 0.9253 (t80) cc_final: 0.8106 (t80) REVERT: C 12 LEU cc_start: 0.9380 (mm) cc_final: 0.9010 (mm) REVERT: C 15 GLN cc_start: 0.8860 (mt0) cc_final: 0.8430 (mt0) REVERT: d 108 TYR cc_start: 0.9308 (t80) cc_final: 0.9104 (t80) REVERT: d 112 LEU cc_start: 0.9542 (mm) cc_final: 0.9288 (mm) REVERT: e 215 GLN cc_start: 0.9083 (mt0) cc_final: 0.8766 (mt0) REVERT: f 308 TYR cc_start: 0.9370 (t80) cc_final: 0.9133 (t80) REVERT: f 312 LEU cc_start: 0.9416 (mm) cc_final: 0.9172 (mm) REVERT: g 415 GLN cc_start: 0.8880 (mt0) cc_final: 0.8616 (mt0) REVERT: i 208 TYR cc_start: 0.9339 (t80) cc_final: 0.8901 (t80) REVERT: j 308 TYR cc_start: 0.9340 (t80) cc_final: 0.8973 (t80) REVERT: j 312 LEU cc_start: 0.9414 (mm) cc_final: 0.9059 (mm) REVERT: k 408 TYR cc_start: 0.9414 (t80) cc_final: 0.9148 (t80) REVERT: E 8 TYR cc_start: 0.9334 (t80) cc_final: 0.9047 (t80) REVERT: E 12 LEU cc_start: 0.9403 (mm) cc_final: 0.9178 (mm) REVERT: m 208 TYR cc_start: 0.9274 (t80) cc_final: 0.8254 (t80) REVERT: m 212 LEU cc_start: 0.9446 (mm) cc_final: 0.9140 (mm) REVERT: m 215 GLN cc_start: 0.9203 (mt0) cc_final: 0.8845 (mt0) REVERT: n 308 TYR cc_start: 0.9366 (t80) cc_final: 0.9145 (t80) REVERT: o 413 GLU cc_start: 0.9352 (pp20) cc_final: 0.9146 (pp20) REVERT: p 108 TYR cc_start: 0.9429 (t80) cc_final: 0.8689 (t80) REVERT: p 112 LEU cc_start: 0.9433 (mm) cc_final: 0.9041 (mm) REVERT: r 308 TYR cc_start: 0.9412 (t80) cc_final: 0.8847 (t80) REVERT: t 108 TYR cc_start: 0.9392 (t80) cc_final: 0.9160 (t80) REVERT: t 112 LEU cc_start: 0.9447 (mm) cc_final: 0.9194 (mm) REVERT: t 115 GLN cc_start: 0.8925 (mt0) cc_final: 0.8633 (mt0) REVERT: u 215 GLN cc_start: 0.9162 (mt0) cc_final: 0.8775 (mt0) REVERT: v 308 TYR cc_start: 0.9309 (t80) cc_final: 0.8839 (t80) REVERT: v 315 GLN cc_start: 0.8904 (mt0) cc_final: 0.8646 (mt0) REVERT: w 413 GLU cc_start: 0.9409 (pp20) cc_final: 0.9162 (pp20) REVERT: H 3 GLU cc_start: 0.8739 (tp30) cc_final: 0.8538 (tp30) REVERT: x 108 TYR cc_start: 0.9340 (t80) cc_final: 0.8687 (t80) REVERT: x 112 LEU cc_start: 0.9524 (mm) cc_final: 0.9106 (mm) REVERT: y 215 GLN cc_start: 0.9194 (mt0) cc_final: 0.8825 (mt0) REVERT: I 8 TYR cc_start: 0.9397 (t80) cc_final: 0.9113 (t80) REVERT: 1 108 TYR cc_start: 0.9398 (t80) cc_final: 0.8828 (t80) REVERT: 1 112 LEU cc_start: 0.9462 (mm) cc_final: 0.9177 (mm) REVERT: 2 215 GLN cc_start: 0.9159 (mt0) cc_final: 0.8703 (mt0) REVERT: 3 312 LEU cc_start: 0.9268 (mm) cc_final: 0.9010 (mm) REVERT: 6 215 GLN cc_start: 0.9140 (mt0) cc_final: 0.8815 (mt0) REVERT: 8 408 TYR cc_start: 0.9287 (t80) cc_final: 0.9034 (t80) REVERT: K 8 TYR cc_start: 0.9365 (t80) cc_final: 0.8388 (t80) REVERT: K 12 LEU cc_start: 0.9349 (mm) cc_final: 0.8917 (mm) REVERT: K 15 GLN cc_start: 0.8848 (mt0) cc_final: 0.8012 (mt0) REVERT: 9 112 LEU cc_start: 0.9486 (mm) cc_final: 0.9247 (mm) REVERT: AA 215 GLN cc_start: 0.9078 (mt0) cc_final: 0.8697 (mt0) REVERT: BA 315 GLN cc_start: 0.8934 (mt0) cc_final: 0.8533 (mt0) REVERT: CA 412 LEU cc_start: 0.9442 (mm) cc_final: 0.9237 (mm) REVERT: L 3 GLU cc_start: 0.8857 (tp30) cc_final: 0.8422 (tp30) REVERT: L 8 TYR cc_start: 0.9277 (t80) cc_final: 0.8394 (t80) REVERT: L 12 LEU cc_start: 0.9439 (mm) cc_final: 0.9059 (mm) REVERT: L 15 GLN cc_start: 0.8947 (mt0) cc_final: 0.8671 (mt0) REVERT: DA 108 TYR cc_start: 0.9266 (t80) cc_final: 0.8421 (t80) REVERT: DA 112 LEU cc_start: 0.9461 (mm) cc_final: 0.9101 (mm) REVERT: EA 208 TYR cc_start: 0.9321 (t80) cc_final: 0.8532 (t80) REVERT: EA 215 GLN cc_start: 0.9060 (mt0) cc_final: 0.8701 (mt0) REVERT: FA 308 TYR cc_start: 0.9266 (t80) cc_final: 0.8365 (t80) REVERT: FA 312 LEU cc_start: 0.9429 (mm) cc_final: 0.9130 (mm) REVERT: FA 315 GLN cc_start: 0.8866 (mt0) cc_final: 0.8401 (mt0) REVERT: GA 408 TYR cc_start: 0.9219 (t80) cc_final: 0.8244 (t80) REVERT: GA 412 LEU cc_start: 0.9426 (mm) cc_final: 0.9095 (mm) REVERT: GA 415 GLN cc_start: 0.8856 (mt0) cc_final: 0.8405 (mt0) REVERT: M 8 TYR cc_start: 0.9289 (t80) cc_final: 0.9081 (t80) REVERT: M 12 LEU cc_start: 0.9418 (mm) cc_final: 0.9184 (mm) REVERT: M 15 GLN cc_start: 0.8877 (mt0) cc_final: 0.8300 (mt0) REVERT: HA 112 LEU cc_start: 0.9506 (mm) cc_final: 0.9247 (mm) REVERT: IA 215 GLN cc_start: 0.9101 (mt0) cc_final: 0.8762 (mt0) REVERT: JA 315 GLN cc_start: 0.8890 (mt0) cc_final: 0.8389 (mt0) REVERT: KA 415 GLN cc_start: 0.8946 (mt0) cc_final: 0.8445 (mt0) REVERT: N 8 TYR cc_start: 0.9353 (t80) cc_final: 0.8993 (t80) REVERT: N 12 LEU cc_start: 0.9388 (mm) cc_final: 0.9136 (mm) REVERT: N 15 GLN cc_start: 0.8823 (mt0) cc_final: 0.8245 (mt0) REVERT: LA 115 GLN cc_start: 0.8895 (mt0) cc_final: 0.8550 (mt0) REVERT: MA 208 TYR cc_start: 0.9314 (t80) cc_final: 0.8965 (t80) REVERT: MA 215 GLN cc_start: 0.9136 (mt0) cc_final: 0.8792 (mt0) REVERT: NA 308 TYR cc_start: 0.9375 (t80) cc_final: 0.9087 (t80) REVERT: NA 315 GLN cc_start: 0.8891 (mt0) cc_final: 0.8450 (mt0) REVERT: OA 408 TYR cc_start: 0.9310 (t80) cc_final: 0.9042 (t80) REVERT: OA 415 GLN cc_start: 0.8988 (mt0) cc_final: 0.8660 (mt0) REVERT: O 8 TYR cc_start: 0.9239 (t80) cc_final: 0.8609 (t80) REVERT: O 12 LEU cc_start: 0.9357 (mm) cc_final: 0.9052 (mm) REVERT: PA 108 TYR cc_start: 0.9372 (t80) cc_final: 0.9050 (t80) REVERT: PA 115 GLN cc_start: 0.8934 (mt0) cc_final: 0.8493 (mt0) REVERT: QA 208 TYR cc_start: 0.9295 (t80) cc_final: 0.8625 (t80) REVERT: QA 215 GLN cc_start: 0.9127 (mt0) cc_final: 0.8760 (mt0) REVERT: RA 308 TYR cc_start: 0.9308 (t80) cc_final: 0.8649 (t80) REVERT: RA 312 LEU cc_start: 0.9411 (mm) cc_final: 0.9067 (mm) REVERT: RA 315 GLN cc_start: 0.8872 (mt0) cc_final: 0.8309 (mt0) REVERT: SA 408 TYR cc_start: 0.9299 (t80) cc_final: 0.8749 (t80) REVERT: SA 412 LEU cc_start: 0.9430 (mm) cc_final: 0.9189 (mm) REVERT: SA 415 GLN cc_start: 0.9023 (mt0) cc_final: 0.8502 (mt0) REVERT: P 15 GLN cc_start: 0.8874 (mt0) cc_final: 0.8407 (mt0) REVERT: UA 212 LEU cc_start: 0.9389 (mm) cc_final: 0.9171 (mm) REVERT: UA 215 GLN cc_start: 0.9123 (mt0) cc_final: 0.8732 (tt0) REVERT: VA 315 GLN cc_start: 0.8730 (mt0) cc_final: 0.8232 (mt0) REVERT: WA 412 LEU cc_start: 0.9403 (mm) cc_final: 0.9120 (mm) REVERT: Q 15 GLN cc_start: 0.8818 (mt0) cc_final: 0.8459 (mt0) REVERT: XA 115 GLN cc_start: 0.8856 (mt0) cc_final: 0.8356 (mt0) REVERT: YA 215 GLN cc_start: 0.9069 (mt0) cc_final: 0.8830 (tt0) REVERT: ZA 315 GLN cc_start: 0.8854 (mt0) cc_final: 0.8322 (mt0) REVERT: aA 415 GLN cc_start: 0.8953 (mt0) cc_final: 0.8536 (mt0) REVERT: R 8 TYR cc_start: 0.9383 (t80) cc_final: 0.9118 (t80) REVERT: R 12 LEU cc_start: 0.9428 (mm) cc_final: 0.9206 (mm) REVERT: cA 211 ILE cc_start: 0.9706 (mt) cc_final: 0.9491 (mm) REVERT: cA 212 LEU cc_start: 0.9387 (mm) cc_final: 0.9173 (mm) REVERT: dA 312 LEU cc_start: 0.9332 (mm) cc_final: 0.9118 (mm) REVERT: eA 408 TYR cc_start: 0.9407 (t80) cc_final: 0.9021 (t80) REVERT: S 8 TYR cc_start: 0.9333 (t80) cc_final: 0.8509 (t80) REVERT: S 12 LEU cc_start: 0.9448 (mm) cc_final: 0.8945 (mm) REVERT: iA 408 TYR cc_start: 0.9292 (t80) cc_final: 0.9024 (t80) REVERT: T 3 GLU cc_start: 0.8810 (tp30) cc_final: 0.8535 (tp30) REVERT: T 11 ILE cc_start: 0.9429 (mt) cc_final: 0.9184 (mm) REVERT: jA 112 LEU cc_start: 0.9202 (mm) cc_final: 0.8963 (mm) REVERT: mA 408 TYR cc_start: 0.9373 (t80) cc_final: 0.8892 (t80) REVERT: mA 412 LEU cc_start: 0.9163 (mm) cc_final: 0.8782 (mm) REVERT: U 8 TYR cc_start: 0.9152 (t80) cc_final: 0.8858 (t80) REVERT: nA 108 TYR cc_start: 0.9235 (t80) cc_final: 0.8887 (t80) REVERT: nA 112 LEU cc_start: 0.9549 (mm) cc_final: 0.9344 (mm) REVERT: oA 215 GLN cc_start: 0.8867 (mt0) cc_final: 0.8630 (mt0) outliers start: 0 outliers final: 0 residues processed: 650 average time/residue: 0.0832 time to fit residues: 85.7550 Evaluate side-chains 623 residues out of total 1155 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 623 time to evaluate : 0.540 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 49 optimal weight: 4.9990 chunk 97 optimal weight: 5.9990 chunk 53 optimal weight: 0.0870 chunk 5 optimal weight: 0.0980 chunk 33 optimal weight: 2.9990 chunk 65 optimal weight: 0.5980 chunk 62 optimal weight: 0.9980 chunk 51 optimal weight: 0.8980 chunk 100 optimal weight: 4.9990 chunk 38 optimal weight: 0.0980 chunk 61 optimal weight: 2.9990 overall best weight: 0.3558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3018 r_free = 0.3018 target = 0.059192 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.2830 r_free = 0.2830 target = 0.052808 restraints weight = 50610.062| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.2884 r_free = 0.2884 target = 0.054738 restraints weight = 27587.488| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.2918 r_free = 0.2918 target = 0.055941 restraints weight = 16597.999| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.2945 r_free = 0.2945 target = 0.056833 restraints weight = 11054.849| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.2965 r_free = 0.2965 target = 0.057527 restraints weight = 7469.797| |-----------------------------------------------------------------------------| r_work (final): 0.2943 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8799 moved from start: 0.3478 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 12915 Z= 0.106 Angle : 0.471 4.230 17325 Z= 0.257 Chirality : 0.035 0.115 1995 Planarity : 0.003 0.014 2310 Dihedral : 3.628 12.063 1890 Min Nonbonded Distance : 2.600 Molprobity Statistics. All-atom Clashscore : 10.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.07 % Favored : 99.93 % Rotamer: Outliers : 0.61 % Allowed : 2.34 % Favored : 97.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.92 (0.24), residues: 1365 helix: 1.33 (0.15), residues: 1365 sheet: None (None), residues: 0 loop : None (None), residues: 0 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARGgA 210 TYR 0.012 0.002 TYRgA 208 Details of bonding type rmsd covalent geometry : bond 0.00240 (12915) covalent geometry : angle 0.47112 (17325) hydrogen bonds : bond 0.03572 ( 1050) hydrogen bonds : angle 3.98424 ( 3150) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2730 Ramachandran restraints generated. 1365 Oldfield, 0 Emsley, 1365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2730 Ramachandran restraints generated. 1365 Oldfield, 0 Emsley, 1365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 653 residues out of total 1155 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 646 time to evaluate : 0.533 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 15 GLN cc_start: 0.8497 (mt0) cc_final: 0.8189 (mt0) REVERT: V 108 TYR cc_start: 0.8960 (t80) cc_final: 0.8626 (t80) REVERT: W 212 LEU cc_start: 0.9246 (mm) cc_final: 0.9036 (mm) REVERT: Y 408 TYR cc_start: 0.8864 (t80) cc_final: 0.8584 (t80) REVERT: Y 412 LEU cc_start: 0.9212 (mm) cc_final: 0.9001 (mm) REVERT: B 15 GLN cc_start: 0.8493 (mt0) cc_final: 0.8141 (mt0) REVERT: b 315 GLN cc_start: 0.8402 (mt0) cc_final: 0.8058 (tt0) REVERT: C 8 TYR cc_start: 0.8809 (t80) cc_final: 0.8096 (t80) REVERT: C 15 GLN cc_start: 0.8569 (mt0) cc_final: 0.8359 (mt0) REVERT: d 108 TYR cc_start: 0.8966 (t80) cc_final: 0.8246 (t80) REVERT: d 112 LEU cc_start: 0.9346 (mm) cc_final: 0.9006 (mm) REVERT: e 208 TYR cc_start: 0.8651 (t80) cc_final: 0.7941 (t80) REVERT: e 215 GLN cc_start: 0.8782 (mt0) cc_final: 0.8489 (tt0) REVERT: f 308 TYR cc_start: 0.8869 (t80) cc_final: 0.8369 (t80) REVERT: g 415 GLN cc_start: 0.8447 (mt0) cc_final: 0.8204 (mt0) REVERT: h 115 GLN cc_start: 0.8655 (mt0) cc_final: 0.8377 (mt0) REVERT: i 208 TYR cc_start: 0.8801 (t80) cc_final: 0.8564 (t80) REVERT: j 308 TYR cc_start: 0.8893 (t80) cc_final: 0.8480 (t80) REVERT: k 408 TYR cc_start: 0.8918 (t80) cc_final: 0.8685 (t80) REVERT: E 3 GLU cc_start: 0.8415 (tp30) cc_final: 0.6875 (mm-30) REVERT: l 115 GLN cc_start: 0.8640 (mt0) cc_final: 0.8413 (tt0) REVERT: o 415 GLN cc_start: 0.8500 (mt0) cc_final: 0.8172 (mt0) REVERT: F 3 GLU cc_start: 0.8556 (tp30) cc_final: 0.7524 (tp30) REVERT: p 108 TYR cc_start: 0.9051 (t80) cc_final: 0.8282 (t80) REVERT: p 112 LEU cc_start: 0.9366 (mm) cc_final: 0.8889 (mm) REVERT: r 311 ILE cc_start: 0.9441 (mt) cc_final: 0.9230 (mt) REVERT: s 415 GLN cc_start: 0.8744 (mt0) cc_final: 0.8013 (mt0) REVERT: t 108 TYR cc_start: 0.8955 (t80) cc_final: 0.8711 (t80) REVERT: u 208 TYR cc_start: 0.8788 (t80) cc_final: 0.8585 (t80) REVERT: u 212 LEU cc_start: 0.9302 (mm) cc_final: 0.9058 (mm) REVERT: u 215 GLN cc_start: 0.8699 (mt0) cc_final: 0.8474 (mt0) REVERT: v 311 ILE cc_start: 0.9512 (mt) cc_final: 0.9220 (mt) REVERT: v 315 GLN cc_start: 0.8375 (mt0) cc_final: 0.8118 (mt0) REVERT: H 15 GLN cc_start: 0.8588 (mt0) cc_final: 0.8362 (mt0) REVERT: x 111 ILE cc_start: 0.9431 (OUTLIER) cc_final: 0.9017 (mt) REVERT: x 112 LEU cc_start: 0.9430 (mm) cc_final: 0.8734 (mm) REVERT: x 115 GLN cc_start: 0.8543 (mt0) cc_final: 0.8232 (mt0) REVERT: y 208 TYR cc_start: 0.8806 (t80) cc_final: 0.8417 (t80) REVERT: I 3 GLU cc_start: 0.8422 (tp30) cc_final: 0.7302 (tp30) REVERT: I 8 TYR cc_start: 0.9044 (t80) cc_final: 0.8644 (t80) REVERT: 1 112 LEU cc_start: 0.9450 (mm) cc_final: 0.9153 (mm) REVERT: 2 211 ILE cc_start: 0.9592 (mt) cc_final: 0.9329 (mt) REVERT: 4 415 GLN cc_start: 0.8500 (mt0) cc_final: 0.7808 (mt0) REVERT: J 15 GLN cc_start: 0.8585 (mt0) cc_final: 0.8290 (mt0) REVERT: 5 115 GLN cc_start: 0.8496 (mt0) cc_final: 0.8232 (tt0) REVERT: K 3 GLU cc_start: 0.8318 (mm-30) cc_final: 0.8009 (tp30) REVERT: K 8 TYR cc_start: 0.8948 (t80) cc_final: 0.8504 (t80) REVERT: K 12 LEU cc_start: 0.9127 (mm) cc_final: 0.8921 (mm) REVERT: K 15 GLN cc_start: 0.8434 (mt0) cc_final: 0.8182 (mt0) REVERT: 9 112 LEU cc_start: 0.9352 (mm) cc_final: 0.9063 (mm) REVERT: BA 315 GLN cc_start: 0.8453 (mt0) cc_final: 0.8182 (tt0) REVERT: L 8 TYR cc_start: 0.8875 (t80) cc_final: 0.8405 (t80) REVERT: DA 108 TYR cc_start: 0.8947 (t80) cc_final: 0.8479 (t80) REVERT: DA 112 LEU cc_start: 0.9341 (mm) cc_final: 0.9081 (mm) REVERT: DA 115 GLN cc_start: 0.8616 (mt0) cc_final: 0.8397 (mt0) REVERT: EA 208 TYR cc_start: 0.8921 (t80) cc_final: 0.8535 (t80) REVERT: EA 215 GLN cc_start: 0.8704 (mt0) cc_final: 0.8478 (tt0) REVERT: FA 308 TYR cc_start: 0.8857 (t80) cc_final: 0.8258 (t80) REVERT: FA 315 GLN cc_start: 0.8449 (mt0) cc_final: 0.8144 (mt0) REVERT: GA 408 TYR cc_start: 0.8877 (t80) cc_final: 0.8310 (t80) REVERT: GA 415 GLN cc_start: 0.8607 (mt0) cc_final: 0.8313 (tt0) REVERT: M 15 GLN cc_start: 0.8386 (mt0) cc_final: 0.8085 (mt0) REVERT: HA 115 GLN cc_start: 0.8603 (mt0) cc_final: 0.8335 (mt0) REVERT: KA 415 GLN cc_start: 0.8413 (mt0) cc_final: 0.8117 (mt0) REVERT: N 15 GLN cc_start: 0.8496 (mt0) cc_final: 0.8279 (mt0) REVERT: LA 115 GLN cc_start: 0.8634 (mt0) cc_final: 0.8428 (mt0) REVERT: O 3 GLU cc_start: 0.8405 (tp30) cc_final: 0.7438 (tp30) REVERT: O 8 TYR cc_start: 0.8741 (t80) cc_final: 0.8371 (t80) REVERT: O 15 GLN cc_start: 0.8520 (mt0) cc_final: 0.8269 (tt0) REVERT: PA 115 GLN cc_start: 0.8697 (mt0) cc_final: 0.8400 (tt0) REVERT: RA 308 TYR cc_start: 0.8866 (t80) cc_final: 0.8533 (t80) REVERT: SA 408 TYR cc_start: 0.8761 (t80) cc_final: 0.8487 (t80) REVERT: SA 415 GLN cc_start: 0.8514 (mt0) cc_final: 0.8234 (mt0) REVERT: P 3 GLU cc_start: 0.8601 (tp30) cc_final: 0.7901 (tp30) REVERT: P 15 GLN cc_start: 0.8523 (mt0) cc_final: 0.8281 (tt0) REVERT: UA 212 LEU cc_start: 0.9278 (mm) cc_final: 0.9015 (mm) REVERT: XA 108 TYR cc_start: 0.8827 (t80) cc_final: 0.8019 (t80) REVERT: YA 208 TYR cc_start: 0.8882 (t80) cc_final: 0.8190 (t80) REVERT: YA 212 LEU cc_start: 0.9195 (mm) cc_final: 0.8988 (mm) REVERT: ZA 315 GLN cc_start: 0.8432 (mt0) cc_final: 0.8104 (mt0) REVERT: aA 415 GLN cc_start: 0.8460 (mt0) cc_final: 0.8148 (tt0) REVERT: R 3 GLU cc_start: 0.8277 (tp30) cc_final: 0.7975 (tp30) REVERT: R 8 TYR cc_start: 0.9032 (t80) cc_final: 0.8573 (t80) REVERT: R 12 LEU cc_start: 0.9214 (mm) cc_final: 0.8961 (mm) REVERT: eA 415 GLN cc_start: 0.8891 (mt0) cc_final: 0.8620 (mt0) REVERT: hA 315 GLN cc_start: 0.8467 (mt0) cc_final: 0.8199 (mt0) REVERT: iA 411 ILE cc_start: 0.9553 (mt) cc_final: 0.9322 (mt) REVERT: T 3 GLU cc_start: 0.8265 (tp30) cc_final: 0.7696 (tp30) REVERT: jA 112 LEU cc_start: 0.9195 (mm) cc_final: 0.8882 (mm) REVERT: lA 308 TYR cc_start: 0.9114 (t80) cc_final: 0.8555 (t80) REVERT: mA 408 TYR cc_start: 0.9054 (t80) cc_final: 0.8765 (t80) REVERT: oA 215 GLN cc_start: 0.8665 (mt0) cc_final: 0.8464 (mt0) outliers start: 7 outliers final: 0 residues processed: 646 average time/residue: 0.0849 time to fit residues: 86.9132 Evaluate side-chains 556 residues out of total 1155 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 555 time to evaluate : 0.571 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 63 optimal weight: 2.9990 chunk 1 optimal weight: 7.9990 chunk 32 optimal weight: 0.9990 chunk 46 optimal weight: 0.8980 chunk 15 optimal weight: 7.9990 chunk 61 optimal weight: 4.9990 chunk 41 optimal weight: 4.9990 chunk 77 optimal weight: 0.6980 chunk 37 optimal weight: 2.9990 chunk 96 optimal weight: 4.9990 chunk 79 optimal weight: 0.9980 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: gA 215 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3033 r_free = 0.3033 target = 0.057343 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2827 r_free = 0.2827 target = 0.050111 restraints weight = 49592.633| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.2883 r_free = 0.2883 target = 0.052105 restraints weight = 28214.349| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.2923 r_free = 0.2923 target = 0.053449 restraints weight = 17785.008| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.2949 r_free = 0.2949 target = 0.054346 restraints weight = 12169.828| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.2970 r_free = 0.2970 target = 0.055041 restraints weight = 8606.109| |-----------------------------------------------------------------------------| r_work (final): 0.2953 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8813 moved from start: 0.4807 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 12915 Z= 0.126 Angle : 0.513 4.356 17325 Z= 0.269 Chirality : 0.041 0.129 1995 Planarity : 0.002 0.013 2310 Dihedral : 2.717 19.201 1890 Min Nonbonded Distance : 2.622 Molprobity Statistics. All-atom Clashscore : 8.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 0.17 % Allowed : 8.31 % Favored : 91.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.74 (0.25), residues: 1365 helix: 1.84 (0.16), residues: 1365 sheet: None (None), residues: 0 loop : None (None), residues: 0 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG l 106 TYR 0.018 0.002 TYRdA 308 Details of bonding type rmsd covalent geometry : bond 0.00294 (12915) covalent geometry : angle 0.51264 (17325) hydrogen bonds : bond 0.03348 ( 1050) hydrogen bonds : angle 3.70069 ( 3150) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2730 Ramachandran restraints generated. 1365 Oldfield, 0 Emsley, 1365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2730 Ramachandran restraints generated. 1365 Oldfield, 0 Emsley, 1365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 638 residues out of total 1155 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 636 time to evaluate : 0.447 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 15 GLN cc_start: 0.8753 (mt0) cc_final: 0.8498 (mt0) REVERT: V 108 TYR cc_start: 0.9116 (t80) cc_final: 0.8855 (t80) REVERT: V 112 LEU cc_start: 0.9413 (mm) cc_final: 0.9191 (mm) REVERT: Y 408 TYR cc_start: 0.9094 (t80) cc_final: 0.8707 (t80) REVERT: Y 412 LEU cc_start: 0.9437 (mm) cc_final: 0.9123 (mm) REVERT: B 3 GLU cc_start: 0.8743 (tp30) cc_final: 0.8295 (tp30) REVERT: a 203 GLU cc_start: 0.8793 (tp30) cc_final: 0.8388 (mm-30) REVERT: b 315 GLN cc_start: 0.8609 (mt0) cc_final: 0.8335 (mt0) REVERT: C 8 TYR cc_start: 0.9089 (t80) cc_final: 0.8431 (t80) REVERT: d 108 TYR cc_start: 0.9171 (t80) cc_final: 0.8415 (t80) REVERT: d 112 LEU cc_start: 0.9469 (mm) cc_final: 0.9256 (mm) REVERT: e 208 TYR cc_start: 0.8813 (t80) cc_final: 0.8110 (t80) REVERT: e 215 GLN cc_start: 0.8916 (mt0) cc_final: 0.8579 (tt0) REVERT: f 308 TYR cc_start: 0.9031 (t80) cc_final: 0.8591 (t80) REVERT: g 408 TYR cc_start: 0.8899 (t80) cc_final: 0.8282 (t80) REVERT: h 115 GLN cc_start: 0.8925 (mt0) cc_final: 0.8664 (mt0) REVERT: i 208 TYR cc_start: 0.9033 (t80) cc_final: 0.8593 (t80) REVERT: j 308 TYR cc_start: 0.9070 (t80) cc_final: 0.8700 (t80) REVERT: k 408 TYR cc_start: 0.9156 (t80) cc_final: 0.8490 (t80) REVERT: l 115 GLN cc_start: 0.8881 (mt0) cc_final: 0.8657 (mt0) REVERT: m 208 TYR cc_start: 0.8955 (t80) cc_final: 0.8748 (t80) REVERT: n 315 GLN cc_start: 0.8844 (mt0) cc_final: 0.8586 (mt0) REVERT: t 108 TYR cc_start: 0.9110 (t80) cc_final: 0.8760 (t80) REVERT: t 112 LEU cc_start: 0.9435 (mm) cc_final: 0.9121 (mm) REVERT: u 208 TYR cc_start: 0.9095 (t80) cc_final: 0.8724 (t80) REVERT: u 212 LEU cc_start: 0.9365 (mm) cc_final: 0.9117 (mm) REVERT: u 215 GLN cc_start: 0.8892 (mt0) cc_final: 0.8669 (mt0) REVERT: v 315 GLN cc_start: 0.8644 (mt0) cc_final: 0.8270 (mt0) REVERT: H 15 GLN cc_start: 0.8766 (mt0) cc_final: 0.8555 (mt0) REVERT: x 115 GLN cc_start: 0.9020 (mt0) cc_final: 0.8469 (mt0) REVERT: y 203 GLU cc_start: 0.8533 (tp30) cc_final: 0.8270 (tp30) REVERT: I 8 TYR cc_start: 0.9241 (t80) cc_final: 0.8850 (t80) REVERT: I 12 LEU cc_start: 0.9534 (mm) cc_final: 0.9299 (mm) REVERT: J 15 GLN cc_start: 0.8812 (mt0) cc_final: 0.8518 (mt0) REVERT: 5 115 GLN cc_start: 0.8719 (mt0) cc_final: 0.8398 (mt0) REVERT: 7 303 GLU cc_start: 0.8642 (tp30) cc_final: 0.8391 (mm-30) REVERT: 8 408 TYR cc_start: 0.8979 (t80) cc_final: 0.8778 (t80) REVERT: K 8 TYR cc_start: 0.9120 (t80) cc_final: 0.8609 (t80) REVERT: K 12 LEU cc_start: 0.9310 (mm) cc_final: 0.8994 (mm) REVERT: 9 112 LEU cc_start: 0.9454 (mm) cc_final: 0.9180 (mm) REVERT: BA 315 GLN cc_start: 0.8777 (mt0) cc_final: 0.8428 (tt0) REVERT: CA 412 LEU cc_start: 0.9453 (mm) cc_final: 0.9188 (mm) REVERT: L 8 TYR cc_start: 0.9081 (t80) cc_final: 0.8619 (t80) REVERT: DA 108 TYR cc_start: 0.9042 (t80) cc_final: 0.8483 (t80) REVERT: DA 112 LEU cc_start: 0.9507 (mm) cc_final: 0.9277 (mm) REVERT: EA 208 TYR cc_start: 0.9157 (t80) cc_final: 0.8736 (t80) REVERT: EA 215 GLN cc_start: 0.8853 (mt0) cc_final: 0.8516 (tt0) REVERT: FA 308 TYR cc_start: 0.9152 (t80) cc_final: 0.8585 (t80) REVERT: FA 312 LEU cc_start: 0.9354 (mm) cc_final: 0.9151 (mm) REVERT: GA 408 TYR cc_start: 0.9058 (t80) cc_final: 0.8463 (t80) REVERT: HA 115 GLN cc_start: 0.8881 (mt0) cc_final: 0.8592 (mt0) REVERT: KA 415 GLN cc_start: 0.8708 (mt0) cc_final: 0.8348 (mt0) REVERT: N 3 GLU cc_start: 0.8645 (tp30) cc_final: 0.8339 (tp30) REVERT: MA 215 GLN cc_start: 0.8996 (mt0) cc_final: 0.8785 (mt0) REVERT: O 8 TYR cc_start: 0.9047 (t80) cc_final: 0.8715 (t80) REVERT: RA 308 TYR cc_start: 0.9077 (t80) cc_final: 0.8834 (t80) REVERT: SA 408 TYR cc_start: 0.9042 (t80) cc_final: 0.8719 (t80) REVERT: P 15 GLN cc_start: 0.8822 (mt0) cc_final: 0.8560 (mt0) REVERT: Q 8 TYR cc_start: 0.8911 (t80) cc_final: 0.8159 (t80) REVERT: XA 108 TYR cc_start: 0.9078 (t80) cc_final: 0.8207 (t80) REVERT: XA 112 LEU cc_start: 0.9362 (mm) cc_final: 0.9124 (mm) REVERT: YA 208 TYR cc_start: 0.9116 (t80) cc_final: 0.8533 (t80) REVERT: ZA 303 GLU cc_start: 0.8697 (tp30) cc_final: 0.8172 (mm-30) REVERT: ZA 315 GLN cc_start: 0.8669 (mt0) cc_final: 0.8338 (mt0) REVERT: aA 408 TYR cc_start: 0.8809 (t80) cc_final: 0.8207 (t80) REVERT: R 8 TYR cc_start: 0.9199 (t80) cc_final: 0.8599 (t80) REVERT: R 12 LEU cc_start: 0.9493 (mm) cc_final: 0.9127 (mm) REVERT: T 11 ILE cc_start: 0.9068 (tt) cc_final: 0.8790 (tp) REVERT: jA 112 LEU cc_start: 0.9446 (mm) cc_final: 0.9135 (mm) REVERT: oA 215 GLN cc_start: 0.8709 (mt0) cc_final: 0.8473 (mt0) REVERT: qA 408 TYR cc_start: 0.8840 (t80) cc_final: 0.8563 (t80) outliers start: 2 outliers final: 0 residues processed: 637 average time/residue: 0.0849 time to fit residues: 84.5555 Evaluate side-chains 562 residues out of total 1155 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 562 time to evaluate : 0.475 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 29 optimal weight: 6.9990 chunk 70 optimal weight: 5.9990 chunk 32 optimal weight: 0.9990 chunk 99 optimal weight: 7.9990 chunk 98 optimal weight: 5.9990 chunk 61 optimal weight: 0.5980 chunk 87 optimal weight: 5.9990 chunk 80 optimal weight: 0.9990 chunk 81 optimal weight: 0.8980 chunk 14 optimal weight: 0.7980 chunk 78 optimal weight: 6.9990 overall best weight: 0.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: W 215 GLN X 315 GLN Z 115 GLN i 215 GLN k 415 GLN E 15 GLN m 215 GLN y 215 GLN 2 215 GLN 6 215 GLN 7 315 GLN AA 215 GLN IA 215 GLN JA 315 GLN XA 115 GLN YA 215 GLN S 15 GLN gA 215 GLN T 15 GLN lA 315 GLN U 15 GLN Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3159 r_free = 0.3159 target = 0.059681 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2932 r_free = 0.2932 target = 0.051584 restraints weight = 47541.691| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.2991 r_free = 0.2991 target = 0.053658 restraints weight = 28324.308| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3032 r_free = 0.3032 target = 0.055037 restraints weight = 18636.068| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3061 r_free = 0.3061 target = 0.056033 restraints weight = 13130.348| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3083 r_free = 0.3083 target = 0.056774 restraints weight = 9546.206| |-----------------------------------------------------------------------------| r_work (final): 0.3067 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8808 moved from start: 0.5683 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 12915 Z= 0.114 Angle : 0.517 5.957 17325 Z= 0.258 Chirality : 0.041 0.141 1995 Planarity : 0.002 0.015 2310 Dihedral : 3.342 25.009 1890 Min Nonbonded Distance : 2.602 Molprobity Statistics. All-atom Clashscore : 4.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 0.69 % Allowed : 9.78 % Favored : 89.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.16 (0.25), residues: 1365 helix: 2.10 (0.15), residues: 1365 sheet: None (None), residues: 0 loop : None (None), residues: 0 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG 7 306 TYR 0.030 0.002 TYRZA 308 Details of bonding type rmsd covalent geometry : bond 0.00289 (12915) covalent geometry : angle 0.51748 (17325) hydrogen bonds : bond 0.02545 ( 1050) hydrogen bonds : angle 3.44546 ( 3150) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2730 Ramachandran restraints generated. 1365 Oldfield, 0 Emsley, 1365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2730 Ramachandran restraints generated. 1365 Oldfield, 0 Emsley, 1365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 643 residues out of total 1155 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 635 time to evaluate : 0.446 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 3 GLU cc_start: 0.8571 (tp30) cc_final: 0.7398 (tp30) REVERT: V 108 TYR cc_start: 0.9064 (t80) cc_final: 0.8814 (t80) REVERT: W 212 LEU cc_start: 0.9580 (mm) cc_final: 0.9317 (mm) REVERT: Y 408 TYR cc_start: 0.9089 (t80) cc_final: 0.8730 (t80) REVERT: Y 412 LEU cc_start: 0.9437 (mm) cc_final: 0.9204 (mm) REVERT: B 3 GLU cc_start: 0.8629 (tp30) cc_final: 0.7523 (tp30) REVERT: B 12 LEU cc_start: 0.9436 (mm) cc_final: 0.9205 (mm) REVERT: Z 115 GLN cc_start: 0.8939 (OUTLIER) cc_final: 0.8670 (tp40) REVERT: c 415 GLN cc_start: 0.8766 (mt0) cc_final: 0.8354 (mt0) REVERT: C 3 GLU cc_start: 0.8564 (mm-30) cc_final: 0.7734 (tp30) REVERT: C 8 TYR cc_start: 0.9048 (t80) cc_final: 0.8454 (t80) REVERT: C 12 LEU cc_start: 0.9430 (mm) cc_final: 0.9214 (mm) REVERT: d 108 TYR cc_start: 0.9173 (t80) cc_final: 0.8488 (t80) REVERT: d 112 LEU cc_start: 0.9594 (mm) cc_final: 0.9329 (mm) REVERT: e 203 GLU cc_start: 0.8955 (mm-30) cc_final: 0.8542 (mp0) REVERT: e 208 TYR cc_start: 0.8648 (t80) cc_final: 0.7995 (t80) REVERT: e 215 GLN cc_start: 0.8881 (mt0) cc_final: 0.8551 (tt0) REVERT: f 308 TYR cc_start: 0.9013 (t80) cc_final: 0.8560 (t80) REVERT: g 408 TYR cc_start: 0.8836 (t80) cc_final: 0.8286 (t80) REVERT: h 111 ILE cc_start: 0.9484 (mt) cc_final: 0.9284 (mt) REVERT: i 208 TYR cc_start: 0.9017 (t80) cc_final: 0.8553 (t80) REVERT: j 303 GLU cc_start: 0.9005 (mm-30) cc_final: 0.8698 (mm-30) REVERT: j 308 TYR cc_start: 0.9013 (t80) cc_final: 0.8707 (t80) REVERT: k 408 TYR cc_start: 0.9067 (t80) cc_final: 0.8548 (t80) REVERT: E 15 GLN cc_start: 0.9197 (OUTLIER) cc_final: 0.7022 (tp40) REVERT: l 115 GLN cc_start: 0.8766 (mt0) cc_final: 0.8485 (tt0) REVERT: m 208 TYR cc_start: 0.8857 (t80) cc_final: 0.8591 (t80) REVERT: n 308 TYR cc_start: 0.8869 (t80) cc_final: 0.8647 (t80) REVERT: F 3 GLU cc_start: 0.8765 (mm-30) cc_final: 0.7836 (mm-30) REVERT: p 108 TYR cc_start: 0.8843 (t80) cc_final: 0.8633 (t80) REVERT: q 208 TYR cc_start: 0.8812 (t80) cc_final: 0.8583 (t80) REVERT: r 308 TYR cc_start: 0.8719 (t80) cc_final: 0.8450 (t80) REVERT: s 411 ILE cc_start: 0.9389 (mt) cc_final: 0.9171 (mt) REVERT: t 108 TYR cc_start: 0.9035 (t80) cc_final: 0.8641 (t80) REVERT: t 112 LEU cc_start: 0.9498 (mm) cc_final: 0.9066 (mm) REVERT: u 208 TYR cc_start: 0.9077 (t80) cc_final: 0.8628 (t80) REVERT: v 315 GLN cc_start: 0.8708 (mt0) cc_final: 0.8380 (mt0) REVERT: x 115 GLN cc_start: 0.9004 (mt0) cc_final: 0.8800 (mt0) REVERT: y 203 GLU cc_start: 0.8492 (tp30) cc_final: 0.8231 (mm-30) REVERT: y 212 LEU cc_start: 0.9527 (mm) cc_final: 0.9264 (mm) REVERT: y 215 GLN cc_start: 0.9291 (OUTLIER) cc_final: 0.7129 (tp40) REVERT: z 308 TYR cc_start: 0.8589 (t80) cc_final: 0.8388 (t80) REVERT: z 315 GLN cc_start: 0.9009 (mt0) cc_final: 0.8275 (mt0) REVERT: 0 403 GLU cc_start: 0.8533 (tp30) cc_final: 0.8145 (tp30) REVERT: I 8 TYR cc_start: 0.9186 (t80) cc_final: 0.8711 (t80) REVERT: I 12 LEU cc_start: 0.9544 (mm) cc_final: 0.9285 (mm) REVERT: 1 108 TYR cc_start: 0.8723 (t80) cc_final: 0.8474 (t80) REVERT: J 3 GLU cc_start: 0.8780 (mm-30) cc_final: 0.8540 (mm-30) REVERT: J 8 TYR cc_start: 0.8576 (t80) cc_final: 0.8058 (t80) REVERT: 5 115 GLN cc_start: 0.8752 (mt0) cc_final: 0.8419 (tt0) REVERT: 6 208 TYR cc_start: 0.8856 (t80) cc_final: 0.8217 (t80) REVERT: 7 308 TYR cc_start: 0.8644 (t80) cc_final: 0.7962 (t80) REVERT: 8 408 TYR cc_start: 0.8871 (t80) cc_final: 0.7785 (t80) REVERT: K 3 GLU cc_start: 0.8908 (mm-30) cc_final: 0.8673 (mm-30) REVERT: K 8 TYR cc_start: 0.9055 (t80) cc_final: 0.8621 (t80) REVERT: K 15 GLN cc_start: 0.8684 (mt0) cc_final: 0.8410 (mt0) REVERT: BA 303 GLU cc_start: 0.9012 (mm-30) cc_final: 0.8801 (mm-30) REVERT: BA 315 GLN cc_start: 0.8647 (mt0) cc_final: 0.8389 (tt0) REVERT: CA 412 LEU cc_start: 0.9447 (mm) cc_final: 0.9238 (mm) REVERT: L 8 TYR cc_start: 0.9097 (t80) cc_final: 0.8664 (t80) REVERT: L 12 LEU cc_start: 0.9567 (mm) cc_final: 0.9286 (mm) REVERT: DA 108 TYR cc_start: 0.9019 (t80) cc_final: 0.8686 (t80) REVERT: EA 208 TYR cc_start: 0.9101 (t80) cc_final: 0.8768 (t80) REVERT: FA 308 TYR cc_start: 0.9089 (t80) cc_final: 0.8490 (t80) REVERT: FA 312 LEU cc_start: 0.9416 (mm) cc_final: 0.9120 (mm) REVERT: GA 408 TYR cc_start: 0.9011 (t80) cc_final: 0.8514 (t80) REVERT: HA 115 GLN cc_start: 0.8859 (mt0) cc_final: 0.8604 (mt0) REVERT: IA 212 LEU cc_start: 0.9553 (mm) cc_final: 0.9318 (mm) REVERT: IA 215 GLN cc_start: 0.9285 (OUTLIER) cc_final: 0.7701 (tp-100) REVERT: JA 312 LEU cc_start: 0.9522 (mm) cc_final: 0.9285 (mm) REVERT: N 3 GLU cc_start: 0.8642 (tp30) cc_final: 0.8364 (tp30) REVERT: O 8 TYR cc_start: 0.8990 (t80) cc_final: 0.8742 (t80) REVERT: QA 203 GLU cc_start: 0.8717 (tp30) cc_final: 0.8385 (mm-30) REVERT: RA 303 GLU cc_start: 0.8667 (tp30) cc_final: 0.8163 (mm-30) REVERT: RA 308 TYR cc_start: 0.9057 (t80) cc_final: 0.8816 (t80) REVERT: RA 312 LEU cc_start: 0.9552 (mm) cc_final: 0.9281 (mm) REVERT: SA 408 TYR cc_start: 0.8944 (t80) cc_final: 0.8672 (t80) REVERT: P 15 GLN cc_start: 0.8793 (mt0) cc_final: 0.8565 (mt0) REVERT: VA 312 LEU cc_start: 0.9577 (mm) cc_final: 0.9299 (mm) REVERT: Q 3 GLU cc_start: 0.8459 (mm-30) cc_final: 0.8240 (tp30) REVERT: Q 8 TYR cc_start: 0.8820 (t80) cc_final: 0.8210 (t80) REVERT: XA 108 TYR cc_start: 0.9048 (t80) cc_final: 0.8131 (t80) REVERT: XA 112 LEU cc_start: 0.9480 (mm) cc_final: 0.9075 (mm) REVERT: YA 208 TYR cc_start: 0.9066 (t80) cc_final: 0.8575 (t80) REVERT: YA 212 LEU cc_start: 0.9528 (mm) cc_final: 0.9270 (mm) REVERT: YA 215 GLN cc_start: 0.8679 (OUTLIER) cc_final: 0.8390 (tp40) REVERT: ZA 308 TYR cc_start: 0.8614 (t80) cc_final: 0.8276 (t80) REVERT: aA 408 TYR cc_start: 0.8628 (t80) cc_final: 0.7989 (t80) REVERT: R 3 GLU cc_start: 0.8588 (mm-30) cc_final: 0.8142 (tp30) REVERT: R 8 TYR cc_start: 0.9160 (t80) cc_final: 0.8559 (t80) REVERT: R 12 LEU cc_start: 0.9616 (mm) cc_final: 0.9123 (mm) REVERT: T 11 ILE cc_start: 0.8794 (tt) cc_final: 0.8508 (tp) REVERT: jA 112 LEU cc_start: 0.9290 (mm) cc_final: 0.9037 (mm) REVERT: U 3 GLU cc_start: 0.8697 (tp30) cc_final: 0.7847 (mm-30) REVERT: U 15 GLN cc_start: 0.9293 (OUTLIER) cc_final: 0.6674 (tp40) REVERT: qA 415 GLN cc_start: 0.8812 (mt0) cc_final: 0.8393 (mt0) outliers start: 8 outliers final: 0 residues processed: 643 average time/residue: 0.0832 time to fit residues: 84.0670 Evaluate side-chains 590 residues out of total 1155 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 584 time to evaluate : 0.519 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 88 optimal weight: 3.9990 chunk 35 optimal weight: 3.9990 chunk 96 optimal weight: 8.9990 chunk 1 optimal weight: 7.9990 chunk 70 optimal weight: 0.9980 chunk 23 optimal weight: 10.0000 chunk 74 optimal weight: 6.9990 chunk 19 optimal weight: 5.9990 chunk 76 optimal weight: 4.9990 chunk 80 optimal weight: 2.9990 chunk 0 optimal weight: 10.0000 overall best weight: 3.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: a 215 GLN d 115 GLN p 115 GLN QA 215 GLN S 15 GLN gA 215 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2982 r_free = 0.2982 target = 0.048727 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2704 r_free = 0.2704 target = 0.040803 restraints weight = 49064.553| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.2766 r_free = 0.2766 target = 0.042583 restraints weight = 30875.940| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.2807 r_free = 0.2807 target = 0.043789 restraints weight = 21225.235| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.2841 r_free = 0.2841 target = 0.044770 restraints weight = 15670.096| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.2868 r_free = 0.2868 target = 0.045511 restraints weight = 11821.555| |-----------------------------------------------------------------------------| r_work (final): 0.2876 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8941 moved from start: 0.5471 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 12915 Z= 0.235 Angle : 0.559 5.426 17325 Z= 0.307 Chirality : 0.046 0.142 1995 Planarity : 0.002 0.017 2310 Dihedral : 3.124 16.181 1890 Min Nonbonded Distance : 2.569 Molprobity Statistics. All-atom Clashscore : 6.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 0.17 % Allowed : 9.09 % Favored : 90.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.97 (0.25), residues: 1365 helix: 1.98 (0.16), residues: 1365 sheet: None (None), residues: 0 loop : None (None), residues: 0 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARGnA 110 TYR 0.025 0.002 TYR 3 308 Details of bonding type rmsd covalent geometry : bond 0.00515 (12915) covalent geometry : angle 0.55909 (17325) hydrogen bonds : bond 0.04026 ( 1050) hydrogen bonds : angle 4.34622 ( 3150) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2730 Ramachandran restraints generated. 1365 Oldfield, 0 Emsley, 1365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2730 Ramachandran restraints generated. 1365 Oldfield, 0 Emsley, 1365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 597 residues out of total 1155 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 595 time to evaluate : 0.369 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 12 LEU cc_start: 0.9495 (mm) cc_final: 0.9284 (mm) REVERT: V 108 TYR cc_start: 0.9126 (t80) cc_final: 0.8771 (t80) REVERT: V 112 LEU cc_start: 0.9545 (mm) cc_final: 0.9273 (mm) REVERT: W 212 LEU cc_start: 0.9623 (mm) cc_final: 0.9323 (mm) REVERT: Y 408 TYR cc_start: 0.9149 (t80) cc_final: 0.8779 (t80) REVERT: B 3 GLU cc_start: 0.8641 (tp30) cc_final: 0.6944 (tp30) REVERT: B 12 LEU cc_start: 0.9564 (mm) cc_final: 0.9231 (mm) REVERT: a 212 LEU cc_start: 0.9538 (mm) cc_final: 0.9219 (mm) REVERT: b 303 GLU cc_start: 0.9039 (mm-30) cc_final: 0.8536 (mm-30) REVERT: c 415 GLN cc_start: 0.8971 (mt0) cc_final: 0.8454 (mt0) REVERT: C 8 TYR cc_start: 0.9137 (t80) cc_final: 0.8304 (t80) REVERT: C 12 LEU cc_start: 0.9435 (mm) cc_final: 0.9178 (mm) REVERT: d 108 TYR cc_start: 0.8983 (t80) cc_final: 0.8556 (t80) REVERT: e 208 TYR cc_start: 0.8755 (t80) cc_final: 0.8170 (t80) REVERT: e 215 GLN cc_start: 0.8936 (mt0) cc_final: 0.8526 (mt0) REVERT: f 308 TYR cc_start: 0.9109 (t80) cc_final: 0.8565 (t80) REVERT: g 403 GLU cc_start: 0.9083 (mp0) cc_final: 0.8827 (mp0) REVERT: g 408 TYR cc_start: 0.8832 (t80) cc_final: 0.8314 (t80) REVERT: D 3 GLU cc_start: 0.9006 (mp0) cc_final: 0.8746 (mm-30) REVERT: i 208 TYR cc_start: 0.8985 (t80) cc_final: 0.8504 (t80) REVERT: j 303 GLU cc_start: 0.9104 (mm-30) cc_final: 0.8897 (mm-30) REVERT: j 308 TYR cc_start: 0.9052 (t80) cc_final: 0.8561 (t80) REVERT: j 312 LEU cc_start: 0.9516 (mm) cc_final: 0.9127 (mm) REVERT: k 408 TYR cc_start: 0.9112 (t80) cc_final: 0.8748 (t80) REVERT: E 3 GLU cc_start: 0.8700 (mm-30) cc_final: 0.8003 (mm-30) REVERT: l 103 GLU cc_start: 0.8993 (mm-30) cc_final: 0.8554 (mm-30) REVERT: l 115 GLN cc_start: 0.8827 (mt0) cc_final: 0.8461 (mt0) REVERT: m 208 TYR cc_start: 0.8888 (t80) cc_final: 0.8661 (t80) REVERT: F 3 GLU cc_start: 0.9121 (mm-30) cc_final: 0.8883 (mm-30) REVERT: p 108 TYR cc_start: 0.8862 (t80) cc_final: 0.8567 (t80) REVERT: q 208 TYR cc_start: 0.8881 (t80) cc_final: 0.8612 (t80) REVERT: r 308 TYR cc_start: 0.8826 (t80) cc_final: 0.8527 (t80) REVERT: G 15 GLN cc_start: 0.8758 (mt0) cc_final: 0.8429 (mt0) REVERT: t 103 GLU cc_start: 0.8687 (mm-30) cc_final: 0.8160 (mm-30) REVERT: t 112 LEU cc_start: 0.9533 (mm) cc_final: 0.9127 (mm) REVERT: u 208 TYR cc_start: 0.9212 (t80) cc_final: 0.8959 (t80) REVERT: u 212 LEU cc_start: 0.9447 (mm) cc_final: 0.9188 (mm) REVERT: x 111 ILE cc_start: 0.9609 (mt) cc_final: 0.9077 (mp) REVERT: x 112 LEU cc_start: 0.9358 (mm) cc_final: 0.8677 (mm) REVERT: x 115 GLN cc_start: 0.9208 (mt0) cc_final: 0.8602 (mt0) REVERT: y 212 LEU cc_start: 0.9574 (mm) cc_final: 0.9269 (mm) REVERT: z 303 GLU cc_start: 0.8995 (mm-30) cc_final: 0.8593 (mm-30) REVERT: z 308 TYR cc_start: 0.8710 (t80) cc_final: 0.8409 (t80) REVERT: z 315 GLN cc_start: 0.9014 (mt0) cc_final: 0.8693 (mt0) REVERT: 0 408 TYR cc_start: 0.9080 (t80) cc_final: 0.8688 (t80) REVERT: 0 412 LEU cc_start: 0.9341 (mm) cc_final: 0.9058 (mm) REVERT: I 3 GLU cc_start: 0.8655 (mm-30) cc_final: 0.7573 (mm-30) REVERT: I 12 LEU cc_start: 0.9555 (mm) cc_final: 0.9289 (mm) REVERT: 1 112 LEU cc_start: 0.9644 (mm) cc_final: 0.9389 (mm) REVERT: 3 303 GLU cc_start: 0.9047 (mm-30) cc_final: 0.8717 (mm-30) REVERT: 4 415 GLN cc_start: 0.8884 (mt0) cc_final: 0.8452 (mt0) REVERT: 5 115 GLN cc_start: 0.8898 (mt0) cc_final: 0.8583 (tt0) REVERT: 7 303 GLU cc_start: 0.8996 (mm-30) cc_final: 0.8477 (mm-30) REVERT: 7 308 TYR cc_start: 0.8804 (t80) cc_final: 0.8521 (t80) REVERT: 8 408 TYR cc_start: 0.8926 (t80) cc_final: 0.7873 (t80) REVERT: K 8 TYR cc_start: 0.9056 (t80) cc_final: 0.8465 (t80) REVERT: K 12 LEU cc_start: 0.9347 (mm) cc_final: 0.9072 (mm) REVERT: 9 112 LEU cc_start: 0.9492 (mm) cc_final: 0.9230 (mm) REVERT: AA 208 TYR cc_start: 0.8837 (t80) cc_final: 0.8586 (t80) REVERT: BA 312 LEU cc_start: 0.9403 (mm) cc_final: 0.9152 (mm) REVERT: CA 412 LEU cc_start: 0.9548 (mm) cc_final: 0.9282 (mm) REVERT: L 8 TYR cc_start: 0.9186 (t80) cc_final: 0.8599 (t80) REVERT: L 12 LEU cc_start: 0.9577 (mm) cc_final: 0.9254 (mm) REVERT: DA 108 TYR cc_start: 0.9090 (t80) cc_final: 0.8659 (t80) REVERT: DA 112 LEU cc_start: 0.9634 (mm) cc_final: 0.9381 (mm) REVERT: EA 208 TYR cc_start: 0.9156 (t80) cc_final: 0.8723 (t80) REVERT: FA 308 TYR cc_start: 0.9170 (t80) cc_final: 0.8510 (t80) REVERT: FA 312 LEU cc_start: 0.9477 (mm) cc_final: 0.9123 (mm) REVERT: GA 408 TYR cc_start: 0.9085 (t80) cc_final: 0.8548 (t80) REVERT: M 12 LEU cc_start: 0.9518 (mm) cc_final: 0.9228 (mm) REVERT: HA 103 GLU cc_start: 0.8649 (mm-30) cc_final: 0.8406 (tp30) REVERT: HA 112 LEU cc_start: 0.9486 (mm) cc_final: 0.9277 (mm) REVERT: HA 115 GLN cc_start: 0.8985 (mt0) cc_final: 0.8639 (mt0) REVERT: IA 212 LEU cc_start: 0.9520 (mm) cc_final: 0.9245 (mm) REVERT: JA 303 GLU cc_start: 0.8963 (mm-30) cc_final: 0.8366 (mm-30) REVERT: N 3 GLU cc_start: 0.8579 (tp30) cc_final: 0.8243 (tp30) REVERT: NA 303 GLU cc_start: 0.8656 (tp30) cc_final: 0.8268 (mm-30) REVERT: NA 315 GLN cc_start: 0.8952 (mt0) cc_final: 0.8660 (mt0) REVERT: OA 412 LEU cc_start: 0.9490 (mm) cc_final: 0.9181 (mm) REVERT: O 8 TYR cc_start: 0.9058 (t80) cc_final: 0.8713 (t80) REVERT: O 12 LEU cc_start: 0.9454 (mm) cc_final: 0.9199 (mm) REVERT: PA 108 TYR cc_start: 0.9176 (t80) cc_final: 0.8845 (t80) REVERT: QA 208 TYR cc_start: 0.9107 (t80) cc_final: 0.8712 (t80) REVERT: QA 212 LEU cc_start: 0.9586 (mm) cc_final: 0.9300 (mm) REVERT: RA 308 TYR cc_start: 0.9131 (t80) cc_final: 0.8793 (t80) REVERT: RA 312 LEU cc_start: 0.9566 (mm) cc_final: 0.9306 (mm) REVERT: SA 403 GLU cc_start: 0.8811 (mm-30) cc_final: 0.8438 (mm-30) REVERT: SA 408 TYR cc_start: 0.9021 (t80) cc_final: 0.8709 (t80) REVERT: P 3 GLU cc_start: 0.8699 (mm-30) cc_final: 0.8461 (mm-30) REVERT: P 15 GLN cc_start: 0.8956 (mt0) cc_final: 0.8682 (mt0) REVERT: UA 212 LEU cc_start: 0.9538 (mm) cc_final: 0.9328 (mm) REVERT: VA 312 LEU cc_start: 0.9609 (mm) cc_final: 0.9331 (mm) REVERT: Q 3 GLU cc_start: 0.8655 (mm-30) cc_final: 0.8421 (mm-30) REVERT: Q 8 TYR cc_start: 0.8865 (t80) cc_final: 0.8189 (t80) REVERT: YA 208 TYR cc_start: 0.9152 (t80) cc_final: 0.8418 (t80) REVERT: ZA 303 GLU cc_start: 0.8969 (mm-30) cc_final: 0.8521 (mm-30) REVERT: ZA 308 TYR cc_start: 0.8835 (t80) cc_final: 0.8024 (t80) REVERT: aA 408 TYR cc_start: 0.8777 (t80) cc_final: 0.7965 (t80) REVERT: R 8 TYR cc_start: 0.9201 (t80) cc_final: 0.8759 (t80) REVERT: R 12 LEU cc_start: 0.9625 (mm) cc_final: 0.9196 (mm) REVERT: cA 212 LEU cc_start: 0.9648 (mm) cc_final: 0.9399 (mm) REVERT: S 3 GLU cc_start: 0.8758 (mm-30) cc_final: 0.8477 (mm-30) REVERT: fA 108 TYR cc_start: 0.9071 (t80) cc_final: 0.8830 (t80) REVERT: iA 403 GLU cc_start: 0.9029 (mm-30) cc_final: 0.8716 (mm-30) REVERT: T 3 GLU cc_start: 0.8951 (mm-30) cc_final: 0.8622 (mm-30) REVERT: T 11 ILE cc_start: 0.9196 (tt) cc_final: 0.8904 (tp) REVERT: jA 112 LEU cc_start: 0.9420 (mm) cc_final: 0.9166 (mm) REVERT: lA 312 LEU cc_start: 0.9437 (mt) cc_final: 0.9143 (mp) REVERT: mA 408 TYR cc_start: 0.9096 (t80) cc_final: 0.8671 (t80) REVERT: mA 411 ILE cc_start: 0.9296 (tt) cc_final: 0.9039 (tp) REVERT: oA 203 GLU cc_start: 0.9254 (mm-30) cc_final: 0.8984 (mm-30) REVERT: pA 303 GLU cc_start: 0.8855 (tp30) cc_final: 0.8527 (mm-30) REVERT: qA 403 GLU cc_start: 0.8839 (mm-30) cc_final: 0.8631 (mm-30) outliers start: 2 outliers final: 0 residues processed: 597 average time/residue: 0.0837 time to fit residues: 78.7278 Evaluate side-chains 559 residues out of total 1155 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 559 time to evaluate : 0.362 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 74 optimal weight: 6.9990 chunk 53 optimal weight: 5.9990 chunk 37 optimal weight: 0.9980 chunk 95 optimal weight: 0.5980 chunk 17 optimal weight: 1.9990 chunk 82 optimal weight: 0.8980 chunk 52 optimal weight: 1.9990 chunk 18 optimal weight: 7.9990 chunk 21 optimal weight: 4.9990 chunk 36 optimal weight: 4.9990 chunk 78 optimal weight: 1.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: g 415 GLN w 415 GLN J 15 GLN ** 8 415 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 15 GLN MA 215 GLN PA 115 GLN RA 315 GLN gA 215 GLN hA 315 GLN mA 415 GLN U 15 GLN oA 215 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3136 r_free = 0.3136 target = 0.058164 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2896 r_free = 0.2896 target = 0.049851 restraints weight = 47610.950| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.2956 r_free = 0.2956 target = 0.051869 restraints weight = 29357.405| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.2998 r_free = 0.2998 target = 0.053263 restraints weight = 19780.386| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3027 r_free = 0.3027 target = 0.054265 restraints weight = 14163.147| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3050 r_free = 0.3050 target = 0.055030 restraints weight = 10466.405| |-----------------------------------------------------------------------------| r_work (final): 0.3034 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8860 moved from start: 0.6081 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 12915 Z= 0.130 Angle : 0.554 4.900 17325 Z= 0.279 Chirality : 0.041 0.161 1995 Planarity : 0.002 0.013 2310 Dihedral : 3.373 23.336 1890 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 5.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 0.26 % Allowed : 1.56 % Favored : 98.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.58 (0.24), residues: 1365 helix: 2.36 (0.15), residues: 1365 sheet: None (None), residues: 0 loop : None (None), residues: 0 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARGfA 106 TYR 0.024 0.002 TYRZA 308 Details of bonding type rmsd covalent geometry : bond 0.00333 (12915) covalent geometry : angle 0.55390 (17325) hydrogen bonds : bond 0.02653 ( 1050) hydrogen bonds : angle 3.63482 ( 3150) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2730 Ramachandran restraints generated. 1365 Oldfield, 0 Emsley, 1365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2730 Ramachandran restraints generated. 1365 Oldfield, 0 Emsley, 1365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 614 residues out of total 1155 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 611 time to evaluate : 0.527 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 12 LEU cc_start: 0.9524 (mm) cc_final: 0.9293 (mm) REVERT: V 108 TYR cc_start: 0.9081 (t80) cc_final: 0.8797 (t80) REVERT: V 112 LEU cc_start: 0.9551 (mm) cc_final: 0.9277 (mm) REVERT: W 212 LEU cc_start: 0.9599 (mm) cc_final: 0.9365 (mm) REVERT: Y 412 LEU cc_start: 0.9556 (mm) cc_final: 0.9322 (mm) REVERT: B 3 GLU cc_start: 0.8617 (tp30) cc_final: 0.7596 (tp30) REVERT: B 12 LEU cc_start: 0.9555 (mm) cc_final: 0.9227 (mm) REVERT: a 212 LEU cc_start: 0.9532 (mm) cc_final: 0.9234 (mm) REVERT: b 303 GLU cc_start: 0.9136 (mm-30) cc_final: 0.8586 (mm-30) REVERT: b 312 LEU cc_start: 0.9373 (mm) cc_final: 0.9156 (mm) REVERT: c 415 GLN cc_start: 0.8942 (mt0) cc_final: 0.8386 (mt0) REVERT: C 8 TYR cc_start: 0.9068 (t80) cc_final: 0.8384 (t80) REVERT: d 108 TYR cc_start: 0.9017 (t80) cc_final: 0.8263 (t80) REVERT: d 112 LEU cc_start: 0.9564 (mm) cc_final: 0.9307 (mm) REVERT: e 208 TYR cc_start: 0.8714 (t80) cc_final: 0.8123 (t80) REVERT: e 215 GLN cc_start: 0.8953 (mt0) cc_final: 0.8733 (mt0) REVERT: f 308 TYR cc_start: 0.9058 (t80) cc_final: 0.8621 (t80) REVERT: g 403 GLU cc_start: 0.9105 (mp0) cc_final: 0.8828 (mp0) REVERT: D 3 GLU cc_start: 0.9021 (mp0) cc_final: 0.8821 (mp0) REVERT: i 208 TYR cc_start: 0.8950 (t80) cc_final: 0.8455 (t80) REVERT: j 303 GLU cc_start: 0.9094 (mm-30) cc_final: 0.8886 (mm-30) REVERT: j 308 TYR cc_start: 0.9001 (t80) cc_final: 0.8614 (t80) REVERT: j 312 LEU cc_start: 0.9494 (mm) cc_final: 0.9142 (mm) REVERT: k 408 TYR cc_start: 0.9007 (t80) cc_final: 0.8617 (t80) REVERT: l 103 GLU cc_start: 0.9038 (mm-30) cc_final: 0.8580 (mm-30) REVERT: l 108 TYR cc_start: 0.8913 (t80) cc_final: 0.8636 (t80) REVERT: l 111 ILE cc_start: 0.9498 (tp) cc_final: 0.9196 (pt) REVERT: m 208 TYR cc_start: 0.8844 (t80) cc_final: 0.8507 (t80) REVERT: F 3 GLU cc_start: 0.9100 (mm-30) cc_final: 0.8802 (mm-30) REVERT: p 108 TYR cc_start: 0.8820 (t80) cc_final: 0.8509 (t80) REVERT: q 208 TYR cc_start: 0.8795 (t80) cc_final: 0.8453 (t80) REVERT: t 103 GLU cc_start: 0.8772 (mm-30) cc_final: 0.8234 (mm-30) REVERT: t 112 LEU cc_start: 0.9547 (mm) cc_final: 0.9098 (mm) REVERT: u 208 TYR cc_start: 0.9198 (t80) cc_final: 0.8805 (t80) REVERT: u 212 LEU cc_start: 0.9431 (mm) cc_final: 0.9223 (mm) REVERT: v 315 GLN cc_start: 0.8865 (mt0) cc_final: 0.8558 (mt0) REVERT: H 12 LEU cc_start: 0.9584 (mm) cc_final: 0.9320 (mm) REVERT: y 212 LEU cc_start: 0.9592 (mm) cc_final: 0.9242 (mm) REVERT: z 303 GLU cc_start: 0.9018 (mm-30) cc_final: 0.8722 (mm-30) REVERT: z 308 TYR cc_start: 0.8592 (t80) cc_final: 0.7722 (t80) REVERT: z 315 GLN cc_start: 0.8993 (mt0) cc_final: 0.8562 (tt0) REVERT: 0 403 GLU cc_start: 0.8528 (tp30) cc_final: 0.8065 (tp30) REVERT: 0 408 TYR cc_start: 0.9015 (t80) cc_final: 0.8556 (t80) REVERT: 0 412 LEU cc_start: 0.9288 (mm) cc_final: 0.8791 (mm) REVERT: 0 415 GLN cc_start: 0.9132 (mt0) cc_final: 0.8372 (mt0) REVERT: I 8 TYR cc_start: 0.8988 (t80) cc_final: 0.8745 (t80) REVERT: I 12 LEU cc_start: 0.9681 (mm) cc_final: 0.9133 (mm) REVERT: 2 208 TYR cc_start: 0.8679 (t80) cc_final: 0.8451 (t80) REVERT: J 15 GLN cc_start: 0.9272 (OUTLIER) cc_final: 0.6260 (tp40) REVERT: 5 115 GLN cc_start: 0.8860 (mt0) cc_final: 0.8559 (mt0) REVERT: 7 303 GLU cc_start: 0.9007 (mm-30) cc_final: 0.8619 (mm-30) REVERT: 7 308 TYR cc_start: 0.8704 (t80) cc_final: 0.7786 (t80) REVERT: 8 408 TYR cc_start: 0.8911 (t80) cc_final: 0.7881 (t80) REVERT: K 3 GLU cc_start: 0.8979 (mm-30) cc_final: 0.7929 (mm-30) REVERT: K 8 TYR cc_start: 0.8891 (t80) cc_final: 0.8512 (t80) REVERT: K 15 GLN cc_start: 0.8818 (mt0) cc_final: 0.8569 (mt0) REVERT: 9 112 LEU cc_start: 0.9473 (mm) cc_final: 0.9268 (mm) REVERT: AA 208 TYR cc_start: 0.8733 (t80) cc_final: 0.8387 (t80) REVERT: BA 303 GLU cc_start: 0.9136 (mm-30) cc_final: 0.8934 (mm-30) REVERT: BA 315 GLN cc_start: 0.8834 (mt0) cc_final: 0.8619 (tt0) REVERT: CA 412 LEU cc_start: 0.9562 (mm) cc_final: 0.9282 (mm) REVERT: CA 415 GLN cc_start: 0.8971 (mt0) cc_final: 0.8379 (tt0) REVERT: L 8 TYR cc_start: 0.9080 (t80) cc_final: 0.8519 (t80) REVERT: L 12 LEU cc_start: 0.9536 (mm) cc_final: 0.9240 (mm) REVERT: DA 108 TYR cc_start: 0.9045 (t80) cc_final: 0.8636 (t80) REVERT: DA 112 LEU cc_start: 0.9632 (mm) cc_final: 0.9428 (mm) REVERT: EA 208 TYR cc_start: 0.9073 (t80) cc_final: 0.8674 (t80) REVERT: FA 308 TYR cc_start: 0.9118 (t80) cc_final: 0.8412 (t80) REVERT: FA 312 LEU cc_start: 0.9435 (mm) cc_final: 0.9106 (mm) REVERT: GA 408 TYR cc_start: 0.8980 (t80) cc_final: 0.8512 (t80) REVERT: M 12 LEU cc_start: 0.9538 (mm) cc_final: 0.9318 (mm) REVERT: M 15 GLN cc_start: 0.8788 (mt0) cc_final: 0.8391 (tt0) REVERT: HA 103 GLU cc_start: 0.8639 (mm-30) cc_final: 0.7481 (mm-30) REVERT: HA 115 GLN cc_start: 0.8972 (mt0) cc_final: 0.8642 (mt0) REVERT: JA 303 GLU cc_start: 0.8972 (mm-30) cc_final: 0.8493 (mm-30) REVERT: KA 403 GLU cc_start: 0.8708 (mm-30) cc_final: 0.8279 (mm-30) REVERT: N 12 LEU cc_start: 0.9629 (mm) cc_final: 0.9377 (mm) REVERT: MA 212 LEU cc_start: 0.9604 (mm) cc_final: 0.9333 (mm) REVERT: OA 412 LEU cc_start: 0.9466 (mm) cc_final: 0.9203 (mm) REVERT: O 8 TYR cc_start: 0.8932 (t80) cc_final: 0.8616 (t80) REVERT: O 12 LEU cc_start: 0.9440 (mm) cc_final: 0.9183 (mm) REVERT: PA 115 GLN cc_start: 0.9339 (OUTLIER) cc_final: 0.7627 (tp40) REVERT: QA 208 TYR cc_start: 0.9029 (t80) cc_final: 0.8784 (t80) REVERT: QA 212 LEU cc_start: 0.9542 (mm) cc_final: 0.9271 (mm) REVERT: RA 303 GLU cc_start: 0.8905 (mm-30) cc_final: 0.8475 (mm-30) REVERT: RA 308 TYR cc_start: 0.9124 (t80) cc_final: 0.8869 (t80) REVERT: SA 408 TYR cc_start: 0.8940 (t80) cc_final: 0.8666 (t80) REVERT: P 3 GLU cc_start: 0.9016 (mm-30) cc_final: 0.7976 (mm-30) REVERT: P 15 GLN cc_start: 0.8898 (mt0) cc_final: 0.8597 (mt0) REVERT: TA 112 LEU cc_start: 0.9602 (mm) cc_final: 0.9383 (mm) REVERT: VA 312 LEU cc_start: 0.9586 (mm) cc_final: 0.9324 (mm) REVERT: Q 3 GLU cc_start: 0.8625 (mm-30) cc_final: 0.7752 (mm-30) REVERT: Q 8 TYR cc_start: 0.8780 (t80) cc_final: 0.8127 (t80) REVERT: XA 108 TYR cc_start: 0.8582 (t80) cc_final: 0.7898 (t80) REVERT: YA 208 TYR cc_start: 0.9069 (t80) cc_final: 0.8394 (t80) REVERT: YA 212 LEU cc_start: 0.9494 (mm) cc_final: 0.9269 (mm) REVERT: ZA 303 GLU cc_start: 0.9025 (mm-30) cc_final: 0.8633 (mm-30) REVERT: ZA 308 TYR cc_start: 0.8563 (t80) cc_final: 0.8063 (t80) REVERT: aA 415 GLN cc_start: 0.8667 (mt0) cc_final: 0.8452 (mt0) REVERT: R 8 TYR cc_start: 0.9135 (t80) cc_final: 0.8935 (t80) REVERT: R 12 LEU cc_start: 0.9537 (mm) cc_final: 0.9279 (mm) REVERT: cA 212 LEU cc_start: 0.9657 (mm) cc_final: 0.9393 (mm) REVERT: fA 108 TYR cc_start: 0.8973 (t80) cc_final: 0.8602 (t80) REVERT: iA 403 GLU cc_start: 0.8971 (mm-30) cc_final: 0.8600 (mm-30) REVERT: T 11 ILE cc_start: 0.8824 (tt) cc_final: 0.8535 (tp) REVERT: oA 203 GLU cc_start: 0.9248 (mm-30) cc_final: 0.8941 (mm-30) REVERT: qA 415 GLN cc_start: 0.8686 (mt0) cc_final: 0.8395 (mt0) outliers start: 3 outliers final: 0 residues processed: 614 average time/residue: 0.0816 time to fit residues: 79.4019 Evaluate side-chains 571 residues out of total 1155 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 569 time to evaluate : 0.524 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 90 optimal weight: 3.9990 chunk 15 optimal weight: 5.9990 chunk 103 optimal weight: 1.9990 chunk 1 optimal weight: 7.9990 chunk 101 optimal weight: 0.9990 chunk 73 optimal weight: 5.9990 chunk 4 optimal weight: 4.9990 chunk 67 optimal weight: 0.8980 chunk 84 optimal weight: 8.9990 chunk 38 optimal weight: 7.9990 chunk 33 optimal weight: 5.9990 overall best weight: 2.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: o 415 GLN ** q 215 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 8 415 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** gA 215 GLN hA 315 GLN ** iA 415 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 15 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3089 r_free = 0.3089 target = 0.056127 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.2853 r_free = 0.2853 target = 0.048143 restraints weight = 48284.014| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2914 r_free = 0.2914 target = 0.050138 restraints weight = 29197.169| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.2957 r_free = 0.2957 target = 0.051485 restraints weight = 19357.553| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.2988 r_free = 0.2988 target = 0.052460 restraints weight = 13739.123| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3012 r_free = 0.3012 target = 0.053210 restraints weight = 10010.647| |-----------------------------------------------------------------------------| r_work (final): 0.3006 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8912 moved from start: 0.5990 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 12915 Z= 0.189 Angle : 0.571 5.330 17325 Z= 0.300 Chirality : 0.044 0.149 1995 Planarity : 0.002 0.020 2310 Dihedral : 3.056 28.215 1890 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 5.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 0.09 % Allowed : 6.41 % Favored : 93.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.76 (0.24), residues: 1365 helix: 2.47 (0.15), residues: 1365 sheet: None (None), residues: 0 loop : None (None), residues: 0 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARGIA 206 TYR 0.026 0.002 TYR 3 308 Details of bonding type rmsd covalent geometry : bond 0.00439 (12915) covalent geometry : angle 0.57145 (17325) hydrogen bonds : bond 0.03269 ( 1050) hydrogen bonds : angle 3.97232 ( 3150) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2730 Ramachandran restraints generated. 1365 Oldfield, 0 Emsley, 1365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2730 Ramachandran restraints generated. 1365 Oldfield, 0 Emsley, 1365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 592 residues out of total 1155 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 591 time to evaluate : 0.397 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 3 GLU cc_start: 0.8952 (mp0) cc_final: 0.8720 (mp0) REVERT: A 12 LEU cc_start: 0.9534 (mm) cc_final: 0.9293 (mm) REVERT: V 108 TYR cc_start: 0.9106 (t80) cc_final: 0.8829 (t80) REVERT: V 112 LEU cc_start: 0.9550 (mm) cc_final: 0.9338 (mm) REVERT: W 212 LEU cc_start: 0.9604 (mm) cc_final: 0.9375 (mm) REVERT: B 12 LEU cc_start: 0.9558 (mm) cc_final: 0.9230 (mm) REVERT: a 212 LEU cc_start: 0.9552 (mm) cc_final: 0.9207 (mm) REVERT: b 303 GLU cc_start: 0.9146 (mm-30) cc_final: 0.8497 (mm-30) REVERT: b 312 LEU cc_start: 0.9415 (mm) cc_final: 0.9156 (mm) REVERT: C 8 TYR cc_start: 0.9069 (t80) cc_final: 0.8461 (t80) REVERT: d 108 TYR cc_start: 0.9056 (t80) cc_final: 0.8304 (t80) REVERT: d 112 LEU cc_start: 0.9556 (mm) cc_final: 0.9337 (mm) REVERT: e 208 TYR cc_start: 0.8718 (t80) cc_final: 0.8109 (t80) REVERT: e 215 GLN cc_start: 0.8998 (mt0) cc_final: 0.8529 (mt0) REVERT: f 308 TYR cc_start: 0.9066 (t80) cc_final: 0.8680 (t80) REVERT: i 208 TYR cc_start: 0.8961 (t80) cc_final: 0.8587 (t80) REVERT: j 303 GLU cc_start: 0.9056 (mm-30) cc_final: 0.8825 (mm-30) REVERT: j 308 TYR cc_start: 0.9044 (t80) cc_final: 0.8492 (t80) REVERT: j 312 LEU cc_start: 0.9543 (mm) cc_final: 0.9095 (mm) REVERT: k 408 TYR cc_start: 0.8974 (t80) cc_final: 0.8667 (t80) REVERT: E 3 GLU cc_start: 0.8542 (mm-30) cc_final: 0.7988 (mm-30) REVERT: l 103 GLU cc_start: 0.9015 (mm-30) cc_final: 0.8534 (mm-30) REVERT: l 108 TYR cc_start: 0.8927 (t80) cc_final: 0.8643 (t80) REVERT: m 208 TYR cc_start: 0.8852 (t80) cc_final: 0.8555 (t80) REVERT: F 3 GLU cc_start: 0.9086 (mm-30) cc_final: 0.8657 (mm-30) REVERT: q 208 TYR cc_start: 0.8860 (t80) cc_final: 0.8575 (t80) REVERT: G 11 ILE cc_start: 0.9475 (mt) cc_final: 0.9224 (mt) REVERT: G 15 GLN cc_start: 0.9086 (mt0) cc_final: 0.8821 (mt0) REVERT: t 103 GLU cc_start: 0.8912 (mm-30) cc_final: 0.8605 (mm-30) REVERT: t 112 LEU cc_start: 0.9530 (mm) cc_final: 0.9277 (mm) REVERT: u 208 TYR cc_start: 0.9232 (t80) cc_final: 0.9001 (t80) REVERT: u 212 LEU cc_start: 0.9575 (mm) cc_final: 0.9295 (mm) REVERT: v 315 GLN cc_start: 0.8773 (mt0) cc_final: 0.8233 (mt0) REVERT: w 403 GLU cc_start: 0.8656 (mm-30) cc_final: 0.7639 (mm-30) REVERT: w 411 ILE cc_start: 0.9502 (tt) cc_final: 0.9174 (tt) REVERT: w 412 LEU cc_start: 0.9427 (mt) cc_final: 0.8944 (mt) REVERT: H 12 LEU cc_start: 0.9552 (mm) cc_final: 0.9344 (mm) REVERT: y 212 LEU cc_start: 0.9582 (mm) cc_final: 0.9221 (mm) REVERT: z 303 GLU cc_start: 0.8964 (mm-30) cc_final: 0.8645 (mm-30) REVERT: z 308 TYR cc_start: 0.8635 (t80) cc_final: 0.7885 (t80) REVERT: z 315 GLN cc_start: 0.8891 (mt0) cc_final: 0.8526 (tt0) REVERT: 0 403 GLU cc_start: 0.8523 (tp30) cc_final: 0.8131 (mm-30) REVERT: 0 408 TYR cc_start: 0.9068 (t80) cc_final: 0.8676 (t80) REVERT: 0 412 LEU cc_start: 0.9350 (mm) cc_final: 0.9090 (mm) REVERT: 0 415 GLN cc_start: 0.8935 (mt0) cc_final: 0.8597 (mt0) REVERT: I 8 TYR cc_start: 0.9023 (t80) cc_final: 0.8736 (t80) REVERT: I 12 LEU cc_start: 0.9649 (mm) cc_final: 0.9121 (mm) REVERT: 2 208 TYR cc_start: 0.8785 (t80) cc_final: 0.8549 (t80) REVERT: 5 115 GLN cc_start: 0.8918 (mt0) cc_final: 0.8593 (mt0) REVERT: 7 303 GLU cc_start: 0.9000 (mm-30) cc_final: 0.8486 (mm-30) REVERT: 8 408 TYR cc_start: 0.8952 (t80) cc_final: 0.7973 (t80) REVERT: 8 411 ILE cc_start: 0.9485 (mt) cc_final: 0.9118 (mt) REVERT: 8 412 LEU cc_start: 0.9358 (mm) cc_final: 0.8918 (mm) REVERT: 8 415 GLN cc_start: 0.8788 (mt0) cc_final: 0.8263 (mt0) REVERT: K 3 GLU cc_start: 0.8987 (mm-30) cc_final: 0.8170 (mm-30) REVERT: K 8 TYR cc_start: 0.8960 (t80) cc_final: 0.8386 (t80) REVERT: K 12 LEU cc_start: 0.9386 (mm) cc_final: 0.9179 (mm) REVERT: K 15 GLN cc_start: 0.8797 (mt0) cc_final: 0.8462 (mt0) REVERT: 9 112 LEU cc_start: 0.9513 (mm) cc_final: 0.9267 (mm) REVERT: BA 303 GLU cc_start: 0.9057 (mm-30) cc_final: 0.8787 (mm-30) REVERT: CA 412 LEU cc_start: 0.9593 (mm) cc_final: 0.9349 (mm) REVERT: CA 415 GLN cc_start: 0.9028 (mt0) cc_final: 0.8581 (tt0) REVERT: L 8 TYR cc_start: 0.9122 (t80) cc_final: 0.8534 (t80) REVERT: DA 108 TYR cc_start: 0.9033 (t80) cc_final: 0.8628 (t80) REVERT: EA 208 TYR cc_start: 0.9098 (t80) cc_final: 0.8656 (t80) REVERT: FA 308 TYR cc_start: 0.9157 (t80) cc_final: 0.8531 (t80) REVERT: FA 312 LEU cc_start: 0.9440 (mm) cc_final: 0.9125 (mm) REVERT: GA 408 TYR cc_start: 0.9013 (t80) cc_final: 0.8526 (t80) REVERT: M 12 LEU cc_start: 0.9557 (mm) cc_final: 0.9290 (mm) REVERT: M 15 GLN cc_start: 0.8877 (mt0) cc_final: 0.8457 (tt0) REVERT: HA 103 GLU cc_start: 0.8636 (mm-30) cc_final: 0.7534 (mm-30) REVERT: HA 115 GLN cc_start: 0.8884 (mt0) cc_final: 0.8648 (mt0) REVERT: JA 303 GLU cc_start: 0.8953 (mm-30) cc_final: 0.8379 (mm-30) REVERT: N 12 LEU cc_start: 0.9612 (mm) cc_final: 0.9313 (mm) REVERT: LA 103 GLU cc_start: 0.9095 (mm-30) cc_final: 0.8662 (mm-30) REVERT: MA 212 LEU cc_start: 0.9631 (mm) cc_final: 0.9317 (mm) REVERT: NA 303 GLU cc_start: 0.9106 (mm-30) cc_final: 0.8435 (mm-30) REVERT: OA 412 LEU cc_start: 0.9550 (mm) cc_final: 0.9197 (mm) REVERT: O 8 TYR cc_start: 0.8998 (t80) cc_final: 0.8610 (t80) REVERT: O 12 LEU cc_start: 0.9483 (mm) cc_final: 0.9152 (mm) REVERT: QA 208 TYR cc_start: 0.9094 (t80) cc_final: 0.8758 (t80) REVERT: QA 212 LEU cc_start: 0.9593 (mm) cc_final: 0.9273 (mm) REVERT: RA 303 GLU cc_start: 0.8919 (mm-30) cc_final: 0.8642 (mm-30) REVERT: RA 308 TYR cc_start: 0.9143 (t80) cc_final: 0.8876 (t80) REVERT: SA 408 TYR cc_start: 0.8940 (t80) cc_final: 0.8708 (t80) REVERT: P 15 GLN cc_start: 0.8940 (mt0) cc_final: 0.8731 (mt0) REVERT: TA 112 LEU cc_start: 0.9608 (mm) cc_final: 0.9370 (mm) REVERT: VA 312 LEU cc_start: 0.9588 (mm) cc_final: 0.9311 (mm) REVERT: Q 3 GLU cc_start: 0.8592 (mm-30) cc_final: 0.8329 (mm-30) REVERT: Q 8 TYR cc_start: 0.8771 (t80) cc_final: 0.8152 (t80) REVERT: XA 103 GLU cc_start: 0.8928 (mp0) cc_final: 0.8691 (mp0) REVERT: XA 108 TYR cc_start: 0.8996 (t80) cc_final: 0.8489 (t80) REVERT: XA 112 LEU cc_start: 0.9517 (mm) cc_final: 0.9132 (mm) REVERT: YA 208 TYR cc_start: 0.9083 (t80) cc_final: 0.8455 (t80) REVERT: ZA 303 GLU cc_start: 0.9004 (mm-30) cc_final: 0.8628 (mm-30) REVERT: ZA 308 TYR cc_start: 0.8784 (t80) cc_final: 0.7994 (t80) REVERT: R 8 TYR cc_start: 0.9171 (t80) cc_final: 0.8937 (t80) REVERT: R 12 LEU cc_start: 0.9650 (mm) cc_final: 0.9291 (mm) REVERT: iA 403 GLU cc_start: 0.8938 (mm-30) cc_final: 0.8607 (mm-30) REVERT: iA 412 LEU cc_start: 0.9500 (mm) cc_final: 0.9213 (mm) REVERT: iA 415 GLN cc_start: 0.8966 (mt0) cc_final: 0.8446 (mt0) REVERT: T 11 ILE cc_start: 0.8877 (tt) cc_final: 0.8578 (tp) REVERT: oA 203 GLU cc_start: 0.9183 (mm-30) cc_final: 0.8849 (mm-30) REVERT: pA 315 GLN cc_start: 0.8683 (mt0) cc_final: 0.8162 (mt0) REVERT: qA 403 GLU cc_start: 0.8823 (mm-30) cc_final: 0.7198 (mm-30) outliers start: 1 outliers final: 0 residues processed: 592 average time/residue: 0.0794 time to fit residues: 74.2563 Evaluate side-chains 563 residues out of total 1155 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 563 time to evaluate : 0.378 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 51 optimal weight: 0.9980 chunk 87 optimal weight: 4.9990 chunk 8 optimal weight: 2.9990 chunk 70 optimal weight: 5.9990 chunk 49 optimal weight: 1.9990 chunk 11 optimal weight: 6.9990 chunk 54 optimal weight: 2.9990 chunk 61 optimal weight: 0.8980 chunk 75 optimal weight: 0.9980 chunk 53 optimal weight: 5.9990 chunk 66 optimal weight: 2.9990 overall best weight: 1.5784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: n 315 GLN ** q 215 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 8 415 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** NA 315 GLN PA 115 GLN gA 215 GLN hA 315 GLN ** iA 415 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3113 r_free = 0.3113 target = 0.057340 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2874 r_free = 0.2874 target = 0.049183 restraints weight = 47737.376| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.2935 r_free = 0.2935 target = 0.051170 restraints weight = 29374.900| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.2974 r_free = 0.2974 target = 0.052460 restraints weight = 19730.264| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3005 r_free = 0.3005 target = 0.053495 restraints weight = 14254.662| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3032 r_free = 0.3032 target = 0.054288 restraints weight = 10501.913| |-----------------------------------------------------------------------------| r_work (final): 0.3024 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8878 moved from start: 0.6303 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 12915 Z= 0.146 Angle : 0.591 4.658 17325 Z= 0.300 Chirality : 0.042 0.153 1995 Planarity : 0.002 0.016 2310 Dihedral : 3.172 27.853 1890 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 4.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 0.09 % Allowed : 1.56 % Favored : 98.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 4.08 (0.24), residues: 1365 helix: 2.67 (0.15), residues: 1365 sheet: None (None), residues: 0 loop : None (None), residues: 0 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG o 406 TYR 0.027 0.002 TYR o 408 Details of bonding type rmsd covalent geometry : bond 0.00374 (12915) covalent geometry : angle 0.59141 (17325) hydrogen bonds : bond 0.02860 ( 1050) hydrogen bonds : angle 3.73901 ( 3150) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2730 Ramachandran restraints generated. 1365 Oldfield, 0 Emsley, 1365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2730 Ramachandran restraints generated. 1365 Oldfield, 0 Emsley, 1365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 597 residues out of total 1155 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 596 time to evaluate : 0.354 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 12 LEU cc_start: 0.9544 (mm) cc_final: 0.9307 (mm) REVERT: V 108 TYR cc_start: 0.9067 (t80) cc_final: 0.8843 (t80) REVERT: B 12 LEU cc_start: 0.9558 (mm) cc_final: 0.9185 (mm) REVERT: a 212 LEU cc_start: 0.9566 (mm) cc_final: 0.9223 (mm) REVERT: b 303 GLU cc_start: 0.9134 (mm-30) cc_final: 0.8432 (mm-30) REVERT: b 312 LEU cc_start: 0.9410 (mm) cc_final: 0.9090 (mm) REVERT: C 8 TYR cc_start: 0.9016 (t80) cc_final: 0.8457 (t80) REVERT: d 108 TYR cc_start: 0.9035 (t80) cc_final: 0.8324 (t80) REVERT: e 208 TYR cc_start: 0.8930 (t80) cc_final: 0.8692 (t80) REVERT: e 215 GLN cc_start: 0.8945 (mt0) cc_final: 0.8715 (mt0) REVERT: f 308 TYR cc_start: 0.8984 (t80) cc_final: 0.8592 (t80) REVERT: g 408 TYR cc_start: 0.8785 (t80) cc_final: 0.8190 (t80) REVERT: i 208 TYR cc_start: 0.8930 (t80) cc_final: 0.8598 (t80) REVERT: j 303 GLU cc_start: 0.9077 (mm-30) cc_final: 0.8862 (mm-30) REVERT: j 308 TYR cc_start: 0.9002 (t80) cc_final: 0.8593 (t80) REVERT: j 312 LEU cc_start: 0.9576 (mm) cc_final: 0.9288 (mm) REVERT: k 408 TYR cc_start: 0.8915 (t80) cc_final: 0.8521 (t80) REVERT: E 3 GLU cc_start: 0.8716 (mm-30) cc_final: 0.7618 (mm-30) REVERT: l 103 GLU cc_start: 0.9007 (mm-30) cc_final: 0.8686 (mm-30) REVERT: m 208 TYR cc_start: 0.8854 (t80) cc_final: 0.8561 (t80) REVERT: o 408 TYR cc_start: 0.8978 (t80) cc_final: 0.8688 (t80) REVERT: o 415 GLN cc_start: 0.8491 (pt0) cc_final: 0.8105 (pt0) REVERT: F 3 GLU cc_start: 0.9062 (mm-30) cc_final: 0.8622 (mm-30) REVERT: q 208 TYR cc_start: 0.8818 (t80) cc_final: 0.8499 (t80) REVERT: r 308 TYR cc_start: 0.8945 (t80) cc_final: 0.8742 (t80) REVERT: s 412 LEU cc_start: 0.9554 (mp) cc_final: 0.9341 (mp) REVERT: G 11 ILE cc_start: 0.9424 (mt) cc_final: 0.9196 (mt) REVERT: t 112 LEU cc_start: 0.9581 (mm) cc_final: 0.9164 (mm) REVERT: u 208 TYR cc_start: 0.9182 (t80) cc_final: 0.8868 (t80) REVERT: u 212 LEU cc_start: 0.9593 (mm) cc_final: 0.9282 (mm) REVERT: w 411 ILE cc_start: 0.9632 (tt) cc_final: 0.9289 (tp) REVERT: w 415 GLN cc_start: 0.8761 (mt0) cc_final: 0.8506 (mt0) REVERT: H 12 LEU cc_start: 0.9560 (mm) cc_final: 0.9355 (mm) REVERT: x 108 TYR cc_start: 0.8571 (t80) cc_final: 0.8321 (t80) REVERT: x 115 GLN cc_start: 0.8800 (mt0) cc_final: 0.8467 (mt0) REVERT: y 203 GLU cc_start: 0.8791 (mm-30) cc_final: 0.8205 (mm-30) REVERT: y 212 LEU cc_start: 0.9583 (mm) cc_final: 0.9202 (mm) REVERT: z 303 GLU cc_start: 0.8950 (mm-30) cc_final: 0.8672 (mm-30) REVERT: z 308 TYR cc_start: 0.8564 (t80) cc_final: 0.7823 (t80) REVERT: z 315 GLN cc_start: 0.8908 (mt0) cc_final: 0.8487 (tt0) REVERT: 0 403 GLU cc_start: 0.8483 (tp30) cc_final: 0.8135 (mm-30) REVERT: 0 408 TYR cc_start: 0.9094 (t80) cc_final: 0.8705 (t80) REVERT: 0 412 LEU cc_start: 0.9340 (mm) cc_final: 0.9080 (mm) REVERT: I 8 TYR cc_start: 0.8900 (t80) cc_final: 0.8689 (t80) REVERT: I 12 LEU cc_start: 0.9640 (mm) cc_final: 0.9297 (mm) REVERT: 2 208 TYR cc_start: 0.8771 (t80) cc_final: 0.8467 (t80) REVERT: 5 103 GLU cc_start: 0.8740 (mm-30) cc_final: 0.8539 (mm-30) REVERT: 5 115 GLN cc_start: 0.8872 (mt0) cc_final: 0.8614 (mt0) REVERT: 7 303 GLU cc_start: 0.8991 (mm-30) cc_final: 0.8516 (mm-30) REVERT: 8 408 TYR cc_start: 0.8923 (t80) cc_final: 0.7892 (t80) REVERT: 8 411 ILE cc_start: 0.9446 (mt) cc_final: 0.9018 (mt) REVERT: 8 412 LEU cc_start: 0.9348 (mm) cc_final: 0.9015 (mm) REVERT: 8 415 GLN cc_start: 0.8921 (mt0) cc_final: 0.8081 (mt0) REVERT: K 8 TYR cc_start: 0.8971 (t80) cc_final: 0.8613 (t80) REVERT: K 15 GLN cc_start: 0.8786 (mt0) cc_final: 0.8462 (tt0) REVERT: 9 112 LEU cc_start: 0.9529 (mm) cc_final: 0.9326 (mm) REVERT: BA 303 GLU cc_start: 0.9057 (mm-30) cc_final: 0.8774 (mm-30) REVERT: L 8 TYR cc_start: 0.9106 (t80) cc_final: 0.8672 (t80) REVERT: DA 108 TYR cc_start: 0.9033 (t80) cc_final: 0.8631 (t80) REVERT: EA 203 GLU cc_start: 0.9070 (mp0) cc_final: 0.8868 (mp0) REVERT: EA 208 TYR cc_start: 0.9104 (t80) cc_final: 0.8689 (t80) REVERT: FA 308 TYR cc_start: 0.9150 (t80) cc_final: 0.8467 (t80) REVERT: FA 312 LEU cc_start: 0.9440 (mm) cc_final: 0.9110 (mm) REVERT: GA 408 TYR cc_start: 0.8974 (t80) cc_final: 0.8498 (t80) REVERT: M 12 LEU cc_start: 0.9570 (mm) cc_final: 0.9257 (mm) REVERT: M 15 GLN cc_start: 0.8813 (mt0) cc_final: 0.8488 (tt0) REVERT: HA 103 GLU cc_start: 0.8596 (mm-30) cc_final: 0.7405 (mm-30) REVERT: HA 115 GLN cc_start: 0.8922 (mt0) cc_final: 0.8457 (mt0) REVERT: IA 203 GLU cc_start: 0.8579 (tp30) cc_final: 0.7945 (mm-30) REVERT: JA 303 GLU cc_start: 0.8963 (mm-30) cc_final: 0.8373 (mm-30) REVERT: N 12 LEU cc_start: 0.9637 (mm) cc_final: 0.9337 (mm) REVERT: LA 103 GLU cc_start: 0.9109 (mm-30) cc_final: 0.8673 (mm-30) REVERT: MA 212 LEU cc_start: 0.9622 (mm) cc_final: 0.9293 (mm) REVERT: NA 303 GLU cc_start: 0.9086 (mm-30) cc_final: 0.8315 (mm-30) REVERT: OA 403 GLU cc_start: 0.9031 (mp0) cc_final: 0.8769 (mp0) REVERT: OA 412 LEU cc_start: 0.9554 (mm) cc_final: 0.9257 (mm) REVERT: O 8 TYR cc_start: 0.8943 (t80) cc_final: 0.8547 (t80) REVERT: O 12 LEU cc_start: 0.9522 (mm) cc_final: 0.9190 (mm) REVERT: QA 203 GLU cc_start: 0.8992 (mm-30) cc_final: 0.8637 (mm-30) REVERT: QA 208 TYR cc_start: 0.9059 (t80) cc_final: 0.8675 (t80) REVERT: QA 212 LEU cc_start: 0.9578 (mm) cc_final: 0.9186 (mm) REVERT: RA 303 GLU cc_start: 0.8939 (mm-30) cc_final: 0.8670 (mm-30) REVERT: RA 308 TYR cc_start: 0.9085 (t80) cc_final: 0.8863 (t80) REVERT: SA 408 TYR cc_start: 0.8925 (t80) cc_final: 0.8705 (t80) REVERT: P 15 GLN cc_start: 0.8890 (mt0) cc_final: 0.8649 (mt0) REVERT: TA 112 LEU cc_start: 0.9606 (mm) cc_final: 0.9342 (mm) REVERT: Q 3 GLU cc_start: 0.8609 (mm-30) cc_final: 0.7434 (mm-30) REVERT: Q 8 TYR cc_start: 0.8815 (t80) cc_final: 0.8405 (t80) REVERT: Q 12 LEU cc_start: 0.9521 (mm) cc_final: 0.9238 (mm) REVERT: XA 103 GLU cc_start: 0.8919 (mp0) cc_final: 0.8695 (mp0) REVERT: XA 112 LEU cc_start: 0.9470 (mm) cc_final: 0.9246 (mm) REVERT: YA 208 TYR cc_start: 0.9028 (t80) cc_final: 0.8445 (t80) REVERT: ZA 303 GLU cc_start: 0.9007 (mm-30) cc_final: 0.8520 (mm-30) REVERT: aA 415 GLN cc_start: 0.8665 (mt0) cc_final: 0.8162 (mt0) REVERT: R 3 GLU cc_start: 0.8711 (mm-30) cc_final: 0.8003 (mm-30) REVERT: R 12 LEU cc_start: 0.9634 (mm) cc_final: 0.9311 (mm) REVERT: bA 112 LEU cc_start: 0.9603 (mm) cc_final: 0.9384 (mm) REVERT: dA 303 GLU cc_start: 0.8931 (mm-30) cc_final: 0.8691 (mm-30) REVERT: eA 415 GLN cc_start: 0.8642 (mt0) cc_final: 0.7640 (mt0) REVERT: iA 408 TYR cc_start: 0.8891 (t80) cc_final: 0.8655 (t80) REVERT: iA 411 ILE cc_start: 0.9461 (mt) cc_final: 0.9224 (tt) REVERT: iA 415 GLN cc_start: 0.8908 (mt0) cc_final: 0.8568 (mt0) REVERT: T 11 ILE cc_start: 0.8840 (tt) cc_final: 0.8506 (tp) REVERT: lA 308 TYR cc_start: 0.9140 (t80) cc_final: 0.8934 (t80) REVERT: oA 203 GLU cc_start: 0.9168 (mm-30) cc_final: 0.8861 (mm-30) REVERT: pA 303 GLU cc_start: 0.9129 (mm-30) cc_final: 0.8872 (mm-30) REVERT: pA 315 GLN cc_start: 0.8614 (mt0) cc_final: 0.8082 (mt0) REVERT: qA 403 GLU cc_start: 0.8802 (mm-30) cc_final: 0.7328 (mm-30) outliers start: 1 outliers final: 0 residues processed: 597 average time/residue: 0.0822 time to fit residues: 77.1075 Evaluate side-chains 564 residues out of total 1155 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 564 time to evaluate : 0.551 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 67 optimal weight: 0.9990 chunk 46 optimal weight: 5.9990 chunk 87 optimal weight: 2.9990 chunk 59 optimal weight: 4.9990 chunk 8 optimal weight: 0.7980 chunk 34 optimal weight: 4.9990 chunk 40 optimal weight: 0.8980 chunk 15 optimal weight: 7.9990 chunk 100 optimal weight: 0.4980 chunk 83 optimal weight: 1.9990 chunk 73 optimal weight: 1.9990 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: o 415 GLN ** 8 415 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** XA 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** cA 215 GLN gA 215 GLN iA 415 GLN qA 415 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3165 r_free = 0.3165 target = 0.059246 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2927 r_free = 0.2927 target = 0.050891 restraints weight = 47352.075| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2985 r_free = 0.2985 target = 0.052922 restraints weight = 29232.556| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3028 r_free = 0.3028 target = 0.054324 restraints weight = 19612.552| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3056 r_free = 0.3056 target = 0.055321 restraints weight = 14041.827| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3080 r_free = 0.3080 target = 0.056106 restraints weight = 10350.236| |-----------------------------------------------------------------------------| r_work (final): 0.3074 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8850 moved from start: 0.6497 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 12915 Z= 0.131 Angle : 0.613 5.015 17325 Z= 0.305 Chirality : 0.042 0.144 1995 Planarity : 0.002 0.024 2310 Dihedral : 3.267 25.506 1890 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 4.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 0.09 % Allowed : 0.52 % Favored : 99.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 4.30 (0.23), residues: 1365 helix: 2.80 (0.14), residues: 1365 sheet: None (None), residues: 0 loop : None (None), residues: 0 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARGKA 406 TYR 0.022 0.002 TYRPA 108 Details of bonding type rmsd covalent geometry : bond 0.00345 (12915) covalent geometry : angle 0.61286 (17325) hydrogen bonds : bond 0.02617 ( 1050) hydrogen bonds : angle 3.61336 ( 3150) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2730 Ramachandran restraints generated. 1365 Oldfield, 0 Emsley, 1365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2730 Ramachandran restraints generated. 1365 Oldfield, 0 Emsley, 1365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 619 residues out of total 1155 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 618 time to evaluate : 0.503 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 12 LEU cc_start: 0.9607 (mm) cc_final: 0.9227 (mm) REVERT: a 212 LEU cc_start: 0.9576 (mm) cc_final: 0.9325 (mm) REVERT: b 303 GLU cc_start: 0.9116 (mm-30) cc_final: 0.8435 (mm-30) REVERT: b 312 LEU cc_start: 0.9415 (mm) cc_final: 0.9165 (mm) REVERT: C 8 TYR cc_start: 0.8989 (t80) cc_final: 0.8479 (t80) REVERT: d 108 TYR cc_start: 0.8997 (t80) cc_final: 0.8384 (t80) REVERT: e 208 TYR cc_start: 0.8895 (t80) cc_final: 0.8645 (t80) REVERT: e 215 GLN cc_start: 0.8910 (mt0) cc_final: 0.8527 (mt0) REVERT: f 308 TYR cc_start: 0.8926 (t80) cc_final: 0.8592 (t80) REVERT: g 408 TYR cc_start: 0.8775 (t80) cc_final: 0.8205 (t80) REVERT: i 208 TYR cc_start: 0.8912 (t80) cc_final: 0.8622 (t80) REVERT: j 303 GLU cc_start: 0.9082 (mm-30) cc_final: 0.8862 (mm-30) REVERT: j 308 TYR cc_start: 0.8996 (t80) cc_final: 0.8630 (t80) REVERT: j 312 LEU cc_start: 0.9603 (mm) cc_final: 0.9324 (mm) REVERT: k 408 TYR cc_start: 0.8831 (t80) cc_final: 0.8433 (t80) REVERT: E 3 GLU cc_start: 0.8760 (mm-30) cc_final: 0.8550 (mm-30) REVERT: l 103 GLU cc_start: 0.9021 (mm-30) cc_final: 0.8699 (mm-30) REVERT: o 408 TYR cc_start: 0.8909 (t80) cc_final: 0.8616 (t80) REVERT: F 3 GLU cc_start: 0.9058 (mm-30) cc_final: 0.8629 (mm-30) REVERT: q 208 TYR cc_start: 0.8830 (t80) cc_final: 0.8472 (t80) REVERT: t 112 LEU cc_start: 0.9568 (mm) cc_final: 0.9117 (mm) REVERT: u 208 TYR cc_start: 0.9144 (t80) cc_final: 0.8875 (t80) REVERT: u 212 LEU cc_start: 0.9577 (mm) cc_final: 0.9275 (mm) REVERT: x 108 TYR cc_start: 0.8554 (t80) cc_final: 0.8313 (t80) REVERT: x 115 GLN cc_start: 0.8731 (mt0) cc_final: 0.8485 (mt0) REVERT: y 203 GLU cc_start: 0.8799 (mm-30) cc_final: 0.8267 (mm-30) REVERT: y 212 LEU cc_start: 0.9585 (mm) cc_final: 0.9170 (mm) REVERT: z 303 GLU cc_start: 0.8973 (mm-30) cc_final: 0.8753 (mm-30) REVERT: z 315 GLN cc_start: 0.8911 (mt0) cc_final: 0.8474 (tt0) REVERT: 0 403 GLU cc_start: 0.8496 (tp30) cc_final: 0.8109 (mm-30) REVERT: 0 408 TYR cc_start: 0.9089 (t80) cc_final: 0.8653 (t80) REVERT: 0 412 LEU cc_start: 0.9345 (mm) cc_final: 0.9094 (mm) REVERT: I 12 LEU cc_start: 0.9623 (mm) cc_final: 0.9316 (mm) REVERT: 5 115 GLN cc_start: 0.8846 (mt0) cc_final: 0.8558 (mt0) REVERT: 6 208 TYR cc_start: 0.8815 (t80) cc_final: 0.8137 (t80) REVERT: 7 303 GLU cc_start: 0.8991 (mm-30) cc_final: 0.8544 (mm-30) REVERT: 8 408 TYR cc_start: 0.8903 (t80) cc_final: 0.7826 (t80) REVERT: 8 411 ILE cc_start: 0.9386 (mt) cc_final: 0.9021 (tp) REVERT: 8 412 LEU cc_start: 0.9365 (mm) cc_final: 0.8988 (mm) REVERT: 8 415 GLN cc_start: 0.8740 (mt0) cc_final: 0.8181 (mt0) REVERT: K 3 GLU cc_start: 0.8917 (mm-30) cc_final: 0.7933 (mm-30) REVERT: K 8 TYR cc_start: 0.8969 (t80) cc_final: 0.8562 (t80) REVERT: K 15 GLN cc_start: 0.8777 (mt0) cc_final: 0.8488 (tt0) REVERT: 9 112 LEU cc_start: 0.9561 (mm) cc_final: 0.9354 (mm) REVERT: BA 303 GLU cc_start: 0.9038 (mm-30) cc_final: 0.8776 (mm-30) REVERT: CA 411 ILE cc_start: 0.9395 (mt) cc_final: 0.9178 (mt) REVERT: L 8 TYR cc_start: 0.9091 (t80) cc_final: 0.8681 (t80) REVERT: DA 108 TYR cc_start: 0.9012 (t80) cc_final: 0.8636 (t80) REVERT: EA 203 GLU cc_start: 0.9103 (mp0) cc_final: 0.8901 (mp0) REVERT: EA 208 TYR cc_start: 0.9079 (t80) cc_final: 0.8644 (t80) REVERT: FA 308 TYR cc_start: 0.9133 (t80) cc_final: 0.8496 (t80) REVERT: FA 312 LEU cc_start: 0.9445 (mm) cc_final: 0.9100 (mm) REVERT: GA 408 TYR cc_start: 0.8949 (t80) cc_final: 0.8494 (t80) REVERT: M 12 LEU cc_start: 0.9578 (mm) cc_final: 0.9315 (mm) REVERT: M 15 GLN cc_start: 0.8827 (mt0) cc_final: 0.8482 (tt0) REVERT: HA 103 GLU cc_start: 0.8590 (mm-30) cc_final: 0.7376 (mm-30) REVERT: KA 403 GLU cc_start: 0.8934 (mm-30) cc_final: 0.8514 (mm-30) REVERT: N 3 GLU cc_start: 0.8620 (mm-30) cc_final: 0.8396 (mm-30) REVERT: N 12 LEU cc_start: 0.9642 (mm) cc_final: 0.9350 (mm) REVERT: LA 103 GLU cc_start: 0.9103 (mm-30) cc_final: 0.8687 (mm-30) REVERT: MA 212 LEU cc_start: 0.9626 (mm) cc_final: 0.9306 (mm) REVERT: NA 303 GLU cc_start: 0.9072 (mm-30) cc_final: 0.8777 (mm-30) REVERT: OA 412 LEU cc_start: 0.9551 (mm) cc_final: 0.9254 (mm) REVERT: O 8 TYR cc_start: 0.8933 (t80) cc_final: 0.8604 (t80) REVERT: O 12 LEU cc_start: 0.9500 (mm) cc_final: 0.9200 (mm) REVERT: PA 108 TYR cc_start: 0.8935 (t80) cc_final: 0.8576 (t80) REVERT: QA 203 GLU cc_start: 0.9010 (mm-30) cc_final: 0.8549 (mm-30) REVERT: QA 212 LEU cc_start: 0.9517 (mm) cc_final: 0.9297 (mm) REVERT: RA 303 GLU cc_start: 0.8908 (mm-30) cc_final: 0.8636 (mm-30) REVERT: TA 112 LEU cc_start: 0.9572 (mm) cc_final: 0.9316 (mm) REVERT: VA 312 LEU cc_start: 0.9595 (mm) cc_final: 0.9373 (mm) REVERT: Q 3 GLU cc_start: 0.8636 (mm-30) cc_final: 0.8341 (mm-30) REVERT: Q 8 TYR cc_start: 0.8809 (t80) cc_final: 0.8470 (t80) REVERT: Q 12 LEU cc_start: 0.9519 (mm) cc_final: 0.9268 (mm) REVERT: XA 103 GLU cc_start: 0.8938 (mp0) cc_final: 0.8725 (mp0) REVERT: YA 208 TYR cc_start: 0.9005 (t80) cc_final: 0.8420 (t80) REVERT: ZA 303 GLU cc_start: 0.8992 (mm-30) cc_final: 0.8614 (mm-30) REVERT: aA 408 TYR cc_start: 0.8882 (t80) cc_final: 0.8191 (t80) REVERT: R 12 LEU cc_start: 0.9649 (mm) cc_final: 0.9279 (mm) REVERT: bA 112 LEU cc_start: 0.9624 (mm) cc_final: 0.9400 (mm) REVERT: iA 403 GLU cc_start: 0.8962 (mm-30) cc_final: 0.8496 (mm-30) REVERT: iA 415 GLN cc_start: 0.8749 (mt0) cc_final: 0.8426 (mt0) REVERT: T 11 ILE cc_start: 0.8812 (tt) cc_final: 0.8485 (tp) REVERT: lA 308 TYR cc_start: 0.9122 (t80) cc_final: 0.8877 (t80) REVERT: U 15 GLN cc_start: 0.8595 (tp40) cc_final: 0.8324 (tp40) REVERT: oA 203 GLU cc_start: 0.9200 (mm-30) cc_final: 0.8913 (mm-30) REVERT: pA 303 GLU cc_start: 0.9136 (mm-30) cc_final: 0.8881 (mm-30) REVERT: pA 315 GLN cc_start: 0.8605 (mt0) cc_final: 0.8079 (mt0) REVERT: qA 403 GLU cc_start: 0.8780 (mm-30) cc_final: 0.7335 (mm-30) outliers start: 1 outliers final: 0 residues processed: 619 average time/residue: 0.0810 time to fit residues: 79.2644 Evaluate side-chains 579 residues out of total 1155 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 579 time to evaluate : 0.546 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 27 optimal weight: 1.9990 chunk 14 optimal weight: 6.9990 chunk 82 optimal weight: 2.9990 chunk 41 optimal weight: 0.8980 chunk 73 optimal weight: 0.9990 chunk 104 optimal weight: 6.9990 chunk 100 optimal weight: 0.8980 chunk 71 optimal weight: 0.7980 chunk 39 optimal weight: 1.9990 chunk 76 optimal weight: 3.9990 chunk 44 optimal weight: 3.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 8 415 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** XA 115 GLN fA 115 GLN gA 215 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3179 r_free = 0.3179 target = 0.059772 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2942 r_free = 0.2942 target = 0.051381 restraints weight = 46986.995| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3001 r_free = 0.3001 target = 0.053422 restraints weight = 28948.656| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3047 r_free = 0.3047 target = 0.054879 restraints weight = 19307.563| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3076 r_free = 0.3076 target = 0.055882 restraints weight = 13670.517| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3098 r_free = 0.3098 target = 0.056625 restraints weight = 10057.546| |-----------------------------------------------------------------------------| r_work (final): 0.3083 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8845 moved from start: 0.6586 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 12915 Z= 0.137 Angle : 0.640 5.519 17325 Z= 0.321 Chirality : 0.042 0.160 1995 Planarity : 0.002 0.030 2310 Dihedral : 3.209 23.198 1890 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 5.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.07 % Favored : 99.93 % Rotamer: Outliers : 0.17 % Allowed : 0.43 % Favored : 99.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 4.46 (0.23), residues: 1365 helix: 2.90 (0.14), residues: 1365 sheet: None (None), residues: 0 loop : None (None), residues: 0 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG 8 406 TYR 0.023 0.002 TYR o 408 Details of bonding type rmsd covalent geometry : bond 0.00360 (12915) covalent geometry : angle 0.63951 (17325) hydrogen bonds : bond 0.02770 ( 1050) hydrogen bonds : angle 3.68058 ( 3150) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2730 Ramachandran restraints generated. 1365 Oldfield, 0 Emsley, 1365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2730 Ramachandran restraints generated. 1365 Oldfield, 0 Emsley, 1365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 611 residues out of total 1155 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 609 time to evaluate : 0.517 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: X 303 GLU cc_start: 0.9064 (mp0) cc_final: 0.8859 (mp0) REVERT: B 12 LEU cc_start: 0.9611 (mm) cc_final: 0.9247 (mm) REVERT: a 212 LEU cc_start: 0.9600 (mm) cc_final: 0.9320 (mm) REVERT: b 303 GLU cc_start: 0.9133 (mm-30) cc_final: 0.8495 (mm-30) REVERT: b 312 LEU cc_start: 0.9436 (mm) cc_final: 0.9195 (mm) REVERT: C 8 TYR cc_start: 0.8993 (t80) cc_final: 0.8489 (t80) REVERT: d 108 TYR cc_start: 0.9009 (t80) cc_final: 0.8445 (t80) REVERT: e 208 TYR cc_start: 0.8924 (t80) cc_final: 0.8678 (t80) REVERT: f 308 TYR cc_start: 0.8947 (t80) cc_final: 0.8657 (t80) REVERT: g 412 LEU cc_start: 0.9568 (mm) cc_final: 0.9299 (mm) REVERT: i 208 TYR cc_start: 0.8919 (t80) cc_final: 0.8687 (t80) REVERT: j 303 GLU cc_start: 0.9094 (mm-30) cc_final: 0.8858 (mm-30) REVERT: j 308 TYR cc_start: 0.8985 (t80) cc_final: 0.8657 (t80) REVERT: j 312 LEU cc_start: 0.9596 (mm) cc_final: 0.9357 (mm) REVERT: k 408 TYR cc_start: 0.8890 (t80) cc_final: 0.8486 (t80) REVERT: l 103 GLU cc_start: 0.9056 (mm-30) cc_final: 0.8702 (mm-30) REVERT: o 408 TYR cc_start: 0.8848 (t80) cc_final: 0.8578 (t80) REVERT: F 3 GLU cc_start: 0.9077 (mm-30) cc_final: 0.8658 (mm-30) REVERT: q 212 LEU cc_start: 0.9488 (mm) cc_final: 0.9266 (mm) REVERT: G 12 LEU cc_start: 0.9614 (mm) cc_final: 0.9379 (mm) REVERT: t 112 LEU cc_start: 0.9566 (mm) cc_final: 0.9130 (mm) REVERT: u 208 TYR cc_start: 0.9146 (t80) cc_final: 0.8875 (t80) REVERT: u 212 LEU cc_start: 0.9581 (mm) cc_final: 0.9284 (mm) REVERT: v 315 GLN cc_start: 0.8673 (mt0) cc_final: 0.8112 (mt0) REVERT: w 403 GLU cc_start: 0.8728 (mm-30) cc_final: 0.7189 (mm-30) REVERT: x 115 GLN cc_start: 0.8649 (mt0) cc_final: 0.8421 (mt0) REVERT: y 203 GLU cc_start: 0.8812 (mm-30) cc_final: 0.8319 (mm-30) REVERT: y 212 LEU cc_start: 0.9565 (mm) cc_final: 0.9205 (mm) REVERT: z 303 GLU cc_start: 0.9003 (mm-30) cc_final: 0.8772 (mm-30) REVERT: z 315 GLN cc_start: 0.8981 (mt0) cc_final: 0.8553 (tt0) REVERT: 0 403 GLU cc_start: 0.8470 (tp30) cc_final: 0.8159 (mm-30) REVERT: 0 408 TYR cc_start: 0.9093 (t80) cc_final: 0.8646 (t80) REVERT: 0 412 LEU cc_start: 0.9354 (mm) cc_final: 0.9095 (mm) REVERT: I 3 GLU cc_start: 0.8859 (mm-30) cc_final: 0.8333 (mm-30) REVERT: I 8 TYR cc_start: 0.8973 (t80) cc_final: 0.8713 (t80) REVERT: I 12 LEU cc_start: 0.9696 (mm) cc_final: 0.9317 (mm) REVERT: 5 103 GLU cc_start: 0.9011 (mm-30) cc_final: 0.8487 (mm-30) REVERT: 5 115 GLN cc_start: 0.8841 (mt0) cc_final: 0.8573 (mt0) REVERT: 7 303 GLU cc_start: 0.8998 (mm-30) cc_final: 0.8520 (mm-30) REVERT: 8 408 TYR cc_start: 0.8950 (t80) cc_final: 0.7865 (t80) REVERT: 8 411 ILE cc_start: 0.9383 (mt) cc_final: 0.9035 (tp) REVERT: 8 412 LEU cc_start: 0.9386 (mm) cc_final: 0.8953 (mm) REVERT: 8 415 GLN cc_start: 0.8745 (mt0) cc_final: 0.8165 (mt0) REVERT: K 3 GLU cc_start: 0.8912 (mm-30) cc_final: 0.8298 (mm-30) REVERT: K 8 TYR cc_start: 0.8949 (t80) cc_final: 0.8543 (t80) REVERT: K 15 GLN cc_start: 0.8797 (mt0) cc_final: 0.8559 (tt0) REVERT: 9 112 LEU cc_start: 0.9592 (mm) cc_final: 0.9366 (mm) REVERT: BA 303 GLU cc_start: 0.9059 (mm-30) cc_final: 0.8774 (mm-30) REVERT: CA 411 ILE cc_start: 0.9406 (mt) cc_final: 0.9168 (mt) REVERT: L 8 TYR cc_start: 0.9100 (t80) cc_final: 0.8697 (t80) REVERT: DA 108 TYR cc_start: 0.9018 (t80) cc_final: 0.8641 (t80) REVERT: EA 208 TYR cc_start: 0.9102 (t80) cc_final: 0.8690 (t80) REVERT: FA 308 TYR cc_start: 0.9132 (t80) cc_final: 0.8490 (t80) REVERT: FA 312 LEU cc_start: 0.9423 (mm) cc_final: 0.9089 (mm) REVERT: GA 408 TYR cc_start: 0.8949 (t80) cc_final: 0.8507 (t80) REVERT: M 12 LEU cc_start: 0.9581 (mm) cc_final: 0.9327 (mm) REVERT: HA 103 GLU cc_start: 0.8643 (mm-30) cc_final: 0.7877 (mm-30) REVERT: HA 115 GLN cc_start: 0.8928 (mt0) cc_final: 0.8347 (mt0) REVERT: IA 203 GLU cc_start: 0.8719 (tp30) cc_final: 0.7944 (tp30) REVERT: IA 208 TYR cc_start: 0.9041 (t80) cc_final: 0.8651 (t80) REVERT: KA 403 GLU cc_start: 0.8928 (mm-30) cc_final: 0.8532 (mm-30) REVERT: N 3 GLU cc_start: 0.8647 (mm-30) cc_final: 0.8394 (mm-30) REVERT: N 12 LEU cc_start: 0.9643 (mm) cc_final: 0.9368 (mm) REVERT: LA 103 GLU cc_start: 0.9110 (mm-30) cc_final: 0.8687 (mm-30) REVERT: MA 212 LEU cc_start: 0.9629 (mm) cc_final: 0.9308 (mm) REVERT: NA 303 GLU cc_start: 0.9083 (mm-30) cc_final: 0.8789 (mm-30) REVERT: OA 412 LEU cc_start: 0.9558 (mm) cc_final: 0.9237 (mm) REVERT: O 8 TYR cc_start: 0.8915 (t80) cc_final: 0.8625 (t80) REVERT: O 12 LEU cc_start: 0.9522 (mm) cc_final: 0.9239 (mm) REVERT: QA 203 GLU cc_start: 0.9028 (mm-30) cc_final: 0.8594 (mm-30) REVERT: QA 212 LEU cc_start: 0.9506 (mm) cc_final: 0.9273 (mm) REVERT: RA 303 GLU cc_start: 0.8981 (mm-30) cc_final: 0.8697 (mm-30) REVERT: P 15 GLN cc_start: 0.8798 (mt0) cc_final: 0.8532 (mt0) REVERT: TA 112 LEU cc_start: 0.9578 (mm) cc_final: 0.9297 (mm) REVERT: Q 8 TYR cc_start: 0.8835 (t80) cc_final: 0.8504 (t80) REVERT: Q 12 LEU cc_start: 0.9560 (mm) cc_final: 0.9305 (mm) REVERT: XA 103 GLU cc_start: 0.8975 (mp0) cc_final: 0.8756 (mp0) REVERT: YA 208 TYR cc_start: 0.9003 (t80) cc_final: 0.8396 (t80) REVERT: ZA 303 GLU cc_start: 0.9032 (mm-30) cc_final: 0.8631 (mm-30) REVERT: R 12 LEU cc_start: 0.9653 (mm) cc_final: 0.9286 (mm) REVERT: bA 112 LEU cc_start: 0.9625 (mm) cc_final: 0.9391 (mm) REVERT: iA 403 GLU cc_start: 0.9015 (mm-30) cc_final: 0.8620 (mm-30) REVERT: T 11 ILE cc_start: 0.8814 (tt) cc_final: 0.8484 (tp) REVERT: lA 308 TYR cc_start: 0.9141 (t80) cc_final: 0.8880 (t80) REVERT: U 3 GLU cc_start: 0.8514 (tp30) cc_final: 0.7816 (mm-30) REVERT: oA 203 GLU cc_start: 0.9202 (mm-30) cc_final: 0.8938 (mm-30) REVERT: pA 303 GLU cc_start: 0.9169 (mm-30) cc_final: 0.8904 (mm-30) REVERT: pA 315 GLN cc_start: 0.8569 (mt0) cc_final: 0.8086 (mt0) REVERT: qA 403 GLU cc_start: 0.8825 (mm-30) cc_final: 0.7434 (mm-30) REVERT: qA 415 GLN cc_start: 0.8873 (mt0) cc_final: 0.8640 (mt0) outliers start: 2 outliers final: 0 residues processed: 611 average time/residue: 0.0881 time to fit residues: 84.9977 Evaluate side-chains 578 residues out of total 1155 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 578 time to evaluate : 0.455 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 89 optimal weight: 2.9990 chunk 46 optimal weight: 2.9990 chunk 48 optimal weight: 5.9990 chunk 91 optimal weight: 8.9990 chunk 1 optimal weight: 8.9990 chunk 20 optimal weight: 8.9990 chunk 53 optimal weight: 0.9980 chunk 43 optimal weight: 1.9990 chunk 52 optimal weight: 0.5980 chunk 85 optimal weight: 7.9990 chunk 19 optimal weight: 1.9990 overall best weight: 1.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 8 415 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BA 315 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** XA 115 GLN gA 215 GLN U 15 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3133 r_free = 0.3133 target = 0.058403 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.2901 r_free = 0.2901 target = 0.050212 restraints weight = 47319.148| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.2959 r_free = 0.2959 target = 0.052220 restraints weight = 28975.168| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3004 r_free = 0.3004 target = 0.053638 restraints weight = 19285.539| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3033 r_free = 0.3033 target = 0.054625 restraints weight = 13643.280| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3058 r_free = 0.3058 target = 0.055410 restraints weight = 10021.231| |-----------------------------------------------------------------------------| r_work (final): 0.3052 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8879 moved from start: 0.6607 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 12915 Z= 0.160 Angle : 0.646 5.535 17325 Z= 0.332 Chirality : 0.043 0.151 1995 Planarity : 0.002 0.017 2310 Dihedral : 3.274 47.482 1890 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 5.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.07 % Favored : 99.93 % Rotamer: Outliers : 0.17 % Allowed : 0.52 % Favored : 99.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 4.49 (0.23), residues: 1365 helix: 2.92 (0.14), residues: 1365 sheet: None (None), residues: 0 loop : None (None), residues: 0 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG M 6 TYR 0.023 0.002 TYR J 8 Details of bonding type rmsd covalent geometry : bond 0.00403 (12915) covalent geometry : angle 0.64617 (17325) hydrogen bonds : bond 0.03094 ( 1050) hydrogen bonds : angle 3.80786 ( 3150) =============================================================================== Job complete usr+sys time: 1930.68 seconds wall clock time: 33 minutes 53.86 seconds (2033.86 seconds total)