Starting phenix.real_space_refine on Wed Jun 11 07:51:37 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6wkx_21812/06_2025/6wkx_21812.cif Found real_map, /net/cci-nas-00/data/ceres_data/6wkx_21812/06_2025/6wkx_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/6wkx_21812/06_2025/6wkx_21812.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6wkx_21812/06_2025/6wkx_21812.map" model { file = "/net/cci-nas-00/data/ceres_data/6wkx_21812/06_2025/6wkx_21812.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6wkx_21812/06_2025/6wkx_21812.cif" } resolution = 4.2 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 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): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: 8.19, per 1000 atoms: 0.63 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: 3.42 Conformation dependent library (CDL) restraints added in 1.5 seconds 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: 1.22 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: 4.08 Time building geometry restraints manager: 4.00 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: 0.010 Normalize map: mean=0, sd=1: 2.100 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.530 Check model and map are aligned: 0.100 Set scattering table: 0.130 Process input model: 31.220 Find NCS groups from input model: 0.680 Set up NCS constraints: 0.190 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.680 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.650 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -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 TYR 0.012 0.004 TYR X 308 ARG 0.001 0.000 ARGHA 110 Details of bonding type rmsd hydrogen bonds : bond 0.24973 ( 1050) hydrogen bonds : angle 7.62188 ( 3150) covalent geometry : bond 0.00637 (12915) covalent geometry : angle 0.59479 (17325) *********************** 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 : 1.605 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: 0.9145 (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: 0.8849 (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: 0.9460 (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: 0.8966 (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: 0.8310 (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: 0.8875 (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: 0.2021 time to fit residues: 201.0059 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 : 1.583 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 88 optimal weight: 0.2980 chunk 79 optimal weight: 3.9990 chunk 44 optimal weight: 1.9990 chunk 27 optimal weight: 0.9990 chunk 53 optimal weight: 0.0870 chunk 42 optimal weight: 0.9980 chunk 82 optimal weight: 0.0050 chunk 31 optimal weight: 0.7980 chunk 50 optimal weight: 7.9990 chunk 61 optimal weight: 0.9990 chunk 95 optimal weight: 2.9990 overall best weight: 0.4372 ------------------------------------------------------------------------------- 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 = 0.3017 r_free = 0.3017 target = 0.059146 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.2829 r_free = 0.2829 target = 0.052780 restraints weight = 50604.587| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.2882 r_free = 0.2882 target = 0.054707 restraints weight = 27600.362| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.2917 r_free = 0.2917 target = 0.055908 restraints weight = 16584.451| |-----------------------------------------------------------------------------| r_work (final): 0.2897 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8815 moved from start: 0.3516 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 12915 Z= 0.103 Angle : 0.475 4.251 17325 Z= 0.259 Chirality : 0.035 0.125 1995 Planarity : 0.003 0.012 2310 Dihedral : 3.581 11.731 1890 Min Nonbonded Distance : 2.600 Molprobity Statistics. All-atom Clashscore : 10.61 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.03 (0.24), residues: 1365 helix: 1.40 (0.15), residues: 1365 sheet: None (None), residues: 0 loop : None (None), residues: 0 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.012 0.002 TYRgA 208 ARG 0.003 0.001 ARGgA 210 Details of bonding type rmsd hydrogen bonds : bond 0.03466 ( 1050) hydrogen bonds : angle 3.94828 ( 3150) covalent geometry : bond 0.00227 (12915) covalent geometry : angle 0.47454 (17325) *********************** 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 652 residues out of total 1155 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 645 time to evaluate : 1.541 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 15 GLN cc_start: 0.8552 (mt0) cc_final: 0.8323 (mt0) REVERT: V 108 TYR cc_start: 0.9074 (t80) cc_final: 0.8732 (t80) REVERT: W 212 LEU cc_start: 0.9340 (mm) cc_final: 0.9131 (mm) REVERT: Y 408 TYR cc_start: 0.9008 (t80) cc_final: 0.8664 (t80) REVERT: B 15 GLN cc_start: 0.8577 (mt0) cc_final: 0.8284 (mt0) REVERT: b 315 GLN cc_start: 0.8518 (mt0) cc_final: 0.8164 (tt0) REVERT: d 108 TYR cc_start: 0.9110 (t80) cc_final: 0.8331 (t80) REVERT: d 112 LEU cc_start: 0.9431 (mm) cc_final: 0.9104 (mm) REVERT: e 208 TYR cc_start: 0.8806 (t80) cc_final: 0.8030 (t80) REVERT: e 215 GLN cc_start: 0.8871 (mt0) cc_final: 0.8587 (tt0) REVERT: f 308 TYR cc_start: 0.9023 (t80) cc_final: 0.8415 (t80) REVERT: g 408 TYR cc_start: 0.9121 (t80) cc_final: 0.8423 (t80) REVERT: g 415 GLN cc_start: 0.8562 (mt0) cc_final: 0.8357 (mt0) REVERT: h 115 GLN cc_start: 0.8744 (mt0) cc_final: 0.8539 (mt0) REVERT: i 208 TYR cc_start: 0.8948 (t80) cc_final: 0.8656 (t80) REVERT: j 308 TYR cc_start: 0.9029 (t80) cc_final: 0.8626 (t80) REVERT: k 408 TYR cc_start: 0.9052 (t80) cc_final: 0.8784 (t80) REVERT: E 3 GLU cc_start: 0.8677 (tp30) cc_final: 0.7127 (mm-30) REVERT: l 115 GLN cc_start: 0.8725 (mt0) cc_final: 0.8490 (tt0) REVERT: o 415 GLN cc_start: 0.8596 (mt0) cc_final: 0.8311 (mt0) REVERT: F 3 GLU cc_start: 0.8821 (tp30) cc_final: 0.7817 (tp30) REVERT: p 108 TYR cc_start: 0.9161 (t80) cc_final: 0.8352 (t80) REVERT: p 112 LEU cc_start: 0.9444 (mm) cc_final: 0.8982 (mm) REVERT: s 415 GLN cc_start: 0.8871 (mt0) cc_final: 0.8064 (mt0) REVERT: t 108 TYR cc_start: 0.9075 (t80) cc_final: 0.8776 (t80) REVERT: u 208 TYR cc_start: 0.8940 (t80) cc_final: 0.8702 (t80) REVERT: u 212 LEU cc_start: 0.9386 (mm) cc_final: 0.9158 (mm) REVERT: v 311 ILE cc_start: 0.9440 (mt) cc_final: 0.9180 (mt) REVERT: v 315 GLN cc_start: 0.8494 (mt0) cc_final: 0.8236 (mt0) REVERT: x 111 ILE cc_start: 0.9351 (OUTLIER) cc_final: 0.9030 (mt) REVERT: x 112 LEU cc_start: 0.9512 (mm) cc_final: 0.8887 (mm) REVERT: x 115 GLN cc_start: 0.8625 (mt0) cc_final: 0.8097 (mt0) REVERT: y 208 TYR cc_start: 0.8949 (t80) cc_final: 0.8510 (t80) REVERT: I 8 TYR cc_start: 0.9176 (t80) cc_final: 0.8759 (t80) REVERT: 1 112 LEU cc_start: 0.9526 (mm) cc_final: 0.9225 (mm) REVERT: 2 211 ILE cc_start: 0.9519 (mt) cc_final: 0.9261 (mt) REVERT: 4 408 TYR cc_start: 0.9056 (t80) cc_final: 0.8851 (t80) REVERT: J 15 GLN cc_start: 0.8656 (mt0) cc_final: 0.8453 (mt0) REVERT: 5 115 GLN cc_start: 0.8591 (mt0) cc_final: 0.8342 (tt0) REVERT: K 8 TYR cc_start: 0.9080 (t80) cc_final: 0.8541 (t80) REVERT: K 12 LEU cc_start: 0.9228 (mm) cc_final: 0.8968 (mm) REVERT: 9 112 LEU cc_start: 0.9418 (mm) cc_final: 0.9135 (mm) REVERT: BA 315 GLN cc_start: 0.8523 (mt0) cc_final: 0.8275 (tt0) REVERT: CA 412 LEU cc_start: 0.9325 (mm) cc_final: 0.9125 (mm) REVERT: L 8 TYR cc_start: 0.8995 (t80) cc_final: 0.8357 (t80) REVERT: DA 108 TYR cc_start: 0.9063 (t80) cc_final: 0.8470 (t80) REVERT: DA 112 LEU cc_start: 0.9398 (mm) cc_final: 0.9166 (mm) REVERT: EA 208 TYR cc_start: 0.9051 (t80) cc_final: 0.8627 (t80) REVERT: FA 308 TYR cc_start: 0.8978 (t80) cc_final: 0.8325 (t80) REVERT: FA 315 GLN cc_start: 0.8558 (mt0) cc_final: 0.8332 (mt0) REVERT: GA 408 TYR cc_start: 0.9023 (t80) cc_final: 0.8404 (t80) REVERT: GA 415 GLN cc_start: 0.8698 (mt0) cc_final: 0.8420 (tt0) REVERT: M 15 GLN cc_start: 0.8509 (mt0) cc_final: 0.8279 (mt0) REVERT: JA 315 GLN cc_start: 0.8480 (mt0) cc_final: 0.8263 (tt0) REVERT: KA 415 GLN cc_start: 0.8494 (mt0) cc_final: 0.8213 (mt0) REVERT: N 8 TYR cc_start: 0.9026 (t80) cc_final: 0.8769 (t80) REVERT: O 3 GLU cc_start: 0.8604 (tp30) cc_final: 0.7612 (tp30) REVERT: O 8 TYR cc_start: 0.8915 (t80) cc_final: 0.8478 (t80) REVERT: O 15 GLN cc_start: 0.8603 (mt0) cc_final: 0.8369 (mt0) REVERT: PA 115 GLN cc_start: 0.8759 (mt0) cc_final: 0.8539 (mt0) REVERT: QA 208 TYR cc_start: 0.8924 (t80) cc_final: 0.8709 (t80) REVERT: RA 308 TYR cc_start: 0.9008 (t80) cc_final: 0.8636 (t80) REVERT: SA 408 TYR cc_start: 0.8933 (t80) cc_final: 0.8570 (t80) REVERT: SA 415 GLN cc_start: 0.8586 (mt0) cc_final: 0.8368 (mt0) REVERT: P 3 GLU cc_start: 0.8821 (tp30) cc_final: 0.8162 (tp30) REVERT: UA 212 LEU cc_start: 0.9361 (mm) cc_final: 0.9099 (mm) REVERT: XA 108 TYR cc_start: 0.8972 (t80) cc_final: 0.8108 (t80) REVERT: YA 208 TYR cc_start: 0.9019 (t80) cc_final: 0.8313 (t80) REVERT: ZA 315 GLN cc_start: 0.8510 (mt0) cc_final: 0.8284 (mt0) REVERT: aA 415 GLN cc_start: 0.8560 (mt0) cc_final: 0.8294 (tt0) REVERT: R 3 GLU cc_start: 0.8442 (tp30) cc_final: 0.8111 (tp30) REVERT: R 8 TYR cc_start: 0.9164 (t80) cc_final: 0.8690 (t80) REVERT: R 12 LEU cc_start: 0.9275 (mm) cc_final: 0.9014 (mm) REVERT: cA 208 TYR cc_start: 0.8999 (t80) cc_final: 0.8762 (t80) REVERT: eA 415 GLN cc_start: 0.8964 (mt0) cc_final: 0.8644 (mt0) REVERT: hA 315 GLN cc_start: 0.8531 (mt0) cc_final: 0.8215 (mt0) REVERT: iA 411 ILE cc_start: 0.9463 (mt) cc_final: 0.9238 (mt) REVERT: T 3 GLU cc_start: 0.8476 (tp30) cc_final: 0.7888 (tp30) REVERT: jA 112 LEU cc_start: 0.9238 (mm) cc_final: 0.8967 (mm) REVERT: lA 308 TYR cc_start: 0.9172 (t80) cc_final: 0.8629 (t80) REVERT: mA 408 TYR cc_start: 0.9172 (t80) cc_final: 0.8812 (t80) REVERT: pA 315 GLN cc_start: 0.8587 (mt0) cc_final: 0.8351 (tt0) outliers start: 7 outliers final: 0 residues processed: 645 average time/residue: 0.2029 time to fit residues: 199.5048 Evaluate side-chains 554 residues out of total 1155 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 553 time to evaluate : 1.544 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 79 optimal weight: 0.9980 chunk 78 optimal weight: 1.9990 chunk 29 optimal weight: 0.9980 chunk 16 optimal weight: 2.9990 chunk 99 optimal weight: 0.9990 chunk 72 optimal weight: 0.9990 chunk 40 optimal weight: 7.9990 chunk 0 optimal weight: 10.0000 chunk 22 optimal weight: 0.9990 chunk 51 optimal weight: 0.9980 chunk 55 optimal weight: 3.9990 overall best weight: 0.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: T 15 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3066 r_free = 0.3066 target = 0.058735 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2862 r_free = 0.2862 target = 0.051369 restraints weight = 48917.114| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2918 r_free = 0.2918 target = 0.053403 restraints weight = 27944.016| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.2956 r_free = 0.2956 target = 0.054748 restraints weight = 17785.117| |-----------------------------------------------------------------------------| r_work (final): 0.2929 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8808 moved from start: 0.4983 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 12915 Z= 0.117 Angle : 0.521 4.529 17325 Z= 0.270 Chirality : 0.040 0.130 1995 Planarity : 0.002 0.017 2310 Dihedral : 2.843 15.920 1890 Min Nonbonded Distance : 2.603 Molprobity Statistics. All-atom Clashscore : 8.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 0.09 % Allowed : 8.66 % Favored : 91.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.72 (0.25), residues: 1365 helix: 1.82 (0.15), residues: 1365 sheet: None (None), residues: 0 loop : None (None), residues: 0 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.019 0.002 TYR n 308 ARG 0.002 0.000 ARG l 106 Details of bonding type rmsd hydrogen bonds : bond 0.03165 ( 1050) hydrogen bonds : angle 3.57908 ( 3150) covalent geometry : bond 0.00278 (12915) covalent geometry : angle 0.52114 (17325) *********************** 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 650 residues out of total 1155 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 649 time to evaluate : 1.582 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: A 3 GLU cc_start: 0.8683 (tp30) cc_final: 0.7802 (tp30) REVERT: V 108 TYR cc_start: 0.9107 (t80) cc_final: 0.8790 (t80) REVERT: Y 408 TYR cc_start: 0.9070 (t80) cc_final: 0.8801 (t80) REVERT: Y 415 GLN cc_start: 0.8649 (mt0) cc_final: 0.8307 (mt0) REVERT: B 3 GLU cc_start: 0.8789 (tp30) cc_final: 0.8310 (tp30) REVERT: b 315 GLN cc_start: 0.8628 (mt0) cc_final: 0.8168 (tt0) REVERT: C 8 TYR cc_start: 0.8818 (t80) cc_final: 0.8076 (t80) REVERT: d 108 TYR cc_start: 0.9161 (t80) cc_final: 0.8369 (t80) REVERT: d 112 LEU cc_start: 0.9489 (mm) cc_final: 0.9120 (mm) REVERT: e 208 TYR cc_start: 0.8888 (t80) cc_final: 0.8061 (t80) REVERT: e 215 GLN cc_start: 0.8914 (mt0) cc_final: 0.8591 (tt0) REVERT: f 308 TYR cc_start: 0.9016 (t80) cc_final: 0.8586 (t80) REVERT: g 408 TYR cc_start: 0.9143 (t80) cc_final: 0.8478 (t80) REVERT: g 412 LEU cc_start: 0.9326 (mm) cc_final: 0.9119 (mm) REVERT: h 115 GLN cc_start: 0.8913 (mt0) cc_final: 0.8712 (mt0) REVERT: i 208 TYR cc_start: 0.9037 (t80) cc_final: 0.8586 (t80) REVERT: j 308 TYR cc_start: 0.9064 (t80) cc_final: 0.8705 (t80) REVERT: k 408 TYR cc_start: 0.9155 (t80) cc_final: 0.8520 (t80) REVERT: l 115 GLN cc_start: 0.8883 (mt0) cc_final: 0.8666 (mt0) REVERT: p 108 TYR cc_start: 0.9165 (t80) cc_final: 0.8472 (t80) REVERT: p 112 LEU cc_start: 0.9332 (mm) cc_final: 0.9113 (mm) REVERT: t 108 TYR cc_start: 0.9065 (t80) cc_final: 0.8764 (t80) REVERT: t 112 LEU cc_start: 0.9438 (mm) cc_final: 0.9152 (mm) REVERT: u 208 TYR cc_start: 0.9099 (t80) cc_final: 0.8813 (t80) REVERT: v 315 GLN cc_start: 0.8713 (mt0) cc_final: 0.8295 (mt0) REVERT: x 111 ILE cc_start: 0.9357 (mp) cc_final: 0.9080 (mt) REVERT: x 112 LEU cc_start: 0.9447 (mm) cc_final: 0.8854 (mm) REVERT: x 115 GLN cc_start: 0.8847 (mt0) cc_final: 0.8349 (mt0) REVERT: I 3 GLU cc_start: 0.8935 (mm-30) cc_final: 0.7460 (tp30) REVERT: I 8 TYR cc_start: 0.9243 (t80) cc_final: 0.8799 (t80) REVERT: I 12 LEU cc_start: 0.9540 (mm) cc_final: 0.9289 (mm) REVERT: 4 412 LEU cc_start: 0.9488 (mp) cc_final: 0.9259 (mp) REVERT: 4 415 GLN cc_start: 0.8724 (mt0) cc_final: 0.8410 (mt0) REVERT: J 15 GLN cc_start: 0.8736 (mt0) cc_final: 0.8505 (mt0) REVERT: 5 115 GLN cc_start: 0.8810 (mt0) cc_final: 0.8522 (mt0) REVERT: 7 303 GLU cc_start: 0.8689 (tp30) cc_final: 0.8413 (mm-30) REVERT: K 8 TYR cc_start: 0.9142 (t80) cc_final: 0.8590 (t80) REVERT: K 12 LEU cc_start: 0.9383 (mm) cc_final: 0.9168 (mm) REVERT: 9 112 LEU cc_start: 0.9436 (mm) cc_final: 0.9212 (mm) REVERT: AA 215 GLN cc_start: 0.8793 (mt0) cc_final: 0.8259 (mt0) REVERT: BA 315 GLN cc_start: 0.8765 (mt0) cc_final: 0.8507 (mt0) REVERT: L 8 TYR cc_start: 0.9074 (t80) cc_final: 0.8615 (t80) REVERT: DA 108 TYR cc_start: 0.9086 (t80) cc_final: 0.8552 (t80) REVERT: EA 208 TYR cc_start: 0.9154 (t80) cc_final: 0.8736 (t80) REVERT: FA 308 TYR cc_start: 0.9138 (t80) cc_final: 0.8653 (t80) REVERT: GA 408 TYR cc_start: 0.9035 (t80) cc_final: 0.8446 (t80) REVERT: M 15 GLN cc_start: 0.8770 (mt0) cc_final: 0.8475 (mt0) REVERT: KA 415 GLN cc_start: 0.8733 (mt0) cc_final: 0.8381 (mt0) REVERT: N 3 GLU cc_start: 0.8725 (tp30) cc_final: 0.8439 (tp30) REVERT: O 8 TYR cc_start: 0.8989 (t80) cc_final: 0.8646 (t80) REVERT: PA 115 GLN cc_start: 0.8858 (mt0) cc_final: 0.8623 (mt0) REVERT: RA 308 TYR cc_start: 0.9054 (t80) cc_final: 0.8815 (t80) REVERT: SA 408 TYR cc_start: 0.9009 (t80) cc_final: 0.8713 (t80) REVERT: Q 3 GLU cc_start: 0.8627 (tp30) cc_final: 0.7706 (tp30) REVERT: Q 8 TYR cc_start: 0.8900 (t80) cc_final: 0.8235 (t80) REVERT: XA 108 TYR cc_start: 0.9087 (t80) cc_final: 0.8229 (t80) REVERT: XA 112 LEU cc_start: 0.9397 (mm) cc_final: 0.9166 (mm) REVERT: YA 208 TYR cc_start: 0.9078 (t80) cc_final: 0.8488 (t80) REVERT: ZA 303 GLU cc_start: 0.8690 (tp30) cc_final: 0.8126 (mm-30) REVERT: aA 408 TYR cc_start: 0.8795 (t80) cc_final: 0.8232 (t80) REVERT: aA 415 GLN cc_start: 0.8869 (mt0) cc_final: 0.8545 (mt0) REVERT: R 8 TYR cc_start: 0.9208 (t80) cc_final: 0.8583 (t80) REVERT: R 12 LEU cc_start: 0.9502 (mm) cc_final: 0.9137 (mm) REVERT: eA 415 GLN cc_start: 0.9133 (mt0) cc_final: 0.8659 (mt0) REVERT: T 11 ILE cc_start: 0.9104 (tt) cc_final: 0.8830 (tp) REVERT: jA 112 LEU cc_start: 0.9480 (mm) cc_final: 0.9199 (mm) REVERT: kA 208 TYR cc_start: 0.8872 (t80) cc_final: 0.8590 (t80) REVERT: lA 303 GLU cc_start: 0.8715 (mm-30) cc_final: 0.7256 (mm-30) REVERT: mA 411 ILE cc_start: 0.9277 (tt) cc_final: 0.9018 (tp) REVERT: U 8 TYR cc_start: 0.8796 (t80) cc_final: 0.8571 (t80) REVERT: oA 211 ILE cc_start: 0.9336 (mt) cc_final: 0.9122 (mt) REVERT: pA 315 GLN cc_start: 0.8726 (mt0) cc_final: 0.8458 (mt0) REVERT: qA 408 TYR cc_start: 0.8807 (t80) cc_final: 0.8546 (t80) outliers start: 1 outliers final: 0 residues processed: 650 average time/residue: 0.2026 time to fit residues: 199.8492 Evaluate side-chains 561 residues out of total 1155 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 561 time to evaluate : 1.452 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 87 optimal weight: 6.9990 chunk 93 optimal weight: 2.9990 chunk 35 optimal weight: 0.8980 chunk 46 optimal weight: 0.1980 chunk 90 optimal weight: 4.9990 chunk 26 optimal weight: 9.9990 chunk 49 optimal weight: 0.5980 chunk 50 optimal weight: 0.8980 chunk 74 optimal weight: 9.9990 chunk 84 optimal weight: 6.9990 chunk 91 optimal weight: 0.9990 overall best weight: 0.7182 ------------------------------------------------------------------------------- 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 i 215 GLN k 415 GLN E 15 GLN m 215 GLN H 15 GLN y 215 GLN 6 215 GLN 7 315 GLN K 15 GLN XA 115 GLN YA 215 GLN ** dA 315 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 15 GLN mA 415 GLN U 15 GLN oA 215 GLN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3191 r_free = 0.3191 target = 0.060626 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2961 r_free = 0.2961 target = 0.052301 restraints weight = 46686.775| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3018 r_free = 0.3018 target = 0.054339 restraints weight = 28538.340| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3059 r_free = 0.3059 target = 0.055731 restraints weight = 19085.404| |-----------------------------------------------------------------------------| r_work (final): 0.3044 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8817 moved from start: 0.5973 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 12915 Z= 0.112 Angle : 0.530 5.511 17325 Z= 0.262 Chirality : 0.040 0.141 1995 Planarity : 0.002 0.013 2310 Dihedral : 3.587 27.232 1890 Min Nonbonded Distance : 2.602 Molprobity Statistics. All-atom Clashscore : 4.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 0.61 % Allowed : 8.74 % Favored : 90.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.09 (0.25), residues: 1365 helix: 2.06 (0.15), residues: 1365 sheet: None (None), residues: 0 loop : None (None), residues: 0 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.027 0.002 TYR r 308 ARG 0.002 0.000 ARGgA 206 Details of bonding type rmsd hydrogen bonds : bond 0.02542 ( 1050) hydrogen bonds : angle 3.44010 ( 3150) covalent geometry : bond 0.00286 (12915) covalent geometry : angle 0.53012 (17325) *********************** 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 647 residues out of total 1155 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 640 time to evaluate : 1.595 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: V 108 TYR cc_start: 0.8923 (t80) cc_final: 0.8402 (t80) REVERT: W 212 LEU cc_start: 0.9601 (mm) cc_final: 0.9301 (mm) REVERT: Y 408 TYR cc_start: 0.9079 (t80) cc_final: 0.8851 (t80) REVERT: B 12 LEU cc_start: 0.9465 (mm) cc_final: 0.9225 (mm) REVERT: a 215 GLN cc_start: 0.8684 (mt0) cc_final: 0.8449 (mt0) REVERT: b 311 ILE cc_start: 0.9482 (mt) cc_final: 0.9186 (mt) REVERT: C 3 GLU cc_start: 0.8656 (mm-30) cc_final: 0.8451 (tp30) REVERT: C 8 TYR cc_start: 0.8689 (t80) cc_final: 0.8124 (t80) REVERT: d 111 ILE cc_start: 0.9600 (tt) cc_final: 0.9388 (tt) REVERT: d 112 LEU cc_start: 0.9518 (mm) cc_final: 0.9265 (mm) REVERT: e 203 GLU cc_start: 0.9005 (mm-30) cc_final: 0.8618 (mp0) REVERT: e 208 TYR cc_start: 0.8710 (t80) cc_final: 0.8330 (t80) REVERT: e 215 GLN cc_start: 0.8852 (mt0) cc_final: 0.8560 (tt0) REVERT: f 308 TYR cc_start: 0.9018 (t80) cc_final: 0.8538 (t80) REVERT: g 408 TYR cc_start: 0.9073 (t80) cc_final: 0.8500 (t80) REVERT: D 11 ILE cc_start: 0.9413 (mt) cc_final: 0.9207 (mt) REVERT: i 208 TYR cc_start: 0.8990 (t80) cc_final: 0.8415 (t80) REVERT: j 303 GLU cc_start: 0.9040 (mm-30) cc_final: 0.8687 (mm-30) REVERT: j 308 TYR cc_start: 0.8996 (t80) cc_final: 0.8733 (t80) REVERT: k 408 TYR cc_start: 0.9070 (t80) cc_final: 0.8681 (t80) REVERT: m 208 TYR cc_start: 0.8809 (t80) cc_final: 0.8584 (t80) REVERT: n 308 TYR cc_start: 0.8874 (t80) cc_final: 0.8642 (t80) REVERT: F 3 GLU cc_start: 0.8812 (mm-30) cc_final: 0.7607 (mm-30) REVERT: p 108 TYR cc_start: 0.9125 (t80) cc_final: 0.8364 (t80) REVERT: p 112 LEU cc_start: 0.9605 (mm) cc_final: 0.9168 (mm) REVERT: s 411 ILE cc_start: 0.9403 (mt) cc_final: 0.9166 (mt) REVERT: s 415 GLN cc_start: 0.8792 (mt0) cc_final: 0.8178 (mt0) REVERT: t 108 TYR cc_start: 0.9012 (t80) cc_final: 0.8726 (t80) REVERT: t 112 LEU cc_start: 0.9515 (mm) cc_final: 0.9171 (mm) REVERT: u 208 TYR cc_start: 0.9073 (t80) cc_final: 0.8632 (t80) REVERT: v 315 GLN cc_start: 0.8663 (mt0) cc_final: 0.8289 (mt0) REVERT: H 15 GLN cc_start: 0.9058 (OUTLIER) cc_final: 0.6588 (tp40) REVERT: x 111 ILE cc_start: 0.9400 (mp) cc_final: 0.9065 (mt) REVERT: x 112 LEU cc_start: 0.9413 (mm) cc_final: 0.8863 (mm) REVERT: x 115 GLN cc_start: 0.8793 (mt0) cc_final: 0.8368 (mt0) REVERT: y 212 LEU cc_start: 0.9557 (mm) cc_final: 0.9201 (mm) REVERT: y 215 GLN cc_start: 0.9255 (OUTLIER) cc_final: 0.7499 (tp40) REVERT: I 3 GLU cc_start: 0.8810 (mm-30) cc_final: 0.7633 (mm-30) REVERT: I 8 TYR cc_start: 0.9177 (t80) cc_final: 0.8715 (t80) REVERT: I 12 LEU cc_start: 0.9552 (mm) cc_final: 0.9281 (mm) REVERT: 1 108 TYR cc_start: 0.8700 (t80) cc_final: 0.8425 (t80) REVERT: 4 415 GLN cc_start: 0.8788 (mt0) cc_final: 0.8260 (mt0) REVERT: J 3 GLU cc_start: 0.8818 (mm-30) cc_final: 0.8588 (mm-30) REVERT: J 8 TYR cc_start: 0.8404 (t80) cc_final: 0.7882 (t80) REVERT: 5 115 GLN cc_start: 0.8800 (mt0) cc_final: 0.8546 (mt0) REVERT: 6 208 TYR cc_start: 0.8865 (t80) cc_final: 0.8108 (t80) REVERT: 7 308 TYR cc_start: 0.8614 (t80) cc_final: 0.7880 (t80) REVERT: 8 408 TYR cc_start: 0.8805 (t80) cc_final: 0.8572 (t80) REVERT: K 8 TYR cc_start: 0.9119 (t80) cc_final: 0.8641 (t80) REVERT: K 12 LEU cc_start: 0.9586 (mm) cc_final: 0.9222 (mm) REVERT: 9 108 TYR cc_start: 0.9125 (t80) cc_final: 0.8743 (t80) REVERT: 9 112 LEU cc_start: 0.9432 (mm) cc_final: 0.9032 (mm) REVERT: L 8 TYR cc_start: 0.9090 (t80) cc_final: 0.8660 (t80) REVERT: L 12 LEU cc_start: 0.9554 (mm) cc_final: 0.9309 (mm) REVERT: DA 108 TYR cc_start: 0.9035 (t80) cc_final: 0.8674 (t80) REVERT: DA 112 LEU cc_start: 0.9644 (mm) cc_final: 0.9391 (mm) REVERT: EA 208 TYR cc_start: 0.9089 (t80) cc_final: 0.8759 (t80) REVERT: FA 308 TYR cc_start: 0.9112 (t80) cc_final: 0.8666 (t80) REVERT: FA 312 LEU cc_start: 0.9379 (mm) cc_final: 0.9177 (mm) REVERT: GA 408 TYR cc_start: 0.8999 (t80) cc_final: 0.8569 (t80) REVERT: M 15 GLN cc_start: 0.8731 (mt0) cc_final: 0.8519 (mt0) REVERT: IA 212 LEU cc_start: 0.9581 (mm) cc_final: 0.9296 (mm) REVERT: N 3 GLU cc_start: 0.8769 (tp30) cc_final: 0.8478 (tp30) REVERT: N 12 LEU cc_start: 0.9583 (mm) cc_final: 0.9302 (mm) REVERT: LA 103 GLU cc_start: 0.9113 (mm-30) cc_final: 0.8101 (mm-30) REVERT: NA 303 GLU cc_start: 0.8725 (tp30) cc_final: 0.8510 (mm-30) REVERT: PA 103 GLU cc_start: 0.8640 (mm-30) cc_final: 0.7950 (mm-30) REVERT: PA 115 GLN cc_start: 0.8912 (mt0) cc_final: 0.8665 (mt0) REVERT: RA 303 GLU cc_start: 0.8695 (tp30) cc_final: 0.8489 (mm-30) REVERT: RA 308 TYR cc_start: 0.9027 (t80) cc_final: 0.8826 (t80) REVERT: RA 312 LEU cc_start: 0.9576 (mm) cc_final: 0.9296 (mm) REVERT: SA 408 TYR cc_start: 0.8915 (t80) cc_final: 0.8684 (t80) REVERT: VA 312 LEU cc_start: 0.9579 (mm) cc_final: 0.9313 (mm) REVERT: Q 8 TYR cc_start: 0.8799 (t80) cc_final: 0.8207 (t80) REVERT: XA 108 TYR cc_start: 0.9022 (t80) cc_final: 0.8249 (t80) REVERT: XA 112 LEU cc_start: 0.9501 (mm) cc_final: 0.9185 (mm) REVERT: YA 208 TYR cc_start: 0.9068 (t80) cc_final: 0.8590 (t80) REVERT: YA 212 LEU cc_start: 0.9545 (mm) cc_final: 0.9259 (mm) REVERT: ZA 308 TYR cc_start: 0.8561 (t80) cc_final: 0.8179 (t80) REVERT: aA 408 TYR cc_start: 0.8644 (t80) cc_final: 0.8074 (t80) REVERT: R 3 GLU cc_start: 0.8758 (tp30) cc_final: 0.8525 (mm-30) REVERT: R 8 TYR cc_start: 0.9134 (t80) cc_final: 0.8552 (t80) REVERT: R 12 LEU cc_start: 0.9628 (mm) cc_final: 0.9121 (mm) REVERT: T 11 ILE cc_start: 0.8802 (tt) cc_final: 0.8483 (tp) REVERT: jA 112 LEU cc_start: 0.9288 (mm) cc_final: 0.9062 (mm) REVERT: kA 208 TYR cc_start: 0.8804 (t80) cc_final: 0.8521 (t80) REVERT: kA 213 GLU cc_start: 0.8804 (tm-30) cc_final: 0.8598 (tm-30) REVERT: U 3 GLU cc_start: 0.8732 (tp30) cc_final: 0.7839 (mm-30) REVERT: U 8 TYR cc_start: 0.8643 (t80) cc_final: 0.8146 (t80) REVERT: qA 415 GLN cc_start: 0.8747 (mt0) cc_final: 0.8355 (mt0) outliers start: 7 outliers final: 1 residues processed: 647 average time/residue: 0.2126 time to fit residues: 211.0821 Evaluate side-chains 581 residues out of total 1155 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 578 time to evaluate : 1.571 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 39 optimal weight: 0.7980 chunk 69 optimal weight: 6.9990 chunk 67 optimal weight: 0.7980 chunk 77 optimal weight: 0.8980 chunk 14 optimal weight: 0.6980 chunk 46 optimal weight: 0.7980 chunk 97 optimal weight: 0.0470 chunk 93 optimal weight: 8.9990 chunk 62 optimal weight: 0.5980 chunk 11 optimal weight: 0.9990 chunk 99 optimal weight: 4.9990 overall best weight: 0.5878 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: c 415 GLN u 215 GLN MA 215 GLN QA 215 GLN P 15 GLN YA 215 GLN cA 215 GLN dA 315 GLN S 15 GLN T 15 GLN kA 215 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3241 r_free = 0.3241 target = 0.061479 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3004 r_free = 0.3004 target = 0.052831 restraints weight = 46541.126| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3061 r_free = 0.3061 target = 0.054922 restraints weight = 28921.874| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3101 r_free = 0.3101 target = 0.056337 restraints weight = 19454.214| |-----------------------------------------------------------------------------| r_work (final): 0.3088 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8812 moved from start: 0.6339 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 12915 Z= 0.110 Angle : 0.538 4.917 17325 Z= 0.265 Chirality : 0.039 0.165 1995 Planarity : 0.002 0.013 2310 Dihedral : 3.489 22.752 1890 Min Nonbonded Distance : 2.587 Molprobity Statistics. All-atom Clashscore : 4.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 0.26 % Allowed : 3.12 % Favored : 96.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.23 (0.24), residues: 1365 helix: 2.14 (0.15), residues: 1365 sheet: None (None), residues: 0 loop : None (None), residues: 0 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.019 0.002 TYR J 8 ARG 0.002 0.000 ARG n 306 Details of bonding type rmsd hydrogen bonds : bond 0.02294 ( 1050) hydrogen bonds : angle 3.44928 ( 3150) covalent geometry : bond 0.00288 (12915) covalent geometry : angle 0.53849 (17325) *********************** 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 649 residues out of total 1155 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 646 time to evaluate : 1.640 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: V 108 TYR cc_start: 0.8773 (t80) cc_final: 0.8314 (t80) REVERT: W 212 LEU cc_start: 0.9638 (mm) cc_final: 0.9415 (mm) REVERT: B 12 LEU cc_start: 0.9530 (mm) cc_final: 0.9258 (mm) REVERT: a 215 GLN cc_start: 0.8675 (mt0) cc_final: 0.8455 (mt0) REVERT: b 311 ILE cc_start: 0.9455 (mt) cc_final: 0.9193 (mt) REVERT: C 8 TYR cc_start: 0.8668 (t80) cc_final: 0.8152 (t80) REVERT: d 108 TYR cc_start: 0.8513 (t80) cc_final: 0.8029 (t80) REVERT: d 111 ILE cc_start: 0.9577 (tt) cc_final: 0.9305 (tt) REVERT: e 211 ILE cc_start: 0.9592 (tt) cc_final: 0.9332 (tt) REVERT: e 215 GLN cc_start: 0.8733 (mt0) cc_final: 0.8461 (tt0) REVERT: f 308 TYR cc_start: 0.9015 (t80) cc_final: 0.8630 (t80) REVERT: g 403 GLU cc_start: 0.9092 (mp0) cc_final: 0.8846 (mp0) REVERT: g 408 TYR cc_start: 0.9013 (t80) cc_final: 0.8638 (t80) REVERT: D 3 GLU cc_start: 0.8992 (mp0) cc_final: 0.8658 (mm-30) REVERT: i 208 TYR cc_start: 0.8951 (t80) cc_final: 0.8522 (t80) REVERT: j 303 GLU cc_start: 0.9132 (mm-30) cc_final: 0.8578 (mm-30) REVERT: j 308 TYR cc_start: 0.8967 (t80) cc_final: 0.8672 (t80) REVERT: j 312 LEU cc_start: 0.9472 (mm) cc_final: 0.9203 (mm) REVERT: k 408 TYR cc_start: 0.8992 (t80) cc_final: 0.8596 (t80) REVERT: m 208 TYR cc_start: 0.8773 (t80) cc_final: 0.8528 (t80) REVERT: F 3 GLU cc_start: 0.8696 (mm-30) cc_final: 0.8305 (tp30) REVERT: p 112 LEU cc_start: 0.9584 (mm) cc_final: 0.9333 (mm) REVERT: s 411 ILE cc_start: 0.9429 (mt) cc_final: 0.9216 (mt) REVERT: G 3 GLU cc_start: 0.8374 (tp30) cc_final: 0.7690 (mm-30) REVERT: G 15 GLN cc_start: 0.9001 (mt0) cc_final: 0.8629 (mt0) REVERT: t 103 GLU cc_start: 0.8479 (tp30) cc_final: 0.7933 (mm-30) REVERT: t 112 LEU cc_start: 0.9516 (mm) cc_final: 0.9159 (mm) REVERT: u 208 TYR cc_start: 0.9005 (t80) cc_final: 0.8770 (t80) REVERT: u 212 LEU cc_start: 0.9529 (mm) cc_final: 0.9200 (mm) REVERT: u 215 GLN cc_start: 0.9047 (tp-100) cc_final: 0.8788 (tp40) REVERT: v 303 GLU cc_start: 0.9163 (mm-30) cc_final: 0.8654 (mm-30) REVERT: v 315 GLN cc_start: 0.8738 (mt0) cc_final: 0.8311 (mt0) REVERT: w 415 GLN cc_start: 0.9023 (mt0) cc_final: 0.8615 (mt0) REVERT: x 103 GLU cc_start: 0.9201 (mm-30) cc_final: 0.8869 (mm-30) REVERT: x 111 ILE cc_start: 0.9396 (mp) cc_final: 0.9040 (mt) REVERT: x 112 LEU cc_start: 0.9524 (mm) cc_final: 0.9061 (mm) REVERT: x 115 GLN cc_start: 0.8766 (mt0) cc_final: 0.8449 (mt0) REVERT: y 212 LEU cc_start: 0.9534 (mm) cc_final: 0.9198 (mm) REVERT: z 303 GLU cc_start: 0.9072 (mm-30) cc_final: 0.8586 (mm-30) REVERT: I 3 GLU cc_start: 0.8763 (mm-30) cc_final: 0.7542 (mm-30) REVERT: I 8 TYR cc_start: 0.8847 (t80) cc_final: 0.8548 (t80) REVERT: I 12 LEU cc_start: 0.9470 (mm) cc_final: 0.9149 (mm) REVERT: 1 112 LEU cc_start: 0.9597 (mm) cc_final: 0.9380 (mm) REVERT: 3 311 ILE cc_start: 0.9511 (mt) cc_final: 0.9252 (mt) REVERT: 4 415 GLN cc_start: 0.8763 (mt0) cc_final: 0.8260 (mt0) REVERT: J 3 GLU cc_start: 0.8851 (mm-30) cc_final: 0.8620 (mm-30) REVERT: J 8 TYR cc_start: 0.8335 (t80) cc_final: 0.7833 (t80) REVERT: 5 115 GLN cc_start: 0.8821 (mt0) cc_final: 0.8609 (mt0) REVERT: 7 308 TYR cc_start: 0.8649 (t80) cc_final: 0.7817 (t80) REVERT: 8 408 TYR cc_start: 0.8746 (t80) cc_final: 0.7833 (t80) REVERT: K 3 GLU cc_start: 0.8973 (mm-30) cc_final: 0.8729 (tp30) REVERT: K 8 TYR cc_start: 0.8984 (t80) cc_final: 0.8747 (t80) REVERT: 9 108 TYR cc_start: 0.9007 (t80) cc_final: 0.8665 (t80) REVERT: 9 112 LEU cc_start: 0.9397 (mm) cc_final: 0.9104 (mm) REVERT: BA 303 GLU cc_start: 0.8696 (mm-30) cc_final: 0.8484 (mm-30) REVERT: L 8 TYR cc_start: 0.9089 (t80) cc_final: 0.8647 (t80) REVERT: L 12 LEU cc_start: 0.9561 (mm) cc_final: 0.9289 (mm) REVERT: DA 108 TYR cc_start: 0.8994 (t80) cc_final: 0.8643 (t80) REVERT: DA 112 LEU cc_start: 0.9649 (mm) cc_final: 0.9409 (mm) REVERT: EA 208 TYR cc_start: 0.9118 (t80) cc_final: 0.8785 (t80) REVERT: FA 308 TYR cc_start: 0.9108 (t80) cc_final: 0.8607 (t80) REVERT: FA 312 LEU cc_start: 0.9426 (mm) cc_final: 0.9161 (mm) REVERT: GA 408 TYR cc_start: 0.8964 (t80) cc_final: 0.8618 (t80) REVERT: M 15 GLN cc_start: 0.8807 (mt0) cc_final: 0.8528 (mt0) REVERT: N 3 GLU cc_start: 0.8736 (tp30) cc_final: 0.8461 (tp30) REVERT: N 12 LEU cc_start: 0.9616 (mm) cc_final: 0.9335 (mm) REVERT: MA 212 LEU cc_start: 0.9597 (mm) cc_final: 0.9389 (mm) REVERT: O 12 LEU cc_start: 0.9462 (mm) cc_final: 0.9177 (mm) REVERT: QA 212 LEU cc_start: 0.9666 (mm) cc_final: 0.9402 (mm) REVERT: RA 312 LEU cc_start: 0.9549 (mm) cc_final: 0.9293 (mm) REVERT: TA 103 GLU cc_start: 0.8829 (mm-30) cc_final: 0.8598 (mm-30) REVERT: VA 312 LEU cc_start: 0.9529 (mm) cc_final: 0.9293 (mm) REVERT: WA 403 GLU cc_start: 0.8937 (mm-30) cc_final: 0.8603 (mm-30) REVERT: Q 8 TYR cc_start: 0.8754 (t80) cc_final: 0.8173 (t80) REVERT: XA 108 TYR cc_start: 0.8705 (t80) cc_final: 0.8451 (t80) REVERT: YA 208 TYR cc_start: 0.9061 (t80) cc_final: 0.8565 (t80) REVERT: YA 212 LEU cc_start: 0.9554 (mm) cc_final: 0.9321 (mm) REVERT: YA 215 GLN cc_start: 0.9027 (OUTLIER) cc_final: 0.7844 (tp40) REVERT: ZA 303 GLU cc_start: 0.9106 (mm-30) cc_final: 0.8703 (mm-30) REVERT: ZA 308 TYR cc_start: 0.8767 (t80) cc_final: 0.8274 (t80) REVERT: aA 408 TYR cc_start: 0.8632 (t80) cc_final: 0.8057 (t80) REVERT: R 3 GLU cc_start: 0.8675 (tp30) cc_final: 0.7719 (mm-30) REVERT: R 8 TYR cc_start: 0.9137 (t80) cc_final: 0.8930 (t80) REVERT: R 12 LEU cc_start: 0.9490 (mm) cc_final: 0.9268 (mm) REVERT: eA 415 GLN cc_start: 0.8973 (mt0) cc_final: 0.8228 (mt0) REVERT: S 3 GLU cc_start: 0.8671 (mm-30) cc_final: 0.8245 (mm-30) REVERT: S 8 TYR cc_start: 0.8970 (t80) cc_final: 0.8619 (t80) REVERT: S 12 LEU cc_start: 0.9591 (mm) cc_final: 0.9342 (mm) REVERT: T 11 ILE cc_start: 0.8788 (tt) cc_final: 0.8473 (tp) REVERT: U 3 GLU cc_start: 0.8864 (tp30) cc_final: 0.7558 (mm-30) REVERT: oA 203 GLU cc_start: 0.9279 (mm-30) cc_final: 0.9023 (mm-30) REVERT: oA 211 ILE cc_start: 0.9258 (mt) cc_final: 0.8964 (mt) REVERT: qA 415 GLN cc_start: 0.8663 (mt0) cc_final: 0.7928 (mt0) outliers start: 3 outliers final: 0 residues processed: 649 average time/residue: 0.1984 time to fit residues: 196.6074 Evaluate side-chains 601 residues out of total 1155 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 600 time to evaluate : 1.527 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 20 optimal weight: 1.9990 chunk 33 optimal weight: 0.9990 chunk 14 optimal weight: 0.4980 chunk 78 optimal weight: 2.9990 chunk 31 optimal weight: 3.9990 chunk 84 optimal weight: 0.9990 chunk 87 optimal weight: 5.9990 chunk 52 optimal weight: 3.9990 chunk 95 optimal weight: 0.0970 chunk 18 optimal weight: 5.9990 chunk 85 optimal weight: 5.9990 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: c 415 GLN d 115 GLN i 215 GLN y 215 GLN JA 315 GLN O 15 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3236 r_free = 0.3236 target = 0.061430 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.2998 r_free = 0.2998 target = 0.052498 restraints weight = 46735.775| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3057 r_free = 0.3057 target = 0.054606 restraints weight = 29159.198| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3099 r_free = 0.3099 target = 0.056065 restraints weight = 19725.549| |-----------------------------------------------------------------------------| r_work (final): 0.3083 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8832 moved from start: 0.6469 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 12915 Z= 0.117 Angle : 0.558 5.864 17325 Z= 0.278 Chirality : 0.040 0.168 1995 Planarity : 0.002 0.013 2310 Dihedral : 3.435 20.398 1890 Min Nonbonded Distance : 2.563 Molprobity Statistics. All-atom Clashscore : 4.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 0.09 % Allowed : 4.68 % Favored : 95.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.53 (0.24), residues: 1365 helix: 2.33 (0.15), residues: 1365 sheet: None (None), residues: 0 loop : None (None), residues: 0 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.018 0.002 TYRdA 308 ARG 0.002 0.000 ARGQA 206 Details of bonding type rmsd hydrogen bonds : bond 0.02386 ( 1050) hydrogen bonds : angle 3.46809 ( 3150) covalent geometry : bond 0.00305 (12915) covalent geometry : angle 0.55791 (17325) *********************** 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 640 residues out of total 1155 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 639 time to evaluate : 1.561 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: A 3 GLU cc_start: 0.8576 (mm-30) cc_final: 0.8374 (tp30) REVERT: V 108 TYR cc_start: 0.8600 (t80) cc_final: 0.8207 (t80) REVERT: W 208 TYR cc_start: 0.9025 (t80) cc_final: 0.8795 (t80) REVERT: Y 412 LEU cc_start: 0.9417 (mm) cc_final: 0.9192 (mm) REVERT: B 12 LEU cc_start: 0.9561 (mm) cc_final: 0.9277 (mm) REVERT: b 311 ILE cc_start: 0.9431 (mt) cc_final: 0.9180 (mt) REVERT: b 312 LEU cc_start: 0.9390 (mm) cc_final: 0.9179 (mm) REVERT: C 8 TYR cc_start: 0.8683 (t80) cc_final: 0.8139 (t80) REVERT: d 108 TYR cc_start: 0.9014 (t80) cc_final: 0.8801 (t80) REVERT: d 111 ILE cc_start: 0.9535 (tt) cc_final: 0.9307 (tt) REVERT: d 112 LEU cc_start: 0.9639 (mm) cc_final: 0.9393 (mm) REVERT: e 211 ILE cc_start: 0.9571 (tt) cc_final: 0.9360 (tt) REVERT: e 215 GLN cc_start: 0.8690 (mt0) cc_final: 0.8435 (tt0) REVERT: f 308 TYR cc_start: 0.8995 (t80) cc_final: 0.8675 (t80) REVERT: g 403 GLU cc_start: 0.9144 (mp0) cc_final: 0.8795 (mp0) REVERT: g 408 TYR cc_start: 0.9020 (t80) cc_final: 0.8625 (t80) REVERT: D 3 GLU cc_start: 0.9066 (mp0) cc_final: 0.8719 (mm-30) REVERT: D 12 LEU cc_start: 0.9595 (mm) cc_final: 0.9328 (mm) REVERT: i 208 TYR cc_start: 0.8967 (t80) cc_final: 0.8498 (t80) REVERT: i 215 GLN cc_start: 0.8930 (tp-100) cc_final: 0.8293 (tp40) REVERT: j 303 GLU cc_start: 0.9067 (mm-30) cc_final: 0.8446 (mm-30) REVERT: j 308 TYR cc_start: 0.8938 (t80) cc_final: 0.8587 (t80) REVERT: j 312 LEU cc_start: 0.9452 (mm) cc_final: 0.9089 (mm) REVERT: k 408 TYR cc_start: 0.9016 (t80) cc_final: 0.8645 (t80) REVERT: E 3 GLU cc_start: 0.8679 (mm-30) cc_final: 0.7972 (mm-30) REVERT: l 108 TYR cc_start: 0.9033 (t80) cc_final: 0.8753 (t80) REVERT: m 208 TYR cc_start: 0.8787 (t80) cc_final: 0.8518 (t80) REVERT: n 303 GLU cc_start: 0.9051 (mm-30) cc_final: 0.8671 (mm-30) REVERT: n 315 GLN cc_start: 0.8750 (mt0) cc_final: 0.8482 (tt0) REVERT: F 3 GLU cc_start: 0.8816 (mm-30) cc_final: 0.8530 (tp30) REVERT: p 108 TYR cc_start: 0.8824 (t80) cc_final: 0.8572 (t80) REVERT: G 3 GLU cc_start: 0.8236 (tp30) cc_final: 0.7571 (mm-30) REVERT: G 8 TYR cc_start: 0.8920 (t80) cc_final: 0.8641 (t80) REVERT: G 15 GLN cc_start: 0.8973 (mt0) cc_final: 0.8718 (mt0) REVERT: t 103 GLU cc_start: 0.8516 (tp30) cc_final: 0.8119 (mm-30) REVERT: t 112 LEU cc_start: 0.9509 (mm) cc_final: 0.9048 (mm) REVERT: u 208 TYR cc_start: 0.9148 (t80) cc_final: 0.8904 (t80) REVERT: u 212 LEU cc_start: 0.9532 (mm) cc_final: 0.9247 (mm) REVERT: v 315 GLN cc_start: 0.8699 (mt0) cc_final: 0.8314 (mt0) REVERT: w 415 GLN cc_start: 0.9056 (mt0) cc_final: 0.8604 (mt0) REVERT: x 103 GLU cc_start: 0.9176 (mm-30) cc_final: 0.8691 (mm-30) REVERT: y 212 LEU cc_start: 0.9559 (mm) cc_final: 0.9247 (mm) REVERT: I 3 GLU cc_start: 0.8784 (mm-30) cc_final: 0.8564 (tp30) REVERT: I 8 TYR cc_start: 0.8745 (t80) cc_final: 0.8445 (t80) REVERT: 1 108 TYR cc_start: 0.8742 (t80) cc_final: 0.8529 (t80) REVERT: 2 212 LEU cc_start: 0.9556 (mm) cc_final: 0.9332 (mm) REVERT: 3 311 ILE cc_start: 0.9539 (mt) cc_final: 0.9323 (mt) REVERT: J 3 GLU cc_start: 0.8900 (mm-30) cc_final: 0.8660 (mm-30) REVERT: 5 115 GLN cc_start: 0.8851 (mt0) cc_final: 0.8590 (mt0) REVERT: 7 308 TYR cc_start: 0.8654 (t80) cc_final: 0.7967 (t80) REVERT: 8 408 TYR cc_start: 0.8799 (t80) cc_final: 0.7931 (t80) REVERT: K 3 GLU cc_start: 0.8912 (mm-30) cc_final: 0.8680 (tp30) REVERT: K 8 TYR cc_start: 0.8950 (t80) cc_final: 0.8621 (t80) REVERT: 9 108 TYR cc_start: 0.8905 (t80) cc_final: 0.8681 (t80) REVERT: 9 112 LEU cc_start: 0.9469 (mm) cc_final: 0.9213 (mm) REVERT: BA 303 GLU cc_start: 0.8743 (mm-30) cc_final: 0.8514 (mm-30) REVERT: BA 312 LEU cc_start: 0.9469 (mm) cc_final: 0.9245 (mm) REVERT: L 8 TYR cc_start: 0.9086 (t80) cc_final: 0.8642 (t80) REVERT: L 12 LEU cc_start: 0.9546 (mm) cc_final: 0.9287 (mm) REVERT: DA 108 TYR cc_start: 0.9031 (t80) cc_final: 0.8677 (t80) REVERT: DA 112 LEU cc_start: 0.9657 (mm) cc_final: 0.9420 (mm) REVERT: EA 208 TYR cc_start: 0.9065 (t80) cc_final: 0.8746 (t80) REVERT: FA 308 TYR cc_start: 0.9105 (t80) cc_final: 0.8563 (t80) REVERT: FA 312 LEU cc_start: 0.9415 (mm) cc_final: 0.9171 (mm) REVERT: GA 408 TYR cc_start: 0.8990 (t80) cc_final: 0.8578 (t80) REVERT: M 15 GLN cc_start: 0.8781 (mt0) cc_final: 0.8453 (mt0) REVERT: IA 212 LEU cc_start: 0.9416 (mm) cc_final: 0.9210 (mm) REVERT: N 3 GLU cc_start: 0.8706 (tp30) cc_final: 0.8462 (tp30) REVERT: N 12 LEU cc_start: 0.9624 (mm) cc_final: 0.9388 (mm) REVERT: LA 103 GLU cc_start: 0.8931 (mm-30) cc_final: 0.8684 (mm-30) REVERT: MA 212 LEU cc_start: 0.9630 (mm) cc_final: 0.9379 (mm) REVERT: NA 303 GLU cc_start: 0.8943 (mm-30) cc_final: 0.8484 (mm-30) REVERT: O 12 LEU cc_start: 0.9591 (mm) cc_final: 0.9223 (mm) REVERT: QA 212 LEU cc_start: 0.9552 (mm) cc_final: 0.9344 (mm) REVERT: RA 303 GLU cc_start: 0.8941 (mm-30) cc_final: 0.8507 (mm-30) REVERT: RA 312 LEU cc_start: 0.9581 (mm) cc_final: 0.9321 (mm) REVERT: P 3 GLU cc_start: 0.8746 (tp30) cc_final: 0.7742 (mm-30) REVERT: VA 312 LEU cc_start: 0.9549 (mm) cc_final: 0.9323 (mm) REVERT: WA 403 GLU cc_start: 0.8965 (mm-30) cc_final: 0.8734 (mm-30) REVERT: Q 8 TYR cc_start: 0.8697 (t80) cc_final: 0.8350 (t80) REVERT: YA 208 TYR cc_start: 0.9086 (t80) cc_final: 0.8570 (t80) REVERT: YA 212 LEU cc_start: 0.9566 (mm) cc_final: 0.9334 (mm) REVERT: ZA 303 GLU cc_start: 0.9247 (mm-30) cc_final: 0.8771 (mm-30) REVERT: ZA 308 TYR cc_start: 0.8441 (t80) cc_final: 0.7880 (t80) REVERT: aA 408 TYR cc_start: 0.9037 (t80) cc_final: 0.8678 (t80) REVERT: aA 412 LEU cc_start: 0.9140 (mp) cc_final: 0.8851 (mp) REVERT: R 12 LEU cc_start: 0.9499 (mm) cc_final: 0.9266 (mm) REVERT: S 8 TYR cc_start: 0.8970 (t80) cc_final: 0.8504 (t80) REVERT: S 12 LEU cc_start: 0.9575 (mm) cc_final: 0.9264 (mm) REVERT: fA 108 TYR cc_start: 0.9105 (t80) cc_final: 0.8815 (t80) REVERT: fA 111 ILE cc_start: 0.9438 (tp) cc_final: 0.9235 (pt) REVERT: T 11 ILE cc_start: 0.8788 (tt) cc_final: 0.8446 (tp) REVERT: jA 108 TYR cc_start: 0.8823 (t80) cc_final: 0.8614 (t80) REVERT: U 3 GLU cc_start: 0.8866 (tp30) cc_final: 0.8058 (mm-30) REVERT: nA 108 TYR cc_start: 0.8370 (t80) cc_final: 0.7873 (t80) REVERT: qA 415 GLN cc_start: 0.8791 (mt0) cc_final: 0.8506 (mt0) outliers start: 1 outliers final: 0 residues processed: 640 average time/residue: 0.2003 time to fit residues: 196.4594 Evaluate side-chains 586 residues out of total 1155 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 586 time to evaluate : 1.563 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 22 optimal weight: 3.9990 chunk 13 optimal weight: 2.9990 chunk 87 optimal weight: 0.9980 chunk 24 optimal weight: 3.9990 chunk 31 optimal weight: 0.9980 chunk 0 optimal weight: 10.0000 chunk 40 optimal weight: 7.9990 chunk 50 optimal weight: 5.9990 chunk 64 optimal weight: 0.0980 chunk 102 optimal weight: 7.9990 chunk 94 optimal weight: 2.9990 overall best weight: 1.6184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: d 115 GLN E 15 GLN l 115 GLN PA 115 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3186 r_free = 0.3186 target = 0.059414 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2944 r_free = 0.2944 target = 0.050920 restraints weight = 47033.662| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 19)----------------| | r_work = 0.3004 r_free = 0.3004 target = 0.052965 restraints weight = 29068.261| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3046 r_free = 0.3046 target = 0.054377 restraints weight = 19588.010| |-----------------------------------------------------------------------------| r_work (final): 0.3035 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8878 moved from start: 0.6332 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= 0.146 Angle : 0.569 4.461 17325 Z= 0.291 Chirality : 0.041 0.149 1995 Planarity : 0.002 0.014 2310 Dihedral : 3.168 18.883 1890 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 4.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 0.09 % Allowed : 2.77 % Favored : 97.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.82 (0.24), residues: 1365 helix: 2.50 (0.15), residues: 1365 sheet: None (None), residues: 0 loop : None (None), residues: 0 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.023 0.002 TYR 3 308 ARG 0.003 0.000 ARGAA 206 Details of bonding type rmsd hydrogen bonds : bond 0.02815 ( 1050) hydrogen bonds : angle 3.69350 ( 3150) covalent geometry : bond 0.00372 (12915) covalent geometry : angle 0.56927 (17325) *********************** 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 621 residues out of total 1155 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 620 time to evaluate : 1.616 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 3 GLU cc_start: 0.8548 (mm-30) cc_final: 0.8332 (tp30) REVERT: V 108 TYR cc_start: 0.8574 (t80) cc_final: 0.8236 (t80) REVERT: W 208 TYR cc_start: 0.8950 (t80) cc_final: 0.8715 (t80) REVERT: Y 412 LEU cc_start: 0.9460 (mm) cc_final: 0.9183 (mm) REVERT: B 12 LEU cc_start: 0.9586 (mm) cc_final: 0.9268 (mm) REVERT: b 312 LEU cc_start: 0.9433 (mm) cc_final: 0.9180 (mm) REVERT: C 8 TYR cc_start: 0.8688 (t80) cc_final: 0.8154 (t80) REVERT: d 108 TYR cc_start: 0.8887 (t80) cc_final: 0.8416 (t80) REVERT: d 112 LEU cc_start: 0.9488 (mm) cc_final: 0.9161 (mm) REVERT: d 115 GLN cc_start: 0.8759 (tp-100) cc_final: 0.8135 (tp40) REVERT: e 203 GLU cc_start: 0.9004 (mm-30) cc_final: 0.8358 (mm-30) REVERT: e 215 GLN cc_start: 0.8786 (mt0) cc_final: 0.8493 (mt0) REVERT: f 308 TYR cc_start: 0.9066 (t80) cc_final: 0.8708 (t80) REVERT: g 408 TYR cc_start: 0.9042 (t80) cc_final: 0.8628 (t80) REVERT: D 3 GLU cc_start: 0.9083 (mp0) cc_final: 0.8740 (mm-30) REVERT: D 12 LEU cc_start: 0.9630 (mm) cc_final: 0.9395 (mm) REVERT: i 208 TYR cc_start: 0.8936 (t80) cc_final: 0.8447 (t80) REVERT: j 303 GLU cc_start: 0.9134 (mm-30) cc_final: 0.8896 (mm-30) REVERT: j 308 TYR cc_start: 0.8978 (t80) cc_final: 0.8562 (t80) REVERT: j 312 LEU cc_start: 0.9477 (mm) cc_final: 0.9098 (mm) REVERT: k 408 TYR cc_start: 0.8980 (t80) cc_final: 0.8610 (t80) REVERT: E 3 GLU cc_start: 0.8935 (mm-30) cc_final: 0.8252 (mm-30) REVERT: l 108 TYR cc_start: 0.8985 (t80) cc_final: 0.8777 (t80) REVERT: l 111 ILE cc_start: 0.9436 (tt) cc_final: 0.9208 (tp) REVERT: m 203 GLU cc_start: 0.8951 (mm-30) cc_final: 0.8682 (mm-30) REVERT: n 303 GLU cc_start: 0.9036 (mm-30) cc_final: 0.8556 (mm-30) REVERT: n 315 GLN cc_start: 0.8771 (mt0) cc_final: 0.8509 (tt0) REVERT: o 408 TYR cc_start: 0.9010 (t80) cc_final: 0.8806 (t80) REVERT: F 3 GLU cc_start: 0.8762 (mm-30) cc_final: 0.7724 (tp30) REVERT: p 108 TYR cc_start: 0.8886 (t80) cc_final: 0.8621 (t80) REVERT: q 208 TYR cc_start: 0.8747 (t80) cc_final: 0.8532 (t80) REVERT: r 308 TYR cc_start: 0.8681 (t80) cc_final: 0.8195 (t80) REVERT: s 411 ILE cc_start: 0.9493 (mt) cc_final: 0.9292 (mt) REVERT: s 415 GLN cc_start: 0.8848 (mt0) cc_final: 0.8236 (mt0) REVERT: G 8 TYR cc_start: 0.9162 (t80) cc_final: 0.8774 (t80) REVERT: G 11 ILE cc_start: 0.9515 (mt) cc_final: 0.9301 (mt) REVERT: t 112 LEU cc_start: 0.9561 (mm) cc_final: 0.9157 (mm) REVERT: u 208 TYR cc_start: 0.9202 (t80) cc_final: 0.8971 (t80) REVERT: u 212 LEU cc_start: 0.9566 (mm) cc_final: 0.9246 (mm) REVERT: v 315 GLN cc_start: 0.8700 (mt0) cc_final: 0.8351 (mt0) REVERT: x 103 GLU cc_start: 0.9185 (mm-30) cc_final: 0.8683 (mm-30) REVERT: y 212 LEU cc_start: 0.9566 (mm) cc_final: 0.9273 (mm) REVERT: y 215 GLN cc_start: 0.8730 (tp-100) cc_final: 0.8509 (tp-100) REVERT: z 303 GLU cc_start: 0.8940 (mm-30) cc_final: 0.8570 (mm-30) REVERT: z 308 TYR cc_start: 0.8766 (t80) cc_final: 0.8432 (t80) REVERT: I 3 GLU cc_start: 0.8742 (mm-30) cc_final: 0.8529 (tp30) REVERT: 2 208 TYR cc_start: 0.8704 (t80) cc_final: 0.8501 (t80) REVERT: 3 312 LEU cc_start: 0.9592 (mp) cc_final: 0.9340 (mp) REVERT: 4 412 LEU cc_start: 0.9429 (mm) cc_final: 0.9224 (mm) REVERT: 5 115 GLN cc_start: 0.8895 (mt0) cc_final: 0.8634 (mt0) REVERT: 7 303 GLU cc_start: 0.9031 (mm-30) cc_final: 0.8744 (mm-30) REVERT: K 3 GLU cc_start: 0.8914 (mm-30) cc_final: 0.8685 (tp30) REVERT: K 8 TYR cc_start: 0.9049 (t80) cc_final: 0.8612 (t80) REVERT: 9 103 GLU cc_start: 0.9041 (mm-30) cc_final: 0.8761 (mm-30) REVERT: 9 108 TYR cc_start: 0.8841 (t80) cc_final: 0.8546 (t80) REVERT: 9 112 LEU cc_start: 0.9485 (mm) cc_final: 0.9136 (mm) REVERT: BA 312 LEU cc_start: 0.9459 (mm) cc_final: 0.9221 (mm) REVERT: L 8 TYR cc_start: 0.9134 (t80) cc_final: 0.8621 (t80) REVERT: L 12 LEU cc_start: 0.9554 (mm) cc_final: 0.9263 (mm) REVERT: DA 108 TYR cc_start: 0.9021 (t80) cc_final: 0.8638 (t80) REVERT: EA 208 TYR cc_start: 0.9099 (t80) cc_final: 0.8719 (t80) REVERT: FA 308 TYR cc_start: 0.9123 (t80) cc_final: 0.8513 (t80) REVERT: FA 312 LEU cc_start: 0.9422 (mm) cc_final: 0.9158 (mm) REVERT: GA 403 GLU cc_start: 0.9105 (mp0) cc_final: 0.8855 (mp0) REVERT: GA 408 TYR cc_start: 0.9070 (t80) cc_final: 0.8638 (t80) REVERT: M 15 GLN cc_start: 0.8855 (mt0) cc_final: 0.8520 (mt0) REVERT: N 3 GLU cc_start: 0.8627 (tp30) cc_final: 0.8414 (tp30) REVERT: N 12 LEU cc_start: 0.9640 (mm) cc_final: 0.9384 (mm) REVERT: LA 103 GLU cc_start: 0.8939 (mm-30) cc_final: 0.8535 (mm-30) REVERT: MA 212 LEU cc_start: 0.9635 (mm) cc_final: 0.9379 (mm) REVERT: NA 303 GLU cc_start: 0.9040 (mm-30) cc_final: 0.8835 (mm-30) REVERT: O 12 LEU cc_start: 0.9625 (mm) cc_final: 0.9333 (mm) REVERT: PA 103 GLU cc_start: 0.9117 (mm-30) cc_final: 0.8674 (mm-30) REVERT: QA 203 GLU cc_start: 0.9011 (mm-30) cc_final: 0.8708 (mm-30) REVERT: QA 212 LEU cc_start: 0.9609 (mm) cc_final: 0.9325 (mm) REVERT: RA 303 GLU cc_start: 0.8963 (mm-30) cc_final: 0.8352 (mm-30) REVERT: RA 312 LEU cc_start: 0.9593 (mm) cc_final: 0.9375 (mm) REVERT: VA 312 LEU cc_start: 0.9566 (mm) cc_final: 0.9342 (mm) REVERT: XA 108 TYR cc_start: 0.8857 (t80) cc_final: 0.8085 (t80) REVERT: YA 208 TYR cc_start: 0.9122 (t80) cc_final: 0.8477 (t80) REVERT: YA 212 LEU cc_start: 0.9587 (mm) cc_final: 0.9372 (mm) REVERT: ZA 303 GLU cc_start: 0.9200 (mm-30) cc_final: 0.8672 (mm-30) REVERT: ZA 312 LEU cc_start: 0.9423 (mp) cc_final: 0.9051 (mp) REVERT: aA 408 TYR cc_start: 0.9182 (t80) cc_final: 0.8810 (t80) REVERT: R 3 GLU cc_start: 0.8892 (mm-30) cc_final: 0.7910 (mm-30) REVERT: R 12 LEU cc_start: 0.9531 (mm) cc_final: 0.9262 (mm) REVERT: bA 112 LEU cc_start: 0.9628 (mm) cc_final: 0.9415 (mm) REVERT: cA 212 LEU cc_start: 0.9632 (mm) cc_final: 0.9414 (mm) REVERT: eA 415 GLN cc_start: 0.8963 (mt0) cc_final: 0.8181 (mt0) REVERT: S 3 GLU cc_start: 0.8664 (mm-30) cc_final: 0.8429 (mm-30) REVERT: fA 108 TYR cc_start: 0.8989 (t80) cc_final: 0.8778 (t80) REVERT: fA 111 ILE cc_start: 0.9474 (tp) cc_final: 0.9224 (pt) REVERT: T 11 ILE cc_start: 0.8809 (tt) cc_final: 0.8482 (tp) REVERT: lA 303 GLU cc_start: 0.8936 (mm-30) cc_final: 0.8716 (mm-30) REVERT: U 3 GLU cc_start: 0.8809 (tp30) cc_final: 0.8305 (mm-30) REVERT: oA 203 GLU cc_start: 0.9255 (mm-30) cc_final: 0.8973 (mm-30) REVERT: qA 415 GLN cc_start: 0.8803 (mt0) cc_final: 0.8578 (mt0) outliers start: 1 outliers final: 0 residues processed: 621 average time/residue: 0.2260 time to fit residues: 218.2912 Evaluate side-chains 577 residues out of total 1155 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 577 time to evaluate : 1.389 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 101 optimal weight: 4.9990 chunk 4 optimal weight: 7.9990 chunk 55 optimal weight: 0.8980 chunk 27 optimal weight: 4.9990 chunk 74 optimal weight: 7.9990 chunk 34 optimal weight: 0.1980 chunk 94 optimal weight: 1.9990 chunk 51 optimal weight: 2.9990 chunk 44 optimal weight: 0.9980 chunk 18 optimal weight: 0.9990 chunk 58 optimal weight: 0.4980 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 15 GLN ** x 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** hA 315 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3241 r_free = 0.3241 target = 0.061855 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3007 r_free = 0.3007 target = 0.053137 restraints weight = 46679.431| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3067 r_free = 0.3067 target = 0.055217 restraints weight = 28961.629| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3108 r_free = 0.3108 target = 0.056658 restraints weight = 19671.599| |-----------------------------------------------------------------------------| r_work (final): 0.3092 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8825 moved from start: 0.6767 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 12915 Z= 0.123 Angle : 0.612 5.438 17325 Z= 0.304 Chirality : 0.040 0.136 1995 Planarity : 0.002 0.014 2310 Dihedral : 3.530 19.868 1890 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 5.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 0.09 % Allowed : 1.04 % Favored : 98.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.91 (0.23), residues: 1365 helix: 2.56 (0.14), residues: 1365 sheet: None (None), residues: 0 loop : None (None), residues: 0 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.026 0.002 TYR 3 308 ARG 0.002 0.000 ARG G 10 Details of bonding type rmsd hydrogen bonds : bond 0.02371 ( 1050) hydrogen bonds : angle 3.56206 ( 3150) covalent geometry : bond 0.00327 (12915) covalent geometry : angle 0.61221 (17325) *********************** 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 634 residues out of total 1155 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 633 time to evaluate : 1.630 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: A 3 GLU cc_start: 0.8606 (mm-30) cc_final: 0.8372 (tp30) REVERT: A 12 LEU cc_start: 0.9483 (mm) cc_final: 0.9281 (mm) REVERT: V 108 TYR cc_start: 0.8498 (t80) cc_final: 0.8178 (t80) REVERT: X 303 GLU cc_start: 0.9113 (mp0) cc_final: 0.8895 (mp0) REVERT: Y 412 LEU cc_start: 0.9458 (mm) cc_final: 0.9193 (mm) REVERT: B 12 LEU cc_start: 0.9598 (mm) cc_final: 0.9254 (mm) REVERT: b 312 LEU cc_start: 0.9449 (mm) cc_final: 0.9208 (mm) REVERT: d 103 GLU cc_start: 0.8938 (mm-30) cc_final: 0.8700 (mm-30) REVERT: d 108 TYR cc_start: 0.8737 (t80) cc_final: 0.8353 (t80) REVERT: d 112 LEU cc_start: 0.9416 (mm) cc_final: 0.9175 (mm) REVERT: e 203 GLU cc_start: 0.9045 (mm-30) cc_final: 0.8724 (mm-30) REVERT: e 215 GLN cc_start: 0.8709 (mt0) cc_final: 0.8389 (tt0) REVERT: f 308 TYR cc_start: 0.9018 (t80) cc_final: 0.8639 (t80) REVERT: g 408 TYR cc_start: 0.9020 (t80) cc_final: 0.8595 (t80) REVERT: D 3 GLU cc_start: 0.9100 (mp0) cc_final: 0.8682 (mm-30) REVERT: D 12 LEU cc_start: 0.9598 (mm) cc_final: 0.9378 (mm) REVERT: i 208 TYR cc_start: 0.8929 (t80) cc_final: 0.8491 (t80) REVERT: j 303 GLU cc_start: 0.9121 (mm-30) cc_final: 0.8858 (mm-30) REVERT: j 308 TYR cc_start: 0.8883 (t80) cc_final: 0.8601 (t80) REVERT: j 312 LEU cc_start: 0.9483 (mm) cc_final: 0.9192 (mm) REVERT: k 408 TYR cc_start: 0.8942 (t80) cc_final: 0.8550 (t80) REVERT: l 108 TYR cc_start: 0.8933 (t80) cc_final: 0.8700 (t80) REVERT: n 303 GLU cc_start: 0.9049 (mm-30) cc_final: 0.8616 (mm-30) REVERT: F 3 GLU cc_start: 0.8787 (mm-30) cc_final: 0.7660 (tp30) REVERT: p 108 TYR cc_start: 0.8763 (t80) cc_final: 0.8520 (t80) REVERT: q 208 TYR cc_start: 0.8660 (t80) cc_final: 0.8448 (t80) REVERT: r 308 TYR cc_start: 0.8886 (t80) cc_final: 0.8641 (t80) REVERT: r 312 LEU cc_start: 0.9627 (mt) cc_final: 0.9349 (mt) REVERT: s 415 GLN cc_start: 0.8824 (mt0) cc_final: 0.8159 (mt0) REVERT: G 11 ILE cc_start: 0.9231 (mt) cc_final: 0.9022 (mt) REVERT: G 12 LEU cc_start: 0.9539 (mm) cc_final: 0.9273 (mm) REVERT: t 112 LEU cc_start: 0.9489 (mm) cc_final: 0.9171 (mm) REVERT: u 208 TYR cc_start: 0.9173 (t80) cc_final: 0.8945 (t80) REVERT: u 212 LEU cc_start: 0.9539 (mm) cc_final: 0.9208 (mm) REVERT: v 311 ILE cc_start: 0.9425 (mt) cc_final: 0.9134 (mt) REVERT: v 315 GLN cc_start: 0.8686 (mt0) cc_final: 0.8450 (mt0) REVERT: x 103 GLU cc_start: 0.9192 (mm-30) cc_final: 0.8761 (mm-30) REVERT: x 108 TYR cc_start: 0.8568 (t80) cc_final: 0.8165 (t80) REVERT: y 212 LEU cc_start: 0.9521 (mm) cc_final: 0.9245 (mm) REVERT: y 215 GLN cc_start: 0.8631 (tp-100) cc_final: 0.8406 (tp40) REVERT: z 303 GLU cc_start: 0.8980 (mm-30) cc_final: 0.8666 (mm-30) REVERT: I 3 GLU cc_start: 0.8799 (mm-30) cc_final: 0.7597 (mm-30) REVERT: I 8 TYR cc_start: 0.9025 (t80) cc_final: 0.8752 (t80) REVERT: I 12 LEU cc_start: 0.9474 (mm) cc_final: 0.9230 (mm) REVERT: 3 312 LEU cc_start: 0.9547 (mp) cc_final: 0.9313 (mp) REVERT: 4 415 GLN cc_start: 0.8731 (mt0) cc_final: 0.8373 (mt0) REVERT: J 15 GLN cc_start: 0.8577 (mt0) cc_final: 0.8241 (mt0) REVERT: 5 103 GLU cc_start: 0.8844 (mm-30) cc_final: 0.7611 (mm-30) REVERT: 6 208 TYR cc_start: 0.9003 (t80) cc_final: 0.8775 (t80) REVERT: 7 303 GLU cc_start: 0.9024 (mm-30) cc_final: 0.8787 (mm-30) REVERT: K 3 GLU cc_start: 0.8910 (mm-30) cc_final: 0.8666 (tp30) REVERT: K 8 TYR cc_start: 0.8821 (t80) cc_final: 0.8477 (t80) REVERT: 9 103 GLU cc_start: 0.9072 (mm-30) cc_final: 0.8746 (mm-30) REVERT: 9 108 TYR cc_start: 0.8698 (t80) cc_final: 0.8497 (t80) REVERT: 9 112 LEU cc_start: 0.9348 (mm) cc_final: 0.9129 (mm) REVERT: BA 312 LEU cc_start: 0.9453 (mm) cc_final: 0.9244 (mm) REVERT: L 3 GLU cc_start: 0.8763 (mm-30) cc_final: 0.8495 (tp30) REVERT: L 8 TYR cc_start: 0.9091 (t80) cc_final: 0.8618 (t80) REVERT: L 12 LEU cc_start: 0.9534 (mm) cc_final: 0.9267 (mm) REVERT: DA 108 TYR cc_start: 0.8995 (t80) cc_final: 0.8607 (t80) REVERT: EA 208 TYR cc_start: 0.9051 (t80) cc_final: 0.8678 (t80) REVERT: FA 308 TYR cc_start: 0.9158 (t80) cc_final: 0.8549 (t80) REVERT: FA 312 LEU cc_start: 0.9456 (mm) cc_final: 0.9167 (mm) REVERT: GA 403 GLU cc_start: 0.9140 (mp0) cc_final: 0.8887 (mp0) REVERT: GA 408 TYR cc_start: 0.8977 (t80) cc_final: 0.8605 (t80) REVERT: M 15 GLN cc_start: 0.8765 (mt0) cc_final: 0.8480 (mt0) REVERT: N 12 LEU cc_start: 0.9643 (mm) cc_final: 0.9403 (mm) REVERT: LA 103 GLU cc_start: 0.8963 (mm-30) cc_final: 0.8636 (mm-30) REVERT: MA 212 LEU cc_start: 0.9635 (mm) cc_final: 0.9399 (mm) REVERT: NA 303 GLU cc_start: 0.9068 (mm-30) cc_final: 0.8834 (mm-30) REVERT: O 8 TYR cc_start: 0.9081 (t80) cc_final: 0.8781 (t80) REVERT: O 12 LEU cc_start: 0.9617 (mm) cc_final: 0.9382 (mm) REVERT: PA 103 GLU cc_start: 0.9172 (mm-30) cc_final: 0.8519 (mm-30) REVERT: QA 203 GLU cc_start: 0.9011 (mm-30) cc_final: 0.8734 (mm-30) REVERT: QA 212 LEU cc_start: 0.9589 (mm) cc_final: 0.9172 (mm) REVERT: RA 303 GLU cc_start: 0.8937 (mm-30) cc_final: 0.8389 (mm-30) REVERT: VA 312 LEU cc_start: 0.9609 (mm) cc_final: 0.9394 (mm) REVERT: WA 413 GLU cc_start: 0.8373 (pt0) cc_final: 0.8156 (pp20) REVERT: Q 11 ILE cc_start: 0.9480 (tt) cc_final: 0.9269 (tt) REVERT: XA 108 TYR cc_start: 0.8864 (t80) cc_final: 0.8174 (t80) REVERT: YA 208 TYR cc_start: 0.9079 (t80) cc_final: 0.8503 (t80) REVERT: ZA 303 GLU cc_start: 0.9140 (mm-30) cc_final: 0.8593 (mm-30) REVERT: ZA 312 LEU cc_start: 0.9471 (mp) cc_final: 0.9131 (mp) REVERT: R 3 GLU cc_start: 0.8863 (mm-30) cc_final: 0.8394 (mm-30) REVERT: R 12 LEU cc_start: 0.9503 (mm) cc_final: 0.9273 (mm) REVERT: bA 112 LEU cc_start: 0.9650 (mm) cc_final: 0.9430 (mm) REVERT: dA 303 GLU cc_start: 0.9163 (mm-30) cc_final: 0.8759 (mm-30) REVERT: dA 315 GLN cc_start: 0.8576 (tp40) cc_final: 0.8341 (tp40) REVERT: eA 415 GLN cc_start: 0.8765 (mt0) cc_final: 0.8389 (mt0) REVERT: S 8 TYR cc_start: 0.8973 (t80) cc_final: 0.8671 (t80) REVERT: iA 408 TYR cc_start: 0.8690 (t80) cc_final: 0.7976 (t80) REVERT: iA 411 ILE cc_start: 0.9408 (tt) cc_final: 0.9156 (tt) REVERT: T 11 ILE cc_start: 0.8801 (tt) cc_final: 0.8462 (tp) REVERT: jA 111 ILE cc_start: 0.8131 (tt) cc_final: 0.7865 (tp) REVERT: U 8 TYR cc_start: 0.8353 (t80) cc_final: 0.8084 (t80) REVERT: oA 203 GLU cc_start: 0.9281 (mm-30) cc_final: 0.9052 (mm-30) REVERT: qA 415 GLN cc_start: 0.8811 (mt0) cc_final: 0.8416 (mt0) outliers start: 1 outliers final: 0 residues processed: 634 average time/residue: 0.1964 time to fit residues: 190.2384 Evaluate side-chains 592 residues out of total 1155 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 592 time to evaluate : 1.424 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 21 optimal weight: 7.9990 chunk 77 optimal weight: 3.9990 chunk 40 optimal weight: 6.9990 chunk 99 optimal weight: 1.9990 chunk 7 optimal weight: 10.0000 chunk 104 optimal weight: 7.9990 chunk 89 optimal weight: 0.8980 chunk 52 optimal weight: 4.9990 chunk 86 optimal weight: 0.9990 chunk 26 optimal weight: 1.9990 chunk 69 optimal weight: 1.9990 overall best weight: 1.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 15 GLN E 15 GLN XA 115 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3186 r_free = 0.3186 target = 0.059294 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2953 r_free = 0.2953 target = 0.050760 restraints weight = 46854.128| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3012 r_free = 0.3012 target = 0.052797 restraints weight = 28870.781| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3053 r_free = 0.3053 target = 0.054185 restraints weight = 19344.148| |-----------------------------------------------------------------------------| r_work (final): 0.3040 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8875 moved from start: 0.6630 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 12915 Z= 0.151 Angle : 0.641 5.349 17325 Z= 0.327 Chirality : 0.042 0.145 1995 Planarity : 0.002 0.014 2310 Dihedral : 3.218 18.647 1890 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 5.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 0.17 % Allowed : 1.90 % Favored : 97.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 4.24 (0.23), residues: 1365 helix: 2.77 (0.14), residues: 1365 sheet: None (None), residues: 0 loop : None (None), residues: 0 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.026 0.002 TYR 3 308 ARG 0.003 0.000 ARGCA 406 Details of bonding type rmsd hydrogen bonds : bond 0.02923 ( 1050) hydrogen bonds : angle 3.80931 ( 3150) covalent geometry : bond 0.00389 (12915) covalent geometry : angle 0.64148 (17325) *********************** 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 618 residues out of total 1155 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 616 time to evaluate : 1.405 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: V 108 TYR cc_start: 0.8564 (t80) cc_final: 0.8221 (t80) REVERT: Y 412 LEU cc_start: 0.9489 (mm) cc_final: 0.9187 (mm) REVERT: B 12 LEU cc_start: 0.9595 (mm) cc_final: 0.9241 (mm) REVERT: b 303 GLU cc_start: 0.8758 (mm-30) cc_final: 0.8341 (tp30) REVERT: b 312 LEU cc_start: 0.9472 (mm) cc_final: 0.9211 (mm) REVERT: d 103 GLU cc_start: 0.8750 (mm-30) cc_final: 0.8507 (mm-30) REVERT: d 108 TYR cc_start: 0.8820 (t80) cc_final: 0.8574 (t80) REVERT: e 203 GLU cc_start: 0.9070 (mm-30) cc_final: 0.8434 (mm-30) REVERT: e 215 GLN cc_start: 0.8772 (mt0) cc_final: 0.8472 (tt0) REVERT: f 308 TYR cc_start: 0.9068 (t80) cc_final: 0.8660 (t80) REVERT: g 408 TYR cc_start: 0.9105 (t80) cc_final: 0.8626 (t80) REVERT: D 12 LEU cc_start: 0.9632 (mm) cc_final: 0.9367 (mm) REVERT: i 208 TYR cc_start: 0.8934 (t80) cc_final: 0.8552 (t80) REVERT: j 303 GLU cc_start: 0.9149 (mm-30) cc_final: 0.8772 (mm-30) REVERT: j 308 TYR cc_start: 0.8985 (t80) cc_final: 0.8686 (t80) REVERT: j 312 LEU cc_start: 0.9502 (mm) cc_final: 0.9210 (mm) REVERT: k 408 TYR cc_start: 0.8960 (t80) cc_final: 0.8611 (t80) REVERT: E 12 LEU cc_start: 0.9478 (mm) cc_final: 0.9275 (mm) REVERT: l 108 TYR cc_start: 0.8903 (t80) cc_final: 0.8626 (t80) REVERT: n 303 GLU cc_start: 0.9045 (mm-30) cc_final: 0.8542 (mm-30) REVERT: F 3 GLU cc_start: 0.8785 (mm-30) cc_final: 0.7710 (mm-30) REVERT: p 108 TYR cc_start: 0.8827 (t80) cc_final: 0.8616 (t80) REVERT: q 208 TYR cc_start: 0.8709 (t80) cc_final: 0.8450 (t80) REVERT: r 308 TYR cc_start: 0.8905 (t80) cc_final: 0.8647 (t80) REVERT: r 312 LEU cc_start: 0.9606 (mt) cc_final: 0.9345 (mt) REVERT: s 411 ILE cc_start: 0.9527 (mt) cc_final: 0.9316 (mt) REVERT: s 415 GLN cc_start: 0.8859 (mt0) cc_final: 0.8536 (mt0) REVERT: G 11 ILE cc_start: 0.9426 (mt) cc_final: 0.9153 (mt) REVERT: G 12 LEU cc_start: 0.9630 (mm) cc_final: 0.9364 (mm) REVERT: t 112 LEU cc_start: 0.9470 (mm) cc_final: 0.9127 (mm) REVERT: u 208 TYR cc_start: 0.9203 (t80) cc_final: 0.8994 (t80) REVERT: u 212 LEU cc_start: 0.9560 (mm) cc_final: 0.9225 (mm) REVERT: v 303 GLU cc_start: 0.9116 (mm-30) cc_final: 0.8761 (mm-30) REVERT: v 315 GLN cc_start: 0.8725 (mt0) cc_final: 0.8414 (mt0) REVERT: x 103 GLU cc_start: 0.9193 (mm-30) cc_final: 0.8749 (mm-30) REVERT: y 212 LEU cc_start: 0.9575 (mm) cc_final: 0.9224 (mm) REVERT: I 3 GLU cc_start: 0.8767 (mm-30) cc_final: 0.7723 (mm-30) REVERT: I 8 TYR cc_start: 0.9039 (t80) cc_final: 0.8793 (t80) REVERT: I 12 LEU cc_start: 0.9465 (mm) cc_final: 0.9193 (mm) REVERT: 3 312 LEU cc_start: 0.9530 (mp) cc_final: 0.9316 (mp) REVERT: 4 415 GLN cc_start: 0.8857 (mt0) cc_final: 0.8657 (mt0) REVERT: 6 208 TYR cc_start: 0.9030 (t80) cc_final: 0.8787 (t80) REVERT: 7 303 GLU cc_start: 0.9015 (mm-30) cc_final: 0.8666 (mm-30) REVERT: K 3 GLU cc_start: 0.8865 (mm-30) cc_final: 0.8623 (tp30) REVERT: K 8 TYR cc_start: 0.8914 (t80) cc_final: 0.8692 (t80) REVERT: 9 103 GLU cc_start: 0.9058 (mm-30) cc_final: 0.8744 (mm-30) REVERT: 9 108 TYR cc_start: 0.8750 (t80) cc_final: 0.8519 (t80) REVERT: L 8 TYR cc_start: 0.9099 (t80) cc_final: 0.8555 (t80) REVERT: L 12 LEU cc_start: 0.9556 (mm) cc_final: 0.9252 (mm) REVERT: DA 108 TYR cc_start: 0.9013 (t80) cc_final: 0.8677 (t80) REVERT: EA 208 TYR cc_start: 0.9104 (t80) cc_final: 0.8707 (t80) REVERT: FA 308 TYR cc_start: 0.9174 (t80) cc_final: 0.8520 (t80) REVERT: FA 312 LEU cc_start: 0.9439 (mm) cc_final: 0.9131 (mm) REVERT: GA 403 GLU cc_start: 0.9135 (mp0) cc_final: 0.8875 (mp0) REVERT: GA 408 TYR cc_start: 0.9043 (t80) cc_final: 0.8635 (t80) REVERT: M 15 GLN cc_start: 0.8866 (mt0) cc_final: 0.8554 (mt0) REVERT: JA 312 LEU cc_start: 0.9538 (mm) cc_final: 0.9312 (mm) REVERT: N 3 GLU cc_start: 0.8686 (mm-30) cc_final: 0.8483 (tp30) REVERT: N 12 LEU cc_start: 0.9633 (mm) cc_final: 0.9343 (mm) REVERT: LA 103 GLU cc_start: 0.8970 (mm-30) cc_final: 0.8581 (mm-30) REVERT: MA 212 LEU cc_start: 0.9644 (mm) cc_final: 0.9388 (mm) REVERT: NA 303 GLU cc_start: 0.9053 (mm-30) cc_final: 0.8820 (mm-30) REVERT: OA 412 LEU cc_start: 0.9512 (mm) cc_final: 0.9307 (mm) REVERT: O 12 LEU cc_start: 0.9601 (mm) cc_final: 0.9336 (mm) REVERT: PA 103 GLU cc_start: 0.9181 (mm-30) cc_final: 0.8533 (mm-30) REVERT: QA 203 GLU cc_start: 0.9072 (mm-30) cc_final: 0.8530 (mm-30) REVERT: QA 212 LEU cc_start: 0.9481 (mm) cc_final: 0.9273 (mm) REVERT: RA 303 GLU cc_start: 0.8985 (mm-30) cc_final: 0.8336 (mm-30) REVERT: SA 412 LEU cc_start: 0.9539 (mm) cc_final: 0.9335 (mm) REVERT: TA 112 LEU cc_start: 0.9588 (mm) cc_final: 0.9365 (mm) REVERT: VA 312 LEU cc_start: 0.9631 (mm) cc_final: 0.9422 (mm) REVERT: WA 412 LEU cc_start: 0.9642 (mm) cc_final: 0.9440 (mm) REVERT: WA 413 GLU cc_start: 0.8509 (pt0) cc_final: 0.8151 (pp20) REVERT: XA 108 TYR cc_start: 0.8912 (t80) cc_final: 0.8204 (t80) REVERT: YA 208 TYR cc_start: 0.9107 (t80) cc_final: 0.8481 (t80) REVERT: YA 212 LEU cc_start: 0.9581 (mm) cc_final: 0.9378 (mm) REVERT: ZA 303 GLU cc_start: 0.9171 (mm-30) cc_final: 0.8576 (mm-30) REVERT: aA 408 TYR cc_start: 0.8982 (t80) cc_final: 0.8650 (t80) REVERT: R 3 GLU cc_start: 0.8860 (mm-30) cc_final: 0.8353 (mm-30) REVERT: R 12 LEU cc_start: 0.9526 (mm) cc_final: 0.9240 (mm) REVERT: bA 112 LEU cc_start: 0.9643 (mm) cc_final: 0.9424 (mm) REVERT: dA 303 GLU cc_start: 0.9208 (mm-30) cc_final: 0.8850 (mm-30) REVERT: dA 315 GLN cc_start: 0.8722 (tp40) cc_final: 0.8222 (tp40) REVERT: eA 415 GLN cc_start: 0.8831 (mt0) cc_final: 0.8392 (mt0) REVERT: S 8 TYR cc_start: 0.8914 (t80) cc_final: 0.8633 (t80) REVERT: iA 403 GLU cc_start: 0.8952 (mm-30) cc_final: 0.8460 (mm-30) REVERT: iA 408 TYR cc_start: 0.8786 (t80) cc_final: 0.8004 (t80) REVERT: T 11 ILE cc_start: 0.8840 (tt) cc_final: 0.8506 (tp) REVERT: kA 215 GLN cc_start: 0.8811 (mt0) cc_final: 0.8597 (mt0) REVERT: lA 303 GLU cc_start: 0.8885 (mm-30) cc_final: 0.7500 (mm-30) REVERT: U 8 TYR cc_start: 0.8512 (t80) cc_final: 0.8292 (t80) REVERT: oA 203 GLU cc_start: 0.9261 (mm-30) cc_final: 0.8984 (mm-30) outliers start: 2 outliers final: 0 residues processed: 618 average time/residue: 0.2015 time to fit residues: 191.4480 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 : 1.571 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 46 optimal weight: 5.9990 chunk 51 optimal weight: 4.9990 chunk 34 optimal weight: 2.9990 chunk 84 optimal weight: 7.9990 chunk 58 optimal weight: 0.9980 chunk 44 optimal weight: 2.9990 chunk 80 optimal weight: 0.7980 chunk 31 optimal weight: 0.9990 chunk 23 optimal weight: 0.9990 chunk 22 optimal weight: 4.9990 chunk 13 optimal weight: 6.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 15 GLN G 15 GLN XA 115 GLN fA 115 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 = 0.3194 r_free = 0.3194 target = 0.059850 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.2960 r_free = 0.2960 target = 0.051255 restraints weight = 46731.755| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3019 r_free = 0.3019 target = 0.053294 restraints weight = 29111.902| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3062 r_free = 0.3062 target = 0.054722 restraints weight = 19650.969| |-----------------------------------------------------------------------------| r_work (final): 0.3048 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8865 moved from start: 0.6796 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 12915 Z= 0.150 Angle : 0.670 5.673 17325 Z= 0.341 Chirality : 0.041 0.142 1995 Planarity : 0.002 0.014 2310 Dihedral : 3.344 18.946 1890 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 6.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 0.26 % Allowed : 0.61 % Favored : 99.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 4.32 (0.23), residues: 1365 helix: 2.81 (0.14), residues: 1365 sheet: None (None), residues: 0 loop : None (None), residues: 0 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.025 0.002 TYR 3 308 ARG 0.002 0.000 ARGCA 406 Details of bonding type rmsd hydrogen bonds : bond 0.02826 ( 1050) hydrogen bonds : angle 3.73487 ( 3150) covalent geometry : bond 0.00394 (12915) covalent geometry : angle 0.66963 (17325) ********************** 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 612 residues out of total 1155 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 609 time to evaluate : 1.570 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: W 208 TYR cc_start: 0.8924 (t80) cc_final: 0.8673 (t80) REVERT: X 303 GLU cc_start: 0.9086 (mp0) cc_final: 0.8881 (mp0) REVERT: B 12 LEU cc_start: 0.9619 (mm) cc_final: 0.9232 (mm) REVERT: b 303 GLU cc_start: 0.8787 (mm-30) cc_final: 0.8369 (tp30) REVERT: b 312 LEU cc_start: 0.9483 (mm) cc_final: 0.9232 (mm) REVERT: d 108 TYR cc_start: 0.8867 (t80) cc_final: 0.8612 (t80) REVERT: e 203 GLU cc_start: 0.9103 (mm-30) cc_final: 0.8424 (mm-30) REVERT: e 215 GLN cc_start: 0.8772 (mt0) cc_final: 0.8451 (tt0) REVERT: f 308 TYR cc_start: 0.9065 (t80) cc_final: 0.8628 (t80) REVERT: g 408 TYR cc_start: 0.9076 (t80) cc_final: 0.8581 (t80) REVERT: D 3 GLU cc_start: 0.9141 (mp0) cc_final: 0.8874 (mp0) REVERT: D 12 LEU cc_start: 0.9618 (mm) cc_final: 0.9376 (mm) REVERT: h 112 LEU cc_start: 0.9461 (mm) cc_final: 0.9237 (mm) REVERT: i 208 TYR cc_start: 0.8926 (t80) cc_final: 0.8500 (t80) REVERT: j 303 GLU cc_start: 0.9107 (mm-30) cc_final: 0.8736 (mm-30) REVERT: j 308 TYR cc_start: 0.8998 (t80) cc_final: 0.8710 (t80) REVERT: j 312 LEU cc_start: 0.9486 (mm) cc_final: 0.9197 (mm) REVERT: k 408 TYR cc_start: 0.8949 (t80) cc_final: 0.8582 (t80) REVERT: l 108 TYR cc_start: 0.8865 (t80) cc_final: 0.8635 (t80) REVERT: n 303 GLU cc_start: 0.9068 (mm-30) cc_final: 0.8547 (mm-30) REVERT: o 403 GLU cc_start: 0.9061 (mm-30) cc_final: 0.8827 (mp0) REVERT: F 3 GLU cc_start: 0.8759 (mm-30) cc_final: 0.7662 (mm-30) REVERT: q 208 TYR cc_start: 0.8711 (t80) cc_final: 0.8447 (t80) REVERT: r 308 TYR cc_start: 0.8857 (t80) cc_final: 0.8574 (t80) REVERT: r 312 LEU cc_start: 0.9604 (mt) cc_final: 0.9350 (mt) REVERT: s 411 ILE cc_start: 0.9528 (mt) cc_final: 0.9313 (mt) REVERT: s 415 GLN cc_start: 0.8817 (mt0) cc_final: 0.8512 (mt0) REVERT: G 12 LEU cc_start: 0.9653 (mm) cc_final: 0.9404 (mm) REVERT: t 112 LEU cc_start: 0.9488 (mm) cc_final: 0.9125 (mm) REVERT: u 208 TYR cc_start: 0.9196 (t80) cc_final: 0.8991 (t80) REVERT: u 212 LEU cc_start: 0.9544 (mm) cc_final: 0.9208 (mm) REVERT: v 303 GLU cc_start: 0.9124 (mm-30) cc_final: 0.8819 (mm-30) REVERT: v 315 GLN cc_start: 0.8781 (mt0) cc_final: 0.8456 (mt0) REVERT: x 103 GLU cc_start: 0.9194 (mm-30) cc_final: 0.8741 (mm-30) REVERT: y 212 LEU cc_start: 0.9566 (mm) cc_final: 0.9211 (mm) REVERT: I 3 GLU cc_start: 0.8782 (mm-30) cc_final: 0.8010 (mm-30) REVERT: I 8 TYR cc_start: 0.9053 (t80) cc_final: 0.8804 (t80) REVERT: I 12 LEU cc_start: 0.9474 (mm) cc_final: 0.9209 (mm) REVERT: 5 103 GLU cc_start: 0.8847 (mm-30) cc_final: 0.8621 (tp30) REVERT: 6 208 TYR cc_start: 0.9012 (t80) cc_final: 0.8789 (t80) REVERT: 7 303 GLU cc_start: 0.9026 (mm-30) cc_final: 0.8672 (mm-30) REVERT: K 3 GLU cc_start: 0.8843 (mm-30) cc_final: 0.8582 (tp30) REVERT: 9 103 GLU cc_start: 0.9077 (mm-30) cc_final: 0.8740 (mm-30) REVERT: L 8 TYR cc_start: 0.9106 (t80) cc_final: 0.8607 (t80) REVERT: L 12 LEU cc_start: 0.9538 (mm) cc_final: 0.9268 (mm) REVERT: DA 108 TYR cc_start: 0.8991 (t80) cc_final: 0.8667 (t80) REVERT: EA 208 TYR cc_start: 0.9103 (t80) cc_final: 0.8696 (t80) REVERT: FA 308 TYR cc_start: 0.9155 (t80) cc_final: 0.8549 (t80) REVERT: FA 312 LEU cc_start: 0.9439 (mm) cc_final: 0.9147 (mm) REVERT: GA 403 GLU cc_start: 0.9146 (mp0) cc_final: 0.8872 (mp0) REVERT: GA 408 TYR cc_start: 0.9043 (t80) cc_final: 0.8636 (t80) REVERT: M 15 GLN cc_start: 0.8838 (mt0) cc_final: 0.8523 (mt0) REVERT: IA 208 TYR cc_start: 0.9013 (t80) cc_final: 0.8676 (t80) REVERT: JA 312 LEU cc_start: 0.9527 (mm) cc_final: 0.9278 (mm) REVERT: N 3 GLU cc_start: 0.8686 (mm-30) cc_final: 0.7562 (mm-30) REVERT: N 12 LEU cc_start: 0.9646 (mm) cc_final: 0.9378 (mm) REVERT: LA 103 GLU cc_start: 0.8964 (mm-30) cc_final: 0.8578 (mm-30) REVERT: MA 212 LEU cc_start: 0.9646 (mm) cc_final: 0.9391 (mm) REVERT: NA 303 GLU cc_start: 0.9052 (mm-30) cc_final: 0.8372 (mm-30) REVERT: PA 103 GLU cc_start: 0.9171 (mm-30) cc_final: 0.8487 (mm-30) REVERT: QA 203 GLU cc_start: 0.9089 (mm-30) cc_final: 0.8567 (mm-30) REVERT: QA 212 LEU cc_start: 0.9499 (mm) cc_final: 0.9265 (mm) REVERT: RA 303 GLU cc_start: 0.8984 (mm-30) cc_final: 0.8547 (mm-30) REVERT: SA 412 LEU cc_start: 0.9560 (mm) cc_final: 0.9338 (mm) REVERT: TA 112 LEU cc_start: 0.9576 (mm) cc_final: 0.9372 (mm) REVERT: VA 312 LEU cc_start: 0.9596 (mm) cc_final: 0.9362 (mm) REVERT: WA 413 GLU cc_start: 0.8423 (pt0) cc_final: 0.8135 (pp20) REVERT: Q 12 LEU cc_start: 0.9572 (mm) cc_final: 0.9320 (mm) REVERT: XA 108 TYR cc_start: 0.8871 (t80) cc_final: 0.8160 (t80) REVERT: YA 208 TYR cc_start: 0.9115 (t80) cc_final: 0.8508 (t80) REVERT: ZA 303 GLU cc_start: 0.9167 (mm-30) cc_final: 0.8590 (mm-30) REVERT: aA 408 TYR cc_start: 0.8895 (t80) cc_final: 0.8556 (t80) REVERT: R 3 GLU cc_start: 0.8865 (mm-30) cc_final: 0.8357 (mm-30) REVERT: R 12 LEU cc_start: 0.9499 (mm) cc_final: 0.9226 (mm) REVERT: bA 112 LEU cc_start: 0.9646 (mm) cc_final: 0.9440 (mm) REVERT: dA 315 GLN cc_start: 0.8713 (tp40) cc_final: 0.8159 (tp40) REVERT: eA 403 GLU cc_start: 0.8598 (tp30) cc_final: 0.8373 (mm-30) REVERT: eA 415 GLN cc_start: 0.8870 (mt0) cc_final: 0.8376 (mt0) REVERT: iA 408 TYR cc_start: 0.8763 (t80) cc_final: 0.7978 (t80) REVERT: T 11 ILE cc_start: 0.8851 (tt) cc_final: 0.8513 (tp) REVERT: oA 203 GLU cc_start: 0.9267 (mm-30) cc_final: 0.8524 (mm-30) outliers start: 3 outliers final: 0 residues processed: 612 average time/residue: 0.2001 time to fit residues: 187.5911 Evaluate side-chains 571 residues out of total 1155 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 571 time to evaluate : 1.612 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 70 optimal weight: 0.0010 chunk 50 optimal weight: 3.9990 chunk 16 optimal weight: 3.9990 chunk 72 optimal weight: 7.9990 chunk 23 optimal weight: 3.9990 chunk 37 optimal weight: 2.9990 chunk 14 optimal weight: 3.9990 chunk 46 optimal weight: 3.9990 chunk 69 optimal weight: 0.9990 chunk 104 optimal weight: 1.9990 chunk 29 optimal weight: 1.9990 overall best weight: 1.5994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 15 GLN n 315 GLN ** 9 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** XA 115 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3180 r_free = 0.3180 target = 0.059102 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2944 r_free = 0.2944 target = 0.050663 restraints weight = 46860.290| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3003 r_free = 0.3003 target = 0.052668 restraints weight = 29178.285| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3045 r_free = 0.3045 target = 0.054047 restraints weight = 19679.740| |-----------------------------------------------------------------------------| r_work (final): 0.3031 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8876 moved from start: 0.6781 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 12915 Z= 0.160 Angle : 0.687 6.954 17325 Z= 0.352 Chirality : 0.043 0.156 1995 Planarity : 0.002 0.015 2310 Dihedral : 3.280 19.054 1890 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 6.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 0.17 % Allowed : 0.26 % Favored : 99.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 4.45 (0.22), residues: 1365 helix: 2.89 (0.14), residues: 1365 sheet: None (None), residues: 0 loop : None (None), residues: 0 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.025 0.002 TYR o 408 ARG 0.002 0.000 ARG 6 206 Details of bonding type rmsd hydrogen bonds : bond 0.03105 ( 1050) hydrogen bonds : angle 3.82581 ( 3150) covalent geometry : bond 0.00415 (12915) covalent geometry : angle 0.68685 (17325) =============================================================================== Job complete usr+sys time: 4409.35 seconds wall clock time: 76 minutes 41.11 seconds (4601.11 seconds total)