Starting phenix.real_space_refine on Thu Sep 26 08:21:09 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wkx_21812/09_2024/6wkx_21812.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wkx_21812/09_2024/6wkx_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wkx_21812/09_2024/6wkx_21812.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wkx_21812/09_2024/6wkx_21812.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wkx_21812/09_2024/6wkx_21812.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wkx_21812/09_2024/6wkx_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): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/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: 8.72, per 1000 atoms: 0.68 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: 3.43 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: 1.23 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: 4.02 Time building geometry restraints manager: 3.93 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.29: 2310 1.29 - 1.35: 2310 1.35 - 1.41: 735 1.41 - 1.47: 1785 1.47 - 1.54: 5775 Bond restraints: 12915 Sorted by residual: bond pdb=" CA ILEgA 211 " pdb=" C ILEgA 211 " ideal model delta sigma weight residual 1.524 1.516 0.008 1.18e-02 7.18e+03 4.90e-01 bond pdb=" CA GLUoA 213 " pdb=" C GLUoA 213 " ideal model delta sigma weight residual 1.527 1.518 0.008 1.21e-02 6.83e+03 4.73e-01 bond pdb=" CA ILEYA 211 " pdb=" C ILEYA 211 " ideal model delta sigma weight residual 1.524 1.516 0.008 1.18e-02 7.18e+03 4.69e-01 bond pdb=" CA ILE a 211 " pdb=" C ILE a 211 " ideal model delta sigma weight residual 1.524 1.516 0.008 1.18e-02 7.18e+03 4.58e-01 bond pdb=" CA GLU a 213 " pdb=" C GLU a 213 " ideal model delta sigma weight residual 1.527 1.519 0.008 1.21e-02 6.83e+03 4.57e-01 ... (remaining 12910 not shown) Histogram of bond angle deviations from ideal: 0.00 - 0.68: 14524 0.68 - 1.37: 2161 1.37 - 2.05: 452 2.05 - 2.73: 26 2.73 - 3.42: 162 Bond angle restraints: 17325 Sorted by residual: angle pdb=" NE ARGWA 406 " pdb=" CZ ARGWA 406 " pdb=" NH1 ARGWA 406 " ideal model delta sigma weight residual 121.50 119.78 1.72 1.00e+00 1.00e+00 2.96e+00 angle pdb=" NE ARG G 6 " pdb=" CZ ARG G 6 " pdb=" NH1 ARG G 6 " ideal model delta sigma weight residual 121.50 119.79 1.71 1.00e+00 1.00e+00 2.93e+00 angle pdb=" NE ARG R 6 " pdb=" CZ ARG R 6 " pdb=" NH1 ARG R 6 " ideal model delta sigma weight residual 121.50 119.79 1.71 1.00e+00 1.00e+00 2.91e+00 angle pdb=" NE ARG w 406 " pdb=" CZ ARG w 406 " pdb=" NH1 ARG w 406 " ideal model delta sigma weight residual 121.50 119.79 1.71 1.00e+00 1.00e+00 2.91e+00 angle pdb=" NE ARGOA 406 " pdb=" CZ ARGOA 406 " pdb=" NH1 ARGOA 406 " ideal model delta sigma weight residual 121.50 119.81 1.69 1.00e+00 1.00e+00 2.87e+00 ... (remaining 17320 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 8.02: 5691 8.02 - 16.05: 1232 16.05 - 24.07: 574 24.07 - 32.09: 399 32.09 - 40.11: 294 Dihedral angle restraints: 8190 sinusoidal: 3465 harmonic: 4725 Sorted by residual: dihedral pdb=" CA ILE 6 204 " pdb=" CB ILE 6 204 " pdb=" CG1 ILE 6 204 " pdb=" CD1 ILE 6 204 " ideal model delta sinusoidal sigma weight residual 60.00 100.11 -40.11 3 1.50e+01 4.44e-03 7.14e+00 dihedral pdb=" CA ILEgA 204 " pdb=" CB ILEgA 204 " pdb=" CG1 ILEgA 204 " pdb=" CD1 ILEgA 204 " ideal model delta sinusoidal sigma weight residual 60.00 100.11 -40.11 3 1.50e+01 4.44e-03 7.14e+00 dihedral pdb=" CA ILEIA 204 " pdb=" CB ILEIA 204 " pdb=" CG1 ILEIA 204 " pdb=" CD1 ILEIA 204 " ideal model delta sinusoidal sigma weight residual 60.00 100.11 -40.11 3 1.50e+01 4.44e-03 7.13e+00 ... (remaining 8187 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.017: 612 0.017 - 0.033: 449 0.033 - 0.050: 532 0.050 - 0.066: 205 0.066 - 0.083: 197 Chirality restraints: 1995 Sorted by residual: chirality pdb=" CA ILE 3 311 " pdb=" N ILE 3 311 " pdb=" C ILE 3 311 " pdb=" CB ILE 3 311 " both_signs ideal model delta sigma weight residual False 2.43 2.52 -0.08 2.00e-01 2.50e+01 1.71e-01 chirality pdb=" CA ILEBA 311 " pdb=" N ILEBA 311 " pdb=" C ILEBA 311 " pdb=" CB ILEBA 311 " both_signs ideal model delta sigma weight residual False 2.43 2.52 -0.08 2.00e-01 2.50e+01 1.69e-01 chirality pdb=" CA ILE j 311 " pdb=" N ILE j 311 " pdb=" C ILE j 311 " pdb=" CB ILE j 311 " both_signs ideal model delta sigma weight residual False 2.43 2.52 -0.08 2.00e-01 2.50e+01 1.68e-01 ... (remaining 1992 not shown) Planarity restraints: 2310 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR v 308 " -0.008 2.00e-02 2.50e+03 5.84e-03 6.83e-01 pdb=" CG TYR v 308 " 0.012 2.00e-02 2.50e+03 pdb=" CD1 TYR v 308 " -0.001 2.00e-02 2.50e+03 pdb=" CD2 TYR v 308 " 0.004 2.00e-02 2.50e+03 pdb=" CE1 TYR v 308 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 TYR v 308 " -0.006 2.00e-02 2.50e+03 pdb=" CZ TYR v 308 " -0.000 2.00e-02 2.50e+03 pdb=" OH TYR v 308 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYRdA 308 " -0.008 2.00e-02 2.50e+03 5.83e-03 6.80e-01 pdb=" CG TYRdA 308 " 0.012 2.00e-02 2.50e+03 pdb=" CD1 TYRdA 308 " -0.001 2.00e-02 2.50e+03 pdb=" CD2 TYRdA 308 " 0.004 2.00e-02 2.50e+03 pdb=" CE1 TYRdA 308 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 TYRdA 308 " -0.006 2.00e-02 2.50e+03 pdb=" CZ TYRdA 308 " 0.000 2.00e-02 2.50e+03 pdb=" OH TYRdA 308 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYRRA 308 " 0.008 2.00e-02 2.50e+03 5.79e-03 6.71e-01 pdb=" CG TYRRA 308 " -0.012 2.00e-02 2.50e+03 pdb=" CD1 TYRRA 308 " 0.001 2.00e-02 2.50e+03 pdb=" CD2 TYRRA 308 " -0.004 2.00e-02 2.50e+03 pdb=" CE1 TYRRA 308 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 TYRRA 308 " 0.007 2.00e-02 2.50e+03 pdb=" CZ TYRRA 308 " -0.001 2.00e-02 2.50e+03 pdb=" OH TYRRA 308 " -0.000 2.00e-02 2.50e+03 ... (remaining 2307 not shown) Histogram of nonbonded interaction distances: 2.30 - 2.82: 4158 2.82 - 3.34: 15647 3.34 - 3.86: 21033 3.86 - 4.38: 25256 4.38 - 4.90: 38427 Nonbonded interactions: 104521 Sorted by model distance: nonbonded pdb=" O GLU I 13 " pdb=" NH2 ARG 9 110 " model vdw 2.298 3.120 nonbonded pdb=" NH2 ARG 0 410 " pdb=" O GLU 7 313 " model vdw 2.311 3.120 nonbonded pdb=" O GLU M 13 " pdb=" NH2 ARGPA 110 " model vdw 2.329 3.120 nonbonded pdb=" O GLU C 13 " pdb=" NH2 ARG l 110 " model vdw 2.335 3.120 nonbonded pdb=" O GLU f 313 " pdb=" NH2 ARG o 410 " model vdw 2.341 3.120 ... (remaining 104516 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain '0' selection = chain '1' selection = chain '2' selection = chain '3' selection = chain '4' selection = chain '5' selection = chain '6' selection = chain '7' selection = chain '8' selection = chain '9' selection = chain 'A' selection = chain 'AA' selection = chain 'B' selection = chain 'BA' selection = chain 'C' selection = chain 'CA' selection = chain 'D' selection = chain 'DA' selection = chain 'E' selection = chain 'EA' selection = chain 'F' selection = chain 'FA' selection = chain 'G' selection = chain 'GA' selection = chain 'H' selection = chain 'HA' selection = chain 'I' selection = chain 'IA' selection = chain 'J' selection = chain 'JA' selection = chain 'K' selection = chain 'KA' selection = chain 'L' selection = chain 'LA' selection = chain 'M' selection = chain 'MA' selection = chain 'N' selection = chain 'NA' selection = chain 'O' selection = chain 'OA' selection = chain 'P' selection = chain 'PA' selection = chain 'Q' selection = chain 'QA' selection = chain 'R' selection = chain 'RA' selection = chain 'S' selection = chain 'SA' selection = chain 'T' selection = chain 'TA' selection = chain 'U' selection = chain 'UA' selection = chain 'V' selection = chain 'VA' selection = chain 'W' selection = chain 'WA' selection = chain 'X' selection = chain 'XA' selection = chain 'Y' selection = chain 'YA' selection = chain 'Z' selection = chain 'ZA' selection = chain 'a' selection = chain 'aA' selection = chain 'b' selection = chain 'bA' selection = chain 'c' selection = chain 'cA' selection = chain 'd' selection = chain 'dA' selection = chain 'e' selection = chain 'eA' selection = chain 'f' selection = chain 'fA' selection = chain 'g' selection = chain 'gA' selection = chain 'h' selection = chain 'hA' selection = chain 'i' selection = chain 'iA' selection = chain 'j' selection = chain 'jA' selection = chain 'k' selection = chain 'kA' selection = chain 'l' selection = chain 'lA' selection = chain 'm' selection = chain 'mA' selection = chain 'n' selection = chain 'nA' selection = chain 'o' selection = chain 'oA' selection = chain 'p' selection = chain 'pA' selection = chain 'q' selection = chain 'qA' selection = chain 'r' selection = chain 's' selection = chain 't' selection = chain 'u' selection = chain 'v' selection = chain 'w' selection = chain 'x' selection = chain 'y' selection = chain 'z' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.420 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: 0.460 Check model and map are aligned: 0.100 Set scattering table: 0.120 Process input model: 31.170 Find NCS groups from input model: 0.700 Set up NCS constraints: 0.180 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:2.700 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.860 ------------------------------------------------------------------------------- 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= 0.403 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 *********************** 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 fitting. rotamer outliers: 0 poor density : 650 time to evaluate : 1.633 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: 0.1989 time to fit residues: 196.4716 Evaluate side-chains 623 residues out of total 1155 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 623 time to evaluate : 1.308 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8759 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= 0.141 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 *********************** 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 fitting. rotamer outliers: 7 poor density : 645 time to evaluate : 1.520 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: V 108 TYR cc_start: 0.9156 (t80) cc_final: 0.8794 (t80) REVERT: W 208 TYR cc_start: 0.9152 (t80) cc_final: 0.8943 (t80) REVERT: W 212 LEU cc_start: 0.9407 (mm) cc_final: 0.9207 (mm) REVERT: Y 408 TYR cc_start: 0.9107 (t80) cc_final: 0.8722 (t80) REVERT: a 212 LEU cc_start: 0.9360 (mm) cc_final: 0.9159 (mm) REVERT: b 315 GLN cc_start: 0.8602 (mt0) cc_final: 0.8244 (tt0) REVERT: c 411 ILE cc_start: 0.9379 (mm) cc_final: 0.9172 (mt) REVERT: d 108 TYR cc_start: 0.9219 (t80) cc_final: 0.8383 (t80) REVERT: d 112 LEU cc_start: 0.9473 (mm) cc_final: 0.9157 (mm) REVERT: e 208 TYR cc_start: 0.8935 (t80) cc_final: 0.8119 (t80) REVERT: f 308 TYR cc_start: 0.9120 (t80) cc_final: 0.8479 (t80) REVERT: g 408 TYR cc_start: 0.9191 (t80) cc_final: 0.8456 (t80) REVERT: i 208 TYR cc_start: 0.9091 (t80) cc_final: 0.8747 (t80) REVERT: j 308 TYR cc_start: 0.9135 (t80) cc_final: 0.8674 (t80) REVERT: k 408 TYR cc_start: 0.9187 (t80) cc_final: 0.8888 (t80) REVERT: E 3 GLU cc_start: 0.8820 (tp30) cc_final: 0.7404 (mm-30) REVERT: l 115 GLN cc_start: 0.8773 (mt0) cc_final: 0.8561 (tt0) REVERT: o 415 GLN cc_start: 0.8666 (mt0) cc_final: 0.8410 (mt0) REVERT: F 3 GLU cc_start: 0.8903 (tp30) cc_final: 0.7962 (tp30) REVERT: p 108 TYR cc_start: 0.9211 (t80) cc_final: 0.8367 (t80) REVERT: p 112 LEU cc_start: 0.9473 (mm) cc_final: 0.9022 (mm) REVERT: s 415 GLN cc_start: 0.8930 (mt0) cc_final: 0.8115 (mt0) REVERT: t 108 TYR cc_start: 0.9150 (t80) cc_final: 0.8807 (t80) REVERT: u 208 TYR cc_start: 0.8991 (t80) cc_final: 0.8744 (t80) REVERT: v 311 ILE cc_start: 0.9340 (mt) cc_final: 0.9090 (mt) REVERT: v 315 GLN cc_start: 0.8584 (mt0) cc_final: 0.8352 (mt0) REVERT: x 111 ILE cc_start: 0.9219 (OUTLIER) cc_final: 0.8924 (mt) REVERT: x 112 LEU cc_start: 0.9545 (mm) cc_final: 0.8964 (mm) REVERT: x 115 GLN cc_start: 0.8689 (mt0) cc_final: 0.8051 (mt0) REVERT: y 208 TYR cc_start: 0.9003 (t80) cc_final: 0.8533 (t80) REVERT: I 8 TYR cc_start: 0.9272 (t80) cc_final: 0.8877 (t80) REVERT: 1 112 LEU cc_start: 0.9535 (mm) cc_final: 0.9279 (mm) REVERT: 2 211 ILE cc_start: 0.9445 (mt) cc_final: 0.9183 (mt) REVERT: 5 115 GLN cc_start: 0.8646 (mt0) cc_final: 0.8430 (tt0) REVERT: K 8 TYR cc_start: 0.9181 (t80) cc_final: 0.8607 (t80) REVERT: K 12 LEU cc_start: 0.9254 (mm) cc_final: 0.9015 (mm) REVERT: 9 112 LEU cc_start: 0.9429 (mm) cc_final: 0.9163 (mm) REVERT: BA 315 GLN cc_start: 0.8612 (mt0) cc_final: 0.8391 (tt0) REVERT: L 8 TYR cc_start: 0.9086 (t80) cc_final: 0.8414 (t80) REVERT: DA 108 TYR cc_start: 0.9132 (t80) cc_final: 0.8499 (t80) REVERT: EA 208 TYR cc_start: 0.9124 (t80) cc_final: 0.8670 (t80) REVERT: FA 308 TYR cc_start: 0.9043 (t80) cc_final: 0.8353 (t80) REVERT: GA 408 TYR cc_start: 0.9098 (t80) cc_final: 0.8447 (t80) REVERT: GA 415 GLN cc_start: 0.8765 (mt0) cc_final: 0.8483 (tt0) REVERT: KA 415 GLN cc_start: 0.8549 (mt0) cc_final: 0.8336 (mt0) REVERT: N 8 TYR cc_start: 0.9098 (t80) cc_final: 0.8819 (t80) REVERT: O 3 GLU cc_start: 0.8826 (tp30) cc_final: 0.7852 (tp30) REVERT: O 8 TYR cc_start: 0.9066 (t80) cc_final: 0.8593 (t80) REVERT: QA 208 TYR cc_start: 0.9019 (t80) cc_final: 0.8771 (t80) REVERT: RA 308 TYR cc_start: 0.9101 (t80) cc_final: 0.8695 (t80) REVERT: SA 408 TYR cc_start: 0.9060 (t80) cc_final: 0.8657 (t80) REVERT: P 3 GLU cc_start: 0.8924 (tp30) cc_final: 0.8311 (tp30) REVERT: UA 212 LEU cc_start: 0.9393 (mm) cc_final: 0.9149 (mm) REVERT: XA 108 TYR cc_start: 0.9073 (t80) cc_final: 0.8160 (t80) REVERT: YA 208 TYR cc_start: 0.9103 (t80) cc_final: 0.8369 (t80) REVERT: R 3 GLU cc_start: 0.8489 (tp30) cc_final: 0.8232 (tp30) REVERT: R 8 TYR cc_start: 0.9218 (t80) cc_final: 0.8714 (t80) REVERT: R 12 LEU cc_start: 0.9251 (mm) cc_final: 0.9017 (mm) REVERT: cA 208 TYR cc_start: 0.9036 (t80) cc_final: 0.8819 (t80) REVERT: eA 415 GLN cc_start: 0.8980 (mt0) cc_final: 0.8747 (mt0) REVERT: hA 315 GLN cc_start: 0.8605 (mt0) cc_final: 0.8311 (mt0) REVERT: iA 411 ILE cc_start: 0.9357 (mt) cc_final: 0.9154 (mt) REVERT: T 3 GLU cc_start: 0.8673 (tp30) cc_final: 0.8156 (tp30) REVERT: jA 112 LEU cc_start: 0.9194 (mm) cc_final: 0.8964 (mm) REVERT: lA 308 TYR cc_start: 0.9199 (t80) cc_final: 0.8673 (t80) REVERT: mA 408 TYR cc_start: 0.9244 (t80) cc_final: 0.8836 (t80) outliers start: 7 outliers final: 0 residues processed: 645 average time/residue: 0.1952 time to fit residues: 190.6544 Evaluate side-chains 548 residues out of total 1155 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 547 time to evaluate : 1.679 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 52 optimal weight: 1.9990 chunk 29 optimal weight: 0.9980 chunk 79 optimal weight: 0.9980 chunk 64 optimal weight: 0.9990 chunk 26 optimal weight: 5.9990 chunk 95 optimal weight: 2.9990 chunk 103 optimal weight: 1.9990 chunk 85 optimal weight: 8.9990 chunk 94 optimal weight: 5.9990 chunk 32 optimal weight: 0.4980 chunk 76 optimal weight: 0.9990 overall best weight: 0.8984 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8753 moved from start: 0.5188 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= 0.177 Angle : 0.544 4.320 17325 Z= 0.284 Chirality : 0.041 0.128 1995 Planarity : 0.002 0.014 2310 Dihedral : 2.994 16.297 1890 Min Nonbonded Distance : 2.616 Molprobity Statistics. All-atom Clashscore : 7.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 0.17 % Allowed : 8.83 % Favored : 91.00 % 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: 2.60 (0.25), residues: 1365 helix: 1.75 (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 0.003 0.000 ARG l 106 *********************** 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 666 residues out of total 1155 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 664 time to evaluate : 1.573 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: A 3 GLU cc_start: 0.8761 (tp30) cc_final: 0.8001 (tp30) REVERT: V 108 TYR cc_start: 0.9140 (t80) cc_final: 0.8798 (t80) REVERT: Y 408 TYR cc_start: 0.9176 (t80) cc_final: 0.8855 (t80) REVERT: Y 415 GLN cc_start: 0.8686 (mt0) cc_final: 0.8394 (mt0) REVERT: b 315 GLN cc_start: 0.8661 (mt0) cc_final: 0.8234 (tt0) REVERT: C 8 TYR cc_start: 0.8912 (t80) cc_final: 0.8157 (t80) REVERT: d 108 TYR cc_start: 0.9224 (t80) cc_final: 0.8380 (t80) REVERT: d 112 LEU cc_start: 0.9483 (mm) cc_final: 0.9117 (mm) REVERT: e 208 TYR cc_start: 0.8906 (t80) cc_final: 0.8064 (t80) REVERT: f 308 TYR cc_start: 0.9062 (t80) cc_final: 0.8632 (t80) REVERT: g 408 TYR cc_start: 0.9208 (t80) cc_final: 0.8613 (t80) REVERT: i 208 TYR cc_start: 0.9096 (t80) cc_final: 0.8647 (t80) REVERT: j 308 TYR cc_start: 0.9102 (t80) cc_final: 0.8768 (t80) REVERT: k 408 TYR cc_start: 0.9174 (t80) cc_final: 0.8670 (t80) REVERT: E 3 GLU cc_start: 0.8839 (tp30) cc_final: 0.7559 (mm-30) REVERT: m 208 TYR cc_start: 0.9019 (t80) cc_final: 0.8776 (t80) REVERT: o 415 GLN cc_start: 0.8929 (mt0) cc_final: 0.8476 (mt0) REVERT: p 108 TYR cc_start: 0.9231 (t80) cc_final: 0.8464 (t80) REVERT: p 112 LEU cc_start: 0.9344 (mm) cc_final: 0.9143 (mm) REVERT: t 108 TYR cc_start: 0.9111 (t80) cc_final: 0.8738 (t80) REVERT: t 112 LEU cc_start: 0.9479 (mm) cc_final: 0.9201 (mm) REVERT: u 208 TYR cc_start: 0.9096 (t80) cc_final: 0.8751 (t80) REVERT: v 315 GLN cc_start: 0.8776 (mt0) cc_final: 0.8389 (mt0) REVERT: H 3 GLU cc_start: 0.8617 (mm-30) cc_final: 0.8386 (tp30) REVERT: x 111 ILE cc_start: 0.9212 (OUTLIER) cc_final: 0.8951 (mt) REVERT: x 112 LEU cc_start: 0.9472 (mm) cc_final: 0.8889 (mm) REVERT: x 115 GLN cc_start: 0.8881 (mt0) cc_final: 0.8293 (mt0) REVERT: I 3 GLU cc_start: 0.8932 (mm-30) cc_final: 0.7484 (tp30) REVERT: I 8 TYR cc_start: 0.9296 (t80) cc_final: 0.8868 (t80) REVERT: I 12 LEU cc_start: 0.9565 (mm) cc_final: 0.9330 (mm) REVERT: 4 412 LEU cc_start: 0.9455 (mp) cc_final: 0.9233 (mp) REVERT: 4 415 GLN cc_start: 0.8742 (mt0) cc_final: 0.8408 (mt0) REVERT: 8 408 TYR cc_start: 0.9017 (t80) cc_final: 0.8798 (t80) REVERT: K 3 GLU cc_start: 0.8875 (tp30) cc_final: 0.8608 (mm-30) REVERT: K 8 TYR cc_start: 0.9220 (t80) cc_final: 0.8620 (t80) REVERT: 9 112 LEU cc_start: 0.9437 (mm) cc_final: 0.9200 (mm) REVERT: AA 215 GLN cc_start: 0.8863 (mt0) cc_final: 0.8300 (mt0) REVERT: L 8 TYR cc_start: 0.9142 (t80) cc_final: 0.8613 (t80) REVERT: DA 108 TYR cc_start: 0.9095 (t80) cc_final: 0.8692 (t80) REVERT: EA 208 TYR cc_start: 0.9183 (t80) cc_final: 0.8736 (t80) REVERT: FA 308 TYR cc_start: 0.9177 (t80) cc_final: 0.8612 (t80) REVERT: FA 312 LEU cc_start: 0.9440 (mm) cc_final: 0.9223 (mm) REVERT: GA 408 TYR cc_start: 0.9078 (t80) cc_final: 0.8513 (t80) REVERT: N 3 GLU cc_start: 0.8826 (tp30) cc_final: 0.8533 (tp30) REVERT: O 8 TYR cc_start: 0.9111 (t80) cc_final: 0.8813 (t80) REVERT: QA 208 TYR cc_start: 0.9094 (t80) cc_final: 0.8868 (t80) REVERT: RA 308 TYR cc_start: 0.9153 (t80) cc_final: 0.8911 (t80) REVERT: SA 408 TYR cc_start: 0.9119 (t80) cc_final: 0.8863 (t80) REVERT: TA 112 LEU cc_start: 0.9466 (mm) cc_final: 0.9266 (mm) REVERT: Q 8 TYR cc_start: 0.8982 (t80) cc_final: 0.8236 (t80) REVERT: XA 108 TYR cc_start: 0.9112 (t80) cc_final: 0.8292 (t80) REVERT: XA 112 LEU cc_start: 0.9384 (mm) cc_final: 0.9150 (mm) REVERT: YA 208 TYR cc_start: 0.9122 (t80) cc_final: 0.8530 (t80) REVERT: R 8 TYR cc_start: 0.9230 (t80) cc_final: 0.8611 (t80) REVERT: R 12 LEU cc_start: 0.9479 (mm) cc_final: 0.9148 (mm) REVERT: eA 415 GLN cc_start: 0.9156 (mt0) cc_final: 0.8694 (mt0) REVERT: gA 208 TYR cc_start: 0.8974 (t80) cc_final: 0.8755 (t80) REVERT: T 11 ILE cc_start: 0.9046 (tt) cc_final: 0.8786 (tp) REVERT: jA 112 LEU cc_start: 0.9431 (mm) cc_final: 0.9131 (mm) REVERT: kA 208 TYR cc_start: 0.8931 (t80) cc_final: 0.8621 (t80) REVERT: lA 303 GLU cc_start: 0.8728 (mm-30) cc_final: 0.7392 (mm-30) REVERT: mA 411 ILE cc_start: 0.9261 (tt) cc_final: 0.9032 (tp) REVERT: U 8 TYR cc_start: 0.8840 (t80) cc_final: 0.8572 (t80) REVERT: qA 408 TYR cc_start: 0.8885 (t80) cc_final: 0.8590 (t80) outliers start: 2 outliers final: 0 residues processed: 665 average time/residue: 0.2002 time to fit residues: 200.4268 Evaluate side-chains 561 residues out of total 1155 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 560 time to evaluate : 1.494 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 94 optimal weight: 4.9990 chunk 71 optimal weight: 1.9990 chunk 49 optimal weight: 2.9990 chunk 10 optimal weight: 4.9990 chunk 45 optimal weight: 7.9990 chunk 64 optimal weight: 9.9990 chunk 95 optimal weight: 6.9990 chunk 101 optimal weight: 0.9990 chunk 50 optimal weight: 1.9990 chunk 90 optimal weight: 7.9990 chunk 27 optimal weight: 0.9990 overall best weight: 1.7990 ------------------------------------------------------------------------------- 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 g 415 GLN h 115 GLN i 215 GLN k 415 GLN E 15 GLN y 215 GLN 6 215 GLN 7 315 GLN K 15 GLN CA 415 GLN JA 315 GLN SA 415 GLN P 15 GLN YA 215 GLN cA 215 GLN S 15 GLN mA 415 GLN oA 215 GLN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8842 moved from start: 0.5876 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 12915 Z= 0.222 Angle : 0.520 5.320 17325 Z= 0.271 Chirality : 0.043 0.136 1995 Planarity : 0.002 0.019 2310 Dihedral : 3.414 22.069 1890 Min Nonbonded Distance : 2.599 Molprobity Statistics. All-atom Clashscore : 6.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 0.52 % Allowed : 9.78 % Favored : 89.70 % 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: 3.10 (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 0.026 0.002 TYR r 308 ARG 0.002 0.000 ARGgA 206 *********************** 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 619 residues out of total 1155 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 613 time to evaluate : 1.533 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 12 LEU cc_start: 0.9543 (mm) cc_final: 0.9290 (mm) REVERT: V 108 TYR cc_start: 0.9005 (t80) cc_final: 0.8445 (t80) REVERT: W 212 LEU cc_start: 0.9592 (mm) cc_final: 0.9280 (mm) REVERT: Y 403 GLU cc_start: 0.9013 (mp0) cc_final: 0.8802 (mp0) REVERT: Y 408 TYR cc_start: 0.9123 (t80) cc_final: 0.8844 (t80) REVERT: b 311 ILE cc_start: 0.9451 (mt) cc_final: 0.9229 (mt) REVERT: b 315 GLN cc_start: 0.8685 (mt0) cc_final: 0.8332 (tt0) REVERT: C 8 TYR cc_start: 0.8866 (t80) cc_final: 0.8118 (t80) REVERT: d 112 LEU cc_start: 0.9548 (mm) cc_final: 0.9305 (mm) REVERT: e 203 GLU cc_start: 0.9149 (mm-30) cc_final: 0.8608 (mp0) REVERT: e 208 TYR cc_start: 0.8830 (t80) cc_final: 0.8357 (t80) REVERT: e 212 LEU cc_start: 0.9507 (mm) cc_final: 0.9276 (mm) REVERT: f 308 TYR cc_start: 0.9128 (t80) cc_final: 0.8699 (t80) REVERT: g 408 TYR cc_start: 0.9208 (t80) cc_final: 0.8512 (t80) REVERT: g 412 LEU cc_start: 0.9524 (mm) cc_final: 0.9233 (mm) REVERT: h 112 LEU cc_start: 0.9595 (mm) cc_final: 0.9382 (mm) REVERT: i 208 TYR cc_start: 0.9110 (t80) cc_final: 0.8589 (t80) REVERT: j 308 TYR cc_start: 0.9090 (t80) cc_final: 0.8692 (t80) REVERT: j 312 LEU cc_start: 0.9514 (mm) cc_final: 0.9189 (mm) REVERT: k 408 TYR cc_start: 0.9181 (t80) cc_final: 0.8931 (t80) REVERT: m 208 TYR cc_start: 0.9022 (t80) cc_final: 0.8768 (t80) REVERT: n 308 TYR cc_start: 0.8974 (t80) cc_final: 0.8708 (t80) REVERT: o 403 GLU cc_start: 0.8713 (mm-30) cc_final: 0.8472 (mm-30) REVERT: F 3 GLU cc_start: 0.8851 (mm-30) cc_final: 0.8615 (mm-30) REVERT: p 108 TYR cc_start: 0.9231 (t80) cc_final: 0.8461 (t80) REVERT: p 112 LEU cc_start: 0.9573 (mm) cc_final: 0.9174 (mm) REVERT: t 108 TYR cc_start: 0.9153 (t80) cc_final: 0.8936 (t80) REVERT: t 112 LEU cc_start: 0.9585 (mm) cc_final: 0.9264 (mm) REVERT: u 208 TYR cc_start: 0.9167 (t80) cc_final: 0.8909 (t80) REVERT: v 315 GLN cc_start: 0.8845 (mt0) cc_final: 0.8451 (mt0) REVERT: H 12 LEU cc_start: 0.9584 (mm) cc_final: 0.9372 (mm) REVERT: x 103 GLU cc_start: 0.9290 (mm-30) cc_final: 0.8525 (mm-30) REVERT: x 111 ILE cc_start: 0.9297 (mp) cc_final: 0.8919 (mt) REVERT: x 112 LEU cc_start: 0.9436 (mm) cc_final: 0.8925 (mm) REVERT: x 115 GLN cc_start: 0.8908 (mt0) cc_final: 0.8368 (mt0) REVERT: y 212 LEU cc_start: 0.9552 (mm) cc_final: 0.9236 (mm) REVERT: z 308 TYR cc_start: 0.8708 (t80) cc_final: 0.8492 (t80) REVERT: z 315 GLN cc_start: 0.9070 (mt0) cc_final: 0.8382 (mt0) REVERT: 0 403 GLU cc_start: 0.8587 (tp30) cc_final: 0.8114 (tp30) REVERT: I 3 GLU cc_start: 0.8827 (mm-30) cc_final: 0.8597 (tp30) REVERT: I 8 TYR cc_start: 0.9280 (t80) cc_final: 0.8758 (t80) REVERT: I 12 LEU cc_start: 0.9583 (mm) cc_final: 0.9287 (mm) REVERT: 1 108 TYR cc_start: 0.8812 (t80) cc_final: 0.8545 (t80) REVERT: J 3 GLU cc_start: 0.8855 (mm-30) cc_final: 0.8537 (mm-30) REVERT: 7 303 GLU cc_start: 0.9009 (mm-30) cc_final: 0.8774 (mm-30) REVERT: 7 308 TYR cc_start: 0.8730 (t80) cc_final: 0.8508 (t80) REVERT: 8 408 TYR cc_start: 0.8974 (t80) cc_final: 0.8696 (t80) REVERT: K 8 TYR cc_start: 0.9215 (t80) cc_final: 0.8714 (t80) REVERT: K 12 LEU cc_start: 0.9518 (mm) cc_final: 0.9225 (mm) REVERT: 9 108 TYR cc_start: 0.9182 (t80) cc_final: 0.8649 (t80) REVERT: 9 112 LEU cc_start: 0.9469 (mm) cc_final: 0.9050 (mm) REVERT: BA 312 LEU cc_start: 0.9479 (mm) cc_final: 0.9195 (mm) REVERT: CA 412 LEU cc_start: 0.9435 (mm) cc_final: 0.9205 (mm) REVERT: L 3 GLU cc_start: 0.8754 (mm-30) cc_final: 0.8540 (mm-30) REVERT: L 8 TYR cc_start: 0.9163 (t80) cc_final: 0.8677 (t80) REVERT: L 12 LEU cc_start: 0.9547 (mm) cc_final: 0.9290 (mm) REVERT: DA 108 TYR cc_start: 0.9123 (t80) cc_final: 0.8684 (t80) REVERT: DA 112 LEU cc_start: 0.9649 (mm) cc_final: 0.9415 (mm) REVERT: EA 208 TYR cc_start: 0.9189 (t80) cc_final: 0.8750 (t80) REVERT: FA 308 TYR cc_start: 0.9167 (t80) cc_final: 0.8541 (t80) REVERT: FA 312 LEU cc_start: 0.9542 (mm) cc_final: 0.9154 (mm) REVERT: GA 408 TYR cc_start: 0.9091 (t80) cc_final: 0.8553 (t80) REVERT: M 12 LEU cc_start: 0.9585 (mm) cc_final: 0.9336 (mm) REVERT: IA 212 LEU cc_start: 0.9572 (mm) cc_final: 0.9313 (mm) REVERT: JA 312 LEU cc_start: 0.9555 (mm) cc_final: 0.9292 (mm) REVERT: N 3 GLU cc_start: 0.8825 (tp30) cc_final: 0.8524 (tp30) REVERT: N 12 LEU cc_start: 0.9589 (mm) cc_final: 0.9275 (mm) REVERT: LA 103 GLU cc_start: 0.9209 (mm-30) cc_final: 0.8140 (mm-30) REVERT: NA 303 GLU cc_start: 0.8768 (tp30) cc_final: 0.8305 (mm-30) REVERT: O 8 TYR cc_start: 0.9127 (t80) cc_final: 0.8839 (t80) REVERT: O 12 LEU cc_start: 0.9503 (mm) cc_final: 0.9269 (mm) REVERT: QA 208 TYR cc_start: 0.9055 (t80) cc_final: 0.8774 (t80) REVERT: RA 303 GLU cc_start: 0.8854 (tp30) cc_final: 0.8482 (mm-30) REVERT: RA 308 TYR cc_start: 0.9149 (t80) cc_final: 0.8854 (t80) REVERT: RA 312 LEU cc_start: 0.9567 (mm) cc_final: 0.9274 (mm) REVERT: SA 403 GLU cc_start: 0.8946 (mp0) cc_final: 0.8700 (mm-30) REVERT: SA 408 TYR cc_start: 0.9111 (t80) cc_final: 0.8783 (t80) REVERT: SA 412 LEU cc_start: 0.9527 (mm) cc_final: 0.9312 (mm) REVERT: P 3 GLU cc_start: 0.8873 (mm-30) cc_final: 0.7927 (mm-30) REVERT: TA 112 LEU cc_start: 0.9605 (mm) cc_final: 0.9300 (mm) REVERT: VA 312 LEU cc_start: 0.9598 (mm) cc_final: 0.9340 (mm) REVERT: WA 415 GLN cc_start: 0.9011 (mt0) cc_final: 0.8240 (mt0) REVERT: Q 8 TYR cc_start: 0.8942 (t80) cc_final: 0.8285 (t80) REVERT: Q 15 GLN cc_start: 0.9613 (mt0) cc_final: 0.9407 (tt0) REVERT: XA 108 TYR cc_start: 0.9091 (t80) cc_final: 0.8147 (t80) REVERT: XA 112 LEU cc_start: 0.9541 (mm) cc_final: 0.9108 (mm) REVERT: YA 208 TYR cc_start: 0.9139 (t80) cc_final: 0.8365 (t80) REVERT: YA 212 LEU cc_start: 0.9541 (mm) cc_final: 0.9240 (mm) REVERT: ZA 308 TYR cc_start: 0.8805 (t80) cc_final: 0.8368 (t80) REVERT: aA 408 TYR cc_start: 0.8673 (t80) cc_final: 0.8205 (t80) REVERT: R 8 TYR cc_start: 0.9209 (t80) cc_final: 0.8635 (t80) REVERT: R 12 LEU cc_start: 0.9644 (mm) cc_final: 0.9154 (mm) REVERT: cA 212 LEU cc_start: 0.9593 (mm) cc_final: 0.9389 (mm) REVERT: fA 103 GLU cc_start: 0.9171 (mm-30) cc_final: 0.8968 (mp0) REVERT: gA 208 TYR cc_start: 0.8926 (t80) cc_final: 0.8676 (t80) REVERT: T 11 ILE cc_start: 0.9091 (tt) cc_final: 0.8816 (tp) REVERT: jA 112 LEU cc_start: 0.9261 (mm) cc_final: 0.8998 (mm) REVERT: kA 208 TYR cc_start: 0.8821 (t80) cc_final: 0.8617 (t80) REVERT: lA 303 GLU cc_start: 0.9050 (mm-30) cc_final: 0.8808 (mp0) REVERT: mA 411 ILE cc_start: 0.9287 (tt) cc_final: 0.9016 (tp) REVERT: U 3 GLU cc_start: 0.8841 (tp30) cc_final: 0.8115 (mm-30) REVERT: U 8 TYR cc_start: 0.8786 (t80) cc_final: 0.8310 (t80) REVERT: oA 203 GLU cc_start: 0.9311 (mm-30) cc_final: 0.9058 (mm-30) REVERT: pA 303 GLU cc_start: 0.9194 (mm-30) cc_final: 0.8989 (mm-30) REVERT: qA 415 GLN cc_start: 0.8890 (mt0) cc_final: 0.8598 (mt0) outliers start: 6 outliers final: 0 residues processed: 619 average time/residue: 0.2053 time to fit residues: 194.2262 Evaluate side-chains 563 residues out of total 1155 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 563 time to evaluate : 1.561 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 84 optimal weight: 1.9990 chunk 57 optimal weight: 1.9990 chunk 1 optimal weight: 0.9980 chunk 75 optimal weight: 0.9980 chunk 41 optimal weight: 4.9990 chunk 86 optimal weight: 0.9980 chunk 70 optimal weight: 6.9990 chunk 0 optimal weight: 10.0000 chunk 51 optimal weight: 1.9990 chunk 91 optimal weight: 10.0000 chunk 25 optimal weight: 4.9990 overall best weight: 1.3984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 15 GLN a 215 GLN d 115 GLN E 15 GLN u 215 GLN y 215 GLN 0 415 GLN MA 215 GLN QA 215 GLN dA 315 GLN S 15 GLN hA 315 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8831 moved from start: 0.6124 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 12915 Z= 0.204 Angle : 0.522 5.095 17325 Z= 0.265 Chirality : 0.041 0.138 1995 Planarity : 0.002 0.012 2310 Dihedral : 3.437 20.753 1890 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 5.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 0.26 % Allowed : 6.84 % Favored : 92.90 % 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: 3.43 (0.25), residues: 1365 helix: 2.27 (0.15), residues: 1365 sheet: None (None), residues: 0 loop : None (None), residues: 0 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.024 0.002 TYR 3 308 ARG 0.004 0.000 ARGIA 206 *********************** 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 619 residues out of total 1155 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 616 time to evaluate : 1.544 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: A 12 LEU cc_start: 0.9526 (mm) cc_final: 0.9316 (mm) REVERT: V 108 TYR cc_start: 0.8903 (t80) cc_final: 0.8385 (t80) REVERT: W 208 TYR cc_start: 0.9058 (t80) cc_final: 0.8838 (t80) REVERT: W 212 LEU cc_start: 0.9589 (mm) cc_final: 0.9359 (mm) REVERT: Y 408 TYR cc_start: 0.9143 (t80) cc_final: 0.8910 (t80) REVERT: B 12 LEU cc_start: 0.9582 (mm) cc_final: 0.9302 (mm) REVERT: a 212 LEU cc_start: 0.9530 (mm) cc_final: 0.9272 (mm) REVERT: b 311 ILE cc_start: 0.9431 (mt) cc_final: 0.9196 (mt) REVERT: b 315 GLN cc_start: 0.8718 (mt0) cc_final: 0.8389 (tt0) REVERT: C 3 GLU cc_start: 0.9148 (mp0) cc_final: 0.8883 (mp0) REVERT: C 8 TYR cc_start: 0.8772 (t80) cc_final: 0.8106 (t80) REVERT: d 111 ILE cc_start: 0.9584 (tt) cc_final: 0.9351 (tt) REVERT: d 112 LEU cc_start: 0.9508 (mm) cc_final: 0.9272 (mm) REVERT: e 203 GLU cc_start: 0.8913 (mm-30) cc_final: 0.8516 (mm-30) REVERT: e 208 TYR cc_start: 0.8841 (t80) cc_final: 0.8590 (t80) REVERT: e 211 ILE cc_start: 0.9488 (tt) cc_final: 0.9242 (tt) REVERT: f 308 TYR cc_start: 0.9116 (t80) cc_final: 0.8685 (t80) REVERT: g 408 TYR cc_start: 0.9149 (t80) cc_final: 0.8535 (t80) REVERT: g 412 LEU cc_start: 0.9500 (mm) cc_final: 0.9204 (mm) REVERT: D 3 GLU cc_start: 0.9103 (mp0) cc_final: 0.8723 (mm-30) REVERT: i 203 GLU cc_start: 0.9213 (mm-30) cc_final: 0.8789 (mm-30) REVERT: i 208 TYR cc_start: 0.9072 (t80) cc_final: 0.8540 (t80) REVERT: j 308 TYR cc_start: 0.9084 (t80) cc_final: 0.8592 (t80) REVERT: j 312 LEU cc_start: 0.9527 (mm) cc_final: 0.9187 (mm) REVERT: k 408 TYR cc_start: 0.9154 (t80) cc_final: 0.8946 (t80) REVERT: E 3 GLU cc_start: 0.8863 (tp30) cc_final: 0.7596 (mm-30) REVERT: m 208 TYR cc_start: 0.8911 (t80) cc_final: 0.8632 (t80) REVERT: o 415 GLN cc_start: 0.8891 (mt0) cc_final: 0.8514 (mt0) REVERT: F 3 GLU cc_start: 0.8755 (mm-30) cc_final: 0.8308 (tp30) REVERT: p 108 TYR cc_start: 0.9184 (t80) cc_final: 0.8331 (t80) REVERT: p 112 LEU cc_start: 0.9417 (mm) cc_final: 0.9044 (mm) REVERT: t 108 TYR cc_start: 0.9120 (t80) cc_final: 0.8882 (t80) REVERT: t 112 LEU cc_start: 0.9606 (mm) cc_final: 0.9281 (mm) REVERT: u 208 TYR cc_start: 0.9187 (t80) cc_final: 0.8823 (t80) REVERT: u 212 LEU cc_start: 0.9578 (mm) cc_final: 0.9285 (mm) REVERT: v 303 GLU cc_start: 0.9189 (mm-30) cc_final: 0.8710 (mm-30) REVERT: v 315 GLN cc_start: 0.8884 (mt0) cc_final: 0.8586 (mt0) REVERT: x 103 GLU cc_start: 0.9184 (mm-30) cc_final: 0.8838 (mm-30) REVERT: x 111 ILE cc_start: 0.9304 (mp) cc_final: 0.8935 (mt) REVERT: x 112 LEU cc_start: 0.9499 (mm) cc_final: 0.9035 (mm) REVERT: x 115 GLN cc_start: 0.8916 (mt0) cc_final: 0.8404 (mt0) REVERT: y 212 LEU cc_start: 0.9591 (mm) cc_final: 0.9232 (mm) REVERT: y 215 GLN cc_start: 0.9249 (OUTLIER) cc_final: 0.7708 (tp-100) REVERT: z 308 TYR cc_start: 0.8651 (t80) cc_final: 0.8386 (t80) REVERT: I 3 GLU cc_start: 0.8748 (mm-30) cc_final: 0.8458 (tp30) REVERT: I 8 TYR cc_start: 0.9236 (t80) cc_final: 0.8665 (t80) REVERT: I 12 LEU cc_start: 0.9505 (mm) cc_final: 0.9288 (mm) REVERT: 1 112 LEU cc_start: 0.9639 (mm) cc_final: 0.9436 (mm) REVERT: 2 208 TYR cc_start: 0.8797 (t80) cc_final: 0.8535 (t80) REVERT: 7 303 GLU cc_start: 0.9037 (mm-30) cc_final: 0.8758 (mm-30) REVERT: 7 308 TYR cc_start: 0.8780 (t80) cc_final: 0.8334 (t80) REVERT: 8 408 TYR cc_start: 0.8937 (t80) cc_final: 0.7852 (t80) REVERT: K 3 GLU cc_start: 0.8457 (tp30) cc_final: 0.7390 (mm-30) REVERT: K 8 TYR cc_start: 0.9162 (t80) cc_final: 0.8668 (t80) REVERT: K 12 LEU cc_start: 0.9514 (mm) cc_final: 0.9169 (mm) REVERT: 9 108 TYR cc_start: 0.8969 (t80) cc_final: 0.8666 (t80) REVERT: 9 112 LEU cc_start: 0.9400 (mm) cc_final: 0.9071 (mm) REVERT: BA 303 GLU cc_start: 0.8747 (mm-30) cc_final: 0.8493 (mm-30) REVERT: BA 312 LEU cc_start: 0.9417 (mm) cc_final: 0.9148 (mm) REVERT: CA 412 LEU cc_start: 0.9491 (mm) cc_final: 0.9168 (mm) REVERT: CA 415 GLN cc_start: 0.8933 (mt0) cc_final: 0.8364 (mt0) REVERT: L 3 GLU cc_start: 0.8761 (mm-30) cc_final: 0.8558 (mm-30) REVERT: L 8 TYR cc_start: 0.9129 (t80) cc_final: 0.8661 (t80) REVERT: L 12 LEU cc_start: 0.9538 (mm) cc_final: 0.9259 (mm) REVERT: DA 108 TYR cc_start: 0.9095 (t80) cc_final: 0.8697 (t80) REVERT: DA 112 LEU cc_start: 0.9641 (mm) cc_final: 0.9423 (mm) REVERT: EA 208 TYR cc_start: 0.9183 (t80) cc_final: 0.8700 (t80) REVERT: FA 308 TYR cc_start: 0.9171 (t80) cc_final: 0.8517 (t80) REVERT: FA 312 LEU cc_start: 0.9547 (mm) cc_final: 0.9157 (mm) REVERT: GA 403 GLU cc_start: 0.9133 (mp0) cc_final: 0.8798 (mp0) REVERT: GA 408 TYR cc_start: 0.9073 (t80) cc_final: 0.8564 (t80) REVERT: M 3 GLU cc_start: 0.8606 (mm-30) cc_final: 0.7818 (tp30) REVERT: M 12 LEU cc_start: 0.9590 (mm) cc_final: 0.9273 (mm) REVERT: HA 103 GLU cc_start: 0.9144 (mm-30) cc_final: 0.8913 (mp0) REVERT: IA 212 LEU cc_start: 0.9518 (mm) cc_final: 0.9304 (mm) REVERT: N 3 GLU cc_start: 0.8763 (tp30) cc_final: 0.8461 (tp30) REVERT: N 12 LEU cc_start: 0.9614 (mm) cc_final: 0.9319 (mm) REVERT: LA 103 GLU cc_start: 0.9062 (mm-30) cc_final: 0.8718 (mm-30) REVERT: MA 212 LEU cc_start: 0.9603 (mm) cc_final: 0.9353 (mm) REVERT: O 3 GLU cc_start: 0.8945 (mp0) cc_final: 0.8693 (mp0) REVERT: O 8 TYR cc_start: 0.9123 (t80) cc_final: 0.8760 (t80) REVERT: O 12 LEU cc_start: 0.9551 (mm) cc_final: 0.9273 (mm) REVERT: QA 208 TYR cc_start: 0.9021 (t80) cc_final: 0.8755 (t80) REVERT: QA 212 LEU cc_start: 0.9597 (mm) cc_final: 0.9387 (mm) REVERT: RA 308 TYR cc_start: 0.9129 (t80) cc_final: 0.8886 (t80) REVERT: RA 312 LEU cc_start: 0.9524 (mm) cc_final: 0.9295 (mm) REVERT: SA 408 TYR cc_start: 0.9064 (t80) cc_final: 0.8771 (t80) REVERT: P 3 GLU cc_start: 0.8813 (mm-30) cc_final: 0.8399 (mm-30) REVERT: TA 112 LEU cc_start: 0.9564 (mm) cc_final: 0.9316 (mm) REVERT: VA 312 LEU cc_start: 0.9560 (mm) cc_final: 0.9347 (mm) REVERT: Q 3 GLU cc_start: 0.8797 (tp30) cc_final: 0.7500 (tp30) REVERT: Q 8 TYR cc_start: 0.8888 (t80) cc_final: 0.8207 (t80) REVERT: XA 112 LEU cc_start: 0.9483 (mm) cc_final: 0.9274 (mm) REVERT: YA 208 TYR cc_start: 0.9107 (t80) cc_final: 0.8332 (t80) REVERT: YA 212 LEU cc_start: 0.9547 (mm) cc_final: 0.9242 (mm) REVERT: ZA 308 TYR cc_start: 0.8674 (t80) cc_final: 0.8240 (t80) REVERT: aA 408 TYR cc_start: 0.8771 (t80) cc_final: 0.8155 (t80) REVERT: aA 415 GLN cc_start: 0.8947 (mt0) cc_final: 0.8743 (mt0) REVERT: R 8 TYR cc_start: 0.9191 (t80) cc_final: 0.8800 (t80) REVERT: R 12 LEU cc_start: 0.9455 (mm) cc_final: 0.9193 (mm) REVERT: cA 212 LEU cc_start: 0.9651 (mm) cc_final: 0.9370 (mm) REVERT: eA 403 GLU cc_start: 0.9120 (mp0) cc_final: 0.8690 (mm-30) REVERT: S 3 GLU cc_start: 0.8845 (mm-30) cc_final: 0.8483 (mm-30) REVERT: S 8 TYR cc_start: 0.9023 (t80) cc_final: 0.8657 (t80) REVERT: fA 103 GLU cc_start: 0.8996 (mm-30) cc_final: 0.8738 (mm-30) REVERT: T 11 ILE cc_start: 0.8784 (tt) cc_final: 0.8450 (tp) REVERT: jA 112 LEU cc_start: 0.9310 (mm) cc_final: 0.9095 (mm) REVERT: kA 211 ILE cc_start: 0.9301 (tt) cc_final: 0.9047 (tp) REVERT: U 3 GLU cc_start: 0.8903 (tp30) cc_final: 0.8254 (mm-30) REVERT: oA 203 GLU cc_start: 0.9346 (mm-30) cc_final: 0.9057 (mm-30) REVERT: qA 403 GLU cc_start: 0.8926 (tp30) cc_final: 0.8715 (mm-30) REVERT: qA 415 GLN cc_start: 0.8890 (mt0) cc_final: 0.8602 (mt0) outliers start: 3 outliers final: 0 residues processed: 619 average time/residue: 0.1975 time to fit residues: 184.7691 Evaluate side-chains 581 residues out of total 1155 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 580 time to evaluate : 1.568 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 34 optimal weight: 3.9990 chunk 91 optimal weight: 0.8980 chunk 20 optimal weight: 0.8980 chunk 59 optimal weight: 0.9980 chunk 25 optimal weight: 5.9990 chunk 101 optimal weight: 0.7980 chunk 84 optimal weight: 0.9980 chunk 47 optimal weight: 0.8980 chunk 8 optimal weight: 2.9990 chunk 33 optimal weight: 1.9990 chunk 53 optimal weight: 0.4980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: a 215 GLN u 215 GLN 5 115 GLN O 15 GLN hA 315 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8797 moved from start: 0.6474 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 12915 Z= 0.183 Angle : 0.535 4.966 17325 Z= 0.261 Chirality : 0.039 0.138 1995 Planarity : 0.002 0.016 2310 Dihedral : 3.565 26.549 1890 Min Nonbonded Distance : 2.565 Molprobity Statistics. All-atom Clashscore : 3.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 0.17 % Allowed : 3.38 % Favored : 96.45 % 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: 3.70 (0.24), residues: 1365 helix: 2.43 (0.15), residues: 1365 sheet: None (None), residues: 0 loop : None (None), residues: 0 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.020 0.002 TYRaA 408 ARG 0.003 0.000 ARGbA 106 *********************** 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 630 residues out of total 1155 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 628 time to evaluate : 1.548 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 3 GLU cc_start: 0.8691 (mm-30) cc_final: 0.8462 (tp30) REVERT: A 12 LEU cc_start: 0.9539 (mm) cc_final: 0.9339 (mm) REVERT: V 108 TYR cc_start: 0.8664 (t80) cc_final: 0.8113 (t80) REVERT: W 208 TYR cc_start: 0.8976 (t80) cc_final: 0.8680 (t80) REVERT: W 212 LEU cc_start: 0.9540 (mm) cc_final: 0.9338 (mm) REVERT: Y 408 TYR cc_start: 0.9096 (t80) cc_final: 0.8885 (t80) REVERT: B 3 GLU cc_start: 0.8816 (mm-30) cc_final: 0.8614 (tp30) REVERT: B 12 LEU cc_start: 0.9586 (mm) cc_final: 0.9295 (mm) REVERT: Z 103 GLU cc_start: 0.9121 (mm-30) cc_final: 0.8819 (mm-30) REVERT: a 212 LEU cc_start: 0.9537 (mm) cc_final: 0.9250 (mm) REVERT: C 3 GLU cc_start: 0.9155 (mp0) cc_final: 0.8871 (mp0) REVERT: C 8 TYR cc_start: 0.8769 (t80) cc_final: 0.8092 (t80) REVERT: e 211 ILE cc_start: 0.9511 (tt) cc_final: 0.9250 (tt) REVERT: e 212 LEU cc_start: 0.9548 (mm) cc_final: 0.9326 (mm) REVERT: f 308 TYR cc_start: 0.9039 (t80) cc_final: 0.8712 (t80) REVERT: g 408 TYR cc_start: 0.9152 (t80) cc_final: 0.8598 (t80) REVERT: g 412 LEU cc_start: 0.9485 (mm) cc_final: 0.9244 (mm) REVERT: h 112 LEU cc_start: 0.9588 (mm) cc_final: 0.9348 (mm) REVERT: i 208 TYR cc_start: 0.9038 (t80) cc_final: 0.8590 (t80) REVERT: j 303 GLU cc_start: 0.9130 (mm-30) cc_final: 0.8697 (mm-30) REVERT: j 308 TYR cc_start: 0.9062 (t80) cc_final: 0.8605 (t80) REVERT: j 312 LEU cc_start: 0.9524 (mm) cc_final: 0.9212 (mm) REVERT: m 208 TYR cc_start: 0.8880 (t80) cc_final: 0.7624 (t80) REVERT: F 3 GLU cc_start: 0.8755 (mm-30) cc_final: 0.7151 (tp30) REVERT: q 208 TYR cc_start: 0.8689 (t80) cc_final: 0.8488 (t80) REVERT: s 411 ILE cc_start: 0.9348 (mt) cc_final: 0.9135 (mt) REVERT: s 415 GLN cc_start: 0.8787 (mt0) cc_final: 0.8442 (mt0) REVERT: G 11 ILE cc_start: 0.9283 (mt) cc_final: 0.9075 (mt) REVERT: t 108 TYR cc_start: 0.9052 (t80) cc_final: 0.8774 (t80) REVERT: t 112 LEU cc_start: 0.9605 (mm) cc_final: 0.9208 (mm) REVERT: u 208 TYR cc_start: 0.8971 (t80) cc_final: 0.8742 (t80) REVERT: u 212 LEU cc_start: 0.9555 (mm) cc_final: 0.9260 (mm) REVERT: v 303 GLU cc_start: 0.9157 (mm-30) cc_final: 0.8781 (mm-30) REVERT: x 103 GLU cc_start: 0.9198 (mm-30) cc_final: 0.8758 (mm-30) REVERT: x 111 ILE cc_start: 0.9271 (mp) cc_final: 0.8886 (mt) REVERT: x 112 LEU cc_start: 0.9533 (mm) cc_final: 0.9191 (mm) REVERT: x 115 GLN cc_start: 0.8923 (mt0) cc_final: 0.8377 (mt0) REVERT: y 212 LEU cc_start: 0.9609 (mm) cc_final: 0.9196 (mm) REVERT: z 308 TYR cc_start: 0.8643 (t80) cc_final: 0.8364 (t80) REVERT: 0 408 TYR cc_start: 0.8937 (t80) cc_final: 0.8662 (t80) REVERT: I 3 GLU cc_start: 0.8752 (mm-30) cc_final: 0.8432 (tp30) REVERT: I 8 TYR cc_start: 0.9178 (t80) cc_final: 0.8514 (t80) REVERT: I 12 LEU cc_start: 0.9508 (mm) cc_final: 0.9203 (mm) REVERT: 1 108 TYR cc_start: 0.8870 (t80) cc_final: 0.8624 (t80) REVERT: 2 212 LEU cc_start: 0.9605 (mm) cc_final: 0.9261 (mm) REVERT: 3 311 ILE cc_start: 0.9462 (mt) cc_final: 0.9257 (mt) REVERT: 4 412 LEU cc_start: 0.9446 (mp) cc_final: 0.9192 (mp) REVERT: J 3 GLU cc_start: 0.8794 (mm-30) cc_final: 0.8502 (mm-30) REVERT: 6 208 TYR cc_start: 0.8847 (t80) cc_final: 0.8204 (t80) REVERT: 7 303 GLU cc_start: 0.9066 (mm-30) cc_final: 0.8774 (mm-30) REVERT: 8 408 TYR cc_start: 0.8892 (t80) cc_final: 0.7701 (t80) REVERT: K 8 TYR cc_start: 0.9121 (t80) cc_final: 0.8791 (t80) REVERT: K 12 LEU cc_start: 0.9562 (mm) cc_final: 0.9329 (mm) REVERT: 9 108 TYR cc_start: 0.8787 (t80) cc_final: 0.8524 (t80) REVERT: 9 112 LEU cc_start: 0.9359 (mm) cc_final: 0.9124 (mm) REVERT: 9 115 GLN cc_start: 0.9064 (mt0) cc_final: 0.8574 (tt0) REVERT: BA 303 GLU cc_start: 0.8773 (mm-30) cc_final: 0.8470 (mm-30) REVERT: BA 312 LEU cc_start: 0.9385 (mm) cc_final: 0.9184 (mm) REVERT: CA 415 GLN cc_start: 0.9064 (mt0) cc_final: 0.8833 (mt0) REVERT: L 3 GLU cc_start: 0.8799 (mm-30) cc_final: 0.8583 (mm-30) REVERT: L 8 TYR cc_start: 0.9094 (t80) cc_final: 0.8619 (t80) REVERT: L 12 LEU cc_start: 0.9523 (mm) cc_final: 0.9272 (mm) REVERT: DA 108 TYR cc_start: 0.9060 (t80) cc_final: 0.8641 (t80) REVERT: DA 112 LEU cc_start: 0.9622 (mm) cc_final: 0.9413 (mm) REVERT: EA 208 TYR cc_start: 0.9111 (t80) cc_final: 0.8635 (t80) REVERT: FA 308 TYR cc_start: 0.9148 (t80) cc_final: 0.8562 (t80) REVERT: FA 312 LEU cc_start: 0.9524 (mm) cc_final: 0.9156 (mm) REVERT: GA 403 GLU cc_start: 0.9156 (mp0) cc_final: 0.8787 (mp0) REVERT: GA 408 TYR cc_start: 0.9012 (t80) cc_final: 0.8588 (t80) REVERT: M 3 GLU cc_start: 0.8702 (mm-30) cc_final: 0.7735 (tp30) REVERT: HA 103 GLU cc_start: 0.9134 (mm-30) cc_final: 0.8823 (mp0) REVERT: KA 415 GLN cc_start: 0.8837 (mt0) cc_final: 0.8240 (mt0) REVERT: N 12 LEU cc_start: 0.9612 (mm) cc_final: 0.9362 (mm) REVERT: LA 103 GLU cc_start: 0.8982 (mm-30) cc_final: 0.8641 (mm-30) REVERT: MA 212 LEU cc_start: 0.9601 (mm) cc_final: 0.9348 (mm) REVERT: NA 303 GLU cc_start: 0.9049 (mm-30) cc_final: 0.8833 (mm-30) REVERT: O 3 GLU cc_start: 0.8984 (mp0) cc_final: 0.8669 (mp0) REVERT: O 8 TYR cc_start: 0.9100 (t80) cc_final: 0.8631 (t80) REVERT: O 12 LEU cc_start: 0.9540 (mm) cc_final: 0.9248 (mm) REVERT: O 15 GLN cc_start: 0.9408 (OUTLIER) cc_final: 0.8856 (mm-40) REVERT: QA 208 TYR cc_start: 0.8997 (t80) cc_final: 0.8665 (t80) REVERT: QA 212 LEU cc_start: 0.9616 (mm) cc_final: 0.9275 (mm) REVERT: RA 303 GLU cc_start: 0.8992 (mm-30) cc_final: 0.8442 (mm-30) REVERT: SA 408 TYR cc_start: 0.9012 (t80) cc_final: 0.8754 (t80) REVERT: P 3 GLU cc_start: 0.9064 (mm-30) cc_final: 0.7968 (mm-30) REVERT: TA 112 LEU cc_start: 0.9539 (mm) cc_final: 0.9297 (mm) REVERT: VA 312 LEU cc_start: 0.9536 (mm) cc_final: 0.9314 (mm) REVERT: Q 8 TYR cc_start: 0.8851 (t80) cc_final: 0.8097 (t80) REVERT: Q 12 LEU cc_start: 0.9403 (mm) cc_final: 0.9147 (mm) REVERT: YA 208 TYR cc_start: 0.9064 (t80) cc_final: 0.8426 (t80) REVERT: YA 212 LEU cc_start: 0.9545 (mm) cc_final: 0.9319 (mm) REVERT: ZA 312 LEU cc_start: 0.9475 (mp) cc_final: 0.9208 (mp) REVERT: R 3 GLU cc_start: 0.8864 (mm-30) cc_final: 0.8296 (mm-30) REVERT: R 8 TYR cc_start: 0.9165 (t80) cc_final: 0.8935 (t80) REVERT: R 12 LEU cc_start: 0.9484 (mm) cc_final: 0.9179 (mm) REVERT: cA 212 LEU cc_start: 0.9614 (mm) cc_final: 0.9292 (mm) REVERT: eA 403 GLU cc_start: 0.9095 (mp0) cc_final: 0.8870 (mm-30) REVERT: eA 415 GLN cc_start: 0.8946 (mt0) cc_final: 0.8674 (mt0) REVERT: S 3 GLU cc_start: 0.8860 (mm-30) cc_final: 0.8512 (mm-30) REVERT: fA 108 TYR cc_start: 0.9173 (t80) cc_final: 0.8936 (t80) REVERT: gA 212 LEU cc_start: 0.9292 (mp) cc_final: 0.9059 (mp) REVERT: T 11 ILE cc_start: 0.8723 (tt) cc_final: 0.8394 (tp) REVERT: jA 108 TYR cc_start: 0.8853 (t80) cc_final: 0.8645 (t80) REVERT: kA 211 ILE cc_start: 0.9180 (tt) cc_final: 0.8939 (tp) REVERT: oA 203 GLU cc_start: 0.9338 (mm-30) cc_final: 0.9055 (mm-30) REVERT: pA 308 TYR cc_start: 0.8757 (t80) cc_final: 0.8541 (t80) REVERT: qA 415 GLN cc_start: 0.8803 (mt0) cc_final: 0.8119 (mt0) outliers start: 2 outliers final: 0 residues processed: 630 average time/residue: 0.2031 time to fit residues: 194.6180 Evaluate side-chains 585 residues out of total 1155 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 584 time to evaluate : 1.534 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 97 optimal weight: 4.9990 chunk 11 optimal weight: 8.9990 chunk 57 optimal weight: 4.9990 chunk 74 optimal weight: 0.9980 chunk 85 optimal weight: 0.9980 chunk 56 optimal weight: 0.9990 chunk 101 optimal weight: 4.9990 chunk 63 optimal weight: 5.9990 chunk 61 optimal weight: 8.9990 chunk 46 optimal weight: 0.9990 chunk 62 optimal weight: 6.9990 overall best weight: 1.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: d 115 GLN y 215 GLN z 315 GLN XA 115 GLN hA 315 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8851 moved from start: 0.6392 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 12915 Z= 0.232 Angle : 0.558 4.012 17325 Z= 0.284 Chirality : 0.042 0.140 1995 Planarity : 0.002 0.013 2310 Dihedral : 3.345 41.032 1890 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 4.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 0.17 % Allowed : 4.24 % Favored : 95.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.95 (0.24), residues: 1365 helix: 2.58 (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 TYR s 408 ARG 0.004 0.000 ARGCA 406 *********************** 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 612 residues out of total 1155 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 610 time to evaluate : 1.653 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: A 3 GLU cc_start: 0.8683 (mm-30) cc_final: 0.8445 (tp30) REVERT: V 108 TYR cc_start: 0.8666 (t80) cc_final: 0.8174 (t80) REVERT: W 208 TYR cc_start: 0.8981 (t80) cc_final: 0.8696 (t80) REVERT: Y 408 TYR cc_start: 0.9141 (t80) cc_final: 0.8920 (t80) REVERT: B 12 LEU cc_start: 0.9608 (mm) cc_final: 0.9258 (mm) REVERT: Z 103 GLU cc_start: 0.9160 (mm-30) cc_final: 0.8749 (mm-30) REVERT: a 212 LEU cc_start: 0.9527 (mm) cc_final: 0.9218 (mm) REVERT: b 312 LEU cc_start: 0.9441 (mm) cc_final: 0.9232 (mm) REVERT: C 3 GLU cc_start: 0.9169 (mp0) cc_final: 0.8865 (mp0) REVERT: C 8 TYR cc_start: 0.8790 (t80) cc_final: 0.8127 (t80) REVERT: d 103 GLU cc_start: 0.8958 (mp0) cc_final: 0.8723 (mm-30) REVERT: d 112 LEU cc_start: 0.9575 (mm) cc_final: 0.9294 (mm) REVERT: e 203 GLU cc_start: 0.9037 (mm-30) cc_final: 0.8697 (mm-30) REVERT: e 211 ILE cc_start: 0.9610 (tt) cc_final: 0.9395 (tt) REVERT: e 212 LEU cc_start: 0.9529 (mm) cc_final: 0.9140 (mm) REVERT: f 308 TYR cc_start: 0.9031 (t80) cc_final: 0.8636 (t80) REVERT: g 408 TYR cc_start: 0.9162 (t80) cc_final: 0.8572 (t80) REVERT: g 412 LEU cc_start: 0.9506 (mm) cc_final: 0.9279 (mm) REVERT: h 112 LEU cc_start: 0.9619 (mm) cc_final: 0.9370 (mm) REVERT: i 203 GLU cc_start: 0.9218 (mm-30) cc_final: 0.8992 (mm-30) REVERT: i 208 TYR cc_start: 0.9072 (t80) cc_final: 0.8690 (t80) REVERT: j 308 TYR cc_start: 0.9088 (t80) cc_final: 0.8705 (t80) REVERT: j 312 LEU cc_start: 0.9634 (mm) cc_final: 0.9334 (mm) REVERT: E 3 GLU cc_start: 0.8839 (mm-30) cc_final: 0.8612 (mm-30) REVERT: m 208 TYR cc_start: 0.8949 (t80) cc_final: 0.8597 (t80) REVERT: F 3 GLU cc_start: 0.8793 (mm-30) cc_final: 0.7762 (mm-30) REVERT: p 108 TYR cc_start: 0.8855 (t80) cc_final: 0.8641 (t80) REVERT: q 208 TYR cc_start: 0.8751 (t80) cc_final: 0.8484 (t80) REVERT: s 415 GLN cc_start: 0.8821 (mt0) cc_final: 0.8602 (mt0) REVERT: G 8 TYR cc_start: 0.9061 (t80) cc_final: 0.8807 (t80) REVERT: G 12 LEU cc_start: 0.9649 (mm) cc_final: 0.9306 (mm) REVERT: t 108 TYR cc_start: 0.9118 (t80) cc_final: 0.8900 (t80) REVERT: t 112 LEU cc_start: 0.9628 (mm) cc_final: 0.9291 (mm) REVERT: u 208 TYR cc_start: 0.8833 (t80) cc_final: 0.8538 (t80) REVERT: u 212 LEU cc_start: 0.9543 (mm) cc_final: 0.9254 (mm) REVERT: v 303 GLU cc_start: 0.9216 (mm-30) cc_final: 0.8941 (mm-30) REVERT: v 315 GLN cc_start: 0.8720 (mt0) cc_final: 0.8471 (mt0) REVERT: w 415 GLN cc_start: 0.9211 (mt0) cc_final: 0.8921 (mt0) REVERT: x 103 GLU cc_start: 0.9161 (mm-30) cc_final: 0.8691 (mm-30) REVERT: y 212 LEU cc_start: 0.9564 (mm) cc_final: 0.9238 (mm) REVERT: y 215 GLN cc_start: 0.8771 (tp-100) cc_final: 0.8545 (tp40) REVERT: z 303 GLU cc_start: 0.9038 (mm-30) cc_final: 0.8505 (mm-30) REVERT: z 308 TYR cc_start: 0.8693 (t80) cc_final: 0.7955 (t80) REVERT: 0 408 TYR cc_start: 0.8891 (t80) cc_final: 0.8561 (t80) REVERT: 0 411 ILE cc_start: 0.9572 (tt) cc_final: 0.9186 (tt) REVERT: 0 412 LEU cc_start: 0.9391 (mm) cc_final: 0.8747 (mm) REVERT: 0 415 GLN cc_start: 0.8554 (mt0) cc_final: 0.8315 (mt0) REVERT: I 8 TYR cc_start: 0.8914 (t80) cc_final: 0.8652 (t80) REVERT: I 12 LEU cc_start: 0.9492 (mm) cc_final: 0.9256 (mm) REVERT: 1 108 TYR cc_start: 0.8868 (t80) cc_final: 0.8654 (t80) REVERT: 2 212 LEU cc_start: 0.9575 (mm) cc_final: 0.9207 (mm) REVERT: 7 303 GLU cc_start: 0.9104 (mm-30) cc_final: 0.8487 (mm-30) REVERT: 7 308 TYR cc_start: 0.8870 (t80) cc_final: 0.8661 (t80) REVERT: K 8 TYR cc_start: 0.9172 (t80) cc_final: 0.8817 (t80) REVERT: K 12 LEU cc_start: 0.9606 (mm) cc_final: 0.9359 (mm) REVERT: 9 108 TYR cc_start: 0.8813 (t80) cc_final: 0.8592 (t80) REVERT: BA 312 LEU cc_start: 0.9403 (mm) cc_final: 0.9162 (mm) REVERT: L 3 GLU cc_start: 0.8769 (mm-30) cc_final: 0.8561 (mm-30) REVERT: L 8 TYR cc_start: 0.9111 (t80) cc_final: 0.8609 (t80) REVERT: L 12 LEU cc_start: 0.9541 (mm) cc_final: 0.9270 (mm) REVERT: DA 108 TYR cc_start: 0.9099 (t80) cc_final: 0.8693 (t80) REVERT: EA 203 GLU cc_start: 0.9109 (mp0) cc_final: 0.8908 (mp0) REVERT: EA 208 TYR cc_start: 0.9153 (t80) cc_final: 0.8675 (t80) REVERT: FA 308 TYR cc_start: 0.9173 (t80) cc_final: 0.8518 (t80) REVERT: FA 312 LEU cc_start: 0.9531 (mm) cc_final: 0.9182 (mm) REVERT: GA 403 GLU cc_start: 0.9178 (mp0) cc_final: 0.8782 (mp0) REVERT: GA 408 TYR cc_start: 0.9047 (t80) cc_final: 0.8550 (t80) REVERT: M 3 GLU cc_start: 0.8715 (mm-30) cc_final: 0.7717 (mm-30) REVERT: M 12 LEU cc_start: 0.9570 (mm) cc_final: 0.9360 (mm) REVERT: HA 103 GLU cc_start: 0.9104 (mm-30) cc_final: 0.8796 (mp0) REVERT: IA 208 TYR cc_start: 0.8977 (t80) cc_final: 0.8508 (t80) REVERT: IA 212 LEU cc_start: 0.9530 (mm) cc_final: 0.9321 (mm) REVERT: KA 403 GLU cc_start: 0.8222 (tp30) cc_final: 0.7994 (mm-30) REVERT: KA 415 GLN cc_start: 0.8841 (mt0) cc_final: 0.8160 (mt0) REVERT: N 3 GLU cc_start: 0.8793 (mm-30) cc_final: 0.8568 (tp30) REVERT: N 12 LEU cc_start: 0.9626 (mm) cc_final: 0.9364 (mm) REVERT: LA 103 GLU cc_start: 0.9048 (mm-30) cc_final: 0.8607 (mm-30) REVERT: MA 212 LEU cc_start: 0.9618 (mm) cc_final: 0.9334 (mm) REVERT: NA 303 GLU cc_start: 0.9062 (mm-30) cc_final: 0.8847 (mm-30) REVERT: OA 412 LEU cc_start: 0.9488 (mm) cc_final: 0.9260 (mm) REVERT: O 3 GLU cc_start: 0.8994 (mp0) cc_final: 0.8683 (mp0) REVERT: O 8 TYR cc_start: 0.9109 (t80) cc_final: 0.8782 (t80) REVERT: O 12 LEU cc_start: 0.9543 (mm) cc_final: 0.9295 (mm) REVERT: QA 212 LEU cc_start: 0.9574 (mm) cc_final: 0.9326 (mm) REVERT: RA 303 GLU cc_start: 0.9050 (mm-30) cc_final: 0.8417 (mm-30) REVERT: RA 312 LEU cc_start: 0.9576 (mm) cc_final: 0.9373 (mm) REVERT: SA 408 TYR cc_start: 0.9022 (t80) cc_final: 0.8783 (t80) REVERT: P 15 GLN cc_start: 0.8813 (tp40) cc_final: 0.8266 (tp40) REVERT: TA 112 LEU cc_start: 0.9544 (mm) cc_final: 0.9298 (mm) REVERT: Q 3 GLU cc_start: 0.8817 (tp30) cc_final: 0.7509 (tp30) REVERT: Q 8 TYR cc_start: 0.8718 (t80) cc_final: 0.8319 (t80) REVERT: YA 208 TYR cc_start: 0.9106 (t80) cc_final: 0.8409 (t80) REVERT: aA 403 GLU cc_start: 0.9206 (mp0) cc_final: 0.8890 (mp0) REVERT: aA 415 GLN cc_start: 0.9026 (mt0) cc_final: 0.8812 (mt0) REVERT: R 3 GLU cc_start: 0.8872 (mm-30) cc_final: 0.8310 (mm-30) REVERT: R 8 TYR cc_start: 0.9200 (t80) cc_final: 0.8998 (t80) REVERT: R 12 LEU cc_start: 0.9560 (mm) cc_final: 0.9247 (mm) REVERT: cA 212 LEU cc_start: 0.9581 (mm) cc_final: 0.9380 (mm) REVERT: eA 415 GLN cc_start: 0.8933 (mt0) cc_final: 0.8701 (mt0) REVERT: S 3 GLU cc_start: 0.8866 (mm-30) cc_final: 0.8544 (mm-30) REVERT: S 8 TYR cc_start: 0.9090 (t80) cc_final: 0.8820 (t80) REVERT: fA 108 TYR cc_start: 0.9068 (t80) cc_final: 0.8836 (t80) REVERT: gA 212 LEU cc_start: 0.9358 (mp) cc_final: 0.9030 (mp) REVERT: T 11 ILE cc_start: 0.8801 (tt) cc_final: 0.8459 (tp) REVERT: jA 108 TYR cc_start: 0.8885 (t80) cc_final: 0.8684 (t80) REVERT: U 8 TYR cc_start: 0.8638 (t80) cc_final: 0.8346 (t80) REVERT: oA 203 GLU cc_start: 0.9331 (mm-30) cc_final: 0.8973 (mm-30) REVERT: pA 308 TYR cc_start: 0.8798 (t80) cc_final: 0.8516 (t80) REVERT: qA 415 GLN cc_start: 0.8702 (mt0) cc_final: 0.8427 (mt0) outliers start: 2 outliers final: 0 residues processed: 612 average time/residue: 0.1951 time to fit residues: 182.3328 Evaluate side-chains 576 residues out of total 1155 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 576 time to evaluate : 1.521 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 40 optimal weight: 4.9990 chunk 60 optimal weight: 2.9990 chunk 30 optimal weight: 0.8980 chunk 19 optimal weight: 0.9980 chunk 64 optimal weight: 2.9990 chunk 68 optimal weight: 0.8980 chunk 50 optimal weight: 0.9990 chunk 9 optimal weight: 0.9980 chunk 79 optimal weight: 0.9980 chunk 92 optimal weight: 0.8980 chunk 96 optimal weight: 2.9990 overall best weight: 0.9380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** x 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 8 415 GLN XA 115 GLN hA 315 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8807 moved from start: 0.6707 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 12915 Z= 0.205 Angle : 0.597 5.355 17325 Z= 0.296 Chirality : 0.041 0.148 1995 Planarity : 0.002 0.013 2310 Dihedral : 3.573 35.041 1890 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 4.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 0.17 % Allowed : 0.95 % 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: 4.25 (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 0.016 0.002 TYR S 8 ARG 0.002 0.000 ARGCA 406 *********************** 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 622 residues out of total 1155 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 620 time to evaluate : 1.474 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: A 3 GLU cc_start: 0.8707 (mm-30) cc_final: 0.8453 (tp30) REVERT: V 108 TYR cc_start: 0.8636 (t80) cc_final: 0.8154 (t80) REVERT: W 208 TYR cc_start: 0.8771 (t80) cc_final: 0.8544 (t80) REVERT: X 303 GLU cc_start: 0.9076 (mp0) cc_final: 0.8862 (mp0) REVERT: B 12 LEU cc_start: 0.9636 (mm) cc_final: 0.9286 (mm) REVERT: Z 103 GLU cc_start: 0.9166 (mm-30) cc_final: 0.8739 (mm-30) REVERT: a 212 LEU cc_start: 0.9541 (mm) cc_final: 0.9229 (mm) REVERT: C 3 GLU cc_start: 0.9177 (mp0) cc_final: 0.8889 (mp0) REVERT: C 8 TYR cc_start: 0.8714 (t80) cc_final: 0.8082 (t80) REVERT: d 112 LEU cc_start: 0.9557 (mm) cc_final: 0.9253 (mm) REVERT: e 203 GLU cc_start: 0.9083 (mm-30) cc_final: 0.8882 (mm-30) REVERT: e 211 ILE cc_start: 0.9522 (tt) cc_final: 0.9289 (tt) REVERT: e 212 LEU cc_start: 0.9525 (mm) cc_final: 0.9183 (mm) REVERT: f 308 TYR cc_start: 0.9022 (t80) cc_final: 0.8652 (t80) REVERT: g 408 TYR cc_start: 0.9111 (t80) cc_final: 0.8456 (t80) REVERT: g 412 LEU cc_start: 0.9501 (mm) cc_final: 0.9276 (mm) REVERT: i 203 GLU cc_start: 0.9201 (mm-30) cc_final: 0.8964 (mm-30) REVERT: i 208 TYR cc_start: 0.9051 (t80) cc_final: 0.8737 (t80) REVERT: j 308 TYR cc_start: 0.9037 (t80) cc_final: 0.8690 (t80) REVERT: j 312 LEU cc_start: 0.9600 (mm) cc_final: 0.9359 (mm) REVERT: E 3 GLU cc_start: 0.8832 (mm-30) cc_final: 0.8566 (mm-30) REVERT: m 208 TYR cc_start: 0.8931 (t80) cc_final: 0.7673 (t80) REVERT: F 3 GLU cc_start: 0.8792 (mm-30) cc_final: 0.7677 (mm-30) REVERT: p 108 TYR cc_start: 0.8838 (t80) cc_final: 0.8534 (t80) REVERT: q 208 TYR cc_start: 0.8730 (t80) cc_final: 0.8422 (t80) REVERT: s 415 GLN cc_start: 0.8865 (mt0) cc_final: 0.8629 (mt0) REVERT: G 3 GLU cc_start: 0.8642 (mm-30) cc_final: 0.8421 (mm-30) REVERT: G 11 ILE cc_start: 0.9336 (mt) cc_final: 0.9136 (mt) REVERT: G 12 LEU cc_start: 0.9698 (mm) cc_final: 0.9349 (mm) REVERT: t 108 TYR cc_start: 0.9044 (t80) cc_final: 0.8819 (t80) REVERT: t 112 LEU cc_start: 0.9624 (mm) cc_final: 0.9248 (mm) REVERT: u 208 TYR cc_start: 0.8602 (t80) cc_final: 0.8397 (t80) REVERT: u 212 LEU cc_start: 0.9528 (mm) cc_final: 0.9320 (mm) REVERT: v 303 GLU cc_start: 0.9213 (mm-30) cc_final: 0.8896 (mm-30) REVERT: x 103 GLU cc_start: 0.9153 (mm-30) cc_final: 0.8597 (mm-30) REVERT: x 108 TYR cc_start: 0.8613 (t80) cc_final: 0.8304 (t80) REVERT: y 212 LEU cc_start: 0.9563 (mm) cc_final: 0.9223 (mm) REVERT: z 303 GLU cc_start: 0.9032 (mm-30) cc_final: 0.8553 (mm-30) REVERT: 0 408 TYR cc_start: 0.8843 (t80) cc_final: 0.8444 (t80) REVERT: 0 411 ILE cc_start: 0.9513 (tt) cc_final: 0.9141 (tt) REVERT: 0 412 LEU cc_start: 0.9347 (mm) cc_final: 0.8695 (mm) REVERT: 0 415 GLN cc_start: 0.8495 (mt0) cc_final: 0.8197 (mt0) REVERT: I 8 TYR cc_start: 0.8907 (t80) cc_final: 0.8619 (t80) REVERT: I 11 ILE cc_start: 0.9386 (tp) cc_final: 0.9165 (tp) REVERT: I 12 LEU cc_start: 0.9482 (mm) cc_final: 0.9204 (mm) REVERT: 1 108 TYR cc_start: 0.8824 (t80) cc_final: 0.8606 (t80) REVERT: 2 212 LEU cc_start: 0.9576 (mm) cc_final: 0.9211 (mm) REVERT: J 3 GLU cc_start: 0.9072 (mm-30) cc_final: 0.8789 (mm-30) REVERT: 7 303 GLU cc_start: 0.9090 (mm-30) cc_final: 0.8407 (mm-30) REVERT: K 8 TYR cc_start: 0.9111 (t80) cc_final: 0.8897 (t80) REVERT: 9 108 TYR cc_start: 0.8715 (t80) cc_final: 0.8466 (t80) REVERT: BA 312 LEU cc_start: 0.9459 (mm) cc_final: 0.9214 (mm) REVERT: L 3 GLU cc_start: 0.8798 (mm-30) cc_final: 0.8571 (mm-30) REVERT: L 8 TYR cc_start: 0.9087 (t80) cc_final: 0.8563 (t80) REVERT: L 12 LEU cc_start: 0.9492 (mm) cc_final: 0.9238 (mm) REVERT: DA 108 TYR cc_start: 0.9029 (t80) cc_final: 0.8589 (t80) REVERT: EA 208 TYR cc_start: 0.9078 (t80) cc_final: 0.8650 (t80) REVERT: FA 308 TYR cc_start: 0.9154 (t80) cc_final: 0.8520 (t80) REVERT: FA 312 LEU cc_start: 0.9487 (mm) cc_final: 0.9140 (mm) REVERT: GA 403 GLU cc_start: 0.9174 (mp0) cc_final: 0.8785 (mp0) REVERT: GA 408 TYR cc_start: 0.8968 (t80) cc_final: 0.8602 (t80) REVERT: M 3 GLU cc_start: 0.8679 (mm-30) cc_final: 0.7715 (mm-30) REVERT: IA 208 TYR cc_start: 0.8874 (t80) cc_final: 0.8413 (t80) REVERT: IA 212 LEU cc_start: 0.9447 (mm) cc_final: 0.9219 (mm) REVERT: JA 312 LEU cc_start: 0.9503 (mm) cc_final: 0.9285 (mm) REVERT: KA 415 GLN cc_start: 0.8762 (mt0) cc_final: 0.8185 (mt0) REVERT: N 3 GLU cc_start: 0.8777 (mm-30) cc_final: 0.7499 (mm-30) REVERT: N 12 LEU cc_start: 0.9617 (mm) cc_final: 0.9346 (mm) REVERT: LA 103 GLU cc_start: 0.9016 (mm-30) cc_final: 0.8580 (mm-30) REVERT: MA 212 LEU cc_start: 0.9614 (mm) cc_final: 0.9378 (mm) REVERT: NA 303 GLU cc_start: 0.9079 (mm-30) cc_final: 0.8836 (mm-30) REVERT: O 3 GLU cc_start: 0.8995 (mp0) cc_final: 0.8661 (mp0) REVERT: O 8 TYR cc_start: 0.8787 (t80) cc_final: 0.8372 (t80) REVERT: O 12 LEU cc_start: 0.9541 (mm) cc_final: 0.9226 (mm) REVERT: QA 212 LEU cc_start: 0.9542 (mm) cc_final: 0.9299 (mm) REVERT: RA 303 GLU cc_start: 0.9015 (mm-30) cc_final: 0.8434 (mm-30) REVERT: TA 112 LEU cc_start: 0.9537 (mm) cc_final: 0.9273 (mm) REVERT: WA 403 GLU cc_start: 0.9034 (mm-30) cc_final: 0.8024 (mm-30) REVERT: Q 11 ILE cc_start: 0.9495 (tt) cc_final: 0.9134 (tt) REVERT: XA 108 TYR cc_start: 0.8932 (t80) cc_final: 0.8585 (t80) REVERT: YA 208 TYR cc_start: 0.9036 (t80) cc_final: 0.8419 (t80) REVERT: aA 403 GLU cc_start: 0.9219 (mp0) cc_final: 0.8912 (mp0) REVERT: R 3 GLU cc_start: 0.8826 (mm-30) cc_final: 0.8317 (mm-30) REVERT: R 12 LEU cc_start: 0.9546 (mm) cc_final: 0.9251 (mm) REVERT: cA 212 LEU cc_start: 0.9624 (mm) cc_final: 0.9387 (mm) REVERT: dA 303 GLU cc_start: 0.9120 (mm-30) cc_final: 0.8666 (mm-30) REVERT: S 3 GLU cc_start: 0.9157 (mm-30) cc_final: 0.8794 (mm-30) REVERT: S 8 TYR cc_start: 0.8915 (t80) cc_final: 0.8459 (t80) REVERT: gA 212 LEU cc_start: 0.9315 (mp) cc_final: 0.8963 (mp) REVERT: T 11 ILE cc_start: 0.8798 (tt) cc_final: 0.8449 (tp) REVERT: jA 108 TYR cc_start: 0.8876 (t80) cc_final: 0.8635 (t80) REVERT: lA 308 TYR cc_start: 0.8711 (t80) cc_final: 0.8489 (t80) REVERT: U 8 TYR cc_start: 0.8536 (t80) cc_final: 0.8258 (t80) REVERT: oA 203 GLU cc_start: 0.9352 (mm-30) cc_final: 0.8596 (mm-30) REVERT: pA 308 TYR cc_start: 0.8757 (t80) cc_final: 0.8440 (t80) REVERT: qA 403 GLU cc_start: 0.8984 (mm-30) cc_final: 0.8741 (mm-30) outliers start: 2 outliers final: 0 residues processed: 622 average time/residue: 0.1945 time to fit residues: 183.9557 Evaluate side-chains 589 residues out of total 1155 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 589 time to evaluate : 1.627 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 88 optimal weight: 0.9980 chunk 94 optimal weight: 4.9990 chunk 96 optimal weight: 2.9990 chunk 56 optimal weight: 3.9990 chunk 41 optimal weight: 1.9990 chunk 74 optimal weight: 8.9990 chunk 28 optimal weight: 0.6980 chunk 85 optimal weight: 0.6980 chunk 89 optimal weight: 0.9990 chunk 93 optimal weight: 0.7980 chunk 61 optimal weight: 8.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: y 215 GLN JA 315 GLN XA 115 GLN iA 415 GLN kA 215 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8795 moved from start: 0.6856 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 12915 Z= 0.206 Angle : 0.628 6.219 17325 Z= 0.309 Chirality : 0.041 0.149 1995 Planarity : 0.002 0.014 2310 Dihedral : 3.570 30.715 1890 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 4.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 0.17 % Allowed : 1.47 % Favored : 98.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 4.44 (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 3 308 ARG 0.002 0.000 ARG 8 406 *********************** 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 623 residues out of total 1155 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 621 time to evaluate : 1.522 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: A 3 GLU cc_start: 0.8713 (mm-30) cc_final: 0.8475 (tp30) REVERT: A 12 LEU cc_start: 0.9494 (mm) cc_final: 0.9287 (mm) REVERT: V 108 TYR cc_start: 0.8937 (t80) cc_final: 0.8707 (t80) REVERT: W 208 TYR cc_start: 0.8697 (t80) cc_final: 0.8376 (t80) REVERT: W 212 LEU cc_start: 0.9432 (mm) cc_final: 0.9224 (mm) REVERT: X 303 GLU cc_start: 0.9111 (mp0) cc_final: 0.8876 (mp0) REVERT: B 12 LEU cc_start: 0.9647 (mm) cc_final: 0.9303 (mm) REVERT: Z 103 GLU cc_start: 0.9154 (mm-30) cc_final: 0.8727 (mm-30) REVERT: a 212 LEU cc_start: 0.9552 (mm) cc_final: 0.9233 (mm) REVERT: C 3 GLU cc_start: 0.9177 (mp0) cc_final: 0.8899 (mp0) REVERT: d 103 GLU cc_start: 0.8915 (mp0) cc_final: 0.8693 (mp0) REVERT: d 112 LEU cc_start: 0.9514 (mm) cc_final: 0.9288 (mm) REVERT: e 203 GLU cc_start: 0.9080 (mm-30) cc_final: 0.8795 (mm-30) REVERT: e 211 ILE cc_start: 0.9502 (tt) cc_final: 0.9145 (tt) REVERT: e 212 LEU cc_start: 0.9521 (mm) cc_final: 0.9151 (mm) REVERT: f 308 TYR cc_start: 0.9005 (t80) cc_final: 0.8662 (t80) REVERT: g 408 TYR cc_start: 0.9109 (t80) cc_final: 0.8488 (t80) REVERT: h 112 LEU cc_start: 0.9551 (mm) cc_final: 0.9350 (mm) REVERT: i 203 GLU cc_start: 0.9199 (mm-30) cc_final: 0.8941 (mm-30) REVERT: i 208 TYR cc_start: 0.9033 (t80) cc_final: 0.8764 (t80) REVERT: j 308 TYR cc_start: 0.9011 (t80) cc_final: 0.8643 (t80) REVERT: j 312 LEU cc_start: 0.9593 (mm) cc_final: 0.9372 (mm) REVERT: m 208 TYR cc_start: 0.8910 (t80) cc_final: 0.8513 (t80) REVERT: F 3 GLU cc_start: 0.8802 (mm-30) cc_final: 0.7696 (mm-30) REVERT: p 108 TYR cc_start: 0.8857 (t80) cc_final: 0.8629 (t80) REVERT: q 208 TYR cc_start: 0.8710 (t80) cc_final: 0.8381 (t80) REVERT: s 411 ILE cc_start: 0.9415 (mt) cc_final: 0.9187 (mt) REVERT: s 415 GLN cc_start: 0.8844 (mt0) cc_final: 0.8635 (mt0) REVERT: G 12 LEU cc_start: 0.9677 (mm) cc_final: 0.9417 (mm) REVERT: t 108 TYR cc_start: 0.9039 (t80) cc_final: 0.8825 (t80) REVERT: t 112 LEU cc_start: 0.9627 (mm) cc_final: 0.9291 (mm) REVERT: u 208 TYR cc_start: 0.8566 (t80) cc_final: 0.8346 (t80) REVERT: u 212 LEU cc_start: 0.9532 (mm) cc_final: 0.9317 (mm) REVERT: v 303 GLU cc_start: 0.9224 (mm-30) cc_final: 0.8890 (mm-30) REVERT: x 103 GLU cc_start: 0.9137 (mm-30) cc_final: 0.8622 (mm-30) REVERT: x 108 TYR cc_start: 0.8603 (t80) cc_final: 0.8319 (t80) REVERT: y 212 LEU cc_start: 0.9532 (mm) cc_final: 0.9154 (mm) REVERT: 0 408 TYR cc_start: 0.8862 (t80) cc_final: 0.8530 (t80) REVERT: 0 411 ILE cc_start: 0.9488 (tt) cc_final: 0.9154 (tt) REVERT: 0 412 LEU cc_start: 0.9341 (mm) cc_final: 0.8694 (mm) REVERT: 0 415 GLN cc_start: 0.8471 (mt0) cc_final: 0.8269 (mt0) REVERT: I 8 TYR cc_start: 0.8908 (t80) cc_final: 0.8615 (t80) REVERT: I 12 LEU cc_start: 0.9467 (mm) cc_final: 0.9214 (mm) REVERT: 1 108 TYR cc_start: 0.8810 (t80) cc_final: 0.8575 (t80) REVERT: 2 212 LEU cc_start: 0.9551 (mm) cc_final: 0.9155 (mm) REVERT: J 3 GLU cc_start: 0.9095 (mm-30) cc_final: 0.8879 (mm-30) REVERT: 7 303 GLU cc_start: 0.9095 (mm-30) cc_final: 0.8403 (mm-30) REVERT: K 3 GLU cc_start: 0.9071 (mm-30) cc_final: 0.8563 (mm-30) REVERT: BA 312 LEU cc_start: 0.9452 (mm) cc_final: 0.9185 (mm) REVERT: L 3 GLU cc_start: 0.8782 (mm-30) cc_final: 0.8446 (mm-30) REVERT: L 8 TYR cc_start: 0.9096 (t80) cc_final: 0.8625 (t80) REVERT: L 12 LEU cc_start: 0.9469 (mm) cc_final: 0.9268 (mm) REVERT: DA 108 TYR cc_start: 0.9010 (t80) cc_final: 0.8673 (t80) REVERT: EA 208 TYR cc_start: 0.9090 (t80) cc_final: 0.8721 (t80) REVERT: FA 308 TYR cc_start: 0.9133 (t80) cc_final: 0.8542 (t80) REVERT: FA 312 LEU cc_start: 0.9476 (mm) cc_final: 0.9179 (mm) REVERT: GA 403 GLU cc_start: 0.9196 (mp0) cc_final: 0.8807 (mp0) REVERT: GA 408 TYR cc_start: 0.8994 (t80) cc_final: 0.8579 (t80) REVERT: M 3 GLU cc_start: 0.8689 (mm-30) cc_final: 0.7728 (mm-30) REVERT: IA 208 TYR cc_start: 0.8841 (t80) cc_final: 0.8395 (t80) REVERT: JA 312 LEU cc_start: 0.9533 (mm) cc_final: 0.9255 (mm) REVERT: KA 412 LEU cc_start: 0.9490 (mm) cc_final: 0.9276 (mm) REVERT: KA 415 GLN cc_start: 0.8801 (mt0) cc_final: 0.8094 (tt0) REVERT: N 12 LEU cc_start: 0.9616 (mm) cc_final: 0.9405 (mm) REVERT: LA 103 GLU cc_start: 0.9052 (mm-30) cc_final: 0.8601 (mm-30) REVERT: MA 212 LEU cc_start: 0.9617 (mm) cc_final: 0.9399 (mm) REVERT: NA 303 GLU cc_start: 0.9092 (mm-30) cc_final: 0.8839 (mm-30) REVERT: O 3 GLU cc_start: 0.9002 (mp0) cc_final: 0.8668 (mp0) REVERT: O 8 TYR cc_start: 0.8753 (t80) cc_final: 0.8332 (t80) REVERT: O 12 LEU cc_start: 0.9546 (mm) cc_final: 0.9207 (mm) REVERT: PA 103 GLU cc_start: 0.9153 (mm-30) cc_final: 0.8415 (mm-30) REVERT: QA 212 LEU cc_start: 0.9526 (mm) cc_final: 0.9267 (mm) REVERT: RA 303 GLU cc_start: 0.9008 (mm-30) cc_final: 0.8386 (mm-30) REVERT: TA 112 LEU cc_start: 0.9487 (mm) cc_final: 0.9217 (mm) REVERT: WA 403 GLU cc_start: 0.9045 (mm-30) cc_final: 0.8507 (mm-30) REVERT: Q 3 GLU cc_start: 0.8929 (mm-30) cc_final: 0.8174 (tp30) REVERT: Q 11 ILE cc_start: 0.9567 (tt) cc_final: 0.9277 (tt) REVERT: XA 108 TYR cc_start: 0.8901 (t80) cc_final: 0.8623 (t80) REVERT: YA 208 TYR cc_start: 0.9025 (t80) cc_final: 0.8493 (t80) REVERT: aA 403 GLU cc_start: 0.9209 (mp0) cc_final: 0.8902 (mp0) REVERT: R 12 LEU cc_start: 0.9587 (mm) cc_final: 0.9266 (mm) REVERT: dA 303 GLU cc_start: 0.9102 (mm-30) cc_final: 0.8649 (mm-30) REVERT: S 3 GLU cc_start: 0.9128 (mm-30) cc_final: 0.8348 (mm-30) REVERT: gA 212 LEU cc_start: 0.9302 (mp) cc_final: 0.8952 (mp) REVERT: iA 415 GLN cc_start: 0.8781 (mt0) cc_final: 0.8479 (mt0) REVERT: T 11 ILE cc_start: 0.8658 (tt) cc_final: 0.8344 (tp) REVERT: jA 108 TYR cc_start: 0.8872 (t80) cc_final: 0.8645 (t80) REVERT: lA 308 TYR cc_start: 0.8633 (t80) cc_final: 0.8432 (t80) REVERT: U 8 TYR cc_start: 0.8535 (t80) cc_final: 0.8259 (t80) REVERT: oA 203 GLU cc_start: 0.9349 (mm-30) cc_final: 0.8981 (mm-30) REVERT: pA 308 TYR cc_start: 0.8762 (t80) cc_final: 0.8433 (t80) REVERT: qA 403 GLU cc_start: 0.9008 (mm-30) cc_final: 0.8766 (mm-30) outliers start: 2 outliers final: 0 residues processed: 623 average time/residue: 0.1982 time to fit residues: 187.7673 Evaluate side-chains 593 residues out of total 1155 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 593 time to evaluate : 1.535 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 99 optimal weight: 2.9990 chunk 60 optimal weight: 0.9980 chunk 47 optimal weight: 0.9990 chunk 69 optimal weight: 0.8980 chunk 104 optimal weight: 0.9980 chunk 96 optimal weight: 3.9990 chunk 83 optimal weight: 0.9980 chunk 8 optimal weight: 0.9980 chunk 64 optimal weight: 0.9980 chunk 51 optimal weight: 4.9990 chunk 66 optimal weight: 0.7980 overall best weight: 0.9380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** o 415 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** RA 315 GLN XA 115 GLN ZA 315 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8799 moved from start: 0.6955 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 12915 Z= 0.229 Angle : 0.654 7.095 17325 Z= 0.326 Chirality : 0.041 0.146 1995 Planarity : 0.002 0.015 2310 Dihedral : 3.516 27.856 1890 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 5.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 0.26 % Allowed : 0.26 % Favored : 99.48 % 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: 4.58 (0.22), residues: 1365 helix: 2.98 (0.14), residues: 1365 sheet: None (None), residues: 0 loop : None (None), residues: 0 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.024 0.002 TYR 3 308 ARG 0.003 0.000 ARG G 10 ********************** 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 622 residues out of total 1155 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 619 time to evaluate : 1.579 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: A 3 GLU cc_start: 0.8726 (mm-30) cc_final: 0.8514 (tp30) REVERT: A 12 LEU cc_start: 0.9525 (mm) cc_final: 0.9295 (mm) REVERT: V 108 TYR cc_start: 0.8945 (t80) cc_final: 0.8702 (t80) REVERT: W 208 TYR cc_start: 0.8702 (t80) cc_final: 0.8383 (t80) REVERT: X 303 GLU cc_start: 0.9114 (mp0) cc_final: 0.8875 (mp0) REVERT: B 12 LEU cc_start: 0.9658 (mm) cc_final: 0.9282 (mm) REVERT: Z 103 GLU cc_start: 0.9172 (mm-30) cc_final: 0.8691 (mm-30) REVERT: a 212 LEU cc_start: 0.9558 (mm) cc_final: 0.9285 (mm) REVERT: C 3 GLU cc_start: 0.9198 (mp0) cc_final: 0.8965 (mp0) REVERT: C 12 LEU cc_start: 0.9596 (mm) cc_final: 0.9396 (mm) REVERT: d 103 GLU cc_start: 0.8944 (mp0) cc_final: 0.8702 (mp0) REVERT: d 112 LEU cc_start: 0.9498 (mm) cc_final: 0.9243 (mm) REVERT: e 203 GLU cc_start: 0.9119 (mm-30) cc_final: 0.8675 (mm-30) REVERT: e 211 ILE cc_start: 0.9497 (tt) cc_final: 0.9122 (tt) REVERT: e 212 LEU cc_start: 0.9515 (mm) cc_final: 0.9184 (mm) REVERT: f 308 TYR cc_start: 0.8970 (t80) cc_final: 0.8652 (t80) REVERT: g 408 TYR cc_start: 0.9094 (t80) cc_final: 0.8579 (t80) REVERT: g 412 LEU cc_start: 0.9487 (mm) cc_final: 0.9284 (mm) REVERT: D 3 GLU cc_start: 0.9056 (mp0) cc_final: 0.8714 (mm-30) REVERT: i 203 GLU cc_start: 0.9199 (mm-30) cc_final: 0.8941 (mm-30) REVERT: i 208 TYR cc_start: 0.9036 (t80) cc_final: 0.8798 (t80) REVERT: j 308 TYR cc_start: 0.9022 (t80) cc_final: 0.8696 (t80) REVERT: m 208 TYR cc_start: 0.8924 (t80) cc_final: 0.8541 (t80) REVERT: o 415 GLN cc_start: 0.8992 (mt0) cc_final: 0.8744 (mt0) REVERT: F 3 GLU cc_start: 0.8786 (mm-30) cc_final: 0.7719 (mm-30) REVERT: q 208 TYR cc_start: 0.8731 (t80) cc_final: 0.8402 (t80) REVERT: G 8 TYR cc_start: 0.9041 (t80) cc_final: 0.8804 (t80) REVERT: G 12 LEU cc_start: 0.9715 (mm) cc_final: 0.9263 (mm) REVERT: t 108 TYR cc_start: 0.9033 (t80) cc_final: 0.8762 (t80) REVERT: t 112 LEU cc_start: 0.9620 (mm) cc_final: 0.9278 (mm) REVERT: u 208 TYR cc_start: 0.8565 (t80) cc_final: 0.8343 (t80) REVERT: u 212 LEU cc_start: 0.9513 (mm) cc_final: 0.9311 (mm) REVERT: v 303 GLU cc_start: 0.9224 (mm-30) cc_final: 0.8884 (mm-30) REVERT: x 103 GLU cc_start: 0.9161 (mm-30) cc_final: 0.8622 (mm-30) REVERT: x 115 GLN cc_start: 0.8917 (mt0) cc_final: 0.8393 (mt0) REVERT: y 203 GLU cc_start: 0.9035 (mm-30) cc_final: 0.8382 (mm-30) REVERT: y 212 LEU cc_start: 0.9571 (mm) cc_final: 0.9281 (mm) REVERT: 0 408 TYR cc_start: 0.8836 (t80) cc_final: 0.8460 (t80) REVERT: 0 411 ILE cc_start: 0.9489 (tt) cc_final: 0.9149 (tt) REVERT: 0 412 LEU cc_start: 0.9368 (mm) cc_final: 0.8755 (mm) REVERT: I 8 TYR cc_start: 0.8841 (t80) cc_final: 0.8631 (t80) REVERT: I 12 LEU cc_start: 0.9441 (mm) cc_final: 0.9161 (mm) REVERT: 1 108 TYR cc_start: 0.8822 (t80) cc_final: 0.8604 (t80) REVERT: 2 212 LEU cc_start: 0.9541 (mm) cc_final: 0.9141 (mm) REVERT: 4 415 GLN cc_start: 0.8978 (mt0) cc_final: 0.8735 (mt0) REVERT: J 3 GLU cc_start: 0.9086 (mm-30) cc_final: 0.8803 (mm-30) REVERT: 7 303 GLU cc_start: 0.9109 (mm-30) cc_final: 0.8537 (mm-30) REVERT: 7 308 TYR cc_start: 0.8648 (t80) cc_final: 0.7939 (t80) REVERT: K 3 GLU cc_start: 0.9057 (mm-30) cc_final: 0.8803 (mm-30) REVERT: CA 408 TYR cc_start: 0.9059 (t80) cc_final: 0.8660 (t80) REVERT: CA 412 LEU cc_start: 0.9418 (mm) cc_final: 0.9157 (mm) REVERT: L 3 GLU cc_start: 0.8795 (mm-30) cc_final: 0.8492 (mm-30) REVERT: L 8 TYR cc_start: 0.9106 (t80) cc_final: 0.8641 (t80) REVERT: L 12 LEU cc_start: 0.9479 (mm) cc_final: 0.9277 (mm) REVERT: DA 108 TYR cc_start: 0.8988 (t80) cc_final: 0.8687 (t80) REVERT: EA 208 TYR cc_start: 0.9068 (t80) cc_final: 0.8709 (t80) REVERT: FA 308 TYR cc_start: 0.9124 (t80) cc_final: 0.8481 (t80) REVERT: FA 312 LEU cc_start: 0.9471 (mm) cc_final: 0.9163 (mm) REVERT: GA 403 GLU cc_start: 0.9202 (mp0) cc_final: 0.8797 (mp0) REVERT: GA 408 TYR cc_start: 0.8997 (t80) cc_final: 0.8588 (t80) REVERT: IA 208 TYR cc_start: 0.8826 (t80) cc_final: 0.8379 (t80) REVERT: JA 312 LEU cc_start: 0.9553 (mm) cc_final: 0.9219 (mm) REVERT: KA 403 GLU cc_start: 0.8869 (mm-30) cc_final: 0.8509 (mm-30) REVERT: LA 103 GLU cc_start: 0.9041 (mm-30) cc_final: 0.8577 (mm-30) REVERT: NA 303 GLU cc_start: 0.9109 (mm-30) cc_final: 0.8849 (mm-30) REVERT: OA 412 LEU cc_start: 0.9528 (mm) cc_final: 0.9320 (mm) REVERT: O 3 GLU cc_start: 0.9016 (mp0) cc_final: 0.8681 (mp0) REVERT: O 8 TYR cc_start: 0.8689 (t80) cc_final: 0.8306 (t80) REVERT: O 12 LEU cc_start: 0.9560 (mm) cc_final: 0.9243 (mm) REVERT: PA 103 GLU cc_start: 0.9162 (mm-30) cc_final: 0.8749 (mm-30) REVERT: QA 212 LEU cc_start: 0.9543 (mm) cc_final: 0.9295 (mm) REVERT: RA 303 GLU cc_start: 0.9019 (mm-30) cc_final: 0.8430 (mm-30) REVERT: TA 112 LEU cc_start: 0.9455 (mm) cc_final: 0.9196 (mm) REVERT: WA 403 GLU cc_start: 0.9077 (mm-30) cc_final: 0.8627 (mm-30) REVERT: Q 3 GLU cc_start: 0.9093 (mm-30) cc_final: 0.8502 (mm-30) REVERT: Q 11 ILE cc_start: 0.9561 (tt) cc_final: 0.9212 (tt) REVERT: YA 208 TYR cc_start: 0.9026 (t80) cc_final: 0.8513 (t80) REVERT: ZA 313 GLU cc_start: 0.8452 (pp20) cc_final: 0.8248 (pp20) REVERT: aA 403 GLU cc_start: 0.9210 (mp0) cc_final: 0.8896 (mp0) REVERT: aA 415 GLN cc_start: 0.8727 (mt0) cc_final: 0.8435 (mt0) REVERT: R 3 GLU cc_start: 0.9012 (mm-30) cc_final: 0.8511 (mm-30) REVERT: R 12 LEU cc_start: 0.9571 (mm) cc_final: 0.9243 (mm) REVERT: dA 303 GLU cc_start: 0.9092 (mm-30) cc_final: 0.8639 (mm-30) REVERT: S 3 GLU cc_start: 0.9171 (mm-30) cc_final: 0.8466 (mm-30) REVERT: gA 212 LEU cc_start: 0.9292 (mp) cc_final: 0.8911 (mp) REVERT: T 11 ILE cc_start: 0.8668 (tt) cc_final: 0.8359 (tp) REVERT: oA 203 GLU cc_start: 0.9341 (mm-30) cc_final: 0.8991 (mm-30) REVERT: pA 308 TYR cc_start: 0.8780 (t80) cc_final: 0.8465 (t80) REVERT: qA 403 GLU cc_start: 0.9011 (mm-30) cc_final: 0.8785 (mm-30) REVERT: qA 411 ILE cc_start: 0.9358 (mt) cc_final: 0.8880 (mp) REVERT: qA 412 LEU cc_start: 0.9230 (mm) cc_final: 0.8924 (mm) REVERT: qA 415 GLN cc_start: 0.9024 (mt0) cc_final: 0.8295 (mt0) outliers start: 3 outliers final: 1 residues processed: 622 average time/residue: 0.1937 time to fit residues: 183.4906 Evaluate side-chains 596 residues out of total 1155 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 595 time to evaluate : 2.266 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 88 optimal weight: 0.9980 chunk 25 optimal weight: 6.9990 chunk 76 optimal weight: 2.9990 chunk 12 optimal weight: 0.9980 chunk 23 optimal weight: 5.9990 chunk 83 optimal weight: 1.9990 chunk 34 optimal weight: 0.0270 chunk 85 optimal weight: 7.9990 chunk 10 optimal weight: 0.9980 chunk 15 optimal weight: 3.9990 chunk 73 optimal weight: 1.9990 overall best weight: 1.0040 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** o 415 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 15 GLN XA 115 GLN hA 315 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3203 r_free = 0.3203 target = 0.060767 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2977 r_free = 0.2977 target = 0.052267 restraints weight = 46498.288| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3034 r_free = 0.3034 target = 0.054293 restraints weight = 29083.672| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3074 r_free = 0.3074 target = 0.055687 restraints weight = 19719.831| |-----------------------------------------------------------------------------| r_work (final): 0.3060 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8852 moved from start: 0.6997 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 12915 Z= 0.230 Angle : 0.657 5.645 17325 Z= 0.328 Chirality : 0.041 0.133 1995 Planarity : 0.002 0.014 2310 Dihedral : 3.521 25.568 1890 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 5.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 0.17 % Allowed : 0.61 % Favored : 99.22 % 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: 4.63 (0.22), residues: 1365 helix: 3.00 (0.14), residues: 1365 sheet: None (None), residues: 0 loop : None (None), residues: 0 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.022 0.002 TYRXA 108 ARG 0.002 0.000 ARGSA 406 =============================================================================== Job complete usr+sys time: 3411.08 seconds wall clock time: 60 minutes 34.06 seconds (3634.06 seconds total)