Starting phenix.real_space_refine on Mon Mar 18 09:18:13 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6hcg_0193/03_2024/6hcg_0193.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6hcg_0193/03_2024/6hcg_0193.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6hcg_0193/03_2024/6hcg_0193.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6hcg_0193/03_2024/6hcg_0193.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6hcg_0193/03_2024/6hcg_0193.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6hcg_0193/03_2024/6hcg_0193.pdb" } resolution = 4.3 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 Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- 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= 0.124 sd= 0.884 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: 4 Type Number sf(0) Gaussians S 180 5.16 5 C 53205 2.51 5 N 15075 2.21 5 O 16725 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 57": "NH1" <-> "NH2" Residue "A ARG 100": "NH1" <-> "NH2" Residue "A ARG 126": "NH1" <-> "NH2" Residue "A ARG 136": "NH1" <-> "NH2" Residue "A ARG 143": "NH1" <-> "NH2" Residue "A ARG 168": "NH1" <-> "NH2" Residue "A ARG 174": "NH1" <-> "NH2" Residue "A ARG 181": "NH1" <-> "NH2" Residue "A ARG 188": "NH1" <-> "NH2" Residue "A ARG 232": "NH1" <-> "NH2" Residue "A ARG 245": "NH1" <-> "NH2" Residue "A ARG 247": "NH1" <-> "NH2" Residue "A ARG 331": "NH1" <-> "NH2" Residue "A ARG 339": "NH1" <-> "NH2" Residue "A ARG 340": "NH1" <-> "NH2" Residue "A ARG 477": "NH1" <-> "NH2" Residue "A ARG 525": "NH1" <-> "NH2" Residue "A ARG 570": "NH1" <-> "NH2" Residue "A ARG 579": "NH1" <-> "NH2" Residue "A ARG 586": "NH1" <-> "NH2" Residue "A ARG 591": "NH1" <-> "NH2" Residue "A ARG 593": "NH1" <-> "NH2" Residue "A ARG 597": "NH1" <-> "NH2" Residue "B ARG 57": "NH1" <-> "NH2" Residue "B ARG 100": "NH1" <-> "NH2" Residue "B ARG 126": "NH1" <-> "NH2" Residue "B ARG 136": "NH1" <-> "NH2" Residue "B ARG 143": "NH1" <-> "NH2" Residue "B ARG 168": "NH1" <-> "NH2" Residue "B ARG 174": "NH1" <-> "NH2" Residue "B ARG 181": "NH1" <-> "NH2" Residue "B ARG 188": "NH1" <-> "NH2" Residue "B ARG 232": "NH1" <-> "NH2" Residue "B ARG 245": "NH1" <-> "NH2" Residue "B ARG 247": "NH1" <-> "NH2" Residue "B ARG 331": "NH1" <-> "NH2" Residue "B ARG 339": "NH1" <-> "NH2" Residue "B ARG 340": "NH1" <-> "NH2" Residue "B ARG 477": "NH1" <-> "NH2" Residue "B ARG 525": "NH1" <-> "NH2" Residue "B ARG 570": "NH1" <-> "NH2" Residue "B ARG 579": "NH1" <-> "NH2" Residue "B ARG 586": "NH1" <-> "NH2" Residue "B ARG 591": "NH1" <-> "NH2" Residue "B ARG 593": "NH1" <-> "NH2" Residue "B ARG 597": "NH1" <-> "NH2" Residue "C ARG 57": "NH1" <-> "NH2" Residue "C ARG 100": "NH1" <-> "NH2" Residue "C ARG 126": "NH1" <-> "NH2" Residue "C ARG 136": "NH1" <-> "NH2" Residue "C ARG 143": "NH1" <-> "NH2" Residue "C ARG 168": "NH1" <-> "NH2" Residue "C ARG 174": "NH1" <-> "NH2" Residue "C ARG 181": "NH1" <-> "NH2" Residue "C ARG 188": "NH1" <-> "NH2" Residue "C ARG 232": "NH1" <-> "NH2" Residue "C ARG 245": "NH1" <-> "NH2" Residue "C ARG 247": "NH1" <-> "NH2" Residue "C ARG 331": "NH1" <-> "NH2" Residue "C ARG 339": "NH1" <-> "NH2" Residue "C ARG 340": "NH1" <-> "NH2" Residue "C ARG 477": "NH1" <-> "NH2" Residue "C ARG 525": "NH1" <-> "NH2" Residue "C ARG 570": "NH1" <-> "NH2" Residue "C ARG 579": "NH1" <-> "NH2" Residue "C ARG 586": "NH1" <-> "NH2" Residue "C ARG 591": "NH1" <-> "NH2" Residue "C ARG 593": "NH1" <-> "NH2" Residue "C ARG 597": "NH1" <-> "NH2" Residue "D ARG 57": "NH1" <-> "NH2" Residue "D ARG 100": "NH1" <-> "NH2" Residue "D ARG 126": "NH1" <-> "NH2" Residue "D ARG 136": "NH1" <-> "NH2" Residue "D ARG 143": "NH1" <-> "NH2" Residue "D ARG 168": "NH1" <-> "NH2" Residue "D ARG 174": "NH1" <-> "NH2" Residue "D ARG 181": "NH1" <-> "NH2" Residue "D ARG 188": "NH1" <-> "NH2" Residue "D ARG 232": "NH1" <-> "NH2" Residue "D ARG 245": "NH1" <-> "NH2" Residue "D ARG 247": "NH1" <-> "NH2" Residue "D ARG 331": "NH1" <-> "NH2" Residue "D ARG 339": "NH1" <-> "NH2" Residue "D ARG 340": "NH1" <-> "NH2" Residue "D ARG 477": "NH1" <-> "NH2" Residue "D ARG 525": "NH1" <-> "NH2" Residue "D ARG 570": "NH1" <-> "NH2" Residue "D ARG 579": "NH1" <-> "NH2" Residue "D ARG 586": "NH1" <-> "NH2" Residue "D ARG 591": "NH1" <-> "NH2" Residue "D ARG 593": "NH1" <-> "NH2" Residue "D ARG 597": "NH1" <-> "NH2" Residue "E ARG 57": "NH1" <-> "NH2" Residue "E ARG 100": "NH1" <-> "NH2" Residue "E ARG 126": "NH1" <-> "NH2" Residue "E ARG 136": "NH1" <-> "NH2" Residue "E ARG 143": "NH1" <-> "NH2" Residue "E ARG 168": "NH1" <-> "NH2" Residue "E ARG 174": "NH1" <-> "NH2" Residue "E ARG 181": "NH1" <-> "NH2" Residue "E ARG 188": "NH1" <-> "NH2" Residue "E ARG 232": "NH1" <-> "NH2" Residue "E ARG 245": "NH1" <-> "NH2" Residue "E ARG 247": "NH1" <-> "NH2" Residue "E ARG 331": "NH1" <-> "NH2" Residue "E ARG 339": "NH1" <-> "NH2" Residue "E ARG 340": "NH1" <-> "NH2" Residue "E ARG 477": "NH1" <-> "NH2" Residue "E ARG 525": "NH1" <-> "NH2" Residue "E ARG 570": "NH1" <-> "NH2" Residue "E ARG 579": "NH1" <-> "NH2" Residue "E ARG 586": "NH1" <-> "NH2" Residue "E ARG 591": "NH1" <-> "NH2" Residue "E ARG 593": "NH1" <-> "NH2" Residue "E ARG 597": "NH1" <-> "NH2" Residue "F ARG 57": "NH1" <-> "NH2" Residue "F ARG 100": "NH1" <-> "NH2" Residue "F ARG 126": "NH1" <-> "NH2" Residue "F ARG 136": "NH1" <-> "NH2" Residue "F ARG 143": "NH1" <-> "NH2" Residue "F ARG 168": "NH1" <-> "NH2" Residue "F ARG 174": "NH1" <-> "NH2" Residue "F ARG 181": "NH1" <-> "NH2" Residue "F ARG 188": "NH1" <-> "NH2" Residue "F ARG 232": "NH1" <-> "NH2" Residue "F ARG 245": "NH1" <-> "NH2" Residue "F ARG 247": "NH1" <-> "NH2" Residue "F ARG 331": "NH1" <-> "NH2" Residue "F ARG 339": "NH1" <-> "NH2" Residue "F ARG 340": "NH1" <-> "NH2" Residue "F ARG 477": "NH1" <-> "NH2" Residue "F ARG 525": "NH1" <-> "NH2" Residue "F ARG 570": "NH1" <-> "NH2" Residue "F ARG 579": "NH1" <-> "NH2" Residue "F ARG 586": "NH1" <-> "NH2" Residue "F ARG 591": "NH1" <-> "NH2" Residue "F ARG 593": "NH1" <-> "NH2" Residue "F ARG 597": "NH1" <-> "NH2" Residue "G ARG 57": "NH1" <-> "NH2" Residue "G ARG 100": "NH1" <-> "NH2" Residue "G ARG 126": "NH1" <-> "NH2" Residue "G ARG 136": "NH1" <-> "NH2" Residue "G ARG 143": "NH1" <-> "NH2" Residue "G ARG 168": "NH1" <-> "NH2" Residue "G ARG 174": "NH1" <-> "NH2" Residue "G ARG 181": "NH1" <-> "NH2" Residue "G ARG 188": "NH1" <-> "NH2" Residue "G ARG 232": "NH1" <-> "NH2" Residue "G ARG 245": "NH1" <-> "NH2" Residue "G ARG 247": "NH1" <-> "NH2" Residue "G ARG 331": "NH1" <-> "NH2" Residue "G ARG 339": "NH1" <-> "NH2" Residue "G ARG 340": "NH1" <-> "NH2" Residue "G ARG 477": "NH1" <-> "NH2" Residue "G ARG 525": "NH1" <-> "NH2" Residue "G ARG 570": "NH1" <-> "NH2" Residue "G ARG 579": "NH1" <-> "NH2" Residue "G ARG 586": "NH1" <-> "NH2" Residue "G ARG 591": "NH1" <-> "NH2" Residue "G ARG 593": "NH1" <-> "NH2" Residue "G ARG 597": "NH1" <-> "NH2" Residue "H ARG 57": "NH1" <-> "NH2" Residue "H ARG 100": "NH1" <-> "NH2" Residue "H ARG 126": "NH1" <-> "NH2" Residue "H ARG 136": "NH1" <-> "NH2" Residue "H ARG 143": "NH1" <-> "NH2" Residue "H ARG 168": "NH1" <-> "NH2" Residue "H ARG 174": "NH1" <-> "NH2" Residue "H ARG 181": "NH1" <-> "NH2" Residue "H ARG 188": "NH1" <-> "NH2" Residue "H ARG 232": "NH1" <-> "NH2" Residue "H ARG 245": "NH1" <-> "NH2" Residue "H ARG 247": "NH1" <-> "NH2" Residue "H ARG 331": "NH1" <-> "NH2" Residue "H ARG 339": "NH1" <-> "NH2" Residue "H ARG 340": "NH1" <-> "NH2" Residue "H ARG 477": "NH1" <-> "NH2" Residue "H ARG 525": "NH1" <-> "NH2" Residue "H ARG 570": "NH1" <-> "NH2" Residue "H ARG 579": "NH1" <-> "NH2" Residue "H ARG 586": "NH1" <-> "NH2" Residue "H ARG 591": "NH1" <-> "NH2" Residue "H ARG 593": "NH1" <-> "NH2" Residue "H ARG 597": "NH1" <-> "NH2" Residue "I ARG 57": "NH1" <-> "NH2" Residue "I ARG 100": "NH1" <-> "NH2" Residue "I ARG 126": "NH1" <-> "NH2" Residue "I ARG 136": "NH1" <-> "NH2" Residue "I ARG 143": "NH1" <-> "NH2" Residue "I ARG 168": "NH1" <-> "NH2" Residue "I ARG 174": "NH1" <-> "NH2" Residue "I ARG 181": "NH1" <-> "NH2" Residue "I ARG 188": "NH1" <-> "NH2" Residue "I ARG 232": "NH1" <-> "NH2" Residue "I ARG 245": "NH1" <-> "NH2" Residue "I ARG 247": "NH1" <-> "NH2" Residue "I ARG 331": "NH1" <-> "NH2" Residue "I ARG 339": "NH1" <-> "NH2" Residue "I ARG 340": "NH1" <-> "NH2" Residue "I ARG 477": "NH1" <-> "NH2" Residue "I ARG 525": "NH1" <-> "NH2" Residue "I ARG 570": "NH1" <-> "NH2" Residue "I ARG 579": "NH1" <-> "NH2" Residue "I ARG 586": "NH1" <-> "NH2" Residue "I ARG 591": "NH1" <-> "NH2" Residue "I ARG 593": "NH1" <-> "NH2" Residue "I ARG 597": "NH1" <-> "NH2" Residue "J ARG 57": "NH1" <-> "NH2" Residue "J ARG 100": "NH1" <-> "NH2" Residue "J ARG 126": "NH1" <-> "NH2" Residue "J ARG 136": "NH1" <-> "NH2" Residue "J ARG 143": "NH1" <-> "NH2" Residue "J ARG 168": "NH1" <-> "NH2" Residue "J ARG 174": "NH1" <-> "NH2" Residue "J ARG 181": "NH1" <-> "NH2" Residue "J ARG 188": "NH1" <-> "NH2" Residue "J ARG 232": "NH1" <-> "NH2" Residue "J ARG 245": "NH1" <-> "NH2" Residue "J ARG 247": "NH1" <-> "NH2" Residue "J ARG 331": "NH1" <-> "NH2" Residue "J ARG 339": "NH1" <-> "NH2" Residue "J ARG 340": "NH1" <-> "NH2" Residue "J ARG 477": "NH1" <-> "NH2" Residue "J ARG 525": "NH1" <-> "NH2" Residue "J ARG 570": "NH1" <-> "NH2" Residue "J ARG 579": "NH1" <-> "NH2" Residue "J ARG 586": "NH1" <-> "NH2" Residue "J ARG 591": "NH1" <-> "NH2" Residue "J ARG 593": "NH1" <-> "NH2" Residue "J ARG 597": "NH1" <-> "NH2" Residue "K ARG 57": "NH1" <-> "NH2" Residue "K ARG 100": "NH1" <-> "NH2" Residue "K ARG 126": "NH1" <-> "NH2" Residue "K ARG 136": "NH1" <-> "NH2" Residue "K ARG 143": "NH1" <-> "NH2" Residue "K ARG 168": "NH1" <-> "NH2" Residue "K ARG 174": "NH1" <-> "NH2" Residue "K ARG 181": "NH1" <-> "NH2" Residue "K ARG 188": "NH1" <-> "NH2" Residue "K ARG 232": "NH1" <-> "NH2" Residue "K ARG 245": "NH1" <-> "NH2" Residue "K ARG 247": "NH1" <-> "NH2" Residue "K ARG 331": "NH1" <-> "NH2" Residue "K ARG 339": "NH1" <-> "NH2" Residue "K ARG 340": "NH1" <-> "NH2" Residue "K ARG 477": "NH1" <-> "NH2" Residue "K ARG 525": "NH1" <-> "NH2" Residue "K ARG 570": "NH1" <-> "NH2" Residue "K ARG 579": "NH1" <-> "NH2" Residue "K ARG 586": "NH1" <-> "NH2" Residue "K ARG 591": "NH1" <-> "NH2" Residue "K ARG 593": "NH1" <-> "NH2" Residue "K ARG 597": "NH1" <-> "NH2" Residue "L ARG 57": "NH1" <-> "NH2" Residue "L ARG 100": "NH1" <-> "NH2" Residue "L ARG 126": "NH1" <-> "NH2" Residue "L ARG 136": "NH1" <-> "NH2" Residue "L ARG 143": "NH1" <-> "NH2" Residue "L ARG 168": "NH1" <-> "NH2" Residue "L ARG 174": "NH1" <-> "NH2" Residue "L ARG 181": "NH1" <-> "NH2" Residue "L ARG 188": "NH1" <-> "NH2" Residue "L ARG 232": "NH1" <-> "NH2" Residue "L ARG 245": "NH1" <-> "NH2" Residue "L ARG 247": "NH1" <-> "NH2" Residue "L ARG 331": "NH1" <-> "NH2" Residue "L ARG 339": "NH1" <-> "NH2" Residue "L ARG 340": "NH1" <-> "NH2" Residue "L ARG 477": "NH1" <-> "NH2" Residue "L ARG 525": "NH1" <-> "NH2" Residue "L ARG 570": "NH1" <-> "NH2" Residue "L ARG 579": "NH1" <-> "NH2" Residue "L ARG 586": "NH1" <-> "NH2" Residue "L ARG 591": "NH1" <-> "NH2" Residue "L ARG 593": "NH1" <-> "NH2" Residue "L ARG 597": "NH1" <-> "NH2" Residue "M ARG 57": "NH1" <-> "NH2" Residue "M ARG 100": "NH1" <-> "NH2" Residue "M ARG 126": "NH1" <-> "NH2" Residue "M ARG 136": "NH1" <-> "NH2" Residue "M ARG 143": "NH1" <-> "NH2" Residue "M ARG 168": "NH1" <-> "NH2" Residue "M ARG 174": "NH1" <-> "NH2" Residue "M ARG 181": "NH1" <-> "NH2" Residue "M ARG 188": "NH1" <-> "NH2" Residue "M ARG 232": "NH1" <-> "NH2" Residue "M ARG 245": "NH1" <-> "NH2" Residue "M ARG 247": "NH1" <-> "NH2" Residue "M ARG 331": "NH1" <-> "NH2" Residue "M ARG 339": "NH1" <-> "NH2" Residue "M ARG 340": "NH1" <-> "NH2" Residue "M ARG 477": "NH1" <-> "NH2" Residue "M ARG 525": "NH1" <-> "NH2" Residue "M ARG 570": "NH1" <-> "NH2" Residue "M ARG 579": "NH1" <-> "NH2" Residue "M ARG 586": "NH1" <-> "NH2" Residue "M ARG 591": "NH1" <-> "NH2" Residue "M ARG 593": "NH1" <-> "NH2" Residue "M ARG 597": "NH1" <-> "NH2" Residue "N ARG 57": "NH1" <-> "NH2" Residue "N ARG 100": "NH1" <-> "NH2" Residue "N ARG 126": "NH1" <-> "NH2" Residue "N ARG 136": "NH1" <-> "NH2" Residue "N ARG 143": "NH1" <-> "NH2" Residue "N ARG 168": "NH1" <-> "NH2" Residue "N ARG 174": "NH1" <-> "NH2" Residue "N ARG 181": "NH1" <-> "NH2" Residue "N ARG 188": "NH1" <-> "NH2" Residue "N ARG 232": "NH1" <-> "NH2" Residue "N ARG 245": "NH1" <-> "NH2" Residue "N ARG 247": "NH1" <-> "NH2" Residue "N ARG 331": "NH1" <-> "NH2" Residue "N ARG 339": "NH1" <-> "NH2" Residue "N ARG 340": "NH1" <-> "NH2" Residue "N ARG 477": "NH1" <-> "NH2" Residue "N ARG 525": "NH1" <-> "NH2" Residue "N ARG 570": "NH1" <-> "NH2" Residue "N ARG 579": "NH1" <-> "NH2" Residue "N ARG 586": "NH1" <-> "NH2" Residue "N ARG 591": "NH1" <-> "NH2" Residue "N ARG 593": "NH1" <-> "NH2" Residue "N ARG 597": "NH1" <-> "NH2" Residue "O ARG 57": "NH1" <-> "NH2" Residue "O ARG 100": "NH1" <-> "NH2" Residue "O ARG 126": "NH1" <-> "NH2" Residue "O ARG 136": "NH1" <-> "NH2" Residue "O ARG 143": "NH1" <-> "NH2" Residue "O ARG 168": "NH1" <-> "NH2" Residue "O ARG 174": "NH1" <-> "NH2" Residue "O ARG 181": "NH1" <-> "NH2" Residue "O ARG 188": "NH1" <-> "NH2" Residue "O ARG 232": "NH1" <-> "NH2" Residue "O ARG 245": "NH1" <-> "NH2" Residue "O ARG 247": "NH1" <-> "NH2" Residue "O ARG 331": "NH1" <-> "NH2" Residue "O ARG 339": "NH1" <-> "NH2" Residue "O ARG 340": "NH1" <-> "NH2" Residue "O ARG 477": "NH1" <-> "NH2" Residue "O ARG 525": "NH1" <-> "NH2" Residue "O ARG 570": "NH1" <-> "NH2" Residue "O ARG 579": "NH1" <-> "NH2" Residue "O ARG 586": "NH1" <-> "NH2" Residue "O ARG 591": "NH1" <-> "NH2" Residue "O ARG 593": "NH1" <-> "NH2" Residue "O ARG 597": "NH1" <-> "NH2" Residue "P ARG 100": "NH1" <-> "NH2" Residue "Q ARG 100": "NH1" <-> "NH2" Residue "R ARG 100": "NH1" <-> "NH2" Residue "S ARG 100": "NH1" <-> "NH2" Residue "T ARG 100": "NH1" <-> "NH2" Residue "U ARG 100": "NH1" <-> "NH2" Residue "V ARG 100": "NH1" <-> "NH2" Residue "W ARG 100": "NH1" <-> "NH2" Residue "X ARG 100": "NH1" <-> "NH2" Residue "Y ARG 100": "NH1" <-> "NH2" Residue "Z ARG 100": "NH1" <-> "NH2" Residue "a ARG 100": "NH1" <-> "NH2" Residue "b ARG 100": "NH1" <-> "NH2" Residue "c ARG 100": "NH1" <-> "NH2" Residue "d ARG 100": "NH1" <-> "NH2" Residue "e ARG 103": "NH1" <-> "NH2" Residue "e ARG 115": "NH1" <-> "NH2" Residue "e ARG 141": "NH1" <-> "NH2" Residue "e ARG 149": "NH1" <-> "NH2" Residue "e ARG 157": "NH1" <-> "NH2" Residue "f ARG 103": "NH1" <-> "NH2" Residue "f ARG 115": "NH1" <-> "NH2" Residue "f ARG 141": "NH1" <-> "NH2" Residue "f ARG 149": "NH1" <-> "NH2" Residue "f ARG 157": "NH1" <-> "NH2" Residue "g ARG 103": "NH1" <-> "NH2" Residue "g ARG 115": "NH1" <-> "NH2" Residue "g ARG 141": "NH1" <-> "NH2" Residue "g ARG 149": "NH1" <-> "NH2" Residue "g ARG 157": "NH1" <-> "NH2" Residue "h ARG 103": "NH1" <-> "NH2" Residue "h ARG 115": "NH1" <-> "NH2" Residue "h ARG 141": "NH1" <-> "NH2" Residue "h ARG 149": "NH1" <-> "NH2" Residue "h ARG 157": "NH1" <-> "NH2" Residue "i ARG 103": "NH1" <-> "NH2" Residue "i ARG 115": "NH1" <-> "NH2" Residue "i ARG 141": "NH1" <-> "NH2" Residue "i ARG 149": "NH1" <-> "NH2" Residue "i ARG 157": "NH1" <-> "NH2" Residue "j ARG 103": "NH1" <-> "NH2" Residue "j ARG 115": "NH1" <-> "NH2" Residue "j ARG 141": "NH1" <-> "NH2" Residue "j ARG 149": "NH1" <-> "NH2" Residue "j ARG 157": "NH1" <-> "NH2" Residue "k ARG 103": "NH1" <-> "NH2" Residue "k ARG 115": "NH1" <-> "NH2" Residue "k ARG 141": "NH1" <-> "NH2" Residue "k ARG 149": "NH1" <-> "NH2" Residue "k ARG 157": "NH1" <-> "NH2" Residue "l ARG 103": "NH1" <-> "NH2" Residue "l ARG 115": "NH1" <-> "NH2" Residue "l ARG 141": "NH1" <-> "NH2" Residue "l ARG 149": "NH1" <-> "NH2" Residue "l ARG 157": "NH1" <-> "NH2" Residue "m ARG 103": "NH1" <-> "NH2" Residue "m ARG 115": "NH1" <-> "NH2" Residue "m ARG 141": "NH1" <-> "NH2" Residue "m ARG 149": "NH1" <-> "NH2" Residue "m ARG 157": "NH1" <-> "NH2" Residue "n ARG 103": "NH1" <-> "NH2" Residue "n ARG 115": "NH1" <-> "NH2" Residue "n ARG 141": "NH1" <-> "NH2" Residue "n ARG 149": "NH1" <-> "NH2" Residue "n ARG 157": "NH1" <-> "NH2" Residue "o ARG 103": "NH1" <-> "NH2" Residue "o ARG 115": "NH1" <-> "NH2" Residue "o ARG 141": "NH1" <-> "NH2" Residue "o ARG 149": "NH1" <-> "NH2" Residue "o ARG 157": "NH1" <-> "NH2" Residue "p ARG 103": "NH1" <-> "NH2" Residue "p ARG 115": "NH1" <-> "NH2" Residue "p ARG 141": "NH1" <-> "NH2" Residue "p ARG 149": "NH1" <-> "NH2" Residue "p ARG 157": "NH1" <-> "NH2" Residue "q ARG 103": "NH1" <-> "NH2" Residue "q ARG 115": "NH1" <-> "NH2" Residue "q ARG 141": "NH1" <-> "NH2" Residue "q ARG 149": "NH1" <-> "NH2" Residue "q ARG 157": "NH1" <-> "NH2" Residue "r ARG 103": "NH1" <-> "NH2" Residue "r ARG 115": "NH1" <-> "NH2" Residue "r ARG 141": "NH1" <-> "NH2" Residue "r ARG 149": "NH1" <-> "NH2" Residue "r ARG 157": "NH1" <-> "NH2" Residue "s ARG 103": "NH1" <-> "NH2" Residue "s ARG 115": "NH1" <-> "NH2" Residue "s ARG 141": "NH1" <-> "NH2" Residue "s ARG 149": "NH1" <-> "NH2" Residue "s ARG 157": "NH1" <-> "NH2" Time to flip residues: 0.21s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 85185 Number of models: 1 Model: "" Number of chains: 45 Chain: "A" Number of atoms: 4447 Number of conformers: 1 Conformer: "" Number of residues, atoms: 592, 4447 Classifications: {'peptide': 592} Link IDs: {'PTRANS': 18, 'TRANS': 573} Chain breaks: 3 Chain: "B" Number of atoms: 4447 Number of conformers: 1 Conformer: "" Number of residues, atoms: 592, 4447 Classifications: {'peptide': 592} Link IDs: {'PTRANS': 18, 'TRANS': 573} Chain breaks: 3 Chain: "C" Number of atoms: 4447 Number of conformers: 1 Conformer: "" Number of residues, atoms: 592, 4447 Classifications: {'peptide': 592} Link IDs: {'PTRANS': 18, 'TRANS': 573} Chain breaks: 3 Chain: "D" Number of atoms: 4447 Number of conformers: 1 Conformer: "" Number of residues, atoms: 592, 4447 Classifications: {'peptide': 592} Link IDs: {'PTRANS': 18, 'TRANS': 573} Chain breaks: 3 Chain: "E" Number of atoms: 4447 Number of conformers: 1 Conformer: "" Number of residues, atoms: 592, 4447 Classifications: {'peptide': 592} Link IDs: {'PTRANS': 18, 'TRANS': 573} Chain breaks: 3 Chain: "F" Number of atoms: 4447 Number of conformers: 1 Conformer: "" Number of residues, atoms: 592, 4447 Classifications: {'peptide': 592} Link IDs: {'PTRANS': 18, 'TRANS': 573} Chain breaks: 3 Chain: "G" Number of atoms: 4447 Number of conformers: 1 Conformer: "" Number of residues, atoms: 592, 4447 Classifications: {'peptide': 592} Link IDs: {'PTRANS': 18, 'TRANS': 573} Chain breaks: 3 Chain: "H" Number of atoms: 4447 Number of conformers: 1 Conformer: "" Number of residues, atoms: 592, 4447 Classifications: {'peptide': 592} Link IDs: {'PTRANS': 18, 'TRANS': 573} Chain breaks: 3 Chain: "I" Number of atoms: 4447 Number of conformers: 1 Conformer: "" Number of residues, atoms: 592, 4447 Classifications: {'peptide': 592} Link IDs: {'PTRANS': 18, 'TRANS': 573} Chain breaks: 3 Chain: "J" Number of atoms: 4447 Number of conformers: 1 Conformer: "" Number of residues, atoms: 592, 4447 Classifications: {'peptide': 592} Link IDs: {'PTRANS': 18, 'TRANS': 573} Chain breaks: 3 Chain: "K" Number of atoms: 4447 Number of conformers: 1 Conformer: "" Number of residues, atoms: 592, 4447 Classifications: {'peptide': 592} Link IDs: {'PTRANS': 18, 'TRANS': 573} Chain breaks: 3 Chain: "L" Number of atoms: 4447 Number of conformers: 1 Conformer: "" Number of residues, atoms: 592, 4447 Classifications: {'peptide': 592} Link IDs: {'PTRANS': 18, 'TRANS': 573} Chain breaks: 3 Chain: "M" Number of atoms: 4447 Number of conformers: 1 Conformer: "" Number of residues, atoms: 592, 4447 Classifications: {'peptide': 592} Link IDs: {'PTRANS': 18, 'TRANS': 573} Chain breaks: 3 Chain: "N" Number of atoms: 4447 Number of conformers: 1 Conformer: "" Number of residues, atoms: 592, 4447 Classifications: {'peptide': 592} Link IDs: {'PTRANS': 18, 'TRANS': 573} Chain breaks: 3 Chain: "O" Number of atoms: 4447 Number of conformers: 1 Conformer: "" Number of residues, atoms: 592, 4447 Classifications: {'peptide': 592} Link IDs: {'PTRANS': 18, 'TRANS': 573} Chain breaks: 3 Chain: "P" Number of atoms: 720 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 720 Classifications: {'peptide': 93} Link IDs: {'PTRANS': 3, 'TRANS': 89} Chain: "Q" Number of atoms: 720 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 720 Classifications: {'peptide': 93} Link IDs: {'PTRANS': 3, 'TRANS': 89} Chain: "R" Number of atoms: 720 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 720 Classifications: {'peptide': 93} Link IDs: {'PTRANS': 3, 'TRANS': 89} Chain: "S" Number of atoms: 720 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 720 Classifications: {'peptide': 93} Link IDs: {'PTRANS': 3, 'TRANS': 89} Chain: "T" Number of atoms: 720 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 720 Classifications: {'peptide': 93} Link IDs: {'PTRANS': 3, 'TRANS': 89} Chain: "U" Number of atoms: 720 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 720 Classifications: {'peptide': 93} Link IDs: {'PTRANS': 3, 'TRANS': 89} Chain: "V" Number of atoms: 720 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 720 Classifications: {'peptide': 93} Link IDs: {'PTRANS': 3, 'TRANS': 89} Chain: "W" Number of atoms: 720 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 720 Classifications: {'peptide': 93} Link IDs: {'PTRANS': 3, 'TRANS': 89} Chain: "X" Number of atoms: 720 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 720 Classifications: {'peptide': 93} Link IDs: {'PTRANS': 3, 'TRANS': 89} Chain: "Y" Number of atoms: 720 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 720 Classifications: {'peptide': 93} Link IDs: {'PTRANS': 3, 'TRANS': 89} Chain: "Z" Number of atoms: 720 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 720 Classifications: {'peptide': 93} Link IDs: {'PTRANS': 3, 'TRANS': 89} Chain: "a" Number of atoms: 720 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 720 Classifications: {'peptide': 93} Link IDs: {'PTRANS': 3, 'TRANS': 89} Chain: "b" Number of atoms: 720 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 720 Classifications: {'peptide': 93} Link IDs: {'PTRANS': 3, 'TRANS': 89} Chain: "c" Number of atoms: 720 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 720 Classifications: {'peptide': 93} Link IDs: {'PTRANS': 3, 'TRANS': 89} Chain: "d" Number of atoms: 720 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 720 Classifications: {'peptide': 93} Link IDs: {'PTRANS': 3, 'TRANS': 89} Chain: "e" Number of atoms: 512 Number of conformers: 1 Conformer: "" Number of residues, atoms: 68, 512 Classifications: {'peptide': 68} Link IDs: {'PTRANS': 4, 'TRANS': 63} Chain: "f" Number of atoms: 512 Number of conformers: 1 Conformer: "" Number of residues, atoms: 68, 512 Classifications: {'peptide': 68} Link IDs: {'PTRANS': 4, 'TRANS': 63} Chain: "g" Number of atoms: 512 Number of conformers: 1 Conformer: "" Number of residues, atoms: 68, 512 Classifications: {'peptide': 68} Link IDs: {'PTRANS': 4, 'TRANS': 63} Chain: "h" Number of atoms: 512 Number of conformers: 1 Conformer: "" Number of residues, atoms: 68, 512 Classifications: {'peptide': 68} Link IDs: {'PTRANS': 4, 'TRANS': 63} Chain: "i" Number of atoms: 512 Number of conformers: 1 Conformer: "" Number of residues, atoms: 68, 512 Classifications: {'peptide': 68} Link IDs: {'PTRANS': 4, 'TRANS': 63} Chain: "j" Number of atoms: 512 Number of conformers: 1 Conformer: "" Number of residues, atoms: 68, 512 Classifications: {'peptide': 68} Link IDs: {'PTRANS': 4, 'TRANS': 63} Chain: "k" Number of atoms: 512 Number of conformers: 1 Conformer: "" Number of residues, atoms: 68, 512 Classifications: {'peptide': 68} Link IDs: {'PTRANS': 4, 'TRANS': 63} Chain: "l" Number of atoms: 512 Number of conformers: 1 Conformer: "" Number of residues, atoms: 68, 512 Classifications: {'peptide': 68} Link IDs: {'PTRANS': 4, 'TRANS': 63} Chain: "m" Number of atoms: 512 Number of conformers: 1 Conformer: "" Number of residues, atoms: 68, 512 Classifications: {'peptide': 68} Link IDs: {'PTRANS': 4, 'TRANS': 63} Chain: "n" Number of atoms: 512 Number of conformers: 1 Conformer: "" Number of residues, atoms: 68, 512 Classifications: {'peptide': 68} Link IDs: {'PTRANS': 4, 'TRANS': 63} Chain: "o" Number of atoms: 512 Number of conformers: 1 Conformer: "" Number of residues, atoms: 68, 512 Classifications: {'peptide': 68} Link IDs: {'PTRANS': 4, 'TRANS': 63} Chain: "p" Number of atoms: 512 Number of conformers: 1 Conformer: "" Number of residues, atoms: 68, 512 Classifications: {'peptide': 68} Link IDs: {'PTRANS': 4, 'TRANS': 63} Chain: "q" Number of atoms: 512 Number of conformers: 1 Conformer: "" Number of residues, atoms: 68, 512 Classifications: {'peptide': 68} Link IDs: {'PTRANS': 4, 'TRANS': 63} Chain: "r" Number of atoms: 512 Number of conformers: 1 Conformer: "" Number of residues, atoms: 68, 512 Classifications: {'peptide': 68} Link IDs: {'PTRANS': 4, 'TRANS': 63} Chain: "s" Number of atoms: 512 Number of conformers: 1 Conformer: "" Number of residues, atoms: 68, 512 Classifications: {'peptide': 68} Link IDs: {'PTRANS': 4, 'TRANS': 63} Time building chain proxies: 32.90, per 1000 atoms: 0.39 Number of scatterers: 85185 At special positions: 0 Unit cell: (227.84, 226.06, 236.74, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 180 16.00 O 16725 8.00 N 15075 7.00 C 53205 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=15, symmetry=0 Simple disulfide: pdb=" SG CYS P 62 " - pdb=" SG CYS P 116 " distance=2.03 Simple disulfide: pdb=" SG CYS Q 62 " - pdb=" SG CYS Q 116 " distance=2.03 Simple disulfide: pdb=" SG CYS R 62 " - pdb=" SG CYS R 116 " distance=2.03 Simple disulfide: pdb=" SG CYS S 62 " - pdb=" SG CYS S 116 " distance=2.03 Simple disulfide: pdb=" SG CYS T 62 " - pdb=" SG CYS T 116 " distance=2.03 Simple disulfide: pdb=" SG CYS U 62 " - pdb=" SG CYS U 116 " distance=2.03 Simple disulfide: pdb=" SG CYS V 62 " - pdb=" SG CYS V 116 " distance=2.03 Simple disulfide: pdb=" SG CYS W 62 " - pdb=" SG CYS W 116 " distance=2.02 Simple disulfide: pdb=" SG CYS X 62 " - pdb=" SG CYS X 116 " distance=2.03 Simple disulfide: pdb=" SG CYS Y 62 " - pdb=" SG CYS Y 116 " distance=2.03 Simple disulfide: pdb=" SG CYS Z 62 " - pdb=" SG CYS Z 116 " distance=2.03 Simple disulfide: pdb=" SG CYS a 62 " - pdb=" SG CYS a 116 " distance=2.03 Simple disulfide: pdb=" SG CYS b 62 " - pdb=" SG CYS b 116 " distance=2.02 Simple disulfide: pdb=" SG CYS c 62 " - pdb=" SG CYS c 116 " distance=2.02 Simple disulfide: pdb=" SG CYS d 62 " - pdb=" SG CYS d 116 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 26.70 Conformation dependent library (CDL) restraints added in 12.2 seconds 22230 Ramachandran restraints generated. 11115 Oldfield, 0 Emsley, 11115 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 21210 Finding SS restraints... Secondary structure from input PDB file: 300 helices and 0 sheets defined 33.2% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.80 Creating SS restraints... Processing helix chain 'A' and resid 34 through 47 removed outlier: 3.926A pdb=" N LYS A 44 " --> pdb=" O ASN A 40 " (cutoff:3.500A) Processing helix chain 'A' and resid 71 through 84 removed outlier: 3.658A pdb=" N TYR A 84 " --> pdb=" O VAL A 80 " (cutoff:3.500A) Processing helix chain 'A' and resid 103 through 107 removed outlier: 3.595A pdb=" N THR A 106 " --> pdb=" O ASP A 103 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N SER A 107 " --> pdb=" O ALA A 104 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 103 through 107' Processing helix chain 'A' and resid 137 through 146 removed outlier: 3.922A pdb=" N LEU A 141 " --> pdb=" O ASP A 137 " (cutoff:3.500A) Processing helix chain 'A' and resid 168 through 184 removed outlier: 3.691A pdb=" N ILE A 172 " --> pdb=" O ARG A 168 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N LYS A 173 " --> pdb=" O ALA A 169 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N ARG A 174 " --> pdb=" O ALA A 170 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N ASN A 184 " --> pdb=" O GLU A 180 " (cutoff:3.500A) Processing helix chain 'A' and resid 200 through 205 removed outlier: 3.618A pdb=" N VAL A 204 " --> pdb=" O ALA A 200 " (cutoff:3.500A) Processing helix chain 'A' and resid 244 through 256 removed outlier: 3.867A pdb=" N ILE A 248 " --> pdb=" O SER A 244 " (cutoff:3.500A) Processing helix chain 'A' and resid 275 through 282 removed outlier: 3.830A pdb=" N GLU A 280 " --> pdb=" O ALA A 276 " (cutoff:3.500A) Processing helix chain 'A' and resid 326 through 335 removed outlier: 3.930A pdb=" N VAL A 332 " --> pdb=" O ASP A 328 " (cutoff:3.500A) Processing helix chain 'A' and resid 381 through 395 removed outlier: 3.646A pdb=" N ASN A 389 " --> pdb=" O ILE A 385 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N GLN A 390 " --> pdb=" O ALA A 386 " (cutoff:3.500A) Processing helix chain 'A' and resid 402 through 407 Processing helix chain 'A' and resid 562 through 567 Processing helix chain 'A' and resid 592 through 612 removed outlier: 3.757A pdb=" N GLN A 598 " --> pdb=" O ASP A 594 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N ALA A 599 " --> pdb=" O GLU A 595 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N ALA A 610 " --> pdb=" O ALA A 606 " (cutoff:3.500A) Processing helix chain 'A' and resid 619 through 631 removed outlier: 3.926A pdb=" N ILE A 631 " --> pdb=" O ASP A 627 " (cutoff:3.500A) Processing helix chain 'A' and resid 639 through 651 removed outlier: 3.731A pdb=" N ALA A 645 " --> pdb=" O ARG A 641 " (cutoff:3.500A) Processing helix chain 'B' and resid 34 through 47 removed outlier: 3.927A pdb=" N LYS B 44 " --> pdb=" O ASN B 40 " (cutoff:3.500A) Processing helix chain 'B' and resid 71 through 84 removed outlier: 3.657A pdb=" N TYR B 84 " --> pdb=" O VAL B 80 " (cutoff:3.500A) Processing helix chain 'B' and resid 103 through 107 removed outlier: 3.595A pdb=" N THR B 106 " --> pdb=" O ASP B 103 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N SER B 107 " --> pdb=" O ALA B 104 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 103 through 107' Processing helix chain 'B' and resid 137 through 146 removed outlier: 3.922A pdb=" N LEU B 141 " --> pdb=" O ASP B 137 " (cutoff:3.500A) Processing helix chain 'B' and resid 168 through 184 removed outlier: 3.691A pdb=" N ILE B 172 " --> pdb=" O ARG B 168 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N LYS B 173 " --> pdb=" O ALA B 169 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N ARG B 174 " --> pdb=" O ALA B 170 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N ASN B 184 " --> pdb=" O GLU B 180 " (cutoff:3.500A) Processing helix chain 'B' and resid 200 through 205 removed outlier: 3.618A pdb=" N VAL B 204 " --> pdb=" O ALA B 200 " (cutoff:3.500A) Processing helix chain 'B' and resid 244 through 256 removed outlier: 3.867A pdb=" N ILE B 248 " --> pdb=" O SER B 244 " (cutoff:3.500A) Processing helix chain 'B' and resid 275 through 282 removed outlier: 3.831A pdb=" N GLU B 280 " --> pdb=" O ALA B 276 " (cutoff:3.500A) Processing helix chain 'B' and resid 326 through 335 removed outlier: 3.930A pdb=" N VAL B 332 " --> pdb=" O ASP B 328 " (cutoff:3.500A) Processing helix chain 'B' and resid 381 through 395 removed outlier: 3.646A pdb=" N ASN B 389 " --> pdb=" O ILE B 385 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N GLN B 390 " --> pdb=" O ALA B 386 " (cutoff:3.500A) Processing helix chain 'B' and resid 402 through 407 Processing helix chain 'B' and resid 562 through 567 Processing helix chain 'B' and resid 592 through 612 removed outlier: 3.758A pdb=" N GLN B 598 " --> pdb=" O ASP B 594 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N ALA B 599 " --> pdb=" O GLU B 595 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N ALA B 610 " --> pdb=" O ALA B 606 " (cutoff:3.500A) Processing helix chain 'B' and resid 619 through 631 removed outlier: 3.926A pdb=" N ILE B 631 " --> pdb=" O ASP B 627 " (cutoff:3.500A) Processing helix chain 'B' and resid 639 through 651 removed outlier: 3.731A pdb=" N ALA B 645 " --> pdb=" O ARG B 641 " (cutoff:3.500A) Processing helix chain 'C' and resid 34 through 47 removed outlier: 3.927A pdb=" N LYS C 44 " --> pdb=" O ASN C 40 " (cutoff:3.500A) Processing helix chain 'C' and resid 71 through 84 removed outlier: 3.657A pdb=" N TYR C 84 " --> pdb=" O VAL C 80 " (cutoff:3.500A) Processing helix chain 'C' and resid 103 through 107 removed outlier: 3.595A pdb=" N THR C 106 " --> pdb=" O ASP C 103 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N SER C 107 " --> pdb=" O ALA C 104 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 103 through 107' Processing helix chain 'C' and resid 137 through 146 removed outlier: 3.922A pdb=" N LEU C 141 " --> pdb=" O ASP C 137 " (cutoff:3.500A) Processing helix chain 'C' and resid 168 through 184 removed outlier: 3.692A pdb=" N ILE C 172 " --> pdb=" O ARG C 168 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N LYS C 173 " --> pdb=" O ALA C 169 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N ARG C 174 " --> pdb=" O ALA C 170 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N ASN C 184 " --> pdb=" O GLU C 180 " (cutoff:3.500A) Processing helix chain 'C' and resid 200 through 205 removed outlier: 3.618A pdb=" N VAL C 204 " --> pdb=" O ALA C 200 " (cutoff:3.500A) Processing helix chain 'C' and resid 244 through 256 removed outlier: 3.867A pdb=" N ILE C 248 " --> pdb=" O SER C 244 " (cutoff:3.500A) Processing helix chain 'C' and resid 275 through 282 removed outlier: 3.830A pdb=" N GLU C 280 " --> pdb=" O ALA C 276 " (cutoff:3.500A) Processing helix chain 'C' and resid 326 through 335 removed outlier: 3.930A pdb=" N VAL C 332 " --> pdb=" O ASP C 328 " (cutoff:3.500A) Processing helix chain 'C' and resid 381 through 395 removed outlier: 3.646A pdb=" N ASN C 389 " --> pdb=" O ILE C 385 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N GLN C 390 " --> pdb=" O ALA C 386 " (cutoff:3.500A) Processing helix chain 'C' and resid 402 through 407 Processing helix chain 'C' and resid 562 through 567 Processing helix chain 'C' and resid 592 through 612 removed outlier: 3.757A pdb=" N GLN C 598 " --> pdb=" O ASP C 594 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N ALA C 599 " --> pdb=" O GLU C 595 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N ALA C 610 " --> pdb=" O ALA C 606 " (cutoff:3.500A) Processing helix chain 'C' and resid 619 through 631 removed outlier: 3.926A pdb=" N ILE C 631 " --> pdb=" O ASP C 627 " (cutoff:3.500A) Processing helix chain 'C' and resid 639 through 651 removed outlier: 3.731A pdb=" N ALA C 645 " --> pdb=" O ARG C 641 " (cutoff:3.500A) Processing helix chain 'D' and resid 34 through 47 removed outlier: 3.926A pdb=" N LYS D 44 " --> pdb=" O ASN D 40 " (cutoff:3.500A) Processing helix chain 'D' and resid 71 through 84 removed outlier: 3.657A pdb=" N TYR D 84 " --> pdb=" O VAL D 80 " (cutoff:3.500A) Processing helix chain 'D' and resid 103 through 107 removed outlier: 3.596A pdb=" N THR D 106 " --> pdb=" O ASP D 103 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N SER D 107 " --> pdb=" O ALA D 104 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 103 through 107' Processing helix chain 'D' and resid 137 through 146 removed outlier: 3.922A pdb=" N LEU D 141 " --> pdb=" O ASP D 137 " (cutoff:3.500A) Processing helix chain 'D' and resid 168 through 184 removed outlier: 3.692A pdb=" N ILE D 172 " --> pdb=" O ARG D 168 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N LYS D 173 " --> pdb=" O ALA D 169 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N ARG D 174 " --> pdb=" O ALA D 170 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N ASN D 184 " --> pdb=" O GLU D 180 " (cutoff:3.500A) Processing helix chain 'D' and resid 200 through 205 removed outlier: 3.618A pdb=" N VAL D 204 " --> pdb=" O ALA D 200 " (cutoff:3.500A) Processing helix chain 'D' and resid 244 through 256 removed outlier: 3.867A pdb=" N ILE D 248 " --> pdb=" O SER D 244 " (cutoff:3.500A) Processing helix chain 'D' and resid 275 through 282 removed outlier: 3.830A pdb=" N GLU D 280 " --> pdb=" O ALA D 276 " (cutoff:3.500A) Processing helix chain 'D' and resid 326 through 335 removed outlier: 3.930A pdb=" N VAL D 332 " --> pdb=" O ASP D 328 " (cutoff:3.500A) Processing helix chain 'D' and resid 381 through 395 removed outlier: 3.645A pdb=" N ASN D 389 " --> pdb=" O ILE D 385 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N GLN D 390 " --> pdb=" O ALA D 386 " (cutoff:3.500A) Processing helix chain 'D' and resid 402 through 407 Processing helix chain 'D' and resid 562 through 567 Processing helix chain 'D' and resid 592 through 612 removed outlier: 3.757A pdb=" N GLN D 598 " --> pdb=" O ASP D 594 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N ALA D 599 " --> pdb=" O GLU D 595 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N ALA D 610 " --> pdb=" O ALA D 606 " (cutoff:3.500A) Processing helix chain 'D' and resid 619 through 631 removed outlier: 3.926A pdb=" N ILE D 631 " --> pdb=" O ASP D 627 " (cutoff:3.500A) Processing helix chain 'D' and resid 639 through 651 removed outlier: 3.732A pdb=" N ALA D 645 " --> pdb=" O ARG D 641 " (cutoff:3.500A) Processing helix chain 'E' and resid 34 through 47 removed outlier: 3.927A pdb=" N LYS E 44 " --> pdb=" O ASN E 40 " (cutoff:3.500A) Processing helix chain 'E' and resid 71 through 84 removed outlier: 3.657A pdb=" N TYR E 84 " --> pdb=" O VAL E 80 " (cutoff:3.500A) Processing helix chain 'E' and resid 103 through 107 removed outlier: 3.596A pdb=" N THR E 106 " --> pdb=" O ASP E 103 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N SER E 107 " --> pdb=" O ALA E 104 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 103 through 107' Processing helix chain 'E' and resid 137 through 146 removed outlier: 3.923A pdb=" N LEU E 141 " --> pdb=" O ASP E 137 " (cutoff:3.500A) Processing helix chain 'E' and resid 168 through 184 removed outlier: 3.691A pdb=" N ILE E 172 " --> pdb=" O ARG E 168 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N LYS E 173 " --> pdb=" O ALA E 169 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N ARG E 174 " --> pdb=" O ALA E 170 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N ASN E 184 " --> pdb=" O GLU E 180 " (cutoff:3.500A) Processing helix chain 'E' and resid 200 through 205 removed outlier: 3.618A pdb=" N VAL E 204 " --> pdb=" O ALA E 200 " (cutoff:3.500A) Processing helix chain 'E' and resid 244 through 256 removed outlier: 3.867A pdb=" N ILE E 248 " --> pdb=" O SER E 244 " (cutoff:3.500A) Processing helix chain 'E' and resid 275 through 282 removed outlier: 3.830A pdb=" N GLU E 280 " --> pdb=" O ALA E 276 " (cutoff:3.500A) Processing helix chain 'E' and resid 326 through 335 removed outlier: 3.930A pdb=" N VAL E 332 " --> pdb=" O ASP E 328 " (cutoff:3.500A) Processing helix chain 'E' and resid 381 through 395 removed outlier: 3.645A pdb=" N ASN E 389 " --> pdb=" O ILE E 385 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N GLN E 390 " --> pdb=" O ALA E 386 " (cutoff:3.500A) Processing helix chain 'E' and resid 402 through 407 Processing helix chain 'E' and resid 562 through 567 Processing helix chain 'E' and resid 592 through 612 removed outlier: 3.757A pdb=" N GLN E 598 " --> pdb=" O ASP E 594 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N ALA E 599 " --> pdb=" O GLU E 595 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N ALA E 610 " --> pdb=" O ALA E 606 " (cutoff:3.500A) Processing helix chain 'E' and resid 619 through 631 removed outlier: 3.926A pdb=" N ILE E 631 " --> pdb=" O ASP E 627 " (cutoff:3.500A) Processing helix chain 'E' and resid 639 through 651 removed outlier: 3.732A pdb=" N ALA E 645 " --> pdb=" O ARG E 641 " (cutoff:3.500A) Processing helix chain 'F' and resid 34 through 47 removed outlier: 3.927A pdb=" N LYS F 44 " --> pdb=" O ASN F 40 " (cutoff:3.500A) Processing helix chain 'F' and resid 71 through 84 removed outlier: 3.658A pdb=" N TYR F 84 " --> pdb=" O VAL F 80 " (cutoff:3.500A) Processing helix chain 'F' and resid 103 through 107 removed outlier: 3.595A pdb=" N THR F 106 " --> pdb=" O ASP F 103 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N SER F 107 " --> pdb=" O ALA F 104 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 103 through 107' Processing helix chain 'F' and resid 137 through 146 removed outlier: 3.922A pdb=" N LEU F 141 " --> pdb=" O ASP F 137 " (cutoff:3.500A) Processing helix chain 'F' and resid 168 through 184 removed outlier: 3.691A pdb=" N ILE F 172 " --> pdb=" O ARG F 168 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N LYS F 173 " --> pdb=" O ALA F 169 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N ARG F 174 " --> pdb=" O ALA F 170 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N ASN F 184 " --> pdb=" O GLU F 180 " (cutoff:3.500A) Processing helix chain 'F' and resid 200 through 205 removed outlier: 3.618A pdb=" N VAL F 204 " --> pdb=" O ALA F 200 " (cutoff:3.500A) Processing helix chain 'F' and resid 244 through 256 removed outlier: 3.867A pdb=" N ILE F 248 " --> pdb=" O SER F 244 " (cutoff:3.500A) Processing helix chain 'F' and resid 275 through 282 removed outlier: 3.830A pdb=" N GLU F 280 " --> pdb=" O ALA F 276 " (cutoff:3.500A) Processing helix chain 'F' and resid 326 through 335 removed outlier: 3.930A pdb=" N VAL F 332 " --> pdb=" O ASP F 328 " (cutoff:3.500A) Processing helix chain 'F' and resid 381 through 395 removed outlier: 3.646A pdb=" N ASN F 389 " --> pdb=" O ILE F 385 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N GLN F 390 " --> pdb=" O ALA F 386 " (cutoff:3.500A) Processing helix chain 'F' and resid 402 through 407 Processing helix chain 'F' and resid 562 through 567 Processing helix chain 'F' and resid 592 through 612 removed outlier: 3.756A pdb=" N GLN F 598 " --> pdb=" O ASP F 594 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N ALA F 599 " --> pdb=" O GLU F 595 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N ALA F 610 " --> pdb=" O ALA F 606 " (cutoff:3.500A) Processing helix chain 'F' and resid 619 through 631 removed outlier: 3.927A pdb=" N ILE F 631 " --> pdb=" O ASP F 627 " (cutoff:3.500A) Processing helix chain 'F' and resid 639 through 651 removed outlier: 3.731A pdb=" N ALA F 645 " --> pdb=" O ARG F 641 " (cutoff:3.500A) Processing helix chain 'G' and resid 34 through 47 removed outlier: 3.927A pdb=" N LYS G 44 " --> pdb=" O ASN G 40 " (cutoff:3.500A) Processing helix chain 'G' and resid 71 through 84 removed outlier: 3.657A pdb=" N TYR G 84 " --> pdb=" O VAL G 80 " (cutoff:3.500A) Processing helix chain 'G' and resid 103 through 107 removed outlier: 3.595A pdb=" N THR G 106 " --> pdb=" O ASP G 103 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N SER G 107 " --> pdb=" O ALA G 104 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 103 through 107' Processing helix chain 'G' and resid 137 through 146 removed outlier: 3.922A pdb=" N LEU G 141 " --> pdb=" O ASP G 137 " (cutoff:3.500A) Processing helix chain 'G' and resid 168 through 184 removed outlier: 3.691A pdb=" N ILE G 172 " --> pdb=" O ARG G 168 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N LYS G 173 " --> pdb=" O ALA G 169 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N ARG G 174 " --> pdb=" O ALA G 170 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N ASN G 184 " --> pdb=" O GLU G 180 " (cutoff:3.500A) Processing helix chain 'G' and resid 200 through 205 removed outlier: 3.618A pdb=" N VAL G 204 " --> pdb=" O ALA G 200 " (cutoff:3.500A) Processing helix chain 'G' and resid 244 through 256 removed outlier: 3.867A pdb=" N ILE G 248 " --> pdb=" O SER G 244 " (cutoff:3.500A) Processing helix chain 'G' and resid 275 through 282 removed outlier: 3.830A pdb=" N GLU G 280 " --> pdb=" O ALA G 276 " (cutoff:3.500A) Processing helix chain 'G' and resid 326 through 335 removed outlier: 3.930A pdb=" N VAL G 332 " --> pdb=" O ASP G 328 " (cutoff:3.500A) Processing helix chain 'G' and resid 381 through 395 removed outlier: 3.646A pdb=" N ASN G 389 " --> pdb=" O ILE G 385 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N GLN G 390 " --> pdb=" O ALA G 386 " (cutoff:3.500A) Processing helix chain 'G' and resid 402 through 407 Processing helix chain 'G' and resid 562 through 567 Processing helix chain 'G' and resid 592 through 612 removed outlier: 3.756A pdb=" N GLN G 598 " --> pdb=" O ASP G 594 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N ALA G 599 " --> pdb=" O GLU G 595 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N ALA G 610 " --> pdb=" O ALA G 606 " (cutoff:3.500A) Processing helix chain 'G' and resid 619 through 631 removed outlier: 3.926A pdb=" N ILE G 631 " --> pdb=" O ASP G 627 " (cutoff:3.500A) Processing helix chain 'G' and resid 639 through 651 removed outlier: 3.731A pdb=" N ALA G 645 " --> pdb=" O ARG G 641 " (cutoff:3.500A) Processing helix chain 'H' and resid 34 through 47 removed outlier: 3.926A pdb=" N LYS H 44 " --> pdb=" O ASN H 40 " (cutoff:3.500A) Processing helix chain 'H' and resid 71 through 84 removed outlier: 3.658A pdb=" N TYR H 84 " --> pdb=" O VAL H 80 " (cutoff:3.500A) Processing helix chain 'H' and resid 103 through 107 removed outlier: 3.596A pdb=" N THR H 106 " --> pdb=" O ASP H 103 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N SER H 107 " --> pdb=" O ALA H 104 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 103 through 107' Processing helix chain 'H' and resid 137 through 146 removed outlier: 3.922A pdb=" N LEU H 141 " --> pdb=" O ASP H 137 " (cutoff:3.500A) Processing helix chain 'H' and resid 168 through 184 removed outlier: 3.691A pdb=" N ILE H 172 " --> pdb=" O ARG H 168 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N LYS H 173 " --> pdb=" O ALA H 169 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N ARG H 174 " --> pdb=" O ALA H 170 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N ASN H 184 " --> pdb=" O GLU H 180 " (cutoff:3.500A) Processing helix chain 'H' and resid 200 through 205 removed outlier: 3.617A pdb=" N VAL H 204 " --> pdb=" O ALA H 200 " (cutoff:3.500A) Processing helix chain 'H' and resid 244 through 256 removed outlier: 3.867A pdb=" N ILE H 248 " --> pdb=" O SER H 244 " (cutoff:3.500A) Processing helix chain 'H' and resid 275 through 282 removed outlier: 3.830A pdb=" N GLU H 280 " --> pdb=" O ALA H 276 " (cutoff:3.500A) Processing helix chain 'H' and resid 326 through 335 removed outlier: 3.929A pdb=" N VAL H 332 " --> pdb=" O ASP H 328 " (cutoff:3.500A) Processing helix chain 'H' and resid 381 through 395 removed outlier: 3.645A pdb=" N ASN H 389 " --> pdb=" O ILE H 385 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N GLN H 390 " --> pdb=" O ALA H 386 " (cutoff:3.500A) Processing helix chain 'H' and resid 402 through 407 Processing helix chain 'H' and resid 562 through 567 Processing helix chain 'H' and resid 592 through 612 removed outlier: 3.757A pdb=" N GLN H 598 " --> pdb=" O ASP H 594 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N ALA H 599 " --> pdb=" O GLU H 595 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N ALA H 610 " --> pdb=" O ALA H 606 " (cutoff:3.500A) Processing helix chain 'H' and resid 619 through 631 removed outlier: 3.926A pdb=" N ILE H 631 " --> pdb=" O ASP H 627 " (cutoff:3.500A) Processing helix chain 'H' and resid 639 through 651 removed outlier: 3.732A pdb=" N ALA H 645 " --> pdb=" O ARG H 641 " (cutoff:3.500A) Processing helix chain 'I' and resid 34 through 47 removed outlier: 3.927A pdb=" N LYS I 44 " --> pdb=" O ASN I 40 " (cutoff:3.500A) Processing helix chain 'I' and resid 71 through 84 removed outlier: 3.657A pdb=" N TYR I 84 " --> pdb=" O VAL I 80 " (cutoff:3.500A) Processing helix chain 'I' and resid 103 through 107 removed outlier: 3.595A pdb=" N THR I 106 " --> pdb=" O ASP I 103 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N SER I 107 " --> pdb=" O ALA I 104 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 103 through 107' Processing helix chain 'I' and resid 137 through 146 removed outlier: 3.923A pdb=" N LEU I 141 " --> pdb=" O ASP I 137 " (cutoff:3.500A) Processing helix chain 'I' and resid 168 through 184 removed outlier: 3.692A pdb=" N ILE I 172 " --> pdb=" O ARG I 168 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N LYS I 173 " --> pdb=" O ALA I 169 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N ARG I 174 " --> pdb=" O ALA I 170 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N ASN I 184 " --> pdb=" O GLU I 180 " (cutoff:3.500A) Processing helix chain 'I' and resid 200 through 205 removed outlier: 3.618A pdb=" N VAL I 204 " --> pdb=" O ALA I 200 " (cutoff:3.500A) Processing helix chain 'I' and resid 244 through 256 removed outlier: 3.868A pdb=" N ILE I 248 " --> pdb=" O SER I 244 " (cutoff:3.500A) Processing helix chain 'I' and resid 275 through 282 removed outlier: 3.830A pdb=" N GLU I 280 " --> pdb=" O ALA I 276 " (cutoff:3.500A) Processing helix chain 'I' and resid 326 through 335 removed outlier: 3.930A pdb=" N VAL I 332 " --> pdb=" O ASP I 328 " (cutoff:3.500A) Processing helix chain 'I' and resid 381 through 395 removed outlier: 3.646A pdb=" N ASN I 389 " --> pdb=" O ILE I 385 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N GLN I 390 " --> pdb=" O ALA I 386 " (cutoff:3.500A) Processing helix chain 'I' and resid 402 through 407 Processing helix chain 'I' and resid 562 through 567 Processing helix chain 'I' and resid 592 through 612 removed outlier: 3.757A pdb=" N GLN I 598 " --> pdb=" O ASP I 594 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N ALA I 599 " --> pdb=" O GLU I 595 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N ALA I 610 " --> pdb=" O ALA I 606 " (cutoff:3.500A) Processing helix chain 'I' and resid 619 through 631 removed outlier: 3.926A pdb=" N ILE I 631 " --> pdb=" O ASP I 627 " (cutoff:3.500A) Processing helix chain 'I' and resid 639 through 651 removed outlier: 3.731A pdb=" N ALA I 645 " --> pdb=" O ARG I 641 " (cutoff:3.500A) Processing helix chain 'J' and resid 34 through 47 removed outlier: 3.927A pdb=" N LYS J 44 " --> pdb=" O ASN J 40 " (cutoff:3.500A) Processing helix chain 'J' and resid 71 through 84 removed outlier: 3.657A pdb=" N TYR J 84 " --> pdb=" O VAL J 80 " (cutoff:3.500A) Processing helix chain 'J' and resid 103 through 107 removed outlier: 3.594A pdb=" N THR J 106 " --> pdb=" O ASP J 103 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N SER J 107 " --> pdb=" O ALA J 104 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 103 through 107' Processing helix chain 'J' and resid 137 through 146 removed outlier: 3.923A pdb=" N LEU J 141 " --> pdb=" O ASP J 137 " (cutoff:3.500A) Processing helix chain 'J' and resid 168 through 184 removed outlier: 3.691A pdb=" N ILE J 172 " --> pdb=" O ARG J 168 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N LYS J 173 " --> pdb=" O ALA J 169 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N ARG J 174 " --> pdb=" O ALA J 170 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ASN J 184 " --> pdb=" O GLU J 180 " (cutoff:3.500A) Processing helix chain 'J' and resid 200 through 205 removed outlier: 3.618A pdb=" N VAL J 204 " --> pdb=" O ALA J 200 " (cutoff:3.500A) Processing helix chain 'J' and resid 244 through 256 removed outlier: 3.867A pdb=" N ILE J 248 " --> pdb=" O SER J 244 " (cutoff:3.500A) Processing helix chain 'J' and resid 275 through 282 removed outlier: 3.831A pdb=" N GLU J 280 " --> pdb=" O ALA J 276 " (cutoff:3.500A) Processing helix chain 'J' and resid 326 through 335 removed outlier: 3.929A pdb=" N VAL J 332 " --> pdb=" O ASP J 328 " (cutoff:3.500A) Processing helix chain 'J' and resid 381 through 395 removed outlier: 3.647A pdb=" N ASN J 389 " --> pdb=" O ILE J 385 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N GLN J 390 " --> pdb=" O ALA J 386 " (cutoff:3.500A) Processing helix chain 'J' and resid 402 through 407 Processing helix chain 'J' and resid 562 through 567 Processing helix chain 'J' and resid 592 through 612 removed outlier: 3.757A pdb=" N GLN J 598 " --> pdb=" O ASP J 594 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N ALA J 599 " --> pdb=" O GLU J 595 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N ALA J 610 " --> pdb=" O ALA J 606 " (cutoff:3.500A) Processing helix chain 'J' and resid 619 through 631 removed outlier: 3.927A pdb=" N ILE J 631 " --> pdb=" O ASP J 627 " (cutoff:3.500A) Processing helix chain 'J' and resid 639 through 651 removed outlier: 3.731A pdb=" N ALA J 645 " --> pdb=" O ARG J 641 " (cutoff:3.500A) Processing helix chain 'K' and resid 34 through 47 removed outlier: 3.926A pdb=" N LYS K 44 " --> pdb=" O ASN K 40 " (cutoff:3.500A) Processing helix chain 'K' and resid 71 through 84 removed outlier: 3.658A pdb=" N TYR K 84 " --> pdb=" O VAL K 80 " (cutoff:3.500A) Processing helix chain 'K' and resid 103 through 107 removed outlier: 3.596A pdb=" N THR K 106 " --> pdb=" O ASP K 103 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N SER K 107 " --> pdb=" O ALA K 104 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 103 through 107' Processing helix chain 'K' and resid 137 through 146 removed outlier: 3.922A pdb=" N LEU K 141 " --> pdb=" O ASP K 137 " (cutoff:3.500A) Processing helix chain 'K' and resid 168 through 184 removed outlier: 3.691A pdb=" N ILE K 172 " --> pdb=" O ARG K 168 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N LYS K 173 " --> pdb=" O ALA K 169 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N ARG K 174 " --> pdb=" O ALA K 170 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N ASN K 184 " --> pdb=" O GLU K 180 " (cutoff:3.500A) Processing helix chain 'K' and resid 200 through 205 removed outlier: 3.618A pdb=" N VAL K 204 " --> pdb=" O ALA K 200 " (cutoff:3.500A) Processing helix chain 'K' and resid 244 through 256 removed outlier: 3.868A pdb=" N ILE K 248 " --> pdb=" O SER K 244 " (cutoff:3.500A) Processing helix chain 'K' and resid 275 through 282 removed outlier: 3.829A pdb=" N GLU K 280 " --> pdb=" O ALA K 276 " (cutoff:3.500A) Processing helix chain 'K' and resid 326 through 335 removed outlier: 3.930A pdb=" N VAL K 332 " --> pdb=" O ASP K 328 " (cutoff:3.500A) Processing helix chain 'K' and resid 381 through 395 removed outlier: 3.646A pdb=" N ASN K 389 " --> pdb=" O ILE K 385 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N GLN K 390 " --> pdb=" O ALA K 386 " (cutoff:3.500A) Processing helix chain 'K' and resid 402 through 407 Processing helix chain 'K' and resid 562 through 567 Processing helix chain 'K' and resid 592 through 612 removed outlier: 3.757A pdb=" N GLN K 598 " --> pdb=" O ASP K 594 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N ALA K 599 " --> pdb=" O GLU K 595 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N ALA K 610 " --> pdb=" O ALA K 606 " (cutoff:3.500A) Processing helix chain 'K' and resid 619 through 631 removed outlier: 3.927A pdb=" N ILE K 631 " --> pdb=" O ASP K 627 " (cutoff:3.500A) Processing helix chain 'K' and resid 639 through 651 removed outlier: 3.732A pdb=" N ALA K 645 " --> pdb=" O ARG K 641 " (cutoff:3.500A) Processing helix chain 'L' and resid 34 through 47 removed outlier: 3.926A pdb=" N LYS L 44 " --> pdb=" O ASN L 40 " (cutoff:3.500A) Processing helix chain 'L' and resid 71 through 84 removed outlier: 3.657A pdb=" N TYR L 84 " --> pdb=" O VAL L 80 " (cutoff:3.500A) Processing helix chain 'L' and resid 103 through 107 removed outlier: 3.595A pdb=" N THR L 106 " --> pdb=" O ASP L 103 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N SER L 107 " --> pdb=" O ALA L 104 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 103 through 107' Processing helix chain 'L' and resid 137 through 146 removed outlier: 3.922A pdb=" N LEU L 141 " --> pdb=" O ASP L 137 " (cutoff:3.500A) Processing helix chain 'L' and resid 168 through 184 removed outlier: 3.691A pdb=" N ILE L 172 " --> pdb=" O ARG L 168 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N LYS L 173 " --> pdb=" O ALA L 169 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N ARG L 174 " --> pdb=" O ALA L 170 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N ASN L 184 " --> pdb=" O GLU L 180 " (cutoff:3.500A) Processing helix chain 'L' and resid 200 through 205 removed outlier: 3.617A pdb=" N VAL L 204 " --> pdb=" O ALA L 200 " (cutoff:3.500A) Processing helix chain 'L' and resid 244 through 256 removed outlier: 3.868A pdb=" N ILE L 248 " --> pdb=" O SER L 244 " (cutoff:3.500A) Processing helix chain 'L' and resid 275 through 282 removed outlier: 3.829A pdb=" N GLU L 280 " --> pdb=" O ALA L 276 " (cutoff:3.500A) Processing helix chain 'L' and resid 326 through 335 removed outlier: 3.929A pdb=" N VAL L 332 " --> pdb=" O ASP L 328 " (cutoff:3.500A) Processing helix chain 'L' and resid 381 through 395 removed outlier: 3.646A pdb=" N ASN L 389 " --> pdb=" O ILE L 385 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N GLN L 390 " --> pdb=" O ALA L 386 " (cutoff:3.500A) Processing helix chain 'L' and resid 402 through 407 Processing helix chain 'L' and resid 562 through 567 Processing helix chain 'L' and resid 592 through 612 removed outlier: 3.756A pdb=" N GLN L 598 " --> pdb=" O ASP L 594 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N ALA L 599 " --> pdb=" O GLU L 595 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N ALA L 610 " --> pdb=" O ALA L 606 " (cutoff:3.500A) Processing helix chain 'L' and resid 619 through 631 removed outlier: 3.926A pdb=" N ILE L 631 " --> pdb=" O ASP L 627 " (cutoff:3.500A) Processing helix chain 'L' and resid 639 through 651 removed outlier: 3.731A pdb=" N ALA L 645 " --> pdb=" O ARG L 641 " (cutoff:3.500A) Processing helix chain 'M' and resid 34 through 47 removed outlier: 3.927A pdb=" N LYS M 44 " --> pdb=" O ASN M 40 " (cutoff:3.500A) Processing helix chain 'M' and resid 71 through 84 removed outlier: 3.658A pdb=" N TYR M 84 " --> pdb=" O VAL M 80 " (cutoff:3.500A) Processing helix chain 'M' and resid 103 through 107 removed outlier: 3.595A pdb=" N THR M 106 " --> pdb=" O ASP M 103 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N SER M 107 " --> pdb=" O ALA M 104 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 103 through 107' Processing helix chain 'M' and resid 137 through 146 removed outlier: 3.922A pdb=" N LEU M 141 " --> pdb=" O ASP M 137 " (cutoff:3.500A) Processing helix chain 'M' and resid 168 through 184 removed outlier: 3.692A pdb=" N ILE M 172 " --> pdb=" O ARG M 168 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N LYS M 173 " --> pdb=" O ALA M 169 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N ARG M 174 " --> pdb=" O ALA M 170 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N ASN M 184 " --> pdb=" O GLU M 180 " (cutoff:3.500A) Processing helix chain 'M' and resid 200 through 205 removed outlier: 3.618A pdb=" N VAL M 204 " --> pdb=" O ALA M 200 " (cutoff:3.500A) Processing helix chain 'M' and resid 244 through 256 removed outlier: 3.868A pdb=" N ILE M 248 " --> pdb=" O SER M 244 " (cutoff:3.500A) Processing helix chain 'M' and resid 275 through 282 removed outlier: 3.830A pdb=" N GLU M 280 " --> pdb=" O ALA M 276 " (cutoff:3.500A) Processing helix chain 'M' and resid 326 through 335 removed outlier: 3.930A pdb=" N VAL M 332 " --> pdb=" O ASP M 328 " (cutoff:3.500A) Processing helix chain 'M' and resid 381 through 395 removed outlier: 3.645A pdb=" N ASN M 389 " --> pdb=" O ILE M 385 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N GLN M 390 " --> pdb=" O ALA M 386 " (cutoff:3.500A) Processing helix chain 'M' and resid 402 through 407 Processing helix chain 'M' and resid 562 through 567 Processing helix chain 'M' and resid 592 through 612 removed outlier: 3.758A pdb=" N GLN M 598 " --> pdb=" O ASP M 594 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N ALA M 599 " --> pdb=" O GLU M 595 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N ALA M 610 " --> pdb=" O ALA M 606 " (cutoff:3.500A) Processing helix chain 'M' and resid 619 through 631 removed outlier: 3.926A pdb=" N ILE M 631 " --> pdb=" O ASP M 627 " (cutoff:3.500A) Processing helix chain 'M' and resid 639 through 651 removed outlier: 3.731A pdb=" N ALA M 645 " --> pdb=" O ARG M 641 " (cutoff:3.500A) Processing helix chain 'N' and resid 34 through 47 removed outlier: 3.926A pdb=" N LYS N 44 " --> pdb=" O ASN N 40 " (cutoff:3.500A) Processing helix chain 'N' and resid 71 through 84 removed outlier: 3.657A pdb=" N TYR N 84 " --> pdb=" O VAL N 80 " (cutoff:3.500A) Processing helix chain 'N' and resid 103 through 107 removed outlier: 3.595A pdb=" N THR N 106 " --> pdb=" O ASP N 103 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N SER N 107 " --> pdb=" O ALA N 104 " (cutoff:3.500A) No H-bonds generated for 'chain 'N' and resid 103 through 107' Processing helix chain 'N' and resid 137 through 146 removed outlier: 3.922A pdb=" N LEU N 141 " --> pdb=" O ASP N 137 " (cutoff:3.500A) Processing helix chain 'N' and resid 168 through 184 removed outlier: 3.691A pdb=" N ILE N 172 " --> pdb=" O ARG N 168 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N LYS N 173 " --> pdb=" O ALA N 169 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N ARG N 174 " --> pdb=" O ALA N 170 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N ASN N 184 " --> pdb=" O GLU N 180 " (cutoff:3.500A) Processing helix chain 'N' and resid 200 through 205 removed outlier: 3.617A pdb=" N VAL N 204 " --> pdb=" O ALA N 200 " (cutoff:3.500A) Processing helix chain 'N' and resid 244 through 256 removed outlier: 3.867A pdb=" N ILE N 248 " --> pdb=" O SER N 244 " (cutoff:3.500A) Processing helix chain 'N' and resid 275 through 282 removed outlier: 3.830A pdb=" N GLU N 280 " --> pdb=" O ALA N 276 " (cutoff:3.500A) Processing helix chain 'N' and resid 326 through 335 removed outlier: 3.930A pdb=" N VAL N 332 " --> pdb=" O ASP N 328 " (cutoff:3.500A) Processing helix chain 'N' and resid 381 through 395 removed outlier: 3.645A pdb=" N ASN N 389 " --> pdb=" O ILE N 385 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N GLN N 390 " --> pdb=" O ALA N 386 " (cutoff:3.500A) Processing helix chain 'N' and resid 402 through 407 Processing helix chain 'N' and resid 562 through 567 Processing helix chain 'N' and resid 592 through 612 removed outlier: 3.757A pdb=" N GLN N 598 " --> pdb=" O ASP N 594 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N ALA N 599 " --> pdb=" O GLU N 595 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N ALA N 610 " --> pdb=" O ALA N 606 " (cutoff:3.500A) Processing helix chain 'N' and resid 619 through 631 removed outlier: 3.926A pdb=" N ILE N 631 " --> pdb=" O ASP N 627 " (cutoff:3.500A) Processing helix chain 'N' and resid 639 through 651 removed outlier: 3.731A pdb=" N ALA N 645 " --> pdb=" O ARG N 641 " (cutoff:3.500A) Processing helix chain 'O' and resid 34 through 47 removed outlier: 3.926A pdb=" N LYS O 44 " --> pdb=" O ASN O 40 " (cutoff:3.500A) Processing helix chain 'O' and resid 71 through 84 removed outlier: 3.657A pdb=" N TYR O 84 " --> pdb=" O VAL O 80 " (cutoff:3.500A) Processing helix chain 'O' and resid 103 through 107 removed outlier: 3.595A pdb=" N THR O 106 " --> pdb=" O ASP O 103 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N SER O 107 " --> pdb=" O ALA O 104 " (cutoff:3.500A) No H-bonds generated for 'chain 'O' and resid 103 through 107' Processing helix chain 'O' and resid 137 through 146 removed outlier: 3.922A pdb=" N LEU O 141 " --> pdb=" O ASP O 137 " (cutoff:3.500A) Processing helix chain 'O' and resid 168 through 184 removed outlier: 3.691A pdb=" N ILE O 172 " --> pdb=" O ARG O 168 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N LYS O 173 " --> pdb=" O ALA O 169 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N ARG O 174 " --> pdb=" O ALA O 170 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N ASN O 184 " --> pdb=" O GLU O 180 " (cutoff:3.500A) Processing helix chain 'O' and resid 200 through 205 removed outlier: 3.618A pdb=" N VAL O 204 " --> pdb=" O ALA O 200 " (cutoff:3.500A) Processing helix chain 'O' and resid 244 through 256 removed outlier: 3.867A pdb=" N ILE O 248 " --> pdb=" O SER O 244 " (cutoff:3.500A) Processing helix chain 'O' and resid 275 through 282 removed outlier: 3.830A pdb=" N GLU O 280 " --> pdb=" O ALA O 276 " (cutoff:3.500A) Processing helix chain 'O' and resid 326 through 335 removed outlier: 3.930A pdb=" N VAL O 332 " --> pdb=" O ASP O 328 " (cutoff:3.500A) Processing helix chain 'O' and resid 381 through 395 removed outlier: 3.646A pdb=" N ASN O 389 " --> pdb=" O ILE O 385 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N GLN O 390 " --> pdb=" O ALA O 386 " (cutoff:3.500A) Processing helix chain 'O' and resid 402 through 407 Processing helix chain 'O' and resid 562 through 567 Processing helix chain 'O' and resid 592 through 612 removed outlier: 3.758A pdb=" N GLN O 598 " --> pdb=" O ASP O 594 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N ALA O 599 " --> pdb=" O GLU O 595 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N ALA O 610 " --> pdb=" O ALA O 606 " (cutoff:3.500A) Processing helix chain 'O' and resid 619 through 631 removed outlier: 3.927A pdb=" N ILE O 631 " --> pdb=" O ASP O 627 " (cutoff:3.500A) Processing helix chain 'O' and resid 639 through 651 removed outlier: 3.731A pdb=" N ALA O 645 " --> pdb=" O ARG O 641 " (cutoff:3.500A) Processing helix chain 'P' and resid 41 through 62 removed outlier: 3.854A pdb=" N LEU P 45 " --> pdb=" O SER P 41 " (cutoff:3.500A) Processing helix chain 'P' and resid 69 through 84 Processing helix chain 'P' and resid 90 through 108 Processing helix chain 'P' and resid 111 through 123 Processing helix chain 'P' and resid 123 through 131 Processing helix chain 'Q' and resid 41 through 62 removed outlier: 3.854A pdb=" N LEU Q 45 " --> pdb=" O SER Q 41 " (cutoff:3.500A) Processing helix chain 'Q' and resid 69 through 84 Processing helix chain 'Q' and resid 90 through 108 Processing helix chain 'Q' and resid 111 through 123 Processing helix chain 'Q' and resid 123 through 131 Processing helix chain 'R' and resid 41 through 62 removed outlier: 3.854A pdb=" N LEU R 45 " --> pdb=" O SER R 41 " (cutoff:3.500A) Processing helix chain 'R' and resid 69 through 84 Processing helix chain 'R' and resid 90 through 108 Processing helix chain 'R' and resid 111 through 123 Processing helix chain 'R' and resid 123 through 131 Processing helix chain 'S' and resid 41 through 62 removed outlier: 3.854A pdb=" N LEU S 45 " --> pdb=" O SER S 41 " (cutoff:3.500A) Processing helix chain 'S' and resid 69 through 84 Processing helix chain 'S' and resid 90 through 108 Processing helix chain 'S' and resid 111 through 123 Processing helix chain 'S' and resid 123 through 131 Processing helix chain 'T' and resid 41 through 62 removed outlier: 3.854A pdb=" N LEU T 45 " --> pdb=" O SER T 41 " (cutoff:3.500A) Processing helix chain 'T' and resid 69 through 84 Processing helix chain 'T' and resid 90 through 108 Processing helix chain 'T' and resid 111 through 123 Processing helix chain 'T' and resid 123 through 131 Processing helix chain 'U' and resid 41 through 62 removed outlier: 3.854A pdb=" N LEU U 45 " --> pdb=" O SER U 41 " (cutoff:3.500A) Processing helix chain 'U' and resid 69 through 84 Processing helix chain 'U' and resid 90 through 108 Processing helix chain 'U' and resid 111 through 123 Processing helix chain 'U' and resid 123 through 131 Processing helix chain 'V' and resid 41 through 62 removed outlier: 3.855A pdb=" N LEU V 45 " --> pdb=" O SER V 41 " (cutoff:3.500A) Processing helix chain 'V' and resid 69 through 84 Processing helix chain 'V' and resid 90 through 108 Processing helix chain 'V' and resid 111 through 123 Processing helix chain 'V' and resid 123 through 131 Processing helix chain 'W' and resid 41 through 62 removed outlier: 3.854A pdb=" N LEU W 45 " --> pdb=" O SER W 41 " (cutoff:3.500A) Processing helix chain 'W' and resid 69 through 84 Processing helix chain 'W' and resid 90 through 108 Processing helix chain 'W' and resid 111 through 123 Processing helix chain 'W' and resid 123 through 131 Processing helix chain 'X' and resid 41 through 62 removed outlier: 3.855A pdb=" N LEU X 45 " --> pdb=" O SER X 41 " (cutoff:3.500A) Processing helix chain 'X' and resid 69 through 84 Processing helix chain 'X' and resid 90 through 108 Processing helix chain 'X' and resid 111 through 123 Processing helix chain 'X' and resid 123 through 131 Processing helix chain 'Y' and resid 41 through 62 removed outlier: 3.855A pdb=" N LEU Y 45 " --> pdb=" O SER Y 41 " (cutoff:3.500A) Processing helix chain 'Y' and resid 69 through 84 Processing helix chain 'Y' and resid 90 through 108 Processing helix chain 'Y' and resid 111 through 123 Processing helix chain 'Y' and resid 123 through 131 Processing helix chain 'Z' and resid 41 through 62 removed outlier: 3.855A pdb=" N LEU Z 45 " --> pdb=" O SER Z 41 " (cutoff:3.500A) Processing helix chain 'Z' and resid 69 through 84 Processing helix chain 'Z' and resid 90 through 108 Processing helix chain 'Z' and resid 111 through 123 Processing helix chain 'Z' and resid 123 through 131 Processing helix chain 'a' and resid 41 through 62 removed outlier: 3.854A pdb=" N LEU a 45 " --> pdb=" O SER a 41 " (cutoff:3.500A) Processing helix chain 'a' and resid 69 through 84 Processing helix chain 'a' and resid 90 through 108 Processing helix chain 'a' and resid 111 through 123 Processing helix chain 'a' and resid 123 through 131 Processing helix chain 'b' and resid 41 through 62 removed outlier: 3.855A pdb=" N LEU b 45 " --> pdb=" O SER b 41 " (cutoff:3.500A) Processing helix chain 'b' and resid 69 through 84 Processing helix chain 'b' and resid 90 through 108 Processing helix chain 'b' and resid 111 through 123 Processing helix chain 'b' and resid 123 through 131 Processing helix chain 'c' and resid 41 through 62 removed outlier: 3.854A pdb=" N LEU c 45 " --> pdb=" O SER c 41 " (cutoff:3.500A) Processing helix chain 'c' and resid 69 through 84 Processing helix chain 'c' and resid 90 through 108 Processing helix chain 'c' and resid 111 through 123 Processing helix chain 'c' and resid 123 through 131 Processing helix chain 'd' and resid 41 through 62 removed outlier: 3.855A pdb=" N LEU d 45 " --> pdb=" O SER d 41 " (cutoff:3.500A) Processing helix chain 'd' and resid 69 through 84 Processing helix chain 'd' and resid 90 through 108 Processing helix chain 'd' and resid 111 through 123 Processing helix chain 'd' and resid 123 through 131 2265 hydrogen bonds defined for protein. 6660 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: 21.26 Time building geometry restraints manager: 29.31 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 21612 1.33 - 1.45: 17129 1.45 - 1.57: 47073 1.57 - 1.70: 1 1.70 - 1.82: 330 Bond restraints: 86145 Sorted by residual: bond pdb=" CD ARG V 100 " pdb=" NE ARG V 100 " ideal model delta sigma weight residual 1.458 1.530 -0.072 1.40e-02 5.10e+03 2.66e+01 bond pdb=" CD ARG X 100 " pdb=" NE ARG X 100 " ideal model delta sigma weight residual 1.458 1.530 -0.072 1.40e-02 5.10e+03 2.65e+01 bond pdb=" CD ARG a 100 " pdb=" NE ARG a 100 " ideal model delta sigma weight residual 1.458 1.530 -0.072 1.40e-02 5.10e+03 2.65e+01 bond pdb=" CD ARG U 100 " pdb=" NE ARG U 100 " ideal model delta sigma weight residual 1.458 1.530 -0.072 1.40e-02 5.10e+03 2.65e+01 bond pdb=" CD ARG P 100 " pdb=" NE ARG P 100 " ideal model delta sigma weight residual 1.458 1.530 -0.072 1.40e-02 5.10e+03 2.63e+01 ... (remaining 86140 not shown) Histogram of bond angle deviations from ideal: 97.95 - 106.00: 1894 106.00 - 114.05: 51027 114.05 - 122.10: 48105 122.10 - 130.16: 15704 130.16 - 138.21: 180 Bond angle restraints: 116910 Sorted by residual: angle pdb=" CA ALA b 124 " pdb=" C ALA b 124 " pdb=" N PRO b 125 " ideal model delta sigma weight residual 120.58 115.67 4.91 7.40e-01 1.83e+00 4.41e+01 angle pdb=" CA ALA X 124 " pdb=" C ALA X 124 " pdb=" N PRO X 125 " ideal model delta sigma weight residual 120.58 115.67 4.91 7.40e-01 1.83e+00 4.39e+01 angle pdb=" CA ALA Y 124 " pdb=" C ALA Y 124 " pdb=" N PRO Y 125 " ideal model delta sigma weight residual 120.58 115.69 4.89 7.40e-01 1.83e+00 4.37e+01 angle pdb=" CA ALA d 124 " pdb=" C ALA d 124 " pdb=" N PRO d 125 " ideal model delta sigma weight residual 120.58 115.69 4.89 7.40e-01 1.83e+00 4.36e+01 angle pdb=" CA ALA W 124 " pdb=" C ALA W 124 " pdb=" N PRO W 125 " ideal model delta sigma weight residual 120.58 115.70 4.88 7.40e-01 1.83e+00 4.35e+01 ... (remaining 116905 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.82: 50611 17.82 - 35.64: 1962 35.64 - 53.46: 362 53.46 - 71.28: 0 71.28 - 89.10: 60 Dihedral angle restraints: 52995 sinusoidal: 20340 harmonic: 32655 Sorted by residual: dihedral pdb=" CA GLN B 313 " pdb=" C GLN B 313 " pdb=" N THR B 314 " pdb=" CA THR B 314 " ideal model delta harmonic sigma weight residual 180.00 158.57 21.43 0 5.00e+00 4.00e-02 1.84e+01 dihedral pdb=" CA GLN D 313 " pdb=" C GLN D 313 " pdb=" N THR D 314 " pdb=" CA THR D 314 " ideal model delta harmonic sigma weight residual 180.00 158.57 21.43 0 5.00e+00 4.00e-02 1.84e+01 dihedral pdb=" CA GLN N 313 " pdb=" C GLN N 313 " pdb=" N THR N 314 " pdb=" CA THR N 314 " ideal model delta harmonic sigma weight residual 180.00 158.59 21.41 0 5.00e+00 4.00e-02 1.83e+01 ... (remaining 52992 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.069: 10073 0.069 - 0.138: 3244 0.138 - 0.207: 681 0.207 - 0.276: 222 0.276 - 0.345: 30 Chirality restraints: 14250 Sorted by residual: chirality pdb=" CA SER W 41 " pdb=" N SER W 41 " pdb=" C SER W 41 " pdb=" CB SER W 41 " both_signs ideal model delta sigma weight residual False 2.51 2.17 0.35 2.00e-01 2.50e+01 2.98e+00 chirality pdb=" CA SER Z 41 " pdb=" N SER Z 41 " pdb=" C SER Z 41 " pdb=" CB SER Z 41 " both_signs ideal model delta sigma weight residual False 2.51 2.17 0.35 2.00e-01 2.50e+01 2.98e+00 chirality pdb=" CA SER R 41 " pdb=" N SER R 41 " pdb=" C SER R 41 " pdb=" CB SER R 41 " both_signs ideal model delta sigma weight residual False 2.51 2.17 0.34 2.00e-01 2.50e+01 2.96e+00 ... (remaining 14247 not shown) Planarity restraints: 15195 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP U 86 " 0.014 2.00e-02 2.50e+03 2.24e-02 1.26e+01 pdb=" CG TRP U 86 " -0.007 2.00e-02 2.50e+03 pdb=" CD1 TRP U 86 " 0.014 2.00e-02 2.50e+03 pdb=" CD2 TRP U 86 " -0.022 2.00e-02 2.50e+03 pdb=" NE1 TRP U 86 " 0.018 2.00e-02 2.50e+03 pdb=" CE2 TRP U 86 " -0.016 2.00e-02 2.50e+03 pdb=" CE3 TRP U 86 " -0.028 2.00e-02 2.50e+03 pdb=" CZ2 TRP U 86 " -0.032 2.00e-02 2.50e+03 pdb=" CZ3 TRP U 86 " 0.024 2.00e-02 2.50e+03 pdb=" CH2 TRP U 86 " 0.034 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP d 86 " -0.014 2.00e-02 2.50e+03 2.24e-02 1.25e+01 pdb=" CG TRP d 86 " 0.008 2.00e-02 2.50e+03 pdb=" CD1 TRP d 86 " -0.014 2.00e-02 2.50e+03 pdb=" CD2 TRP d 86 " 0.022 2.00e-02 2.50e+03 pdb=" NE1 TRP d 86 " -0.018 2.00e-02 2.50e+03 pdb=" CE2 TRP d 86 " 0.015 2.00e-02 2.50e+03 pdb=" CE3 TRP d 86 " 0.028 2.00e-02 2.50e+03 pdb=" CZ2 TRP d 86 " 0.032 2.00e-02 2.50e+03 pdb=" CZ3 TRP d 86 " -0.025 2.00e-02 2.50e+03 pdb=" CH2 TRP d 86 " -0.034 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP V 86 " 0.014 2.00e-02 2.50e+03 2.24e-02 1.25e+01 pdb=" CG TRP V 86 " -0.008 2.00e-02 2.50e+03 pdb=" CD1 TRP V 86 " 0.014 2.00e-02 2.50e+03 pdb=" CD2 TRP V 86 " -0.022 2.00e-02 2.50e+03 pdb=" NE1 TRP V 86 " 0.018 2.00e-02 2.50e+03 pdb=" CE2 TRP V 86 " -0.016 2.00e-02 2.50e+03 pdb=" CE3 TRP V 86 " -0.028 2.00e-02 2.50e+03 pdb=" CZ2 TRP V 86 " -0.031 2.00e-02 2.50e+03 pdb=" CZ3 TRP V 86 " 0.024 2.00e-02 2.50e+03 pdb=" CH2 TRP V 86 " 0.034 2.00e-02 2.50e+03 ... (remaining 15192 not shown) Histogram of nonbonded interaction distances: 1.94 - 2.53: 1089 2.53 - 3.13: 74736 3.13 - 3.72: 122710 3.72 - 4.31: 170504 4.31 - 4.90: 273598 Nonbonded interactions: 642637 Sorted by model distance: nonbonded pdb=" O PRO G 159 " pdb=" OG SER H 222 " model vdw 1.943 2.440 nonbonded pdb=" O PRO E 159 " pdb=" OG SER F 222 " model vdw 1.945 2.440 nonbonded pdb=" O PRO N 159 " pdb=" OG SER O 222 " model vdw 1.951 2.440 nonbonded pdb=" O PRO J 159 " pdb=" OG SER K 222 " model vdw 1.954 2.440 nonbonded pdb=" O PRO I 159 " pdb=" OG SER J 222 " model vdw 1.955 2.440 ... (remaining 642632 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' } ncs_group { reference = chain 'P' selection = chain 'Q' 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' selection = chain 'a' selection = chain 'b' selection = chain 'c' selection = chain 'd' } ncs_group { reference = chain 'e' selection = chain 'f' selection = chain 'g' selection = chain 'h' selection = chain 'i' selection = chain 'j' selection = chain 'k' selection = chain 'l' selection = chain 'm' selection = chain 'n' selection = chain 'o' selection = chain 'p' selection = chain 'q' selection = chain 'r' selection = chain 's' } 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: 0.650 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.070 Extract box with map and model: 6.220 Check model and map are aligned: 0.930 Set scattering table: 0.590 Process input model: 162.820 Find NCS groups from input model: 5.360 Set up NCS constraints: 1.380 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: 0.020 Load rotamer database and sin/cos tables:2.530 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 180.580 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7271 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 : 0.011 0.086 86145 Z= 0.723 Angle : 1.306 13.207 116910 Z= 0.790 Chirality : 0.073 0.345 14250 Planarity : 0.009 0.077 15195 Dihedral : 10.566 89.096 31740 Min Nonbonded Distance : 1.943 Molprobity Statistics. All-atom Clashscore : 35.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.87 % Favored : 90.13 % Rotamer: Outliers : 0.00 % Allowed : 5.62 % Favored : 94.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.43 (0.06), residues: 11115 helix: -2.07 (0.08), residues: 3300 sheet: -2.87 (0.09), residues: 2415 loop : -3.58 (0.06), residues: 5400 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.008 TRP U 86 HIS 0.029 0.007 HIS J 311 PHE 0.024 0.004 PHE M 607 TYR 0.042 0.005 TYR a 74 ARG 0.030 0.003 ARG U 56 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 22230 Ramachandran restraints generated. 11115 Oldfield, 0 Emsley, 11115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 22230 Ramachandran restraints generated. 11115 Oldfield, 0 Emsley, 11115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1839 residues out of total 9345 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 1839 time to evaluate : 7.753 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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 141 LEU cc_start: 0.9097 (pp) cc_final: 0.8896 (pp) REVERT: A 165 MET cc_start: 0.7697 (pmm) cc_final: 0.7210 (pmm) REVERT: A 359 ASN cc_start: 0.8840 (p0) cc_final: 0.7704 (t0) REVERT: A 415 PHE cc_start: 0.7035 (t80) cc_final: 0.6781 (t80) REVERT: B 165 MET cc_start: 0.8008 (pmm) cc_final: 0.7579 (pmm) REVERT: B 251 MET cc_start: 0.7767 (mpp) cc_final: 0.7516 (mtm) REVERT: B 326 MET cc_start: 0.6551 (mtp) cc_final: 0.6322 (mmt) REVERT: B 555 LYS cc_start: 0.7754 (pttt) cc_final: 0.7341 (pptt) REVERT: B 565 ILE cc_start: 0.8976 (mm) cc_final: 0.8599 (mm) REVERT: C 97 LYS cc_start: 0.8754 (pttt) cc_final: 0.8464 (mptt) REVERT: C 165 MET cc_start: 0.7910 (pmm) cc_final: 0.7707 (pmm) REVERT: C 251 MET cc_start: 0.7292 (mpp) cc_final: 0.7047 (mtm) REVERT: D 97 LYS cc_start: 0.8395 (pttt) cc_final: 0.8126 (mptt) REVERT: D 165 MET cc_start: 0.7139 (pmm) cc_final: 0.6708 (pmm) REVERT: D 502 GLN cc_start: 0.8814 (pm20) cc_final: 0.7927 (pm20) REVERT: D 555 LYS cc_start: 0.7943 (pttt) cc_final: 0.7438 (pptt) REVERT: E 320 THR cc_start: 0.7769 (p) cc_final: 0.7412 (p) REVERT: E 359 ASN cc_start: 0.8503 (p0) cc_final: 0.8036 (t0) REVERT: E 360 LEU cc_start: 0.8622 (tp) cc_final: 0.8403 (tp) REVERT: E 485 LYS cc_start: 0.8381 (pttt) cc_final: 0.8173 (pttm) REVERT: F 71 GLU cc_start: 0.8673 (mm-30) cc_final: 0.8349 (pm20) REVERT: F 100 ARG cc_start: 0.7305 (tpt90) cc_final: 0.7076 (mmm160) REVERT: F 359 ASN cc_start: 0.8688 (p0) cc_final: 0.7374 (t0) REVERT: F 415 PHE cc_start: 0.6514 (t80) cc_final: 0.6091 (m-80) REVERT: F 416 TYR cc_start: 0.6361 (m-80) cc_final: 0.5063 (t80) REVERT: F 629 LEU cc_start: 0.9081 (mt) cc_final: 0.8586 (pp) REVERT: G 100 ARG cc_start: 0.6855 (tpt90) cc_final: 0.6579 (mmm160) REVERT: G 280 GLU cc_start: 0.7589 (tp30) cc_final: 0.7354 (tp30) REVERT: G 416 TYR cc_start: 0.5394 (m-80) cc_final: 0.5105 (t80) REVERT: G 422 MET cc_start: 0.8404 (pmm) cc_final: 0.7989 (mtt) REVERT: H 91 MET cc_start: 0.6824 (tpt) cc_final: 0.6597 (mpp) REVERT: H 100 ARG cc_start: 0.6891 (tpt90) cc_final: 0.6352 (mmm160) REVERT: H 172 ILE cc_start: 0.7878 (mm) cc_final: 0.7673 (mm) REVERT: H 187 ASP cc_start: 0.6776 (m-30) cc_final: 0.6412 (m-30) REVERT: H 359 ASN cc_start: 0.8709 (p0) cc_final: 0.7985 (t0) REVERT: H 506 SER cc_start: 0.9043 (t) cc_final: 0.8791 (p) REVERT: H 564 VAL cc_start: 0.8753 (m) cc_final: 0.8461 (m) REVERT: I 67 MET cc_start: 0.8570 (mtt) cc_final: 0.8258 (tpt) REVERT: I 91 MET cc_start: 0.6930 (tpt) cc_final: 0.6269 (mpp) REVERT: I 165 MET cc_start: 0.8057 (pmm) cc_final: 0.7659 (pmm) REVERT: I 205 LYS cc_start: 0.7923 (tttt) cc_final: 0.7269 (tppp) REVERT: I 345 VAL cc_start: 0.9013 (t) cc_final: 0.8795 (p) REVERT: I 359 ASN cc_start: 0.8919 (p0) cc_final: 0.7845 (t0) REVERT: I 565 ILE cc_start: 0.9274 (mm) cc_final: 0.9046 (mm) REVERT: I 629 LEU cc_start: 0.7714 (mt) cc_final: 0.7316 (pp) REVERT: J 74 TYR cc_start: 0.8406 (t80) cc_final: 0.8155 (t80) REVERT: J 145 LEU cc_start: 0.9140 (tm) cc_final: 0.8710 (pp) REVERT: J 280 GLU cc_start: 0.7147 (tp30) cc_final: 0.6858 (tp30) REVERT: K 97 LYS cc_start: 0.8305 (pttt) cc_final: 0.8051 (mptt) REVERT: K 165 MET cc_start: 0.8270 (pmm) cc_final: 0.7879 (pmm) REVERT: K 545 LEU cc_start: 0.8927 (pp) cc_final: 0.8622 (pp) REVERT: L 67 MET cc_start: 0.8448 (mtt) cc_final: 0.8164 (tpt) REVERT: L 165 MET cc_start: 0.8182 (pmm) cc_final: 0.7791 (pmm) REVERT: L 202 GLU cc_start: 0.7281 (tp30) cc_final: 0.6912 (tp30) REVERT: L 359 ASN cc_start: 0.8746 (p0) cc_final: 0.8164 (t0) REVERT: L 629 LEU cc_start: 0.7740 (mt) cc_final: 0.7494 (pp) REVERT: M 252 ILE cc_start: 0.7846 (pp) cc_final: 0.7454 (pt) REVERT: M 359 ASN cc_start: 0.9072 (p0) cc_final: 0.8313 (t0) REVERT: M 422 MET cc_start: 0.8439 (pmm) cc_final: 0.8006 (pmm) REVERT: N 145 LEU cc_start: 0.9073 (tm) cc_final: 0.8774 (tt) REVERT: N 209 GLU cc_start: 0.7982 (tt0) cc_final: 0.7525 (tp30) REVERT: N 340 ARG cc_start: 0.7350 (mmp-170) cc_final: 0.7004 (mtm180) REVERT: O 67 MET cc_start: 0.8996 (mtt) cc_final: 0.8533 (tpt) REVERT: O 165 MET cc_start: 0.8164 (pmm) cc_final: 0.7899 (pmm) REVERT: O 280 GLU cc_start: 0.7211 (tp30) cc_final: 0.6976 (tp30) REVERT: O 371 MET cc_start: 0.8332 (ttm) cc_final: 0.8016 (tmm) REVERT: O 480 VAL cc_start: 0.9173 (t) cc_final: 0.8899 (p) REVERT: O 629 LEU cc_start: 0.7717 (mt) cc_final: 0.7507 (mt) REVERT: R 73 ILE cc_start: 0.0192 (mt) cc_final: -0.0049 (mm) REVERT: T 73 ILE cc_start: 0.1367 (mt) cc_final: 0.1124 (mm) REVERT: T 121 ARG cc_start: 0.3192 (ttm110) cc_final: 0.2843 (mmt-90) REVERT: U 60 ASN cc_start: 0.7568 (m-40) cc_final: 0.6928 (t0) REVERT: Y 127 ILE cc_start: 0.8182 (mt) cc_final: 0.7958 (mt) REVERT: d 93 THR cc_start: 0.6422 (m) cc_final: 0.6182 (t) REVERT: e 145 ILE cc_start: 0.6500 (mt) cc_final: 0.6234 (mt) REVERT: e 149 ARG cc_start: 0.6802 (ptt180) cc_final: 0.6594 (ptm160) REVERT: e 150 ILE cc_start: 0.7848 (mm) cc_final: 0.6796 (mp) REVERT: f 159 GLU cc_start: 0.2436 (mt-10) cc_final: 0.1828 (mt-10) REVERT: g 158 LYS cc_start: 0.6440 (mttm) cc_final: 0.6200 (mmmt) REVERT: g 159 GLU cc_start: 0.2496 (mt-10) cc_final: 0.1470 (mt-10) REVERT: h 121 GLU cc_start: 0.7122 (tt0) cc_final: 0.6911 (pp20) REVERT: h 149 ARG cc_start: 0.7278 (ptt180) cc_final: 0.6785 (ttp-110) REVERT: i 121 GLU cc_start: 0.7520 (tt0) cc_final: 0.6994 (tm-30) REVERT: i 150 ILE cc_start: 0.7624 (mm) cc_final: 0.7166 (mm) REVERT: i 158 LYS cc_start: 0.6559 (mttm) cc_final: 0.6249 (tptt) REVERT: j 150 ILE cc_start: 0.8116 (mm) cc_final: 0.7848 (mp) REVERT: j 158 LYS cc_start: 0.7121 (mttm) cc_final: 0.6695 (tptt) REVERT: k 149 ARG cc_start: 0.5465 (ptt180) cc_final: 0.4840 (ptm160) REVERT: k 150 ILE cc_start: 0.7891 (mm) cc_final: 0.7047 (mp) REVERT: l 150 ILE cc_start: 0.8426 (mm) cc_final: 0.8220 (mm) REVERT: l 158 LYS cc_start: 0.7909 (mttm) cc_final: 0.7545 (tptt) REVERT: o 121 GLU cc_start: 0.7769 (tt0) cc_final: 0.7262 (tm-30) REVERT: o 158 LYS cc_start: 0.6532 (mttm) cc_final: 0.6019 (tptt) REVERT: p 121 GLU cc_start: 0.7241 (tt0) cc_final: 0.6829 (tm-30) REVERT: p 158 LYS cc_start: 0.5498 (mttm) cc_final: 0.5112 (tptt) REVERT: s 149 ARG cc_start: 0.6553 (ptt180) cc_final: 0.6301 (ttp-110) outliers start: 0 outliers final: 0 residues processed: 1839 average time/residue: 0.8158 time to fit residues: 2495.1937 Evaluate side-chains 847 residues out of total 9345 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 847 time to evaluate : 7.288 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1110 random chunks: chunk 937 optimal weight: 10.0000 chunk 841 optimal weight: 2.9990 chunk 466 optimal weight: 8.9990 chunk 287 optimal weight: 7.9990 chunk 567 optimal weight: 0.9980 chunk 449 optimal weight: 6.9990 chunk 870 optimal weight: 7.9990 chunk 336 optimal weight: 4.9990 chunk 529 optimal weight: 9.9990 chunk 647 optimal weight: 10.0000 chunk 1008 optimal weight: 9.9990 overall best weight: 4.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 93 ASN A 161 ASN A 254 GLN ** A 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 262 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 373 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 419 ASN A 446 ASN ** A 448 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 489 GLN B 47 ASN B 161 ASN B 254 GLN B 353 GLN B 446 ASN B 448 GLN B 611 GLN C 161 ASN C 254 GLN C 315 ASN ** C 373 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 446 ASN C 448 GLN C 603 GLN D 93 ASN D 148 ASN D 161 ASN D 254 GLN ** D 313 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 446 ASN D 448 GLN D 523 ASN D 603 GLN D 626 ASN E 146 ASN E 148 ASN E 161 ASN E 254 GLN ** E 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 262 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 373 GLN E 446 ASN E 489 GLN ** E 603 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 626 ASN E 630 HIS F 47 ASN F 161 ASN F 254 GLN ** F 313 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 446 ASN F 448 GLN F 489 GLN G 47 ASN G 148 ASN G 161 ASN G 254 GLN ** G 373 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 446 ASN G 448 GLN G 489 GLN H 47 ASN H 161 ASN H 254 GLN ** H 373 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 446 ASN H 448 GLN H 603 GLN ** I 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 161 ASN I 254 GLN I 448 GLN I 523 ASN J 40 ASN J 47 ASN ** J 146 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 161 ASN J 254 GLN ** J 446 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 448 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 603 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 47 ASN K 161 ASN K 184 ASN K 254 GLN ** K 363 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 373 GLN K 446 ASN K 448 GLN K 489 GLN ** K 611 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 40 ASN L 47 ASN ** L 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 161 ASN L 254 GLN ** L 363 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 373 GLN L 446 ASN ** L 448 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 161 ASN M 184 ASN M 254 GLN M 353 GLN ** M 373 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 446 ASN M 448 GLN N 47 ASN ** N 156 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 161 ASN N 254 GLN N 373 GLN N 446 ASN N 448 GLN N 489 GLN ** N 603 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 148 ASN ** O 161 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 254 GLN ** O 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 262 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 353 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 373 GLN O 446 ASN O 448 GLN O 489 GLN O 523 ASN ** O 603 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 626 ASN O 630 HIS R 97 ASN ** R 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 118 GLN U 120 ASN V 44 GLN W 44 GLN ** Z 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 107 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 122 GLN ** c 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 107 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 106 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7544 moved from start: 0.4207 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.077 86145 Z= 0.361 Angle : 0.774 9.555 116910 Z= 0.401 Chirality : 0.050 0.220 14250 Planarity : 0.006 0.082 15195 Dihedral : 5.491 23.626 12030 Min Nonbonded Distance : 2.053 Molprobity Statistics. All-atom Clashscore : 19.17 Ramachandran Plot: Outliers : 0.04 % Allowed : 7.85 % Favored : 92.12 % Rotamer: Outliers : 0.04 % Allowed : 4.55 % Favored : 95.41 % 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: -3.19 (0.07), residues: 11115 helix: -0.42 (0.08), residues: 3450 sheet: -2.44 (0.10), residues: 2130 loop : -3.18 (0.06), residues: 5535 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP T 86 HIS 0.008 0.002 HIS B 156 PHE 0.025 0.002 PHE e 164 TYR 0.030 0.002 TYR I 157 ARG 0.026 0.001 ARG d 64 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 22230 Ramachandran restraints generated. 11115 Oldfield, 0 Emsley, 11115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 22230 Ramachandran restraints generated. 11115 Oldfield, 0 Emsley, 11115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1090 residues out of total 9345 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 1086 time to evaluate : 7.302 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: A 55 SER cc_start: 0.8720 (m) cc_final: 0.8164 (p) REVERT: A 91 MET cc_start: 0.5894 (mpp) cc_final: 0.5316 (mpp) REVERT: A 100 ARG cc_start: 0.6402 (tpt90) cc_final: 0.5516 (mmm160) REVERT: A 143 ARG cc_start: 0.8574 (ttp-110) cc_final: 0.7902 (ttm110) REVERT: A 165 MET cc_start: 0.7642 (pmm) cc_final: 0.7310 (pmm) REVERT: A 205 LYS cc_start: 0.8046 (ptmt) cc_final: 0.7713 (ptpp) REVERT: A 371 MET cc_start: 0.7669 (tmm) cc_final: 0.7172 (tmm) REVERT: A 447 MET cc_start: 0.8110 (mpp) cc_final: 0.7727 (mpp) REVERT: B 351 GLU cc_start: 0.6427 (pp20) cc_final: 0.5427 (pp20) REVERT: B 555 LYS cc_start: 0.7852 (pttt) cc_final: 0.7294 (pttp) REVERT: C 67 MET cc_start: 0.4451 (tpt) cc_final: 0.4226 (tpt) REVERT: C 147 ASP cc_start: 0.6589 (t0) cc_final: 0.6174 (t0) REVERT: C 326 MET cc_start: 0.7399 (ttm) cc_final: 0.7172 (ttm) REVERT: C 422 MET cc_start: 0.8709 (pmm) cc_final: 0.8398 (pmm) REVERT: C 518 LEU cc_start: 0.7658 (mp) cc_final: 0.7444 (mp) REVERT: C 582 MET cc_start: 0.7196 (mmm) cc_final: 0.6952 (mmm) REVERT: C 605 THR cc_start: 0.8652 (m) cc_final: 0.8389 (p) REVERT: D 67 MET cc_start: 0.1343 (tpt) cc_final: 0.1118 (tpt) REVERT: D 97 LYS cc_start: 0.8810 (pttt) cc_final: 0.8423 (ptpt) REVERT: D 141 LEU cc_start: 0.8930 (pp) cc_final: 0.8488 (pp) REVERT: D 148 ASN cc_start: 0.6893 (m110) cc_final: 0.6477 (m-40) REVERT: D 422 MET cc_start: 0.7626 (pmm) cc_final: 0.7035 (pmm) REVERT: E 100 ARG cc_start: 0.7071 (tpt90) cc_final: 0.6736 (mmm160) REVERT: E 172 ILE cc_start: 0.8271 (mm) cc_final: 0.8006 (mm) REVERT: E 326 MET cc_start: 0.7650 (pmm) cc_final: 0.7119 (pmm) REVERT: E 359 ASN cc_start: 0.8591 (p0) cc_final: 0.7863 (t0) REVERT: E 360 LEU cc_start: 0.8830 (tp) cc_final: 0.8495 (mt) REVERT: E 460 LEU cc_start: 0.8196 (mp) cc_final: 0.7765 (mp) REVERT: F 100 ARG cc_start: 0.7469 (tpt90) cc_final: 0.6433 (mmm160) REVERT: F 156 HIS cc_start: 0.5670 (m-70) cc_final: 0.5318 (m-70) REVERT: F 202 GLU cc_start: 0.7115 (tp30) cc_final: 0.6514 (tp30) REVERT: F 206 LEU cc_start: 0.8563 (tt) cc_final: 0.8278 (tp) REVERT: F 422 MET cc_start: 0.8512 (pmm) cc_final: 0.8292 (pmm) REVERT: G 100 ARG cc_start: 0.6919 (tpt90) cc_final: 0.6664 (mmm160) REVERT: G 144 GLN cc_start: 0.8733 (mm-40) cc_final: 0.8417 (mt0) REVERT: G 389 ASN cc_start: 0.8769 (m-40) cc_final: 0.8495 (p0) REVERT: G 416 TYR cc_start: 0.4971 (m-80) cc_final: 0.4430 (t80) REVERT: G 422 MET cc_start: 0.8235 (pmm) cc_final: 0.7905 (pmm) REVERT: H 172 ILE cc_start: 0.7781 (mm) cc_final: 0.7512 (mm) REVERT: H 187 ASP cc_start: 0.6458 (m-30) cc_final: 0.6022 (m-30) REVERT: H 359 ASN cc_start: 0.8808 (p0) cc_final: 0.8457 (t0) REVERT: H 371 MET cc_start: 0.7033 (tmm) cc_final: 0.6742 (tmm) REVERT: H 389 ASN cc_start: 0.8363 (m-40) cc_final: 0.8038 (p0) REVERT: H 506 SER cc_start: 0.8720 (t) cc_final: 0.8370 (m) REVERT: I 67 MET cc_start: 0.8407 (mtt) cc_final: 0.8017 (tpt) REVERT: I 74 TYR cc_start: 0.8802 (t80) cc_final: 0.8591 (t80) REVERT: I 91 MET cc_start: 0.6912 (tpt) cc_final: 0.6375 (mpp) REVERT: I 205 LYS cc_start: 0.8023 (tttt) cc_final: 0.7523 (mmtp) REVERT: I 223 MET cc_start: 0.6664 (mpp) cc_final: 0.6052 (mmt) REVERT: I 326 MET cc_start: 0.7674 (pmm) cc_final: 0.7033 (pmm) REVERT: I 359 ASN cc_start: 0.8718 (p0) cc_final: 0.7918 (t0) REVERT: I 415 PHE cc_start: 0.7063 (t80) cc_final: 0.6704 (t80) REVERT: I 459 VAL cc_start: 0.9439 (t) cc_final: 0.9214 (m) REVERT: J 97 LYS cc_start: 0.8600 (pttt) cc_final: 0.8394 (ptpp) REVERT: J 147 ASP cc_start: 0.7543 (t0) cc_final: 0.7305 (t0) REVERT: J 359 ASN cc_start: 0.8892 (p0) cc_final: 0.8241 (t0) REVERT: J 371 MET cc_start: 0.7508 (ttp) cc_final: 0.7199 (tmm) REVERT: J 447 MET cc_start: 0.7569 (ttp) cc_final: 0.7276 (ttp) REVERT: K 197 TRP cc_start: 0.7264 (p90) cc_final: 0.6627 (p90) REVERT: K 422 MET cc_start: 0.8117 (pmm) cc_final: 0.7715 (pmm) REVERT: K 518 LEU cc_start: 0.7389 (mp) cc_final: 0.7177 (mp) REVERT: L 67 MET cc_start: 0.8657 (mtt) cc_final: 0.8424 (tpt) REVERT: L 205 LYS cc_start: 0.8914 (ttpt) cc_final: 0.8465 (ttpt) REVERT: L 326 MET cc_start: 0.7765 (pmm) cc_final: 0.7184 (pmm) REVERT: L 460 LEU cc_start: 0.8510 (mp) cc_final: 0.8171 (mp) REVERT: M 359 ASN cc_start: 0.8861 (p0) cc_final: 0.8364 (t0) REVERT: M 422 MET cc_start: 0.8663 (pmm) cc_final: 0.8378 (pmm) REVERT: N 143 ARG cc_start: 0.7616 (mtm-85) cc_final: 0.7046 (tpt170) REVERT: N 202 GLU cc_start: 0.7183 (tp30) cc_final: 0.6954 (tp30) REVERT: N 209 GLU cc_start: 0.8238 (tt0) cc_final: 0.7648 (tp30) REVERT: N 422 MET cc_start: 0.8370 (pmm) cc_final: 0.7858 (pmm) REVERT: N 582 MET cc_start: 0.7131 (mmm) cc_final: 0.6568 (tpp) REVERT: O 326 MET cc_start: 0.8473 (pmm) cc_final: 0.7775 (pmm) REVERT: O 371 MET cc_start: 0.7903 (ttm) cc_final: 0.7472 (tmm) REVERT: O 447 MET cc_start: 0.8391 (mpp) cc_final: 0.8011 (mpp) REVERT: O 558 LEU cc_start: 0.8913 (tp) cc_final: 0.8656 (tp) REVERT: P 88 ASN cc_start: 0.4637 (m-40) cc_final: 0.3908 (t0) REVERT: Q 88 ASN cc_start: 0.5132 (m-40) cc_final: 0.4531 (t0) REVERT: S 88 ASN cc_start: 0.4411 (m-40) cc_final: 0.3786 (t0) REVERT: T 73 ILE cc_start: 0.1715 (mt) cc_final: 0.1412 (mm) REVERT: T 121 ARG cc_start: 0.3762 (ttm110) cc_final: 0.3486 (mmt-90) REVERT: U 88 ASN cc_start: 0.4630 (m-40) cc_final: 0.4395 (m-40) REVERT: W 88 ASN cc_start: 0.4602 (m-40) cc_final: 0.3798 (t0) REVERT: X 88 ASN cc_start: 0.4693 (m-40) cc_final: 0.4124 (t0) REVERT: Y 88 ASN cc_start: 0.5035 (m-40) cc_final: 0.4611 (t0) REVERT: a 73 ILE cc_start: 0.0659 (mt) cc_final: 0.0298 (mm) REVERT: b 73 ILE cc_start: 0.1893 (mt) cc_final: 0.1637 (mm) REVERT: c 88 ASN cc_start: 0.4123 (m-40) cc_final: 0.3351 (t0) REVERT: d 88 ASN cc_start: 0.5213 (m-40) cc_final: 0.4526 (t0) REVERT: e 149 ARG cc_start: 0.7272 (ptt180) cc_final: 0.6947 (tmm-80) REVERT: e 150 ILE cc_start: 0.8092 (mm) cc_final: 0.7833 (mt) REVERT: g 150 ILE cc_start: 0.8529 (mp) cc_final: 0.8173 (mp) REVERT: h 121 GLU cc_start: 0.6957 (tt0) cc_final: 0.6432 (pp20) REVERT: h 149 ARG cc_start: 0.6637 (ptt180) cc_final: 0.6180 (tmm-80) REVERT: h 150 ILE cc_start: 0.8338 (mm) cc_final: 0.7879 (mm) REVERT: i 121 GLU cc_start: 0.7467 (tt0) cc_final: 0.6713 (tm-30) REVERT: i 150 ILE cc_start: 0.7712 (mm) cc_final: 0.7262 (mm) REVERT: j 150 ILE cc_start: 0.8539 (mm) cc_final: 0.8156 (mp) REVERT: k 149 ARG cc_start: 0.5148 (ptt180) cc_final: 0.4896 (tmm-80) REVERT: k 150 ILE cc_start: 0.8006 (mm) cc_final: 0.7736 (mm) REVERT: l 103 ARG cc_start: 0.5500 (ttp-170) cc_final: 0.4561 (ptm-80) REVERT: l 150 ILE cc_start: 0.8390 (mm) cc_final: 0.8090 (mm) REVERT: p 107 LEU cc_start: 0.4859 (tt) cc_final: 0.4292 (mt) REVERT: p 121 GLU cc_start: 0.6926 (tt0) cc_final: 0.6426 (tm-30) REVERT: s 149 ARG cc_start: 0.6492 (ptt180) cc_final: 0.5723 (tmm-80) outliers start: 4 outliers final: 0 residues processed: 1089 average time/residue: 0.8089 time to fit residues: 1532.9595 Evaluate side-chains 726 residues out of total 9345 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 726 time to evaluate : 7.186 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1110 random chunks: chunk 560 optimal weight: 6.9990 chunk 312 optimal weight: 0.6980 chunk 838 optimal weight: 20.0000 chunk 686 optimal weight: 9.9990 chunk 278 optimal weight: 4.9990 chunk 1009 optimal weight: 6.9990 chunk 1090 optimal weight: 0.0570 chunk 899 optimal weight: 8.9990 chunk 1001 optimal weight: 5.9990 chunk 344 optimal weight: 40.0000 chunk 810 optimal weight: 6.9990 overall best weight: 3.7504 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 47 ASN A 93 ASN ** A 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 262 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 448 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 489 GLN A 630 HIS ** B 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 373 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 523 ASN C 146 ASN C 603 GLN D 47 ASN D 156 HIS ** D 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 262 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 313 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 419 ASN D 603 GLN ** D 611 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 47 ASN E 419 ASN E 489 GLN ** E 603 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 313 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 315 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 489 GLN F 523 ASN ** F 603 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 353 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 373 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 489 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 630 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 353 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 523 ASN ** I 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 315 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 419 ASN J 446 ASN ** J 448 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 603 GLN ** K 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 156 HIS K 315 ASN ** K 363 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 489 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 448 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 523 ASN L 603 GLN L 630 HIS ** M 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 373 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 419 ASN M 523 ASN ** N 156 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 184 ASN N 315 ASN N 419 ASN O 47 ASN O 161 ASN O 184 ASN O 315 ASN ** O 373 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 419 ASN O 489 GLN O 603 GLN ** P 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 44 GLN ** V 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 63 ASN ** Z 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 97 ASN b 104 GLN ** c 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 107 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 155 GLN ** h 126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** i 155 GLN ** j 126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** j 155 GLN k 155 GLN l 155 GLN ** m 126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** n 155 GLN ** q 126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** s 155 GLN Total number of N/Q/H flips: 48 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7579 moved from start: 0.5121 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 86145 Z= 0.286 Angle : 0.650 8.765 116910 Z= 0.335 Chirality : 0.046 0.211 14250 Planarity : 0.005 0.077 15195 Dihedral : 5.005 19.964 12030 Min Nonbonded Distance : 2.095 Molprobity Statistics. All-atom Clashscore : 17.85 Ramachandran Plot: Outliers : 0.03 % Allowed : 7.71 % Favored : 92.26 % Rotamer: Outliers : 0.06 % Allowed : 4.69 % Favored : 95.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.60 (0.07), residues: 11115 helix: 0.36 (0.09), residues: 3555 sheet: -2.11 (0.10), residues: 2145 loop : -3.10 (0.07), residues: 5415 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP N 364 HIS 0.012 0.001 HIS L 156 PHE 0.023 0.002 PHE i 164 TYR 0.022 0.002 TYR K 65 ARG 0.014 0.001 ARG I 143 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 22230 Ramachandran restraints generated. 11115 Oldfield, 0 Emsley, 11115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 22230 Ramachandran restraints generated. 11115 Oldfield, 0 Emsley, 11115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 939 residues out of total 9345 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 933 time to evaluate : 7.308 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: A 165 MET cc_start: 0.7877 (pmm) cc_final: 0.7538 (pmm) REVERT: A 205 LYS cc_start: 0.8089 (ptmt) cc_final: 0.7388 (ptpp) REVERT: A 359 ASN cc_start: 0.8625 (p0) cc_final: 0.7941 (t0) REVERT: A 447 MET cc_start: 0.8023 (mpp) cc_final: 0.7611 (mpp) REVERT: B 555 LYS cc_start: 0.7881 (pttt) cc_final: 0.7265 (pttp) REVERT: C 145 LEU cc_start: 0.9031 (pp) cc_final: 0.8821 (pp) REVERT: C 146 ASN cc_start: 0.8653 (t0) cc_final: 0.8149 (p0) REVERT: C 422 MET cc_start: 0.8579 (pmm) cc_final: 0.8327 (pmm) REVERT: C 447 MET cc_start: 0.7509 (mpp) cc_final: 0.6960 (mpp) REVERT: C 605 THR cc_start: 0.8591 (m) cc_final: 0.8347 (p) REVERT: D 141 LEU cc_start: 0.9003 (pp) cc_final: 0.8321 (pp) REVERT: D 144 GLN cc_start: 0.8902 (mt0) cc_final: 0.8216 (mp10) REVERT: D 422 MET cc_start: 0.8117 (pmm) cc_final: 0.7752 (pmm) REVERT: D 509 ASP cc_start: 0.8053 (m-30) cc_final: 0.7480 (t0) REVERT: E 100 ARG cc_start: 0.7130 (tpt90) cc_final: 0.6509 (mmm160) REVERT: E 172 ILE cc_start: 0.8032 (mm) cc_final: 0.7798 (mm) REVERT: E 326 MET cc_start: 0.7576 (pmm) cc_final: 0.6714 (pmm) REVERT: E 359 ASN cc_start: 0.8412 (p0) cc_final: 0.7679 (t0) REVERT: E 518 LEU cc_start: 0.7804 (mt) cc_final: 0.7586 (mt) REVERT: F 156 HIS cc_start: 0.5367 (m-70) cc_final: 0.4971 (m-70) REVERT: F 202 GLU cc_start: 0.7047 (tp30) cc_final: 0.6685 (tp30) REVERT: F 251 MET cc_start: 0.7154 (mtt) cc_final: 0.6951 (mtp) REVERT: G 100 ARG cc_start: 0.7168 (tpt90) cc_final: 0.6872 (mmm160) REVERT: G 144 GLN cc_start: 0.8764 (mm-40) cc_final: 0.8411 (mt0) REVERT: G 389 ASN cc_start: 0.8783 (m-40) cc_final: 0.8521 (p0) REVERT: G 422 MET cc_start: 0.7876 (pmm) cc_final: 0.7597 (pmm) REVERT: H 172 ILE cc_start: 0.7790 (mm) cc_final: 0.7574 (mm) REVERT: H 187 ASP cc_start: 0.6080 (m-30) cc_final: 0.5630 (m-30) REVERT: H 359 ASN cc_start: 0.8941 (p0) cc_final: 0.8448 (t0) REVERT: H 371 MET cc_start: 0.6944 (tmm) cc_final: 0.6447 (tmm) REVERT: H 389 ASN cc_start: 0.9013 (m-40) cc_final: 0.8491 (p0) REVERT: H 506 SER cc_start: 0.8886 (t) cc_final: 0.8316 (m) REVERT: I 39 ILE cc_start: 0.9429 (mm) cc_final: 0.9223 (pt) REVERT: I 74 TYR cc_start: 0.8789 (t80) cc_final: 0.8505 (t80) REVERT: I 174 ARG cc_start: 0.7624 (ptt180) cc_final: 0.6612 (ptm160) REVERT: I 205 LYS cc_start: 0.7865 (tttt) cc_final: 0.7548 (mmtp) REVERT: I 206 LEU cc_start: 0.8560 (tt) cc_final: 0.8301 (tp) REVERT: I 359 ASN cc_start: 0.8599 (p0) cc_final: 0.7634 (t0) REVERT: J 67 MET cc_start: 0.2766 (tpt) cc_final: 0.2312 (tpt) REVERT: J 206 LEU cc_start: 0.8969 (tt) cc_final: 0.8745 (tt) REVERT: J 359 ASN cc_start: 0.8709 (p0) cc_final: 0.8119 (t0) REVERT: J 371 MET cc_start: 0.7333 (ttp) cc_final: 0.6954 (tmm) REVERT: J 603 GLN cc_start: 0.8092 (OUTLIER) cc_final: 0.7832 (tm-30) REVERT: K 91 MET cc_start: 0.6811 (mpp) cc_final: 0.6405 (mpp) REVERT: K 223 MET cc_start: 0.7114 (mpp) cc_final: 0.6397 (mpp) REVERT: K 349 ILE cc_start: 0.9443 (mp) cc_final: 0.8933 (tp) REVERT: L 67 MET cc_start: 0.8614 (mtt) cc_final: 0.8348 (tpp) REVERT: L 156 HIS cc_start: 0.5305 (m-70) cc_final: 0.5087 (m90) REVERT: L 165 MET cc_start: 0.8211 (pmm) cc_final: 0.7897 (pmm) REVERT: L 326 MET cc_start: 0.7927 (pmm) cc_final: 0.7198 (pmm) REVERT: L 371 MET cc_start: 0.6957 (tmm) cc_final: 0.6576 (tmm) REVERT: L 509 ASP cc_start: 0.8503 (m-30) cc_final: 0.7677 (t70) REVERT: L 521 THR cc_start: 0.8787 (p) cc_final: 0.8533 (p) REVERT: M 39 ILE cc_start: 0.9318 (mm) cc_final: 0.9094 (pt) REVERT: M 144 GLN cc_start: 0.8267 (tm-30) cc_final: 0.7873 (pp30) REVERT: M 205 LYS cc_start: 0.8883 (mttt) cc_final: 0.8621 (mmtp) REVERT: M 359 ASN cc_start: 0.8647 (p0) cc_final: 0.8373 (t0) REVERT: N 202 GLU cc_start: 0.6882 (tp30) cc_final: 0.6526 (tp30) REVERT: N 251 MET cc_start: 0.7310 (ptp) cc_final: 0.7065 (ptp) REVERT: N 422 MET cc_start: 0.8543 (pmm) cc_final: 0.7965 (pmm) REVERT: O 143 ARG cc_start: 0.7642 (tpt170) cc_final: 0.7009 (tpt170) REVERT: O 147 ASP cc_start: 0.7908 (t0) cc_final: 0.7640 (t0) REVERT: O 326 MET cc_start: 0.8298 (pmm) cc_final: 0.8064 (pmm) REVERT: O 371 MET cc_start: 0.8480 (ttm) cc_final: 0.7625 (tmm) REVERT: O 447 MET cc_start: 0.8418 (mpp) cc_final: 0.8140 (mpp) REVERT: O 603 GLN cc_start: 0.8618 (OUTLIER) cc_final: 0.8208 (tm-30) REVERT: P 88 ASN cc_start: 0.4258 (m-40) cc_final: 0.3668 (t0) REVERT: Q 88 ASN cc_start: 0.5149 (m-40) cc_final: 0.4675 (t0) REVERT: T 73 ILE cc_start: 0.1513 (mt) cc_final: 0.1109 (mm) REVERT: T 121 ARG cc_start: 0.3867 (ttm110) cc_final: 0.3509 (mmt-90) REVERT: U 75 ARG cc_start: 0.3222 (mmm160) cc_final: 0.2445 (ppt170) REVERT: U 88 ASN cc_start: 0.4790 (m-40) cc_final: 0.4544 (m-40) REVERT: V 45 LEU cc_start: 0.7478 (tp) cc_final: 0.7133 (mm) REVERT: W 88 ASN cc_start: 0.4592 (m-40) cc_final: 0.3783 (t0) REVERT: X 88 ASN cc_start: 0.4767 (m-40) cc_final: 0.4301 (t0) REVERT: Y 88 ASN cc_start: 0.4962 (m-40) cc_final: 0.4570 (t0) REVERT: c 88 ASN cc_start: 0.3201 (m-40) cc_final: 0.2475 (t0) REVERT: d 88 ASN cc_start: 0.4792 (m-40) cc_final: 0.4274 (t0) REVERT: h 121 GLU cc_start: 0.7078 (tt0) cc_final: 0.6556 (pp20) REVERT: i 121 GLU cc_start: 0.7528 (tt0) cc_final: 0.6812 (tm-30) REVERT: i 150 ILE cc_start: 0.7409 (mm) cc_final: 0.7103 (mt) REVERT: i 155 GLN cc_start: 0.8331 (OUTLIER) cc_final: 0.8042 (pp30) REVERT: k 103 ARG cc_start: 0.5799 (ptp90) cc_final: 0.5411 (ptp90) REVERT: k 120 ILE cc_start: 0.4533 (pt) cc_final: 0.4286 (pt) REVERT: k 149 ARG cc_start: 0.5295 (ptt180) cc_final: 0.5039 (tmm-80) REVERT: m 120 ILE cc_start: 0.5759 (pt) cc_final: 0.5398 (pt) REVERT: r 120 ILE cc_start: 0.5373 (pt) cc_final: 0.5093 (pt) REVERT: s 149 ARG cc_start: 0.6103 (ptt180) cc_final: 0.5475 (tmm-80) REVERT: s 150 ILE cc_start: 0.7967 (mm) cc_final: 0.7612 (mt) outliers start: 6 outliers final: 0 residues processed: 938 average time/residue: 0.7279 time to fit residues: 1195.4294 Evaluate side-chains 702 residues out of total 9345 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 699 time to evaluate : 7.272 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1110 random chunks: chunk 997 optimal weight: 7.9990 chunk 759 optimal weight: 0.9980 chunk 524 optimal weight: 5.9990 chunk 111 optimal weight: 5.9990 chunk 481 optimal weight: 10.0000 chunk 678 optimal weight: 5.9990 chunk 1013 optimal weight: 8.9990 chunk 1072 optimal weight: 1.9990 chunk 529 optimal weight: 10.0000 chunk 960 optimal weight: 6.9990 chunk 289 optimal weight: 2.9990 overall best weight: 3.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 93 ASN ** A 448 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 489 GLN ** B 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 373 GLN B 419 ASN ** B 626 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 47 ASN ** C 156 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 315 ASN C 603 GLN ** D 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 148 ASN ** D 313 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 448 GLN D 603 GLN ** D 611 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 626 ASN ** E 262 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 313 GLN ** E 603 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 313 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 315 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 353 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 373 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 419 ASN ** G 489 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 630 HIS ** H 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 156 HIS H 161 ASN ** H 353 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 373 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 47 ASN I 419 ASN I 448 GLN I 630 HIS J 446 ASN ** J 448 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 156 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 258 GLN K 315 ASN K 363 GLN K 419 ASN ** L 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 315 ASN ** L 363 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 448 GLN L 603 GLN ** M 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 47 ASN ** M 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 373 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 40 ASN ** N 156 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 373 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 489 GLN ** O 626 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 122 GLN Q 97 ASN Q 122 GLN ** R 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 107 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 115 GLN T 122 GLN ** U 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 107 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 115 GLN ** V 120 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 122 GLN Y 122 GLN ** Z 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 122 GLN ** c 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 107 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 107 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** h 155 GLN ** i 126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** l 155 GLN ** m 126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** n 155 GLN p 155 GLN ** q 126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 44 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7614 moved from start: 0.5816 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 86145 Z= 0.272 Angle : 0.634 10.069 116910 Z= 0.324 Chirality : 0.046 0.298 14250 Planarity : 0.005 0.069 15195 Dihedral : 4.886 20.295 12030 Min Nonbonded Distance : 2.084 Molprobity Statistics. All-atom Clashscore : 17.53 Ramachandran Plot: Outliers : 0.01 % Allowed : 8.57 % Favored : 91.43 % Rotamer: Outliers : 0.00 % Allowed : 5.23 % Favored : 94.77 % 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: -2.26 (0.07), residues: 11115 helix: 0.78 (0.09), residues: 3525 sheet: -2.13 (0.11), residues: 2040 loop : -2.89 (0.07), residues: 5550 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.001 TRP J 197 HIS 0.013 0.001 HIS A 156 PHE 0.026 0.002 PHE N 584 TYR 0.027 0.002 TYR B 604 ARG 0.012 0.001 ARG H 143 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 22230 Ramachandran restraints generated. 11115 Oldfield, 0 Emsley, 11115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 22230 Ramachandran restraints generated. 11115 Oldfield, 0 Emsley, 11115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 874 residues out of total 9345 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 874 time to evaluate : 7.306 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: A 165 MET cc_start: 0.7722 (pmm) cc_final: 0.7444 (pmm) REVERT: A 447 MET cc_start: 0.8086 (mpp) cc_final: 0.7468 (mpp) REVERT: B 555 LYS cc_start: 0.7810 (pttt) cc_final: 0.7303 (pttp) REVERT: C 137 ASP cc_start: 0.7990 (p0) cc_final: 0.7631 (p0) REVERT: C 145 LEU cc_start: 0.9013 (pp) cc_final: 0.8804 (pp) REVERT: C 422 MET cc_start: 0.8584 (pmm) cc_final: 0.8339 (pmm) REVERT: C 447 MET cc_start: 0.7741 (mpp) cc_final: 0.7178 (mpp) REVERT: D 91 MET cc_start: 0.5814 (mpp) cc_final: 0.5608 (mpp) REVERT: D 144 GLN cc_start: 0.8611 (mt0) cc_final: 0.8072 (mt0) REVERT: D 422 MET cc_start: 0.8073 (pmm) cc_final: 0.7832 (pmm) REVERT: D 509 ASP cc_start: 0.7876 (m-30) cc_final: 0.7326 (t0) REVERT: E 100 ARG cc_start: 0.7140 (tpt90) cc_final: 0.6534 (mmm160) REVERT: E 326 MET cc_start: 0.7591 (pmm) cc_final: 0.6998 (pmm) REVERT: E 359 ASN cc_start: 0.8577 (p0) cc_final: 0.7716 (t0) REVERT: E 360 LEU cc_start: 0.7946 (mt) cc_final: 0.7641 (mt) REVERT: F 100 ARG cc_start: 0.7550 (tpt90) cc_final: 0.6604 (mmm160) REVERT: G 100 ARG cc_start: 0.7241 (tpt90) cc_final: 0.6870 (mmm160) REVERT: G 144 GLN cc_start: 0.8769 (mm-40) cc_final: 0.8390 (mt0) REVERT: G 389 ASN cc_start: 0.8873 (m-40) cc_final: 0.8544 (p0) REVERT: H 172 ILE cc_start: 0.7879 (mm) cc_final: 0.7659 (mm) REVERT: H 187 ASP cc_start: 0.6948 (m-30) cc_final: 0.6503 (m-30) REVERT: H 389 ASN cc_start: 0.8759 (m-40) cc_final: 0.8438 (p0) REVERT: H 416 TYR cc_start: 0.5411 (m-80) cc_final: 0.4274 (t80) REVERT: H 506 SER cc_start: 0.8897 (t) cc_final: 0.8381 (m) REVERT: I 39 ILE cc_start: 0.9448 (mm) cc_final: 0.9245 (pt) REVERT: I 74 TYR cc_start: 0.8823 (t80) cc_final: 0.8619 (t80) REVERT: I 105 LYS cc_start: 0.8062 (ptmm) cc_final: 0.7810 (ptmm) REVERT: I 156 HIS cc_start: 0.5599 (m-70) cc_final: 0.5372 (m90) REVERT: I 174 ARG cc_start: 0.7134 (ptt180) cc_final: 0.6273 (ptm160) REVERT: I 205 LYS cc_start: 0.7858 (tttt) cc_final: 0.7637 (mmtp) REVERT: I 256 ASP cc_start: 0.7129 (p0) cc_final: 0.6900 (p0) REVERT: I 326 MET cc_start: 0.8285 (pmm) cc_final: 0.8059 (pmm) REVERT: I 359 ASN cc_start: 0.8631 (p0) cc_final: 0.7637 (t0) REVERT: I 484 LEU cc_start: 0.9006 (tp) cc_final: 0.8736 (tp) REVERT: J 67 MET cc_start: 0.2790 (tpt) cc_final: 0.2286 (tpt) REVERT: J 371 MET cc_start: 0.7813 (ttp) cc_final: 0.6953 (tmm) REVERT: J 422 MET cc_start: 0.8856 (pmm) cc_final: 0.8650 (pmm) REVERT: K 223 MET cc_start: 0.7091 (mpp) cc_final: 0.6222 (mpp) REVERT: K 509 ASP cc_start: 0.8294 (m-30) cc_final: 0.7723 (t0) REVERT: L 67 MET cc_start: 0.8476 (mtt) cc_final: 0.7938 (tpp) REVERT: L 165 MET cc_start: 0.8223 (pmm) cc_final: 0.7946 (pmm) REVERT: L 256 ASP cc_start: 0.7990 (t0) cc_final: 0.7690 (t0) REVERT: L 326 MET cc_start: 0.8057 (pmm) cc_final: 0.7170 (pmm) REVERT: L 330 GLU cc_start: 0.8963 (mp0) cc_final: 0.8718 (mp0) REVERT: L 509 ASP cc_start: 0.8559 (m-30) cc_final: 0.7817 (t70) REVERT: L 521 THR cc_start: 0.8989 (p) cc_final: 0.8678 (p) REVERT: M 39 ILE cc_start: 0.9346 (mm) cc_final: 0.9132 (pt) REVERT: M 359 ASN cc_start: 0.8670 (p0) cc_final: 0.8375 (t0) REVERT: M 460 LEU cc_start: 0.9022 (tt) cc_final: 0.8471 (tt) REVERT: N 371 MET cc_start: 0.7965 (tmm) cc_final: 0.7671 (tmm) REVERT: O 143 ARG cc_start: 0.7842 (tpt170) cc_final: 0.7080 (tpt170) REVERT: O 147 ASP cc_start: 0.7743 (t0) cc_final: 0.7540 (t0) REVERT: O 326 MET cc_start: 0.8702 (pmm) cc_final: 0.8475 (pmm) REVERT: P 73 ILE cc_start: 0.1309 (mt) cc_final: 0.1064 (mm) REVERT: R 127 ILE cc_start: 0.8249 (mt) cc_final: 0.7999 (mt) REVERT: T 73 ILE cc_start: 0.1733 (mt) cc_final: 0.1441 (mm) REVERT: T 121 ARG cc_start: 0.3599 (ttm110) cc_final: 0.3242 (mmt-90) REVERT: U 75 ARG cc_start: 0.3111 (mmm160) cc_final: 0.2536 (ppt170) REVERT: X 88 ASN cc_start: 0.4664 (m-40) cc_final: 0.4142 (t0) REVERT: Y 88 ASN cc_start: 0.3961 (m-40) cc_final: 0.3506 (t0) REVERT: b 46 GLU cc_start: 0.7006 (tm-30) cc_final: 0.6721 (tm-30) REVERT: b 73 ILE cc_start: 0.1863 (mt) cc_final: 0.1558 (mm) REVERT: d 80 VAL cc_start: 0.5600 (t) cc_final: 0.5390 (t) REVERT: d 88 ASN cc_start: 0.4747 (m-40) cc_final: 0.4215 (t0) REVERT: d 97 ASN cc_start: 0.9327 (t0) cc_final: 0.8954 (m-40) REVERT: e 141 ARG cc_start: 0.9125 (ppt170) cc_final: 0.8867 (tmm-80) REVERT: e 149 ARG cc_start: 0.6696 (ptt180) cc_final: 0.6354 (tmm-80) REVERT: e 150 ILE cc_start: 0.8850 (mm) cc_final: 0.8551 (mm) REVERT: h 121 GLU cc_start: 0.7028 (tt0) cc_final: 0.6653 (pp20) REVERT: i 121 GLU cc_start: 0.7894 (tt0) cc_final: 0.6932 (tm-30) REVERT: k 149 ARG cc_start: 0.5200 (ptt180) cc_final: 0.4922 (tmm-80) REVERT: m 120 ILE cc_start: 0.4949 (pt) cc_final: 0.4669 (pt) REVERT: p 107 LEU cc_start: 0.4842 (tt) cc_final: 0.4156 (mt) REVERT: q 103 ARG cc_start: 0.4306 (ttp80) cc_final: 0.3878 (ttp80) REVERT: r 120 ILE cc_start: 0.4686 (pt) cc_final: 0.4425 (pt) REVERT: s 149 ARG cc_start: 0.6056 (ptt180) cc_final: 0.5364 (tmm-80) REVERT: s 150 ILE cc_start: 0.7955 (mm) cc_final: 0.7545 (mt) REVERT: s 158 LYS cc_start: 0.5633 (mttm) cc_final: 0.5330 (tptt) outliers start: 0 outliers final: 0 residues processed: 874 average time/residue: 0.7586 time to fit residues: 1168.1519 Evaluate side-chains 664 residues out of total 9345 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 664 time to evaluate : 7.280 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1110 random chunks: chunk 893 optimal weight: 9.9990 chunk 609 optimal weight: 5.9990 chunk 15 optimal weight: 9.9990 chunk 798 optimal weight: 7.9990 chunk 442 optimal weight: 1.9990 chunk 915 optimal weight: 7.9990 chunk 741 optimal weight: 5.9990 chunk 1 optimal weight: 7.9990 chunk 547 optimal weight: 9.9990 chunk 963 optimal weight: 7.9990 chunk 270 optimal weight: 6.9990 overall best weight: 5.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 40 ASN A 93 ASN ** A 156 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 373 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 448 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 489 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 523 ASN ** A 630 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 156 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 446 ASN B 448 GLN B 611 GLN B 626 ASN C 40 ASN C 156 HIS C 315 ASN C 446 ASN C 448 GLN C 523 ASN ** C 611 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 313 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 603 GLN ** D 611 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 262 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 446 ASN ** E 603 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 626 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 40 ASN F 132 ASN ** F 313 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 315 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 446 ASN F 448 GLN ** G 353 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 373 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 448 GLN ** G 489 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 630 HIS H 40 ASN ** H 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 156 HIS H 315 ASN ** H 353 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 373 GLN I 40 ASN ** J 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 258 GLN J 313 GLN J 446 ASN ** J 448 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 523 ASN J 603 GLN J 630 HIS K 40 ASN ** K 156 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 315 ASN K 363 GLN K 523 ASN ** L 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 315 ASN L 363 GLN L 419 ASN L 448 GLN M 40 ASN ** M 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 373 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 603 GLN ** N 156 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 315 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 448 GLN ** N 523 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 40 ASN O 258 GLN ** O 315 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 373 GLN O 448 GLN ** O 489 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 626 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 107 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 122 GLN S 122 GLN ** U 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 107 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 122 GLN ** V 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 107 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 120 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 122 GLN ** W 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 107 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 122 GLN ** Z 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 115 GLN ** a 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 107 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 115 GLN a 122 GLN ** c 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 107 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 115 GLN ** c 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 122 GLN ** d 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 107 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 122 GLN ** e 126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** f 153 ASN f 155 GLN ** g 126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** l 155 GLN ** m 126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** n 155 GLN ** q 126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 62 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7704 moved from start: 0.6784 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.090 86145 Z= 0.405 Angle : 0.762 9.399 116910 Z= 0.396 Chirality : 0.049 0.328 14250 Planarity : 0.006 0.089 15195 Dihedral : 5.596 23.534 12030 Min Nonbonded Distance : 1.994 Molprobity Statistics. All-atom Clashscore : 22.72 Ramachandran Plot: Outliers : 0.04 % Allowed : 10.49 % Favored : 89.47 % Rotamer: Outliers : 0.03 % Allowed : 5.09 % Favored : 94.87 % 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: -2.62 (0.07), residues: 11115 helix: 0.25 (0.09), residues: 3525 sheet: -2.05 (0.10), residues: 2250 loop : -3.06 (0.07), residues: 5340 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP L 197 HIS 0.008 0.002 HIS M 156 PHE 0.025 0.003 PHE b 126 TYR 0.041 0.002 TYR O 596 ARG 0.010 0.001 ARG J 477 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 22230 Ramachandran restraints generated. 11115 Oldfield, 0 Emsley, 11115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 22230 Ramachandran restraints generated. 11115 Oldfield, 0 Emsley, 11115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 790 residues out of total 9345 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 787 time to evaluate : 7.290 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: A 165 MET cc_start: 0.7480 (pmm) cc_final: 0.7205 (pmm) REVERT: B 555 LYS cc_start: 0.8027 (pttt) cc_final: 0.7224 (pttp) REVERT: C 422 MET cc_start: 0.8566 (pmm) cc_final: 0.8317 (pmm) REVERT: C 447 MET cc_start: 0.7949 (mpp) cc_final: 0.7336 (mpp) REVERT: C 582 MET cc_start: 0.7096 (mmm) cc_final: 0.6852 (tpp) REVERT: D 144 GLN cc_start: 0.8528 (mt0) cc_final: 0.7884 (mt0) REVERT: D 146 ASN cc_start: 0.9112 (t0) cc_final: 0.8627 (p0) REVERT: D 415 PHE cc_start: 0.7172 (m-80) cc_final: 0.6862 (m-80) REVERT: D 422 MET cc_start: 0.8180 (pmm) cc_final: 0.7812 (pmm) REVERT: D 509 ASP cc_start: 0.8005 (m-30) cc_final: 0.7486 (t0) REVERT: E 100 ARG cc_start: 0.7258 (tpt90) cc_final: 0.6661 (mmm160) REVERT: E 326 MET cc_start: 0.7963 (pmm) cc_final: 0.7520 (pmm) REVERT: E 359 ASN cc_start: 0.8474 (p0) cc_final: 0.7866 (t0) REVERT: E 360 LEU cc_start: 0.8453 (mt) cc_final: 0.8077 (mt) REVERT: F 100 ARG cc_start: 0.7823 (tpt90) cc_final: 0.7030 (tpm170) REVERT: F 251 MET cc_start: 0.6995 (mtt) cc_final: 0.6772 (mtp) REVERT: F 422 MET cc_start: 0.8544 (pmm) cc_final: 0.8239 (pmm) REVERT: G 326 MET cc_start: 0.7177 (ttp) cc_final: 0.6976 (ttm) REVERT: G 389 ASN cc_start: 0.8973 (m-40) cc_final: 0.8579 (p0) REVERT: G 422 MET cc_start: 0.8365 (pmm) cc_final: 0.7964 (pmm) REVERT: H 157 TYR cc_start: 0.7423 (p90) cc_final: 0.7059 (p90) REVERT: H 187 ASP cc_start: 0.6468 (m-30) cc_final: 0.6100 (m-30) REVERT: H 389 ASN cc_start: 0.8852 (m-40) cc_final: 0.8474 (p0) REVERT: H 506 SER cc_start: 0.8810 (t) cc_final: 0.8431 (m) REVERT: I 39 ILE cc_start: 0.9407 (mm) cc_final: 0.9184 (pt) REVERT: I 105 LYS cc_start: 0.8164 (ptmm) cc_final: 0.7892 (ptmm) REVERT: I 174 ARG cc_start: 0.7376 (ptt180) cc_final: 0.6843 (ptm160) REVERT: I 202 GLU cc_start: 0.7694 (tp30) cc_final: 0.7492 (tp30) REVERT: I 223 MET cc_start: 0.6933 (mpp) cc_final: 0.6613 (mmt) REVERT: I 251 MET cc_start: 0.7850 (mtp) cc_final: 0.7521 (mtm) REVERT: I 256 ASP cc_start: 0.7469 (p0) cc_final: 0.7192 (p0) REVERT: I 326 MET cc_start: 0.8348 (pmm) cc_final: 0.8053 (pmm) REVERT: I 359 ASN cc_start: 0.8495 (p0) cc_final: 0.7274 (t0) REVERT: I 554 ASP cc_start: 0.8169 (p0) cc_final: 0.7538 (p0) REVERT: J 67 MET cc_start: 0.2500 (tpt) cc_final: 0.1945 (tpt) REVERT: J 77 PHE cc_start: 0.8542 (t80) cc_final: 0.8322 (t80) REVERT: J 147 ASP cc_start: 0.7557 (t0) cc_final: 0.6595 (m-30) REVERT: J 358 LEU cc_start: 0.9032 (tp) cc_final: 0.8824 (tt) REVERT: J 371 MET cc_start: 0.7693 (ttp) cc_final: 0.6780 (tmm) REVERT: K 223 MET cc_start: 0.6551 (mpp) cc_final: 0.6116 (mpp) REVERT: K 256 ASP cc_start: 0.7771 (t0) cc_final: 0.7354 (t0) REVERT: K 371 MET cc_start: 0.7576 (tmm) cc_final: 0.7368 (tmm) REVERT: K 509 ASP cc_start: 0.8384 (m-30) cc_final: 0.7980 (t0) REVERT: L 67 MET cc_start: 0.8524 (mtt) cc_final: 0.8013 (tpp) REVERT: L 172 ILE cc_start: 0.7724 (mm) cc_final: 0.7448 (tp) REVERT: L 205 LYS cc_start: 0.8411 (ttpt) cc_final: 0.8181 (ptmt) REVERT: L 256 ASP cc_start: 0.8010 (t0) cc_final: 0.7703 (t0) REVERT: L 326 MET cc_start: 0.8594 (pmm) cc_final: 0.8171 (pmm) REVERT: L 359 ASN cc_start: 0.8808 (p0) cc_final: 0.8225 (t0) REVERT: L 509 ASP cc_start: 0.8537 (m-30) cc_final: 0.8182 (t70) REVERT: M 256 ASP cc_start: 0.7854 (t0) cc_final: 0.7483 (t70) REVERT: M 359 ASN cc_start: 0.8780 (p0) cc_final: 0.8322 (t0) REVERT: N 251 MET cc_start: 0.7699 (ptp) cc_final: 0.7087 (ptp) REVERT: O 143 ARG cc_start: 0.7971 (tpt170) cc_final: 0.7305 (tpt170) REVERT: O 371 MET cc_start: 0.7897 (ttt) cc_final: 0.7385 (tmm) REVERT: R 127 ILE cc_start: 0.8189 (mt) cc_final: 0.7960 (mt) REVERT: T 121 ARG cc_start: 0.3946 (ttm110) cc_final: 0.3501 (mmt-90) REVERT: Z 46 GLU cc_start: 0.7870 (tm-30) cc_final: 0.7657 (tm-30) REVERT: c 46 GLU cc_start: 0.7028 (tm-30) cc_final: 0.6802 (tm-30) REVERT: d 80 VAL cc_start: 0.5214 (t) cc_final: 0.4953 (t) REVERT: e 133 ASP cc_start: 0.7105 (m-30) cc_final: 0.6857 (m-30) REVERT: h 121 GLU cc_start: 0.7140 (tt0) cc_final: 0.6861 (pp20) REVERT: i 121 GLU cc_start: 0.7111 (tt0) cc_final: 0.6898 (mp0) REVERT: m 120 ILE cc_start: 0.5358 (pt) cc_final: 0.5035 (pt) REVERT: p 120 ILE cc_start: 0.6274 (pt) cc_final: 0.6065 (pt) REVERT: q 155 GLN cc_start: 0.7365 (pt0) cc_final: 0.7158 (pt0) REVERT: r 120 ILE cc_start: 0.5067 (pt) cc_final: 0.4773 (pt) REVERT: s 149 ARG cc_start: 0.5938 (ptt180) cc_final: 0.5288 (tmm-80) outliers start: 3 outliers final: 0 residues processed: 790 average time/residue: 0.7154 time to fit residues: 1008.5712 Evaluate side-chains 591 residues out of total 9345 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 591 time to evaluate : 7.350 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1110 random chunks: chunk 360 optimal weight: 8.9990 chunk 966 optimal weight: 10.0000 chunk 212 optimal weight: 7.9990 chunk 629 optimal weight: 6.9990 chunk 264 optimal weight: 4.9990 chunk 1073 optimal weight: 4.9990 chunk 891 optimal weight: 10.0000 chunk 497 optimal weight: 3.9990 chunk 89 optimal weight: 1.9990 chunk 355 optimal weight: 5.9990 chunk 563 optimal weight: 10.0000 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 93 ASN ** A 156 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 373 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 448 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 489 GLN C 93 ASN ** C 603 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 611 GLN ** D 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 433 ASN D 603 GLN ** D 611 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 262 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 626 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 313 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 315 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 353 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 373 GLN ** G 489 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 630 HIS ** H 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 156 HIS ** H 262 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 353 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 373 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 419 ASN I 603 GLN I 626 ASN I 630 HIS ** J 363 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 446 ASN ** J 448 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 47 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 363 GLN ** K 603 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 47 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 146 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 373 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 156 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 315 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 373 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 523 ASN ** O 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 262 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 315 ASN ** O 489 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 626 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 115 GLN ** R 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 107 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 120 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 115 GLN ** Z 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 107 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 107 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** e 155 GLN ** g 126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** n 155 GLN ** q 126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7683 moved from start: 0.7027 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.062 86145 Z= 0.311 Angle : 0.670 9.168 116910 Z= 0.344 Chirality : 0.047 0.254 14250 Planarity : 0.005 0.063 15195 Dihedral : 5.220 22.826 12030 Min Nonbonded Distance : 2.022 Molprobity Statistics. All-atom Clashscore : 19.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.98 % Favored : 91.02 % Rotamer: Outliers : 0.01 % Allowed : 3.60 % Favored : 96.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -2.50 (0.07), residues: 11115 helix: 0.44 (0.09), residues: 3540 sheet: -2.17 (0.10), residues: 2385 loop : -2.98 (0.07), residues: 5190 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP O 197 HIS 0.015 0.002 HIS I 630 PHE 0.034 0.002 PHE T 119 TYR 0.030 0.002 TYR I 604 ARG 0.008 0.001 ARG f 103 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 22230 Ramachandran restraints generated. 11115 Oldfield, 0 Emsley, 11115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 22230 Ramachandran restraints generated. 11115 Oldfield, 0 Emsley, 11115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 783 residues out of total 9345 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 782 time to evaluate : 7.397 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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 326 MET cc_start: 0.7841 (pmm) cc_final: 0.7582 (pmm) REVERT: A 423 LEU cc_start: 0.8487 (mm) cc_final: 0.8267 (mt) REVERT: A 460 LEU cc_start: 0.8908 (tt) cc_final: 0.8662 (tt) REVERT: B 100 ARG cc_start: 0.7839 (tmt-80) cc_final: 0.6781 (ttp80) REVERT: B 156 HIS cc_start: 0.6631 (m-70) cc_final: 0.6402 (m-70) REVERT: B 555 LYS cc_start: 0.7737 (pttt) cc_final: 0.7077 (pttp) REVERT: C 422 MET cc_start: 0.8531 (pmm) cc_final: 0.8280 (pmm) REVERT: C 447 MET cc_start: 0.7950 (mpp) cc_final: 0.7319 (mpp) REVERT: D 144 GLN cc_start: 0.8482 (mt0) cc_final: 0.7796 (mt0) REVERT: D 146 ASN cc_start: 0.9181 (t0) cc_final: 0.8597 (p0) REVERT: D 274 LYS cc_start: 0.7161 (tttt) cc_final: 0.6779 (tttp) REVERT: D 422 MET cc_start: 0.7657 (pmm) cc_final: 0.7277 (pmm) REVERT: D 509 ASP cc_start: 0.8048 (m-30) cc_final: 0.7577 (t0) REVERT: D 518 LEU cc_start: 0.7607 (tt) cc_final: 0.7398 (tp) REVERT: D 586 ARG cc_start: 0.7702 (ttm170) cc_final: 0.7399 (ttm-80) REVERT: E 100 ARG cc_start: 0.7247 (tpt90) cc_final: 0.6668 (mmm160) REVERT: E 209 GLU cc_start: 0.8918 (tt0) cc_final: 0.8717 (tt0) REVERT: E 359 ASN cc_start: 0.8705 (p0) cc_final: 0.7876 (t0) REVERT: F 88 VAL cc_start: 0.9069 (m) cc_final: 0.8482 (t) REVERT: F 96 LEU cc_start: 0.8694 (pp) cc_final: 0.8160 (pp) REVERT: F 100 ARG cc_start: 0.7850 (tpt90) cc_final: 0.6999 (tpm170) REVERT: F 202 GLU cc_start: 0.6721 (mm-30) cc_final: 0.6324 (tp30) REVERT: F 422 MET cc_start: 0.8393 (pmm) cc_final: 0.8133 (pmm) REVERT: G 100 ARG cc_start: 0.7536 (tpt90) cc_final: 0.7046 (mmm160) REVERT: G 156 HIS cc_start: 0.6076 (m-70) cc_final: 0.5860 (m90) REVERT: G 389 ASN cc_start: 0.8944 (m-40) cc_final: 0.8585 (p0) REVERT: G 422 MET cc_start: 0.8078 (pmm) cc_final: 0.7737 (pmm) REVERT: H 157 TYR cc_start: 0.7575 (p90) cc_final: 0.7142 (p90) REVERT: H 187 ASP cc_start: 0.5932 (m-30) cc_final: 0.5511 (m-30) REVERT: H 359 ASN cc_start: 0.8574 (p0) cc_final: 0.8361 (t0) REVERT: H 371 MET cc_start: 0.7127 (tmm) cc_final: 0.6857 (tmm) REVERT: H 506 SER cc_start: 0.8992 (t) cc_final: 0.8518 (m) REVERT: I 39 ILE cc_start: 0.9389 (mm) cc_final: 0.9165 (pt) REVERT: I 105 LYS cc_start: 0.8123 (ptmm) cc_final: 0.7851 (ptmm) REVERT: I 174 ARG cc_start: 0.7535 (ptt180) cc_final: 0.6736 (ptm160) REVERT: I 256 ASP cc_start: 0.7228 (p0) cc_final: 0.6955 (p0) REVERT: I 326 MET cc_start: 0.8537 (pmm) cc_final: 0.8242 (pmm) REVERT: I 359 ASN cc_start: 0.8454 (p0) cc_final: 0.7261 (t0) REVERT: I 518 LEU cc_start: 0.7879 (mp) cc_final: 0.7664 (mp) REVERT: I 554 ASP cc_start: 0.7507 (p0) cc_final: 0.7022 (p0) REVERT: J 67 MET cc_start: 0.3696 (tpt) cc_final: 0.2733 (tpt) REVERT: J 77 PHE cc_start: 0.8450 (t80) cc_final: 0.8174 (t80) REVERT: J 147 ASP cc_start: 0.7761 (t0) cc_final: 0.6484 (m-30) REVERT: J 371 MET cc_start: 0.7740 (tmm) cc_final: 0.6935 (tmm) REVERT: K 67 MET cc_start: 0.1480 (tpt) cc_final: 0.0056 (tpt) REVERT: K 197 TRP cc_start: 0.7438 (p90) cc_final: 0.7219 (p90) REVERT: K 223 MET cc_start: 0.7173 (mpp) cc_final: 0.6765 (mpp) REVERT: K 256 ASP cc_start: 0.7994 (t0) cc_final: 0.7416 (t0) REVERT: K 509 ASP cc_start: 0.8340 (m-30) cc_final: 0.8007 (t0) REVERT: L 67 MET cc_start: 0.8564 (mtt) cc_final: 0.8140 (tpp) REVERT: L 165 MET cc_start: 0.8184 (pmm) cc_final: 0.7950 (pmm) REVERT: L 172 ILE cc_start: 0.7299 (mm) cc_final: 0.7073 (mm) REVERT: L 205 LYS cc_start: 0.8385 (ttpt) cc_final: 0.8169 (ptmt) REVERT: L 256 ASP cc_start: 0.8013 (t0) cc_final: 0.7731 (t0) REVERT: L 326 MET cc_start: 0.8465 (pmm) cc_final: 0.8066 (pmm) REVERT: L 359 ASN cc_start: 0.8846 (p0) cc_final: 0.8175 (t0) REVERT: L 509 ASP cc_start: 0.8443 (m-30) cc_final: 0.8151 (t70) REVERT: M 256 ASP cc_start: 0.7832 (t0) cc_final: 0.7258 (t0) REVERT: M 359 ASN cc_start: 0.8734 (p0) cc_final: 0.8341 (t0) REVERT: N 251 MET cc_start: 0.7580 (ptp) cc_final: 0.7321 (ptp) REVERT: O 202 GLU cc_start: 0.6764 (tp30) cc_final: 0.6562 (tp30) REVERT: O 371 MET cc_start: 0.8328 (ttt) cc_final: 0.7333 (tmm) REVERT: R 127 ILE cc_start: 0.8120 (mt) cc_final: 0.7859 (mt) REVERT: T 121 ARG cc_start: 0.3457 (ttm110) cc_final: 0.3030 (mmt-90) REVERT: U 119 PHE cc_start: -0.2328 (m-10) cc_final: -0.2586 (m-10) REVERT: b 73 ILE cc_start: 0.1761 (mm) cc_final: 0.1496 (mm) REVERT: h 121 GLU cc_start: 0.7106 (tt0) cc_final: 0.6808 (pp20) REVERT: i 121 GLU cc_start: 0.7543 (tt0) cc_final: 0.7314 (mp0) REVERT: m 120 ILE cc_start: 0.5272 (pt) cc_final: 0.4954 (pt) REVERT: q 155 GLN cc_start: 0.7353 (pt0) cc_final: 0.7137 (pt0) REVERT: r 120 ILE cc_start: 0.4760 (pt) cc_final: 0.4406 (pt) REVERT: s 149 ARG cc_start: 0.5849 (ptt180) cc_final: 0.5449 (tmm-80) outliers start: 1 outliers final: 1 residues processed: 783 average time/residue: 0.7420 time to fit residues: 1030.4191 Evaluate side-chains 614 residues out of total 9345 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 613 time to evaluate : 7.492 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1110 random chunks: chunk 1035 optimal weight: 40.0000 chunk 121 optimal weight: 5.9990 chunk 611 optimal weight: 0.0570 chunk 784 optimal weight: 6.9990 chunk 607 optimal weight: 8.9990 chunk 904 optimal weight: 20.0000 chunk 599 optimal weight: 6.9990 chunk 1069 optimal weight: 0.7980 chunk 669 optimal weight: 7.9990 chunk 652 optimal weight: 8.9990 chunk 493 optimal weight: 7.9990 overall best weight: 4.1704 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 93 ASN ** A 156 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 373 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 448 GLN ** B 47 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 156 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 603 GLN C 93 ASN ** D 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 313 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 433 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 603 GLN D 611 GLN ** E 262 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 603 GLN ** E 626 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 313 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 315 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 353 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 489 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 630 HIS ** H 47 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 156 HIS ** H 161 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 262 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 353 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 373 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 262 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 448 GLN I 603 GLN J 75 GLN ** J 363 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 448 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 603 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 47 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 258 GLN K 315 ASN K 363 GLN ** L 47 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 315 ASN L 363 GLN M 258 GLN ** M 373 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 156 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 315 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 373 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 262 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 489 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 107 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 115 GLN ** R 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 107 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 107 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 120 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 107 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 107 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 115 GLN ** e 126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** n 155 GLN o 155 GLN ** q 126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7688 moved from start: 0.7333 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.060 86145 Z= 0.299 Angle : 0.666 9.951 116910 Z= 0.342 Chirality : 0.047 0.208 14250 Planarity : 0.005 0.062 15195 Dihedral : 5.167 23.597 12030 Min Nonbonded Distance : 2.030 Molprobity Statistics. All-atom Clashscore : 19.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.93 % Favored : 90.07 % Rotamer: Outliers : 0.02 % Allowed : 2.86 % Favored : 97.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.40 (0.08), residues: 11115 helix: 0.52 (0.09), residues: 3540 sheet: -2.12 (0.10), residues: 2340 loop : -2.91 (0.07), residues: 5235 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 197 HIS 0.008 0.002 HIS K 156 PHE 0.040 0.002 PHE T 119 TYR 0.032 0.002 TYR O 596 ARG 0.014 0.001 ARG I 143 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 22230 Ramachandran restraints generated. 11115 Oldfield, 0 Emsley, 11115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 22230 Ramachandran restraints generated. 11115 Oldfield, 0 Emsley, 11115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 754 residues out of total 9345 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 752 time to evaluate : 7.481 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 136 ARG cc_start: 0.7388 (mmp80) cc_final: 0.6810 (mmp80) REVERT: A 326 MET cc_start: 0.7978 (pmm) cc_final: 0.7495 (pmm) REVERT: A 423 LEU cc_start: 0.8500 (mm) cc_final: 0.8281 (mt) REVERT: B 100 ARG cc_start: 0.7753 (tmt-80) cc_final: 0.6703 (ttp80) REVERT: B 509 ASP cc_start: 0.8221 (m-30) cc_final: 0.7742 (t0) REVERT: B 555 LYS cc_start: 0.7767 (pttt) cc_final: 0.7096 (pttp) REVERT: C 202 GLU cc_start: 0.6875 (tp30) cc_final: 0.6631 (tp30) REVERT: C 422 MET cc_start: 0.8465 (pmm) cc_final: 0.8250 (pmm) REVERT: C 447 MET cc_start: 0.7906 (mpp) cc_final: 0.7240 (mpp) REVERT: D 67 MET cc_start: 0.2244 (tpt) cc_final: 0.1921 (tpt) REVERT: D 144 GLN cc_start: 0.8522 (mt0) cc_final: 0.8233 (pp30) REVERT: D 146 ASN cc_start: 0.9041 (t0) cc_final: 0.8319 (p0) REVERT: D 172 ILE cc_start: 0.8223 (mm) cc_final: 0.7983 (mm) REVERT: D 274 LYS cc_start: 0.7110 (tttt) cc_final: 0.6709 (tttp) REVERT: D 422 MET cc_start: 0.7624 (pmm) cc_final: 0.7254 (pmm) REVERT: D 509 ASP cc_start: 0.7857 (m-30) cc_final: 0.7407 (t0) REVERT: D 586 ARG cc_start: 0.7687 (ttm170) cc_final: 0.7384 (ttm-80) REVERT: E 67 MET cc_start: 0.2806 (tpt) cc_final: 0.2566 (tpt) REVERT: E 100 ARG cc_start: 0.7230 (tpt90) cc_final: 0.6671 (mmm160) REVERT: E 209 GLU cc_start: 0.9032 (tt0) cc_final: 0.8823 (tt0) REVERT: E 359 ASN cc_start: 0.8526 (p0) cc_final: 0.7654 (t0) REVERT: E 603 GLN cc_start: 0.8658 (OUTLIER) cc_final: 0.8199 (tm-30) REVERT: G 100 ARG cc_start: 0.7571 (tpt90) cc_final: 0.6944 (mmm160) REVERT: G 144 GLN cc_start: 0.8775 (mm-40) cc_final: 0.8481 (mt0) REVERT: G 389 ASN cc_start: 0.8934 (m-40) cc_final: 0.8571 (p0) REVERT: G 422 MET cc_start: 0.8079 (pmm) cc_final: 0.7784 (pmm) REVERT: H 157 TYR cc_start: 0.7756 (p90) cc_final: 0.7290 (p90) REVERT: H 187 ASP cc_start: 0.6020 (m-30) cc_final: 0.5695 (m-30) REVERT: H 359 ASN cc_start: 0.8602 (p0) cc_final: 0.8382 (t0) REVERT: H 506 SER cc_start: 0.8951 (t) cc_final: 0.8483 (m) REVERT: I 251 MET cc_start: 0.7843 (mtp) cc_final: 0.7630 (mtm) REVERT: I 256 ASP cc_start: 0.7221 (p0) cc_final: 0.6953 (p0) REVERT: I 326 MET cc_start: 0.8529 (pmm) cc_final: 0.8217 (pmm) REVERT: I 359 ASN cc_start: 0.8450 (p0) cc_final: 0.7207 (t0) REVERT: I 554 ASP cc_start: 0.7471 (p0) cc_final: 0.7011 (p0) REVERT: J 77 PHE cc_start: 0.8447 (t80) cc_final: 0.8140 (t80) REVERT: J 371 MET cc_start: 0.7749 (tmm) cc_final: 0.6937 (tmm) REVERT: J 422 MET cc_start: 0.8869 (pmm) cc_final: 0.8606 (pmm) REVERT: K 67 MET cc_start: 0.1678 (tpt) cc_final: 0.0150 (tpt) REVERT: K 197 TRP cc_start: 0.8135 (p90) cc_final: 0.7714 (p90) REVERT: K 223 MET cc_start: 0.7039 (mpp) cc_final: 0.6660 (mpp) REVERT: K 256 ASP cc_start: 0.7877 (t0) cc_final: 0.7273 (t0) REVERT: L 67 MET cc_start: 0.8567 (mtt) cc_final: 0.8184 (tpp) REVERT: L 165 MET cc_start: 0.8171 (pmm) cc_final: 0.7917 (pmm) REVERT: L 172 ILE cc_start: 0.7061 (mm) cc_final: 0.6764 (mm) REVERT: L 187 ASP cc_start: 0.7420 (m-30) cc_final: 0.7066 (m-30) REVERT: L 205 LYS cc_start: 0.8489 (ttpt) cc_final: 0.8225 (ptmt) REVERT: L 256 ASP cc_start: 0.7963 (t0) cc_final: 0.7629 (t0) REVERT: L 326 MET cc_start: 0.8465 (pmm) cc_final: 0.8120 (pmm) REVERT: L 359 ASN cc_start: 0.8868 (p0) cc_final: 0.8218 (t0) REVERT: L 509 ASP cc_start: 0.8437 (m-30) cc_final: 0.8146 (t70) REVERT: M 359 ASN cc_start: 0.8711 (p0) cc_final: 0.8379 (t0) REVERT: N 67 MET cc_start: 0.3359 (tpt) cc_final: 0.2329 (tpt) REVERT: N 251 MET cc_start: 0.7767 (ptp) cc_final: 0.7300 (ptp) REVERT: N 371 MET cc_start: 0.8469 (ttp) cc_final: 0.8096 (ppp) REVERT: O 371 MET cc_start: 0.8049 (ttt) cc_final: 0.7129 (tmm) REVERT: R 127 ILE cc_start: 0.8113 (mt) cc_final: 0.7850 (mt) REVERT: T 121 ARG cc_start: 0.3791 (ttm110) cc_final: 0.3369 (mmt-90) REVERT: U 119 PHE cc_start: -0.2060 (m-10) cc_final: -0.2292 (m-10) REVERT: b 73 ILE cc_start: 0.1662 (mm) cc_final: 0.1391 (mm) REVERT: h 121 GLU cc_start: 0.7115 (tt0) cc_final: 0.6821 (pp20) REVERT: i 121 GLU cc_start: 0.7104 (tt0) cc_final: 0.6852 (mp0) REVERT: m 120 ILE cc_start: 0.5099 (pt) cc_final: 0.4801 (pt) REVERT: p 155 GLN cc_start: 0.8075 (tm-30) cc_final: 0.7573 (pt0) REVERT: r 120 ILE cc_start: 0.5112 (pt) cc_final: 0.4850 (pt) REVERT: s 149 ARG cc_start: 0.5714 (ptt180) cc_final: 0.5458 (tmm-80) REVERT: s 150 ILE cc_start: 0.7917 (mp) cc_final: 0.7705 (mp) outliers start: 2 outliers final: 0 residues processed: 754 average time/residue: 0.7226 time to fit residues: 973.4400 Evaluate side-chains 585 residues out of total 9345 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 584 time to evaluate : 7.280 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1110 random chunks: chunk 661 optimal weight: 8.9990 chunk 427 optimal weight: 1.9990 chunk 638 optimal weight: 20.0000 chunk 322 optimal weight: 20.0000 chunk 210 optimal weight: 3.9990 chunk 207 optimal weight: 3.9990 chunk 680 optimal weight: 8.9990 chunk 728 optimal weight: 5.9990 chunk 528 optimal weight: 20.0000 chunk 99 optimal weight: 8.9990 chunk 840 optimal weight: 8.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 93 ASN ** A 373 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 446 ASN ** B 47 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 448 GLN C 315 ASN C 448 GLN ** C 603 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 132 ASN ** D 313 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 262 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 626 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 156 HIS ** F 313 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 315 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 243 ASN ** G 353 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 489 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 630 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 47 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 156 HIS ** H 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 262 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 353 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 262 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 315 ASN ** I 603 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 156 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 353 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 363 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 448 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 603 GLN ** K 47 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 315 ASN K 363 GLN ** L 47 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 315 ASN L 446 ASN ** M 373 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 448 GLN ** N 156 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 315 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 335 GLN ** N 373 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 262 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 489 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 626 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 107 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 115 GLN ** R 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 107 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 107 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 107 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 120 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 107 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 107 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 115 GLN ** Z 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 107 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 115 GLN ** c 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 107 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** m 124 ASN n 155 GLN ** q 126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7713 moved from start: 0.7721 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.076 86145 Z= 0.346 Angle : 0.710 10.144 116910 Z= 0.367 Chirality : 0.048 0.270 14250 Planarity : 0.005 0.089 15195 Dihedral : 5.413 33.238 12030 Min Nonbonded Distance : 2.005 Molprobity Statistics. All-atom Clashscore : 21.19 Ramachandran Plot: Outliers : 0.01 % Allowed : 10.63 % Favored : 89.36 % Rotamer: Outliers : 0.00 % Allowed : 2.02 % Favored : 97.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.01 % 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: -2.50 (0.08), residues: 11115 helix: 0.37 (0.09), residues: 3540 sheet: -2.21 (0.10), residues: 2340 loop : -2.90 (0.08), residues: 5235 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.002 TRP J 197 HIS 0.009 0.002 HIS H 156 PHE 0.037 0.002 PHE T 119 TYR 0.037 0.002 TYR O 596 ARG 0.011 0.001 ARG K 143 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 22230 Ramachandran restraints generated. 11115 Oldfield, 0 Emsley, 11115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 22230 Ramachandran restraints generated. 11115 Oldfield, 0 Emsley, 11115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 727 residues out of total 9345 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 727 time to evaluate : 7.471 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 57 ARG cc_start: 0.8534 (mtt90) cc_final: 0.7970 (mpp80) REVERT: B 100 ARG cc_start: 0.7530 (tmt-80) cc_final: 0.6585 (ttp80) REVERT: B 156 HIS cc_start: 0.6651 (m-70) cc_final: 0.6411 (m-70) REVERT: B 555 LYS cc_start: 0.7722 (pttt) cc_final: 0.6928 (pttp) REVERT: C 422 MET cc_start: 0.8052 (pmm) cc_final: 0.7505 (pmm) REVERT: C 447 MET cc_start: 0.7780 (mpp) cc_final: 0.7066 (mpp) REVERT: D 67 MET cc_start: 0.3333 (tpt) cc_final: 0.2986 (tpt) REVERT: D 146 ASN cc_start: 0.8917 (t0) cc_final: 0.8245 (p0) REVERT: D 172 ILE cc_start: 0.8185 (mm) cc_final: 0.7914 (mm) REVERT: D 274 LYS cc_start: 0.7134 (tttt) cc_final: 0.6749 (tttp) REVERT: D 422 MET cc_start: 0.7470 (pmm) cc_final: 0.7062 (pmm) REVERT: D 509 ASP cc_start: 0.7857 (m-30) cc_final: 0.7426 (t0) REVERT: D 586 ARG cc_start: 0.7600 (ttm170) cc_final: 0.7331 (ttm-80) REVERT: E 100 ARG cc_start: 0.7310 (tpt90) cc_final: 0.6818 (mmm160) REVERT: E 209 GLU cc_start: 0.9043 (tt0) cc_final: 0.8824 (tt0) REVERT: E 422 MET cc_start: 0.8473 (pmm) cc_final: 0.8225 (pmm) REVERT: E 509 ASP cc_start: 0.8080 (m-30) cc_final: 0.7544 (t0) REVERT: F 88 VAL cc_start: 0.9106 (m) cc_final: 0.8518 (t) REVERT: F 96 LEU cc_start: 0.8674 (pp) cc_final: 0.8160 (pp) REVERT: F 100 ARG cc_start: 0.7945 (tpt90) cc_final: 0.6952 (tpm170) REVERT: F 155 VAL cc_start: 0.7352 (t) cc_final: 0.7024 (t) REVERT: F 209 GLU cc_start: 0.8973 (tt0) cc_final: 0.8290 (mp0) REVERT: F 251 MET cc_start: 0.6815 (mtt) cc_final: 0.6552 (mtp) REVERT: G 67 MET cc_start: 0.1927 (tpt) cc_final: 0.0409 (tpt) REVERT: G 68 LEU cc_start: 0.7384 (pp) cc_final: 0.7120 (pp) REVERT: G 100 ARG cc_start: 0.7711 (tpt90) cc_final: 0.7128 (mmm160) REVERT: G 389 ASN cc_start: 0.8963 (m-40) cc_final: 0.8591 (p0) REVERT: G 422 MET cc_start: 0.8373 (pmm) cc_final: 0.8006 (pmm) REVERT: H 187 ASP cc_start: 0.5965 (m-30) cc_final: 0.5667 (m-30) REVERT: H 359 ASN cc_start: 0.8644 (p0) cc_final: 0.8372 (t0) REVERT: H 506 SER cc_start: 0.8947 (t) cc_final: 0.8498 (m) REVERT: I 67 MET cc_start: 0.2708 (tpt) cc_final: 0.1457 (tpt) REVERT: I 251 MET cc_start: 0.7686 (mtp) cc_final: 0.7472 (mtm) REVERT: I 256 ASP cc_start: 0.7226 (p0) cc_final: 0.7014 (p0) REVERT: I 326 MET cc_start: 0.8647 (pmm) cc_final: 0.8301 (pmm) REVERT: I 359 ASN cc_start: 0.8503 (p0) cc_final: 0.7240 (t0) REVERT: I 554 ASP cc_start: 0.7492 (p0) cc_final: 0.7049 (p0) REVERT: J 77 PHE cc_start: 0.8446 (t80) cc_final: 0.8133 (t80) REVERT: J 371 MET cc_start: 0.8102 (tmm) cc_final: 0.7332 (tmm) REVERT: J 422 MET cc_start: 0.8585 (pmm) cc_final: 0.8312 (pmm) REVERT: K 67 MET cc_start: 0.1517 (tpt) cc_final: 0.0210 (tpt) REVERT: K 165 MET cc_start: 0.8017 (pmm) cc_final: 0.7629 (pmm) REVERT: K 223 MET cc_start: 0.7191 (mpp) cc_final: 0.6732 (mpp) REVERT: K 256 ASP cc_start: 0.7615 (t0) cc_final: 0.6987 (t0) REVERT: L 67 MET cc_start: 0.8419 (mtt) cc_final: 0.8153 (tpp) REVERT: L 165 MET cc_start: 0.8199 (pmm) cc_final: 0.7954 (pmm) REVERT: L 172 ILE cc_start: 0.7228 (mm) cc_final: 0.6940 (mm) REVERT: L 205 LYS cc_start: 0.8482 (ttpt) cc_final: 0.8232 (ptmt) REVERT: L 256 ASP cc_start: 0.8019 (t0) cc_final: 0.7621 (t0) REVERT: L 326 MET cc_start: 0.8095 (pmm) cc_final: 0.7422 (pmm) REVERT: L 330 GLU cc_start: 0.9146 (mp0) cc_final: 0.8602 (mp0) REVERT: L 359 ASN cc_start: 0.8910 (p0) cc_final: 0.8188 (t0) REVERT: L 509 ASP cc_start: 0.8365 (m-30) cc_final: 0.8118 (t70) REVERT: M 67 MET cc_start: 0.3079 (tpt) cc_final: 0.2059 (tpt) REVERT: M 256 ASP cc_start: 0.7661 (t0) cc_final: 0.7393 (t0) REVERT: N 67 MET cc_start: 0.3449 (tpt) cc_final: 0.2469 (tpt) REVERT: N 165 MET cc_start: 0.8213 (pmm) cc_final: 0.7936 (pmm) REVERT: N 251 MET cc_start: 0.7624 (ptp) cc_final: 0.7366 (ptp) REVERT: N 371 MET cc_start: 0.8473 (ttp) cc_final: 0.8069 (ppp) REVERT: O 371 MET cc_start: 0.8262 (ttt) cc_final: 0.7320 (tmm) REVERT: R 127 ILE cc_start: 0.8122 (mt) cc_final: 0.7848 (mt) REVERT: T 121 ARG cc_start: 0.3821 (ttm110) cc_final: 0.3356 (mmt-90) REVERT: X 119 PHE cc_start: 0.0635 (m-80) cc_final: 0.0188 (m-80) REVERT: g 103 ARG cc_start: 0.5296 (ttp80) cc_final: 0.4343 (ttp80) REVERT: i 121 GLU cc_start: 0.7050 (tt0) cc_final: 0.6656 (mp0) REVERT: m 120 ILE cc_start: 0.5271 (pt) cc_final: 0.5066 (pt) REVERT: m 164 PHE cc_start: 0.4951 (t80) cc_final: 0.4574 (t80) REVERT: r 120 ILE cc_start: 0.5282 (pt) cc_final: 0.4982 (pt) outliers start: 0 outliers final: 0 residues processed: 727 average time/residue: 0.7185 time to fit residues: 927.7410 Evaluate side-chains 556 residues out of total 9345 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 556 time to evaluate : 7.181 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1110 random chunks: chunk 973 optimal weight: 1.9990 chunk 1024 optimal weight: 5.9990 chunk 935 optimal weight: 30.0000 chunk 996 optimal weight: 8.9990 chunk 600 optimal weight: 5.9990 chunk 434 optimal weight: 10.0000 chunk 782 optimal weight: 8.9990 chunk 305 optimal weight: 7.9990 chunk 900 optimal weight: 6.9990 chunk 942 optimal weight: 6.9990 chunk 993 optimal weight: 20.0000 overall best weight: 5.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 373 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 446 ASN ** B 47 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 315 ASN C 603 GLN D 40 ASN D 603 GLN ** E 262 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 626 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 156 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 313 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 315 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 363 GLN ** G 353 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 489 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 630 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 47 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 132 ASN ** H 146 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 156 HIS H 161 ASN ** H 262 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 353 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 262 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 603 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 156 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 353 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 448 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 47 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 315 ASN K 363 GLN ** L 47 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 315 ASN ** M 359 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 373 GLN ** N 156 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 315 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 373 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 262 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 489 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 626 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 107 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 107 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 107 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 107 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 120 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 107 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 47 GLN ** Y 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 107 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 107 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 107 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 115 GLN ** e 126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** l 155 GLN n 155 GLN o 153 ASN ** o 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7731 moved from start: 0.8069 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.083 86145 Z= 0.382 Angle : 0.741 10.765 116910 Z= 0.383 Chirality : 0.049 0.283 14250 Planarity : 0.006 0.088 15195 Dihedral : 5.613 25.639 12030 Min Nonbonded Distance : 2.022 Molprobity Statistics. All-atom Clashscore : 22.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.17 % Favored : 88.83 % Rotamer: Outliers : 0.00 % Allowed : 1.24 % Favored : 98.76 % 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: -2.64 (0.08), residues: 11115 helix: 0.19 (0.09), residues: 3555 sheet: -2.39 (0.10), residues: 2175 loop : -2.90 (0.07), residues: 5385 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.002 TRP L 197 HIS 0.009 0.002 HIS H 156 PHE 0.035 0.002 PHE T 119 TYR 0.036 0.002 TYR O 596 ARG 0.012 0.001 ARG K 143 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 22230 Ramachandran restraints generated. 11115 Oldfield, 0 Emsley, 11115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 22230 Ramachandran restraints generated. 11115 Oldfield, 0 Emsley, 11115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 683 residues out of total 9345 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 683 time to evaluate : 7.422 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: A 57 ARG cc_start: 0.8524 (mtt90) cc_final: 0.8002 (mpp80) REVERT: A 165 MET cc_start: 0.7513 (pmm) cc_final: 0.7259 (pmm) REVERT: A 172 ILE cc_start: 0.8391 (mm) cc_final: 0.8104 (mm) REVERT: A 415 PHE cc_start: 0.7289 (t80) cc_final: 0.7069 (t80) REVERT: A 422 MET cc_start: 0.8195 (pmm) cc_final: 0.7576 (pmm) REVERT: B 100 ARG cc_start: 0.7527 (tmt-80) cc_final: 0.6533 (ttp80) REVERT: B 509 ASP cc_start: 0.8245 (m-30) cc_final: 0.7792 (t0) REVERT: B 555 LYS cc_start: 0.7699 (pttt) cc_final: 0.6943 (pttp) REVERT: C 223 MET cc_start: 0.7375 (mmt) cc_final: 0.7061 (mmp) REVERT: C 422 MET cc_start: 0.8171 (pmm) cc_final: 0.7706 (pmm) REVERT: C 641 ARG cc_start: 0.6687 (ttm170) cc_final: 0.6406 (mmt180) REVERT: D 67 MET cc_start: 0.2445 (tpt) cc_final: 0.2007 (tpt) REVERT: D 144 GLN cc_start: 0.8146 (pp30) cc_final: 0.7839 (pt0) REVERT: D 146 ASN cc_start: 0.8965 (t0) cc_final: 0.8430 (p0) REVERT: D 172 ILE cc_start: 0.8408 (mm) cc_final: 0.8140 (mm) REVERT: D 274 LYS cc_start: 0.7317 (tttt) cc_final: 0.6950 (tttp) REVERT: D 415 PHE cc_start: 0.6842 (t80) cc_final: 0.6621 (t80) REVERT: D 422 MET cc_start: 0.7515 (pmm) cc_final: 0.7169 (pmm) REVERT: D 509 ASP cc_start: 0.7878 (m-30) cc_final: 0.7431 (t0) REVERT: E 67 MET cc_start: 0.1446 (tpt) cc_final: 0.0770 (tpt) REVERT: E 100 ARG cc_start: 0.7236 (tpt90) cc_final: 0.6793 (mmm160) REVERT: E 415 PHE cc_start: 0.7620 (t80) cc_final: 0.7345 (t80) REVERT: E 422 MET cc_start: 0.8478 (pmm) cc_final: 0.8229 (pmm) REVERT: E 509 ASP cc_start: 0.7922 (m-30) cc_final: 0.7416 (t0) REVERT: F 209 GLU cc_start: 0.8835 (tt0) cc_final: 0.8318 (mp0) REVERT: F 251 MET cc_start: 0.7087 (mtt) cc_final: 0.6846 (mtp) REVERT: G 67 MET cc_start: 0.2034 (tpt) cc_final: 0.0816 (tpt) REVERT: G 68 LEU cc_start: 0.6458 (pp) cc_final: 0.6179 (pp) REVERT: G 74 TYR cc_start: 0.8959 (t80) cc_final: 0.8607 (t80) REVERT: G 100 ARG cc_start: 0.7626 (tpt90) cc_final: 0.7080 (mmm160) REVERT: G 326 MET cc_start: 0.6830 (ptm) cc_final: 0.6548 (ptm) REVERT: G 389 ASN cc_start: 0.8839 (m-40) cc_final: 0.8400 (p0) REVERT: H 187 ASP cc_start: 0.5979 (m-30) cc_final: 0.5717 (m-30) REVERT: H 251 MET cc_start: 0.8755 (mtt) cc_final: 0.8484 (mtm) REVERT: H 506 SER cc_start: 0.8698 (t) cc_final: 0.8413 (m) REVERT: I 67 MET cc_start: 0.2824 (tpt) cc_final: 0.1542 (tpt) REVERT: I 77 PHE cc_start: 0.9028 (t80) cc_final: 0.8749 (t80) REVERT: I 251 MET cc_start: 0.7704 (mtp) cc_final: 0.7444 (mtm) REVERT: I 256 ASP cc_start: 0.7293 (p0) cc_final: 0.7068 (p0) REVERT: I 326 MET cc_start: 0.8635 (pmm) cc_final: 0.8311 (pmm) REVERT: I 359 ASN cc_start: 0.8125 (p0) cc_final: 0.7108 (t0) REVERT: I 554 ASP cc_start: 0.7480 (p0) cc_final: 0.7054 (p0) REVERT: J 67 MET cc_start: 0.2361 (tpt) cc_final: 0.1306 (tpt) REVERT: J 371 MET cc_start: 0.8122 (tmm) cc_final: 0.7339 (tmm) REVERT: J 422 MET cc_start: 0.8424 (pmm) cc_final: 0.8130 (pmm) REVERT: K 67 MET cc_start: 0.1007 (tpt) cc_final: -0.0516 (tpt) REVERT: K 165 MET cc_start: 0.7901 (pmm) cc_final: 0.7626 (pmm) REVERT: K 223 MET cc_start: 0.7393 (mpp) cc_final: 0.6938 (mpp) REVERT: K 256 ASP cc_start: 0.7572 (t0) cc_final: 0.6959 (t0) REVERT: L 165 MET cc_start: 0.8116 (pmm) cc_final: 0.7854 (pmm) REVERT: L 172 ILE cc_start: 0.7324 (mm) cc_final: 0.7035 (mm) REVERT: L 205 LYS cc_start: 0.8468 (ttpt) cc_final: 0.8241 (ptmt) REVERT: L 256 ASP cc_start: 0.8245 (t0) cc_final: 0.7992 (t0) REVERT: L 326 MET cc_start: 0.7989 (pmm) cc_final: 0.7465 (pmm) REVERT: L 330 GLU cc_start: 0.9017 (mp0) cc_final: 0.8772 (mp0) REVERT: L 333 ILE cc_start: 0.9542 (mt) cc_final: 0.9339 (mt) REVERT: L 422 MET cc_start: 0.8833 (pmm) cc_final: 0.8619 (pmm) REVERT: L 509 ASP cc_start: 0.8377 (m-30) cc_final: 0.8138 (t70) REVERT: M 67 MET cc_start: 0.3336 (tpt) cc_final: 0.2214 (tpt) REVERT: M 100 ARG cc_start: 0.7412 (tpt90) cc_final: 0.6613 (mtm-85) REVERT: M 256 ASP cc_start: 0.7629 (t0) cc_final: 0.7404 (t0) REVERT: N 67 MET cc_start: 0.2256 (tpt) cc_final: 0.1364 (tpt) REVERT: N 165 MET cc_start: 0.8156 (pmm) cc_final: 0.7745 (pmm) REVERT: O 251 MET cc_start: 0.7698 (mtp) cc_final: 0.7492 (mtm) REVERT: O 371 MET cc_start: 0.8326 (ttt) cc_final: 0.7408 (tmm) REVERT: O 422 MET cc_start: 0.8345 (pmm) cc_final: 0.8119 (pmm) REVERT: R 127 ILE cc_start: 0.8354 (mt) cc_final: 0.8095 (mt) REVERT: T 121 ARG cc_start: 0.4139 (ttm110) cc_final: 0.3577 (mmt-90) REVERT: U 39 ILE cc_start: 0.8488 (tt) cc_final: 0.8276 (mp) REVERT: X 119 PHE cc_start: -0.0236 (m-80) cc_final: -0.0480 (m-10) REVERT: g 103 ARG cc_start: 0.5399 (ttp80) cc_final: 0.5013 (ttp80) REVERT: i 121 GLU cc_start: 0.7049 (tt0) cc_final: 0.6630 (mp0) REVERT: m 103 ARG cc_start: 0.5078 (ttp80) cc_final: 0.4771 (ttp80) REVERT: p 149 ARG cc_start: 0.5748 (ptt180) cc_final: 0.5481 (tmm-80) REVERT: p 155 GLN cc_start: 0.7575 (tm-30) cc_final: 0.7351 (tm-30) REVERT: r 120 ILE cc_start: 0.5197 (pt) cc_final: 0.4881 (pt) outliers start: 0 outliers final: 0 residues processed: 683 average time/residue: 0.7364 time to fit residues: 898.3632 Evaluate side-chains 538 residues out of total 9345 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 538 time to evaluate : 7.230 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1110 random chunks: chunk 654 optimal weight: 8.9990 chunk 1054 optimal weight: 8.9990 chunk 643 optimal weight: 0.6980 chunk 500 optimal weight: 2.9990 chunk 732 optimal weight: 6.9990 chunk 1105 optimal weight: 0.2980 chunk 1017 optimal weight: 9.9990 chunk 880 optimal weight: 4.9990 chunk 91 optimal weight: 0.9990 chunk 680 optimal weight: 7.9990 chunk 539 optimal weight: 0.0010 overall best weight: 0.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 373 GLN ** A 630 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 47 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 446 ASN ** D 313 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 489 GLN ** D 603 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 156 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 262 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 626 ASN ** F 156 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 313 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 315 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 446 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 353 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 363 GLN ** G 489 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 630 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 47 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 146 ASN ** H 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 262 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 353 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 373 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 156 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 262 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 626 ASN ** J 156 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 363 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 448 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 47 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 363 GLN K 523 ASN K 603 GLN L 40 ASN ** L 47 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 373 GLN L 448 GLN L 523 ASN ** M 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 315 ASN M 359 ASN M 448 GLN ** N 156 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 315 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 373 GLN N 489 GLN ** O 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 262 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 489 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 115 GLN ** U 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 107 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 107 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 120 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 115 GLN ** Z 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** j 155 GLN m 124 ASN ** q 126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7618 moved from start: 0.7933 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.054 86145 Z= 0.163 Angle : 0.610 10.764 116910 Z= 0.304 Chirality : 0.046 0.234 14250 Planarity : 0.005 0.070 15195 Dihedral : 4.716 22.416 12030 Min Nonbonded Distance : 2.057 Molprobity Statistics. All-atom Clashscore : 16.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.94 % Favored : 93.06 % Rotamer: Outliers : 0.00 % Allowed : 0.31 % Favored : 99.69 % 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: -2.02 (0.08), residues: 11115 helix: 0.83 (0.09), residues: 3555 sheet: -1.99 (0.11), residues: 1995 loop : -2.65 (0.07), residues: 5565 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP I 197 HIS 0.014 0.002 HIS E 156 PHE 0.035 0.001 PHE Y 119 TYR 0.019 0.001 TYR I 604 ARG 0.017 0.000 ARG O 641 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 22230 Ramachandran restraints generated. 11115 Oldfield, 0 Emsley, 11115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 22230 Ramachandran restraints generated. 11115 Oldfield, 0 Emsley, 11115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 801 residues out of total 9345 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 801 time to evaluate : 7.388 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 57 ARG cc_start: 0.8598 (mtt90) cc_final: 0.7952 (mpp80) REVERT: A 165 MET cc_start: 0.7174 (pmm) cc_final: 0.6911 (pmm) REVERT: A 172 ILE cc_start: 0.8339 (mm) cc_final: 0.8124 (mm) REVERT: A 326 MET cc_start: 0.8691 (pmm) cc_final: 0.8227 (pmm) REVERT: A 422 MET cc_start: 0.7999 (pmm) cc_final: 0.7711 (pmm) REVERT: A 518 LEU cc_start: 0.8408 (tp) cc_final: 0.8177 (tt) REVERT: B 100 ARG cc_start: 0.7810 (tmt-80) cc_final: 0.6753 (ttp80) REVERT: B 555 LYS cc_start: 0.7595 (pttt) cc_final: 0.6918 (pttp) REVERT: C 202 GLU cc_start: 0.6925 (tp30) cc_final: 0.6556 (tp30) REVERT: C 422 MET cc_start: 0.8010 (pmm) cc_final: 0.7671 (pmm) REVERT: C 447 MET cc_start: 0.7956 (mmt) cc_final: 0.7674 (mpp) REVERT: C 509 ASP cc_start: 0.8270 (m-30) cc_final: 0.7988 (m-30) REVERT: D 67 MET cc_start: 0.2267 (tpt) cc_final: 0.1765 (tpt) REVERT: D 144 GLN cc_start: 0.8141 (pp30) cc_final: 0.7940 (pt0) REVERT: D 146 ASN cc_start: 0.8848 (t0) cc_final: 0.8398 (p0) REVERT: D 172 ILE cc_start: 0.8150 (mm) cc_final: 0.7845 (mm) REVERT: D 415 PHE cc_start: 0.6859 (t80) cc_final: 0.6649 (t80) REVERT: D 422 MET cc_start: 0.7467 (pmm) cc_final: 0.7073 (pmm) REVERT: D 509 ASP cc_start: 0.8109 (m-30) cc_final: 0.7623 (t0) REVERT: D 586 ARG cc_start: 0.7706 (ttm170) cc_final: 0.7398 (ttm-80) REVERT: E 359 ASN cc_start: 0.8459 (p0) cc_final: 0.7402 (t0) REVERT: F 67 MET cc_start: 0.1818 (tpt) cc_final: 0.1499 (tpt) REVERT: F 202 GLU cc_start: 0.6493 (mm-30) cc_final: 0.6092 (tp30) REVERT: F 209 GLU cc_start: 0.8547 (tt0) cc_final: 0.8193 (mp0) REVERT: F 251 MET cc_start: 0.7066 (mtt) cc_final: 0.6844 (mtp) REVERT: F 311 HIS cc_start: 0.8095 (t-170) cc_final: 0.7751 (t70) REVERT: G 67 MET cc_start: 0.2032 (tpt) cc_final: 0.0899 (tpt) REVERT: G 68 LEU cc_start: 0.6192 (pp) cc_final: 0.5913 (pp) REVERT: G 74 TYR cc_start: 0.8867 (t80) cc_final: 0.8624 (t80) REVERT: G 156 HIS cc_start: 0.5719 (m-70) cc_final: 0.5503 (m-70) REVERT: G 326 MET cc_start: 0.7794 (ptm) cc_final: 0.7535 (ptm) REVERT: G 389 ASN cc_start: 0.8724 (m-40) cc_final: 0.8348 (p0) REVERT: G 422 MET cc_start: 0.7922 (pmm) cc_final: 0.7679 (pmm) REVERT: H 157 TYR cc_start: 0.7706 (p90) cc_final: 0.7389 (p90) REVERT: H 187 ASP cc_start: 0.6912 (m-30) cc_final: 0.5965 (p0) REVERT: H 251 MET cc_start: 0.8773 (mtt) cc_final: 0.8373 (mtm) REVERT: H 359 ASN cc_start: 0.8151 (p0) cc_final: 0.7912 (t0) REVERT: H 506 SER cc_start: 0.8745 (t) cc_final: 0.8268 (m) REVERT: I 39 ILE cc_start: 0.9361 (mm) cc_final: 0.9086 (pt) REVERT: I 251 MET cc_start: 0.7816 (mtp) cc_final: 0.7603 (mtm) REVERT: I 326 MET cc_start: 0.8553 (pmm) cc_final: 0.8276 (pmm) REVERT: I 554 ASP cc_start: 0.7148 (p0) cc_final: 0.6641 (p0) REVERT: J 46 LEU cc_start: 0.9067 (tt) cc_final: 0.8659 (pp) REVERT: J 371 MET cc_start: 0.7719 (tmm) cc_final: 0.6788 (tmm) REVERT: J 422 MET cc_start: 0.8341 (pmm) cc_final: 0.7913 (pmm) REVERT: K 67 MET cc_start: 0.1227 (tpt) cc_final: 0.0044 (tpt) REVERT: K 165 MET cc_start: 0.7858 (pmm) cc_final: 0.7515 (pmm) REVERT: K 223 MET cc_start: 0.7513 (mpp) cc_final: 0.6848 (mpp) REVERT: K 256 ASP cc_start: 0.7682 (t0) cc_final: 0.7085 (t0) REVERT: K 349 ILE cc_start: 0.9344 (mp) cc_final: 0.8843 (tp) REVERT: L 67 MET cc_start: 0.3872 (tpt) cc_final: 0.2664 (tpt) REVERT: L 74 TYR cc_start: 0.8946 (t80) cc_final: 0.8498 (t80) REVERT: L 172 ILE cc_start: 0.7205 (mm) cc_final: 0.6956 (mm) REVERT: L 205 LYS cc_start: 0.8434 (ttpt) cc_final: 0.8213 (ptmt) REVERT: L 256 ASP cc_start: 0.8355 (t0) cc_final: 0.8095 (t0) REVERT: L 326 MET cc_start: 0.8349 (pmm) cc_final: 0.7687 (pmm) REVERT: L 330 GLU cc_start: 0.9021 (mp0) cc_final: 0.8566 (mp0) REVERT: L 333 ILE cc_start: 0.9554 (mt) cc_final: 0.9313 (mt) REVERT: L 359 ASN cc_start: 0.8479 (p0) cc_final: 0.7988 (t0) REVERT: L 415 PHE cc_start: 0.6583 (m-80) cc_final: 0.5955 (m-80) REVERT: L 422 MET cc_start: 0.8629 (pmm) cc_final: 0.8357 (pmm) REVERT: L 509 ASP cc_start: 0.8325 (m-30) cc_final: 0.7784 (t70) REVERT: L 521 THR cc_start: 0.8828 (p) cc_final: 0.8536 (p) REVERT: M 74 TYR cc_start: 0.9058 (t80) cc_final: 0.8533 (t80) REVERT: M 100 ARG cc_start: 0.7339 (tpt90) cc_final: 0.6694 (mtm180) REVERT: N 67 MET cc_start: 0.3304 (tpt) cc_final: 0.2346 (tpt) REVERT: N 251 MET cc_start: 0.7513 (ptp) cc_final: 0.7131 (ptp) REVERT: N 371 MET cc_start: 0.8335 (ttp) cc_final: 0.8071 (ppp) REVERT: N 423 LEU cc_start: 0.8488 (mm) cc_final: 0.8222 (mt) REVERT: O 143 ARG cc_start: 0.8297 (tpt170) cc_final: 0.7460 (tpt170) REVERT: O 172 ILE cc_start: 0.8749 (mm) cc_final: 0.8417 (mm) REVERT: O 202 GLU cc_start: 0.7002 (tp30) cc_final: 0.6760 (tp30) REVERT: X 119 PHE cc_start: 0.0177 (m-80) cc_final: -0.0047 (m-10) REVERT: f 163 LEU cc_start: 0.7899 (mt) cc_final: 0.7429 (pp) REVERT: g 103 ARG cc_start: 0.5326 (ttp80) cc_final: 0.4849 (ttp80) REVERT: p 155 GLN cc_start: 0.7746 (tm-30) cc_final: 0.7502 (tm-30) REVERT: r 120 ILE cc_start: 0.5333 (pt) cc_final: 0.4907 (pt) outliers start: 0 outliers final: 0 residues processed: 801 average time/residue: 0.7252 time to fit residues: 1031.6078 Evaluate side-chains 601 residues out of total 9345 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 601 time to evaluate : 7.181 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1110 random chunks: chunk 699 optimal weight: 2.9990 chunk 938 optimal weight: 0.2980 chunk 269 optimal weight: 0.9980 chunk 811 optimal weight: 0.0060 chunk 130 optimal weight: 5.9990 chunk 244 optimal weight: 9.9990 chunk 881 optimal weight: 8.9990 chunk 369 optimal weight: 2.9990 chunk 905 optimal weight: 9.9990 chunk 111 optimal weight: 5.9990 chunk 162 optimal weight: 7.9990 overall best weight: 1.4600 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 373 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 47 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 262 GLN ** B 353 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 315 ASN C 446 ASN ** D 313 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 489 GLN ** D 603 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 262 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 156 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 313 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 315 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 446 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 489 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 630 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 47 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 262 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 353 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 373 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 262 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 626 ASN J 156 HIS ** J 353 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 363 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 448 GLN ** K 47 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 363 GLN ** L 47 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 258 GLN L 448 GLN ** M 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 156 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 315 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 262 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 489 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 107 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 107 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 120 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 107 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 60 ASN ** d 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 115 GLN ** g 126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** i 124 ASN ** i 126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** l 153 ASN ** q 126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3885 r_free = 0.3885 target = 0.096751 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.074361 restraints weight = 409429.842| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.075149 restraints weight = 309237.829| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.075571 restraints weight = 225480.701| |-----------------------------------------------------------------------------| r_work (final): 0.3400 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7610 moved from start: 0.7993 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 86145 Z= 0.171 Angle : 0.595 10.964 116910 Z= 0.297 Chirality : 0.045 0.208 14250 Planarity : 0.005 0.067 15195 Dihedral : 4.537 22.307 12030 Min Nonbonded Distance : 2.037 Molprobity Statistics. All-atom Clashscore : 16.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.81 % Favored : 92.19 % Rotamer: Outliers : 0.01 % Allowed : 0.21 % Favored : 99.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.86 (0.08), residues: 11115 helix: 0.95 (0.09), residues: 3555 sheet: -1.86 (0.11), residues: 1965 loop : -2.56 (0.08), residues: 5595 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP L 197 HIS 0.014 0.002 HIS A 156 PHE 0.033 0.001 PHE T 119 TYR 0.018 0.001 TYR I 604 ARG 0.011 0.000 ARG E 136 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 18282.80 seconds wall clock time: 324 minutes 5.06 seconds (19445.06 seconds total)