Starting phenix.real_space_refine on Wed Nov 15 18:20:04 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6kfk_9974/11_2023/6kfk_9974.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6kfk_9974/11_2023/6kfk_9974.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6kfk_9974/11_2023/6kfk_9974.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6kfk_9974/11_2023/6kfk_9974.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6kfk_9974/11_2023/6kfk_9974.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6kfk_9974/11_2023/6kfk_9974.pdb" } resolution = 4.1 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.009 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 176 5.16 5 C 40040 2.51 5 N 11242 2.21 5 O 13618 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B PHE 2": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 29": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 38": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 82": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 92": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 99": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 169": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 186": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 258": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 262": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 283": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 303": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 381": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 2": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 29": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 38": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 82": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 92": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 99": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 169": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 186": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 258": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 262": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 283": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 303": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 381": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 2": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 29": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 38": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 82": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 92": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 99": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 169": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 186": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 258": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 262": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 283": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 303": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 381": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 2": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 29": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 38": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 82": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 92": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 99": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 169": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 186": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 258": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 262": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 283": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 303": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 381": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 2": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 29": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 38": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 82": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 92": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 99": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 169": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 186": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 258": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 262": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 283": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 303": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 381": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 2": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 29": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 38": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 82": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 92": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 99": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 169": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 186": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 258": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 262": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 283": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 303": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 381": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 2": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 29": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 38": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 82": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 92": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 99": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 169": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 186": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 258": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 262": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 283": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 303": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 381": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 2": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 29": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 38": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 82": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 92": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 99": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 169": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 186": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 258": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 262": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 283": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 303": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 381": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 2": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 29": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 38": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 82": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 92": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 99": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 169": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 186": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 258": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 262": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 283": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 303": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 381": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 2": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 29": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 38": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 82": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 92": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 99": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 169": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 186": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 258": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 262": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 283": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 303": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 381": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 2": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 29": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 38": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 82": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 92": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 99": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 169": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 186": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 258": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 262": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 283": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 303": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 381": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 2": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 29": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 38": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 82": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 92": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 99": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 169": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 186": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 258": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 262": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 283": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 303": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 381": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M PHE 2": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M TYR 29": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M PHE 38": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M PHE 82": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M PHE 92": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M PHE 99": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M PHE 169": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M TYR 186": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M PHE 258": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M PHE 262": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M TYR 283": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M TYR 303": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M TYR 381": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N PHE 2": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N TYR 29": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N PHE 38": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N PHE 82": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N PHE 92": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N PHE 99": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N PHE 169": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N TYR 186": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N PHE 258": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N PHE 262": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N TYR 283": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N TYR 303": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N TYR 381": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O PHE 2": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O TYR 29": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O PHE 38": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O PHE 82": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O PHE 92": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O PHE 99": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O PHE 169": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O TYR 186": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O PHE 258": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O PHE 262": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O TYR 283": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O TYR 303": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O TYR 381": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P PHE 2": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P TYR 29": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P PHE 38": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P PHE 82": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P PHE 92": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P PHE 99": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P PHE 169": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P TYR 186": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P PHE 258": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P PHE 262": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P TYR 283": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P TYR 303": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P TYR 381": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q PHE 2": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q TYR 29": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q PHE 38": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q PHE 82": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q PHE 92": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q PHE 99": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q PHE 169": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q TYR 186": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q PHE 258": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q PHE 262": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q TYR 283": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q TYR 303": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q TYR 381": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R PHE 2": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R TYR 29": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R PHE 38": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R PHE 82": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R PHE 92": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R PHE 99": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R PHE 169": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R TYR 186": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R PHE 258": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R PHE 262": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R TYR 283": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R TYR 303": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R TYR 381": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S PHE 2": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S TYR 29": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S PHE 38": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S PHE 82": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S PHE 92": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S PHE 99": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S PHE 169": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S TYR 186": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S PHE 258": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S PHE 262": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S TYR 283": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S TYR 303": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S TYR 381": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T PHE 2": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T TYR 29": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T PHE 38": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T PHE 82": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T PHE 92": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T PHE 99": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T PHE 169": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T TYR 186": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T PHE 258": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T PHE 262": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T TYR 283": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T TYR 303": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T TYR 381": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U PHE 2": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U TYR 29": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U PHE 38": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U PHE 82": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U PHE 92": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U PHE 99": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U PHE 169": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U TYR 186": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U PHE 258": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U PHE 262": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U TYR 283": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U TYR 303": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U TYR 381": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V PHE 2": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V TYR 29": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V PHE 38": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V PHE 82": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V PHE 92": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V PHE 99": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V PHE 169": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V TYR 186": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V PHE 258": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V PHE 262": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V TYR 283": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V TYR 303": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V TYR 381": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.15s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5144/modules/chem_data/mon_lib" Total number of atoms: 65076 Number of models: 1 Model: "" Number of chains: 22 Chain: "B" Number of atoms: 2958 Number of conformers: 1 Conformer: "" Number of residues, atoms: 402, 2958 Classifications: {'peptide': 402} Link IDs: {'CIS': 2, 'PCIS': 1, 'PTRANS': 11, 'TRANS': 387} Chain: "C" Number of atoms: 2958 Number of conformers: 1 Conformer: "" Number of residues, atoms: 402, 2958 Classifications: {'peptide': 402} Link IDs: {'CIS': 2, 'PCIS': 1, 'PTRANS': 11, 'TRANS': 387} Chain: "D" Number of atoms: 2958 Number of conformers: 1 Conformer: "" Number of residues, atoms: 402, 2958 Classifications: {'peptide': 402} Link IDs: {'CIS': 2, 'PCIS': 1, 'PTRANS': 11, 'TRANS': 387} Chain: "E" Number of atoms: 2958 Number of conformers: 1 Conformer: "" Number of residues, atoms: 402, 2958 Classifications: {'peptide': 402} Link IDs: {'CIS': 2, 'PCIS': 1, 'PTRANS': 11, 'TRANS': 387} Chain: "F" Number of atoms: 2958 Number of conformers: 1 Conformer: "" Number of residues, atoms: 402, 2958 Classifications: {'peptide': 402} Link IDs: {'CIS': 2, 'PCIS': 1, 'PTRANS': 11, 'TRANS': 387} Chain: "G" Number of atoms: 2958 Number of conformers: 1 Conformer: "" Number of residues, atoms: 402, 2958 Classifications: {'peptide': 402} Link IDs: {'CIS': 2, 'PCIS': 1, 'PTRANS': 11, 'TRANS': 387} Chain: "H" Number of atoms: 2958 Number of conformers: 1 Conformer: "" Number of residues, atoms: 402, 2958 Classifications: {'peptide': 402} Link IDs: {'CIS': 2, 'PCIS': 1, 'PTRANS': 11, 'TRANS': 387} Chain: "I" Number of atoms: 2958 Number of conformers: 1 Conformer: "" Number of residues, atoms: 402, 2958 Classifications: {'peptide': 402} Link IDs: {'CIS': 2, 'PCIS': 1, 'PTRANS': 11, 'TRANS': 387} Chain: "J" Number of atoms: 2958 Number of conformers: 1 Conformer: "" Number of residues, atoms: 402, 2958 Classifications: {'peptide': 402} Link IDs: {'CIS': 2, 'PCIS': 1, 'PTRANS': 11, 'TRANS': 387} Chain: "K" Number of atoms: 2958 Number of conformers: 1 Conformer: "" Number of residues, atoms: 402, 2958 Classifications: {'peptide': 402} Link IDs: {'CIS': 2, 'PCIS': 1, 'PTRANS': 11, 'TRANS': 387} Chain: "L" Number of atoms: 2958 Number of conformers: 1 Conformer: "" Number of residues, atoms: 402, 2958 Classifications: {'peptide': 402} Link IDs: {'CIS': 2, 'PCIS': 1, 'PTRANS': 11, 'TRANS': 387} Chain: "A" Number of atoms: 2958 Number of conformers: 1 Conformer: "" Number of residues, atoms: 402, 2958 Classifications: {'peptide': 402} Link IDs: {'CIS': 2, 'PCIS': 1, 'PTRANS': 11, 'TRANS': 387} Chain: "M" Number of atoms: 2958 Number of conformers: 1 Conformer: "" Number of residues, atoms: 402, 2958 Classifications: {'peptide': 402} Link IDs: {'CIS': 2, 'PCIS': 1, 'PTRANS': 11, 'TRANS': 387} Chain: "N" Number of atoms: 2958 Number of conformers: 1 Conformer: "" Number of residues, atoms: 402, 2958 Classifications: {'peptide': 402} Link IDs: {'CIS': 2, 'PCIS': 1, 'PTRANS': 11, 'TRANS': 387} Chain: "O" Number of atoms: 2958 Number of conformers: 1 Conformer: "" Number of residues, atoms: 402, 2958 Classifications: {'peptide': 402} Link IDs: {'CIS': 2, 'PCIS': 1, 'PTRANS': 11, 'TRANS': 387} Chain: "P" Number of atoms: 2958 Number of conformers: 1 Conformer: "" Number of residues, atoms: 402, 2958 Classifications: {'peptide': 402} Link IDs: {'CIS': 2, 'PCIS': 1, 'PTRANS': 11, 'TRANS': 387} Chain: "Q" Number of atoms: 2958 Number of conformers: 1 Conformer: "" Number of residues, atoms: 402, 2958 Classifications: {'peptide': 402} Link IDs: {'CIS': 2, 'PCIS': 1, 'PTRANS': 11, 'TRANS': 387} Chain: "R" Number of atoms: 2958 Number of conformers: 1 Conformer: "" Number of residues, atoms: 402, 2958 Classifications: {'peptide': 402} Link IDs: {'CIS': 2, 'PCIS': 1, 'PTRANS': 11, 'TRANS': 387} Chain: "S" Number of atoms: 2958 Number of conformers: 1 Conformer: "" Number of residues, atoms: 402, 2958 Classifications: {'peptide': 402} Link IDs: {'CIS': 2, 'PCIS': 1, 'PTRANS': 11, 'TRANS': 387} Chain: "T" Number of atoms: 2958 Number of conformers: 1 Conformer: "" Number of residues, atoms: 402, 2958 Classifications: {'peptide': 402} Link IDs: {'CIS': 2, 'PCIS': 1, 'PTRANS': 11, 'TRANS': 387} Chain: "U" Number of atoms: 2958 Number of conformers: 1 Conformer: "" Number of residues, atoms: 402, 2958 Classifications: {'peptide': 402} Link IDs: {'CIS': 2, 'PCIS': 1, 'PTRANS': 11, 'TRANS': 387} Chain: "V" Number of atoms: 2958 Number of conformers: 1 Conformer: "" Number of residues, atoms: 402, 2958 Classifications: {'peptide': 402} Link IDs: {'CIS': 2, 'PCIS': 1, 'PTRANS': 11, 'TRANS': 387} Time building chain proxies: 25.33, per 1000 atoms: 0.39 Number of scatterers: 65076 At special positions: 0 Unit cell: (186.14, 187.78, 218.94, 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 176 16.00 O 13618 8.00 N 11242 7.00 C 40040 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 20.98 Conformation dependent library (CDL) restraints added in 9.7 seconds 17600 Ramachandran restraints generated. 8800 Oldfield, 0 Emsley, 8800 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 15972 Finding SS restraints... Secondary structure from input PDB file: 88 helices and 198 sheets defined 17.2% alpha, 32.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 6.76 Creating SS restraints... Processing helix chain 'A' and resid 2 through 25 removed outlier: 4.895A pdb=" N GLY A 8 " --> pdb=" O GLN A 4 " (cutoff:3.500A) Processing helix chain 'A' and resid 26 through 28 No H-bonds generated for 'chain 'A' and resid 26 through 28' Processing helix chain 'A' and resid 173 through 177 Processing helix chain 'A' and resid 366 through 402 removed outlier: 4.530A pdb=" N VAL A 372 " --> pdb=" O SER A 368 " (cutoff:3.500A) Processing helix chain 'B' and resid 2 through 25 removed outlier: 4.894A pdb=" N GLY B 8 " --> pdb=" O GLN B 4 " (cutoff:3.500A) Processing helix chain 'B' and resid 26 through 28 No H-bonds generated for 'chain 'B' and resid 26 through 28' Processing helix chain 'B' and resid 173 through 177 Processing helix chain 'B' and resid 366 through 402 removed outlier: 4.530A pdb=" N VAL B 372 " --> pdb=" O SER B 368 " (cutoff:3.500A) Processing helix chain 'C' and resid 2 through 25 removed outlier: 4.894A pdb=" N GLY C 8 " --> pdb=" O GLN C 4 " (cutoff:3.500A) Processing helix chain 'C' and resid 26 through 28 No H-bonds generated for 'chain 'C' and resid 26 through 28' Processing helix chain 'C' and resid 173 through 177 Processing helix chain 'C' and resid 366 through 402 removed outlier: 4.530A pdb=" N VAL C 372 " --> pdb=" O SER C 368 " (cutoff:3.500A) Processing helix chain 'D' and resid 2 through 25 removed outlier: 4.894A pdb=" N GLY D 8 " --> pdb=" O GLN D 4 " (cutoff:3.500A) Processing helix chain 'D' and resid 26 through 28 No H-bonds generated for 'chain 'D' and resid 26 through 28' Processing helix chain 'D' and resid 173 through 177 Processing helix chain 'D' and resid 366 through 402 removed outlier: 4.530A pdb=" N VAL D 372 " --> pdb=" O SER D 368 " (cutoff:3.500A) Processing helix chain 'E' and resid 2 through 25 removed outlier: 4.894A pdb=" N GLY E 8 " --> pdb=" O GLN E 4 " (cutoff:3.500A) Processing helix chain 'E' and resid 26 through 28 No H-bonds generated for 'chain 'E' and resid 26 through 28' Processing helix chain 'E' and resid 173 through 177 Processing helix chain 'E' and resid 366 through 402 removed outlier: 4.530A pdb=" N VAL E 372 " --> pdb=" O SER E 368 " (cutoff:3.500A) Processing helix chain 'F' and resid 2 through 25 removed outlier: 4.895A pdb=" N GLY F 8 " --> pdb=" O GLN F 4 " (cutoff:3.500A) Processing helix chain 'F' and resid 26 through 28 No H-bonds generated for 'chain 'F' and resid 26 through 28' Processing helix chain 'F' and resid 173 through 177 Processing helix chain 'F' and resid 366 through 402 removed outlier: 4.530A pdb=" N VAL F 372 " --> pdb=" O SER F 368 " (cutoff:3.500A) Processing helix chain 'G' and resid 2 through 25 removed outlier: 4.895A pdb=" N GLY G 8 " --> pdb=" O GLN G 4 " (cutoff:3.500A) Processing helix chain 'G' and resid 26 through 28 No H-bonds generated for 'chain 'G' and resid 26 through 28' Processing helix chain 'G' and resid 173 through 177 Processing helix chain 'G' and resid 366 through 402 removed outlier: 4.530A pdb=" N VAL G 372 " --> pdb=" O SER G 368 " (cutoff:3.500A) Processing helix chain 'H' and resid 2 through 25 removed outlier: 4.895A pdb=" N GLY H 8 " --> pdb=" O GLN H 4 " (cutoff:3.500A) Processing helix chain 'H' and resid 26 through 28 No H-bonds generated for 'chain 'H' and resid 26 through 28' Processing helix chain 'H' and resid 173 through 177 Processing helix chain 'H' and resid 366 through 402 removed outlier: 4.530A pdb=" N VAL H 372 " --> pdb=" O SER H 368 " (cutoff:3.500A) Processing helix chain 'I' and resid 2 through 25 removed outlier: 4.894A pdb=" N GLY I 8 " --> pdb=" O GLN I 4 " (cutoff:3.500A) Processing helix chain 'I' and resid 26 through 28 No H-bonds generated for 'chain 'I' and resid 26 through 28' Processing helix chain 'I' and resid 173 through 177 Processing helix chain 'I' and resid 366 through 402 removed outlier: 4.530A pdb=" N VAL I 372 " --> pdb=" O SER I 368 " (cutoff:3.500A) Processing helix chain 'J' and resid 2 through 25 removed outlier: 4.895A pdb=" N GLY J 8 " --> pdb=" O GLN J 4 " (cutoff:3.500A) Processing helix chain 'J' and resid 26 through 28 No H-bonds generated for 'chain 'J' and resid 26 through 28' Processing helix chain 'J' and resid 173 through 177 Processing helix chain 'J' and resid 366 through 402 removed outlier: 4.530A pdb=" N VAL J 372 " --> pdb=" O SER J 368 " (cutoff:3.500A) Processing helix chain 'K' and resid 2 through 25 removed outlier: 4.894A pdb=" N GLY K 8 " --> pdb=" O GLN K 4 " (cutoff:3.500A) Processing helix chain 'K' and resid 26 through 28 No H-bonds generated for 'chain 'K' and resid 26 through 28' Processing helix chain 'K' and resid 173 through 177 Processing helix chain 'K' and resid 366 through 402 removed outlier: 4.529A pdb=" N VAL K 372 " --> pdb=" O SER K 368 " (cutoff:3.500A) Processing helix chain 'L' and resid 2 through 25 removed outlier: 4.895A pdb=" N GLY L 8 " --> pdb=" O GLN L 4 " (cutoff:3.500A) Processing helix chain 'L' and resid 26 through 28 No H-bonds generated for 'chain 'L' and resid 26 through 28' Processing helix chain 'L' and resid 173 through 177 Processing helix chain 'L' and resid 366 through 402 removed outlier: 4.529A pdb=" N VAL L 372 " --> pdb=" O SER L 368 " (cutoff:3.500A) Processing helix chain 'M' and resid 2 through 25 removed outlier: 4.894A pdb=" N GLY M 8 " --> pdb=" O GLN M 4 " (cutoff:3.500A) Processing helix chain 'M' and resid 26 through 28 No H-bonds generated for 'chain 'M' and resid 26 through 28' Processing helix chain 'M' and resid 173 through 177 Processing helix chain 'M' and resid 366 through 402 removed outlier: 4.530A pdb=" N VAL M 372 " --> pdb=" O SER M 368 " (cutoff:3.500A) Processing helix chain 'N' and resid 2 through 25 removed outlier: 4.895A pdb=" N GLY N 8 " --> pdb=" O GLN N 4 " (cutoff:3.500A) Processing helix chain 'N' and resid 26 through 28 No H-bonds generated for 'chain 'N' and resid 26 through 28' Processing helix chain 'N' and resid 173 through 177 Processing helix chain 'N' and resid 366 through 402 removed outlier: 4.530A pdb=" N VAL N 372 " --> pdb=" O SER N 368 " (cutoff:3.500A) Processing helix chain 'O' and resid 2 through 25 removed outlier: 4.895A pdb=" N GLY O 8 " --> pdb=" O GLN O 4 " (cutoff:3.500A) Processing helix chain 'O' and resid 26 through 28 No H-bonds generated for 'chain 'O' and resid 26 through 28' Processing helix chain 'O' and resid 173 through 177 Processing helix chain 'O' and resid 366 through 402 removed outlier: 4.530A pdb=" N VAL O 372 " --> pdb=" O SER O 368 " (cutoff:3.500A) Processing helix chain 'P' and resid 2 through 25 removed outlier: 4.895A pdb=" N GLY P 8 " --> pdb=" O GLN P 4 " (cutoff:3.500A) Processing helix chain 'P' and resid 26 through 28 No H-bonds generated for 'chain 'P' and resid 26 through 28' Processing helix chain 'P' and resid 173 through 177 Processing helix chain 'P' and resid 366 through 402 removed outlier: 4.530A pdb=" N VAL P 372 " --> pdb=" O SER P 368 " (cutoff:3.500A) Processing helix chain 'Q' and resid 2 through 25 removed outlier: 4.895A pdb=" N GLY Q 8 " --> pdb=" O GLN Q 4 " (cutoff:3.500A) Processing helix chain 'Q' and resid 26 through 28 No H-bonds generated for 'chain 'Q' and resid 26 through 28' Processing helix chain 'Q' and resid 173 through 177 Processing helix chain 'Q' and resid 366 through 402 removed outlier: 4.530A pdb=" N VAL Q 372 " --> pdb=" O SER Q 368 " (cutoff:3.500A) Processing helix chain 'R' and resid 2 through 25 removed outlier: 4.895A pdb=" N GLY R 8 " --> pdb=" O GLN R 4 " (cutoff:3.500A) Processing helix chain 'R' and resid 26 through 28 No H-bonds generated for 'chain 'R' and resid 26 through 28' Processing helix chain 'R' and resid 173 through 177 Processing helix chain 'R' and resid 366 through 402 removed outlier: 4.530A pdb=" N VAL R 372 " --> pdb=" O SER R 368 " (cutoff:3.500A) Processing helix chain 'S' and resid 2 through 25 removed outlier: 4.895A pdb=" N GLY S 8 " --> pdb=" O GLN S 4 " (cutoff:3.500A) Processing helix chain 'S' and resid 26 through 28 No H-bonds generated for 'chain 'S' and resid 26 through 28' Processing helix chain 'S' and resid 173 through 177 Processing helix chain 'S' and resid 366 through 402 removed outlier: 4.529A pdb=" N VAL S 372 " --> pdb=" O SER S 368 " (cutoff:3.500A) Processing helix chain 'T' and resid 2 through 25 removed outlier: 4.895A pdb=" N GLY T 8 " --> pdb=" O GLN T 4 " (cutoff:3.500A) Processing helix chain 'T' and resid 26 through 28 No H-bonds generated for 'chain 'T' and resid 26 through 28' Processing helix chain 'T' and resid 173 through 177 Processing helix chain 'T' and resid 366 through 402 removed outlier: 4.530A pdb=" N VAL T 372 " --> pdb=" O SER T 368 " (cutoff:3.500A) Processing helix chain 'U' and resid 2 through 25 removed outlier: 4.895A pdb=" N GLY U 8 " --> pdb=" O GLN U 4 " (cutoff:3.500A) Processing helix chain 'U' and resid 26 through 28 No H-bonds generated for 'chain 'U' and resid 26 through 28' Processing helix chain 'U' and resid 173 through 177 Processing helix chain 'U' and resid 366 through 402 removed outlier: 4.529A pdb=" N VAL U 372 " --> pdb=" O SER U 368 " (cutoff:3.500A) Processing helix chain 'V' and resid 2 through 25 removed outlier: 4.895A pdb=" N GLY V 8 " --> pdb=" O GLN V 4 " (cutoff:3.500A) Processing helix chain 'V' and resid 26 through 28 No H-bonds generated for 'chain 'V' and resid 26 through 28' Processing helix chain 'V' and resid 173 through 177 Processing helix chain 'V' and resid 366 through 402 removed outlier: 4.530A pdb=" N VAL V 372 " --> pdb=" O SER V 368 " (cutoff:3.500A) Processing sheet with id= 1, first strand: chain 'A' and resid 34 through 40 Processing sheet with id= 2, first strand: chain 'A' and resid 90 through 94 removed outlier: 16.047A pdb=" N PHE A 81 " --> pdb=" O TYR A 118 " (cutoff:3.500A) removed outlier: 11.217A pdb=" N TYR A 118 " --> pdb=" O PHE A 81 " (cutoff:3.500A) removed outlier: 5.245A pdb=" N ARG A 83 " --> pdb=" O THR A 116 " (cutoff:3.500A) removed outlier: 5.981A pdb=" N GLU A 308 " --> pdb=" O TYR A 303 " (cutoff:3.500A) removed outlier: 7.389A pdb=" N TYR A 303 " --> pdb=" O GLU A 308 " (cutoff:3.500A) removed outlier: 5.816A pdb=" N VAL A 310 " --> pdb=" O GLY A 301 " (cutoff:3.500A) removed outlier: 6.058A pdb=" N GLY A 301 " --> pdb=" O VAL A 310 " (cutoff:3.500A) Processing sheet with id= 3, first strand: chain 'A' and resid 134 through 135 removed outlier: 5.245A pdb=" N ARG A 83 " --> pdb=" O THR A 116 " (cutoff:3.500A) removed outlier: 11.217A pdb=" N TYR A 118 " --> pdb=" O PHE A 81 " (cutoff:3.500A) removed outlier: 16.047A pdb=" N PHE A 81 " --> pdb=" O TYR A 118 " (cutoff:3.500A) Processing sheet with id= 4, first strand: chain 'A' and resid 100 through 101 Processing sheet with id= 5, first strand: chain 'A' and resid 120 through 121 Processing sheet with id= 6, first strand: chain 'A' and resid 242 through 245 removed outlier: 6.726A pdb=" N ALA A 151 " --> pdb=" O SER A 261 " (cutoff:3.500A) Processing sheet with id= 7, first strand: chain 'A' and resid 242 through 245 removed outlier: 6.726A pdb=" N ALA A 151 " --> pdb=" O SER A 261 " (cutoff:3.500A) removed outlier: 7.124A pdb=" N THR A 150 " --> pdb=" O GLN A 280 " (cutoff:3.500A) removed outlier: 5.077A pdb=" N GLN A 280 " --> pdb=" O THR A 150 " (cutoff:3.500A) removed outlier: 6.042A pdb=" N SER A 152 " --> pdb=" O THR A 278 " (cutoff:3.500A) removed outlier: 4.444A pdb=" N THR A 278 " --> pdb=" O SER A 152 " (cutoff:3.500A) removed outlier: 4.763A pdb=" N GLN A 154 " --> pdb=" O VAL A 276 " (cutoff:3.500A) Processing sheet with id= 8, first strand: chain 'A' and resid 179 through 186 removed outlier: 6.852A pdb=" N GLU A 206 " --> pdb=" O THR A 202 " (cutoff:3.500A) removed outlier: 6.422A pdb=" N LYS A 230 " --> pdb=" O GLU A 238 " (cutoff:3.500A) Processing sheet with id= 9, first strand: chain 'A' and resid 326 through 328 Processing sheet with id= 10, first strand: chain 'B' and resid 34 through 40 Processing sheet with id= 11, first strand: chain 'B' and resid 90 through 94 removed outlier: 16.048A pdb=" N PHE B 81 " --> pdb=" O TYR B 118 " (cutoff:3.500A) removed outlier: 11.217A pdb=" N TYR B 118 " --> pdb=" O PHE B 81 " (cutoff:3.500A) removed outlier: 5.245A pdb=" N ARG B 83 " --> pdb=" O THR B 116 " (cutoff:3.500A) removed outlier: 5.980A pdb=" N GLU B 308 " --> pdb=" O TYR B 303 " (cutoff:3.500A) removed outlier: 7.389A pdb=" N TYR B 303 " --> pdb=" O GLU B 308 " (cutoff:3.500A) removed outlier: 5.817A pdb=" N VAL B 310 " --> pdb=" O GLY B 301 " (cutoff:3.500A) removed outlier: 6.059A pdb=" N GLY B 301 " --> pdb=" O VAL B 310 " (cutoff:3.500A) Processing sheet with id= 12, first strand: chain 'B' and resid 134 through 135 removed outlier: 5.245A pdb=" N ARG B 83 " --> pdb=" O THR B 116 " (cutoff:3.500A) removed outlier: 11.217A pdb=" N TYR B 118 " --> pdb=" O PHE B 81 " (cutoff:3.500A) removed outlier: 16.048A pdb=" N PHE B 81 " --> pdb=" O TYR B 118 " (cutoff:3.500A) Processing sheet with id= 13, first strand: chain 'B' and resid 100 through 101 Processing sheet with id= 14, first strand: chain 'B' and resid 120 through 121 Processing sheet with id= 15, first strand: chain 'B' and resid 242 through 245 removed outlier: 6.726A pdb=" N ALA B 151 " --> pdb=" O SER B 261 " (cutoff:3.500A) Processing sheet with id= 16, first strand: chain 'B' and resid 242 through 245 removed outlier: 6.726A pdb=" N ALA B 151 " --> pdb=" O SER B 261 " (cutoff:3.500A) removed outlier: 7.123A pdb=" N THR B 150 " --> pdb=" O GLN B 280 " (cutoff:3.500A) removed outlier: 5.076A pdb=" N GLN B 280 " --> pdb=" O THR B 150 " (cutoff:3.500A) removed outlier: 6.041A pdb=" N SER B 152 " --> pdb=" O THR B 278 " (cutoff:3.500A) removed outlier: 4.444A pdb=" N THR B 278 " --> pdb=" O SER B 152 " (cutoff:3.500A) removed outlier: 4.763A pdb=" N GLN B 154 " --> pdb=" O VAL B 276 " (cutoff:3.500A) Processing sheet with id= 17, first strand: chain 'B' and resid 179 through 186 removed outlier: 6.851A pdb=" N GLU B 206 " --> pdb=" O THR B 202 " (cutoff:3.500A) removed outlier: 6.422A pdb=" N LYS B 230 " --> pdb=" O GLU B 238 " (cutoff:3.500A) Processing sheet with id= 18, first strand: chain 'B' and resid 326 through 328 Processing sheet with id= 19, first strand: chain 'C' and resid 34 through 40 Processing sheet with id= 20, first strand: chain 'C' and resid 90 through 94 removed outlier: 16.047A pdb=" N PHE C 81 " --> pdb=" O TYR C 118 " (cutoff:3.500A) removed outlier: 11.217A pdb=" N TYR C 118 " --> pdb=" O PHE C 81 " (cutoff:3.500A) removed outlier: 5.245A pdb=" N ARG C 83 " --> pdb=" O THR C 116 " (cutoff:3.500A) removed outlier: 5.980A pdb=" N GLU C 308 " --> pdb=" O TYR C 303 " (cutoff:3.500A) removed outlier: 7.389A pdb=" N TYR C 303 " --> pdb=" O GLU C 308 " (cutoff:3.500A) removed outlier: 5.816A pdb=" N VAL C 310 " --> pdb=" O GLY C 301 " (cutoff:3.500A) removed outlier: 6.059A pdb=" N GLY C 301 " --> pdb=" O VAL C 310 " (cutoff:3.500A) Processing sheet with id= 21, first strand: chain 'C' and resid 134 through 135 removed outlier: 5.245A pdb=" N ARG C 83 " --> pdb=" O THR C 116 " (cutoff:3.500A) removed outlier: 11.217A pdb=" N TYR C 118 " --> pdb=" O PHE C 81 " (cutoff:3.500A) removed outlier: 16.047A pdb=" N PHE C 81 " --> pdb=" O TYR C 118 " (cutoff:3.500A) Processing sheet with id= 22, first strand: chain 'C' and resid 100 through 101 Processing sheet with id= 23, first strand: chain 'C' and resid 120 through 121 Processing sheet with id= 24, first strand: chain 'C' and resid 242 through 245 removed outlier: 6.725A pdb=" N ALA C 151 " --> pdb=" O SER C 261 " (cutoff:3.500A) Processing sheet with id= 25, first strand: chain 'C' and resid 242 through 245 removed outlier: 6.725A pdb=" N ALA C 151 " --> pdb=" O SER C 261 " (cutoff:3.500A) removed outlier: 7.124A pdb=" N THR C 150 " --> pdb=" O GLN C 280 " (cutoff:3.500A) removed outlier: 5.077A pdb=" N GLN C 280 " --> pdb=" O THR C 150 " (cutoff:3.500A) removed outlier: 6.042A pdb=" N SER C 152 " --> pdb=" O THR C 278 " (cutoff:3.500A) removed outlier: 4.444A pdb=" N THR C 278 " --> pdb=" O SER C 152 " (cutoff:3.500A) removed outlier: 4.764A pdb=" N GLN C 154 " --> pdb=" O VAL C 276 " (cutoff:3.500A) Processing sheet with id= 26, first strand: chain 'C' and resid 179 through 186 removed outlier: 6.852A pdb=" N GLU C 206 " --> pdb=" O THR C 202 " (cutoff:3.500A) removed outlier: 6.421A pdb=" N LYS C 230 " --> pdb=" O GLU C 238 " (cutoff:3.500A) Processing sheet with id= 27, first strand: chain 'C' and resid 326 through 328 Processing sheet with id= 28, first strand: chain 'D' and resid 34 through 40 Processing sheet with id= 29, first strand: chain 'D' and resid 90 through 94 removed outlier: 16.047A pdb=" N PHE D 81 " --> pdb=" O TYR D 118 " (cutoff:3.500A) removed outlier: 11.217A pdb=" N TYR D 118 " --> pdb=" O PHE D 81 " (cutoff:3.500A) removed outlier: 5.245A pdb=" N ARG D 83 " --> pdb=" O THR D 116 " (cutoff:3.500A) removed outlier: 5.980A pdb=" N GLU D 308 " --> pdb=" O TYR D 303 " (cutoff:3.500A) removed outlier: 7.390A pdb=" N TYR D 303 " --> pdb=" O GLU D 308 " (cutoff:3.500A) removed outlier: 5.816A pdb=" N VAL D 310 " --> pdb=" O GLY D 301 " (cutoff:3.500A) removed outlier: 6.058A pdb=" N GLY D 301 " --> pdb=" O VAL D 310 " (cutoff:3.500A) Processing sheet with id= 30, first strand: chain 'D' and resid 134 through 135 removed outlier: 5.245A pdb=" N ARG D 83 " --> pdb=" O THR D 116 " (cutoff:3.500A) removed outlier: 11.217A pdb=" N TYR D 118 " --> pdb=" O PHE D 81 " (cutoff:3.500A) removed outlier: 16.047A pdb=" N PHE D 81 " --> pdb=" O TYR D 118 " (cutoff:3.500A) Processing sheet with id= 31, first strand: chain 'D' and resid 100 through 101 Processing sheet with id= 32, first strand: chain 'D' and resid 120 through 121 Processing sheet with id= 33, first strand: chain 'D' and resid 242 through 245 removed outlier: 6.725A pdb=" N ALA D 151 " --> pdb=" O SER D 261 " (cutoff:3.500A) Processing sheet with id= 34, first strand: chain 'D' and resid 242 through 245 removed outlier: 6.725A pdb=" N ALA D 151 " --> pdb=" O SER D 261 " (cutoff:3.500A) removed outlier: 7.124A pdb=" N THR D 150 " --> pdb=" O GLN D 280 " (cutoff:3.500A) removed outlier: 5.076A pdb=" N GLN D 280 " --> pdb=" O THR D 150 " (cutoff:3.500A) removed outlier: 6.041A pdb=" N SER D 152 " --> pdb=" O THR D 278 " (cutoff:3.500A) removed outlier: 4.444A pdb=" N THR D 278 " --> pdb=" O SER D 152 " (cutoff:3.500A) removed outlier: 4.763A pdb=" N GLN D 154 " --> pdb=" O VAL D 276 " (cutoff:3.500A) Processing sheet with id= 35, first strand: chain 'D' and resid 179 through 186 removed outlier: 6.852A pdb=" N GLU D 206 " --> pdb=" O THR D 202 " (cutoff:3.500A) removed outlier: 6.422A pdb=" N LYS D 230 " --> pdb=" O GLU D 238 " (cutoff:3.500A) Processing sheet with id= 36, first strand: chain 'D' and resid 326 through 328 Processing sheet with id= 37, first strand: chain 'E' and resid 34 through 40 Processing sheet with id= 38, first strand: chain 'E' and resid 90 through 94 removed outlier: 16.047A pdb=" N PHE E 81 " --> pdb=" O TYR E 118 " (cutoff:3.500A) removed outlier: 11.217A pdb=" N TYR E 118 " --> pdb=" O PHE E 81 " (cutoff:3.500A) removed outlier: 5.245A pdb=" N ARG E 83 " --> pdb=" O THR E 116 " (cutoff:3.500A) removed outlier: 5.980A pdb=" N GLU E 308 " --> pdb=" O TYR E 303 " (cutoff:3.500A) removed outlier: 7.390A pdb=" N TYR E 303 " --> pdb=" O GLU E 308 " (cutoff:3.500A) removed outlier: 5.816A pdb=" N VAL E 310 " --> pdb=" O GLY E 301 " (cutoff:3.500A) removed outlier: 6.059A pdb=" N GLY E 301 " --> pdb=" O VAL E 310 " (cutoff:3.500A) Processing sheet with id= 39, first strand: chain 'E' and resid 134 through 135 removed outlier: 5.245A pdb=" N ARG E 83 " --> pdb=" O THR E 116 " (cutoff:3.500A) removed outlier: 11.217A pdb=" N TYR E 118 " --> pdb=" O PHE E 81 " (cutoff:3.500A) removed outlier: 16.047A pdb=" N PHE E 81 " --> pdb=" O TYR E 118 " (cutoff:3.500A) Processing sheet with id= 40, first strand: chain 'E' and resid 100 through 101 Processing sheet with id= 41, first strand: chain 'E' and resid 120 through 121 Processing sheet with id= 42, first strand: chain 'E' and resid 242 through 245 removed outlier: 6.725A pdb=" N ALA E 151 " --> pdb=" O SER E 261 " (cutoff:3.500A) Processing sheet with id= 43, first strand: chain 'E' and resid 242 through 245 removed outlier: 6.725A pdb=" N ALA E 151 " --> pdb=" O SER E 261 " (cutoff:3.500A) removed outlier: 7.124A pdb=" N THR E 150 " --> pdb=" O GLN E 280 " (cutoff:3.500A) removed outlier: 5.077A pdb=" N GLN E 280 " --> pdb=" O THR E 150 " (cutoff:3.500A) removed outlier: 6.041A pdb=" N SER E 152 " --> pdb=" O THR E 278 " (cutoff:3.500A) removed outlier: 4.444A pdb=" N THR E 278 " --> pdb=" O SER E 152 " (cutoff:3.500A) removed outlier: 4.763A pdb=" N GLN E 154 " --> pdb=" O VAL E 276 " (cutoff:3.500A) Processing sheet with id= 44, first strand: chain 'E' and resid 179 through 186 removed outlier: 6.852A pdb=" N GLU E 206 " --> pdb=" O THR E 202 " (cutoff:3.500A) removed outlier: 6.422A pdb=" N LYS E 230 " --> pdb=" O GLU E 238 " (cutoff:3.500A) Processing sheet with id= 45, first strand: chain 'E' and resid 326 through 328 Processing sheet with id= 46, first strand: chain 'F' and resid 34 through 40 Processing sheet with id= 47, first strand: chain 'F' and resid 90 through 94 removed outlier: 16.047A pdb=" N PHE F 81 " --> pdb=" O TYR F 118 " (cutoff:3.500A) removed outlier: 11.217A pdb=" N TYR F 118 " --> pdb=" O PHE F 81 " (cutoff:3.500A) removed outlier: 5.244A pdb=" N ARG F 83 " --> pdb=" O THR F 116 " (cutoff:3.500A) removed outlier: 5.980A pdb=" N GLU F 308 " --> pdb=" O TYR F 303 " (cutoff:3.500A) removed outlier: 7.389A pdb=" N TYR F 303 " --> pdb=" O GLU F 308 " (cutoff:3.500A) removed outlier: 5.816A pdb=" N VAL F 310 " --> pdb=" O GLY F 301 " (cutoff:3.500A) removed outlier: 6.059A pdb=" N GLY F 301 " --> pdb=" O VAL F 310 " (cutoff:3.500A) Processing sheet with id= 48, first strand: chain 'F' and resid 134 through 135 removed outlier: 5.244A pdb=" N ARG F 83 " --> pdb=" O THR F 116 " (cutoff:3.500A) removed outlier: 11.217A pdb=" N TYR F 118 " --> pdb=" O PHE F 81 " (cutoff:3.500A) removed outlier: 16.047A pdb=" N PHE F 81 " --> pdb=" O TYR F 118 " (cutoff:3.500A) Processing sheet with id= 49, first strand: chain 'F' and resid 100 through 101 Processing sheet with id= 50, first strand: chain 'F' and resid 120 through 121 Processing sheet with id= 51, first strand: chain 'F' and resid 242 through 245 removed outlier: 6.725A pdb=" N ALA F 151 " --> pdb=" O SER F 261 " (cutoff:3.500A) Processing sheet with id= 52, first strand: chain 'F' and resid 242 through 245 removed outlier: 6.725A pdb=" N ALA F 151 " --> pdb=" O SER F 261 " (cutoff:3.500A) removed outlier: 7.123A pdb=" N THR F 150 " --> pdb=" O GLN F 280 " (cutoff:3.500A) removed outlier: 5.077A pdb=" N GLN F 280 " --> pdb=" O THR F 150 " (cutoff:3.500A) removed outlier: 6.042A pdb=" N SER F 152 " --> pdb=" O THR F 278 " (cutoff:3.500A) removed outlier: 4.443A pdb=" N THR F 278 " --> pdb=" O SER F 152 " (cutoff:3.500A) removed outlier: 4.764A pdb=" N GLN F 154 " --> pdb=" O VAL F 276 " (cutoff:3.500A) Processing sheet with id= 53, first strand: chain 'F' and resid 179 through 186 removed outlier: 6.851A pdb=" N GLU F 206 " --> pdb=" O THR F 202 " (cutoff:3.500A) removed outlier: 6.422A pdb=" N LYS F 230 " --> pdb=" O GLU F 238 " (cutoff:3.500A) Processing sheet with id= 54, first strand: chain 'F' and resid 326 through 328 Processing sheet with id= 55, first strand: chain 'G' and resid 34 through 40 Processing sheet with id= 56, first strand: chain 'G' and resid 90 through 94 removed outlier: 16.047A pdb=" N PHE G 81 " --> pdb=" O TYR G 118 " (cutoff:3.500A) removed outlier: 11.217A pdb=" N TYR G 118 " --> pdb=" O PHE G 81 " (cutoff:3.500A) removed outlier: 5.244A pdb=" N ARG G 83 " --> pdb=" O THR G 116 " (cutoff:3.500A) removed outlier: 5.981A pdb=" N GLU G 308 " --> pdb=" O TYR G 303 " (cutoff:3.500A) removed outlier: 7.389A pdb=" N TYR G 303 " --> pdb=" O GLU G 308 " (cutoff:3.500A) removed outlier: 5.816A pdb=" N VAL G 310 " --> pdb=" O GLY G 301 " (cutoff:3.500A) removed outlier: 6.058A pdb=" N GLY G 301 " --> pdb=" O VAL G 310 " (cutoff:3.500A) Processing sheet with id= 57, first strand: chain 'G' and resid 134 through 135 removed outlier: 5.244A pdb=" N ARG G 83 " --> pdb=" O THR G 116 " (cutoff:3.500A) removed outlier: 11.217A pdb=" N TYR G 118 " --> pdb=" O PHE G 81 " (cutoff:3.500A) removed outlier: 16.047A pdb=" N PHE G 81 " --> pdb=" O TYR G 118 " (cutoff:3.500A) Processing sheet with id= 58, first strand: chain 'G' and resid 100 through 101 Processing sheet with id= 59, first strand: chain 'G' and resid 120 through 121 Processing sheet with id= 60, first strand: chain 'G' and resid 242 through 245 removed outlier: 6.725A pdb=" N ALA G 151 " --> pdb=" O SER G 261 " (cutoff:3.500A) Processing sheet with id= 61, first strand: chain 'G' and resid 242 through 245 removed outlier: 6.725A pdb=" N ALA G 151 " --> pdb=" O SER G 261 " (cutoff:3.500A) removed outlier: 7.123A pdb=" N THR G 150 " --> pdb=" O GLN G 280 " (cutoff:3.500A) removed outlier: 5.076A pdb=" N GLN G 280 " --> pdb=" O THR G 150 " (cutoff:3.500A) removed outlier: 6.041A pdb=" N SER G 152 " --> pdb=" O THR G 278 " (cutoff:3.500A) removed outlier: 4.444A pdb=" N THR G 278 " --> pdb=" O SER G 152 " (cutoff:3.500A) removed outlier: 4.764A pdb=" N GLN G 154 " --> pdb=" O VAL G 276 " (cutoff:3.500A) Processing sheet with id= 62, first strand: chain 'G' and resid 179 through 186 removed outlier: 6.852A pdb=" N GLU G 206 " --> pdb=" O THR G 202 " (cutoff:3.500A) removed outlier: 6.422A pdb=" N LYS G 230 " --> pdb=" O GLU G 238 " (cutoff:3.500A) Processing sheet with id= 63, first strand: chain 'G' and resid 326 through 328 Processing sheet with id= 64, first strand: chain 'H' and resid 34 through 40 Processing sheet with id= 65, first strand: chain 'H' and resid 90 through 94 removed outlier: 16.047A pdb=" N PHE H 81 " --> pdb=" O TYR H 118 " (cutoff:3.500A) removed outlier: 11.217A pdb=" N TYR H 118 " --> pdb=" O PHE H 81 " (cutoff:3.500A) removed outlier: 5.245A pdb=" N ARG H 83 " --> pdb=" O THR H 116 " (cutoff:3.500A) removed outlier: 5.980A pdb=" N GLU H 308 " --> pdb=" O TYR H 303 " (cutoff:3.500A) removed outlier: 7.389A pdb=" N TYR H 303 " --> pdb=" O GLU H 308 " (cutoff:3.500A) removed outlier: 5.816A pdb=" N VAL H 310 " --> pdb=" O GLY H 301 " (cutoff:3.500A) removed outlier: 6.058A pdb=" N GLY H 301 " --> pdb=" O VAL H 310 " (cutoff:3.500A) Processing sheet with id= 66, first strand: chain 'H' and resid 134 through 135 removed outlier: 5.245A pdb=" N ARG H 83 " --> pdb=" O THR H 116 " (cutoff:3.500A) removed outlier: 11.217A pdb=" N TYR H 118 " --> pdb=" O PHE H 81 " (cutoff:3.500A) removed outlier: 16.047A pdb=" N PHE H 81 " --> pdb=" O TYR H 118 " (cutoff:3.500A) Processing sheet with id= 67, first strand: chain 'H' and resid 100 through 101 Processing sheet with id= 68, first strand: chain 'H' and resid 120 through 121 Processing sheet with id= 69, first strand: chain 'H' and resid 242 through 245 removed outlier: 6.725A pdb=" N ALA H 151 " --> pdb=" O SER H 261 " (cutoff:3.500A) Processing sheet with id= 70, first strand: chain 'H' and resid 242 through 245 removed outlier: 6.725A pdb=" N ALA H 151 " --> pdb=" O SER H 261 " (cutoff:3.500A) removed outlier: 7.123A pdb=" N THR H 150 " --> pdb=" O GLN H 280 " (cutoff:3.500A) removed outlier: 5.077A pdb=" N GLN H 280 " --> pdb=" O THR H 150 " (cutoff:3.500A) removed outlier: 6.042A pdb=" N SER H 152 " --> pdb=" O THR H 278 " (cutoff:3.500A) removed outlier: 4.444A pdb=" N THR H 278 " --> pdb=" O SER H 152 " (cutoff:3.500A) removed outlier: 4.764A pdb=" N GLN H 154 " --> pdb=" O VAL H 276 " (cutoff:3.500A) Processing sheet with id= 71, first strand: chain 'H' and resid 179 through 186 removed outlier: 6.852A pdb=" N GLU H 206 " --> pdb=" O THR H 202 " (cutoff:3.500A) removed outlier: 6.422A pdb=" N LYS H 230 " --> pdb=" O GLU H 238 " (cutoff:3.500A) Processing sheet with id= 72, first strand: chain 'H' and resid 326 through 328 Processing sheet with id= 73, first strand: chain 'I' and resid 34 through 40 Processing sheet with id= 74, first strand: chain 'I' and resid 90 through 94 removed outlier: 16.047A pdb=" N PHE I 81 " --> pdb=" O TYR I 118 " (cutoff:3.500A) removed outlier: 11.217A pdb=" N TYR I 118 " --> pdb=" O PHE I 81 " (cutoff:3.500A) removed outlier: 5.244A pdb=" N ARG I 83 " --> pdb=" O THR I 116 " (cutoff:3.500A) removed outlier: 5.980A pdb=" N GLU I 308 " --> pdb=" O TYR I 303 " (cutoff:3.500A) removed outlier: 7.389A pdb=" N TYR I 303 " --> pdb=" O GLU I 308 " (cutoff:3.500A) removed outlier: 5.816A pdb=" N VAL I 310 " --> pdb=" O GLY I 301 " (cutoff:3.500A) removed outlier: 6.059A pdb=" N GLY I 301 " --> pdb=" O VAL I 310 " (cutoff:3.500A) Processing sheet with id= 75, first strand: chain 'I' and resid 134 through 135 removed outlier: 5.244A pdb=" N ARG I 83 " --> pdb=" O THR I 116 " (cutoff:3.500A) removed outlier: 11.217A pdb=" N TYR I 118 " --> pdb=" O PHE I 81 " (cutoff:3.500A) removed outlier: 16.047A pdb=" N PHE I 81 " --> pdb=" O TYR I 118 " (cutoff:3.500A) Processing sheet with id= 76, first strand: chain 'I' and resid 100 through 101 Processing sheet with id= 77, first strand: chain 'I' and resid 120 through 121 Processing sheet with id= 78, first strand: chain 'I' and resid 242 through 245 removed outlier: 6.726A pdb=" N ALA I 151 " --> pdb=" O SER I 261 " (cutoff:3.500A) Processing sheet with id= 79, first strand: chain 'I' and resid 242 through 245 removed outlier: 6.726A pdb=" N ALA I 151 " --> pdb=" O SER I 261 " (cutoff:3.500A) removed outlier: 7.124A pdb=" N THR I 150 " --> pdb=" O GLN I 280 " (cutoff:3.500A) removed outlier: 5.077A pdb=" N GLN I 280 " --> pdb=" O THR I 150 " (cutoff:3.500A) removed outlier: 6.040A pdb=" N SER I 152 " --> pdb=" O THR I 278 " (cutoff:3.500A) removed outlier: 4.444A pdb=" N THR I 278 " --> pdb=" O SER I 152 " (cutoff:3.500A) removed outlier: 4.763A pdb=" N GLN I 154 " --> pdb=" O VAL I 276 " (cutoff:3.500A) Processing sheet with id= 80, first strand: chain 'I' and resid 179 through 186 removed outlier: 6.851A pdb=" N GLU I 206 " --> pdb=" O THR I 202 " (cutoff:3.500A) removed outlier: 6.422A pdb=" N LYS I 230 " --> pdb=" O GLU I 238 " (cutoff:3.500A) Processing sheet with id= 81, first strand: chain 'I' and resid 326 through 328 Processing sheet with id= 82, first strand: chain 'J' and resid 34 through 40 Processing sheet with id= 83, first strand: chain 'J' and resid 90 through 94 removed outlier: 16.047A pdb=" N PHE J 81 " --> pdb=" O TYR J 118 " (cutoff:3.500A) removed outlier: 11.216A pdb=" N TYR J 118 " --> pdb=" O PHE J 81 " (cutoff:3.500A) removed outlier: 5.245A pdb=" N ARG J 83 " --> pdb=" O THR J 116 " (cutoff:3.500A) removed outlier: 5.980A pdb=" N GLU J 308 " --> pdb=" O TYR J 303 " (cutoff:3.500A) removed outlier: 7.390A pdb=" N TYR J 303 " --> pdb=" O GLU J 308 " (cutoff:3.500A) removed outlier: 5.816A pdb=" N VAL J 310 " --> pdb=" O GLY J 301 " (cutoff:3.500A) removed outlier: 6.058A pdb=" N GLY J 301 " --> pdb=" O VAL J 310 " (cutoff:3.500A) Processing sheet with id= 84, first strand: chain 'J' and resid 134 through 135 removed outlier: 5.245A pdb=" N ARG J 83 " --> pdb=" O THR J 116 " (cutoff:3.500A) removed outlier: 11.216A pdb=" N TYR J 118 " --> pdb=" O PHE J 81 " (cutoff:3.500A) removed outlier: 16.047A pdb=" N PHE J 81 " --> pdb=" O TYR J 118 " (cutoff:3.500A) Processing sheet with id= 85, first strand: chain 'J' and resid 100 through 101 Processing sheet with id= 86, first strand: chain 'J' and resid 120 through 121 Processing sheet with id= 87, first strand: chain 'J' and resid 242 through 245 removed outlier: 6.726A pdb=" N ALA J 151 " --> pdb=" O SER J 261 " (cutoff:3.500A) Processing sheet with id= 88, first strand: chain 'J' and resid 242 through 245 removed outlier: 6.726A pdb=" N ALA J 151 " --> pdb=" O SER J 261 " (cutoff:3.500A) removed outlier: 7.123A pdb=" N THR J 150 " --> pdb=" O GLN J 280 " (cutoff:3.500A) removed outlier: 5.077A pdb=" N GLN J 280 " --> pdb=" O THR J 150 " (cutoff:3.500A) removed outlier: 6.042A pdb=" N SER J 152 " --> pdb=" O THR J 278 " (cutoff:3.500A) removed outlier: 4.444A pdb=" N THR J 278 " --> pdb=" O SER J 152 " (cutoff:3.500A) removed outlier: 4.763A pdb=" N GLN J 154 " --> pdb=" O VAL J 276 " (cutoff:3.500A) Processing sheet with id= 89, first strand: chain 'J' and resid 179 through 186 removed outlier: 6.852A pdb=" N GLU J 206 " --> pdb=" O THR J 202 " (cutoff:3.500A) removed outlier: 6.422A pdb=" N LYS J 230 " --> pdb=" O GLU J 238 " (cutoff:3.500A) Processing sheet with id= 90, first strand: chain 'J' and resid 326 through 328 Processing sheet with id= 91, first strand: chain 'K' and resid 34 through 40 Processing sheet with id= 92, first strand: chain 'K' and resid 90 through 94 removed outlier: 16.047A pdb=" N PHE K 81 " --> pdb=" O TYR K 118 " (cutoff:3.500A) removed outlier: 11.217A pdb=" N TYR K 118 " --> pdb=" O PHE K 81 " (cutoff:3.500A) removed outlier: 5.245A pdb=" N ARG K 83 " --> pdb=" O THR K 116 " (cutoff:3.500A) removed outlier: 5.981A pdb=" N GLU K 308 " --> pdb=" O TYR K 303 " (cutoff:3.500A) removed outlier: 7.389A pdb=" N TYR K 303 " --> pdb=" O GLU K 308 " (cutoff:3.500A) removed outlier: 5.816A pdb=" N VAL K 310 " --> pdb=" O GLY K 301 " (cutoff:3.500A) removed outlier: 6.058A pdb=" N GLY K 301 " --> pdb=" O VAL K 310 " (cutoff:3.500A) Processing sheet with id= 93, first strand: chain 'K' and resid 134 through 135 removed outlier: 5.245A pdb=" N ARG K 83 " --> pdb=" O THR K 116 " (cutoff:3.500A) removed outlier: 11.217A pdb=" N TYR K 118 " --> pdb=" O PHE K 81 " (cutoff:3.500A) removed outlier: 16.047A pdb=" N PHE K 81 " --> pdb=" O TYR K 118 " (cutoff:3.500A) Processing sheet with id= 94, first strand: chain 'K' and resid 100 through 101 Processing sheet with id= 95, first strand: chain 'K' and resid 120 through 121 Processing sheet with id= 96, first strand: chain 'K' and resid 242 through 245 removed outlier: 6.726A pdb=" N ALA K 151 " --> pdb=" O SER K 261 " (cutoff:3.500A) Processing sheet with id= 97, first strand: chain 'K' and resid 242 through 245 removed outlier: 6.726A pdb=" N ALA K 151 " --> pdb=" O SER K 261 " (cutoff:3.500A) removed outlier: 7.123A pdb=" N THR K 150 " --> pdb=" O GLN K 280 " (cutoff:3.500A) removed outlier: 5.076A pdb=" N GLN K 280 " --> pdb=" O THR K 150 " (cutoff:3.500A) removed outlier: 6.041A pdb=" N SER K 152 " --> pdb=" O THR K 278 " (cutoff:3.500A) removed outlier: 4.444A pdb=" N THR K 278 " --> pdb=" O SER K 152 " (cutoff:3.500A) removed outlier: 4.763A pdb=" N GLN K 154 " --> pdb=" O VAL K 276 " (cutoff:3.500A) Processing sheet with id= 98, first strand: chain 'K' and resid 179 through 186 removed outlier: 6.852A pdb=" N GLU K 206 " --> pdb=" O THR K 202 " (cutoff:3.500A) removed outlier: 6.421A pdb=" N LYS K 230 " --> pdb=" O GLU K 238 " (cutoff:3.500A) Processing sheet with id= 99, first strand: chain 'K' and resid 326 through 328 Processing sheet with id=100, first strand: chain 'L' and resid 34 through 40 Processing sheet with id=101, first strand: chain 'L' and resid 90 through 94 removed outlier: 16.047A pdb=" N PHE L 81 " --> pdb=" O TYR L 118 " (cutoff:3.500A) removed outlier: 11.217A pdb=" N TYR L 118 " --> pdb=" O PHE L 81 " (cutoff:3.500A) removed outlier: 5.245A pdb=" N ARG L 83 " --> pdb=" O THR L 116 " (cutoff:3.500A) removed outlier: 5.981A pdb=" N GLU L 308 " --> pdb=" O TYR L 303 " (cutoff:3.500A) removed outlier: 7.389A pdb=" N TYR L 303 " --> pdb=" O GLU L 308 " (cutoff:3.500A) removed outlier: 5.817A pdb=" N VAL L 310 " --> pdb=" O GLY L 301 " (cutoff:3.500A) removed outlier: 6.058A pdb=" N GLY L 301 " --> pdb=" O VAL L 310 " (cutoff:3.500A) Processing sheet with id=102, first strand: chain 'L' and resid 134 through 135 removed outlier: 5.245A pdb=" N ARG L 83 " --> pdb=" O THR L 116 " (cutoff:3.500A) removed outlier: 11.217A pdb=" N TYR L 118 " --> pdb=" O PHE L 81 " (cutoff:3.500A) removed outlier: 16.047A pdb=" N PHE L 81 " --> pdb=" O TYR L 118 " (cutoff:3.500A) Processing sheet with id=103, first strand: chain 'L' and resid 100 through 101 Processing sheet with id=104, first strand: chain 'L' and resid 120 through 121 Processing sheet with id=105, first strand: chain 'L' and resid 242 through 245 removed outlier: 6.726A pdb=" N ALA L 151 " --> pdb=" O SER L 261 " (cutoff:3.500A) Processing sheet with id=106, first strand: chain 'L' and resid 242 through 245 removed outlier: 6.726A pdb=" N ALA L 151 " --> pdb=" O SER L 261 " (cutoff:3.500A) removed outlier: 7.124A pdb=" N THR L 150 " --> pdb=" O GLN L 280 " (cutoff:3.500A) removed outlier: 5.077A pdb=" N GLN L 280 " --> pdb=" O THR L 150 " (cutoff:3.500A) removed outlier: 6.042A pdb=" N SER L 152 " --> pdb=" O THR L 278 " (cutoff:3.500A) removed outlier: 4.445A pdb=" N THR L 278 " --> pdb=" O SER L 152 " (cutoff:3.500A) removed outlier: 4.763A pdb=" N GLN L 154 " --> pdb=" O VAL L 276 " (cutoff:3.500A) Processing sheet with id=107, first strand: chain 'L' and resid 179 through 186 removed outlier: 6.851A pdb=" N GLU L 206 " --> pdb=" O THR L 202 " (cutoff:3.500A) removed outlier: 6.422A pdb=" N LYS L 230 " --> pdb=" O GLU L 238 " (cutoff:3.500A) Processing sheet with id=108, first strand: chain 'L' and resid 326 through 328 Processing sheet with id=109, first strand: chain 'M' and resid 34 through 40 Processing sheet with id=110, first strand: chain 'M' and resid 90 through 94 removed outlier: 16.048A pdb=" N PHE M 81 " --> pdb=" O TYR M 118 " (cutoff:3.500A) removed outlier: 11.217A pdb=" N TYR M 118 " --> pdb=" O PHE M 81 " (cutoff:3.500A) removed outlier: 5.245A pdb=" N ARG M 83 " --> pdb=" O THR M 116 " (cutoff:3.500A) removed outlier: 5.980A pdb=" N GLU M 308 " --> pdb=" O TYR M 303 " (cutoff:3.500A) removed outlier: 7.389A pdb=" N TYR M 303 " --> pdb=" O GLU M 308 " (cutoff:3.500A) removed outlier: 5.816A pdb=" N VAL M 310 " --> pdb=" O GLY M 301 " (cutoff:3.500A) removed outlier: 6.058A pdb=" N GLY M 301 " --> pdb=" O VAL M 310 " (cutoff:3.500A) Processing sheet with id=111, first strand: chain 'M' and resid 134 through 135 removed outlier: 5.245A pdb=" N ARG M 83 " --> pdb=" O THR M 116 " (cutoff:3.500A) removed outlier: 11.217A pdb=" N TYR M 118 " --> pdb=" O PHE M 81 " (cutoff:3.500A) removed outlier: 16.048A pdb=" N PHE M 81 " --> pdb=" O TYR M 118 " (cutoff:3.500A) Processing sheet with id=112, first strand: chain 'M' and resid 100 through 101 Processing sheet with id=113, first strand: chain 'M' and resid 120 through 121 Processing sheet with id=114, first strand: chain 'M' and resid 242 through 245 removed outlier: 6.726A pdb=" N ALA M 151 " --> pdb=" O SER M 261 " (cutoff:3.500A) Processing sheet with id=115, first strand: chain 'M' and resid 242 through 245 removed outlier: 6.726A pdb=" N ALA M 151 " --> pdb=" O SER M 261 " (cutoff:3.500A) removed outlier: 7.123A pdb=" N THR M 150 " --> pdb=" O GLN M 280 " (cutoff:3.500A) removed outlier: 5.077A pdb=" N GLN M 280 " --> pdb=" O THR M 150 " (cutoff:3.500A) removed outlier: 6.041A pdb=" N SER M 152 " --> pdb=" O THR M 278 " (cutoff:3.500A) removed outlier: 4.444A pdb=" N THR M 278 " --> pdb=" O SER M 152 " (cutoff:3.500A) removed outlier: 4.764A pdb=" N GLN M 154 " --> pdb=" O VAL M 276 " (cutoff:3.500A) Processing sheet with id=116, first strand: chain 'M' and resid 179 through 186 removed outlier: 6.852A pdb=" N GLU M 206 " --> pdb=" O THR M 202 " (cutoff:3.500A) removed outlier: 6.422A pdb=" N LYS M 230 " --> pdb=" O GLU M 238 " (cutoff:3.500A) Processing sheet with id=117, first strand: chain 'M' and resid 326 through 328 Processing sheet with id=118, first strand: chain 'N' and resid 34 through 40 Processing sheet with id=119, first strand: chain 'N' and resid 90 through 94 removed outlier: 16.047A pdb=" N PHE N 81 " --> pdb=" O TYR N 118 " (cutoff:3.500A) removed outlier: 11.217A pdb=" N TYR N 118 " --> pdb=" O PHE N 81 " (cutoff:3.500A) removed outlier: 5.246A pdb=" N ARG N 83 " --> pdb=" O THR N 116 " (cutoff:3.500A) removed outlier: 5.981A pdb=" N GLU N 308 " --> pdb=" O TYR N 303 " (cutoff:3.500A) removed outlier: 7.390A pdb=" N TYR N 303 " --> pdb=" O GLU N 308 " (cutoff:3.500A) removed outlier: 5.816A pdb=" N VAL N 310 " --> pdb=" O GLY N 301 " (cutoff:3.500A) removed outlier: 6.058A pdb=" N GLY N 301 " --> pdb=" O VAL N 310 " (cutoff:3.500A) Processing sheet with id=120, first strand: chain 'N' and resid 134 through 135 removed outlier: 5.246A pdb=" N ARG N 83 " --> pdb=" O THR N 116 " (cutoff:3.500A) removed outlier: 11.217A pdb=" N TYR N 118 " --> pdb=" O PHE N 81 " (cutoff:3.500A) removed outlier: 16.047A pdb=" N PHE N 81 " --> pdb=" O TYR N 118 " (cutoff:3.500A) Processing sheet with id=121, first strand: chain 'N' and resid 100 through 101 Processing sheet with id=122, first strand: chain 'N' and resid 120 through 121 Processing sheet with id=123, first strand: chain 'N' and resid 242 through 245 removed outlier: 6.726A pdb=" N ALA N 151 " --> pdb=" O SER N 261 " (cutoff:3.500A) Processing sheet with id=124, first strand: chain 'N' and resid 242 through 245 removed outlier: 6.726A pdb=" N ALA N 151 " --> pdb=" O SER N 261 " (cutoff:3.500A) removed outlier: 7.123A pdb=" N THR N 150 " --> pdb=" O GLN N 280 " (cutoff:3.500A) removed outlier: 5.077A pdb=" N GLN N 280 " --> pdb=" O THR N 150 " (cutoff:3.500A) removed outlier: 6.041A pdb=" N SER N 152 " --> pdb=" O THR N 278 " (cutoff:3.500A) removed outlier: 4.444A pdb=" N THR N 278 " --> pdb=" O SER N 152 " (cutoff:3.500A) removed outlier: 4.764A pdb=" N GLN N 154 " --> pdb=" O VAL N 276 " (cutoff:3.500A) Processing sheet with id=125, first strand: chain 'N' and resid 179 through 186 removed outlier: 6.852A pdb=" N GLU N 206 " --> pdb=" O THR N 202 " (cutoff:3.500A) removed outlier: 6.421A pdb=" N LYS N 230 " --> pdb=" O GLU N 238 " (cutoff:3.500A) Processing sheet with id=126, first strand: chain 'N' and resid 326 through 328 Processing sheet with id=127, first strand: chain 'O' and resid 34 through 40 Processing sheet with id=128, first strand: chain 'O' and resid 90 through 94 removed outlier: 16.047A pdb=" N PHE O 81 " --> pdb=" O TYR O 118 " (cutoff:3.500A) removed outlier: 11.216A pdb=" N TYR O 118 " --> pdb=" O PHE O 81 " (cutoff:3.500A) removed outlier: 5.245A pdb=" N ARG O 83 " --> pdb=" O THR O 116 " (cutoff:3.500A) removed outlier: 5.980A pdb=" N GLU O 308 " --> pdb=" O TYR O 303 " (cutoff:3.500A) removed outlier: 7.390A pdb=" N TYR O 303 " --> pdb=" O GLU O 308 " (cutoff:3.500A) removed outlier: 5.816A pdb=" N VAL O 310 " --> pdb=" O GLY O 301 " (cutoff:3.500A) removed outlier: 6.059A pdb=" N GLY O 301 " --> pdb=" O VAL O 310 " (cutoff:3.500A) Processing sheet with id=129, first strand: chain 'O' and resid 134 through 135 removed outlier: 5.245A pdb=" N ARG O 83 " --> pdb=" O THR O 116 " (cutoff:3.500A) removed outlier: 11.216A pdb=" N TYR O 118 " --> pdb=" O PHE O 81 " (cutoff:3.500A) removed outlier: 16.047A pdb=" N PHE O 81 " --> pdb=" O TYR O 118 " (cutoff:3.500A) Processing sheet with id=130, first strand: chain 'O' and resid 100 through 101 Processing sheet with id=131, first strand: chain 'O' and resid 120 through 121 Processing sheet with id=132, first strand: chain 'O' and resid 242 through 245 removed outlier: 6.725A pdb=" N ALA O 151 " --> pdb=" O SER O 261 " (cutoff:3.500A) Processing sheet with id=133, first strand: chain 'O' and resid 242 through 245 removed outlier: 6.725A pdb=" N ALA O 151 " --> pdb=" O SER O 261 " (cutoff:3.500A) removed outlier: 7.124A pdb=" N THR O 150 " --> pdb=" O GLN O 280 " (cutoff:3.500A) removed outlier: 5.077A pdb=" N GLN O 280 " --> pdb=" O THR O 150 " (cutoff:3.500A) removed outlier: 6.041A pdb=" N SER O 152 " --> pdb=" O THR O 278 " (cutoff:3.500A) removed outlier: 4.444A pdb=" N THR O 278 " --> pdb=" O SER O 152 " (cutoff:3.500A) removed outlier: 4.763A pdb=" N GLN O 154 " --> pdb=" O VAL O 276 " (cutoff:3.500A) Processing sheet with id=134, first strand: chain 'O' and resid 179 through 186 removed outlier: 6.851A pdb=" N GLU O 206 " --> pdb=" O THR O 202 " (cutoff:3.500A) removed outlier: 6.422A pdb=" N LYS O 230 " --> pdb=" O GLU O 238 " (cutoff:3.500A) Processing sheet with id=135, first strand: chain 'O' and resid 326 through 328 Processing sheet with id=136, first strand: chain 'P' and resid 34 through 40 Processing sheet with id=137, first strand: chain 'P' and resid 90 through 94 removed outlier: 16.047A pdb=" N PHE P 81 " --> pdb=" O TYR P 118 " (cutoff:3.500A) removed outlier: 11.216A pdb=" N TYR P 118 " --> pdb=" O PHE P 81 " (cutoff:3.500A) removed outlier: 5.245A pdb=" N ARG P 83 " --> pdb=" O THR P 116 " (cutoff:3.500A) removed outlier: 5.981A pdb=" N GLU P 308 " --> pdb=" O TYR P 303 " (cutoff:3.500A) removed outlier: 7.389A pdb=" N TYR P 303 " --> pdb=" O GLU P 308 " (cutoff:3.500A) removed outlier: 5.815A pdb=" N VAL P 310 " --> pdb=" O GLY P 301 " (cutoff:3.500A) removed outlier: 6.059A pdb=" N GLY P 301 " --> pdb=" O VAL P 310 " (cutoff:3.500A) Processing sheet with id=138, first strand: chain 'P' and resid 134 through 135 removed outlier: 5.245A pdb=" N ARG P 83 " --> pdb=" O THR P 116 " (cutoff:3.500A) removed outlier: 11.216A pdb=" N TYR P 118 " --> pdb=" O PHE P 81 " (cutoff:3.500A) removed outlier: 16.047A pdb=" N PHE P 81 " --> pdb=" O TYR P 118 " (cutoff:3.500A) Processing sheet with id=139, first strand: chain 'P' and resid 100 through 101 Processing sheet with id=140, first strand: chain 'P' and resid 120 through 121 Processing sheet with id=141, first strand: chain 'P' and resid 242 through 245 removed outlier: 6.725A pdb=" N ALA P 151 " --> pdb=" O SER P 261 " (cutoff:3.500A) Processing sheet with id=142, first strand: chain 'P' and resid 242 through 245 removed outlier: 6.725A pdb=" N ALA P 151 " --> pdb=" O SER P 261 " (cutoff:3.500A) removed outlier: 7.124A pdb=" N THR P 150 " --> pdb=" O GLN P 280 " (cutoff:3.500A) removed outlier: 5.076A pdb=" N GLN P 280 " --> pdb=" O THR P 150 " (cutoff:3.500A) removed outlier: 6.042A pdb=" N SER P 152 " --> pdb=" O THR P 278 " (cutoff:3.500A) removed outlier: 4.444A pdb=" N THR P 278 " --> pdb=" O SER P 152 " (cutoff:3.500A) removed outlier: 4.763A pdb=" N GLN P 154 " --> pdb=" O VAL P 276 " (cutoff:3.500A) Processing sheet with id=143, first strand: chain 'P' and resid 179 through 186 removed outlier: 6.852A pdb=" N GLU P 206 " --> pdb=" O THR P 202 " (cutoff:3.500A) removed outlier: 6.422A pdb=" N LYS P 230 " --> pdb=" O GLU P 238 " (cutoff:3.500A) Processing sheet with id=144, first strand: chain 'P' and resid 326 through 328 Processing sheet with id=145, first strand: chain 'Q' and resid 34 through 40 Processing sheet with id=146, first strand: chain 'Q' and resid 90 through 94 removed outlier: 16.047A pdb=" N PHE Q 81 " --> pdb=" O TYR Q 118 " (cutoff:3.500A) removed outlier: 11.217A pdb=" N TYR Q 118 " --> pdb=" O PHE Q 81 " (cutoff:3.500A) removed outlier: 5.245A pdb=" N ARG Q 83 " --> pdb=" O THR Q 116 " (cutoff:3.500A) removed outlier: 5.980A pdb=" N GLU Q 308 " --> pdb=" O TYR Q 303 " (cutoff:3.500A) removed outlier: 7.389A pdb=" N TYR Q 303 " --> pdb=" O GLU Q 308 " (cutoff:3.500A) removed outlier: 5.816A pdb=" N VAL Q 310 " --> pdb=" O GLY Q 301 " (cutoff:3.500A) removed outlier: 6.058A pdb=" N GLY Q 301 " --> pdb=" O VAL Q 310 " (cutoff:3.500A) Processing sheet with id=147, first strand: chain 'Q' and resid 134 through 135 removed outlier: 5.245A pdb=" N ARG Q 83 " --> pdb=" O THR Q 116 " (cutoff:3.500A) removed outlier: 11.217A pdb=" N TYR Q 118 " --> pdb=" O PHE Q 81 " (cutoff:3.500A) removed outlier: 16.047A pdb=" N PHE Q 81 " --> pdb=" O TYR Q 118 " (cutoff:3.500A) Processing sheet with id=148, first strand: chain 'Q' and resid 100 through 101 Processing sheet with id=149, first strand: chain 'Q' and resid 120 through 121 Processing sheet with id=150, first strand: chain 'Q' and resid 242 through 245 removed outlier: 6.726A pdb=" N ALA Q 151 " --> pdb=" O SER Q 261 " (cutoff:3.500A) Processing sheet with id=151, first strand: chain 'Q' and resid 242 through 245 removed outlier: 6.726A pdb=" N ALA Q 151 " --> pdb=" O SER Q 261 " (cutoff:3.500A) removed outlier: 7.124A pdb=" N THR Q 150 " --> pdb=" O GLN Q 280 " (cutoff:3.500A) removed outlier: 5.076A pdb=" N GLN Q 280 " --> pdb=" O THR Q 150 " (cutoff:3.500A) removed outlier: 6.041A pdb=" N SER Q 152 " --> pdb=" O THR Q 278 " (cutoff:3.500A) removed outlier: 4.444A pdb=" N THR Q 278 " --> pdb=" O SER Q 152 " (cutoff:3.500A) removed outlier: 4.764A pdb=" N GLN Q 154 " --> pdb=" O VAL Q 276 " (cutoff:3.500A) Processing sheet with id=152, first strand: chain 'Q' and resid 179 through 186 removed outlier: 6.852A pdb=" N GLU Q 206 " --> pdb=" O THR Q 202 " (cutoff:3.500A) removed outlier: 6.422A pdb=" N LYS Q 230 " --> pdb=" O GLU Q 238 " (cutoff:3.500A) Processing sheet with id=153, first strand: chain 'Q' and resid 326 through 328 Processing sheet with id=154, first strand: chain 'R' and resid 34 through 40 Processing sheet with id=155, first strand: chain 'R' and resid 90 through 94 removed outlier: 16.047A pdb=" N PHE R 81 " --> pdb=" O TYR R 118 " (cutoff:3.500A) removed outlier: 11.216A pdb=" N TYR R 118 " --> pdb=" O PHE R 81 " (cutoff:3.500A) removed outlier: 5.244A pdb=" N ARG R 83 " --> pdb=" O THR R 116 " (cutoff:3.500A) removed outlier: 5.981A pdb=" N GLU R 308 " --> pdb=" O TYR R 303 " (cutoff:3.500A) removed outlier: 7.389A pdb=" N TYR R 303 " --> pdb=" O GLU R 308 " (cutoff:3.500A) removed outlier: 5.816A pdb=" N VAL R 310 " --> pdb=" O GLY R 301 " (cutoff:3.500A) removed outlier: 6.058A pdb=" N GLY R 301 " --> pdb=" O VAL R 310 " (cutoff:3.500A) Processing sheet with id=156, first strand: chain 'R' and resid 134 through 135 removed outlier: 5.244A pdb=" N ARG R 83 " --> pdb=" O THR R 116 " (cutoff:3.500A) removed outlier: 11.216A pdb=" N TYR R 118 " --> pdb=" O PHE R 81 " (cutoff:3.500A) removed outlier: 16.047A pdb=" N PHE R 81 " --> pdb=" O TYR R 118 " (cutoff:3.500A) Processing sheet with id=157, first strand: chain 'R' and resid 100 through 101 Processing sheet with id=158, first strand: chain 'R' and resid 120 through 121 Processing sheet with id=159, first strand: chain 'R' and resid 242 through 245 removed outlier: 6.726A pdb=" N ALA R 151 " --> pdb=" O SER R 261 " (cutoff:3.500A) Processing sheet with id=160, first strand: chain 'R' and resid 242 through 245 removed outlier: 6.726A pdb=" N ALA R 151 " --> pdb=" O SER R 261 " (cutoff:3.500A) removed outlier: 7.124A pdb=" N THR R 150 " --> pdb=" O GLN R 280 " (cutoff:3.500A) removed outlier: 5.077A pdb=" N GLN R 280 " --> pdb=" O THR R 150 " (cutoff:3.500A) removed outlier: 6.041A pdb=" N SER R 152 " --> pdb=" O THR R 278 " (cutoff:3.500A) removed outlier: 4.444A pdb=" N THR R 278 " --> pdb=" O SER R 152 " (cutoff:3.500A) removed outlier: 4.763A pdb=" N GLN R 154 " --> pdb=" O VAL R 276 " (cutoff:3.500A) Processing sheet with id=161, first strand: chain 'R' and resid 179 through 186 removed outlier: 6.851A pdb=" N GLU R 206 " --> pdb=" O THR R 202 " (cutoff:3.500A) removed outlier: 6.422A pdb=" N LYS R 230 " --> pdb=" O GLU R 238 " (cutoff:3.500A) Processing sheet with id=162, first strand: chain 'R' and resid 326 through 328 Processing sheet with id=163, first strand: chain 'S' and resid 34 through 40 Processing sheet with id=164, first strand: chain 'S' and resid 90 through 94 removed outlier: 16.047A pdb=" N PHE S 81 " --> pdb=" O TYR S 118 " (cutoff:3.500A) removed outlier: 11.217A pdb=" N TYR S 118 " --> pdb=" O PHE S 81 " (cutoff:3.500A) removed outlier: 5.245A pdb=" N ARG S 83 " --> pdb=" O THR S 116 " (cutoff:3.500A) removed outlier: 5.981A pdb=" N GLU S 308 " --> pdb=" O TYR S 303 " (cutoff:3.500A) removed outlier: 7.390A pdb=" N TYR S 303 " --> pdb=" O GLU S 308 " (cutoff:3.500A) removed outlier: 5.816A pdb=" N VAL S 310 " --> pdb=" O GLY S 301 " (cutoff:3.500A) removed outlier: 6.058A pdb=" N GLY S 301 " --> pdb=" O VAL S 310 " (cutoff:3.500A) Processing sheet with id=165, first strand: chain 'S' and resid 134 through 135 removed outlier: 5.245A pdb=" N ARG S 83 " --> pdb=" O THR S 116 " (cutoff:3.500A) removed outlier: 11.217A pdb=" N TYR S 118 " --> pdb=" O PHE S 81 " (cutoff:3.500A) removed outlier: 16.047A pdb=" N PHE S 81 " --> pdb=" O TYR S 118 " (cutoff:3.500A) Processing sheet with id=166, first strand: chain 'S' and resid 100 through 101 Processing sheet with id=167, first strand: chain 'S' and resid 120 through 121 Processing sheet with id=168, first strand: chain 'S' and resid 242 through 245 removed outlier: 6.726A pdb=" N ALA S 151 " --> pdb=" O SER S 261 " (cutoff:3.500A) Processing sheet with id=169, first strand: chain 'S' and resid 242 through 245 removed outlier: 6.726A pdb=" N ALA S 151 " --> pdb=" O SER S 261 " (cutoff:3.500A) removed outlier: 7.123A pdb=" N THR S 150 " --> pdb=" O GLN S 280 " (cutoff:3.500A) removed outlier: 5.077A pdb=" N GLN S 280 " --> pdb=" O THR S 150 " (cutoff:3.500A) removed outlier: 6.041A pdb=" N SER S 152 " --> pdb=" O THR S 278 " (cutoff:3.500A) removed outlier: 4.444A pdb=" N THR S 278 " --> pdb=" O SER S 152 " (cutoff:3.500A) removed outlier: 4.764A pdb=" N GLN S 154 " --> pdb=" O VAL S 276 " (cutoff:3.500A) Processing sheet with id=170, first strand: chain 'S' and resid 179 through 186 removed outlier: 6.852A pdb=" N GLU S 206 " --> pdb=" O THR S 202 " (cutoff:3.500A) removed outlier: 6.422A pdb=" N LYS S 230 " --> pdb=" O GLU S 238 " (cutoff:3.500A) Processing sheet with id=171, first strand: chain 'S' and resid 326 through 328 Processing sheet with id=172, first strand: chain 'T' and resid 34 through 40 Processing sheet with id=173, first strand: chain 'T' and resid 90 through 94 removed outlier: 16.047A pdb=" N PHE T 81 " --> pdb=" O TYR T 118 " (cutoff:3.500A) removed outlier: 11.217A pdb=" N TYR T 118 " --> pdb=" O PHE T 81 " (cutoff:3.500A) removed outlier: 5.244A pdb=" N ARG T 83 " --> pdb=" O THR T 116 " (cutoff:3.500A) removed outlier: 5.980A pdb=" N GLU T 308 " --> pdb=" O TYR T 303 " (cutoff:3.500A) removed outlier: 7.389A pdb=" N TYR T 303 " --> pdb=" O GLU T 308 " (cutoff:3.500A) removed outlier: 5.816A pdb=" N VAL T 310 " --> pdb=" O GLY T 301 " (cutoff:3.500A) removed outlier: 6.058A pdb=" N GLY T 301 " --> pdb=" O VAL T 310 " (cutoff:3.500A) Processing sheet with id=174, first strand: chain 'T' and resid 134 through 135 removed outlier: 5.244A pdb=" N ARG T 83 " --> pdb=" O THR T 116 " (cutoff:3.500A) removed outlier: 11.217A pdb=" N TYR T 118 " --> pdb=" O PHE T 81 " (cutoff:3.500A) removed outlier: 16.047A pdb=" N PHE T 81 " --> pdb=" O TYR T 118 " (cutoff:3.500A) Processing sheet with id=175, first strand: chain 'T' and resid 100 through 101 Processing sheet with id=176, first strand: chain 'T' and resid 120 through 121 Processing sheet with id=177, first strand: chain 'T' and resid 242 through 245 removed outlier: 6.726A pdb=" N ALA T 151 " --> pdb=" O SER T 261 " (cutoff:3.500A) Processing sheet with id=178, first strand: chain 'T' and resid 242 through 245 removed outlier: 6.726A pdb=" N ALA T 151 " --> pdb=" O SER T 261 " (cutoff:3.500A) removed outlier: 7.123A pdb=" N THR T 150 " --> pdb=" O GLN T 280 " (cutoff:3.500A) removed outlier: 5.077A pdb=" N GLN T 280 " --> pdb=" O THR T 150 " (cutoff:3.500A) removed outlier: 6.042A pdb=" N SER T 152 " --> pdb=" O THR T 278 " (cutoff:3.500A) removed outlier: 4.444A pdb=" N THR T 278 " --> pdb=" O SER T 152 " (cutoff:3.500A) removed outlier: 4.764A pdb=" N GLN T 154 " --> pdb=" O VAL T 276 " (cutoff:3.500A) Processing sheet with id=179, first strand: chain 'T' and resid 179 through 186 removed outlier: 6.851A pdb=" N GLU T 206 " --> pdb=" O THR T 202 " (cutoff:3.500A) removed outlier: 6.421A pdb=" N LYS T 230 " --> pdb=" O GLU T 238 " (cutoff:3.500A) Processing sheet with id=180, first strand: chain 'T' and resid 326 through 328 Processing sheet with id=181, first strand: chain 'U' and resid 34 through 40 Processing sheet with id=182, first strand: chain 'U' and resid 90 through 94 removed outlier: 16.047A pdb=" N PHE U 81 " --> pdb=" O TYR U 118 " (cutoff:3.500A) removed outlier: 11.216A pdb=" N TYR U 118 " --> pdb=" O PHE U 81 " (cutoff:3.500A) removed outlier: 5.245A pdb=" N ARG U 83 " --> pdb=" O THR U 116 " (cutoff:3.500A) removed outlier: 5.981A pdb=" N GLU U 308 " --> pdb=" O TYR U 303 " (cutoff:3.500A) removed outlier: 7.390A pdb=" N TYR U 303 " --> pdb=" O GLU U 308 " (cutoff:3.500A) removed outlier: 5.816A pdb=" N VAL U 310 " --> pdb=" O GLY U 301 " (cutoff:3.500A) removed outlier: 6.058A pdb=" N GLY U 301 " --> pdb=" O VAL U 310 " (cutoff:3.500A) Processing sheet with id=183, first strand: chain 'U' and resid 134 through 135 removed outlier: 5.245A pdb=" N ARG U 83 " --> pdb=" O THR U 116 " (cutoff:3.500A) removed outlier: 11.216A pdb=" N TYR U 118 " --> pdb=" O PHE U 81 " (cutoff:3.500A) removed outlier: 16.047A pdb=" N PHE U 81 " --> pdb=" O TYR U 118 " (cutoff:3.500A) Processing sheet with id=184, first strand: chain 'U' and resid 100 through 101 Processing sheet with id=185, first strand: chain 'U' and resid 120 through 121 Processing sheet with id=186, first strand: chain 'U' and resid 242 through 245 removed outlier: 6.726A pdb=" N ALA U 151 " --> pdb=" O SER U 261 " (cutoff:3.500A) Processing sheet with id=187, first strand: chain 'U' and resid 242 through 245 removed outlier: 6.726A pdb=" N ALA U 151 " --> pdb=" O SER U 261 " (cutoff:3.500A) removed outlier: 7.123A pdb=" N THR U 150 " --> pdb=" O GLN U 280 " (cutoff:3.500A) removed outlier: 5.076A pdb=" N GLN U 280 " --> pdb=" O THR U 150 " (cutoff:3.500A) removed outlier: 6.041A pdb=" N SER U 152 " --> pdb=" O THR U 278 " (cutoff:3.500A) removed outlier: 4.443A pdb=" N THR U 278 " --> pdb=" O SER U 152 " (cutoff:3.500A) removed outlier: 4.763A pdb=" N GLN U 154 " --> pdb=" O VAL U 276 " (cutoff:3.500A) Processing sheet with id=188, first strand: chain 'U' and resid 179 through 186 removed outlier: 6.852A pdb=" N GLU U 206 " --> pdb=" O THR U 202 " (cutoff:3.500A) removed outlier: 6.422A pdb=" N LYS U 230 " --> pdb=" O GLU U 238 " (cutoff:3.500A) Processing sheet with id=189, first strand: chain 'U' and resid 326 through 328 Processing sheet with id=190, first strand: chain 'V' and resid 34 through 40 Processing sheet with id=191, first strand: chain 'V' and resid 90 through 94 removed outlier: 16.047A pdb=" N PHE V 81 " --> pdb=" O TYR V 118 " (cutoff:3.500A) removed outlier: 11.216A pdb=" N TYR V 118 " --> pdb=" O PHE V 81 " (cutoff:3.500A) removed outlier: 5.245A pdb=" N ARG V 83 " --> pdb=" O THR V 116 " (cutoff:3.500A) removed outlier: 5.980A pdb=" N GLU V 308 " --> pdb=" O TYR V 303 " (cutoff:3.500A) removed outlier: 7.390A pdb=" N TYR V 303 " --> pdb=" O GLU V 308 " (cutoff:3.500A) removed outlier: 5.816A pdb=" N VAL V 310 " --> pdb=" O GLY V 301 " (cutoff:3.500A) removed outlier: 6.059A pdb=" N GLY V 301 " --> pdb=" O VAL V 310 " (cutoff:3.500A) Processing sheet with id=192, first strand: chain 'V' and resid 134 through 135 removed outlier: 5.245A pdb=" N ARG V 83 " --> pdb=" O THR V 116 " (cutoff:3.500A) removed outlier: 11.216A pdb=" N TYR V 118 " --> pdb=" O PHE V 81 " (cutoff:3.500A) removed outlier: 16.047A pdb=" N PHE V 81 " --> pdb=" O TYR V 118 " (cutoff:3.500A) Processing sheet with id=193, first strand: chain 'V' and resid 100 through 101 Processing sheet with id=194, first strand: chain 'V' and resid 120 through 121 Processing sheet with id=195, first strand: chain 'V' and resid 242 through 245 removed outlier: 6.726A pdb=" N ALA V 151 " --> pdb=" O SER V 261 " (cutoff:3.500A) Processing sheet with id=196, first strand: chain 'V' and resid 242 through 245 removed outlier: 6.726A pdb=" N ALA V 151 " --> pdb=" O SER V 261 " (cutoff:3.500A) removed outlier: 7.124A pdb=" N THR V 150 " --> pdb=" O GLN V 280 " (cutoff:3.500A) removed outlier: 5.076A pdb=" N GLN V 280 " --> pdb=" O THR V 150 " (cutoff:3.500A) removed outlier: 6.042A pdb=" N SER V 152 " --> pdb=" O THR V 278 " (cutoff:3.500A) removed outlier: 4.445A pdb=" N THR V 278 " --> pdb=" O SER V 152 " (cutoff:3.500A) removed outlier: 4.764A pdb=" N GLN V 154 " --> pdb=" O VAL V 276 " (cutoff:3.500A) Processing sheet with id=197, first strand: chain 'V' and resid 179 through 186 removed outlier: 6.851A pdb=" N GLU V 206 " --> pdb=" O THR V 202 " (cutoff:3.500A) removed outlier: 6.422A pdb=" N LYS V 230 " --> pdb=" O GLU V 238 " (cutoff:3.500A) Processing sheet with id=198, first strand: chain 'V' and resid 326 through 328 2838 hydrogen bonds defined for protein. 7260 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: 30.29 Time building geometry restraints manager: 22.86 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 16230 1.32 - 1.44: 14596 1.44 - 1.56: 34822 1.56 - 1.68: 44 1.68 - 1.81: 352 Bond restraints: 66044 Sorted by residual: bond pdb=" CA ASN F 305 " pdb=" CB ASN F 305 " ideal model delta sigma weight residual 1.528 1.447 0.081 1.37e-02 5.33e+03 3.50e+01 bond pdb=" CA ASN T 305 " pdb=" CB ASN T 305 " ideal model delta sigma weight residual 1.528 1.447 0.081 1.37e-02 5.33e+03 3.49e+01 bond pdb=" CA ASN S 305 " pdb=" CB ASN S 305 " ideal model delta sigma weight residual 1.528 1.447 0.081 1.37e-02 5.33e+03 3.49e+01 bond pdb=" CA ASN K 305 " pdb=" CB ASN K 305 " ideal model delta sigma weight residual 1.528 1.447 0.081 1.37e-02 5.33e+03 3.48e+01 bond pdb=" CA ASN P 305 " pdb=" CB ASN P 305 " ideal model delta sigma weight residual 1.528 1.448 0.081 1.37e-02 5.33e+03 3.47e+01 ... (remaining 66039 not shown) Histogram of bond angle deviations from ideal: 98.95 - 109.83: 15411 109.83 - 120.70: 51697 120.70 - 131.58: 22696 131.58 - 142.45: 110 142.45 - 153.33: 66 Bond angle restraints: 89980 Sorted by residual: angle pdb=" C GLY E 329 " pdb=" N ASP E 330 " pdb=" CA ASP E 330 " ideal model delta sigma weight residual 120.58 153.33 -32.75 1.71e+00 3.42e-01 3.67e+02 angle pdb=" C GLY L 329 " pdb=" N ASP L 330 " pdb=" CA ASP L 330 " ideal model delta sigma weight residual 120.58 153.32 -32.74 1.71e+00 3.42e-01 3.67e+02 angle pdb=" C GLY I 329 " pdb=" N ASP I 330 " pdb=" CA ASP I 330 " ideal model delta sigma weight residual 120.58 153.31 -32.73 1.71e+00 3.42e-01 3.66e+02 angle pdb=" C GLY O 329 " pdb=" N ASP O 330 " pdb=" CA ASP O 330 " ideal model delta sigma weight residual 120.58 153.31 -32.73 1.71e+00 3.42e-01 3.66e+02 angle pdb=" C GLY N 329 " pdb=" N ASP N 330 " pdb=" CA ASP N 330 " ideal model delta sigma weight residual 120.58 153.30 -32.72 1.71e+00 3.42e-01 3.66e+02 ... (remaining 89975 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.70: 37444 16.70 - 33.39: 1056 33.39 - 50.09: 308 50.09 - 66.78: 154 66.78 - 83.48: 110 Dihedral angle restraints: 39072 sinusoidal: 14036 harmonic: 25036 Sorted by residual: dihedral pdb=" CA THR E 65 " pdb=" C THR E 65 " pdb=" N THR E 66 " pdb=" CA THR E 66 " ideal model delta harmonic sigma weight residual -180.00 -144.63 -35.37 0 5.00e+00 4.00e-02 5.00e+01 dihedral pdb=" CA THR M 65 " pdb=" C THR M 65 " pdb=" N THR M 66 " pdb=" CA THR M 66 " ideal model delta harmonic sigma weight residual 180.00 -144.63 -35.37 0 5.00e+00 4.00e-02 5.00e+01 dihedral pdb=" CA THR F 65 " pdb=" C THR F 65 " pdb=" N THR F 66 " pdb=" CA THR F 66 " ideal model delta harmonic sigma weight residual 180.00 -144.64 -35.36 0 5.00e+00 4.00e-02 5.00e+01 ... (remaining 39069 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.067: 6545 0.067 - 0.134: 3117 0.134 - 0.201: 563 0.201 - 0.269: 269 0.269 - 0.336: 66 Chirality restraints: 10560 Sorted by residual: chirality pdb=" CA ASN E 400 " pdb=" N ASN E 400 " pdb=" C ASN E 400 " pdb=" CB ASN E 400 " both_signs ideal model delta sigma weight residual False 2.51 2.17 0.34 2.00e-01 2.50e+01 2.82e+00 chirality pdb=" CA ASN K 400 " pdb=" N ASN K 400 " pdb=" C ASN K 400 " pdb=" CB ASN K 400 " both_signs ideal model delta sigma weight residual False 2.51 2.18 0.33 2.00e-01 2.50e+01 2.80e+00 chirality pdb=" CA TYR Q 303 " pdb=" N TYR Q 303 " pdb=" C TYR Q 303 " pdb=" CB TYR Q 303 " both_signs ideal model delta sigma weight residual False 2.51 2.18 0.33 2.00e-01 2.50e+01 2.80e+00 ... (remaining 10557 not shown) Planarity restraints: 12078 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA THR C 141 " 0.062 2.00e-02 2.50e+03 1.30e-01 1.68e+02 pdb=" C THR C 141 " -0.224 2.00e-02 2.50e+03 pdb=" O THR C 141 " 0.086 2.00e-02 2.50e+03 pdb=" N LEU C 142 " 0.076 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR N 141 " 0.062 2.00e-02 2.50e+03 1.30e-01 1.68e+02 pdb=" C THR N 141 " -0.224 2.00e-02 2.50e+03 pdb=" O THR N 141 " 0.086 2.00e-02 2.50e+03 pdb=" N LEU N 142 " 0.076 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR E 141 " 0.062 2.00e-02 2.50e+03 1.30e-01 1.68e+02 pdb=" C THR E 141 " -0.224 2.00e-02 2.50e+03 pdb=" O THR E 141 " 0.086 2.00e-02 2.50e+03 pdb=" N LEU E 142 " 0.076 2.00e-02 2.50e+03 ... (remaining 12075 not shown) Histogram of nonbonded interaction distances: 1.44 - 2.13: 304 2.13 - 2.83: 25353 2.83 - 3.52: 100481 3.52 - 4.21: 173374 4.21 - 4.90: 282035 Nonbonded interactions: 581547 Sorted by model distance: nonbonded pdb=" CG2 THR J 65 " pdb=" CZ PHE T 42 " model vdw 1.444 3.760 nonbonded pdb=" CG2 THR K 65 " pdb=" CZ PHE U 42 " model vdw 1.444 3.760 nonbonded pdb=" CG2 THR I 65 " pdb=" CZ PHE S 42 " model vdw 1.444 3.760 nonbonded pdb=" CG2 THR L 65 " pdb=" CZ PHE V 42 " model vdw 1.444 3.760 nonbonded pdb=" CG2 THR H 65 " pdb=" CZ PHE R 42 " model vdw 1.444 3.760 ... (remaining 581542 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' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' selection = chain 'U' selection = chain 'V' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.440 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.060 Extract box with map and model: 14.420 Check model and map are aligned: 0.760 Set scattering table: 0.480 Process input model: 143.470 Find NCS groups from input model: 3.800 Set up NCS constraints: 0.460 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: 0.010 Load rotamer database and sin/cos tables:2.350 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 168.250 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.0635 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 : 0.015 0.090 66044 Z= 0.982 Angle : 1.991 32.750 89980 Z= 1.293 Chirality : 0.083 0.336 10560 Planarity : 0.011 0.130 12078 Dihedral : 10.936 83.477 23100 Min Nonbonded Distance : 1.444 Molprobity Statistics. All-atom Clashscore : 20.13 Ramachandran Plot: Outliers : 2.25 % Allowed : 8.25 % Favored : 89.50 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.51 % Twisted Proline : 0.00 % Twisted General : 0.77 % 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: -1.03 (0.09), residues: 8800 helix: 1.29 (0.14), residues: 1276 sheet: -0.90 (0.10), residues: 2442 loop : -1.08 (0.08), residues: 5082 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17600 Ramachandran restraints generated. 8800 Oldfield, 0 Emsley, 8800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17600 Ramachandran restraints generated. 8800 Oldfield, 0 Emsley, 8800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 863 residues out of total 7084 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 863 time to evaluate : 4.989 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 outliers start: 0 outliers final: 0 residues processed: 863 average time/residue: 0.5711 time to fit residues: 861.5340 Evaluate side-chains 518 residues out of total 7084 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 518 time to evaluate : 5.340 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 7.3400 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 880 random chunks: chunk 743 optimal weight: 0.0970 chunk 666 optimal weight: 5.9990 chunk 370 optimal weight: 5.9990 chunk 227 optimal weight: 20.0000 chunk 449 optimal weight: 1.9990 chunk 356 optimal weight: 0.7980 chunk 689 optimal weight: 5.9990 chunk 266 optimal weight: 0.9990 chunk 419 optimal weight: 6.9990 chunk 513 optimal weight: 9.9990 chunk 799 optimal weight: 5.9990 overall best weight: 1.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 25 ASN B 191 ASN ** B 269 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 364 ASN ** C 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 25 ASN C 78 GLN C 191 ASN ** C 269 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 305 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 364 ASN ** D 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 25 ASN ** D 269 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 305 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 309 GLN ** E 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 25 ASN E 191 ASN ** E 269 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 292 GLN ** E 305 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 309 GLN E 364 ASN F 25 ASN F 191 ASN ** F 269 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 305 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 309 GLN ** G 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 25 ASN ** G 269 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 305 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 309 GLN ** G 321 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 25 ASN ** H 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 191 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 251 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 269 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 292 GLN ** H 305 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 25 ASN ** I 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 191 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 251 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 269 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 305 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 309 GLN ** J 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 25 ASN ** J 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 191 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 251 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 269 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 305 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 309 GLN ** K 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 25 ASN ** K 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 191 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 251 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 269 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 292 GLN ** K 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 380 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 25 ASN ** L 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 191 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 251 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 269 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 295 ASN ** L 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 25 ASN ** A 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 191 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 251 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 269 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 281 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 321 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 328 GLN M 25 ASN ** M 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 191 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 251 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 269 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 25 ASN ** N 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 191 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 251 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 269 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 295 ASN ** N 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 321 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 25 ASN ** O 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 191 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 251 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 269 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 281 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 305 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 321 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 25 ASN ** P 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 191 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 251 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 269 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 281 ASN ** P 305 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 25 ASN ** Q 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 191 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 251 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 281 ASN Q 295 ASN ** Q 305 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 78 GLN ** R 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 191 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 251 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 305 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 191 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 251 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 305 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 321 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 191 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 251 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 191 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 251 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 268 GLN U 281 ASN ** U 305 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 191 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 251 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 268 GLN V 281 ASN ** V 305 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 45 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.0915 moved from start: 0.2700 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 66044 Z= 0.233 Angle : 0.859 13.915 89980 Z= 0.478 Chirality : 0.049 0.233 10560 Planarity : 0.004 0.058 12078 Dihedral : 5.718 26.200 9196 Min Nonbonded Distance : 2.215 Molprobity Statistics. All-atom Clashscore : 14.36 Ramachandran Plot: Outliers : 1.00 % Allowed : 6.15 % Favored : 92.85 % Rotamer: Outliers : 0.04 % Allowed : 1.54 % Favored : 98.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.51 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.18 (0.09), residues: 8800 helix: 3.53 (0.13), residues: 1276 sheet: -0.90 (0.09), residues: 2486 loop : -0.64 (0.09), residues: 5038 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17600 Ramachandran restraints generated. 8800 Oldfield, 0 Emsley, 8800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17600 Ramachandran restraints generated. 8800 Oldfield, 0 Emsley, 8800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 616 residues out of total 7084 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 613 time to evaluate : 5.126 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 outliers start: 3 outliers final: 2 residues processed: 613 average time/residue: 0.6124 time to fit residues: 656.0778 Evaluate side-chains 464 residues out of total 7084 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 462 time to evaluate : 4.989 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.4579 time to fit residues: 9.0221 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 880 random chunks: chunk 444 optimal weight: 8.9990 chunk 248 optimal weight: 10.0000 chunk 665 optimal weight: 9.9990 chunk 544 optimal weight: 0.6980 chunk 220 optimal weight: 30.0000 chunk 800 optimal weight: 9.9990 chunk 864 optimal weight: 30.0000 chunk 712 optimal weight: 3.9990 chunk 793 optimal weight: 5.9990 chunk 272 optimal weight: 4.9990 chunk 642 optimal weight: 9.9990 overall best weight: 4.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 15 ASN ** B 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 280 GLN B 281 ASN B 307 GLN ** B 313 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 386 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 15 ASN C 67 ASN ** C 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 205 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 280 GLN C 281 ASN ** C 313 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 378 GLN C 380 ASN ** C 386 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 15 ASN ** D 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 191 ASN ** D 205 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 280 GLN D 281 ASN ** D 313 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 378 GLN E 15 ASN E 67 ASN ** E 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 280 GLN E 281 ASN E 309 GLN ** E 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 378 GLN E 380 ASN ** E 386 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 15 ASN F 67 ASN ** F 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 280 GLN F 281 ASN ** F 313 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 378 GLN F 380 ASN ** F 386 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 15 ASN G 280 GLN G 281 ASN G 309 GLN ** G 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 322 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 378 GLN ** G 380 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 15 ASN H 269 ASN H 280 GLN H 281 ASN ** H 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 313 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 322 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 378 GLN H 380 ASN I 15 ASN I 280 GLN I 281 ASN ** I 313 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 322 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 378 GLN I 380 ASN J 15 ASN ** J 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 280 GLN J 281 ASN ** J 313 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 322 ASN J 378 GLN J 380 ASN K 15 ASN K 67 ASN K 280 GLN K 281 ASN ** K 313 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 378 GLN ** K 380 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 15 ASN L 267 GLN L 280 GLN L 281 ASN L 307 GLN ** L 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 322 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 378 GLN ** L 380 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 15 ASN ** A 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 280 GLN A 307 GLN ** A 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 378 GLN ** A 380 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 15 ASN M 78 GLN ** M 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 191 ASN M 280 GLN M 281 ASN ** M 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 378 GLN N 15 ASN N 78 GLN ** N 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 280 GLN N 281 ASN ** N 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 313 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 378 GLN N 380 ASN O 15 ASN O 78 GLN ** O 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 280 GLN ** O 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 322 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 378 GLN O 380 ASN P 15 ASN P 78 GLN P 280 GLN ** P 281 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 322 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 378 GLN P 380 ASN Q 15 ASN Q 78 GLN ** Q 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 280 GLN ** Q 281 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 307 GLN ** Q 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 322 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 378 GLN R 15 ASN R 280 GLN R 281 ASN ** R 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 322 ASN R 380 ASN S 15 ASN S 280 GLN S 281 ASN ** S 313 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 322 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 15 ASN T 280 GLN T 281 ASN ** T 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 313 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 322 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 380 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 15 ASN U 268 GLN U 280 GLN ** U 281 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 305 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 313 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 322 ASN V 15 ASN V 212 HIS V 280 GLN ** V 281 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 313 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 322 ASN ** V 380 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 111 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1561 moved from start: 0.4851 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.092 66044 Z= 0.331 Angle : 0.930 14.476 89980 Z= 0.502 Chirality : 0.050 0.228 10560 Planarity : 0.005 0.129 12078 Dihedral : 6.113 25.024 9196 Min Nonbonded Distance : 1.994 Molprobity Statistics. All-atom Clashscore : 22.26 Ramachandran Plot: Outliers : 0.75 % Allowed : 8.19 % Favored : 91.06 % Rotamer: Outliers : 0.27 % Allowed : 3.43 % Favored : 96.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.51 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.59 (0.09), residues: 8800 helix: 2.02 (0.13), residues: 1188 sheet: -1.05 (0.09), residues: 2728 loop : -0.53 (0.09), residues: 4884 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17600 Ramachandran restraints generated. 8800 Oldfield, 0 Emsley, 8800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17600 Ramachandran restraints generated. 8800 Oldfield, 0 Emsley, 8800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 534 residues out of total 7084 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 515 time to evaluate : 5.120 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 outliers start: 19 outliers final: 14 residues processed: 533 average time/residue: 0.6305 time to fit residues: 580.7618 Evaluate side-chains 403 residues out of total 7084 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 389 time to evaluate : 5.037 Switching outliers to nearest non-outliers outliers start: 14 outliers final: 0 residues processed: 14 average time/residue: 0.4693 time to fit residues: 20.0043 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 880 random chunks: chunk 790 optimal weight: 0.8980 chunk 601 optimal weight: 6.9990 chunk 415 optimal weight: 7.9990 chunk 88 optimal weight: 7.9990 chunk 382 optimal weight: 8.9990 chunk 537 optimal weight: 10.0000 chunk 803 optimal weight: 8.9990 chunk 850 optimal weight: 9.9990 chunk 419 optimal weight: 7.9990 chunk 761 optimal weight: 6.9990 chunk 229 optimal weight: 20.0000 overall best weight: 6.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 4 GLN B 280 GLN B 281 ASN ** B 313 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 322 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 4 GLN C 280 GLN C 281 ASN ** C 313 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 322 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 4 GLN D 212 HIS D 280 GLN D 281 ASN ** D 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 313 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 322 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 4 GLN ** E 205 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 212 HIS ** E 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 280 GLN E 281 ASN ** E 305 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 313 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 322 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 4 GLN ** F 205 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 212 HIS F 280 GLN F 281 ASN ** F 305 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 313 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 322 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 205 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 212 HIS G 280 GLN G 281 ASN ** G 313 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 322 ASN G 380 ASN ** H 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 212 HIS H 280 GLN ** H 281 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 307 GLN ** H 313 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 322 ASN H 380 ASN ** I 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 212 HIS I 280 GLN I 281 ASN ** I 313 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 322 ASN J 212 HIS J 280 GLN ** J 281 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 292 GLN ** J 305 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 313 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 380 ASN K 212 HIS K 280 GLN ** K 281 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 292 GLN K 307 GLN ** K 313 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 322 ASN ** K 380 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 212 HIS L 280 GLN ** L 281 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 313 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 322 ASN L 380 ASN A 189 GLN A 212 HIS A 280 GLN ** A 313 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 322 ASN A 380 ASN ** M 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 212 HIS M 280 GLN M 281 ASN M 307 GLN ** M 313 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 322 ASN ** N 132 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 212 HIS N 232 ASN N 244 ASN N 280 GLN ** N 281 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 307 GLN ** N 313 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 322 ASN N 386 GLN ** O 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 212 HIS O 280 GLN O 292 GLN O 307 GLN ** O 313 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 322 ASN P 212 HIS P 280 GLN ** P 281 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 307 GLN ** P 313 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 322 ASN ** P 386 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 212 HIS Q 280 GLN ** Q 281 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 292 GLN ** Q 313 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 322 ASN ** R 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 212 HIS R 280 GLN ** R 281 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 313 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 22 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 78 GLN S 212 HIS S 280 GLN ** S 281 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 313 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 322 ASN T 78 GLN T 212 HIS T 280 GLN ** T 281 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 313 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 322 ASN T 380 ASN U 78 GLN U 212 HIS U 280 GLN ** U 281 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 313 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 78 GLN V 280 GLN ** V 313 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 380 ASN Total number of N/Q/H flips: 92 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1899 moved from start: 0.6515 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.065 66044 Z= 0.356 Angle : 0.937 15.472 89980 Z= 0.503 Chirality : 0.052 0.257 10560 Planarity : 0.005 0.114 12078 Dihedral : 6.498 28.073 9196 Min Nonbonded Distance : 2.020 Molprobity Statistics. All-atom Clashscore : 24.13 Ramachandran Plot: Outliers : 1.00 % Allowed : 7.75 % Favored : 91.25 % Rotamer: Outliers : 0.00 % Allowed : 4.18 % Favored : 95.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.51 % 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: -1.07 (0.09), residues: 8800 helix: 1.30 (0.13), residues: 1188 sheet: -0.86 (0.10), residues: 2354 loop : -1.11 (0.08), residues: 5258 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17600 Ramachandran restraints generated. 8800 Oldfield, 0 Emsley, 8800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17600 Ramachandran restraints generated. 8800 Oldfield, 0 Emsley, 8800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 502 residues out of total 7084 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 502 time to evaluate : 5.137 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 outliers start: 0 outliers final: 0 residues processed: 502 average time/residue: 0.6118 time to fit residues: 530.3292 Evaluate side-chains 410 residues out of total 7084 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 410 time to evaluate : 5.024 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 7.2777 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 880 random chunks: chunk 708 optimal weight: 9.9990 chunk 482 optimal weight: 7.9990 chunk 12 optimal weight: 20.0000 chunk 633 optimal weight: 20.0000 chunk 350 optimal weight: 6.9990 chunk 725 optimal weight: 6.9990 chunk 587 optimal weight: 2.9990 chunk 1 optimal weight: 2.9990 chunk 434 optimal weight: 5.9990 chunk 763 optimal weight: 5.9990 chunk 214 optimal weight: 10.0000 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 212 HIS B 280 GLN B 281 ASN ** B 313 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 322 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 386 GLN ** C 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 212 HIS C 280 GLN ** C 281 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 313 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 322 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 386 GLN D 280 GLN ** D 305 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 313 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 322 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 269 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 280 GLN ** E 305 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 313 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 322 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 386 GLN F 280 GLN ** F 313 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 322 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 386 GLN ** G 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 280 GLN ** G 313 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 25 ASN H 78 GLN H 280 GLN H 281 ASN ** H 313 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 280 GLN ** I 313 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 280 GLN J 281 ASN J 292 GLN ** J 313 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 191 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 280 GLN ** K 281 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 313 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 269 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 280 GLN ** L 281 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 313 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 386 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 280 GLN A 281 ASN ** A 313 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 280 GLN ** M 313 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 280 GLN ** N 281 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 313 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 364 ASN N 380 ASN ** O 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 280 GLN ** O 281 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 313 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 380 ASN ** O 386 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 280 GLN P 281 ASN ** P 313 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 129 GLN ** Q 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 191 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 280 GLN Q 281 ASN ** Q 313 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 280 GLN ** R 281 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 313 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 380 ASN ** S 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 280 GLN ** S 281 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 313 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 280 GLN ** T 281 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 313 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 280 GLN ** U 313 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 268 GLN V 280 GLN ** V 313 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 43 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.2029 moved from start: 0.7504 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.068 66044 Z= 0.305 Angle : 0.841 14.372 89980 Z= 0.452 Chirality : 0.049 0.272 10560 Planarity : 0.005 0.074 12078 Dihedral : 6.155 29.003 9196 Min Nonbonded Distance : 2.032 Molprobity Statistics. All-atom Clashscore : 22.59 Ramachandran Plot: Outliers : 1.08 % Allowed : 7.41 % Favored : 91.51 % Rotamer: Outliers : 0.00 % Allowed : 3.50 % Favored : 96.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.51 % 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: -1.01 (0.09), residues: 8800 helix: 1.93 (0.13), residues: 1188 sheet: -1.08 (0.10), residues: 2398 loop : -1.09 (0.08), residues: 5214 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17600 Ramachandran restraints generated. 8800 Oldfield, 0 Emsley, 8800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17600 Ramachandran restraints generated. 8800 Oldfield, 0 Emsley, 8800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 518 residues out of total 7084 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 518 time to evaluate : 5.140 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 outliers start: 0 outliers final: 0 residues processed: 518 average time/residue: 0.5984 time to fit residues: 540.7094 Evaluate side-chains 437 residues out of total 7084 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 437 time to evaluate : 5.034 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 7.3949 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 880 random chunks: chunk 286 optimal weight: 0.9980 chunk 766 optimal weight: 0.2980 chunk 168 optimal weight: 10.0000 chunk 499 optimal weight: 8.9990 chunk 209 optimal weight: 10.0000 chunk 851 optimal weight: 0.9980 chunk 706 optimal weight: 9.9990 chunk 394 optimal weight: 8.9990 chunk 70 optimal weight: 7.9990 chunk 281 optimal weight: 0.7980 chunk 446 optimal weight: 0.8980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 280 GLN ** B 313 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 322 ASN C 25 ASN C 280 GLN ** C 305 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 313 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 322 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 280 GLN ** D 305 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 307 GLN ** D 313 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 322 ASN ** E 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 25 ASN ** E 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 269 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 280 GLN ** E 305 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 313 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 322 ASN F 280 GLN ** F 305 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 313 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 322 ASN F 378 GLN ** G 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 25 ASN ** G 269 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 280 GLN ** G 313 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 378 GLN H 280 GLN ** H 313 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 380 ASN ** I 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 25 ASN ** I 313 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 25 ASN J 58 GLN J 280 GLN J 292 GLN ** J 313 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 378 GLN ** K 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 25 ASN ** K 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 191 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 280 GLN ** K 313 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 380 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 269 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 280 GLN ** L 305 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 313 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 25 ASN ** A 191 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 280 GLN ** A 305 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 313 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 25 ASN M 280 GLN ** M 313 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 380 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 25 ASN N 280 GLN N 295 ASN ** N 313 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 4 GLN ** O 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 25 ASN ** O 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 280 GLN O 281 ASN ** O 313 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 378 GLN ** P 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 25 ASN P 280 GLN P 281 ASN ** P 313 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 4 GLN ** Q 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 25 ASN ** Q 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 191 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 280 GLN Q 281 ASN ** Q 313 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 4 GLN R 280 GLN ** R 313 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 4 GLN S 280 GLN ** S 313 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 58 GLN T 280 GLN ** T 305 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 313 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 58 GLN U 280 GLN ** U 305 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 313 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 328 GLN V 58 GLN V 280 GLN ** V 305 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 313 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 57 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1810 moved from start: 0.7477 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 66044 Z= 0.165 Angle : 0.677 12.363 89980 Z= 0.365 Chirality : 0.044 0.215 10560 Planarity : 0.004 0.048 12078 Dihedral : 5.416 29.460 9196 Min Nonbonded Distance : 2.081 Molprobity Statistics. All-atom Clashscore : 17.56 Ramachandran Plot: Outliers : 1.10 % Allowed : 6.27 % Favored : 92.62 % Rotamer: Outliers : 0.00 % Allowed : 1.33 % Favored : 98.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.51 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.57 (0.09), residues: 8800 helix: 3.09 (0.13), residues: 1188 sheet: -0.49 (0.10), residues: 2288 loop : -1.19 (0.08), residues: 5324 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17600 Ramachandran restraints generated. 8800 Oldfield, 0 Emsley, 8800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17600 Ramachandran restraints generated. 8800 Oldfield, 0 Emsley, 8800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 487 residues out of total 7084 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 487 time to evaluate : 5.885 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 outliers start: 0 outliers final: 0 residues processed: 487 average time/residue: 0.6124 time to fit residues: 520.1054 Evaluate side-chains 411 residues out of total 7084 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 411 time to evaluate : 5.105 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 7.6689 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 880 random chunks: chunk 820 optimal weight: 0.8980 chunk 95 optimal weight: 5.9990 chunk 485 optimal weight: 2.9990 chunk 621 optimal weight: 0.0070 chunk 481 optimal weight: 3.9990 chunk 716 optimal weight: 9.9990 chunk 475 optimal weight: 1.9990 chunk 848 optimal weight: 9.9990 chunk 530 optimal weight: 0.9990 chunk 517 optimal weight: 0.9980 chunk 391 optimal weight: 0.9990 overall best weight: 0.7802 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 25 ASN ** B 313 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 280 GLN ** C 305 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 313 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 322 ASN C 378 GLN D 25 ASN D 280 GLN ** D 305 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 313 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 280 GLN ** E 305 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 313 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 280 GLN ** F 305 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 313 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 269 ASN G 280 GLN ** G 313 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 309 GLN ** H 313 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 380 ASN I 4 GLN ** I 313 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 292 GLN ** J 313 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 380 ASN K 4 GLN ** K 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 280 GLN ** K 313 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 380 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 25 ASN ** L 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 269 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 280 GLN L 292 GLN ** L 305 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 313 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 191 ASN A 280 GLN ** A 305 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 313 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 280 GLN ** M 313 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 380 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 313 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 313 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 280 GLN ** P 313 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 191 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 280 GLN ** Q 313 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 58 GLN ** R 313 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 58 GLN S 280 GLN ** S 305 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 313 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 280 GLN ** T 305 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 313 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 4 GLN U 280 GLN ** U 305 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 313 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 280 GLN ** V 305 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 313 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 32 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1759 moved from start: 0.7569 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.048 66044 Z= 0.159 Angle : 0.646 11.709 89980 Z= 0.347 Chirality : 0.043 0.218 10560 Planarity : 0.004 0.057 12078 Dihedral : 5.063 29.487 9196 Min Nonbonded Distance : 2.104 Molprobity Statistics. All-atom Clashscore : 16.21 Ramachandran Plot: Outliers : 1.14 % Allowed : 6.55 % Favored : 92.32 % Rotamer: Outliers : 0.01 % Allowed : 0.96 % Favored : 99.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.51 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.37 (0.09), residues: 8800 helix: 3.54 (0.13), residues: 1210 sheet: -0.50 (0.10), residues: 2332 loop : -1.07 (0.08), residues: 5258 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17600 Ramachandran restraints generated. 8800 Oldfield, 0 Emsley, 8800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17600 Ramachandran restraints generated. 8800 Oldfield, 0 Emsley, 8800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 488 residues out of total 7084 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 487 time to evaluate : 5.337 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 outliers start: 1 outliers final: 0 residues processed: 487 average time/residue: 0.6027 time to fit residues: 513.0076 Evaluate side-chains 410 residues out of total 7084 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 410 time to evaluate : 5.078 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 7.2929 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 880 random chunks: chunk 524 optimal weight: 2.9990 chunk 338 optimal weight: 7.9990 chunk 506 optimal weight: 7.9990 chunk 255 optimal weight: 5.9990 chunk 166 optimal weight: 20.0000 chunk 164 optimal weight: 5.9990 chunk 539 optimal weight: 7.9990 chunk 577 optimal weight: 10.0000 chunk 419 optimal weight: 20.0000 chunk 79 optimal weight: 6.9990 chunk 666 optimal weight: 7.9990 overall best weight: 5.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 313 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 391 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 280 GLN ** C 305 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 313 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 391 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 280 GLN ** D 305 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 313 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 391 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 280 GLN ** E 305 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 313 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 391 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 280 GLN ** F 305 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 313 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 391 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 280 GLN ** G 313 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 386 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 313 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 380 ASN ** I 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 313 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 58 GLN ** J 313 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 380 ASN ** K 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 280 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 281 ASN ** K 313 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 15 ASN ** L 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 269 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 280 GLN ** L 281 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 292 GLN ** L 305 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 313 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 386 GLN ** A 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 280 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 305 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 313 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 380 ASN ** M 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 280 GLN ** M 313 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 154 GLN ** N 269 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 281 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 313 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 313 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 280 GLN ** P 313 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 380 ASN ** P 386 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 191 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 280 GLN Q 292 GLN ** Q 313 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 22 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 58 GLN ** R 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 281 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 313 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 328 GLN S 58 GLN S 280 GLN ** S 281 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 305 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 313 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 380 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 22 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 191 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 280 GLN ** T 281 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 305 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 313 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 15 ASN ** U 22 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 280 GLN ** U 305 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 313 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 22 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 280 GLN ** V 281 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 305 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 313 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 28 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.2317 moved from start: 0.8997 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.080 66044 Z= 0.352 Angle : 0.931 14.225 89980 Z= 0.498 Chirality : 0.052 0.260 10560 Planarity : 0.005 0.065 12078 Dihedral : 6.325 33.851 9196 Min Nonbonded Distance : 1.990 Molprobity Statistics. All-atom Clashscore : 26.72 Ramachandran Plot: Outliers : 1.14 % Allowed : 8.52 % Favored : 90.34 % Rotamer: Outliers : 0.00 % Allowed : 1.52 % Favored : 98.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.51 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: -1.18 (0.09), residues: 8800 helix: 1.54 (0.13), residues: 1254 sheet: -1.00 (0.10), residues: 2288 loop : -1.29 (0.08), residues: 5258 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17600 Ramachandran restraints generated. 8800 Oldfield, 0 Emsley, 8800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17600 Ramachandran restraints generated. 8800 Oldfield, 0 Emsley, 8800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 578 residues out of total 7084 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 578 time to evaluate : 5.027 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 outliers start: 0 outliers final: 0 residues processed: 578 average time/residue: 0.5888 time to fit residues: 597.8964 Evaluate side-chains 483 residues out of total 7084 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 483 time to evaluate : 5.014 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 7.2583 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 880 random chunks: chunk 771 optimal weight: 7.9990 chunk 812 optimal weight: 0.0770 chunk 741 optimal weight: 40.0000 chunk 790 optimal weight: 0.9990 chunk 475 optimal weight: 9.9990 chunk 344 optimal weight: 8.9990 chunk 620 optimal weight: 7.9990 chunk 242 optimal weight: 0.8980 chunk 714 optimal weight: 6.9990 chunk 747 optimal weight: 10.0000 chunk 787 optimal weight: 10.0000 overall best weight: 3.3944 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 313 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 280 GLN ** C 305 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 313 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 280 GLN ** D 305 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 313 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 378 GLN ** E 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 280 GLN ** E 305 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 313 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 328 GLN E 378 GLN ** F 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 280 GLN ** F 305 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 313 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 4 GLN ** G 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 280 GLN ** G 313 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 380 ASN ** H 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 313 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 378 GLN ** H 386 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 391 GLN ** I 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 292 GLN ** I 305 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 313 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 380 ASN J 4 GLN ** J 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 58 GLN ** J 305 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 313 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 280 GLN ** K 305 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 313 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 380 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 4 GLN ** L 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 269 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 280 GLN L 292 GLN ** L 305 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 313 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 380 ASN A 4 GLN ** A 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 280 GLN ** A 305 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 313 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 4 GLN ** M 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 280 GLN ** M 313 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 380 ASN N 4 GLN ** N 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 269 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 305 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 313 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 380 ASN ** O 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 292 GLN O 295 ASN ** O 313 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 4 GLN ** P 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 280 GLN ** P 313 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 191 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 280 GLN ** Q 305 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 313 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 58 GLN ** R 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 305 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 313 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 386 GLN S 58 GLN S 244 ASN S 280 GLN ** S 305 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 313 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 380 ASN S 386 GLN S 391 GLN ** T 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 191 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 280 GLN T 281 ASN ** T 305 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 313 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 380 ASN T 386 GLN U 280 GLN ** U 305 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 313 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 280 GLN ** V 305 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 313 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 337 GLN V 380 ASN Total number of N/Q/H flips: 49 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.2209 moved from start: 0.9198 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 66044 Z= 0.215 Angle : 0.737 16.939 89980 Z= 0.396 Chirality : 0.046 0.224 10560 Planarity : 0.004 0.054 12078 Dihedral : 5.786 30.213 9196 Min Nonbonded Distance : 2.084 Molprobity Statistics. All-atom Clashscore : 19.91 Ramachandran Plot: Outliers : 0.99 % Allowed : 7.39 % Favored : 91.62 % Rotamer: Outliers : 0.01 % Allowed : 0.73 % Favored : 99.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.51 % 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: -1.05 (0.09), residues: 8800 helix: 2.15 (0.13), residues: 1254 sheet: -1.03 (0.10), residues: 2310 loop : -1.28 (0.08), residues: 5236 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17600 Ramachandran restraints generated. 8800 Oldfield, 0 Emsley, 8800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17600 Ramachandran restraints generated. 8800 Oldfield, 0 Emsley, 8800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 573 residues out of total 7084 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 572 time to evaluate : 5.145 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 outliers start: 1 outliers final: 0 residues processed: 572 average time/residue: 0.5976 time to fit residues: 601.4852 Evaluate side-chains 501 residues out of total 7084 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 501 time to evaluate : 5.064 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 7.5502 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 880 random chunks: chunk 519 optimal weight: 7.9990 chunk 835 optimal weight: 20.0000 chunk 510 optimal weight: 0.0010 chunk 396 optimal weight: 1.9990 chunk 581 optimal weight: 20.0000 chunk 876 optimal weight: 0.0970 chunk 806 optimal weight: 6.9990 chunk 698 optimal weight: 9.9990 chunk 72 optimal weight: 8.9990 chunk 539 optimal weight: 10.0000 chunk 428 optimal weight: 0.9980 overall best weight: 2.0188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 313 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 280 GLN ** C 305 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 313 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 280 GLN ** D 305 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 313 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 280 GLN ** E 305 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 313 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 25 ASN F 280 GLN ** F 305 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 309 GLN ** F 313 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 280 GLN G 295 ASN ** G 313 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 313 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 292 GLN ** I 305 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 313 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 378 GLN ** J 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 58 GLN ** J 305 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 313 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 280 GLN ** K 313 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 380 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 391 GLN ** L 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 269 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 280 GLN L 292 GLN ** L 305 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 313 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 378 GLN L 380 ASN L 391 GLN ** A 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 280 GLN ** A 305 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 313 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 280 GLN ** M 313 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 378 GLN M 391 GLN ** N 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 269 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 295 ASN ** N 305 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 313 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 378 GLN ** O 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 292 GLN ** O 313 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 280 GLN ** P 313 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 380 ASN ** Q 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 191 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 280 GLN Q 292 GLN ** Q 313 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 305 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 313 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 386 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 280 GLN ** S 305 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 313 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 380 ASN ** S 386 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 191 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 280 GLN ** T 305 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 313 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 386 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 280 GLN ** U 305 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 313 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 4 GLN V 280 GLN ** V 305 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 313 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 35 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.2147 moved from start: 0.9353 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 66044 Z= 0.182 Angle : 0.685 12.034 89980 Z= 0.370 Chirality : 0.045 0.316 10560 Planarity : 0.004 0.073 12078 Dihedral : 5.381 29.874 9196 Min Nonbonded Distance : 2.099 Molprobity Statistics. All-atom Clashscore : 17.81 Ramachandran Plot: Outliers : 0.92 % Allowed : 7.41 % Favored : 91.67 % Rotamer: Outliers : 0.00 % Allowed : 0.51 % Favored : 99.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.51 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.84 (0.09), residues: 8800 helix: 2.58 (0.14), residues: 1276 sheet: -0.80 (0.10), residues: 2420 loop : -1.28 (0.08), residues: 5104 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17600 Ramachandran restraints generated. 8800 Oldfield, 0 Emsley, 8800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17600 Ramachandran restraints generated. 8800 Oldfield, 0 Emsley, 8800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 581 residues out of total 7084 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 581 time to evaluate : 5.090 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 outliers start: 0 outliers final: 0 residues processed: 581 average time/residue: 0.5859 time to fit residues: 595.8579 Evaluate side-chains 503 residues out of total 7084 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 503 time to evaluate : 5.042 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 7.3660 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 880 random chunks: chunk 554 optimal weight: 4.9990 chunk 743 optimal weight: 10.0000 chunk 213 optimal weight: 3.9990 chunk 643 optimal weight: 9.9990 chunk 103 optimal weight: 9.9990 chunk 194 optimal weight: 6.9990 chunk 699 optimal weight: 3.9990 chunk 292 optimal weight: 4.9990 chunk 718 optimal weight: 0.9980 chunk 88 optimal weight: 0.2980 chunk 128 optimal weight: 6.9990 overall best weight: 2.8586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 313 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 280 GLN ** C 305 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 313 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 280 GLN ** D 305 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 313 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 280 GLN ** E 305 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 313 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 328 GLN ** F 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 280 GLN F 292 GLN ** F 305 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 309 GLN ** F 313 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 280 GLN G 295 ASN ** G 313 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 4 GLN ** H 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 313 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 380 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 292 GLN ** I 305 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 313 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 305 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 313 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 391 GLN ** K 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 280 GLN ** K 313 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 378 GLN ** K 380 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 391 GLN ** L 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 269 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 280 GLN L 292 GLN ** L 305 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 313 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 280 GLN ** A 305 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 313 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 378 GLN ** M 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 280 GLN ** M 313 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 269 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 305 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 313 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 380 ASN ** O 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 292 GLN ** O 313 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 280 GLN ** P 313 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 378 GLN P 380 ASN ** Q 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 191 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 280 GLN Q 292 GLN ** Q 313 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 378 GLN ** R 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 305 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 313 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 280 GLN ** S 305 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 313 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 191 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 280 GLN ** T 305 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 313 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 386 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 280 GLN U 292 GLN ** U 305 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 313 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 380 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 391 GLN V 280 GLN ** V 305 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 313 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 364 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 34 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5437 r_free = 0.5437 target = 0.327811 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.5260 r_free = 0.5260 target = 0.313839 restraints weight = 1134887.293| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.5309 r_free = 0.5309 target = 0.318533 restraints weight = 711167.616| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.5297 r_free = 0.5297 target = 0.317046 restraints weight = 619972.982| |-----------------------------------------------------------------------------| r_work (final): 0.5292 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.2761 moved from start: 0.9614 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.086 66044 Z= 0.199 Angle : 0.701 12.196 89980 Z= 0.376 Chirality : 0.046 0.270 10560 Planarity : 0.004 0.048 12078 Dihedral : 5.397 29.768 9196 Min Nonbonded Distance : 2.091 Molprobity Statistics. All-atom Clashscore : 18.31 Ramachandran Plot: Outliers : 0.86 % Allowed : 7.39 % Favored : 91.75 % Rotamer: Outliers : 0.01 % Allowed : 0.41 % Favored : 99.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.51 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.89 (0.09), residues: 8800 helix: 2.65 (0.14), residues: 1276 sheet: -0.91 (0.10), residues: 2310 loop : -1.31 (0.08), residues: 5214 =============================================================================== Job complete usr+sys time: 11373.10 seconds wall clock time: 205 minutes 4.62 seconds (12304.62 seconds total)