Starting phenix.real_space_refine on Tue Mar 12 22:42:05 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6kfk_9974/03_2024/6kfk_9974.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6kfk_9974/03_2024/6kfk_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_9974/03_2024/6kfk_9974.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6kfk_9974/03_2024/6kfk_9974.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6kfk_9974/03_2024/6kfk_9974.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6kfk_9974/03_2024/6kfk_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: 0.20s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/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: 29.98, per 1000 atoms: 0.46 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: 21.49 Conformation dependent library (CDL) restraints added in 9.4 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: 7.36 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: 29.20 Time building geometry restraints manager: 23.70 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: 3.370 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.050 Extract box with map and model: 14.920 Check model and map are aligned: 0.730 Set scattering table: 0.460 Process input model: 148.760 Find NCS groups from input model: 3.820 Set up NCS constraints: 0.470 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:2.370 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 174.970 ------------------------------------------------------------------------------- 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 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.009 TRP D 207 HIS 0.004 0.002 HIS Q 212 PHE 0.030 0.004 PHE V 169 TYR 0.050 0.008 TYR F 198 ARG 0.007 0.001 ARG C 95 *********************** 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 : 5.051 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: B 195 MET cc_start: -0.1147 (mmp) cc_final: -0.1802 (tpt) REVERT: B 364 ASN cc_start: 0.4763 (p0) cc_final: 0.3988 (m-40) REVERT: C 113 MET cc_start: 0.0530 (mtt) cc_final: 0.0184 (mtp) REVERT: C 143 MET cc_start: -0.1474 (tpt) cc_final: -0.1963 (tpt) REVERT: C 195 MET cc_start: -0.0304 (mmp) cc_final: -0.0835 (tpt) REVERT: C 364 ASN cc_start: 0.4725 (p0) cc_final: 0.3914 (m-40) REVERT: D 143 MET cc_start: -0.1818 (tpt) cc_final: -0.2167 (tpt) REVERT: D 195 MET cc_start: -0.0716 (mmp) cc_final: -0.1241 (tpt) REVERT: E 143 MET cc_start: -0.1839 (tpt) cc_final: -0.2210 (tpt) REVERT: E 195 MET cc_start: -0.0407 (mmp) cc_final: -0.1116 (tpt) REVERT: E 266 MET cc_start: -0.1453 (mtm) cc_final: -0.1963 (mtt) REVERT: E 364 ASN cc_start: 0.4779 (p0) cc_final: 0.4095 (m-40) REVERT: F 113 MET cc_start: 0.0536 (mtt) cc_final: -0.0057 (mtp) REVERT: F 195 MET cc_start: -0.0563 (mmp) cc_final: -0.1133 (tpt) REVERT: F 266 MET cc_start: -0.1507 (mtm) cc_final: -0.1864 (mtt) REVERT: G 113 MET cc_start: 0.0374 (mtt) cc_final: 0.0048 (mtp) REVERT: G 143 MET cc_start: -0.1475 (tpt) cc_final: -0.1823 (tpt) REVERT: G 195 MET cc_start: -0.0185 (mmp) cc_final: -0.1172 (tpt) REVERT: H 41 MET cc_start: 0.1151 (mmm) cc_final: 0.0925 (mmm) REVERT: H 143 MET cc_start: -0.1866 (tpt) cc_final: -0.2282 (tpt) REVERT: H 195 MET cc_start: -0.0381 (mmp) cc_final: -0.0926 (tpt) REVERT: H 266 MET cc_start: -0.1552 (mtm) cc_final: -0.1932 (mtt) REVERT: I 41 MET cc_start: 0.0786 (mmm) cc_final: 0.0065 (mmm) REVERT: I 143 MET cc_start: -0.2140 (tpt) cc_final: -0.2407 (tpt) REVERT: I 195 MET cc_start: -0.0250 (mmp) cc_final: -0.0858 (tpt) REVERT: J 143 MET cc_start: -0.1913 (tpt) cc_final: -0.2291 (tpt) REVERT: J 195 MET cc_start: -0.0419 (mmp) cc_final: -0.1484 (tpt) REVERT: K 41 MET cc_start: 0.0981 (mmm) cc_final: 0.0226 (mmt) REVERT: K 113 MET cc_start: 0.0901 (mtt) cc_final: 0.0052 (mtp) REVERT: K 195 MET cc_start: -0.0833 (mmp) cc_final: -0.2111 (tpt) REVERT: K 266 MET cc_start: -0.1885 (mtm) cc_final: -0.2373 (mtt) REVERT: K 309 GLN cc_start: 0.4972 (pt0) cc_final: 0.4682 (pm20) REVERT: L 113 MET cc_start: 0.0573 (mtt) cc_final: -0.0023 (mtp) REVERT: L 195 MET cc_start: -0.1005 (mmp) cc_final: -0.1962 (tpt) REVERT: L 266 MET cc_start: -0.1933 (mtm) cc_final: -0.2421 (mtt) REVERT: L 295 ASN cc_start: 0.5048 (p0) cc_final: 0.3893 (m-40) REVERT: A 41 MET cc_start: 0.0904 (mmm) cc_final: 0.0558 (mmt) REVERT: A 195 MET cc_start: -0.0973 (mmp) cc_final: -0.1849 (tpt) REVERT: A 266 MET cc_start: -0.2135 (mtm) cc_final: -0.2540 (mtt) REVERT: A 309 GLN cc_start: 0.5027 (pt0) cc_final: 0.4652 (pm20) REVERT: M 41 MET cc_start: 0.1465 (mmm) cc_final: 0.1127 (mmt) REVERT: M 195 MET cc_start: -0.0961 (mmp) cc_final: -0.2267 (tpt) REVERT: N 195 MET cc_start: -0.1052 (mmp) cc_final: -0.2017 (tpt) REVERT: N 295 ASN cc_start: 0.5330 (p0) cc_final: 0.4319 (m-40) REVERT: O 41 MET cc_start: 0.1257 (mmm) cc_final: 0.0411 (mmt) REVERT: O 195 MET cc_start: -0.1460 (mmp) cc_final: -0.2046 (tpt) REVERT: O 295 ASN cc_start: 0.5379 (p0) cc_final: 0.4110 (m110) REVERT: P 41 MET cc_start: 0.1238 (mmm) cc_final: 0.0633 (mmm) REVERT: P 195 MET cc_start: -0.1503 (mmp) cc_final: -0.1878 (tpt) REVERT: P 295 ASN cc_start: 0.5106 (p0) cc_final: 0.4331 (m-40) REVERT: Q 41 MET cc_start: 0.1160 (mmm) cc_final: 0.0503 (mmt) REVERT: Q 195 MET cc_start: -0.0966 (mmp) cc_final: -0.1505 (tpt) REVERT: Q 204 ASP cc_start: 0.2712 (t0) cc_final: 0.2250 (m-30) REVERT: Q 295 ASN cc_start: 0.5358 (p0) cc_final: 0.4344 (m-40) REVERT: R 41 MET cc_start: 0.1398 (mmm) cc_final: 0.0485 (mmt) REVERT: R 143 MET cc_start: -0.1639 (tpt) cc_final: -0.1962 (tpt) REVERT: R 195 MET cc_start: -0.0685 (mmp) cc_final: -0.1437 (tpt) REVERT: R 295 ASN cc_start: 0.5249 (p0) cc_final: 0.4133 (m110) REVERT: S 41 MET cc_start: 0.1444 (mmm) cc_final: 0.0526 (mmt) REVERT: S 143 MET cc_start: -0.1965 (tpt) cc_final: -0.2199 (tpt) REVERT: S 195 MET cc_start: -0.0735 (mmp) cc_final: -0.1347 (tpt) REVERT: S 204 ASP cc_start: 0.2355 (t0) cc_final: 0.1963 (m-30) REVERT: T 41 MET cc_start: 0.1242 (mmm) cc_final: 0.0213 (mmt) REVERT: T 204 ASP cc_start: 0.2591 (t0) cc_final: 0.2200 (m-30) REVERT: T 309 GLN cc_start: 0.5020 (pt0) cc_final: 0.4638 (pt0) REVERT: U 204 ASP cc_start: 0.3361 (t0) cc_final: 0.2758 (m-30) REVERT: V 41 MET cc_start: 0.1320 (mmm) cc_final: 0.0316 (mmt) REVERT: V 204 ASP cc_start: 0.3242 (t0) cc_final: 0.2926 (m-30) REVERT: V 266 MET cc_start: -0.2253 (mtm) cc_final: -0.2465 (ttm) outliers start: 0 outliers final: 0 residues processed: 863 average time/residue: 0.5582 time to fit residues: 841.1423 Evaluate side-chains 531 residues out of total 7084 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 531 time to evaluate : 5.028 ------------------------------------------------------------------------------- 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: 4.9990 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: 2.9990 chunk 419 optimal weight: 7.9990 chunk 513 optimal weight: 9.9990 chunk 799 optimal weight: 5.9990 overall best weight: 2.1784 ------------------------------------------------------------------------------- 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 305 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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** ** D 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 191 ASN ** D 269 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 305 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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** ** H 307 GLN ** 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 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 25 ASN ** 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 251 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 269 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 292 GLN ** K 305 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 380 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 305 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 307 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 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 305 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 321 ASN ** M 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 305 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 305 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 ** P 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 305 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 378 GLN 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** ** R 307 GLN ** 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 307 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 251 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 305 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 309 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 281 ASN ** V 305 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 26 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.0950 moved from start: 0.2720 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.068 66044 Z= 0.238 Angle : 0.855 14.002 89980 Z= 0.475 Chirality : 0.049 0.249 10560 Planarity : 0.004 0.054 12078 Dihedral : 5.727 25.490 9196 Min Nonbonded Distance : 2.175 Molprobity Statistics. All-atom Clashscore : 15.61 Ramachandran Plot: Outliers : 1.00 % Allowed : 6.01 % Favored : 92.99 % Rotamer: Outliers : 0.00 % Allowed : 1.40 % Favored : 98.60 % 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: -0.16 (0.09), residues: 8800 helix: 3.48 (0.13), residues: 1276 sheet: -1.00 (0.10), residues: 2376 loop : -0.56 (0.09), residues: 5148 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP M 207 HIS 0.002 0.001 HIS M 212 PHE 0.028 0.002 PHE D 231 TYR 0.020 0.002 TYR J 303 ARG 0.016 0.002 ARG A 70 *********************** 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 623 residues out of total 7084 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 623 time to evaluate : 5.320 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: B 195 MET cc_start: -0.0700 (mmp) cc_final: -0.1099 (tpp) REVERT: C 110 MET cc_start: 0.2212 (tmm) cc_final: 0.0812 (ttt) REVERT: C 143 MET cc_start: -0.1860 (tpt) cc_final: -0.2330 (tpt) REVERT: C 195 MET cc_start: -0.0063 (mmp) cc_final: -0.0589 (tpp) REVERT: C 364 ASN cc_start: 0.4686 (p0) cc_final: 0.4085 (m110) REVERT: D 143 MET cc_start: -0.1734 (tpt) cc_final: -0.2240 (tpt) REVERT: D 195 MET cc_start: -0.0402 (mmp) cc_final: -0.1010 (tpt) REVERT: E 110 MET cc_start: 0.2405 (tmm) cc_final: 0.1576 (ttt) REVERT: E 143 MET cc_start: -0.2055 (tpt) cc_final: -0.2417 (tpt) REVERT: E 195 MET cc_start: -0.0036 (mmp) cc_final: -0.0632 (tpp) REVERT: F 110 MET cc_start: 0.2137 (tmm) cc_final: 0.0593 (ttt) REVERT: F 113 MET cc_start: 0.0454 (mtt) cc_final: 0.0088 (mtp) REVERT: F 195 MET cc_start: -0.0202 (mmp) cc_final: -0.0922 (tpt) REVERT: G 113 MET cc_start: 0.0647 (mtt) cc_final: 0.0415 (mtp) REVERT: G 143 MET cc_start: -0.1940 (tpt) cc_final: -0.2478 (tpt) REVERT: G 195 MET cc_start: 0.0139 (mmp) cc_final: -0.0764 (tpt) REVERT: H 143 MET cc_start: -0.1954 (tpt) cc_final: -0.2453 (tpt) REVERT: H 195 MET cc_start: 0.0042 (mmp) cc_final: -0.1062 (tpt) REVERT: I 143 MET cc_start: -0.2185 (tpt) cc_final: -0.2595 (tpt) REVERT: I 195 MET cc_start: 0.0156 (mmp) cc_final: -0.0780 (tpt) REVERT: J 143 MET cc_start: -0.1989 (tpt) cc_final: -0.2532 (tpt) REVERT: J 195 MET cc_start: -0.0260 (mmp) cc_final: -0.1763 (tpt) REVERT: K 195 MET cc_start: -0.0547 (mmp) cc_final: -0.1984 (tpt) REVERT: L 113 MET cc_start: 0.0534 (mtt) cc_final: 0.0332 (mtp) REVERT: L 195 MET cc_start: -0.0571 (mmp) cc_final: -0.1549 (tpt) REVERT: L 295 ASN cc_start: 0.4569 (p0) cc_final: 0.4213 (m110) REVERT: L 309 GLN cc_start: 0.5304 (pm20) cc_final: 0.4577 (pm20) REVERT: A 41 MET cc_start: 0.1460 (mmm) cc_final: 0.0965 (mmm) REVERT: A 113 MET cc_start: 0.0992 (mtt) cc_final: 0.0785 (mtp) REVERT: A 195 MET cc_start: -0.0556 (mmp) cc_final: -0.1867 (tpt) REVERT: M 195 MET cc_start: -0.0966 (mmp) cc_final: -0.1908 (tpt) REVERT: N 113 MET cc_start: 0.1031 (mtt) cc_final: 0.0791 (mtp) REVERT: N 195 MET cc_start: -0.0686 (mmp) cc_final: -0.1816 (tpt) REVERT: N 295 ASN cc_start: 0.4716 (p0) cc_final: 0.4311 (m-40) REVERT: O 41 MET cc_start: 0.1395 (mmm) cc_final: 0.1128 (mmm) REVERT: O 113 MET cc_start: 0.0883 (mtt) cc_final: 0.0511 (mtp) REVERT: O 195 MET cc_start: -0.1466 (mmp) cc_final: -0.2065 (tpt) REVERT: O 295 ASN cc_start: 0.5136 (p0) cc_final: 0.4166 (m110) REVERT: P 195 MET cc_start: -0.1271 (mmp) cc_final: -0.2066 (tpt) REVERT: P 295 ASN cc_start: 0.4988 (p0) cc_final: 0.4296 (m-40) REVERT: Q 113 MET cc_start: -0.1397 (mtm) cc_final: -0.1624 (mtp) REVERT: Q 195 MET cc_start: -0.0740 (mmp) cc_final: -0.1613 (tpt) REVERT: Q 204 ASP cc_start: 0.2519 (t0) cc_final: 0.2317 (m-30) REVERT: Q 295 ASN cc_start: 0.5373 (p0) cc_final: 0.4559 (m-40) REVERT: R 143 MET cc_start: -0.2461 (tpt) cc_final: -0.2670 (tpt) REVERT: R 195 MET cc_start: -0.0454 (mmp) cc_final: -0.1319 (tpt) REVERT: R 292 GLN cc_start: 0.3689 (tp-100) cc_final: 0.3468 (tp-100) REVERT: R 295 ASN cc_start: 0.5220 (p0) cc_final: 0.4297 (m110) REVERT: S 195 MET cc_start: -0.0561 (mmp) cc_final: -0.0989 (tpt) REVERT: T 195 MET cc_start: 0.0471 (tpt) cc_final: 0.0058 (tpp) REVERT: U 204 ASP cc_start: 0.3175 (t0) cc_final: 0.2926 (m-30) outliers start: 0 outliers final: 0 residues processed: 623 average time/residue: 0.6012 time to fit residues: 652.7392 Evaluate side-chains 467 residues out of total 7084 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 467 time to evaluate : 5.053 ------------------------------------------------------------------------------- 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: 0.7980 chunk 248 optimal weight: 8.9990 chunk 665 optimal weight: 20.0000 chunk 544 optimal weight: 40.0000 chunk 220 optimal weight: 20.0000 chunk 800 optimal weight: 1.9990 chunk 864 optimal weight: 30.0000 chunk 712 optimal weight: 0.8980 chunk 793 optimal weight: 7.9990 chunk 272 optimal weight: 5.9990 chunk 642 optimal weight: 8.9990 overall best weight: 3.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 15 ASN B 267 GLN B 280 GLN B 281 ASN B 307 GLN B 378 GLN ** B 386 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 15 ASN C 67 ASN ** C 205 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 267 GLN C 280 GLN C 281 ASN ** C 305 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 307 GLN C 378 GLN C 380 ASN D 15 ASN D 267 GLN D 280 GLN D 281 ASN ** D 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 322 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 378 GLN E 15 ASN ** E 269 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 280 GLN E 281 ASN ** E 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 378 GLN E 380 ASN F 15 ASN ** F 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 205 ASN F 267 GLN F 280 GLN F 281 ASN F 309 GLN ** F 322 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 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 322 ASN G 378 GLN H 15 ASN H 269 ASN H 280 GLN H 281 ASN ** H 305 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 322 ASN H 378 GLN H 380 ASN I 15 ASN I 67 ASN ** I 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 280 GLN I 281 ASN ** I 305 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 307 GLN ** 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 322 ASN I 378 GLN J 15 ASN J 67 ASN J 267 GLN J 280 GLN J 281 ASN ** J 305 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 309 GLN ** 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 322 ASN J 378 GLN J 380 ASN K 15 ASN ** K 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 67 ASN ** K 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 191 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 269 ASN K 280 GLN K 281 ASN K 309 GLN ** K 313 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 322 ASN K 378 GLN ** K 380 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 15 ASN ** L 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 67 ASN L 267 GLN L 280 GLN L 281 ASN ** L 305 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 307 GLN ** L 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 322 ASN L 378 GLN ** L 380 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 15 ASN ** A 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 280 GLN ** A 281 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 307 GLN ** A 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 321 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 322 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 378 GLN ** A 380 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 15 ASN ** M 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 78 GLN M 191 ASN ** M 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 280 GLN ** M 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 322 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 378 GLN N 15 ASN ** N 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 78 GLN 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 322 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 378 GLN ** N 380 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 15 ASN ** O 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 321 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 322 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 378 GLN P 15 ASN ** P 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 78 GLN P 189 GLN P 191 ASN ** P 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 P 378 GLN P 380 ASN Q 15 ASN ** Q 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 313 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 322 ASN R 15 ASN R 280 GLN R 281 ASN ** R 305 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 307 GLN ** R 313 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 322 ASN R 380 ASN S 15 ASN ** S 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 280 GLN S 281 ASN ** 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 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 309 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 U 15 ASN 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 322 ASN V 15 ASN 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 322 ASN Total number of N/Q/H flips: 122 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1389 moved from start: 0.4444 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.087 66044 Z= 0.256 Angle : 0.825 14.142 89980 Z= 0.450 Chirality : 0.047 0.187 10560 Planarity : 0.005 0.101 12078 Dihedral : 5.711 23.930 9196 Min Nonbonded Distance : 2.014 Molprobity Statistics. All-atom Clashscore : 18.09 Ramachandran Plot: Outliers : 0.75 % Allowed : 7.57 % Favored : 91.68 % Rotamer: Outliers : 0.25 % Allowed : 3.44 % 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: -0.38 (0.09), residues: 8800 helix: 2.94 (0.12), residues: 1210 sheet: -1.10 (0.09), residues: 2860 loop : -0.47 (0.10), residues: 4730 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.005 TRP G 207 HIS 0.003 0.001 HIS V 212 PHE 0.028 0.003 PHE E 231 TYR 0.034 0.003 TYR K 303 ARG 0.026 0.001 ARG O 402 *********************** 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 572 residues out of total 7084 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 554 time to evaluate : 5.432 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 113 MET cc_start: 0.0241 (mtt) cc_final: 0.0020 (mtp) REVERT: B 143 MET cc_start: -0.1842 (ttt) cc_final: -0.3300 (ttt) REVERT: C 110 MET cc_start: 0.2464 (tmm) cc_final: 0.1182 (ttt) REVERT: C 143 MET cc_start: -0.2024 (tpt) cc_final: -0.2536 (tpt) REVERT: C 266 MET cc_start: -0.3115 (mtt) cc_final: -0.3701 (ttm) REVERT: D 110 MET cc_start: 0.2874 (tmm) cc_final: 0.2671 (tmm) REVERT: D 143 MET cc_start: -0.2159 (tpt) cc_final: -0.2774 (tpt) REVERT: D 266 MET cc_start: -0.2651 (mtt) cc_final: -0.3336 (ttm) REVERT: E 110 MET cc_start: 0.2539 (tmm) cc_final: 0.1611 (ttt) REVERT: E 143 MET cc_start: -0.2421 (tpt) cc_final: -0.2825 (tpt) REVERT: E 266 MET cc_start: -0.3045 (mtt) cc_final: -0.4036 (ttm) REVERT: F 110 MET cc_start: 0.2223 (tmm) cc_final: 0.0820 (ttt) REVERT: F 113 MET cc_start: 0.0357 (mtt) cc_final: 0.0127 (mtp) REVERT: F 195 MET cc_start: -0.0115 (mmp) cc_final: -0.1072 (tpt) REVERT: G 113 MET cc_start: 0.0827 (mtt) cc_final: 0.0483 (mtp) REVERT: G 143 MET cc_start: -0.2220 (tpt) cc_final: -0.2732 (tpt) REVERT: H 143 MET cc_start: -0.2143 (tpt) cc_final: -0.2575 (tpt) REVERT: I 143 MET cc_start: -0.2554 (tpt) cc_final: -0.3002 (tpt) REVERT: J 113 MET cc_start: -0.0536 (ttp) cc_final: -0.0845 (ttp) REVERT: J 143 MET cc_start: -0.2126 (tpt) cc_final: -0.2634 (tpt) REVERT: J 195 MET cc_start: -0.0129 (mmp) cc_final: -0.1880 (tpt) REVERT: J 266 MET cc_start: -0.2226 (mtm) cc_final: -0.2710 (mtt) REVERT: K 266 MET cc_start: -0.2971 (mtt) cc_final: -0.4083 (ttm) REVERT: L 266 MET cc_start: -0.3453 (mtt) cc_final: -0.4456 (ttm) REVERT: L 295 ASN cc_start: 0.4619 (p0) cc_final: 0.4081 (m110) REVERT: A 143 MET cc_start: -0.1748 (ttt) cc_final: -0.2162 (ttt) REVERT: A 266 MET cc_start: -0.3093 (mtt) cc_final: -0.4202 (ttm) REVERT: A 295 ASN cc_start: 0.5388 (p0) cc_final: 0.4040 (m110) REVERT: M 266 MET cc_start: -0.3135 (mtt) cc_final: -0.4308 (ttm) REVERT: M 295 ASN cc_start: 0.5195 (p0) cc_final: 0.3909 (m-40) REVERT: M 376 VAL cc_start: 0.1304 (t) cc_final: 0.1058 (t) REVERT: N 110 MET cc_start: 0.2841 (tmm) cc_final: 0.1854 (ttt) REVERT: N 266 MET cc_start: -0.3313 (mtt) cc_final: -0.4258 (ttm) REVERT: N 295 ASN cc_start: 0.5475 (p0) cc_final: 0.4139 (m-40) REVERT: O 110 MET cc_start: 0.2563 (tmm) cc_final: 0.1562 (ttt) REVERT: O 113 MET cc_start: 0.0923 (mtt) cc_final: 0.0694 (mtp) REVERT: O 143 MET cc_start: -0.1974 (ttt) cc_final: -0.2409 (ttt) REVERT: O 195 MET cc_start: -0.1194 (mmp) cc_final: -0.1957 (tpt) REVERT: O 402 ARG cc_start: 0.0689 (mpp80) cc_final: 0.0026 (ptm160) REVERT: P 143 MET cc_start: -0.1830 (ttt) cc_final: -0.2138 (ttt) REVERT: P 295 ASN cc_start: 0.5214 (p0) cc_final: 0.4055 (m-40) REVERT: Q 110 MET cc_start: 0.2707 (tmm) cc_final: 0.1563 (ttt) REVERT: Q 143 MET cc_start: -0.1756 (ttt) cc_final: -0.2842 (ttt) REVERT: Q 195 MET cc_start: -0.0688 (mmp) cc_final: -0.1327 (tpt) REVERT: Q 204 ASP cc_start: 0.2533 (t0) cc_final: 0.2302 (m-30) REVERT: Q 266 MET cc_start: -0.3022 (mtm) cc_final: -0.3693 (mtt) REVERT: Q 295 ASN cc_start: 0.5399 (p0) cc_final: 0.4488 (m110) REVERT: R 195 MET cc_start: -0.0090 (mmp) cc_final: -0.1189 (tpt) REVERT: R 295 ASN cc_start: 0.5283 (p0) cc_final: 0.3999 (m110) REVERT: S 195 MET cc_start: -0.0061 (mmp) cc_final: -0.1233 (tpt) REVERT: S 266 MET cc_start: -0.3531 (mtt) cc_final: -0.4422 (ttm) REVERT: S 295 ASN cc_start: 0.5673 (p0) cc_final: 0.4571 (m-40) REVERT: T 143 MET cc_start: -0.1710 (ttt) cc_final: -0.2839 (ttt) REVERT: T 292 GLN cc_start: 0.4097 (tp-100) cc_final: 0.3858 (tp-100) REVERT: V 31 PHE cc_start: 0.6439 (t80) cc_final: 0.6175 (t80) outliers start: 18 outliers final: 14 residues processed: 572 average time/residue: 0.5687 time to fit residues: 567.6066 Evaluate side-chains 440 residues out of total 7084 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 426 time to evaluate : 5.000 ------------------------------------------------------------------------------- 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: 7.9990 chunk 601 optimal weight: 4.9990 chunk 415 optimal weight: 7.9990 chunk 88 optimal weight: 0.7980 chunk 382 optimal weight: 10.0000 chunk 537 optimal weight: 10.0000 chunk 803 optimal weight: 9.9990 chunk 850 optimal weight: 8.9990 chunk 419 optimal weight: 10.0000 chunk 761 optimal weight: 5.9990 chunk 229 optimal weight: 5.9990 overall best weight: 5.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 4 GLN 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** C 4 GLN C 212 HIS ** C 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 280 GLN C 281 ASN ** 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 212 HIS D 280 GLN D 281 ASN D 307 GLN D 309 GLN ** 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** D 386 GLN E 4 GLN E 212 HIS E 280 GLN E 281 ASN E 307 GLN ** 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 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 212 HIS G 280 GLN ** G 305 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 307 GLN ** G 313 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 212 HIS H 280 GLN H 281 ASN ** H 305 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 380 ASN I 212 HIS I 280 GLN I 281 ASN ** I 305 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 307 GLN ** I 313 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 212 HIS J 280 GLN J 281 ASN J 307 GLN J 309 GLN ** J 313 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 380 ASN ** K 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 212 HIS K 280 GLN K 281 ASN K 307 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 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 212 HIS ** L 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 269 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 280 GLN L 281 ASN ** L 313 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 321 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 322 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 380 ASN ** M 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 212 HIS M 232 ASN 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 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 212 HIS N 280 GLN N 281 ASN 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 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 212 HIS O 280 GLN O 307 GLN ** O 313 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 321 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 322 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 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** ** 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 212 HIS Q 280 GLN ** Q 281 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 292 GLN Q 307 GLN ** Q 313 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 380 ASN R 212 HIS R 280 GLN R 281 ASN ** 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 22 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 78 GLN ** S 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 212 HIS S 280 GLN S 281 ASN ** 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 T 307 GLN T 309 GLN ** T 313 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 196 ASN V 212 HIS 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: 96 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1803 moved from start: 0.6236 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.060 66044 Z= 0.321 Angle : 0.906 14.621 89980 Z= 0.485 Chirality : 0.051 0.240 10560 Planarity : 0.005 0.183 12078 Dihedral : 6.217 25.451 9196 Min Nonbonded Distance : 2.003 Molprobity Statistics. All-atom Clashscore : 22.97 Ramachandran Plot: Outliers : 1.00 % Allowed : 6.78 % Favored : 92.22 % Rotamer: Outliers : 0.07 % Allowed : 3.36 % Favored : 96.57 % 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: -0.86 (0.09), residues: 8800 helix: 1.66 (0.13), residues: 1188 sheet: -0.83 (0.09), residues: 2618 loop : -0.96 (0.09), residues: 4994 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.005 TRP E 333 HIS 0.007 0.001 HIS T 212 PHE 0.053 0.003 PHE U 42 TYR 0.029 0.003 TYR F 303 ARG 0.034 0.002 ARG H 402 *********************** 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 501 residues out of total 7084 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 496 time to evaluate : 5.142 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: B 143 MET cc_start: -0.1922 (ttt) cc_final: -0.3328 (ttt) REVERT: B 195 MET cc_start: 0.0229 (mmp) cc_final: -0.0031 (tpp) REVERT: C 110 MET cc_start: 0.2768 (tmm) cc_final: 0.1738 (ttt) REVERT: C 266 MET cc_start: -0.3567 (mtt) cc_final: -0.4550 (ttm) REVERT: C 295 ASN cc_start: 0.5619 (p0) cc_final: 0.4267 (m-40) REVERT: D 31 PHE cc_start: 0.6228 (t80) cc_final: 0.6007 (t80) REVERT: D 110 MET cc_start: 0.3359 (tmm) cc_final: 0.3031 (tmm) REVERT: D 143 MET cc_start: -0.2211 (tpt) cc_final: -0.3002 (tpt) REVERT: D 231 PHE cc_start: 0.1909 (m-80) cc_final: 0.0501 (m-80) REVERT: E 110 MET cc_start: 0.3618 (tmm) cc_final: 0.2684 (ttt) REVERT: E 143 MET cc_start: -0.2482 (tpt) cc_final: -0.3141 (tpt) REVERT: E 195 MET cc_start: 0.0372 (mmp) cc_final: -0.0389 (tpp) REVERT: E 266 MET cc_start: -0.3067 (mtt) cc_final: -0.4502 (ttp) REVERT: F 110 MET cc_start: 0.3230 (tmm) cc_final: 0.2779 (tmm) REVERT: F 113 MET cc_start: 0.0737 (mtt) cc_final: 0.0464 (mtp) REVERT: F 205 ASN cc_start: 0.2130 (m-40) cc_final: 0.1626 (p0) REVERT: G 143 MET cc_start: -0.2599 (tpt) cc_final: -0.3187 (tpt) REVERT: G 266 MET cc_start: -0.2397 (mtm) cc_final: -0.2715 (mtt) REVERT: H 143 MET cc_start: -0.2178 (tpt) cc_final: -0.2764 (tpt) REVERT: H 195 MET cc_start: 0.0473 (mmp) cc_final: -0.0644 (tpt) REVERT: I 143 MET cc_start: -0.2338 (tpt) cc_final: -0.2913 (tpt) REVERT: J 143 MET cc_start: -0.2084 (tpt) cc_final: -0.2856 (tpt) REVERT: J 266 MET cc_start: -0.2398 (mtm) cc_final: -0.2773 (mtt) REVERT: J 292 GLN cc_start: 0.4776 (tp-100) cc_final: 0.4517 (tp40) REVERT: J 295 ASN cc_start: 0.5669 (p0) cc_final: 0.4355 (m110) REVERT: K 143 MET cc_start: -0.2212 (ttt) cc_final: -0.3212 (ttp) REVERT: K 195 MET cc_start: -0.0413 (mmp) cc_final: -0.0834 (tpp) REVERT: L 143 MET cc_start: -0.1617 (ttt) cc_final: -0.2033 (ttt) REVERT: L 195 MET cc_start: 0.0080 (mmp) cc_final: -0.0619 (tpp) REVERT: A 143 MET cc_start: -0.1904 (ttt) cc_final: -0.3208 (ttt) REVERT: A 195 MET cc_start: -0.0325 (mmp) cc_final: -0.1426 (tpt) REVERT: M 195 MET cc_start: -0.0603 (mmp) cc_final: -0.1715 (mmm) REVERT: N 110 MET cc_start: 0.2970 (tmm) cc_final: 0.2411 (ttt) REVERT: N 195 MET cc_start: -0.0368 (mmp) cc_final: -0.1181 (tpt) REVERT: O 110 MET cc_start: 0.2574 (tmm) cc_final: 0.2146 (ttt) REVERT: O 143 MET cc_start: -0.2357 (ttt) cc_final: -0.2799 (ttt) REVERT: O 195 MET cc_start: -0.0948 (mmp) cc_final: -0.1188 (tpp) REVERT: O 292 GLN cc_start: 0.4247 (tp-100) cc_final: 0.3959 (tp-100) REVERT: P 143 MET cc_start: -0.1910 (ttt) cc_final: -0.2258 (ttt) REVERT: P 195 MET cc_start: -0.0688 (mmp) cc_final: -0.1187 (tpp) REVERT: Q 110 MET cc_start: 0.2862 (tmm) cc_final: 0.2130 (ttt) REVERT: Q 143 MET cc_start: -0.1659 (ttt) cc_final: -0.2974 (ttt) REVERT: Q 195 MET cc_start: -0.0247 (mmp) cc_final: -0.0564 (tpp) REVERT: Q 266 MET cc_start: -0.3345 (mtt) cc_final: -0.4839 (ttm) REVERT: Q 292 GLN cc_start: 0.4473 (tp-100) cc_final: 0.4194 (tp-100) REVERT: R 143 MET cc_start: -0.2801 (ttt) cc_final: -0.3880 (ttt) REVERT: R 195 MET cc_start: 0.0033 (mmp) cc_final: -0.0683 (tpt) REVERT: R 374 MET cc_start: 0.0529 (ttp) cc_final: 0.0306 (ttp) REVERT: S 143 MET cc_start: -0.1990 (mmm) cc_final: -0.2585 (mtt) REVERT: S 309 GLN cc_start: 0.5422 (pp30) cc_final: 0.5205 (pp30) outliers start: 5 outliers final: 3 residues processed: 501 average time/residue: 0.5910 time to fit residues: 514.1828 Evaluate side-chains 414 residues out of total 7084 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 411 time to evaluate : 5.022 ------------------------------------------------------------------------------- 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: 20.0000 chunk 482 optimal weight: 9.9990 chunk 12 optimal weight: 0.2980 chunk 633 optimal weight: 4.9990 chunk 350 optimal weight: 0.4980 chunk 725 optimal weight: 4.9990 chunk 587 optimal weight: 9.9990 chunk 1 optimal weight: 6.9990 chunk 434 optimal weight: 4.9990 chunk 763 optimal weight: 1.9990 chunk 214 optimal weight: 0.0570 overall best weight: 1.5702 ------------------------------------------------------------------------------- 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 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 280 GLN ** 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 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 267 GLN ** 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 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 205 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 322 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 386 GLN ** G 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 280 GLN ** G 305 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 313 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 280 GLN ** H 305 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 280 GLN 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 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 269 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 280 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 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 280 GLN K 292 GLN ** K 313 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 364 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 380 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 313 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 189 GLN A 280 GLN A 281 ASN ** A 313 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 321 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 322 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 189 GLN M 280 GLN ** M 313 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 280 GLN ** N 313 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 364 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 25 ASN ** 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 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 321 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 322 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 25 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 25 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 280 GLN ** R 313 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 128 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** T 280 GLN ** T 309 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 280 GLN ** U 313 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 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: 28 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1637 moved from start: 0.6323 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.082 66044 Z= 0.181 Angle : 0.699 13.319 89980 Z= 0.378 Chirality : 0.044 0.221 10560 Planarity : 0.004 0.058 12078 Dihedral : 5.469 25.877 9196 Min Nonbonded Distance : 2.113 Molprobity Statistics. All-atom Clashscore : 16.91 Ramachandran Plot: Outliers : 1.00 % Allowed : 6.52 % Favored : 92.48 % Rotamer: Outliers : 0.00 % Allowed : 1.40 % Favored : 98.60 % 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: -0.49 (0.09), residues: 8800 helix: 2.70 (0.13), residues: 1210 sheet: -0.66 (0.11), residues: 1980 loop : -0.90 (0.08), residues: 5610 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP K 207 HIS 0.001 0.001 HIS B 212 PHE 0.012 0.001 PHE Q 231 TYR 0.020 0.002 TYR I 177 ARG 0.006 0.001 ARG T 402 *********************** 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 483 residues out of total 7084 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 483 time to evaluate : 5.017 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: B 143 MET cc_start: -0.1875 (ttt) cc_final: -0.3159 (ttt) REVERT: B 231 PHE cc_start: 0.1701 (m-80) cc_final: 0.0506 (m-80) REVERT: B 266 MET cc_start: -0.1950 (ttt) cc_final: -0.2174 (ttt) REVERT: C 110 MET cc_start: 0.2817 (tmm) cc_final: 0.2025 (ttt) REVERT: C 195 MET cc_start: 0.0645 (mmp) cc_final: -0.0660 (tpt) REVERT: C 266 MET cc_start: -0.3747 (mtt) cc_final: -0.4594 (ttm) REVERT: C 295 ASN cc_start: 0.5315 (p0) cc_final: 0.4131 (m-40) REVERT: D 143 MET cc_start: -0.2280 (tpt) cc_final: -0.3008 (tpt) REVERT: D 195 MET cc_start: 0.0417 (mmp) cc_final: -0.1101 (tpt) REVERT: D 231 PHE cc_start: 0.2296 (m-80) cc_final: 0.0795 (m-80) REVERT: E 110 MET cc_start: 0.3471 (tmm) cc_final: 0.2718 (ttt) REVERT: E 143 MET cc_start: -0.2343 (tpt) cc_final: -0.3032 (tpt) REVERT: E 195 MET cc_start: 0.0531 (mmp) cc_final: -0.1070 (tpt) REVERT: E 266 MET cc_start: -0.3042 (mtt) cc_final: -0.4502 (ttp) REVERT: F 110 MET cc_start: 0.3074 (tmm) cc_final: 0.2679 (tmm) REVERT: F 113 MET cc_start: 0.0562 (mtt) cc_final: 0.0231 (mtp) REVERT: F 266 MET cc_start: -0.3484 (mtt) cc_final: -0.4674 (ttm) REVERT: G 402 ARG cc_start: 0.2389 (mmp80) cc_final: 0.1767 (mtm110) REVERT: H 195 MET cc_start: 0.0460 (mmp) cc_final: -0.0846 (tpt) REVERT: H 231 PHE cc_start: 0.1669 (m-80) cc_final: 0.0502 (m-80) REVERT: I 143 MET cc_start: -0.2377 (tpt) cc_final: -0.2900 (tpt) REVERT: I 295 ASN cc_start: 0.5140 (p0) cc_final: 0.4337 (m-40) REVERT: J 143 MET cc_start: -0.2151 (tpt) cc_final: -0.2879 (tpt) REVERT: J 266 MET cc_start: -0.2349 (mtm) cc_final: -0.2747 (ttm) REVERT: J 295 ASN cc_start: 0.5528 (p0) cc_final: 0.4418 (m110) REVERT: K 143 MET cc_start: -0.2472 (ttt) cc_final: -0.3430 (ttp) REVERT: K 195 MET cc_start: -0.0359 (mmp) cc_final: -0.1450 (tpp) REVERT: L 143 MET cc_start: -0.1671 (ttt) cc_final: -0.2064 (ttt) REVERT: L 195 MET cc_start: -0.0029 (mmp) cc_final: -0.1640 (tpt) REVERT: L 266 MET cc_start: -0.3872 (mtt) cc_final: -0.4849 (ttm) REVERT: A 143 MET cc_start: -0.2107 (ttt) cc_final: -0.3278 (ttt) REVERT: A 195 MET cc_start: -0.0196 (mmp) cc_final: -0.1526 (tpt) REVERT: A 266 MET cc_start: -0.3425 (mtm) cc_final: -0.4688 (ttm) REVERT: M 143 MET cc_start: -0.1443 (ttt) cc_final: -0.3156 (ttt) REVERT: M 195 MET cc_start: -0.0699 (mmp) cc_final: -0.1674 (mmm) REVERT: M 266 MET cc_start: -0.3639 (mtt) cc_final: -0.5065 (ttm) REVERT: N 143 MET cc_start: -0.1528 (ttt) cc_final: -0.2903 (ttt) REVERT: N 177 TYR cc_start: 0.3756 (p90) cc_final: 0.3527 (p90) REVERT: N 195 MET cc_start: -0.0628 (mmp) cc_final: -0.1145 (tpp) REVERT: N 295 ASN cc_start: 0.5634 (p0) cc_final: 0.4144 (m110) REVERT: O 65 THR cc_start: 0.7251 (t) cc_final: 0.6773 (p) REVERT: O 110 MET cc_start: 0.2432 (tmm) cc_final: 0.2144 (ttt) REVERT: O 143 MET cc_start: -0.2397 (ttt) cc_final: -0.2696 (ttt) REVERT: O 195 MET cc_start: -0.1183 (mmp) cc_final: -0.1761 (tpp) REVERT: P 143 MET cc_start: -0.2098 (ttt) cc_final: -0.2431 (ttt) REVERT: P 195 MET cc_start: -0.0782 (mmp) cc_final: -0.1300 (tpp) REVERT: Q 110 MET cc_start: 0.2676 (tmm) cc_final: 0.1957 (ttt) REVERT: Q 143 MET cc_start: -0.1732 (ttt) cc_final: -0.2250 (pmm) REVERT: Q 195 MET cc_start: -0.0455 (mmp) cc_final: -0.0754 (tpp) REVERT: Q 295 ASN cc_start: 0.5695 (p0) cc_final: 0.4577 (m110) REVERT: R 195 MET cc_start: 0.0391 (mmp) cc_final: -0.1418 (tpt) REVERT: S 309 GLN cc_start: 0.5406 (pp30) cc_final: 0.5169 (pp30) REVERT: T 143 MET cc_start: -0.1863 (ttt) cc_final: -0.2460 (pmm) outliers start: 0 outliers final: 0 residues processed: 483 average time/residue: 0.5822 time to fit residues: 485.3210 Evaluate side-chains 396 residues out of total 7084 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 396 time to evaluate : 4.980 ------------------------------------------------------------------------------- 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: 20.0000 chunk 766 optimal weight: 0.5980 chunk 168 optimal weight: 9.9990 chunk 499 optimal weight: 30.0000 chunk 209 optimal weight: 9.9990 chunk 851 optimal weight: 20.0000 chunk 706 optimal weight: 5.9990 chunk 394 optimal weight: 10.0000 chunk 70 optimal weight: 9.9990 chunk 281 optimal weight: 2.9990 chunk 446 optimal weight: 1.9990 overall best weight: 4.3188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 205 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 268 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 280 GLN ** B 281 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** B 322 ASN ** C 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 205 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 280 GLN ** C 313 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 322 ASN 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 ** E 25 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 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 280 GLN ** F 313 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 322 ASN ** G 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 280 GLN G 309 GLN ** G 313 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 78 GLN ** H 313 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 386 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 25 ASN 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 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 267 GLN ** 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 313 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 386 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 292 GLN ** K 313 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 364 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 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 292 GLN ** L 313 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 364 ASN ** 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 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 281 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 321 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 322 ASN ** M 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 25 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 4 GLN ** 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** ** N 364 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 25 ASN ** 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 281 ASN ** O 313 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 321 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 322 ASN ** 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 281 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 313 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 364 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 380 ASN ** Q 4 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 281 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** Q 380 ASN ** R 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 22 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 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** T 280 GLN ** T 281 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 309 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 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 ** both conformations clash, **PLEASE CHECK MANUALLY** 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: 27 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1978 moved from start: 0.7468 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 66044 Z= 0.271 Angle : 0.823 13.660 89980 Z= 0.437 Chirality : 0.048 0.235 10560 Planarity : 0.004 0.094 12078 Dihedral : 5.803 29.863 9196 Min Nonbonded Distance : 2.060 Molprobity Statistics. All-atom Clashscore : 21.41 Ramachandran Plot: Outliers : 1.07 % Allowed : 7.76 % Favored : 91.17 % Rotamer: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % 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: -0.88 (0.09), residues: 8800 helix: 2.01 (0.14), residues: 1254 sheet: -0.72 (0.10), residues: 2574 loop : -1.21 (0.08), residues: 4972 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.004 TRP T 333 HIS 0.002 0.001 HIS A 193 PHE 0.021 0.002 PHE Q 231 TYR 0.023 0.002 TYR F 303 ARG 0.007 0.002 ARG I 402 *********************** 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 485 residues out of total 7084 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 485 time to evaluate : 5.141 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: B 143 MET cc_start: -0.1859 (ttt) cc_final: -0.3233 (ttt) REVERT: B 195 MET cc_start: 0.0299 (mmp) cc_final: -0.1130 (tpt) REVERT: C 110 MET cc_start: 0.3033 (tmm) cc_final: 0.2189 (ttt) REVERT: C 266 MET cc_start: -0.3618 (mtt) cc_final: -0.4955 (ttp) REVERT: C 402 ARG cc_start: 0.3223 (mmp80) cc_final: 0.2467 (mtm110) REVERT: D 110 MET cc_start: 0.3314 (tmm) cc_final: 0.1930 (ttt) REVERT: D 143 MET cc_start: -0.2261 (tpt) cc_final: -0.3093 (tpt) REVERT: D 195 MET cc_start: 0.0718 (mmp) cc_final: -0.1055 (tpt) REVERT: D 231 PHE cc_start: 0.2265 (m-80) cc_final: 0.0754 (m-80) REVERT: D 402 ARG cc_start: 0.2949 (mmp80) cc_final: 0.2734 (mtm110) REVERT: E 110 MET cc_start: 0.3654 (tmm) cc_final: 0.2913 (ttt) REVERT: E 143 MET cc_start: -0.2233 (tpt) cc_final: -0.2941 (tpt) REVERT: E 195 MET cc_start: 0.0877 (mmp) cc_final: -0.0747 (tpt) REVERT: F 110 MET cc_start: 0.3375 (tmm) cc_final: 0.3006 (tmm) REVERT: G 195 MET cc_start: 0.0892 (mmp) cc_final: -0.0700 (tpt) REVERT: G 266 MET cc_start: -0.2172 (mtm) cc_final: -0.3588 (mmt) REVERT: H 143 MET cc_start: -0.1423 (ttt) cc_final: -0.2234 (ttt) REVERT: H 195 MET cc_start: 0.1025 (mmp) cc_final: -0.0434 (tpt) REVERT: I 143 MET cc_start: -0.2491 (tpt) cc_final: -0.3172 (tpt) REVERT: I 195 MET cc_start: 0.0818 (mmp) cc_final: -0.0602 (tpt) REVERT: J 143 MET cc_start: -0.2208 (tpt) cc_final: -0.3035 (tpt) REVERT: J 195 MET cc_start: 0.0097 (mmp) cc_final: -0.1628 (tpt) REVERT: J 266 MET cc_start: -0.2227 (mtm) cc_final: -0.2842 (ttm) REVERT: K 143 MET cc_start: -0.2157 (ttt) cc_final: -0.3505 (ttp) REVERT: K 195 MET cc_start: -0.0033 (mmp) cc_final: -0.0515 (tpp) REVERT: L 143 MET cc_start: -0.1690 (ttt) cc_final: -0.2197 (ttt) REVERT: L 195 MET cc_start: 0.0364 (mmp) cc_final: -0.1381 (tpt) REVERT: L 266 MET cc_start: -0.3683 (mtt) cc_final: -0.4802 (ttm) REVERT: A 143 MET cc_start: -0.2006 (ttt) cc_final: -0.3183 (ttt) REVERT: A 266 MET cc_start: -0.3405 (mtm) cc_final: -0.4836 (ttm) REVERT: M 195 MET cc_start: -0.0422 (mmp) cc_final: -0.1589 (mmm) REVERT: N 110 MET cc_start: 0.2829 (tmm) cc_final: 0.2142 (ttt) REVERT: N 143 MET cc_start: -0.1972 (ttt) cc_final: -0.3319 (ttt) REVERT: N 195 MET cc_start: -0.0292 (mmp) cc_final: -0.1093 (tpt) REVERT: O 65 THR cc_start: 0.7619 (t) cc_final: 0.7027 (p) REVERT: O 143 MET cc_start: -0.2451 (ttt) cc_final: -0.2700 (ttt) REVERT: O 195 MET cc_start: -0.1059 (mmp) cc_final: -0.1499 (tpt) REVERT: P 143 MET cc_start: -0.2068 (ttt) cc_final: -0.2354 (ttt) REVERT: P 195 MET cc_start: -0.0680 (mmp) cc_final: -0.1012 (tpp) REVERT: Q 110 MET cc_start: 0.2699 (tmm) cc_final: 0.2285 (ttt) REVERT: Q 143 MET cc_start: -0.1767 (ttt) cc_final: -0.2380 (pmm) REVERT: Q 195 MET cc_start: -0.0190 (mmp) cc_final: -0.0811 (tpt) REVERT: R 143 MET cc_start: 0.0270 (pmm) cc_final: -0.1007 (mtt) REVERT: R 195 MET cc_start: 0.0280 (mmp) cc_final: -0.0753 (tpt) outliers start: 0 outliers final: 0 residues processed: 485 average time/residue: 0.5836 time to fit residues: 494.2146 Evaluate side-chains 422 residues out of total 7084 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 422 time to evaluate : 5.003 ------------------------------------------------------------------------------- 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: 4.9990 chunk 95 optimal weight: 8.9990 chunk 485 optimal weight: 5.9990 chunk 621 optimal weight: 0.0470 chunk 481 optimal weight: 5.9990 chunk 716 optimal weight: 9.9990 chunk 475 optimal weight: 20.0000 chunk 848 optimal weight: 3.9990 chunk 530 optimal weight: 0.0670 chunk 517 optimal weight: 7.9990 chunk 391 optimal weight: 0.6980 overall best weight: 1.9620 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 25 ASN ** B 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 280 GLN ** B 313 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 25 ASN ** C 267 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** 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 25 ASN 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 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 205 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 ** both conformations clash, **PLEASE CHECK MANUALLY** G 25 ASN 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 232 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** ** J 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 25 ASN ** J 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 269 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 386 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 4 GLN K 292 GLN ** K 313 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 364 ASN ** 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 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 364 ASN L 386 GLN ** A 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 189 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 321 ASN ** 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 21 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 O 4 GLN ** 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 313 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 321 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 322 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 380 ASN O 386 GLN ** P 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 313 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 364 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 4 GLN ** 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 313 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 318 ASN ** 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 305 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 307 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 309 GLN ** T 313 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 318 ASN ** 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** 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: 34 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1849 moved from start: 0.7606 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 66044 Z= 0.176 Angle : 0.680 12.509 89980 Z= 0.365 Chirality : 0.044 0.225 10560 Planarity : 0.004 0.051 12078 Dihedral : 5.345 30.793 9196 Min Nonbonded Distance : 2.101 Molprobity Statistics. All-atom Clashscore : 17.86 Ramachandran Plot: Outliers : 1.07 % Allowed : 6.38 % Favored : 92.56 % Rotamer: Outliers : 0.00 % Allowed : 0.95 % Favored : 99.05 % 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: -0.56 (0.09), residues: 8800 helix: 2.68 (0.13), residues: 1254 sheet: -0.62 (0.10), residues: 2552 loop : -1.04 (0.09), residues: 4994 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP U 333 HIS 0.007 0.001 HIS H 193 PHE 0.012 0.001 PHE K 42 TYR 0.018 0.002 TYR I 177 ARG 0.009 0.001 ARG G 402 *********************** 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 494 residues out of total 7084 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 494 time to evaluate : 5.075 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: B 143 MET cc_start: -0.1828 (ttt) cc_final: -0.3145 (ttt) REVERT: B 231 PHE cc_start: 0.1893 (m-80) cc_final: 0.0592 (m-80) REVERT: C 110 MET cc_start: 0.3130 (tmm) cc_final: 0.2368 (ttt) REVERT: C 143 MET cc_start: -0.1410 (ttt) cc_final: -0.1933 (ttt) REVERT: C 402 ARG cc_start: 0.3272 (mmp80) cc_final: 0.2734 (mtm110) REVERT: D 110 MET cc_start: 0.3267 (tmm) cc_final: 0.1827 (ttt) REVERT: D 143 MET cc_start: -0.2481 (tpt) cc_final: -0.3209 (tpt) REVERT: D 195 MET cc_start: 0.0870 (mmp) cc_final: -0.0946 (tpt) REVERT: E 110 MET cc_start: 0.3499 (tmm) cc_final: 0.2928 (ttt) REVERT: E 143 MET cc_start: -0.2213 (tpt) cc_final: -0.2827 (tpt) REVERT: F 110 MET cc_start: 0.3202 (tmm) cc_final: 0.2973 (tmm) REVERT: F 195 MET cc_start: 0.0348 (mmp) cc_final: -0.0912 (tpt) REVERT: G 143 MET cc_start: -0.2113 (ttt) cc_final: -0.3468 (ttt) REVERT: G 195 MET cc_start: 0.1025 (mmp) cc_final: -0.0675 (tpt) REVERT: G 266 MET cc_start: -0.2470 (mtm) cc_final: -0.3748 (mmt) REVERT: H 143 MET cc_start: -0.1679 (ttt) cc_final: -0.2013 (ttt) REVERT: H 231 PHE cc_start: 0.1695 (m-80) cc_final: 0.0507 (m-80) REVERT: I 143 MET cc_start: -0.2761 (tpt) cc_final: -0.3463 (tpt) REVERT: I 195 MET cc_start: 0.0934 (mmp) cc_final: -0.0598 (tpt) REVERT: J 266 MET cc_start: -0.2276 (mtm) cc_final: -0.2956 (ttm) REVERT: K 143 MET cc_start: -0.2539 (ttt) cc_final: -0.3609 (ttp) REVERT: K 177 TYR cc_start: 0.2248 (p90) cc_final: 0.2041 (p90) REVERT: K 195 MET cc_start: -0.0315 (mmp) cc_final: -0.0755 (tpp) REVERT: L 143 MET cc_start: -0.2079 (ttt) cc_final: -0.2850 (ttt) REVERT: L 195 MET cc_start: 0.0443 (mmp) cc_final: -0.1310 (tpt) REVERT: L 266 MET cc_start: -0.3994 (mtt) cc_final: -0.5061 (ttm) REVERT: A 143 MET cc_start: -0.1880 (ttt) cc_final: -0.2400 (ttt) REVERT: A 266 MET cc_start: -0.3405 (mtm) cc_final: -0.4805 (ttm) REVERT: M 195 MET cc_start: -0.0520 (mmp) cc_final: -0.1552 (mmm) REVERT: N 110 MET cc_start: 0.2908 (tmm) cc_final: 0.2365 (ttt) REVERT: N 143 MET cc_start: -0.2401 (ttt) cc_final: -0.3583 (ttt) REVERT: N 195 MET cc_start: -0.0252 (mmp) cc_final: -0.0988 (tpt) REVERT: O 65 THR cc_start: 0.7683 (t) cc_final: 0.7047 (p) REVERT: O 143 MET cc_start: -0.2680 (ttt) cc_final: -0.2908 (ttt) REVERT: O 195 MET cc_start: -0.1155 (mmp) cc_final: -0.1414 (tpt) REVERT: P 143 MET cc_start: -0.2401 (ttt) cc_final: -0.2716 (ttt) REVERT: P 195 MET cc_start: -0.0685 (mmp) cc_final: -0.1107 (tpp) REVERT: Q 110 MET cc_start: 0.2882 (tmm) cc_final: 0.2677 (ttt) REVERT: Q 143 MET cc_start: -0.1982 (ttt) cc_final: -0.3090 (ttt) REVERT: Q 195 MET cc_start: -0.0365 (mmp) cc_final: -0.0905 (tpt) REVERT: R 143 MET cc_start: -0.0643 (pmm) cc_final: -0.1426 (mtt) REVERT: R 195 MET cc_start: 0.0234 (mmp) cc_final: -0.0798 (tpt) REVERT: S 309 GLN cc_start: 0.5248 (pp30) cc_final: 0.4760 (pp30) REVERT: T 143 MET cc_start: -0.2225 (ttt) cc_final: -0.2733 (pmm) REVERT: V 266 MET cc_start: -0.3247 (ttt) cc_final: -0.5883 (mtt) outliers start: 0 outliers final: 0 residues processed: 494 average time/residue: 0.5760 time to fit residues: 497.5301 Evaluate side-chains 425 residues out of total 7084 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 425 time to evaluate : 4.993 ------------------------------------------------------------------------------- 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: 30.0000 chunk 506 optimal weight: 9.9990 chunk 255 optimal weight: 7.9990 chunk 166 optimal weight: 20.0000 chunk 164 optimal weight: 0.3980 chunk 539 optimal weight: 5.9990 chunk 577 optimal weight: 20.0000 chunk 419 optimal weight: 30.0000 chunk 79 optimal weight: 10.0000 chunk 666 optimal weight: 7.9990 overall best weight: 5.0788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 268 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 280 GLN ** B 313 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 391 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 205 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 267 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 378 GLN ** C 391 GLN ** 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 280 GLN ** F 309 GLN ** 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 ** 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** ** H 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 269 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 H 386 GLN I 15 ASN ** 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 313 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 386 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 25 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 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 191 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 292 GLN ** 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 189 GLN ** 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 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 191 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 281 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 309 GLN ** 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** O 321 ASN O 322 ASN ** P 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 313 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 364 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 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 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 281 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 305 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 380 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 15 ASN ** T 273 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 280 GLN ** T 313 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 380 ASN U 15 ASN ** U 273 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 4 GLN V 280 GLN ** V 292 GLN ** 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** Total number of N/Q/H flips: 25 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.2247 moved from start: 0.8879 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.099 66044 Z= 0.296 Angle : 0.865 13.251 89980 Z= 0.462 Chirality : 0.050 0.245 10560 Planarity : 0.005 0.056 12078 Dihedral : 6.096 32.903 9196 Min Nonbonded Distance : 2.020 Molprobity Statistics. All-atom Clashscore : 25.12 Ramachandran Plot: Outliers : 1.10 % Allowed : 8.50 % Favored : 90.40 % Rotamer: Outliers : 0.00 % Allowed : 0.89 % Favored : 99.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.51 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: -1.16 (0.09), residues: 8800 helix: 1.47 (0.14), residues: 1254 sheet: -0.77 (0.10), residues: 2464 loop : -1.37 (0.08), residues: 5082 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.004 TRP V 333 HIS 0.008 0.001 HIS R 193 PHE 0.031 0.003 PHE L 42 TYR 0.022 0.002 TYR J 303 ARG 0.008 0.002 ARG E 105 *********************** 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 567 residues out of total 7084 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 567 time to evaluate : 5.121 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: B 143 MET cc_start: -0.2103 (ttt) cc_final: -0.3496 (ttt) REVERT: C 110 MET cc_start: 0.3490 (tmm) cc_final: 0.3005 (ttt) REVERT: C 143 MET cc_start: -0.1782 (ttt) cc_final: -0.3167 (ttt) REVERT: C 195 MET cc_start: 0.0806 (mmp) cc_final: -0.0703 (tpt) REVERT: D 110 MET cc_start: 0.3610 (tmm) cc_final: 0.2097 (ttt) REVERT: D 195 MET cc_start: 0.1043 (mmp) cc_final: -0.0800 (tpt) REVERT: E 110 MET cc_start: 0.3913 (tmm) cc_final: 0.3568 (ttt) REVERT: E 195 MET cc_start: 0.1227 (mmp) cc_final: -0.0621 (tpt) REVERT: F 195 MET cc_start: 0.0840 (mmp) cc_final: -0.0543 (tpt) REVERT: G 143 MET cc_start: -0.2093 (ttt) cc_final: -0.3587 (ttt) REVERT: G 195 MET cc_start: 0.1025 (mmp) cc_final: -0.0578 (tpt) REVERT: G 266 MET cc_start: -0.2414 (mtm) cc_final: -0.3798 (mmt) REVERT: H 143 MET cc_start: -0.1893 (ttt) cc_final: -0.2345 (ttt) REVERT: H 195 MET cc_start: 0.0852 (mmp) cc_final: -0.0423 (tpt) REVERT: H 231 PHE cc_start: 0.2021 (m-80) cc_final: 0.0667 (m-80) REVERT: H 281 ASN cc_start: 0.4545 (t0) cc_final: 0.4248 (t0) REVERT: H 374 MET cc_start: 0.1728 (ptt) cc_final: 0.1127 (mmt) REVERT: I 374 MET cc_start: 0.2032 (ptt) cc_final: 0.1269 (mmt) REVERT: J 266 MET cc_start: -0.2349 (mtm) cc_final: -0.2620 (mtt) REVERT: J 374 MET cc_start: 0.1771 (ptt) cc_final: 0.1023 (mmt) REVERT: K 143 MET cc_start: -0.2360 (ttt) cc_final: -0.3505 (ttp) REVERT: K 195 MET cc_start: 0.0059 (mmp) cc_final: -0.0717 (tpp) REVERT: L 195 MET cc_start: 0.0942 (mmp) cc_final: -0.0925 (tpt) REVERT: A 143 MET cc_start: -0.2012 (ttt) cc_final: -0.2293 (ttt) REVERT: A 195 MET cc_start: 0.0538 (mmp) cc_final: -0.1462 (tpt) REVERT: M 177 TYR cc_start: 0.2624 (p90) cc_final: 0.2402 (p90) REVERT: M 195 MET cc_start: -0.0214 (mmp) cc_final: -0.1586 (tpt) REVERT: N 110 MET cc_start: 0.3150 (tmm) cc_final: 0.2485 (ttt) REVERT: N 195 MET cc_start: -0.0207 (mmp) cc_final: -0.1014 (tpt) REVERT: O 143 MET cc_start: -0.2676 (ttt) cc_final: -0.3165 (ttt) REVERT: O 195 MET cc_start: -0.0895 (mmp) cc_final: -0.1265 (tpt) REVERT: O 292 GLN cc_start: 0.4421 (tp-100) cc_final: 0.4173 (tp-100) REVERT: P 143 MET cc_start: -0.2176 (ttt) cc_final: -0.2434 (ttt) REVERT: P 195 MET cc_start: -0.0481 (mmp) cc_final: -0.0958 (tpt) REVERT: Q 143 MET cc_start: -0.1841 (ttt) cc_final: -0.3189 (ttt) REVERT: Q 195 MET cc_start: 0.0165 (mmp) cc_final: -0.0575 (tpt) REVERT: R 143 MET cc_start: -0.0177 (pmm) cc_final: -0.1576 (mtt) REVERT: S 309 GLN cc_start: 0.5578 (pp30) cc_final: 0.4861 (pp30) REVERT: S 380 ASN cc_start: 0.6241 (m-40) cc_final: 0.5923 (m-40) REVERT: S 398 LEU cc_start: 0.5982 (tp) cc_final: 0.5304 (mm) REVERT: V 266 MET cc_start: -0.3055 (ttt) cc_final: -0.5768 (mtt) outliers start: 0 outliers final: 0 residues processed: 567 average time/residue: 0.5794 time to fit residues: 575.2386 Evaluate side-chains 477 residues out of total 7084 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 477 time to evaluate : 5.008 ------------------------------------------------------------------------------- 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: 6.9990 chunk 812 optimal weight: 0.0010 chunk 741 optimal weight: 40.0000 chunk 790 optimal weight: 20.0000 chunk 475 optimal weight: 8.9990 chunk 344 optimal weight: 5.9990 chunk 620 optimal weight: 6.9990 chunk 242 optimal weight: 4.9990 chunk 714 optimal weight: 9.9990 chunk 747 optimal weight: 6.9990 chunk 787 optimal weight: 0.0270 overall best weight: 3.6050 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 280 GLN ** B 313 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 378 GLN ** C 267 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** ** D 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 280 GLN ** 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 313 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 378 GLN ** F 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 269 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 280 GLN ** F 305 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 309 GLN ** 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 378 GLN ** 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 378 GLN G 380 ASN ** H 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 232 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 ** I 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 292 GLN I 309 GLN ** 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 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 269 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 378 GLN ** K 21 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 ** L 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 191 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 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 189 GLN ** 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** ** N 21 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 378 GLN ** N 386 GLN ** 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 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 191 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 305 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 382 GLN ** P 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 313 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 364 ASN P 382 GLN ** 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 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 281 ASN ** 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 128 GLN ** 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** S 386 GLN 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** T 386 GLN U 268 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 15 ASN V 280 GLN ** V 292 GLN ** 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 380 ASN Total number of N/Q/H flips: 34 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.2193 moved from start: 0.9180 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= 0.216 Angle : 0.727 12.568 89980 Z= 0.392 Chirality : 0.046 0.229 10560 Planarity : 0.004 0.078 12078 Dihedral : 5.719 31.610 9196 Min Nonbonded Distance : 2.093 Molprobity Statistics. All-atom Clashscore : 20.42 Ramachandran Plot: Outliers : 1.00 % Allowed : 6.92 % Favored : 92.08 % Rotamer: Outliers : 0.00 % Allowed : 0.85 % Favored : 99.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.51 % Twisted Proline : 0.00 % Twisted General : 0.02 % 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: -1.10 (0.09), residues: 8800 helix: 1.87 (0.14), residues: 1276 sheet: -1.07 (0.10), residues: 2310 loop : -1.25 (0.08), residues: 5214 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP S 333 HIS 0.005 0.001 HIS S 193 PHE 0.017 0.002 PHE H 31 TYR 0.026 0.002 TYR Q 303 ARG 0.008 0.001 ARG Q 379 *********************** 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 565 residues out of total 7084 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 565 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: B 143 MET cc_start: -0.2134 (ttt) cc_final: -0.3494 (ttt) REVERT: C 110 MET cc_start: 0.3226 (tmm) cc_final: 0.2904 (ttt) REVERT: C 143 MET cc_start: -0.1786 (ttt) cc_final: -0.2018 (ttt) REVERT: D 110 MET cc_start: 0.3777 (tmm) cc_final: 0.2521 (ttt) REVERT: D 195 MET cc_start: 0.1149 (mmp) cc_final: -0.0719 (tpt) REVERT: E 143 MET cc_start: -0.1914 (ttt) cc_final: -0.2272 (ttt) REVERT: E 195 MET cc_start: 0.1292 (mmp) cc_final: -0.0509 (tpt) REVERT: F 110 MET cc_start: 0.3472 (tmm) cc_final: 0.3243 (ttt) REVERT: F 195 MET cc_start: 0.0987 (mmp) cc_final: -0.0386 (tpt) REVERT: G 143 MET cc_start: -0.2330 (ttt) cc_final: -0.3633 (ttt) REVERT: G 195 MET cc_start: 0.1167 (mmp) cc_final: -0.0488 (tpt) REVERT: G 266 MET cc_start: -0.2561 (mtm) cc_final: -0.3955 (mmt) REVERT: G 374 MET cc_start: 0.1808 (ptt) cc_final: 0.0855 (mtm) REVERT: G 380 ASN cc_start: 0.5737 (m110) cc_final: 0.5530 (m110) REVERT: H 143 MET cc_start: -0.1879 (ttt) cc_final: -0.2219 (ttt) REVERT: H 195 MET cc_start: 0.0959 (mmp) cc_final: -0.0535 (tpt) REVERT: I 143 MET cc_start: -0.2155 (ttt) cc_final: -0.3596 (ttt) REVERT: I 195 MET cc_start: 0.1189 (mmp) cc_final: -0.0330 (tpt) REVERT: J 143 MET cc_start: -0.2328 (ttt) cc_final: -0.3535 (ttt) REVERT: J 266 MET cc_start: -0.2439 (mtm) cc_final: -0.2765 (mtt) REVERT: K 143 MET cc_start: -0.2430 (ttt) cc_final: -0.3524 (ttp) REVERT: K 195 MET cc_start: 0.0254 (mmp) cc_final: -0.0503 (tpp) REVERT: L 143 MET cc_start: -0.1766 (ttt) cc_final: -0.2171 (ttt) REVERT: L 374 MET cc_start: 0.3873 (ptm) cc_final: 0.2692 (mmt) REVERT: A 143 MET cc_start: -0.2307 (ttt) cc_final: -0.2608 (ttt) REVERT: A 195 MET cc_start: 0.0646 (mmp) cc_final: -0.1422 (tpt) REVERT: M 195 MET cc_start: -0.0112 (mmp) cc_final: -0.1583 (tpt) REVERT: M 380 ASN cc_start: 0.6624 (m-40) cc_final: 0.6204 (t0) REVERT: M 398 LEU cc_start: 0.5359 (tt) cc_final: 0.4357 (mm) REVERT: N 110 MET cc_start: 0.3337 (tmm) cc_final: 0.3051 (ttt) REVERT: N 195 MET cc_start: 0.0095 (mmp) cc_final: -0.0724 (tpt) REVERT: O 143 MET cc_start: -0.2886 (ttt) cc_final: -0.3270 (ttt) REVERT: O 195 MET cc_start: -0.0697 (mmp) cc_final: -0.1088 (tpt) REVERT: P 143 MET cc_start: -0.2115 (ttt) cc_final: -0.2400 (ttt) REVERT: P 195 MET cc_start: -0.0364 (mmp) cc_final: -0.0899 (tpt) REVERT: P 398 LEU cc_start: 0.4796 (tt) cc_final: 0.4130 (mm) REVERT: Q 143 MET cc_start: -0.1723 (ttt) cc_final: -0.2986 (ttt) REVERT: Q 195 MET cc_start: 0.0270 (mmp) cc_final: -0.0472 (tpt) REVERT: Q 379 ARG cc_start: 0.3999 (mmp80) cc_final: 0.3014 (ttt180) REVERT: Q 391 GLN cc_start: 0.5699 (mt0) cc_final: 0.4785 (mp10) REVERT: Q 398 LEU cc_start: 0.5930 (tp) cc_final: 0.5633 (mm) REVERT: R 143 MET cc_start: -0.0099 (pmm) cc_final: -0.1640 (mtt) REVERT: R 380 ASN cc_start: 0.6571 (m-40) cc_final: 0.6357 (m-40) REVERT: R 398 LEU cc_start: 0.5635 (tt) cc_final: 0.4807 (mm) REVERT: S 380 ASN cc_start: 0.6214 (m-40) cc_final: 0.5863 (m-40) REVERT: S 398 LEU cc_start: 0.6062 (tp) cc_final: 0.5476 (mm) REVERT: T 143 MET cc_start: -0.2431 (ttt) cc_final: -0.2760 (pmm) REVERT: T 374 MET cc_start: 0.2975 (tmm) cc_final: 0.2557 (tmm) REVERT: V 266 MET cc_start: -0.3086 (ttt) cc_final: -0.5739 (mtt) outliers start: 0 outliers final: 0 residues processed: 565 average time/residue: 0.5686 time to fit residues: 562.6155 Evaluate side-chains 499 residues out of total 7084 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 499 time to evaluate : 5.375 ------------------------------------------------------------------------------- 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: 0.0170 chunk 396 optimal weight: 20.0000 chunk 581 optimal weight: 30.0000 chunk 876 optimal weight: 9.9990 chunk 806 optimal weight: 6.9990 chunk 698 optimal weight: 10.0000 chunk 72 optimal weight: 7.9990 chunk 539 optimal weight: 20.0000 chunk 428 optimal weight: 9.9990 overall best weight: 6.6026 ------------------------------------------------------------------------------- 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 154 GLN B 280 GLN ** B 313 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 391 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 154 GLN ** C 267 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 154 GLN D 280 GLN ** 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 154 GLN E 280 GLN ** E 313 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 328 GLN ** E 391 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 154 GLN ** F 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 269 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 280 GLN F 292 GLN ** F 309 GLN ** 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 154 GLN 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 154 GLN ** H 269 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 391 GLN ** I 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 154 GLN I 292 GLN ** I 313 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 378 GLN ** I 380 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 154 GLN ** J 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 269 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 154 GLN ** 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 386 GLN K 391 GLN ** L 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 154 GLN ** L 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 191 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 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 196 ASN ** A 313 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 15 ASN ** M 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 154 GLN ** M 191 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 391 GLN ** N 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 154 GLN ** 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 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 128 GLN O 154 GLN ** O 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 191 ASN ** 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** O 382 GLN ** P 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 154 GLN ** P 313 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 378 GLN ** 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 292 GLN ** Q 313 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 378 GLN ** R 22 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 ** R 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 386 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 22 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 58 GLN ** S 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 281 ASN ** 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 386 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 58 GLN ** T 273 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 280 GLN T 302 ASN ** 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 22 ASN ** 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** ** U 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 386 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 391 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 280 GLN ** V 292 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 302 ASN ** 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** Total number of N/Q/H flips: 48 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.2528 moved from start: 1.0305 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.131 66044 Z= 0.350 Angle : 0.937 18.561 89980 Z= 0.503 Chirality : 0.052 0.251 10560 Planarity : 0.005 0.083 12078 Dihedral : 6.623 37.931 9196 Min Nonbonded Distance : 2.009 Molprobity Statistics. All-atom Clashscore : 27.48 Ramachandran Plot: Outliers : 0.99 % Allowed : 9.72 % Favored : 89.30 % Rotamer: Outliers : 0.00 % Allowed : 0.76 % Favored : 99.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.51 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: -1.71 (0.08), residues: 8800 helix: 0.75 (0.14), residues: 1254 sheet: -1.44 (0.10), residues: 2112 loop : -1.50 (0.08), residues: 5434 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.004 TRP R 333 HIS 0.004 0.001 HIS U 193 PHE 0.045 0.003 PHE H 42 TYR 0.021 0.002 TYR B 303 ARG 0.012 0.002 ARG V 95 ********************** 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 602 residues out of total 7084 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 602 time to evaluate : 5.392 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: B 143 MET cc_start: -0.1814 (ttt) cc_final: -0.3312 (ttt) REVERT: C 110 MET cc_start: 0.3540 (tmm) cc_final: 0.3339 (ttt) REVERT: C 143 MET cc_start: -0.1794 (ttt) cc_final: -0.2084 (ttt) REVERT: C 195 MET cc_start: 0.1607 (mmp) cc_final: -0.0052 (tpt) REVERT: D 110 MET cc_start: 0.3592 (tmm) cc_final: 0.2543 (ttt) REVERT: D 143 MET cc_start: -0.1886 (ttt) cc_final: -0.3253 (ttt) REVERT: D 195 MET cc_start: 0.1274 (mmp) cc_final: -0.0453 (tpt) REVERT: E 143 MET cc_start: -0.2023 (ttt) cc_final: -0.2247 (ttt) REVERT: E 195 MET cc_start: 0.1838 (mmp) cc_final: 0.0198 (tpt) REVERT: F 150 THR cc_start: 0.3203 (p) cc_final: 0.2751 (p) REVERT: G 143 MET cc_start: -0.2122 (ttt) cc_final: -0.2431 (ttt) REVERT: G 195 MET cc_start: 0.1966 (mmp) cc_final: 0.0273 (tpt) REVERT: G 266 MET cc_start: -0.2531 (mtm) cc_final: -0.3919 (mmt) REVERT: G 374 MET cc_start: 0.2767 (ptt) cc_final: 0.1274 (mtt) REVERT: H 143 MET cc_start: -0.1559 (ttt) cc_final: -0.2115 (ttt) REVERT: H 231 PHE cc_start: 0.2355 (m-80) cc_final: 0.0859 (m-80) REVERT: I 143 MET cc_start: -0.2020 (ttt) cc_final: -0.3425 (ttt) REVERT: J 59 ASP cc_start: 0.6007 (m-30) cc_final: 0.4771 (m-30) REVERT: J 143 MET cc_start: -0.1909 (ttt) cc_final: -0.3348 (ttt) REVERT: J 266 MET cc_start: -0.2599 (mtm) cc_final: -0.2822 (mtt) REVERT: K 143 MET cc_start: -0.2277 (ttt) cc_final: -0.3347 (ttp) REVERT: K 195 MET cc_start: 0.0962 (mmp) cc_final: -0.0723 (tpt) REVERT: L 143 MET cc_start: -0.1722 (ttt) cc_final: -0.2028 (ttt) REVERT: A 143 MET cc_start: -0.2137 (ttt) cc_final: -0.2507 (ttt) REVERT: A 195 MET cc_start: 0.0459 (mmp) cc_final: -0.0992 (tpt) REVERT: M 195 MET cc_start: 0.0208 (mmp) cc_final: -0.1046 (tpt) REVERT: M 380 ASN cc_start: 0.7176 (m-40) cc_final: 0.6645 (t0) REVERT: N 195 MET cc_start: 0.0481 (mmp) cc_final: -0.0436 (tpt) REVERT: O 143 MET cc_start: -0.2674 (ttt) cc_final: -0.3026 (ttt) REVERT: O 195 MET cc_start: -0.0235 (mmp) cc_final: -0.0767 (tpt) REVERT: O 292 GLN cc_start: 0.4361 (tp-100) cc_final: 0.4103 (tp-100) REVERT: P 143 MET cc_start: -0.1853 (ttt) cc_final: -0.2285 (ttt) REVERT: P 374 MET cc_start: 0.3446 (ptt) cc_final: 0.2049 (mmt) REVERT: Q 143 MET cc_start: -0.1737 (ttt) cc_final: -0.2065 (ttt) REVERT: Q 195 MET cc_start: 0.0666 (mmp) cc_final: -0.0069 (tpt) REVERT: R 32 LYS cc_start: 0.6568 (mmpt) cc_final: 0.6365 (mmpt) REVERT: R 143 MET cc_start: 0.0339 (pmm) cc_final: -0.1046 (mmt) REVERT: R 195 MET cc_start: 0.0577 (mmp) cc_final: -0.0104 (tpt) REVERT: R 380 ASN cc_start: 0.7084 (m-40) cc_final: 0.6754 (m-40) REVERT: S 380 ASN cc_start: 0.7114 (m-40) cc_final: 0.6652 (m-40) REVERT: T 143 MET cc_start: -0.2320 (ttt) cc_final: -0.2560 (ttt) REVERT: T 380 ASN cc_start: 0.6808 (m-40) cc_final: 0.6274 (t0) REVERT: U 379 ARG cc_start: 0.4355 (mmp80) cc_final: 0.3373 (ttt180) REVERT: U 380 ASN cc_start: 0.7078 (m-40) cc_final: 0.6645 (t0) REVERT: V 266 MET cc_start: -0.2910 (ttt) cc_final: -0.5596 (mtt) outliers start: 0 outliers final: 0 residues processed: 602 average time/residue: 0.5601 time to fit residues: 592.8178 Evaluate side-chains 506 residues out of total 7084 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 506 time to evaluate : 6.551 ------------------------------------------------------------------------------- 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: 8.9990 chunk 743 optimal weight: 0.0970 chunk 213 optimal weight: 7.9990 chunk 643 optimal weight: 5.9990 chunk 103 optimal weight: 4.9990 chunk 194 optimal weight: 8.9990 chunk 699 optimal weight: 9.9990 chunk 292 optimal weight: 6.9990 chunk 718 optimal weight: 9.9990 chunk 88 optimal weight: 2.9990 chunk 128 optimal weight: 8.9990 overall best weight: 4.2186 ------------------------------------------------------------------------------- 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 154 GLN ** B 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 268 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 280 GLN ** 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 154 GLN ** C 267 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** ** D 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 154 GLN D 280 GLN ** 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 154 GLN E 280 GLN ** E 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 154 GLN ** F 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 269 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 280 GLN F 292 GLN ** F 305 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 309 GLN ** 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 280 GLN ** G 313 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 391 GLN H 4 GLN ** H 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 269 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 15 ASN ** I 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 154 GLN I 292 GLN ** 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 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 269 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 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 154 GLN ** 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 378 GLN ** L 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 191 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 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 ** A 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 189 GLN ** 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 A 391 GLN ** M 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 191 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 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 391 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 21 ASN ** 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 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 307 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 268 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 268 GLN ** R 281 ASN ** 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 58 GLN ** S 128 GLN ** 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 386 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 273 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 280 GLN ** T 313 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 386 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 22 ASN ** 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** V 280 GLN ** 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 391 GLN Total number of N/Q/H flips: 34 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5409 r_free = 0.5409 target = 0.324566 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.5226 r_free = 0.5226 target = 0.310083 restraints weight = 1130326.230| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.5277 r_free = 0.5277 target = 0.314929 restraints weight = 703258.321| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.5267 r_free = 0.5267 target = 0.313576 restraints weight = 601586.135| |-----------------------------------------------------------------------------| r_work (final): 0.5258 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3057 moved from start: 1.0483 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 66044 Z= 0.240 Angle : 0.773 12.662 89980 Z= 0.420 Chirality : 0.048 0.314 10560 Planarity : 0.004 0.042 12078 Dihedral : 6.193 32.641 9196 Min Nonbonded Distance : 2.067 Molprobity Statistics. All-atom Clashscore : 21.77 Ramachandran Plot: Outliers : 0.93 % Allowed : 7.77 % Favored : 91.30 % Rotamer: Outliers : 0.00 % Allowed : 0.48 % Favored : 99.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.51 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: -1.51 (0.09), residues: 8800 helix: 1.42 (0.14), residues: 1254 sheet: -1.19 (0.10), residues: 2288 loop : -1.57 (0.08), residues: 5258 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP R 333 HIS 0.002 0.001 HIS E 193 PHE 0.027 0.002 PHE L 31 TYR 0.017 0.002 TYR I 177 ARG 0.012 0.001 ARG I 379 =============================================================================== Job complete usr+sys time: 11402.02 seconds wall clock time: 205 minutes 34.51 seconds (12334.51 seconds total)