Starting phenix.real_space_refine on Fri Feb 23 15:38:41 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5kyh_8298/02_2024/5kyh_8298.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5kyh_8298/02_2024/5kyh_8298.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5kyh_8298/02_2024/5kyh_8298.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5kyh_8298/02_2024/5kyh_8298.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5kyh_8298/02_2024/5kyh_8298.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5kyh_8298/02_2024/5kyh_8298.pdb" } resolution = 4.0 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.951 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 105 5.16 5 C 25053 2.51 5 N 6321 2.21 5 O 7413 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 22": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 76": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 95": "OD1" <-> "OD2" Residue "A PHE 109": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 129": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 133": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 197": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 201": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 203": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 220": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 225": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 234": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 236": "NH1" <-> "NH2" Residue "A PHE 237": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 242": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 256": "OD1" <-> "OD2" Residue "B TYR 22": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 76": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 95": "OD1" <-> "OD2" Residue "B PHE 109": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 129": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 133": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 197": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 201": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 203": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 220": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 225": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 234": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 236": "NH1" <-> "NH2" Residue "B PHE 237": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 242": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 256": "OD1" <-> "OD2" Residue "C TYR 22": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 76": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 95": "OD1" <-> "OD2" Residue "C PHE 109": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 129": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 197": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 201": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 203": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 220": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 225": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 234": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 236": "NH1" <-> "NH2" Residue "C PHE 237": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 242": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 256": "OD1" <-> "OD2" Residue "D TYR 22": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 76": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 95": "OD1" <-> "OD2" Residue "D PHE 109": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 129": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 197": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 201": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 203": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 220": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 225": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 234": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 236": "NH1" <-> "NH2" Residue "D PHE 237": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 242": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 256": "OD1" <-> "OD2" Residue "E TYR 22": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 76": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 95": "OD1" <-> "OD2" Residue "E PHE 109": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 129": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 197": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 201": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 203": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 220": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 225": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 234": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 236": "NH1" <-> "NH2" Residue "E PHE 237": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 242": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 256": "OD1" <-> "OD2" Residue "F TYR 22": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 76": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 95": "OD1" <-> "OD2" Residue "F PHE 109": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 129": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 197": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 201": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 203": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 220": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 225": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 234": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 236": "NH1" <-> "NH2" Residue "F PHE 237": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 242": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 256": "OD1" <-> "OD2" Residue "G TYR 22": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 76": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 95": "OD1" <-> "OD2" Residue "G PHE 109": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 129": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 133": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 197": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 201": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 203": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 220": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 225": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 234": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ARG 236": "NH1" <-> "NH2" Residue "G PHE 237": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 242": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 256": "OD1" <-> "OD2" Residue "H TYR 22": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 76": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ASP 95": "OD1" <-> "OD2" Residue "H PHE 109": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 129": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 197": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 201": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 203": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 220": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 225": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 234": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ARG 236": "NH1" <-> "NH2" Residue "H PHE 237": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 242": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ASP 256": "OD1" <-> "OD2" Residue "I TYR 22": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 76": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ASP 95": "OD1" <-> "OD2" Residue "I PHE 109": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 129": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 197": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 201": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 203": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 220": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 225": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 234": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ARG 236": "NH1" <-> "NH2" Residue "I PHE 237": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 242": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ASP 256": "OD1" <-> "OD2" Residue "J TYR 22": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 76": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ASP 95": "OD1" <-> "OD2" Residue "J PHE 109": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 129": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 197": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 201": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 203": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 220": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 225": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 234": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ARG 236": "NH1" <-> "NH2" Residue "J PHE 237": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 242": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ASP 256": "OD1" <-> "OD2" Residue "K TYR 22": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 76": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ASP 95": "OD1" <-> "OD2" Residue "K PHE 109": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 129": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 197": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 201": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 203": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 220": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 225": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 234": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ARG 236": "NH1" <-> "NH2" Residue "K PHE 237": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 242": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ASP 256": "OD1" <-> "OD2" Residue "L TYR 22": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 76": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ASP 95": "OD1" <-> "OD2" Residue "L PHE 109": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 129": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 133": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 197": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 201": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 203": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 220": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 225": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 234": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ARG 236": "NH1" <-> "NH2" Residue "L PHE 237": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 242": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ASP 256": "OD1" <-> "OD2" Residue "M TYR 22": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M PHE 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M PHE 76": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M ASP 95": "OD1" <-> "OD2" Residue "M PHE 109": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M PHE 129": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M PHE 133": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M PHE 197": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M TYR 201": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M PHE 203": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M TYR 220": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M PHE 225": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M PHE 234": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M ARG 236": "NH1" <-> "NH2" Residue "M PHE 237": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M TYR 242": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M ASP 256": "OD1" <-> "OD2" Residue "N TYR 22": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N PHE 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N PHE 76": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N ASP 95": "OD1" <-> "OD2" Residue "N PHE 109": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N PHE 129": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N PHE 197": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N TYR 201": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N PHE 203": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N TYR 220": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N PHE 225": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N PHE 234": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N ARG 236": "NH1" <-> "NH2" Residue "N PHE 237": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N TYR 242": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N ASP 256": "OD1" <-> "OD2" Residue "O TYR 22": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O PHE 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O PHE 76": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O ASP 95": "OD1" <-> "OD2" Residue "O PHE 109": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O PHE 129": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O PHE 197": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O TYR 201": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O PHE 203": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O TYR 220": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O PHE 225": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O PHE 234": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O ARG 236": "NH1" <-> "NH2" Residue "O PHE 237": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O TYR 242": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O ASP 256": "OD1" <-> "OD2" Residue "P TYR 22": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P PHE 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P PHE 76": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P ASP 95": "OD1" <-> "OD2" Residue "P PHE 109": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P PHE 129": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P PHE 197": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P TYR 201": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P PHE 203": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P TYR 220": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P PHE 225": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P PHE 234": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P ARG 236": "NH1" <-> "NH2" Residue "P PHE 237": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P TYR 242": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P ASP 256": "OD1" <-> "OD2" Residue "Q TYR 22": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q PHE 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q PHE 76": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q ASP 95": "OD1" <-> "OD2" Residue "Q PHE 109": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q PHE 129": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q PHE 197": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q TYR 201": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q PHE 203": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q TYR 220": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q PHE 225": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q PHE 234": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q ARG 236": "NH1" <-> "NH2" Residue "Q PHE 237": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q TYR 242": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q ASP 256": "OD1" <-> "OD2" Residue "R TYR 22": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R PHE 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R PHE 76": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R ASP 95": "OD1" <-> "OD2" Residue "R PHE 109": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R PHE 129": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R PHE 197": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R TYR 201": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R PHE 203": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R TYR 220": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R PHE 225": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R PHE 234": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R ARG 236": "NH1" <-> "NH2" Residue "R PHE 237": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R TYR 242": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R ASP 256": "OD1" <-> "OD2" Residue "S TYR 22": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S PHE 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S PHE 76": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S ASP 95": "OD1" <-> "OD2" Residue "S PHE 109": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S PHE 129": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S PHE 197": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S TYR 201": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S PHE 203": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S TYR 220": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S PHE 225": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S PHE 234": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S ARG 236": "NH1" <-> "NH2" Residue "S PHE 237": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S TYR 242": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S ASP 256": "OD1" <-> "OD2" Residue "T TYR 22": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T PHE 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T PHE 76": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T ASP 95": "OD1" <-> "OD2" Residue "T PHE 109": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T PHE 129": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T PHE 133": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T PHE 197": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T TYR 201": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T PHE 203": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T TYR 220": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T PHE 225": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T PHE 234": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T ARG 236": "NH1" <-> "NH2" Residue "T PHE 237": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T TYR 242": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T ASP 256": "OD1" <-> "OD2" Residue "U TYR 22": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U PHE 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U PHE 76": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U ASP 95": "OD1" <-> "OD2" Residue "U PHE 109": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U PHE 129": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U PHE 197": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U TYR 201": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U PHE 203": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U TYR 220": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U PHE 225": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U PHE 234": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U ARG 236": "NH1" <-> "NH2" Residue "U PHE 237": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U TYR 242": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U ASP 256": "OD1" <-> "OD2" Time to flip residues: 0.14s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 38892 Number of models: 1 Model: "" Number of chains: 21 Chain: "A" Number of atoms: 1852 Number of conformers: 1 Conformer: "" Number of residues, atoms: 242, 1852 Classifications: {'peptide': 242} Link IDs: {'PTRANS': 11, 'TRANS': 230} Chain breaks: 1 Chain: "B" Number of atoms: 1852 Number of conformers: 1 Conformer: "" Number of residues, atoms: 242, 1852 Classifications: {'peptide': 242} Link IDs: {'PTRANS': 11, 'TRANS': 230} Chain breaks: 1 Chain: "C" Number of atoms: 1852 Number of conformers: 1 Conformer: "" Number of residues, atoms: 242, 1852 Classifications: {'peptide': 242} Link IDs: {'PTRANS': 11, 'TRANS': 230} Chain breaks: 1 Chain: "D" Number of atoms: 1852 Number of conformers: 1 Conformer: "" Number of residues, atoms: 242, 1852 Classifications: {'peptide': 242} Link IDs: {'PTRANS': 11, 'TRANS': 230} Chain breaks: 1 Chain: "E" Number of atoms: 1852 Number of conformers: 1 Conformer: "" Number of residues, atoms: 242, 1852 Classifications: {'peptide': 242} Link IDs: {'PTRANS': 11, 'TRANS': 230} Chain breaks: 1 Chain: "F" Number of atoms: 1852 Number of conformers: 1 Conformer: "" Number of residues, atoms: 242, 1852 Classifications: {'peptide': 242} Link IDs: {'PTRANS': 11, 'TRANS': 230} Chain breaks: 1 Chain: "G" Number of atoms: 1852 Number of conformers: 1 Conformer: "" Number of residues, atoms: 242, 1852 Classifications: {'peptide': 242} Link IDs: {'PTRANS': 11, 'TRANS': 230} Chain breaks: 1 Chain: "H" Number of atoms: 1852 Number of conformers: 1 Conformer: "" Number of residues, atoms: 242, 1852 Classifications: {'peptide': 242} Link IDs: {'PTRANS': 11, 'TRANS': 230} Chain breaks: 1 Chain: "I" Number of atoms: 1852 Number of conformers: 1 Conformer: "" Number of residues, atoms: 242, 1852 Classifications: {'peptide': 242} Link IDs: {'PTRANS': 11, 'TRANS': 230} Chain breaks: 1 Chain: "J" Number of atoms: 1852 Number of conformers: 1 Conformer: "" Number of residues, atoms: 242, 1852 Classifications: {'peptide': 242} Link IDs: {'PTRANS': 11, 'TRANS': 230} Chain breaks: 1 Chain: "K" Number of atoms: 1852 Number of conformers: 1 Conformer: "" Number of residues, atoms: 242, 1852 Classifications: {'peptide': 242} Link IDs: {'PTRANS': 11, 'TRANS': 230} Chain breaks: 1 Chain: "L" Number of atoms: 1852 Number of conformers: 1 Conformer: "" Number of residues, atoms: 242, 1852 Classifications: {'peptide': 242} Link IDs: {'PTRANS': 11, 'TRANS': 230} Chain breaks: 1 Chain: "M" Number of atoms: 1852 Number of conformers: 1 Conformer: "" Number of residues, atoms: 242, 1852 Classifications: {'peptide': 242} Link IDs: {'PTRANS': 11, 'TRANS': 230} Chain breaks: 1 Chain: "N" Number of atoms: 1852 Number of conformers: 1 Conformer: "" Number of residues, atoms: 242, 1852 Classifications: {'peptide': 242} Link IDs: {'PTRANS': 11, 'TRANS': 230} Chain breaks: 1 Chain: "O" Number of atoms: 1852 Number of conformers: 1 Conformer: "" Number of residues, atoms: 242, 1852 Classifications: {'peptide': 242} Link IDs: {'PTRANS': 11, 'TRANS': 230} Chain breaks: 1 Chain: "P" Number of atoms: 1852 Number of conformers: 1 Conformer: "" Number of residues, atoms: 242, 1852 Classifications: {'peptide': 242} Link IDs: {'PTRANS': 11, 'TRANS': 230} Chain breaks: 1 Chain: "Q" Number of atoms: 1852 Number of conformers: 1 Conformer: "" Number of residues, atoms: 242, 1852 Classifications: {'peptide': 242} Link IDs: {'PTRANS': 11, 'TRANS': 230} Chain breaks: 1 Chain: "R" Number of atoms: 1852 Number of conformers: 1 Conformer: "" Number of residues, atoms: 242, 1852 Classifications: {'peptide': 242} Link IDs: {'PTRANS': 11, 'TRANS': 230} Chain breaks: 1 Chain: "S" Number of atoms: 1852 Number of conformers: 1 Conformer: "" Number of residues, atoms: 242, 1852 Classifications: {'peptide': 242} Link IDs: {'PTRANS': 11, 'TRANS': 230} Chain breaks: 1 Chain: "T" Number of atoms: 1852 Number of conformers: 1 Conformer: "" Number of residues, atoms: 242, 1852 Classifications: {'peptide': 242} Link IDs: {'PTRANS': 11, 'TRANS': 230} Chain breaks: 1 Chain: "U" Number of atoms: 1852 Number of conformers: 1 Conformer: "" Number of residues, atoms: 242, 1852 Classifications: {'peptide': 242} Link IDs: {'PTRANS': 11, 'TRANS': 230} Chain breaks: 1 Time building chain proxies: 19.64, per 1000 atoms: 0.50 Number of scatterers: 38892 At special positions: 0 Unit cell: (143.64, 145.8, 228.96, 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 105 16.00 O 7413 8.00 N 6321 7.00 C 25053 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=21, symmetry=0 Simple disulfide: pdb=" SG CYS A 104 " - pdb=" SG CYS A 271 " distance=2.05 Simple disulfide: pdb=" SG CYS B 104 " - pdb=" SG CYS B 271 " distance=2.05 Simple disulfide: pdb=" SG CYS C 104 " - pdb=" SG CYS C 271 " distance=2.05 Simple disulfide: pdb=" SG CYS D 104 " - pdb=" SG CYS D 271 " distance=2.05 Simple disulfide: pdb=" SG CYS E 104 " - pdb=" SG CYS E 271 " distance=2.05 Simple disulfide: pdb=" SG CYS F 104 " - pdb=" SG CYS F 271 " distance=2.05 Simple disulfide: pdb=" SG CYS G 104 " - pdb=" SG CYS G 271 " distance=2.05 Simple disulfide: pdb=" SG CYS H 104 " - pdb=" SG CYS H 271 " distance=2.05 Simple disulfide: pdb=" SG CYS I 104 " - pdb=" SG CYS I 271 " distance=2.05 Simple disulfide: pdb=" SG CYS J 104 " - pdb=" SG CYS J 271 " distance=2.05 Simple disulfide: pdb=" SG CYS K 104 " - pdb=" SG CYS K 271 " distance=2.05 Simple disulfide: pdb=" SG CYS L 104 " - pdb=" SG CYS L 271 " distance=2.05 Simple disulfide: pdb=" SG CYS M 104 " - pdb=" SG CYS M 271 " distance=2.05 Simple disulfide: pdb=" SG CYS N 104 " - pdb=" SG CYS N 271 " distance=2.05 Simple disulfide: pdb=" SG CYS O 104 " - pdb=" SG CYS O 271 " distance=2.05 Simple disulfide: pdb=" SG CYS P 104 " - pdb=" SG CYS P 271 " distance=2.05 Simple disulfide: pdb=" SG CYS Q 104 " - pdb=" SG CYS Q 271 " distance=2.05 Simple disulfide: pdb=" SG CYS R 104 " - pdb=" SG CYS R 271 " distance=2.05 Simple disulfide: pdb=" SG CYS S 104 " - pdb=" SG CYS S 271 " distance=2.05 Simple disulfide: pdb=" SG CYS T 104 " - pdb=" SG CYS T 271 " distance=2.05 Simple disulfide: pdb=" SG CYS U 104 " - pdb=" SG CYS U 271 " distance=2.05 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: 13.44 Conformation dependent library (CDL) restraints added in 6.9 seconds 9996 Ramachandran restraints generated. 4998 Oldfield, 0 Emsley, 4998 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 9576 Finding SS restraints... Secondary structure from input PDB file: 63 helices and 126 sheets defined 16.1% alpha, 36.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.63 Creating SS restraints... Processing helix chain 'A' and resid 1 through 29 removed outlier: 3.632A pdb=" N LEU A 8 " --> pdb=" O VAL A 4 " (cutoff:3.500A) Processing helix chain 'A' and resid 61 through 65 removed outlier: 3.713A pdb=" N PHE A 65 " --> pdb=" O LYS A 62 " (cutoff:3.500A) Processing helix chain 'A' and resid 115 through 120 removed outlier: 4.379A pdb=" N GLY A 120 " --> pdb=" O LYS A 116 " (cutoff:3.500A) Processing helix chain 'B' and resid 2 through 29 removed outlier: 3.632A pdb=" N LEU B 8 " --> pdb=" O VAL B 4 " (cutoff:3.500A) Processing helix chain 'B' and resid 61 through 65 removed outlier: 3.714A pdb=" N PHE B 65 " --> pdb=" O LYS B 62 " (cutoff:3.500A) Processing helix chain 'B' and resid 115 through 120 removed outlier: 4.380A pdb=" N GLY B 120 " --> pdb=" O LYS B 116 " (cutoff:3.500A) Processing helix chain 'C' and resid 2 through 29 removed outlier: 3.632A pdb=" N LEU C 8 " --> pdb=" O VAL C 4 " (cutoff:3.500A) Processing helix chain 'C' and resid 61 through 65 removed outlier: 3.714A pdb=" N PHE C 65 " --> pdb=" O LYS C 62 " (cutoff:3.500A) Processing helix chain 'C' and resid 115 through 120 removed outlier: 4.379A pdb=" N GLY C 120 " --> pdb=" O LYS C 116 " (cutoff:3.500A) Processing helix chain 'D' and resid 2 through 29 removed outlier: 3.633A pdb=" N LEU D 8 " --> pdb=" O VAL D 4 " (cutoff:3.500A) Processing helix chain 'D' and resid 61 through 65 removed outlier: 3.713A pdb=" N PHE D 65 " --> pdb=" O LYS D 62 " (cutoff:3.500A) Processing helix chain 'D' and resid 115 through 120 removed outlier: 4.380A pdb=" N GLY D 120 " --> pdb=" O LYS D 116 " (cutoff:3.500A) Processing helix chain 'E' and resid 2 through 29 removed outlier: 3.633A pdb=" N LEU E 8 " --> pdb=" O VAL E 4 " (cutoff:3.500A) Processing helix chain 'E' and resid 61 through 65 removed outlier: 3.714A pdb=" N PHE E 65 " --> pdb=" O LYS E 62 " (cutoff:3.500A) Processing helix chain 'E' and resid 115 through 120 removed outlier: 4.379A pdb=" N GLY E 120 " --> pdb=" O LYS E 116 " (cutoff:3.500A) Processing helix chain 'F' and resid 2 through 29 removed outlier: 3.632A pdb=" N LEU F 8 " --> pdb=" O VAL F 4 " (cutoff:3.500A) Processing helix chain 'F' and resid 61 through 65 removed outlier: 3.714A pdb=" N PHE F 65 " --> pdb=" O LYS F 62 " (cutoff:3.500A) Processing helix chain 'F' and resid 115 through 120 removed outlier: 4.380A pdb=" N GLY F 120 " --> pdb=" O LYS F 116 " (cutoff:3.500A) Processing helix chain 'G' and resid 2 through 29 removed outlier: 3.633A pdb=" N LEU G 8 " --> pdb=" O VAL G 4 " (cutoff:3.500A) Processing helix chain 'G' and resid 61 through 65 removed outlier: 3.713A pdb=" N PHE G 65 " --> pdb=" O LYS G 62 " (cutoff:3.500A) Processing helix chain 'G' and resid 115 through 120 removed outlier: 4.380A pdb=" N GLY G 120 " --> pdb=" O LYS G 116 " (cutoff:3.500A) Processing helix chain 'H' and resid 2 through 29 removed outlier: 3.632A pdb=" N LEU H 8 " --> pdb=" O VAL H 4 " (cutoff:3.500A) Processing helix chain 'H' and resid 61 through 65 removed outlier: 3.714A pdb=" N PHE H 65 " --> pdb=" O LYS H 62 " (cutoff:3.500A) Processing helix chain 'H' and resid 115 through 120 removed outlier: 4.379A pdb=" N GLY H 120 " --> pdb=" O LYS H 116 " (cutoff:3.500A) Processing helix chain 'I' and resid 2 through 29 removed outlier: 3.633A pdb=" N LEU I 8 " --> pdb=" O VAL I 4 " (cutoff:3.500A) Processing helix chain 'I' and resid 61 through 65 removed outlier: 3.713A pdb=" N PHE I 65 " --> pdb=" O LYS I 62 " (cutoff:3.500A) Processing helix chain 'I' and resid 115 through 120 removed outlier: 4.380A pdb=" N GLY I 120 " --> pdb=" O LYS I 116 " (cutoff:3.500A) Processing helix chain 'J' and resid 2 through 29 removed outlier: 3.632A pdb=" N LEU J 8 " --> pdb=" O VAL J 4 " (cutoff:3.500A) Processing helix chain 'J' and resid 61 through 65 removed outlier: 3.713A pdb=" N PHE J 65 " --> pdb=" O LYS J 62 " (cutoff:3.500A) Processing helix chain 'J' and resid 115 through 120 removed outlier: 4.380A pdb=" N GLY J 120 " --> pdb=" O LYS J 116 " (cutoff:3.500A) Processing helix chain 'K' and resid 2 through 29 removed outlier: 3.632A pdb=" N LEU K 8 " --> pdb=" O VAL K 4 " (cutoff:3.500A) Processing helix chain 'K' and resid 61 through 65 removed outlier: 3.714A pdb=" N PHE K 65 " --> pdb=" O LYS K 62 " (cutoff:3.500A) Processing helix chain 'K' and resid 115 through 120 removed outlier: 4.380A pdb=" N GLY K 120 " --> pdb=" O LYS K 116 " (cutoff:3.500A) Processing helix chain 'L' and resid 2 through 29 removed outlier: 3.633A pdb=" N LEU L 8 " --> pdb=" O VAL L 4 " (cutoff:3.500A) Processing helix chain 'L' and resid 61 through 65 removed outlier: 3.714A pdb=" N PHE L 65 " --> pdb=" O LYS L 62 " (cutoff:3.500A) Processing helix chain 'L' and resid 115 through 120 removed outlier: 4.379A pdb=" N GLY L 120 " --> pdb=" O LYS L 116 " (cutoff:3.500A) Processing helix chain 'M' and resid 2 through 29 removed outlier: 3.632A pdb=" N LEU M 8 " --> pdb=" O VAL M 4 " (cutoff:3.500A) Processing helix chain 'M' and resid 61 through 65 removed outlier: 3.713A pdb=" N PHE M 65 " --> pdb=" O LYS M 62 " (cutoff:3.500A) Processing helix chain 'M' and resid 115 through 120 removed outlier: 4.380A pdb=" N GLY M 120 " --> pdb=" O LYS M 116 " (cutoff:3.500A) Processing helix chain 'N' and resid 2 through 29 removed outlier: 3.633A pdb=" N LEU N 8 " --> pdb=" O VAL N 4 " (cutoff:3.500A) Processing helix chain 'N' and resid 61 through 65 removed outlier: 3.713A pdb=" N PHE N 65 " --> pdb=" O LYS N 62 " (cutoff:3.500A) Processing helix chain 'N' and resid 115 through 120 removed outlier: 4.379A pdb=" N GLY N 120 " --> pdb=" O LYS N 116 " (cutoff:3.500A) Processing helix chain 'O' and resid 2 through 29 removed outlier: 3.633A pdb=" N LEU O 8 " --> pdb=" O VAL O 4 " (cutoff:3.500A) Processing helix chain 'O' and resid 61 through 65 removed outlier: 3.714A pdb=" N PHE O 65 " --> pdb=" O LYS O 62 " (cutoff:3.500A) Processing helix chain 'O' and resid 115 through 120 removed outlier: 4.379A pdb=" N GLY O 120 " --> pdb=" O LYS O 116 " (cutoff:3.500A) Processing helix chain 'P' and resid 2 through 29 removed outlier: 3.633A pdb=" N LEU P 8 " --> pdb=" O VAL P 4 " (cutoff:3.500A) Processing helix chain 'P' and resid 61 through 65 removed outlier: 3.713A pdb=" N PHE P 65 " --> pdb=" O LYS P 62 " (cutoff:3.500A) Processing helix chain 'P' and resid 115 through 120 removed outlier: 4.380A pdb=" N GLY P 120 " --> pdb=" O LYS P 116 " (cutoff:3.500A) Processing helix chain 'Q' and resid 2 through 29 removed outlier: 3.633A pdb=" N LEU Q 8 " --> pdb=" O VAL Q 4 " (cutoff:3.500A) Processing helix chain 'Q' and resid 61 through 65 removed outlier: 3.713A pdb=" N PHE Q 65 " --> pdb=" O LYS Q 62 " (cutoff:3.500A) Processing helix chain 'Q' and resid 115 through 120 removed outlier: 4.380A pdb=" N GLY Q 120 " --> pdb=" O LYS Q 116 " (cutoff:3.500A) Processing helix chain 'R' and resid 2 through 29 removed outlier: 3.632A pdb=" N LEU R 8 " --> pdb=" O VAL R 4 " (cutoff:3.500A) Processing helix chain 'R' and resid 61 through 65 removed outlier: 3.713A pdb=" N PHE R 65 " --> pdb=" O LYS R 62 " (cutoff:3.500A) Processing helix chain 'R' and resid 115 through 120 removed outlier: 4.380A pdb=" N GLY R 120 " --> pdb=" O LYS R 116 " (cutoff:3.500A) Processing helix chain 'S' and resid 2 through 29 removed outlier: 3.632A pdb=" N LEU S 8 " --> pdb=" O VAL S 4 " (cutoff:3.500A) Processing helix chain 'S' and resid 61 through 65 removed outlier: 3.714A pdb=" N PHE S 65 " --> pdb=" O LYS S 62 " (cutoff:3.500A) Processing helix chain 'S' and resid 115 through 120 removed outlier: 4.380A pdb=" N GLY S 120 " --> pdb=" O LYS S 116 " (cutoff:3.500A) Processing helix chain 'T' and resid 2 through 29 removed outlier: 3.632A pdb=" N LEU T 8 " --> pdb=" O VAL T 4 " (cutoff:3.500A) Processing helix chain 'T' and resid 61 through 65 removed outlier: 3.714A pdb=" N PHE T 65 " --> pdb=" O LYS T 62 " (cutoff:3.500A) Processing helix chain 'T' and resid 115 through 120 removed outlier: 4.380A pdb=" N GLY T 120 " --> pdb=" O LYS T 116 " (cutoff:3.500A) Processing helix chain 'U' and resid 2 through 29 removed outlier: 3.632A pdb=" N LEU U 8 " --> pdb=" O VAL U 4 " (cutoff:3.500A) Processing helix chain 'U' and resid 61 through 65 removed outlier: 3.713A pdb=" N PHE U 65 " --> pdb=" O LYS U 62 " (cutoff:3.500A) Processing helix chain 'U' and resid 115 through 120 removed outlier: 4.379A pdb=" N GLY U 120 " --> pdb=" O LYS U 116 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 43 through 50 removed outlier: 5.890A pdb=" N LEU A 44 " --> pdb=" O GLN A 77 " (cutoff:3.500A) removed outlier: 6.777A pdb=" N GLN A 77 " --> pdb=" O LEU A 44 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N GLN A 46 " --> pdb=" O SER A 75 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 101 through 106 removed outlier: 6.939A pdb=" N VAL A 96 " --> pdb=" O VAL A 103 " (cutoff:3.500A) removed outlier: 5.071A pdb=" N HIS A 105 " --> pdb=" O ILE A 94 " (cutoff:3.500A) removed outlier: 6.962A pdb=" N ILE A 94 " --> pdb=" O HIS A 105 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 101 through 106 removed outlier: 6.939A pdb=" N VAL A 96 " --> pdb=" O VAL A 103 " (cutoff:3.500A) removed outlier: 5.071A pdb=" N HIS A 105 " --> pdb=" O ILE A 94 " (cutoff:3.500A) removed outlier: 6.962A pdb=" N ILE A 94 " --> pdb=" O HIS A 105 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 109 through 110 Processing sheet with id=AA5, first strand: chain 'A' and resid 122 through 123 removed outlier: 5.796A pdb=" N THR A 127 " --> pdb=" O GLY A 251 " (cutoff:3.500A) removed outlier: 5.629A pdb=" N VAL A 252 " --> pdb=" O SER A 243 " (cutoff:3.500A) removed outlier: 6.207A pdb=" N SER A 243 " --> pdb=" O VAL A 252 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 209 through 215 Processing sheet with id=AA7, first strand: chain 'B' and resid 43 through 50 removed outlier: 5.890A pdb=" N LEU B 44 " --> pdb=" O GLN B 77 " (cutoff:3.500A) removed outlier: 6.777A pdb=" N GLN B 77 " --> pdb=" O LEU B 44 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N GLN B 46 " --> pdb=" O SER B 75 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 101 through 106 removed outlier: 6.940A pdb=" N VAL B 96 " --> pdb=" O VAL B 103 " (cutoff:3.500A) removed outlier: 5.070A pdb=" N HIS B 105 " --> pdb=" O ILE B 94 " (cutoff:3.500A) removed outlier: 6.961A pdb=" N ILE B 94 " --> pdb=" O HIS B 105 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 101 through 106 removed outlier: 6.940A pdb=" N VAL B 96 " --> pdb=" O VAL B 103 " (cutoff:3.500A) removed outlier: 5.070A pdb=" N HIS B 105 " --> pdb=" O ILE B 94 " (cutoff:3.500A) removed outlier: 6.961A pdb=" N ILE B 94 " --> pdb=" O HIS B 105 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 109 through 110 Processing sheet with id=AB2, first strand: chain 'B' and resid 122 through 123 removed outlier: 5.795A pdb=" N THR B 127 " --> pdb=" O GLY B 251 " (cutoff:3.500A) removed outlier: 5.629A pdb=" N VAL B 252 " --> pdb=" O SER B 243 " (cutoff:3.500A) removed outlier: 6.206A pdb=" N SER B 243 " --> pdb=" O VAL B 252 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 209 through 215 Processing sheet with id=AB4, first strand: chain 'C' and resid 43 through 50 removed outlier: 5.890A pdb=" N LEU C 44 " --> pdb=" O GLN C 77 " (cutoff:3.500A) removed outlier: 6.777A pdb=" N GLN C 77 " --> pdb=" O LEU C 44 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N GLN C 46 " --> pdb=" O SER C 75 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 101 through 106 removed outlier: 6.940A pdb=" N VAL C 96 " --> pdb=" O VAL C 103 " (cutoff:3.500A) removed outlier: 5.071A pdb=" N HIS C 105 " --> pdb=" O ILE C 94 " (cutoff:3.500A) removed outlier: 6.961A pdb=" N ILE C 94 " --> pdb=" O HIS C 105 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 101 through 106 removed outlier: 6.940A pdb=" N VAL C 96 " --> pdb=" O VAL C 103 " (cutoff:3.500A) removed outlier: 5.071A pdb=" N HIS C 105 " --> pdb=" O ILE C 94 " (cutoff:3.500A) removed outlier: 6.961A pdb=" N ILE C 94 " --> pdb=" O HIS C 105 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 109 through 110 Processing sheet with id=AB8, first strand: chain 'C' and resid 122 through 123 removed outlier: 5.796A pdb=" N THR C 127 " --> pdb=" O GLY C 251 " (cutoff:3.500A) removed outlier: 5.629A pdb=" N VAL C 252 " --> pdb=" O SER C 243 " (cutoff:3.500A) removed outlier: 6.207A pdb=" N SER C 243 " --> pdb=" O VAL C 252 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 209 through 215 Processing sheet with id=AC1, first strand: chain 'D' and resid 43 through 50 removed outlier: 5.890A pdb=" N LEU D 44 " --> pdb=" O GLN D 77 " (cutoff:3.500A) removed outlier: 6.777A pdb=" N GLN D 77 " --> pdb=" O LEU D 44 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N GLN D 46 " --> pdb=" O SER D 75 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'D' and resid 101 through 106 removed outlier: 6.939A pdb=" N VAL D 96 " --> pdb=" O VAL D 103 " (cutoff:3.500A) removed outlier: 5.071A pdb=" N HIS D 105 " --> pdb=" O ILE D 94 " (cutoff:3.500A) removed outlier: 6.961A pdb=" N ILE D 94 " --> pdb=" O HIS D 105 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'D' and resid 101 through 106 removed outlier: 6.939A pdb=" N VAL D 96 " --> pdb=" O VAL D 103 " (cutoff:3.500A) removed outlier: 5.071A pdb=" N HIS D 105 " --> pdb=" O ILE D 94 " (cutoff:3.500A) removed outlier: 6.961A pdb=" N ILE D 94 " --> pdb=" O HIS D 105 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'D' and resid 109 through 110 Processing sheet with id=AC5, first strand: chain 'D' and resid 122 through 123 removed outlier: 5.795A pdb=" N THR D 127 " --> pdb=" O GLY D 251 " (cutoff:3.500A) removed outlier: 5.630A pdb=" N VAL D 252 " --> pdb=" O SER D 243 " (cutoff:3.500A) removed outlier: 6.207A pdb=" N SER D 243 " --> pdb=" O VAL D 252 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'D' and resid 209 through 215 Processing sheet with id=AC7, first strand: chain 'E' and resid 43 through 50 removed outlier: 5.890A pdb=" N LEU E 44 " --> pdb=" O GLN E 77 " (cutoff:3.500A) removed outlier: 6.777A pdb=" N GLN E 77 " --> pdb=" O LEU E 44 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N GLN E 46 " --> pdb=" O SER E 75 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'E' and resid 101 through 106 removed outlier: 6.941A pdb=" N VAL E 96 " --> pdb=" O VAL E 103 " (cutoff:3.500A) removed outlier: 5.071A pdb=" N HIS E 105 " --> pdb=" O ILE E 94 " (cutoff:3.500A) removed outlier: 6.961A pdb=" N ILE E 94 " --> pdb=" O HIS E 105 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'E' and resid 101 through 106 removed outlier: 6.941A pdb=" N VAL E 96 " --> pdb=" O VAL E 103 " (cutoff:3.500A) removed outlier: 5.071A pdb=" N HIS E 105 " --> pdb=" O ILE E 94 " (cutoff:3.500A) removed outlier: 6.961A pdb=" N ILE E 94 " --> pdb=" O HIS E 105 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'E' and resid 109 through 110 Processing sheet with id=AD2, first strand: chain 'E' and resid 122 through 123 removed outlier: 5.796A pdb=" N THR E 127 " --> pdb=" O GLY E 251 " (cutoff:3.500A) removed outlier: 5.630A pdb=" N VAL E 252 " --> pdb=" O SER E 243 " (cutoff:3.500A) removed outlier: 6.207A pdb=" N SER E 243 " --> pdb=" O VAL E 252 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'E' and resid 209 through 215 Processing sheet with id=AD4, first strand: chain 'F' and resid 43 through 50 removed outlier: 5.890A pdb=" N LEU F 44 " --> pdb=" O GLN F 77 " (cutoff:3.500A) removed outlier: 6.777A pdb=" N GLN F 77 " --> pdb=" O LEU F 44 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N GLN F 46 " --> pdb=" O SER F 75 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'F' and resid 101 through 106 removed outlier: 6.939A pdb=" N VAL F 96 " --> pdb=" O VAL F 103 " (cutoff:3.500A) removed outlier: 5.070A pdb=" N HIS F 105 " --> pdb=" O ILE F 94 " (cutoff:3.500A) removed outlier: 6.961A pdb=" N ILE F 94 " --> pdb=" O HIS F 105 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'F' and resid 101 through 106 removed outlier: 6.939A pdb=" N VAL F 96 " --> pdb=" O VAL F 103 " (cutoff:3.500A) removed outlier: 5.070A pdb=" N HIS F 105 " --> pdb=" O ILE F 94 " (cutoff:3.500A) removed outlier: 6.961A pdb=" N ILE F 94 " --> pdb=" O HIS F 105 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'F' and resid 109 through 110 Processing sheet with id=AD8, first strand: chain 'F' and resid 122 through 123 removed outlier: 5.796A pdb=" N THR F 127 " --> pdb=" O GLY F 251 " (cutoff:3.500A) removed outlier: 5.630A pdb=" N VAL F 252 " --> pdb=" O SER F 243 " (cutoff:3.500A) removed outlier: 6.207A pdb=" N SER F 243 " --> pdb=" O VAL F 252 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'F' and resid 209 through 215 Processing sheet with id=AE1, first strand: chain 'G' and resid 43 through 50 removed outlier: 5.891A pdb=" N LEU G 44 " --> pdb=" O GLN G 77 " (cutoff:3.500A) removed outlier: 6.777A pdb=" N GLN G 77 " --> pdb=" O LEU G 44 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N GLN G 46 " --> pdb=" O SER G 75 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'G' and resid 101 through 106 removed outlier: 6.940A pdb=" N VAL G 96 " --> pdb=" O VAL G 103 " (cutoff:3.500A) removed outlier: 5.070A pdb=" N HIS G 105 " --> pdb=" O ILE G 94 " (cutoff:3.500A) removed outlier: 6.961A pdb=" N ILE G 94 " --> pdb=" O HIS G 105 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'G' and resid 101 through 106 removed outlier: 6.940A pdb=" N VAL G 96 " --> pdb=" O VAL G 103 " (cutoff:3.500A) removed outlier: 5.070A pdb=" N HIS G 105 " --> pdb=" O ILE G 94 " (cutoff:3.500A) removed outlier: 6.961A pdb=" N ILE G 94 " --> pdb=" O HIS G 105 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'G' and resid 109 through 110 Processing sheet with id=AE5, first strand: chain 'G' and resid 122 through 123 removed outlier: 5.796A pdb=" N THR G 127 " --> pdb=" O GLY G 251 " (cutoff:3.500A) removed outlier: 5.630A pdb=" N VAL G 252 " --> pdb=" O SER G 243 " (cutoff:3.500A) removed outlier: 6.207A pdb=" N SER G 243 " --> pdb=" O VAL G 252 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'G' and resid 209 through 215 Processing sheet with id=AE7, first strand: chain 'H' and resid 43 through 50 removed outlier: 5.891A pdb=" N LEU H 44 " --> pdb=" O GLN H 77 " (cutoff:3.500A) removed outlier: 6.778A pdb=" N GLN H 77 " --> pdb=" O LEU H 44 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N GLN H 46 " --> pdb=" O SER H 75 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'H' and resid 101 through 106 removed outlier: 6.939A pdb=" N VAL H 96 " --> pdb=" O VAL H 103 " (cutoff:3.500A) removed outlier: 5.071A pdb=" N HIS H 105 " --> pdb=" O ILE H 94 " (cutoff:3.500A) removed outlier: 6.961A pdb=" N ILE H 94 " --> pdb=" O HIS H 105 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'H' and resid 101 through 106 removed outlier: 6.939A pdb=" N VAL H 96 " --> pdb=" O VAL H 103 " (cutoff:3.500A) removed outlier: 5.071A pdb=" N HIS H 105 " --> pdb=" O ILE H 94 " (cutoff:3.500A) removed outlier: 6.961A pdb=" N ILE H 94 " --> pdb=" O HIS H 105 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'H' and resid 109 through 110 Processing sheet with id=AF2, first strand: chain 'H' and resid 122 through 123 removed outlier: 5.796A pdb=" N THR H 127 " --> pdb=" O GLY H 251 " (cutoff:3.500A) removed outlier: 5.630A pdb=" N VAL H 252 " --> pdb=" O SER H 243 " (cutoff:3.500A) removed outlier: 6.207A pdb=" N SER H 243 " --> pdb=" O VAL H 252 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'H' and resid 209 through 215 Processing sheet with id=AF4, first strand: chain 'I' and resid 43 through 50 removed outlier: 5.890A pdb=" N LEU I 44 " --> pdb=" O GLN I 77 " (cutoff:3.500A) removed outlier: 6.777A pdb=" N GLN I 77 " --> pdb=" O LEU I 44 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N GLN I 46 " --> pdb=" O SER I 75 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'I' and resid 101 through 106 removed outlier: 6.940A pdb=" N VAL I 96 " --> pdb=" O VAL I 103 " (cutoff:3.500A) removed outlier: 5.070A pdb=" N HIS I 105 " --> pdb=" O ILE I 94 " (cutoff:3.500A) removed outlier: 6.961A pdb=" N ILE I 94 " --> pdb=" O HIS I 105 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'I' and resid 101 through 106 removed outlier: 6.940A pdb=" N VAL I 96 " --> pdb=" O VAL I 103 " (cutoff:3.500A) removed outlier: 5.070A pdb=" N HIS I 105 " --> pdb=" O ILE I 94 " (cutoff:3.500A) removed outlier: 6.961A pdb=" N ILE I 94 " --> pdb=" O HIS I 105 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'I' and resid 109 through 110 Processing sheet with id=AF8, first strand: chain 'I' and resid 122 through 123 removed outlier: 5.796A pdb=" N THR I 127 " --> pdb=" O GLY I 251 " (cutoff:3.500A) removed outlier: 5.630A pdb=" N VAL I 252 " --> pdb=" O SER I 243 " (cutoff:3.500A) removed outlier: 6.207A pdb=" N SER I 243 " --> pdb=" O VAL I 252 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'I' and resid 209 through 215 Processing sheet with id=AG1, first strand: chain 'J' and resid 43 through 50 removed outlier: 5.890A pdb=" N LEU J 44 " --> pdb=" O GLN J 77 " (cutoff:3.500A) removed outlier: 6.777A pdb=" N GLN J 77 " --> pdb=" O LEU J 44 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N GLN J 46 " --> pdb=" O SER J 75 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'J' and resid 101 through 106 removed outlier: 6.940A pdb=" N VAL J 96 " --> pdb=" O VAL J 103 " (cutoff:3.500A) removed outlier: 5.070A pdb=" N HIS J 105 " --> pdb=" O ILE J 94 " (cutoff:3.500A) removed outlier: 6.962A pdb=" N ILE J 94 " --> pdb=" O HIS J 105 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'J' and resid 101 through 106 removed outlier: 6.940A pdb=" N VAL J 96 " --> pdb=" O VAL J 103 " (cutoff:3.500A) removed outlier: 5.070A pdb=" N HIS J 105 " --> pdb=" O ILE J 94 " (cutoff:3.500A) removed outlier: 6.962A pdb=" N ILE J 94 " --> pdb=" O HIS J 105 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'J' and resid 109 through 110 Processing sheet with id=AG5, first strand: chain 'J' and resid 122 through 123 removed outlier: 5.796A pdb=" N THR J 127 " --> pdb=" O GLY J 251 " (cutoff:3.500A) removed outlier: 5.629A pdb=" N VAL J 252 " --> pdb=" O SER J 243 " (cutoff:3.500A) removed outlier: 6.208A pdb=" N SER J 243 " --> pdb=" O VAL J 252 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'J' and resid 209 through 215 Processing sheet with id=AG7, first strand: chain 'K' and resid 43 through 50 removed outlier: 5.890A pdb=" N LEU K 44 " --> pdb=" O GLN K 77 " (cutoff:3.500A) removed outlier: 6.777A pdb=" N GLN K 77 " --> pdb=" O LEU K 44 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N GLN K 46 " --> pdb=" O SER K 75 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'K' and resid 101 through 106 removed outlier: 6.940A pdb=" N VAL K 96 " --> pdb=" O VAL K 103 " (cutoff:3.500A) removed outlier: 5.070A pdb=" N HIS K 105 " --> pdb=" O ILE K 94 " (cutoff:3.500A) removed outlier: 6.961A pdb=" N ILE K 94 " --> pdb=" O HIS K 105 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'K' and resid 101 through 106 removed outlier: 6.940A pdb=" N VAL K 96 " --> pdb=" O VAL K 103 " (cutoff:3.500A) removed outlier: 5.070A pdb=" N HIS K 105 " --> pdb=" O ILE K 94 " (cutoff:3.500A) removed outlier: 6.961A pdb=" N ILE K 94 " --> pdb=" O HIS K 105 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'K' and resid 109 through 110 Processing sheet with id=AH2, first strand: chain 'K' and resid 122 through 123 removed outlier: 5.795A pdb=" N THR K 127 " --> pdb=" O GLY K 251 " (cutoff:3.500A) removed outlier: 5.629A pdb=" N VAL K 252 " --> pdb=" O SER K 243 " (cutoff:3.500A) removed outlier: 6.207A pdb=" N SER K 243 " --> pdb=" O VAL K 252 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain 'K' and resid 209 through 215 Processing sheet with id=AH4, first strand: chain 'L' and resid 43 through 50 removed outlier: 5.890A pdb=" N LEU L 44 " --> pdb=" O GLN L 77 " (cutoff:3.500A) removed outlier: 6.777A pdb=" N GLN L 77 " --> pdb=" O LEU L 44 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N GLN L 46 " --> pdb=" O SER L 75 " (cutoff:3.500A) Processing sheet with id=AH5, first strand: chain 'L' and resid 101 through 106 removed outlier: 6.940A pdb=" N VAL L 96 " --> pdb=" O VAL L 103 " (cutoff:3.500A) removed outlier: 5.071A pdb=" N HIS L 105 " --> pdb=" O ILE L 94 " (cutoff:3.500A) removed outlier: 6.961A pdb=" N ILE L 94 " --> pdb=" O HIS L 105 " (cutoff:3.500A) Processing sheet with id=AH6, first strand: chain 'L' and resid 101 through 106 removed outlier: 6.940A pdb=" N VAL L 96 " --> pdb=" O VAL L 103 " (cutoff:3.500A) removed outlier: 5.071A pdb=" N HIS L 105 " --> pdb=" O ILE L 94 " (cutoff:3.500A) removed outlier: 6.961A pdb=" N ILE L 94 " --> pdb=" O HIS L 105 " (cutoff:3.500A) Processing sheet with id=AH7, first strand: chain 'L' and resid 109 through 110 Processing sheet with id=AH8, first strand: chain 'L' and resid 122 through 123 removed outlier: 5.796A pdb=" N THR L 127 " --> pdb=" O GLY L 251 " (cutoff:3.500A) removed outlier: 5.630A pdb=" N VAL L 252 " --> pdb=" O SER L 243 " (cutoff:3.500A) removed outlier: 6.206A pdb=" N SER L 243 " --> pdb=" O VAL L 252 " (cutoff:3.500A) Processing sheet with id=AH9, first strand: chain 'L' and resid 209 through 215 Processing sheet with id=AI1, first strand: chain 'M' and resid 43 through 50 removed outlier: 5.890A pdb=" N LEU M 44 " --> pdb=" O GLN M 77 " (cutoff:3.500A) removed outlier: 6.777A pdb=" N GLN M 77 " --> pdb=" O LEU M 44 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N GLN M 46 " --> pdb=" O SER M 75 " (cutoff:3.500A) Processing sheet with id=AI2, first strand: chain 'M' and resid 101 through 106 removed outlier: 6.940A pdb=" N VAL M 96 " --> pdb=" O VAL M 103 " (cutoff:3.500A) removed outlier: 5.071A pdb=" N HIS M 105 " --> pdb=" O ILE M 94 " (cutoff:3.500A) removed outlier: 6.961A pdb=" N ILE M 94 " --> pdb=" O HIS M 105 " (cutoff:3.500A) Processing sheet with id=AI3, first strand: chain 'M' and resid 101 through 106 removed outlier: 6.940A pdb=" N VAL M 96 " --> pdb=" O VAL M 103 " (cutoff:3.500A) removed outlier: 5.071A pdb=" N HIS M 105 " --> pdb=" O ILE M 94 " (cutoff:3.500A) removed outlier: 6.961A pdb=" N ILE M 94 " --> pdb=" O HIS M 105 " (cutoff:3.500A) Processing sheet with id=AI4, first strand: chain 'M' and resid 109 through 110 Processing sheet with id=AI5, first strand: chain 'M' and resid 122 through 123 removed outlier: 5.797A pdb=" N THR M 127 " --> pdb=" O GLY M 251 " (cutoff:3.500A) removed outlier: 5.630A pdb=" N VAL M 252 " --> pdb=" O SER M 243 " (cutoff:3.500A) removed outlier: 6.207A pdb=" N SER M 243 " --> pdb=" O VAL M 252 " (cutoff:3.500A) Processing sheet with id=AI6, first strand: chain 'M' and resid 209 through 215 Processing sheet with id=AI7, first strand: chain 'N' and resid 43 through 50 removed outlier: 5.891A pdb=" N LEU N 44 " --> pdb=" O GLN N 77 " (cutoff:3.500A) removed outlier: 6.777A pdb=" N GLN N 77 " --> pdb=" O LEU N 44 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N GLN N 46 " --> pdb=" O SER N 75 " (cutoff:3.500A) Processing sheet with id=AI8, first strand: chain 'N' and resid 101 through 106 removed outlier: 6.940A pdb=" N VAL N 96 " --> pdb=" O VAL N 103 " (cutoff:3.500A) removed outlier: 5.071A pdb=" N HIS N 105 " --> pdb=" O ILE N 94 " (cutoff:3.500A) removed outlier: 6.961A pdb=" N ILE N 94 " --> pdb=" O HIS N 105 " (cutoff:3.500A) Processing sheet with id=AI9, first strand: chain 'N' and resid 101 through 106 removed outlier: 6.940A pdb=" N VAL N 96 " --> pdb=" O VAL N 103 " (cutoff:3.500A) removed outlier: 5.071A pdb=" N HIS N 105 " --> pdb=" O ILE N 94 " (cutoff:3.500A) removed outlier: 6.961A pdb=" N ILE N 94 " --> pdb=" O HIS N 105 " (cutoff:3.500A) Processing sheet with id=AJ1, first strand: chain 'N' and resid 109 through 110 Processing sheet with id=AJ2, first strand: chain 'N' and resid 122 through 123 removed outlier: 5.797A pdb=" N THR N 127 " --> pdb=" O GLY N 251 " (cutoff:3.500A) removed outlier: 5.629A pdb=" N VAL N 252 " --> pdb=" O SER N 243 " (cutoff:3.500A) removed outlier: 6.207A pdb=" N SER N 243 " --> pdb=" O VAL N 252 " (cutoff:3.500A) Processing sheet with id=AJ3, first strand: chain 'N' and resid 209 through 215 Processing sheet with id=AJ4, first strand: chain 'O' and resid 43 through 50 removed outlier: 5.890A pdb=" N LEU O 44 " --> pdb=" O GLN O 77 " (cutoff:3.500A) removed outlier: 6.777A pdb=" N GLN O 77 " --> pdb=" O LEU O 44 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N GLN O 46 " --> pdb=" O SER O 75 " (cutoff:3.500A) Processing sheet with id=AJ5, first strand: chain 'O' and resid 101 through 106 removed outlier: 6.939A pdb=" N VAL O 96 " --> pdb=" O VAL O 103 " (cutoff:3.500A) removed outlier: 5.070A pdb=" N HIS O 105 " --> pdb=" O ILE O 94 " (cutoff:3.500A) removed outlier: 6.961A pdb=" N ILE O 94 " --> pdb=" O HIS O 105 " (cutoff:3.500A) Processing sheet with id=AJ6, first strand: chain 'O' and resid 101 through 106 removed outlier: 6.939A pdb=" N VAL O 96 " --> pdb=" O VAL O 103 " (cutoff:3.500A) removed outlier: 5.070A pdb=" N HIS O 105 " --> pdb=" O ILE O 94 " (cutoff:3.500A) removed outlier: 6.961A pdb=" N ILE O 94 " --> pdb=" O HIS O 105 " (cutoff:3.500A) Processing sheet with id=AJ7, first strand: chain 'O' and resid 109 through 110 Processing sheet with id=AJ8, first strand: chain 'O' and resid 122 through 123 removed outlier: 5.796A pdb=" N THR O 127 " --> pdb=" O GLY O 251 " (cutoff:3.500A) removed outlier: 5.630A pdb=" N VAL O 252 " --> pdb=" O SER O 243 " (cutoff:3.500A) removed outlier: 6.207A pdb=" N SER O 243 " --> pdb=" O VAL O 252 " (cutoff:3.500A) Processing sheet with id=AJ9, first strand: chain 'O' and resid 209 through 215 Processing sheet with id=AK1, first strand: chain 'P' and resid 43 through 50 removed outlier: 5.890A pdb=" N LEU P 44 " --> pdb=" O GLN P 77 " (cutoff:3.500A) removed outlier: 6.778A pdb=" N GLN P 77 " --> pdb=" O LEU P 44 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N GLN P 46 " --> pdb=" O SER P 75 " (cutoff:3.500A) Processing sheet with id=AK2, first strand: chain 'P' and resid 101 through 106 removed outlier: 6.940A pdb=" N VAL P 96 " --> pdb=" O VAL P 103 " (cutoff:3.500A) removed outlier: 5.071A pdb=" N HIS P 105 " --> pdb=" O ILE P 94 " (cutoff:3.500A) removed outlier: 6.960A pdb=" N ILE P 94 " --> pdb=" O HIS P 105 " (cutoff:3.500A) Processing sheet with id=AK3, first strand: chain 'P' and resid 101 through 106 removed outlier: 6.940A pdb=" N VAL P 96 " --> pdb=" O VAL P 103 " (cutoff:3.500A) removed outlier: 5.071A pdb=" N HIS P 105 " --> pdb=" O ILE P 94 " (cutoff:3.500A) removed outlier: 6.960A pdb=" N ILE P 94 " --> pdb=" O HIS P 105 " (cutoff:3.500A) Processing sheet with id=AK4, first strand: chain 'P' and resid 109 through 110 Processing sheet with id=AK5, first strand: chain 'P' and resid 122 through 123 removed outlier: 5.795A pdb=" N THR P 127 " --> pdb=" O GLY P 251 " (cutoff:3.500A) removed outlier: 5.630A pdb=" N VAL P 252 " --> pdb=" O SER P 243 " (cutoff:3.500A) removed outlier: 6.207A pdb=" N SER P 243 " --> pdb=" O VAL P 252 " (cutoff:3.500A) Processing sheet with id=AK6, first strand: chain 'P' and resid 209 through 215 Processing sheet with id=AK7, first strand: chain 'Q' and resid 43 through 50 removed outlier: 5.890A pdb=" N LEU Q 44 " --> pdb=" O GLN Q 77 " (cutoff:3.500A) removed outlier: 6.777A pdb=" N GLN Q 77 " --> pdb=" O LEU Q 44 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N GLN Q 46 " --> pdb=" O SER Q 75 " (cutoff:3.500A) Processing sheet with id=AK8, first strand: chain 'Q' and resid 101 through 106 removed outlier: 6.940A pdb=" N VAL Q 96 " --> pdb=" O VAL Q 103 " (cutoff:3.500A) removed outlier: 5.071A pdb=" N HIS Q 105 " --> pdb=" O ILE Q 94 " (cutoff:3.500A) removed outlier: 6.961A pdb=" N ILE Q 94 " --> pdb=" O HIS Q 105 " (cutoff:3.500A) Processing sheet with id=AK9, first strand: chain 'Q' and resid 101 through 106 removed outlier: 6.940A pdb=" N VAL Q 96 " --> pdb=" O VAL Q 103 " (cutoff:3.500A) removed outlier: 5.071A pdb=" N HIS Q 105 " --> pdb=" O ILE Q 94 " (cutoff:3.500A) removed outlier: 6.961A pdb=" N ILE Q 94 " --> pdb=" O HIS Q 105 " (cutoff:3.500A) Processing sheet with id=AL1, first strand: chain 'Q' and resid 109 through 110 Processing sheet with id=AL2, first strand: chain 'Q' and resid 122 through 123 removed outlier: 5.796A pdb=" N THR Q 127 " --> pdb=" O GLY Q 251 " (cutoff:3.500A) removed outlier: 5.630A pdb=" N VAL Q 252 " --> pdb=" O SER Q 243 " (cutoff:3.500A) removed outlier: 6.207A pdb=" N SER Q 243 " --> pdb=" O VAL Q 252 " (cutoff:3.500A) Processing sheet with id=AL3, first strand: chain 'Q' and resid 209 through 215 Processing sheet with id=AL4, first strand: chain 'R' and resid 43 through 50 removed outlier: 5.890A pdb=" N LEU R 44 " --> pdb=" O GLN R 77 " (cutoff:3.500A) removed outlier: 6.776A pdb=" N GLN R 77 " --> pdb=" O LEU R 44 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N GLN R 46 " --> pdb=" O SER R 75 " (cutoff:3.500A) Processing sheet with id=AL5, first strand: chain 'R' and resid 101 through 106 removed outlier: 6.940A pdb=" N VAL R 96 " --> pdb=" O VAL R 103 " (cutoff:3.500A) removed outlier: 5.071A pdb=" N HIS R 105 " --> pdb=" O ILE R 94 " (cutoff:3.500A) removed outlier: 6.962A pdb=" N ILE R 94 " --> pdb=" O HIS R 105 " (cutoff:3.500A) Processing sheet with id=AL6, first strand: chain 'R' and resid 101 through 106 removed outlier: 6.940A pdb=" N VAL R 96 " --> pdb=" O VAL R 103 " (cutoff:3.500A) removed outlier: 5.071A pdb=" N HIS R 105 " --> pdb=" O ILE R 94 " (cutoff:3.500A) removed outlier: 6.962A pdb=" N ILE R 94 " --> pdb=" O HIS R 105 " (cutoff:3.500A) Processing sheet with id=AL7, first strand: chain 'R' and resid 109 through 110 Processing sheet with id=AL8, first strand: chain 'R' and resid 122 through 123 removed outlier: 5.796A pdb=" N THR R 127 " --> pdb=" O GLY R 251 " (cutoff:3.500A) removed outlier: 5.630A pdb=" N VAL R 252 " --> pdb=" O SER R 243 " (cutoff:3.500A) removed outlier: 6.207A pdb=" N SER R 243 " --> pdb=" O VAL R 252 " (cutoff:3.500A) Processing sheet with id=AL9, first strand: chain 'R' and resid 209 through 215 Processing sheet with id=AM1, first strand: chain 'S' and resid 43 through 50 removed outlier: 5.890A pdb=" N LEU S 44 " --> pdb=" O GLN S 77 " (cutoff:3.500A) removed outlier: 6.776A pdb=" N GLN S 77 " --> pdb=" O LEU S 44 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N GLN S 46 " --> pdb=" O SER S 75 " (cutoff:3.500A) Processing sheet with id=AM2, first strand: chain 'S' and resid 101 through 106 removed outlier: 6.939A pdb=" N VAL S 96 " --> pdb=" O VAL S 103 " (cutoff:3.500A) removed outlier: 5.070A pdb=" N HIS S 105 " --> pdb=" O ILE S 94 " (cutoff:3.500A) removed outlier: 6.962A pdb=" N ILE S 94 " --> pdb=" O HIS S 105 " (cutoff:3.500A) Processing sheet with id=AM3, first strand: chain 'S' and resid 101 through 106 removed outlier: 6.939A pdb=" N VAL S 96 " --> pdb=" O VAL S 103 " (cutoff:3.500A) removed outlier: 5.070A pdb=" N HIS S 105 " --> pdb=" O ILE S 94 " (cutoff:3.500A) removed outlier: 6.962A pdb=" N ILE S 94 " --> pdb=" O HIS S 105 " (cutoff:3.500A) Processing sheet with id=AM4, first strand: chain 'S' and resid 109 through 110 Processing sheet with id=AM5, first strand: chain 'S' and resid 122 through 123 removed outlier: 5.796A pdb=" N THR S 127 " --> pdb=" O GLY S 251 " (cutoff:3.500A) removed outlier: 5.629A pdb=" N VAL S 252 " --> pdb=" O SER S 243 " (cutoff:3.500A) removed outlier: 6.207A pdb=" N SER S 243 " --> pdb=" O VAL S 252 " (cutoff:3.500A) Processing sheet with id=AM6, first strand: chain 'S' and resid 209 through 215 Processing sheet with id=AM7, first strand: chain 'T' and resid 43 through 50 removed outlier: 5.890A pdb=" N LEU T 44 " --> pdb=" O GLN T 77 " (cutoff:3.500A) removed outlier: 6.777A pdb=" N GLN T 77 " --> pdb=" O LEU T 44 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N GLN T 46 " --> pdb=" O SER T 75 " (cutoff:3.500A) Processing sheet with id=AM8, first strand: chain 'T' and resid 101 through 106 removed outlier: 6.940A pdb=" N VAL T 96 " --> pdb=" O VAL T 103 " (cutoff:3.500A) removed outlier: 5.071A pdb=" N HIS T 105 " --> pdb=" O ILE T 94 " (cutoff:3.500A) removed outlier: 6.962A pdb=" N ILE T 94 " --> pdb=" O HIS T 105 " (cutoff:3.500A) Processing sheet with id=AM9, first strand: chain 'T' and resid 101 through 106 removed outlier: 6.940A pdb=" N VAL T 96 " --> pdb=" O VAL T 103 " (cutoff:3.500A) removed outlier: 5.071A pdb=" N HIS T 105 " --> pdb=" O ILE T 94 " (cutoff:3.500A) removed outlier: 6.962A pdb=" N ILE T 94 " --> pdb=" O HIS T 105 " (cutoff:3.500A) Processing sheet with id=AN1, first strand: chain 'T' and resid 109 through 110 Processing sheet with id=AN2, first strand: chain 'T' and resid 122 through 123 removed outlier: 5.796A pdb=" N THR T 127 " --> pdb=" O GLY T 251 " (cutoff:3.500A) removed outlier: 5.629A pdb=" N VAL T 252 " --> pdb=" O SER T 243 " (cutoff:3.500A) removed outlier: 6.207A pdb=" N SER T 243 " --> pdb=" O VAL T 252 " (cutoff:3.500A) Processing sheet with id=AN3, first strand: chain 'T' and resid 209 through 215 Processing sheet with id=AN4, first strand: chain 'U' and resid 43 through 50 removed outlier: 5.890A pdb=" N LEU U 44 " --> pdb=" O GLN U 77 " (cutoff:3.500A) removed outlier: 6.777A pdb=" N GLN U 77 " --> pdb=" O LEU U 44 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N GLN U 46 " --> pdb=" O SER U 75 " (cutoff:3.500A) Processing sheet with id=AN5, first strand: chain 'U' and resid 101 through 106 removed outlier: 6.940A pdb=" N VAL U 96 " --> pdb=" O VAL U 103 " (cutoff:3.500A) removed outlier: 5.070A pdb=" N HIS U 105 " --> pdb=" O ILE U 94 " (cutoff:3.500A) removed outlier: 6.961A pdb=" N ILE U 94 " --> pdb=" O HIS U 105 " (cutoff:3.500A) Processing sheet with id=AN6, first strand: chain 'U' and resid 101 through 106 removed outlier: 6.940A pdb=" N VAL U 96 " --> pdb=" O VAL U 103 " (cutoff:3.500A) removed outlier: 5.070A pdb=" N HIS U 105 " --> pdb=" O ILE U 94 " (cutoff:3.500A) removed outlier: 6.961A pdb=" N ILE U 94 " --> pdb=" O HIS U 105 " (cutoff:3.500A) Processing sheet with id=AN7, first strand: chain 'U' and resid 109 through 110 Processing sheet with id=AN8, first strand: chain 'U' and resid 122 through 123 removed outlier: 5.795A pdb=" N THR U 127 " --> pdb=" O GLY U 251 " (cutoff:3.500A) removed outlier: 5.629A pdb=" N VAL U 252 " --> pdb=" O SER U 243 " (cutoff:3.500A) removed outlier: 6.207A pdb=" N SER U 243 " --> pdb=" O VAL U 252 " (cutoff:3.500A) Processing sheet with id=AN9, first strand: chain 'U' and resid 209 through 215 1639 hydrogen bonds defined for protein. 4224 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: 15.19 Time building geometry restraints manager: 14.66 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 10622 1.33 - 1.46: 9341 1.46 - 1.59: 19664 1.59 - 1.71: 42 1.71 - 1.84: 168 Bond restraints: 39837 Sorted by residual: bond pdb=" CG GLU F 222 " pdb=" CD GLU F 222 " ideal model delta sigma weight residual 1.516 1.630 -0.114 2.50e-02 1.60e+03 2.10e+01 bond pdb=" CG GLU S 222 " pdb=" CD GLU S 222 " ideal model delta sigma weight residual 1.516 1.630 -0.114 2.50e-02 1.60e+03 2.09e+01 bond pdb=" CG GLU H 222 " pdb=" CD GLU H 222 " ideal model delta sigma weight residual 1.516 1.630 -0.114 2.50e-02 1.60e+03 2.09e+01 bond pdb=" CG GLU U 222 " pdb=" CD GLU U 222 " ideal model delta sigma weight residual 1.516 1.630 -0.114 2.50e-02 1.60e+03 2.09e+01 bond pdb=" CG GLU L 222 " pdb=" CD GLU L 222 " ideal model delta sigma weight residual 1.516 1.630 -0.114 2.50e-02 1.60e+03 2.08e+01 ... (remaining 39832 not shown) Histogram of bond angle deviations from ideal: 100.28 - 108.12: 3500 108.12 - 115.97: 23263 115.97 - 123.81: 25859 123.81 - 131.66: 1873 131.66 - 139.50: 168 Bond angle restraints: 54663 Sorted by residual: angle pdb=" O PRO T 78 " pdb=" C PRO T 78 " pdb=" N PRO T 79 " ideal model delta sigma weight residual 121.15 124.41 -3.26 4.70e-01 4.53e+00 4.82e+01 angle pdb=" O PRO D 78 " pdb=" C PRO D 78 " pdb=" N PRO D 79 " ideal model delta sigma weight residual 121.15 124.41 -3.26 4.70e-01 4.53e+00 4.81e+01 angle pdb=" O PRO K 78 " pdb=" C PRO K 78 " pdb=" N PRO K 79 " ideal model delta sigma weight residual 121.15 124.41 -3.26 4.70e-01 4.53e+00 4.81e+01 angle pdb=" O PRO C 78 " pdb=" C PRO C 78 " pdb=" N PRO C 79 " ideal model delta sigma weight residual 121.15 124.41 -3.26 4.70e-01 4.53e+00 4.80e+01 angle pdb=" O PRO N 78 " pdb=" C PRO N 78 " pdb=" N PRO N 79 " ideal model delta sigma weight residual 121.15 124.40 -3.25 4.70e-01 4.53e+00 4.79e+01 ... (remaining 54658 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.00: 21467 16.00 - 32.01: 1108 32.01 - 48.01: 399 48.01 - 64.02: 84 64.02 - 80.02: 21 Dihedral angle restraints: 23079 sinusoidal: 8295 harmonic: 14784 Sorted by residual: dihedral pdb=" CB CYS A 104 " pdb=" SG CYS A 104 " pdb=" SG CYS A 271 " pdb=" CB CYS A 271 " ideal model delta sinusoidal sigma weight residual -86.00 -145.17 59.17 1 1.00e+01 1.00e-02 4.68e+01 dihedral pdb=" CB CYS L 104 " pdb=" SG CYS L 104 " pdb=" SG CYS L 271 " pdb=" CB CYS L 271 " ideal model delta sinusoidal sigma weight residual -86.00 -145.16 59.16 1 1.00e+01 1.00e-02 4.68e+01 dihedral pdb=" CB CYS N 104 " pdb=" SG CYS N 104 " pdb=" SG CYS N 271 " pdb=" CB CYS N 271 " ideal model delta sinusoidal sigma weight residual -86.00 -145.15 59.15 1 1.00e+01 1.00e-02 4.68e+01 ... (remaining 23076 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.076: 3487 0.076 - 0.151: 1917 0.151 - 0.227: 866 0.227 - 0.303: 261 0.303 - 0.379: 21 Chirality restraints: 6552 Sorted by residual: chirality pdb=" CA TRP K 270 " pdb=" N TRP K 270 " pdb=" C TRP K 270 " pdb=" CB TRP K 270 " both_signs ideal model delta sigma weight residual False 2.51 2.13 0.38 2.00e-01 2.50e+01 3.58e+00 chirality pdb=" CA TRP R 270 " pdb=" N TRP R 270 " pdb=" C TRP R 270 " pdb=" CB TRP R 270 " both_signs ideal model delta sigma weight residual False 2.51 2.13 0.38 2.00e-01 2.50e+01 3.58e+00 chirality pdb=" CA TRP C 270 " pdb=" N TRP C 270 " pdb=" C TRP C 270 " pdb=" CB TRP C 270 " both_signs ideal model delta sigma weight residual False 2.51 2.13 0.38 2.00e-01 2.50e+01 3.58e+00 ... (remaining 6549 not shown) Planarity restraints: 6909 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR E 215 " -0.110 2.00e-02 2.50e+03 5.80e-02 6.72e+01 pdb=" CG TYR E 215 " 0.045 2.00e-02 2.50e+03 pdb=" CD1 TYR E 215 " 0.042 2.00e-02 2.50e+03 pdb=" CD2 TYR E 215 " 0.054 2.00e-02 2.50e+03 pdb=" CE1 TYR E 215 " 0.026 2.00e-02 2.50e+03 pdb=" CE2 TYR E 215 " 0.023 2.00e-02 2.50e+03 pdb=" CZ TYR E 215 " 0.004 2.00e-02 2.50e+03 pdb=" OH TYR E 215 " -0.083 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR U 215 " -0.110 2.00e-02 2.50e+03 5.80e-02 6.72e+01 pdb=" CG TYR U 215 " 0.045 2.00e-02 2.50e+03 pdb=" CD1 TYR U 215 " 0.042 2.00e-02 2.50e+03 pdb=" CD2 TYR U 215 " 0.053 2.00e-02 2.50e+03 pdb=" CE1 TYR U 215 " 0.026 2.00e-02 2.50e+03 pdb=" CE2 TYR U 215 " 0.023 2.00e-02 2.50e+03 pdb=" CZ TYR U 215 " 0.003 2.00e-02 2.50e+03 pdb=" OH TYR U 215 " -0.083 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR B 215 " -0.110 2.00e-02 2.50e+03 5.80e-02 6.72e+01 pdb=" CG TYR B 215 " 0.045 2.00e-02 2.50e+03 pdb=" CD1 TYR B 215 " 0.042 2.00e-02 2.50e+03 pdb=" CD2 TYR B 215 " 0.054 2.00e-02 2.50e+03 pdb=" CE1 TYR B 215 " 0.026 2.00e-02 2.50e+03 pdb=" CE2 TYR B 215 " 0.023 2.00e-02 2.50e+03 pdb=" CZ TYR B 215 " 0.004 2.00e-02 2.50e+03 pdb=" OH TYR B 215 " -0.083 2.00e-02 2.50e+03 ... (remaining 6906 not shown) Histogram of nonbonded interaction distances: 1.69 - 2.33: 280 2.33 - 2.98: 20739 2.98 - 3.62: 51009 3.62 - 4.26: 80703 4.26 - 4.90: 133906 Nonbonded interactions: 286637 Sorted by model distance: nonbonded pdb=" OH TYR K 117 " pdb=" CD1 ILE R 302 " model vdw 1.692 3.460 nonbonded pdb=" OH TYR H 117 " pdb=" CD1 ILE O 302 " model vdw 1.711 3.460 nonbonded pdb=" OH TYR G 117 " pdb=" CD1 ILE N 302 " model vdw 1.725 3.460 nonbonded pdb=" OH TYR E 117 " pdb=" CD1 ILE L 302 " model vdw 1.729 3.460 nonbonded pdb=" OH TYR I 117 " pdb=" CD1 ILE P 302 " model vdw 1.732 3.460 ... (remaining 286632 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' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.680 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.040 Extract box with map and model: 5.120 Check model and map are aligned: 0.580 Set scattering table: 0.330 Process input model: 95.130 Find NCS groups from input model: 2.630 Set up NCS constraints: 0.340 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:3.010 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 107.870 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7831 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 : 0.014 0.114 39837 Z= 0.920 Angle : 1.824 14.502 54663 Z= 1.176 Chirality : 0.110 0.379 6552 Planarity : 0.012 0.081 6909 Dihedral : 11.444 80.024 13440 Min Nonbonded Distance : 1.692 Molprobity Statistics. All-atom Clashscore : 34.34 Ramachandran Plot: Outliers : 1.26 % Allowed : 2.52 % Favored : 96.22 % Rotamer: Outliers : 3.90 % Allowed : 5.85 % Favored : 90.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.68 (0.10), residues: 4998 helix: -0.10 (0.17), residues: 714 sheet: 0.66 (0.14), residues: 1155 loop : -0.99 (0.09), residues: 3129 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.068 0.019 TRP U 294 HIS 0.006 0.002 HIS J 118 PHE 0.060 0.012 PHE Q 133 TYR 0.110 0.016 TYR U 215 ARG 0.021 0.005 ARG L 67 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9996 Ramachandran restraints generated. 4998 Oldfield, 0 Emsley, 4998 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9996 Ramachandran restraints generated. 4998 Oldfield, 0 Emsley, 4998 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1804 residues out of total 4305 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 168 poor density : 1636 time to evaluate : 4.161 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 63 ASP cc_start: 0.8630 (m-30) cc_final: 0.8351 (t70) REVERT: A 107 ASP cc_start: 0.7472 (p0) cc_final: 0.6915 (t0) REVERT: A 115 ASP cc_start: 0.8693 (t0) cc_final: 0.8268 (t0) REVERT: A 200 GLN cc_start: 0.8771 (mm-40) cc_final: 0.8566 (mm110) REVERT: A 232 ILE cc_start: 0.9227 (mt) cc_final: 0.8535 (mt) REVERT: A 233 LYS cc_start: 0.8483 (mttt) cc_final: 0.7923 (mmmm) REVERT: A 239 ASN cc_start: 0.9020 (OUTLIER) cc_final: 0.8605 (p0) REVERT: A 282 VAL cc_start: 0.9555 (m) cc_final: 0.9311 (m) REVERT: A 286 MET cc_start: 0.9188 (mtt) cc_final: 0.8877 (mtp) REVERT: B 63 ASP cc_start: 0.8799 (m-30) cc_final: 0.8406 (t70) REVERT: B 89 ILE cc_start: 0.8330 (mm) cc_final: 0.8118 (mt) REVERT: B 107 ASP cc_start: 0.7423 (p0) cc_final: 0.6744 (t0) REVERT: B 114 ASP cc_start: 0.8673 (t0) cc_final: 0.8134 (m-30) REVERT: B 115 ASP cc_start: 0.8467 (t0) cc_final: 0.8053 (t0) REVERT: B 198 ASP cc_start: 0.8727 (t0) cc_final: 0.8435 (t0) REVERT: B 232 ILE cc_start: 0.9230 (mt) cc_final: 0.8481 (mm) REVERT: B 233 LYS cc_start: 0.8399 (mttt) cc_final: 0.7937 (mmmm) REVERT: B 239 ASN cc_start: 0.8818 (OUTLIER) cc_final: 0.8561 (p0) REVERT: B 267 VAL cc_start: 0.9245 (t) cc_final: 0.8985 (m) REVERT: B 279 MET cc_start: 0.8829 (mtt) cc_final: 0.8171 (mtt) REVERT: B 282 VAL cc_start: 0.9551 (m) cc_final: 0.9265 (m) REVERT: B 286 MET cc_start: 0.9135 (mtt) cc_final: 0.8867 (mtm) REVERT: C 107 ASP cc_start: 0.7391 (p0) cc_final: 0.6776 (t0) REVERT: C 114 ASP cc_start: 0.8557 (t0) cc_final: 0.8148 (m-30) REVERT: C 115 ASP cc_start: 0.8581 (t0) cc_final: 0.7800 (t0) REVERT: C 198 ASP cc_start: 0.8419 (t0) cc_final: 0.8109 (t0) REVERT: C 201 TYR cc_start: 0.8895 (m-80) cc_final: 0.8403 (m-80) REVERT: C 233 LYS cc_start: 0.8498 (mttt) cc_final: 0.8205 (mmmm) REVERT: C 249 ASN cc_start: 0.9323 (m-40) cc_final: 0.8968 (m110) REVERT: C 274 VAL cc_start: 0.9269 (t) cc_final: 0.9031 (p) REVERT: C 279 MET cc_start: 0.8528 (mtt) cc_final: 0.7824 (mtt) REVERT: C 282 VAL cc_start: 0.9446 (m) cc_final: 0.9146 (m) REVERT: D 62 LYS cc_start: 0.8540 (pttp) cc_final: 0.7906 (mttp) REVERT: D 107 ASP cc_start: 0.7406 (p0) cc_final: 0.7154 (t0) REVERT: D 114 ASP cc_start: 0.8881 (t0) cc_final: 0.8656 (t0) REVERT: D 115 ASP cc_start: 0.8563 (t0) cc_final: 0.8340 (t0) REVERT: D 233 LYS cc_start: 0.8441 (mttt) cc_final: 0.8067 (mmmm) REVERT: D 239 ASN cc_start: 0.8941 (OUTLIER) cc_final: 0.8547 (p0) REVERT: D 282 VAL cc_start: 0.9439 (m) cc_final: 0.9145 (m) REVERT: E 75 SER cc_start: 0.8854 (t) cc_final: 0.8639 (t) REVERT: E 91 ILE cc_start: 0.9327 (mt) cc_final: 0.9088 (mt) REVERT: E 114 ASP cc_start: 0.8579 (t0) cc_final: 0.8059 (m-30) REVERT: E 115 ASP cc_start: 0.8377 (t0) cc_final: 0.8076 (t70) REVERT: E 233 LYS cc_start: 0.8086 (mttt) cc_final: 0.7495 (mmmm) REVERT: E 239 ASN cc_start: 0.9049 (OUTLIER) cc_final: 0.8380 (p0) REVERT: E 249 ASN cc_start: 0.9239 (m-40) cc_final: 0.9014 (m-40) REVERT: E 279 MET cc_start: 0.8474 (mtt) cc_final: 0.8214 (mtt) REVERT: E 282 VAL cc_start: 0.9486 (m) cc_final: 0.9244 (m) REVERT: E 286 MET cc_start: 0.9183 (mtt) cc_final: 0.8851 (mtm) REVERT: F 83 LEU cc_start: 0.6960 (OUTLIER) cc_final: 0.6742 (mt) REVERT: F 107 ASP cc_start: 0.7688 (p0) cc_final: 0.7049 (t0) REVERT: F 114 ASP cc_start: 0.8601 (t0) cc_final: 0.8080 (m-30) REVERT: F 232 ILE cc_start: 0.9074 (mt) cc_final: 0.8665 (mt) REVERT: F 233 LYS cc_start: 0.8366 (mttt) cc_final: 0.7933 (mmmm) REVERT: F 239 ASN cc_start: 0.8865 (OUTLIER) cc_final: 0.8368 (p0) REVERT: F 279 MET cc_start: 0.8406 (mtt) cc_final: 0.7972 (mtt) REVERT: F 286 MET cc_start: 0.9152 (mtt) cc_final: 0.8894 (mtm) REVERT: G 8 LEU cc_start: 0.9032 (tp) cc_final: 0.8719 (tt) REVERT: G 62 LYS cc_start: 0.8398 (pttp) cc_final: 0.7973 (mttt) REVERT: G 107 ASP cc_start: 0.7722 (p0) cc_final: 0.7296 (t0) REVERT: G 111 MET cc_start: 0.8265 (ttp) cc_final: 0.8047 (ttt) REVERT: G 114 ASP cc_start: 0.8745 (t0) cc_final: 0.8491 (t0) REVERT: G 115 ASP cc_start: 0.8404 (t0) cc_final: 0.8073 (t0) REVERT: G 233 LYS cc_start: 0.8433 (mttt) cc_final: 0.7881 (mmmm) REVERT: G 282 VAL cc_start: 0.9493 (m) cc_final: 0.9184 (m) REVERT: H 8 LEU cc_start: 0.9071 (tp) cc_final: 0.8812 (tp) REVERT: H 91 ILE cc_start: 0.9389 (mt) cc_final: 0.9165 (mt) REVERT: H 107 ASP cc_start: 0.7397 (p0) cc_final: 0.7000 (t0) REVERT: H 114 ASP cc_start: 0.8671 (t0) cc_final: 0.8009 (m-30) REVERT: H 115 ASP cc_start: 0.8502 (t0) cc_final: 0.7946 (t0) REVERT: H 198 ASP cc_start: 0.8482 (t0) cc_final: 0.8239 (t0) REVERT: H 201 TYR cc_start: 0.8936 (m-80) cc_final: 0.8270 (m-80) REVERT: H 206 ILE cc_start: 0.9309 (mm) cc_final: 0.9060 (mm) REVERT: H 232 ILE cc_start: 0.9052 (mt) cc_final: 0.8770 (mt) REVERT: H 233 LYS cc_start: 0.8305 (mttt) cc_final: 0.7958 (mmmm) REVERT: H 239 ASN cc_start: 0.9076 (OUTLIER) cc_final: 0.8650 (p0) REVERT: H 267 VAL cc_start: 0.9206 (t) cc_final: 0.9005 (m) REVERT: H 274 VAL cc_start: 0.9330 (t) cc_final: 0.9089 (p) REVERT: H 279 MET cc_start: 0.8496 (mtt) cc_final: 0.7539 (mtt) REVERT: H 282 VAL cc_start: 0.9345 (m) cc_final: 0.8997 (m) REVERT: I 8 LEU cc_start: 0.9084 (tp) cc_final: 0.8824 (tp) REVERT: I 62 LYS cc_start: 0.8197 (pttp) cc_final: 0.7678 (mttt) REVERT: I 63 ASP cc_start: 0.8624 (m-30) cc_final: 0.8420 (t0) REVERT: I 107 ASP cc_start: 0.7515 (p0) cc_final: 0.6956 (t0) REVERT: I 114 ASP cc_start: 0.8475 (t0) cc_final: 0.8238 (t0) REVERT: I 115 ASP cc_start: 0.8833 (t0) cc_final: 0.8469 (t70) REVERT: I 226 ARG cc_start: 0.8907 (ttm-80) cc_final: 0.8635 (tpp80) REVERT: I 232 ILE cc_start: 0.9061 (mt) cc_final: 0.8760 (mt) REVERT: I 233 LYS cc_start: 0.8138 (mttt) cc_final: 0.7698 (mmmm) REVERT: I 267 VAL cc_start: 0.9228 (t) cc_final: 0.8958 (m) REVERT: I 282 VAL cc_start: 0.9514 (m) cc_final: 0.9212 (m) REVERT: J 8 LEU cc_start: 0.9074 (tp) cc_final: 0.8802 (tp) REVERT: J 62 LYS cc_start: 0.8188 (pttp) cc_final: 0.7914 (mttp) REVERT: J 63 ASP cc_start: 0.8686 (m-30) cc_final: 0.8345 (t70) REVERT: J 107 ASP cc_start: 0.7606 (p0) cc_final: 0.7202 (t0) REVERT: J 206 ILE cc_start: 0.9437 (mm) cc_final: 0.9211 (mt) REVERT: J 232 ILE cc_start: 0.9126 (mt) cc_final: 0.8772 (mt) REVERT: J 233 LYS cc_start: 0.8338 (mttt) cc_final: 0.7706 (mmmm) REVERT: J 239 ASN cc_start: 0.9057 (OUTLIER) cc_final: 0.8672 (p0) REVERT: J 267 VAL cc_start: 0.8955 (t) cc_final: 0.8699 (m) REVERT: J 279 MET cc_start: 0.8328 (mtt) cc_final: 0.7977 (mtt) REVERT: J 282 VAL cc_start: 0.9519 (m) cc_final: 0.9284 (m) REVERT: K 8 LEU cc_start: 0.9048 (tp) cc_final: 0.8822 (tp) REVERT: K 62 LYS cc_start: 0.8305 (pttp) cc_final: 0.7739 (mttt) REVERT: K 63 ASP cc_start: 0.8518 (m-30) cc_final: 0.8120 (t70) REVERT: K 107 ASP cc_start: 0.7576 (p0) cc_final: 0.7047 (t0) REVERT: K 233 LYS cc_start: 0.8338 (mttt) cc_final: 0.7876 (mmmm) REVERT: K 267 VAL cc_start: 0.9346 (t) cc_final: 0.8990 (m) REVERT: K 279 MET cc_start: 0.8352 (mtt) cc_final: 0.7793 (mtt) REVERT: K 282 VAL cc_start: 0.9374 (m) cc_final: 0.9124 (m) REVERT: L 62 LYS cc_start: 0.8733 (pttp) cc_final: 0.8225 (mttp) REVERT: L 69 LYS cc_start: 0.8884 (mmtt) cc_final: 0.8517 (mmmt) REVERT: L 107 ASP cc_start: 0.7513 (p0) cc_final: 0.6836 (t0) REVERT: L 111 MET cc_start: 0.8300 (ttp) cc_final: 0.8045 (ttm) REVERT: L 114 ASP cc_start: 0.8595 (t0) cc_final: 0.8025 (m-30) REVERT: L 115 ASP cc_start: 0.8614 (t0) cc_final: 0.8300 (t70) REVERT: L 206 ILE cc_start: 0.9467 (mm) cc_final: 0.9259 (mt) REVERT: L 232 ILE cc_start: 0.9234 (mt) cc_final: 0.8570 (mt) REVERT: L 233 LYS cc_start: 0.8305 (mttt) cc_final: 0.7705 (mmmm) REVERT: L 279 MET cc_start: 0.8559 (mtt) cc_final: 0.8274 (mtt) REVERT: L 282 VAL cc_start: 0.9558 (m) cc_final: 0.9354 (m) REVERT: M 62 LYS cc_start: 0.8482 (pttp) cc_final: 0.8039 (mttp) REVERT: M 107 ASP cc_start: 0.7634 (p0) cc_final: 0.6971 (t0) REVERT: M 111 MET cc_start: 0.8348 (ttp) cc_final: 0.8066 (ttt) REVERT: M 206 ILE cc_start: 0.9469 (mm) cc_final: 0.9250 (mt) REVERT: M 232 ILE cc_start: 0.9247 (mt) cc_final: 0.8899 (mt) REVERT: M 233 LYS cc_start: 0.8332 (mttt) cc_final: 0.7723 (mmmm) REVERT: M 267 VAL cc_start: 0.9203 (t) cc_final: 0.8811 (m) REVERT: M 274 VAL cc_start: 0.9219 (t) cc_final: 0.9002 (p) REVERT: M 279 MET cc_start: 0.8500 (mtt) cc_final: 0.7696 (mtt) REVERT: N 62 LYS cc_start: 0.8477 (pttp) cc_final: 0.8161 (mttp) REVERT: N 74 LEU cc_start: 0.9619 (mt) cc_final: 0.9419 (mt) REVERT: N 107 ASP cc_start: 0.7641 (p0) cc_final: 0.7105 (t0) REVERT: N 201 TYR cc_start: 0.8813 (m-80) cc_final: 0.8607 (m-80) REVERT: N 232 ILE cc_start: 0.9319 (mt) cc_final: 0.9013 (mp) REVERT: N 233 LYS cc_start: 0.8307 (mttt) cc_final: 0.7626 (mmmm) REVERT: N 262 GLN cc_start: 0.8712 (pt0) cc_final: 0.8482 (pm20) REVERT: N 267 VAL cc_start: 0.9310 (t) cc_final: 0.9036 (m) REVERT: N 282 VAL cc_start: 0.9456 (m) cc_final: 0.9138 (m) REVERT: O 62 LYS cc_start: 0.8524 (pttp) cc_final: 0.8018 (mttp) REVERT: O 77 GLN cc_start: 0.8818 (tp40) cc_final: 0.8096 (tm-30) REVERT: O 107 ASP cc_start: 0.7475 (p0) cc_final: 0.6815 (t0) REVERT: O 116 LYS cc_start: 0.8713 (mttt) cc_final: 0.8314 (pttt) REVERT: O 132 VAL cc_start: 0.8564 (OUTLIER) cc_final: 0.8326 (m) REVERT: O 232 ILE cc_start: 0.9269 (mt) cc_final: 0.9064 (mt) REVERT: O 233 LYS cc_start: 0.8505 (mttt) cc_final: 0.8294 (mmmm) REVERT: O 279 MET cc_start: 0.8462 (mtt) cc_final: 0.8205 (mtt) REVERT: O 282 VAL cc_start: 0.9439 (m) cc_final: 0.9196 (m) REVERT: P 29 SER cc_start: 0.9289 (t) cc_final: 0.9080 (p) REVERT: P 62 LYS cc_start: 0.8378 (pttp) cc_final: 0.8023 (mttp) REVERT: P 63 ASP cc_start: 0.8584 (m-30) cc_final: 0.8290 (t70) REVERT: P 75 SER cc_start: 0.8861 (t) cc_final: 0.8541 (t) REVERT: P 107 ASP cc_start: 0.7612 (p0) cc_final: 0.7167 (t0) REVERT: P 114 ASP cc_start: 0.8599 (t0) cc_final: 0.8362 (t0) REVERT: P 116 LYS cc_start: 0.8591 (mttt) cc_final: 0.8238 (pttt) REVERT: P 232 ILE cc_start: 0.9181 (mt) cc_final: 0.8844 (mt) REVERT: P 233 LYS cc_start: 0.8408 (mttt) cc_final: 0.7911 (mmmm) REVERT: P 267 VAL cc_start: 0.9203 (t) cc_final: 0.8925 (m) REVERT: P 279 MET cc_start: 0.8378 (mtt) cc_final: 0.7564 (mtt) REVERT: P 290 ASP cc_start: 0.8554 (p0) cc_final: 0.8290 (p0) REVERT: Q 8 LEU cc_start: 0.9046 (tp) cc_final: 0.8791 (tp) REVERT: Q 107 ASP cc_start: 0.7388 (p0) cc_final: 0.7110 (t0) REVERT: Q 116 LYS cc_start: 0.8677 (mttt) cc_final: 0.8237 (pttt) REVERT: Q 232 ILE cc_start: 0.9131 (mt) cc_final: 0.8632 (mt) REVERT: Q 233 LYS cc_start: 0.8483 (mttt) cc_final: 0.8117 (mmmm) REVERT: Q 267 VAL cc_start: 0.9420 (t) cc_final: 0.9217 (m) REVERT: Q 279 MET cc_start: 0.8375 (mtt) cc_final: 0.7747 (mtt) REVERT: Q 282 VAL cc_start: 0.9523 (m) cc_final: 0.9271 (m) REVERT: R 62 LYS cc_start: 0.8643 (pttp) cc_final: 0.7977 (mttp) REVERT: R 107 ASP cc_start: 0.7362 (p0) cc_final: 0.6664 (t0) REVERT: R 232 ILE cc_start: 0.9306 (mt) cc_final: 0.8749 (mt) REVERT: R 233 LYS cc_start: 0.8451 (mttt) cc_final: 0.8054 (mmmm) REVERT: R 239 ASN cc_start: 0.8864 (OUTLIER) cc_final: 0.8615 (p0) REVERT: R 267 VAL cc_start: 0.9294 (t) cc_final: 0.9081 (m) REVERT: S 55 ASN cc_start: 0.8722 (m-40) cc_final: 0.7835 (p0) REVERT: S 62 LYS cc_start: 0.8229 (pttp) cc_final: 0.7678 (mttp) REVERT: S 77 GLN cc_start: 0.8706 (tp40) cc_final: 0.8307 (tm-30) REVERT: S 91 ILE cc_start: 0.9351 (mt) cc_final: 0.9096 (mt) REVERT: S 111 MET cc_start: 0.8206 (ttp) cc_final: 0.7955 (ttm) REVERT: S 115 ASP cc_start: 0.8628 (t0) cc_final: 0.8371 (t70) REVERT: S 116 LYS cc_start: 0.8598 (mttt) cc_final: 0.8374 (pttt) REVERT: S 121 GLN cc_start: 0.7350 (mt0) cc_final: 0.7130 (mt0) REVERT: S 232 ILE cc_start: 0.9230 (mt) cc_final: 0.8917 (mt) REVERT: S 253 PRO cc_start: 0.9425 (Cg_exo) cc_final: 0.8841 (Cg_endo) REVERT: S 274 VAL cc_start: 0.9412 (t) cc_final: 0.9172 (p) REVERT: S 275 ASN cc_start: 0.8715 (t0) cc_final: 0.8071 (t0) REVERT: S 279 MET cc_start: 0.8436 (mtt) cc_final: 0.7659 (mtt) REVERT: S 286 MET cc_start: 0.9170 (mtt) cc_final: 0.8891 (mtm) REVERT: T 54 THR cc_start: 0.8473 (p) cc_final: 0.8260 (p) REVERT: T 55 ASN cc_start: 0.8491 (m-40) cc_final: 0.7849 (p0) REVERT: T 62 LYS cc_start: 0.8559 (pttp) cc_final: 0.7883 (mttp) REVERT: T 77 GLN cc_start: 0.8594 (tp40) cc_final: 0.7894 (tm-30) REVERT: T 116 LYS cc_start: 0.8610 (mttt) cc_final: 0.8242 (pttt) REVERT: T 117 TYR cc_start: 0.8774 (t80) cc_final: 0.8531 (t80) REVERT: T 232 ILE cc_start: 0.9257 (mt) cc_final: 0.8574 (mt) REVERT: T 233 LYS cc_start: 0.8393 (mttt) cc_final: 0.8149 (mmmm) REVERT: T 248 ASN cc_start: 0.8730 (m-40) cc_final: 0.8453 (m110) REVERT: T 275 ASN cc_start: 0.8838 (t0) cc_final: 0.8167 (t0) REVERT: T 279 MET cc_start: 0.8678 (mtt) cc_final: 0.8075 (mtt) REVERT: T 282 VAL cc_start: 0.9505 (m) cc_final: 0.9305 (m) REVERT: T 300 LEU cc_start: 0.9108 (tt) cc_final: 0.8894 (tt) REVERT: U 55 ASN cc_start: 0.8208 (m-40) cc_final: 0.7947 (p0) REVERT: U 115 ASP cc_start: 0.8566 (t0) cc_final: 0.8301 (t70) REVERT: U 116 LYS cc_start: 0.8751 (mttt) cc_final: 0.8305 (pttt) REVERT: U 214 ASN cc_start: 0.8767 (t0) cc_final: 0.8371 (t0) REVERT: U 224 ASN cc_start: 0.8465 (t0) cc_final: 0.8169 (t0) REVERT: U 232 ILE cc_start: 0.9226 (mt) cc_final: 0.8765 (mp) REVERT: U 287 VAL cc_start: 0.9229 (t) cc_final: 0.8843 (p) REVERT: U 300 LEU cc_start: 0.8964 (tt) cc_final: 0.8759 (tt) outliers start: 168 outliers final: 86 residues processed: 1733 average time/residue: 0.5045 time to fit residues: 1453.0501 Evaluate side-chains 1124 residues out of total 4305 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 96 poor density : 1028 time to evaluate : 4.267 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 LEU Chi-restraints excluded: chain A residue 94 ILE Chi-restraints excluded: chain A residue 239 ASN Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 257 VAL Chi-restraints excluded: chain B residue 42 LEU Chi-restraints excluded: chain B residue 94 ILE Chi-restraints excluded: chain B residue 239 ASN Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain B residue 257 VAL Chi-restraints excluded: chain C residue 42 LEU Chi-restraints excluded: chain C residue 239 ASN Chi-restraints excluded: chain C residue 240 THR Chi-restraints excluded: chain C residue 257 VAL Chi-restraints excluded: chain D residue 42 LEU Chi-restraints excluded: chain D residue 239 ASN Chi-restraints excluded: chain D residue 240 THR Chi-restraints excluded: chain D residue 257 VAL Chi-restraints excluded: chain E residue 42 LEU Chi-restraints excluded: chain E residue 83 LEU Chi-restraints excluded: chain E residue 239 ASN Chi-restraints excluded: chain E residue 240 THR Chi-restraints excluded: chain E residue 257 VAL Chi-restraints excluded: chain F residue 42 LEU Chi-restraints excluded: chain F residue 48 THR Chi-restraints excluded: chain F residue 83 LEU Chi-restraints excluded: chain F residue 239 ASN Chi-restraints excluded: chain F residue 240 THR Chi-restraints excluded: chain F residue 257 VAL Chi-restraints excluded: chain G residue 83 LEU Chi-restraints excluded: chain G residue 132 VAL Chi-restraints excluded: chain G residue 240 THR Chi-restraints excluded: chain G residue 257 VAL Chi-restraints excluded: chain H residue 83 LEU Chi-restraints excluded: chain H residue 239 ASN Chi-restraints excluded: chain H residue 240 THR Chi-restraints excluded: chain H residue 257 VAL Chi-restraints excluded: chain I residue 42 LEU Chi-restraints excluded: chain I residue 240 THR Chi-restraints excluded: chain I residue 257 VAL Chi-restraints excluded: chain J residue 42 LEU Chi-restraints excluded: chain J residue 83 LEU Chi-restraints excluded: chain J residue 132 VAL Chi-restraints excluded: chain J residue 239 ASN Chi-restraints excluded: chain J residue 240 THR Chi-restraints excluded: chain J residue 257 VAL Chi-restraints excluded: chain K residue 42 LEU Chi-restraints excluded: chain K residue 48 THR Chi-restraints excluded: chain K residue 83 LEU Chi-restraints excluded: chain K residue 94 ILE Chi-restraints excluded: chain K residue 132 VAL Chi-restraints excluded: chain K residue 240 THR Chi-restraints excluded: chain K residue 257 VAL Chi-restraints excluded: chain L residue 42 LEU Chi-restraints excluded: chain L residue 240 THR Chi-restraints excluded: chain L residue 257 VAL Chi-restraints excluded: chain M residue 94 ILE Chi-restraints excluded: chain M residue 132 VAL Chi-restraints excluded: chain M residue 239 ASN Chi-restraints excluded: chain M residue 240 THR Chi-restraints excluded: chain M residue 257 VAL Chi-restraints excluded: chain N residue 42 LEU Chi-restraints excluded: chain N residue 94 ILE Chi-restraints excluded: chain N residue 240 THR Chi-restraints excluded: chain N residue 257 VAL Chi-restraints excluded: chain O residue 48 THR Chi-restraints excluded: chain O residue 94 ILE Chi-restraints excluded: chain O residue 132 VAL Chi-restraints excluded: chain O residue 240 THR Chi-restraints excluded: chain O residue 257 VAL Chi-restraints excluded: chain P residue 94 ILE Chi-restraints excluded: chain P residue 240 THR Chi-restraints excluded: chain P residue 257 VAL Chi-restraints excluded: chain Q residue 94 ILE Chi-restraints excluded: chain Q residue 239 ASN Chi-restraints excluded: chain Q residue 240 THR Chi-restraints excluded: chain Q residue 257 VAL Chi-restraints excluded: chain R residue 48 THR Chi-restraints excluded: chain R residue 239 ASN Chi-restraints excluded: chain R residue 240 THR Chi-restraints excluded: chain R residue 257 VAL Chi-restraints excluded: chain S residue 83 LEU Chi-restraints excluded: chain S residue 94 ILE Chi-restraints excluded: chain S residue 132 VAL Chi-restraints excluded: chain S residue 239 ASN Chi-restraints excluded: chain S residue 240 THR Chi-restraints excluded: chain S residue 257 VAL Chi-restraints excluded: chain T residue 42 LEU Chi-restraints excluded: chain T residue 48 THR Chi-restraints excluded: chain T residue 94 ILE Chi-restraints excluded: chain T residue 240 THR Chi-restraints excluded: chain T residue 257 VAL Chi-restraints excluded: chain U residue 42 LEU Chi-restraints excluded: chain U residue 94 ILE Chi-restraints excluded: chain U residue 240 THR Chi-restraints excluded: chain U residue 257 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 504 random chunks: chunk 425 optimal weight: 10.0000 chunk 382 optimal weight: 5.9990 chunk 211 optimal weight: 5.9990 chunk 130 optimal weight: 3.9990 chunk 257 optimal weight: 6.9990 chunk 204 optimal weight: 5.9990 chunk 395 optimal weight: 8.9990 chunk 152 optimal weight: 7.9990 chunk 240 optimal weight: 7.9990 chunk 294 optimal weight: 2.9990 chunk 457 optimal weight: 5.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 46 GLN ** A 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 46 GLN ** B 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 264 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 46 GLN C 77 GLN C 118 HIS C 264 ASN D 46 GLN ** E 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 247 GLN ** E 264 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 247 GLN ** H 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 247 GLN ** H 264 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 99 GLN J 118 HIS J 219 ASN J 247 GLN J 262 GLN K 46 GLN K 99 GLN K 118 HIS L 118 HIS L 239 ASN M 46 GLN ** M 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 118 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 264 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 46 GLN ** N 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 118 HIS N 219 ASN N 247 GLN ** N 264 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 219 ASN Q 46 GLN ** Q 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 264 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 280 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 46 GLN R 219 ASN ** R 264 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 277 ASN T 219 ASN U 99 GLN Total number of N/Q/H flips: 32 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7824 moved from start: 0.3065 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 39837 Z= 0.292 Angle : 0.757 9.426 54663 Z= 0.407 Chirality : 0.048 0.187 6552 Planarity : 0.005 0.066 6909 Dihedral : 7.050 56.011 5452 Min Nonbonded Distance : 2.082 Molprobity Statistics. All-atom Clashscore : 12.48 Ramachandran Plot: Outliers : 0.32 % Allowed : 3.06 % Favored : 96.62 % Rotamer: Outliers : 5.13 % Allowed : 12.73 % Favored : 82.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.34 (0.11), residues: 4998 helix: 2.27 (0.18), residues: 714 sheet: 0.78 (0.11), residues: 1722 loop : -0.77 (0.12), residues: 2562 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP H 211 HIS 0.004 0.001 HIS E 241 PHE 0.016 0.002 PHE U 237 TYR 0.025 0.002 TYR L 22 ARG 0.009 0.001 ARG G 236 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9996 Ramachandran restraints generated. 4998 Oldfield, 0 Emsley, 4998 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9996 Ramachandran restraints generated. 4998 Oldfield, 0 Emsley, 4998 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1309 residues out of total 4305 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 221 poor density : 1088 time to evaluate : 4.203 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 63 ASP cc_start: 0.8639 (m-30) cc_final: 0.8399 (t70) REVERT: A 81 GLN cc_start: 0.7931 (tm-30) cc_final: 0.7476 (pm20) REVERT: A 107 ASP cc_start: 0.7582 (p0) cc_final: 0.7005 (t0) REVERT: A 115 ASP cc_start: 0.8795 (t0) cc_final: 0.8455 (t0) REVERT: A 201 TYR cc_start: 0.8670 (m-10) cc_final: 0.8465 (m-10) REVERT: A 233 LYS cc_start: 0.8076 (mttt) cc_final: 0.7795 (mmmm) REVERT: A 239 ASN cc_start: 0.8890 (OUTLIER) cc_final: 0.8444 (p0) REVERT: A 286 MET cc_start: 0.9064 (mtt) cc_final: 0.8786 (mtp) REVERT: B 63 ASP cc_start: 0.8735 (m-30) cc_final: 0.8395 (t70) REVERT: B 198 ASP cc_start: 0.8659 (t0) cc_final: 0.8316 (t0) REVERT: B 201 TYR cc_start: 0.8862 (m-80) cc_final: 0.8492 (m-80) REVERT: B 233 LYS cc_start: 0.8081 (mttt) cc_final: 0.7696 (mmmm) REVERT: B 239 ASN cc_start: 0.8973 (OUTLIER) cc_final: 0.8690 (p0) REVERT: B 279 MET cc_start: 0.8673 (mtt) cc_final: 0.7951 (mtt) REVERT: C 81 GLN cc_start: 0.7818 (tm-30) cc_final: 0.7444 (pm20) REVERT: C 107 ASP cc_start: 0.7369 (p0) cc_final: 0.6967 (t0) REVERT: C 115 ASP cc_start: 0.8664 (t0) cc_final: 0.8288 (t0) REVERT: C 198 ASP cc_start: 0.8404 (t0) cc_final: 0.8074 (t0) REVERT: C 201 TYR cc_start: 0.8988 (m-80) cc_final: 0.8534 (m-80) REVERT: C 249 ASN cc_start: 0.9182 (m-40) cc_final: 0.8981 (m110) REVERT: C 274 VAL cc_start: 0.9257 (t) cc_final: 0.9044 (p) REVERT: C 279 MET cc_start: 0.8421 (mtt) cc_final: 0.7557 (mtt) REVERT: D 62 LYS cc_start: 0.8503 (pttp) cc_final: 0.7949 (mttp) REVERT: D 107 ASP cc_start: 0.7485 (p0) cc_final: 0.7019 (t0) REVERT: D 115 ASP cc_start: 0.8782 (t0) cc_final: 0.8463 (t0) REVERT: D 201 TYR cc_start: 0.8926 (m-10) cc_final: 0.8668 (m-10) REVERT: D 233 LYS cc_start: 0.7983 (mttt) cc_final: 0.7613 (mmmm) REVERT: D 236 ARG cc_start: 0.7482 (ttm-80) cc_final: 0.7138 (ttm-80) REVERT: E 114 ASP cc_start: 0.8641 (t0) cc_final: 0.8174 (m-30) REVERT: E 115 ASP cc_start: 0.8827 (t0) cc_final: 0.8309 (t0) REVERT: E 201 TYR cc_start: 0.8916 (m-10) cc_final: 0.8675 (m-10) REVERT: E 233 LYS cc_start: 0.7667 (mttt) cc_final: 0.7166 (mmmm) REVERT: E 239 ASN cc_start: 0.8877 (OUTLIER) cc_final: 0.8249 (p0) REVERT: E 279 MET cc_start: 0.8472 (mtt) cc_final: 0.8098 (mtt) REVERT: F 116 LYS cc_start: 0.8476 (mmtt) cc_final: 0.8063 (mmtt) REVERT: F 233 LYS cc_start: 0.7946 (mttt) cc_final: 0.7675 (mmmm) REVERT: F 239 ASN cc_start: 0.9055 (OUTLIER) cc_final: 0.8381 (p0) REVERT: F 279 MET cc_start: 0.8113 (mtt) cc_final: 0.7798 (mtt) REVERT: G 62 LYS cc_start: 0.8358 (pttp) cc_final: 0.8020 (mttt) REVERT: G 107 ASP cc_start: 0.7619 (p0) cc_final: 0.7266 (t0) REVERT: G 114 ASP cc_start: 0.8824 (t0) cc_final: 0.8597 (t0) REVERT: G 115 ASP cc_start: 0.8881 (t0) cc_final: 0.8602 (t0) REVERT: G 201 TYR cc_start: 0.9076 (m-80) cc_final: 0.8875 (m-80) REVERT: G 233 LYS cc_start: 0.8056 (mttt) cc_final: 0.7720 (mmmm) REVERT: H 114 ASP cc_start: 0.8698 (t0) cc_final: 0.8315 (t0) REVERT: H 115 ASP cc_start: 0.8864 (t0) cc_final: 0.8496 (t0) REVERT: H 233 LYS cc_start: 0.7715 (mttt) cc_final: 0.7459 (mmmm) REVERT: H 239 ASN cc_start: 0.9031 (OUTLIER) cc_final: 0.8534 (p0) REVERT: I 62 LYS cc_start: 0.8179 (pttp) cc_final: 0.7658 (mttp) REVERT: I 63 ASP cc_start: 0.8613 (m-30) cc_final: 0.8401 (t0) REVERT: I 83 LEU cc_start: 0.7300 (OUTLIER) cc_final: 0.6803 (tp) REVERT: I 107 ASP cc_start: 0.7600 (p0) cc_final: 0.7113 (t0) REVERT: I 115 ASP cc_start: 0.9117 (t0) cc_final: 0.8897 (t0) REVERT: I 233 LYS cc_start: 0.7654 (mttt) cc_final: 0.7448 (mmmm) REVERT: J 62 LYS cc_start: 0.8180 (pttp) cc_final: 0.7827 (mttp) REVERT: J 63 ASP cc_start: 0.8650 (m-30) cc_final: 0.8366 (t70) REVERT: J 107 ASP cc_start: 0.7535 (p0) cc_final: 0.7125 (t0) REVERT: J 233 LYS cc_start: 0.7914 (mttt) cc_final: 0.7435 (mmmm) REVERT: J 239 ASN cc_start: 0.9105 (OUTLIER) cc_final: 0.8580 (p0) REVERT: J 279 MET cc_start: 0.8222 (mtt) cc_final: 0.7245 (mtt) REVERT: K 62 LYS cc_start: 0.8392 (pttp) cc_final: 0.7824 (mttt) REVERT: K 63 ASP cc_start: 0.8559 (m-30) cc_final: 0.8194 (t70) REVERT: K 201 TYR cc_start: 0.8985 (m-80) cc_final: 0.8583 (m-80) REVERT: K 233 LYS cc_start: 0.7957 (mttt) cc_final: 0.7602 (mmmm) REVERT: K 236 ARG cc_start: 0.6857 (ttm-80) cc_final: 0.6537 (ttm-80) REVERT: K 239 ASN cc_start: 0.8579 (m-40) cc_final: 0.7897 (p0) REVERT: K 279 MET cc_start: 0.7992 (mtt) cc_final: 0.7754 (mtt) REVERT: L 62 LYS cc_start: 0.8673 (pttp) cc_final: 0.8143 (mttp) REVERT: L 114 ASP cc_start: 0.8770 (t0) cc_final: 0.8387 (m-30) REVERT: L 233 LYS cc_start: 0.7845 (mttt) cc_final: 0.7452 (mmmm) REVERT: L 236 ARG cc_start: 0.6940 (ttm-80) cc_final: 0.6714 (ttm-80) REVERT: L 254 ILE cc_start: 0.9207 (mm) cc_final: 0.8930 (mt) REVERT: L 279 MET cc_start: 0.8157 (mtt) cc_final: 0.7882 (mtt) REVERT: M 62 LYS cc_start: 0.8335 (pttp) cc_final: 0.7971 (mttp) REVERT: M 83 LEU cc_start: 0.7024 (OUTLIER) cc_final: 0.6490 (tp) REVERT: M 233 LYS cc_start: 0.8082 (mttt) cc_final: 0.7589 (mmmm) REVERT: M 279 MET cc_start: 0.8245 (mtt) cc_final: 0.7650 (mtt) REVERT: N 62 LYS cc_start: 0.8303 (pttp) cc_final: 0.7941 (mttp) REVERT: N 233 LYS cc_start: 0.7824 (mttt) cc_final: 0.7213 (mmmm) REVERT: N 254 ILE cc_start: 0.9181 (mm) cc_final: 0.8966 (mt) REVERT: N 267 VAL cc_start: 0.9222 (t) cc_final: 0.8950 (m) REVERT: N 279 MET cc_start: 0.8209 (mtt) cc_final: 0.7142 (mtt) REVERT: N 300 LEU cc_start: 0.8933 (tp) cc_final: 0.8687 (tp) REVERT: O 62 LYS cc_start: 0.8411 (pttp) cc_final: 0.7926 (mttt) REVERT: O 236 ARG cc_start: 0.4821 (tpm170) cc_final: 0.3986 (tpt170) REVERT: P 62 LYS cc_start: 0.8384 (pttp) cc_final: 0.7935 (mttt) REVERT: P 63 ASP cc_start: 0.8470 (m-30) cc_final: 0.8269 (t70) REVERT: P 114 ASP cc_start: 0.8639 (t0) cc_final: 0.8415 (t70) REVERT: P 233 LYS cc_start: 0.7852 (mttt) cc_final: 0.7436 (mmmm) REVERT: P 290 ASP cc_start: 0.8583 (p0) cc_final: 0.8316 (p0) REVERT: Q 107 ASP cc_start: 0.7330 (p0) cc_final: 0.7104 (t0) REVERT: Q 116 LYS cc_start: 0.8743 (mttt) cc_final: 0.8432 (pttt) REVERT: R 62 LYS cc_start: 0.8468 (pttp) cc_final: 0.7890 (mttp) REVERT: R 63 ASP cc_start: 0.8601 (t70) cc_final: 0.8290 (t70) REVERT: R 239 ASN cc_start: 0.8881 (OUTLIER) cc_final: 0.8477 (p0) REVERT: S 62 LYS cc_start: 0.8180 (pttp) cc_final: 0.7599 (mttp) REVERT: S 91 ILE cc_start: 0.9420 (mt) cc_final: 0.9118 (mt) REVERT: S 111 MET cc_start: 0.7928 (ttp) cc_final: 0.7699 (ttm) REVERT: S 116 LYS cc_start: 0.8713 (mttt) cc_final: 0.8365 (pttt) REVERT: S 198 ASP cc_start: 0.8103 (t0) cc_final: 0.7271 (t0) REVERT: S 253 PRO cc_start: 0.9302 (Cg_exo) cc_final: 0.8870 (Cg_endo) REVERT: S 286 MET cc_start: 0.9120 (mtt) cc_final: 0.8859 (mtm) REVERT: S 287 VAL cc_start: 0.9459 (t) cc_final: 0.9168 (p) REVERT: T 55 ASN cc_start: 0.8431 (m-40) cc_final: 0.7969 (p0) REVERT: T 62 LYS cc_start: 0.8202 (pttp) cc_final: 0.7856 (mttp) REVERT: T 63 ASP cc_start: 0.8620 (t70) cc_final: 0.8346 (t70) REVERT: T 121 GLN cc_start: 0.7634 (mt0) cc_final: 0.7308 (mp10) REVERT: T 275 ASN cc_start: 0.8585 (t0) cc_final: 0.8319 (t0) REVERT: T 279 MET cc_start: 0.8410 (mtt) cc_final: 0.7954 (mtt) REVERT: U 89 ILE cc_start: 0.8072 (mm) cc_final: 0.7854 (mt) REVERT: U 108 SER cc_start: 0.9390 (OUTLIER) cc_final: 0.8957 (t) REVERT: U 115 ASP cc_start: 0.8842 (t0) cc_final: 0.8499 (t0) REVERT: U 116 LYS cc_start: 0.8808 (mttt) cc_final: 0.8459 (pttt) outliers start: 221 outliers final: 114 residues processed: 1212 average time/residue: 0.4449 time to fit residues: 909.0098 Evaluate side-chains 1003 residues out of total 4305 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 124 poor density : 879 time to evaluate : 4.248 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 VAL Chi-restraints excluded: chain A residue 26 SER Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 42 LEU Chi-restraints excluded: chain A residue 82 VAL Chi-restraints excluded: chain A residue 104 CYS Chi-restraints excluded: chain A residue 239 ASN Chi-restraints excluded: chain A residue 293 THR Chi-restraints excluded: chain A residue 302 ILE Chi-restraints excluded: chain B residue 26 SER Chi-restraints excluded: chain B residue 37 VAL Chi-restraints excluded: chain B residue 42 LEU Chi-restraints excluded: chain B residue 199 ASP Chi-restraints excluded: chain B residue 239 ASN Chi-restraints excluded: chain C residue 26 SER Chi-restraints excluded: chain C residue 37 VAL Chi-restraints excluded: chain C residue 42 LEU Chi-restraints excluded: chain C residue 240 THR Chi-restraints excluded: chain D residue 11 ILE Chi-restraints excluded: chain D residue 26 SER Chi-restraints excluded: chain D residue 42 LEU Chi-restraints excluded: chain D residue 46 GLN Chi-restraints excluded: chain D residue 104 CYS Chi-restraints excluded: chain D residue 240 THR Chi-restraints excluded: chain D residue 246 THR Chi-restraints excluded: chain E residue 26 SER Chi-restraints excluded: chain E residue 42 LEU Chi-restraints excluded: chain E residue 83 LEU Chi-restraints excluded: chain E residue 94 ILE Chi-restraints excluded: chain E residue 104 CYS Chi-restraints excluded: chain E residue 198 ASP Chi-restraints excluded: chain E residue 239 ASN Chi-restraints excluded: chain E residue 240 THR Chi-restraints excluded: chain F residue 12 LEU Chi-restraints excluded: chain F residue 26 SER Chi-restraints excluded: chain F residue 37 VAL Chi-restraints excluded: chain F residue 42 LEU Chi-restraints excluded: chain F residue 83 LEU Chi-restraints excluded: chain F residue 94 ILE Chi-restraints excluded: chain F residue 102 VAL Chi-restraints excluded: chain F residue 115 ASP Chi-restraints excluded: chain F residue 198 ASP Chi-restraints excluded: chain F residue 239 ASN Chi-restraints excluded: chain G residue 26 SER Chi-restraints excluded: chain G residue 83 LEU Chi-restraints excluded: chain G residue 104 CYS Chi-restraints excluded: chain G residue 132 VAL Chi-restraints excluded: chain G residue 198 ASP Chi-restraints excluded: chain G residue 240 THR Chi-restraints excluded: chain H residue 26 SER Chi-restraints excluded: chain H residue 42 LEU Chi-restraints excluded: chain H residue 199 ASP Chi-restraints excluded: chain H residue 239 ASN Chi-restraints excluded: chain H residue 240 THR Chi-restraints excluded: chain I residue 12 LEU Chi-restraints excluded: chain I residue 20 LEU Chi-restraints excluded: chain I residue 42 LEU Chi-restraints excluded: chain I residue 83 LEU Chi-restraints excluded: chain I residue 102 VAL Chi-restraints excluded: chain I residue 199 ASP Chi-restraints excluded: chain I residue 240 THR Chi-restraints excluded: chain J residue 20 LEU Chi-restraints excluded: chain J residue 26 SER Chi-restraints excluded: chain J residue 42 LEU Chi-restraints excluded: chain J residue 83 LEU Chi-restraints excluded: chain J residue 102 VAL Chi-restraints excluded: chain J residue 132 VAL Chi-restraints excluded: chain J residue 239 ASN Chi-restraints excluded: chain J residue 240 THR Chi-restraints excluded: chain K residue 42 LEU Chi-restraints excluded: chain K residue 83 LEU Chi-restraints excluded: chain K residue 102 VAL Chi-restraints excluded: chain K residue 132 VAL Chi-restraints excluded: chain K residue 199 ASP Chi-restraints excluded: chain K residue 240 THR Chi-restraints excluded: chain L residue 42 LEU Chi-restraints excluded: chain L residue 45 ILE Chi-restraints excluded: chain L residue 102 VAL Chi-restraints excluded: chain L residue 240 THR Chi-restraints excluded: chain M residue 26 SER Chi-restraints excluded: chain M residue 42 LEU Chi-restraints excluded: chain M residue 83 LEU Chi-restraints excluded: chain M residue 102 VAL Chi-restraints excluded: chain M residue 240 THR Chi-restraints excluded: chain N residue 26 SER Chi-restraints excluded: chain N residue 42 LEU Chi-restraints excluded: chain N residue 104 CYS Chi-restraints excluded: chain N residue 240 THR Chi-restraints excluded: chain N residue 264 ASN Chi-restraints excluded: chain O residue 20 LEU Chi-restraints excluded: chain O residue 42 LEU Chi-restraints excluded: chain O residue 240 THR Chi-restraints excluded: chain P residue 20 LEU Chi-restraints excluded: chain P residue 104 CYS Chi-restraints excluded: chain P residue 216 VAL Chi-restraints excluded: chain P residue 240 THR Chi-restraints excluded: chain Q residue 20 LEU Chi-restraints excluded: chain Q residue 46 GLN Chi-restraints excluded: chain Q residue 104 CYS Chi-restraints excluded: chain Q residue 240 THR Chi-restraints excluded: chain R residue 20 LEU Chi-restraints excluded: chain R residue 199 ASP Chi-restraints excluded: chain R residue 239 ASN Chi-restraints excluded: chain R residue 240 THR Chi-restraints excluded: chain R residue 293 THR Chi-restraints excluded: chain S residue 20 LEU Chi-restraints excluded: chain S residue 23 THR Chi-restraints excluded: chain S residue 42 LEU Chi-restraints excluded: chain S residue 82 VAL Chi-restraints excluded: chain S residue 83 LEU Chi-restraints excluded: chain S residue 108 SER Chi-restraints excluded: chain S residue 132 VAL Chi-restraints excluded: chain S residue 293 THR Chi-restraints excluded: chain T residue 1 VAL Chi-restraints excluded: chain T residue 20 LEU Chi-restraints excluded: chain T residue 42 LEU Chi-restraints excluded: chain T residue 102 VAL Chi-restraints excluded: chain T residue 108 SER Chi-restraints excluded: chain T residue 240 THR Chi-restraints excluded: chain U residue 1 VAL Chi-restraints excluded: chain U residue 42 LEU Chi-restraints excluded: chain U residue 82 VAL Chi-restraints excluded: chain U residue 102 VAL Chi-restraints excluded: chain U residue 108 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 504 random chunks: chunk 254 optimal weight: 8.9990 chunk 142 optimal weight: 4.9990 chunk 380 optimal weight: 9.9990 chunk 311 optimal weight: 10.0000 chunk 126 optimal weight: 4.9990 chunk 458 optimal weight: 8.9990 chunk 495 optimal weight: 9.9990 chunk 408 optimal weight: 0.9990 chunk 454 optimal weight: 9.9990 chunk 156 optimal weight: 8.9990 chunk 367 optimal weight: 8.9990 overall best weight: 5.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 264 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 264 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 264 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 46 GLN H 46 GLN ** H 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 46 GLN ** I 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 46 GLN ** L 280 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 46 GLN ** M 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 46 GLN O 46 GLN ** O 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 239 ASN ** P 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 273 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 280 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 46 GLN ** R 280 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 46 GLN ** S 118 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 46 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7851 moved from start: 0.3765 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.078 39837 Z= 0.279 Angle : 0.698 8.752 54663 Z= 0.373 Chirality : 0.047 0.162 6552 Planarity : 0.004 0.030 6909 Dihedral : 5.978 54.260 5385 Min Nonbonded Distance : 2.036 Molprobity Statistics. All-atom Clashscore : 10.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.80 % Favored : 95.20 % Rotamer: Outliers : 4.97 % Allowed : 15.45 % Favored : 79.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.29 (0.12), residues: 4998 helix: 2.46 (0.18), residues: 714 sheet: 0.52 (0.12), residues: 1764 loop : -0.72 (0.12), residues: 2520 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP O 211 HIS 0.006 0.001 HIS I 105 PHE 0.018 0.001 PHE K 197 TYR 0.020 0.002 TYR S 22 ARG 0.004 0.001 ARG T 236 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9996 Ramachandran restraints generated. 4998 Oldfield, 0 Emsley, 4998 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9996 Ramachandran restraints generated. 4998 Oldfield, 0 Emsley, 4998 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1143 residues out of total 4305 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 214 poor density : 929 time to evaluate : 4.390 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 63 ASP cc_start: 0.8572 (m-30) cc_final: 0.8322 (t70) REVERT: A 81 GLN cc_start: 0.7886 (tm-30) cc_final: 0.7501 (pm20) REVERT: A 115 ASP cc_start: 0.8878 (t0) cc_final: 0.8534 (t0) REVERT: A 201 TYR cc_start: 0.8800 (m-10) cc_final: 0.8490 (m-10) REVERT: A 233 LYS cc_start: 0.8201 (mttt) cc_final: 0.7870 (mmmm) REVERT: A 239 ASN cc_start: 0.8915 (OUTLIER) cc_final: 0.8417 (p0) REVERT: A 286 MET cc_start: 0.9036 (mtt) cc_final: 0.8789 (mtp) REVERT: B 63 ASP cc_start: 0.8712 (m-30) cc_final: 0.8390 (t70) REVERT: B 81 GLN cc_start: 0.8098 (tm-30) cc_final: 0.7528 (pm20) REVERT: B 198 ASP cc_start: 0.8664 (t0) cc_final: 0.8346 (t0) REVERT: B 233 LYS cc_start: 0.8359 (mttt) cc_final: 0.7799 (mmmm) REVERT: B 239 ASN cc_start: 0.9041 (OUTLIER) cc_final: 0.8733 (p0) REVERT: B 279 MET cc_start: 0.8511 (mtt) cc_final: 0.7911 (mtt) REVERT: C 81 GLN cc_start: 0.7439 (tm-30) cc_final: 0.7163 (pm20) REVERT: C 115 ASP cc_start: 0.8833 (t0) cc_final: 0.8558 (t70) REVERT: C 198 ASP cc_start: 0.8435 (t0) cc_final: 0.8136 (t0) REVERT: C 201 TYR cc_start: 0.9020 (m-80) cc_final: 0.8604 (m-80) REVERT: C 279 MET cc_start: 0.8412 (mtt) cc_final: 0.7416 (mtt) REVERT: D 115 ASP cc_start: 0.8754 (t0) cc_final: 0.8473 (t0) REVERT: D 201 TYR cc_start: 0.8923 (m-10) cc_final: 0.8608 (m-10) REVERT: D 233 LYS cc_start: 0.8179 (mttt) cc_final: 0.7809 (mmmm) REVERT: D 236 ARG cc_start: 0.7493 (ttm-80) cc_final: 0.7280 (ttm-80) REVERT: D 239 ASN cc_start: 0.8975 (m110) cc_final: 0.8360 (p0) REVERT: E 115 ASP cc_start: 0.8903 (t0) cc_final: 0.8513 (t0) REVERT: E 201 TYR cc_start: 0.8937 (m-10) cc_final: 0.8573 (m-10) REVERT: E 233 LYS cc_start: 0.7879 (mttt) cc_final: 0.7300 (mmmm) REVERT: E 239 ASN cc_start: 0.8839 (OUTLIER) cc_final: 0.8173 (p0) REVERT: E 279 MET cc_start: 0.8372 (mtt) cc_final: 0.8169 (mtt) REVERT: F 116 LYS cc_start: 0.8552 (mmtt) cc_final: 0.8298 (mmtt) REVERT: F 233 LYS cc_start: 0.8159 (mttt) cc_final: 0.7852 (mmmm) REVERT: F 239 ASN cc_start: 0.9125 (OUTLIER) cc_final: 0.8355 (p0) REVERT: F 279 MET cc_start: 0.8217 (mtt) cc_final: 0.7928 (mtt) REVERT: G 62 LYS cc_start: 0.8457 (pttp) cc_final: 0.8223 (mttt) REVERT: G 114 ASP cc_start: 0.8888 (t0) cc_final: 0.8574 (t0) REVERT: G 115 ASP cc_start: 0.8985 (t0) cc_final: 0.8569 (t0) REVERT: G 233 LYS cc_start: 0.8304 (mttt) cc_final: 0.7839 (mmmm) REVERT: H 114 ASP cc_start: 0.8810 (t0) cc_final: 0.8429 (t0) REVERT: H 201 TYR cc_start: 0.9035 (m-80) cc_final: 0.8815 (m-10) REVERT: H 233 LYS cc_start: 0.8070 (mttt) cc_final: 0.7682 (mmmm) REVERT: H 239 ASN cc_start: 0.9066 (OUTLIER) cc_final: 0.8534 (p0) REVERT: I 62 LYS cc_start: 0.8175 (pttp) cc_final: 0.7783 (mttt) REVERT: I 63 ASP cc_start: 0.8557 (m-30) cc_final: 0.8355 (t0) REVERT: I 115 ASP cc_start: 0.9044 (t0) cc_final: 0.8752 (t0) REVERT: I 201 TYR cc_start: 0.8906 (m-80) cc_final: 0.8557 (m-80) REVERT: I 233 LYS cc_start: 0.7928 (mttt) cc_final: 0.7611 (mmmm) REVERT: J 46 GLN cc_start: 0.8888 (pt0) cc_final: 0.8459 (pp30) REVERT: J 62 LYS cc_start: 0.8398 (pttp) cc_final: 0.8055 (mttp) REVERT: J 63 ASP cc_start: 0.8597 (m-30) cc_final: 0.8313 (t70) REVERT: J 233 LYS cc_start: 0.8214 (mttt) cc_final: 0.7688 (mmmm) REVERT: J 239 ASN cc_start: 0.9133 (OUTLIER) cc_final: 0.8587 (p0) REVERT: J 279 MET cc_start: 0.8288 (mtt) cc_final: 0.7742 (mtt) REVERT: K 62 LYS cc_start: 0.8623 (pttp) cc_final: 0.7942 (mttt) REVERT: K 63 ASP cc_start: 0.8606 (m-30) cc_final: 0.8271 (t70) REVERT: K 198 ASP cc_start: 0.8305 (t70) cc_final: 0.7887 (p0) REVERT: K 201 TYR cc_start: 0.8922 (m-80) cc_final: 0.8215 (m-80) REVERT: K 233 LYS cc_start: 0.8260 (mttt) cc_final: 0.7839 (mmmm) REVERT: K 239 ASN cc_start: 0.8562 (m-40) cc_final: 0.7815 (p0) REVERT: K 267 VAL cc_start: 0.9230 (t) cc_final: 0.8928 (m) REVERT: L 62 LYS cc_start: 0.8701 (pttp) cc_final: 0.8193 (mttp) REVERT: L 83 LEU cc_start: 0.7524 (mt) cc_final: 0.7137 (tp) REVERT: L 114 ASP cc_start: 0.8819 (t0) cc_final: 0.8455 (m-30) REVERT: L 233 LYS cc_start: 0.8280 (mttt) cc_final: 0.7697 (mmmm) REVERT: L 236 ARG cc_start: 0.7401 (ttm-80) cc_final: 0.6937 (ttm-80) REVERT: L 262 GLN cc_start: 0.8283 (pm20) cc_final: 0.7304 (pm20) REVERT: L 279 MET cc_start: 0.8184 (mtt) cc_final: 0.7878 (mtt) REVERT: M 46 GLN cc_start: 0.8640 (OUTLIER) cc_final: 0.8319 (pm20) REVERT: M 233 LYS cc_start: 0.8332 (mttt) cc_final: 0.7776 (mmmm) REVERT: M 279 MET cc_start: 0.8438 (mtt) cc_final: 0.7803 (mtt) REVERT: N 55 ASN cc_start: 0.8691 (m-40) cc_final: 0.7921 (p0) REVERT: N 62 LYS cc_start: 0.8128 (pttp) cc_final: 0.7850 (mttp) REVERT: N 233 LYS cc_start: 0.8051 (mttt) cc_final: 0.7359 (mmmm) REVERT: N 279 MET cc_start: 0.8131 (mtt) cc_final: 0.7320 (mtt) REVERT: O 62 LYS cc_start: 0.8338 (pttp) cc_final: 0.7998 (mttp) REVERT: O 94 ILE cc_start: 0.9279 (mt) cc_final: 0.8971 (tt) REVERT: O 214 ASN cc_start: 0.8670 (t0) cc_final: 0.7652 (p0) REVERT: O 236 ARG cc_start: 0.4765 (tpm170) cc_final: 0.3889 (tpt170) REVERT: O 279 MET cc_start: 0.7641 (mtt) cc_final: 0.6602 (mtt) REVERT: O 300 LEU cc_start: 0.8979 (tp) cc_final: 0.8548 (tt) REVERT: P 62 LYS cc_start: 0.8493 (pttp) cc_final: 0.8170 (mttt) REVERT: P 63 ASP cc_start: 0.8531 (m-30) cc_final: 0.8302 (t70) REVERT: P 114 ASP cc_start: 0.8715 (t0) cc_final: 0.8513 (t70) REVERT: P 232 ILE cc_start: 0.9235 (mt) cc_final: 0.9007 (mm) REVERT: P 233 LYS cc_start: 0.8051 (mttt) cc_final: 0.7593 (mmmm) REVERT: P 262 GLN cc_start: 0.8243 (OUTLIER) cc_final: 0.7894 (pp30) REVERT: P 279 MET cc_start: 0.8100 (mtt) cc_final: 0.7754 (mtp) REVERT: P 300 LEU cc_start: 0.9005 (tp) cc_final: 0.8675 (tt) REVERT: Q 116 LYS cc_start: 0.8840 (mttt) cc_final: 0.8502 (pttt) REVERT: Q 300 LEU cc_start: 0.8924 (tp) cc_final: 0.8722 (tp) REVERT: R 62 LYS cc_start: 0.8591 (pttp) cc_final: 0.8021 (mttp) REVERT: R 63 ASP cc_start: 0.8737 (t70) cc_final: 0.8437 (t70) REVERT: R 239 ASN cc_start: 0.8809 (OUTLIER) cc_final: 0.8379 (p0) REVERT: S 62 LYS cc_start: 0.8136 (pttp) cc_final: 0.7648 (mttp) REVERT: S 91 ILE cc_start: 0.9425 (mt) cc_final: 0.9099 (mt) REVERT: S 253 PRO cc_start: 0.9214 (Cg_exo) cc_final: 0.8779 (Cg_endo) REVERT: S 286 MET cc_start: 0.9169 (mtt) cc_final: 0.8934 (mtm) REVERT: T 62 LYS cc_start: 0.8226 (pttp) cc_final: 0.7882 (mttp) REVERT: T 63 ASP cc_start: 0.8709 (t70) cc_final: 0.8454 (t70) REVERT: T 275 ASN cc_start: 0.8532 (t0) cc_final: 0.8122 (t0) REVERT: T 279 MET cc_start: 0.8262 (mtt) cc_final: 0.7847 (mtt) REVERT: U 89 ILE cc_start: 0.8279 (mm) cc_final: 0.8041 (mt) REVERT: U 115 ASP cc_start: 0.8810 (t0) cc_final: 0.8497 (t0) REVERT: U 116 LYS cc_start: 0.8923 (mttt) cc_final: 0.8494 (pttt) outliers start: 214 outliers final: 159 residues processed: 1066 average time/residue: 0.4759 time to fit residues: 858.7307 Evaluate side-chains 1007 residues out of total 4305 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 168 poor density : 839 time to evaluate : 4.087 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 VAL Chi-restraints excluded: chain A residue 26 SER Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 42 LEU Chi-restraints excluded: chain A residue 239 ASN Chi-restraints excluded: chain A residue 257 VAL Chi-restraints excluded: chain A residue 293 THR Chi-restraints excluded: chain A residue 302 ILE Chi-restraints excluded: chain B residue 26 SER Chi-restraints excluded: chain B residue 37 VAL Chi-restraints excluded: chain B residue 42 LEU Chi-restraints excluded: chain B residue 199 ASP Chi-restraints excluded: chain B residue 239 ASN Chi-restraints excluded: chain B residue 257 VAL Chi-restraints excluded: chain B residue 293 THR Chi-restraints excluded: chain C residue 26 SER Chi-restraints excluded: chain C residue 37 VAL Chi-restraints excluded: chain C residue 42 LEU Chi-restraints excluded: chain C residue 240 THR Chi-restraints excluded: chain C residue 257 VAL Chi-restraints excluded: chain D residue 1 VAL Chi-restraints excluded: chain D residue 11 ILE Chi-restraints excluded: chain D residue 12 LEU Chi-restraints excluded: chain D residue 26 SER Chi-restraints excluded: chain D residue 42 LEU Chi-restraints excluded: chain D residue 81 GLN Chi-restraints excluded: chain D residue 240 THR Chi-restraints excluded: chain E residue 1 VAL Chi-restraints excluded: chain E residue 26 SER Chi-restraints excluded: chain E residue 42 LEU Chi-restraints excluded: chain E residue 94 ILE Chi-restraints excluded: chain E residue 102 VAL Chi-restraints excluded: chain E residue 199 ASP Chi-restraints excluded: chain E residue 239 ASN Chi-restraints excluded: chain E residue 257 VAL Chi-restraints excluded: chain F residue 1 VAL Chi-restraints excluded: chain F residue 12 LEU Chi-restraints excluded: chain F residue 26 SER Chi-restraints excluded: chain F residue 37 VAL Chi-restraints excluded: chain F residue 42 LEU Chi-restraints excluded: chain F residue 102 VAL Chi-restraints excluded: chain F residue 114 ASP Chi-restraints excluded: chain F residue 199 ASP Chi-restraints excluded: chain F residue 239 ASN Chi-restraints excluded: chain F residue 282 VAL Chi-restraints excluded: chain F residue 293 THR Chi-restraints excluded: chain G residue 20 LEU Chi-restraints excluded: chain G residue 26 SER Chi-restraints excluded: chain G residue 198 ASP Chi-restraints excluded: chain G residue 240 THR Chi-restraints excluded: chain G residue 257 VAL Chi-restraints excluded: chain G residue 293 THR Chi-restraints excluded: chain H residue 12 LEU Chi-restraints excluded: chain H residue 26 SER Chi-restraints excluded: chain H residue 42 LEU Chi-restraints excluded: chain H residue 199 ASP Chi-restraints excluded: chain H residue 239 ASN Chi-restraints excluded: chain H residue 240 THR Chi-restraints excluded: chain H residue 257 VAL Chi-restraints excluded: chain H residue 293 THR Chi-restraints excluded: chain I residue 12 LEU Chi-restraints excluded: chain I residue 20 LEU Chi-restraints excluded: chain I residue 26 SER Chi-restraints excluded: chain I residue 42 LEU Chi-restraints excluded: chain I residue 46 GLN Chi-restraints excluded: chain I residue 81 GLN Chi-restraints excluded: chain I residue 95 ASP Chi-restraints excluded: chain I residue 102 VAL Chi-restraints excluded: chain I residue 199 ASP Chi-restraints excluded: chain I residue 240 THR Chi-restraints excluded: chain I residue 257 VAL Chi-restraints excluded: chain J residue 26 SER Chi-restraints excluded: chain J residue 42 LEU Chi-restraints excluded: chain J residue 102 VAL Chi-restraints excluded: chain J residue 199 ASP Chi-restraints excluded: chain J residue 239 ASN Chi-restraints excluded: chain J residue 240 THR Chi-restraints excluded: chain J residue 257 VAL Chi-restraints excluded: chain J residue 293 THR Chi-restraints excluded: chain K residue 12 LEU Chi-restraints excluded: chain K residue 20 LEU Chi-restraints excluded: chain K residue 26 SER Chi-restraints excluded: chain K residue 42 LEU Chi-restraints excluded: chain K residue 83 LEU Chi-restraints excluded: chain K residue 102 VAL Chi-restraints excluded: chain K residue 199 ASP Chi-restraints excluded: chain K residue 240 THR Chi-restraints excluded: chain K residue 257 VAL Chi-restraints excluded: chain L residue 20 LEU Chi-restraints excluded: chain L residue 26 SER Chi-restraints excluded: chain L residue 42 LEU Chi-restraints excluded: chain L residue 45 ILE Chi-restraints excluded: chain L residue 95 ASP Chi-restraints excluded: chain L residue 102 VAL Chi-restraints excluded: chain L residue 240 THR Chi-restraints excluded: chain L residue 257 VAL Chi-restraints excluded: chain M residue 20 LEU Chi-restraints excluded: chain M residue 26 SER Chi-restraints excluded: chain M residue 42 LEU Chi-restraints excluded: chain M residue 46 GLN Chi-restraints excluded: chain M residue 95 ASP Chi-restraints excluded: chain M residue 102 VAL Chi-restraints excluded: chain M residue 240 THR Chi-restraints excluded: chain M residue 257 VAL Chi-restraints excluded: chain N residue 20 LEU Chi-restraints excluded: chain N residue 26 SER Chi-restraints excluded: chain N residue 42 LEU Chi-restraints excluded: chain N residue 46 GLN Chi-restraints excluded: chain N residue 102 VAL Chi-restraints excluded: chain N residue 240 THR Chi-restraints excluded: chain N residue 257 VAL Chi-restraints excluded: chain O residue 20 LEU Chi-restraints excluded: chain O residue 46 GLN Chi-restraints excluded: chain O residue 293 THR Chi-restraints excluded: chain P residue 20 LEU Chi-restraints excluded: chain P residue 26 SER Chi-restraints excluded: chain P residue 95 ASP Chi-restraints excluded: chain P residue 102 VAL Chi-restraints excluded: chain P residue 199 ASP Chi-restraints excluded: chain P residue 216 VAL Chi-restraints excluded: chain P residue 257 VAL Chi-restraints excluded: chain P residue 262 GLN Chi-restraints excluded: chain P residue 293 THR Chi-restraints excluded: chain Q residue 20 LEU Chi-restraints excluded: chain Q residue 95 ASP Chi-restraints excluded: chain Q residue 257 VAL Chi-restraints excluded: chain Q residue 293 THR Chi-restraints excluded: chain R residue 20 LEU Chi-restraints excluded: chain R residue 26 SER Chi-restraints excluded: chain R residue 42 LEU Chi-restraints excluded: chain R residue 46 GLN Chi-restraints excluded: chain R residue 82 VAL Chi-restraints excluded: chain R residue 239 ASN Chi-restraints excluded: chain R residue 257 VAL Chi-restraints excluded: chain R residue 293 THR Chi-restraints excluded: chain S residue 1 VAL Chi-restraints excluded: chain S residue 13 ILE Chi-restraints excluded: chain S residue 20 LEU Chi-restraints excluded: chain S residue 23 THR Chi-restraints excluded: chain S residue 82 VAL Chi-restraints excluded: chain S residue 83 LEU Chi-restraints excluded: chain S residue 108 SER Chi-restraints excluded: chain S residue 126 LEU Chi-restraints excluded: chain S residue 239 ASN Chi-restraints excluded: chain S residue 257 VAL Chi-restraints excluded: chain S residue 293 THR Chi-restraints excluded: chain T residue 1 VAL Chi-restraints excluded: chain T residue 13 ILE Chi-restraints excluded: chain T residue 20 LEU Chi-restraints excluded: chain T residue 42 LEU Chi-restraints excluded: chain T residue 82 VAL Chi-restraints excluded: chain T residue 94 ILE Chi-restraints excluded: chain T residue 102 VAL Chi-restraints excluded: chain T residue 122 THR Chi-restraints excluded: chain T residue 238 VAL Chi-restraints excluded: chain T residue 257 VAL Chi-restraints excluded: chain T residue 293 THR Chi-restraints excluded: chain U residue 13 ILE Chi-restraints excluded: chain U residue 20 LEU Chi-restraints excluded: chain U residue 42 LEU Chi-restraints excluded: chain U residue 46 GLN Chi-restraints excluded: chain U residue 94 ILE Chi-restraints excluded: chain U residue 102 VAL Chi-restraints excluded: chain U residue 104 CYS Chi-restraints excluded: chain U residue 122 THR Chi-restraints excluded: chain U residue 238 VAL Chi-restraints excluded: chain U residue 257 VAL Chi-restraints excluded: chain U residue 293 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 504 random chunks: chunk 453 optimal weight: 20.0000 chunk 344 optimal weight: 3.9990 chunk 237 optimal weight: 0.9990 chunk 50 optimal weight: 9.9990 chunk 218 optimal weight: 3.9990 chunk 307 optimal weight: 20.0000 chunk 460 optimal weight: 0.6980 chunk 487 optimal weight: 6.9990 chunk 240 optimal weight: 6.9990 chunk 436 optimal weight: 0.9980 chunk 131 optimal weight: 10.0000 overall best weight: 2.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 46 GLN ** B 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 264 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 46 GLN ** D 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 264 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 81 GLN ** E 264 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 46 GLN H 77 GLN H 118 HIS I 46 GLN I 77 GLN I 219 ASN J 46 GLN K 239 ASN ** L 280 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 46 GLN ** M 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 118 HIS N 46 GLN ** O 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 219 ASN ** P 273 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 280 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 46 GLN R 280 GLN T 277 ASN U 46 GLN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7806 moved from start: 0.4102 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 39837 Z= 0.180 Angle : 0.630 8.862 54663 Z= 0.328 Chirality : 0.046 0.178 6552 Planarity : 0.003 0.026 6909 Dihedral : 5.508 51.556 5367 Min Nonbonded Distance : 2.127 Molprobity Statistics. All-atom Clashscore : 9.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.16 % Favored : 95.84 % Rotamer: Outliers : 3.53 % Allowed : 18.16 % Favored : 78.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.49 (0.12), residues: 4998 helix: 2.99 (0.19), residues: 714 sheet: 0.58 (0.12), residues: 1764 loop : -0.64 (0.12), residues: 2520 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP R 211 HIS 0.004 0.001 HIS N 105 PHE 0.011 0.001 PHE U 237 TYR 0.022 0.001 TYR D 22 ARG 0.002 0.000 ARG U 226 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9996 Ramachandran restraints generated. 4998 Oldfield, 0 Emsley, 4998 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9996 Ramachandran restraints generated. 4998 Oldfield, 0 Emsley, 4998 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1069 residues out of total 4305 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 152 poor density : 917 time to evaluate : 4.621 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: A 22 TYR cc_start: 0.9176 (t80) cc_final: 0.8884 (t80) REVERT: A 107 ASP cc_start: 0.7182 (p0) cc_final: 0.6958 (t0) REVERT: A 201 TYR cc_start: 0.8767 (m-10) cc_final: 0.8548 (m-10) REVERT: A 233 LYS cc_start: 0.8235 (mttt) cc_final: 0.7873 (mmmm) REVERT: A 239 ASN cc_start: 0.8937 (m-40) cc_final: 0.8373 (p0) REVERT: A 286 MET cc_start: 0.9047 (mtt) cc_final: 0.8812 (mtp) REVERT: B 81 GLN cc_start: 0.7930 (tm-30) cc_final: 0.7628 (pm20) REVERT: B 233 LYS cc_start: 0.8357 (mttt) cc_final: 0.7826 (mmmm) REVERT: B 239 ASN cc_start: 0.8994 (m-40) cc_final: 0.8690 (p0) REVERT: B 279 MET cc_start: 0.8431 (mtt) cc_final: 0.7876 (mtt) REVERT: C 107 ASP cc_start: 0.7450 (p0) cc_final: 0.7218 (t0) REVERT: C 198 ASP cc_start: 0.8412 (t0) cc_final: 0.8170 (t0) REVERT: C 201 TYR cc_start: 0.9016 (m-80) cc_final: 0.8601 (m-80) REVERT: C 279 MET cc_start: 0.8316 (mtt) cc_final: 0.7353 (mtt) REVERT: D 115 ASP cc_start: 0.8721 (t0) cc_final: 0.8416 (t0) REVERT: D 201 TYR cc_start: 0.8893 (m-10) cc_final: 0.8619 (m-10) REVERT: D 233 LYS cc_start: 0.8050 (mttt) cc_final: 0.7732 (mmmm) REVERT: D 236 ARG cc_start: 0.7405 (ttm-80) cc_final: 0.7084 (ttm-80) REVERT: D 239 ASN cc_start: 0.8910 (m110) cc_final: 0.8260 (p0) REVERT: E 115 ASP cc_start: 0.8836 (t0) cc_final: 0.8426 (t0) REVERT: E 201 TYR cc_start: 0.8895 (m-10) cc_final: 0.8671 (m-10) REVERT: E 233 LYS cc_start: 0.7890 (mttt) cc_final: 0.7394 (mmmm) REVERT: E 239 ASN cc_start: 0.8827 (OUTLIER) cc_final: 0.8123 (p0) REVERT: F 116 LYS cc_start: 0.8434 (mmtt) cc_final: 0.8200 (mmtt) REVERT: F 233 LYS cc_start: 0.8218 (mttt) cc_final: 0.7863 (mmmm) REVERT: F 239 ASN cc_start: 0.9040 (m-40) cc_final: 0.8333 (p0) REVERT: F 267 VAL cc_start: 0.8961 (t) cc_final: 0.8702 (m) REVERT: F 279 MET cc_start: 0.8194 (mtt) cc_final: 0.7905 (mtt) REVERT: G 62 LYS cc_start: 0.8442 (pttp) cc_final: 0.8164 (mttt) REVERT: G 115 ASP cc_start: 0.8937 (t0) cc_final: 0.8540 (t0) REVERT: G 233 LYS cc_start: 0.8247 (mttt) cc_final: 0.7812 (mmmm) REVERT: H 114 ASP cc_start: 0.8796 (t0) cc_final: 0.8463 (t0) REVERT: H 201 TYR cc_start: 0.8979 (m-80) cc_final: 0.8559 (m-10) REVERT: H 233 LYS cc_start: 0.8101 (mttt) cc_final: 0.7664 (mmmm) REVERT: H 239 ASN cc_start: 0.9030 (m-40) cc_final: 0.8461 (p0) REVERT: H 267 VAL cc_start: 0.9044 (t) cc_final: 0.8834 (m) REVERT: I 62 LYS cc_start: 0.8181 (pttp) cc_final: 0.7741 (mttt) REVERT: I 201 TYR cc_start: 0.8940 (m-80) cc_final: 0.8584 (m-80) REVERT: I 233 LYS cc_start: 0.7864 (mttt) cc_final: 0.7592 (mmmm) REVERT: I 267 VAL cc_start: 0.9114 (t) cc_final: 0.8909 (m) REVERT: J 62 LYS cc_start: 0.8405 (pttp) cc_final: 0.8089 (mttp) REVERT: J 63 ASP cc_start: 0.8648 (m-30) cc_final: 0.8427 (t70) REVERT: J 117 TYR cc_start: 0.7670 (t80) cc_final: 0.7463 (t80) REVERT: J 233 LYS cc_start: 0.8226 (mttt) cc_final: 0.7709 (mmmm) REVERT: J 239 ASN cc_start: 0.9110 (m-40) cc_final: 0.8483 (p0) REVERT: J 279 MET cc_start: 0.8300 (mtt) cc_final: 0.7772 (mtt) REVERT: K 62 LYS cc_start: 0.8343 (pttp) cc_final: 0.7876 (mttt) REVERT: K 63 ASP cc_start: 0.8541 (m-30) cc_final: 0.8228 (t70) REVERT: K 198 ASP cc_start: 0.8353 (t70) cc_final: 0.7953 (p0) REVERT: K 201 TYR cc_start: 0.8909 (m-80) cc_final: 0.8178 (m-80) REVERT: K 233 LYS cc_start: 0.8143 (mttt) cc_final: 0.7752 (mmmm) REVERT: K 239 ASN cc_start: 0.8497 (m110) cc_final: 0.7834 (p0) REVERT: K 267 VAL cc_start: 0.9200 (t) cc_final: 0.8937 (m) REVERT: L 62 LYS cc_start: 0.8662 (pttp) cc_final: 0.8148 (mttp) REVERT: L 107 ASP cc_start: 0.7300 (p0) cc_final: 0.7007 (t0) REVERT: L 114 ASP cc_start: 0.8834 (t0) cc_final: 0.8628 (t70) REVERT: L 233 LYS cc_start: 0.8167 (mttt) cc_final: 0.7612 (mmmm) REVERT: L 236 ARG cc_start: 0.7393 (ttm-80) cc_final: 0.6910 (ttm-80) REVERT: L 262 GLN cc_start: 0.8255 (pm20) cc_final: 0.7268 (pm20) REVERT: M 233 LYS cc_start: 0.8320 (mttt) cc_final: 0.7764 (mmmm) REVERT: M 279 MET cc_start: 0.8145 (mtt) cc_final: 0.7422 (mtt) REVERT: M 285 LYS cc_start: 0.9080 (ttmt) cc_final: 0.8865 (tttt) REVERT: N 55 ASN cc_start: 0.8670 (m-40) cc_final: 0.7946 (p0) REVERT: N 62 LYS cc_start: 0.8156 (pttp) cc_final: 0.7845 (mttp) REVERT: N 233 LYS cc_start: 0.8027 (mttt) cc_final: 0.7382 (mmmm) REVERT: N 279 MET cc_start: 0.7841 (mtt) cc_final: 0.7054 (mtt) REVERT: O 62 LYS cc_start: 0.8386 (pttp) cc_final: 0.8020 (mttp) REVERT: O 94 ILE cc_start: 0.9290 (mt) cc_final: 0.8994 (tt) REVERT: O 236 ARG cc_start: 0.4549 (tpt170) cc_final: 0.3969 (tpt170) REVERT: P 63 ASP cc_start: 0.8474 (m-30) cc_final: 0.8233 (t70) REVERT: P 233 LYS cc_start: 0.7993 (mttt) cc_final: 0.7510 (mmmm) REVERT: P 262 GLN cc_start: 0.8159 (OUTLIER) cc_final: 0.7809 (pp30) REVERT: Q 107 ASP cc_start: 0.7500 (p0) cc_final: 0.7247 (t0) REVERT: Q 116 LYS cc_start: 0.8787 (mttt) cc_final: 0.8451 (pttt) REVERT: R 62 LYS cc_start: 0.8573 (pttp) cc_final: 0.8022 (mttp) REVERT: R 63 ASP cc_start: 0.8689 (t70) cc_final: 0.8389 (t70) REVERT: R 225 PHE cc_start: 0.8679 (OUTLIER) cc_final: 0.8374 (t80) REVERT: R 239 ASN cc_start: 0.8828 (m-40) cc_final: 0.8370 (p0) REVERT: S 62 LYS cc_start: 0.8139 (pttp) cc_final: 0.7615 (mttp) REVERT: S 253 PRO cc_start: 0.9309 (Cg_exo) cc_final: 0.9040 (Cg_endo) REVERT: S 290 ASP cc_start: 0.8529 (p0) cc_final: 0.8298 (p0) REVERT: T 62 LYS cc_start: 0.8191 (pttp) cc_final: 0.7880 (mttp) REVERT: T 63 ASP cc_start: 0.8664 (t70) cc_final: 0.8433 (t70) REVERT: T 77 GLN cc_start: 0.8384 (tp40) cc_final: 0.8017 (tm-30) REVERT: T 121 GLN cc_start: 0.7689 (mt0) cc_final: 0.7413 (mp10) REVERT: T 225 PHE cc_start: 0.8631 (OUTLIER) cc_final: 0.8349 (t80) REVERT: T 275 ASN cc_start: 0.8607 (t0) cc_final: 0.8375 (t0) REVERT: U 89 ILE cc_start: 0.8269 (mm) cc_final: 0.8048 (mt) REVERT: U 115 ASP cc_start: 0.8767 (t0) cc_final: 0.8423 (t0) REVERT: U 116 LYS cc_start: 0.8888 (mttt) cc_final: 0.8465 (pttt) outliers start: 152 outliers final: 113 residues processed: 1021 average time/residue: 0.4467 time to fit residues: 760.7978 Evaluate side-chains 957 residues out of total 4305 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 117 poor density : 840 time to evaluate : 4.122 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 VAL Chi-restraints excluded: chain A residue 20 LEU Chi-restraints excluded: chain A residue 26 SER Chi-restraints excluded: chain A residue 42 LEU Chi-restraints excluded: chain A residue 257 VAL Chi-restraints excluded: chain A residue 293 THR Chi-restraints excluded: chain B residue 26 SER Chi-restraints excluded: chain B residue 42 LEU Chi-restraints excluded: chain B residue 257 VAL Chi-restraints excluded: chain B residue 293 THR Chi-restraints excluded: chain C residue 20 LEU Chi-restraints excluded: chain C residue 26 SER Chi-restraints excluded: chain C residue 42 LEU Chi-restraints excluded: chain C residue 240 THR Chi-restraints excluded: chain C residue 257 VAL Chi-restraints excluded: chain D residue 1 VAL Chi-restraints excluded: chain D residue 12 LEU Chi-restraints excluded: chain D residue 26 SER Chi-restraints excluded: chain D residue 42 LEU Chi-restraints excluded: chain D residue 246 THR Chi-restraints excluded: chain E residue 1 VAL Chi-restraints excluded: chain E residue 26 SER Chi-restraints excluded: chain E residue 42 LEU Chi-restraints excluded: chain E residue 83 LEU Chi-restraints excluded: chain E residue 94 ILE Chi-restraints excluded: chain E residue 102 VAL Chi-restraints excluded: chain E residue 239 ASN Chi-restraints excluded: chain E residue 257 VAL Chi-restraints excluded: chain E residue 293 THR Chi-restraints excluded: chain F residue 26 SER Chi-restraints excluded: chain F residue 42 LEU Chi-restraints excluded: chain F residue 102 VAL Chi-restraints excluded: chain F residue 199 ASP Chi-restraints excluded: chain F residue 293 THR Chi-restraints excluded: chain G residue 20 LEU Chi-restraints excluded: chain G residue 26 SER Chi-restraints excluded: chain G residue 83 LEU Chi-restraints excluded: chain G residue 102 VAL Chi-restraints excluded: chain G residue 240 THR Chi-restraints excluded: chain G residue 257 VAL Chi-restraints excluded: chain H residue 12 LEU Chi-restraints excluded: chain H residue 26 SER Chi-restraints excluded: chain H residue 42 LEU Chi-restraints excluded: chain H residue 46 GLN Chi-restraints excluded: chain H residue 115 ASP Chi-restraints excluded: chain H residue 199 ASP Chi-restraints excluded: chain H residue 225 PHE Chi-restraints excluded: chain H residue 257 VAL Chi-restraints excluded: chain I residue 26 SER Chi-restraints excluded: chain I residue 42 LEU Chi-restraints excluded: chain I residue 102 VAL Chi-restraints excluded: chain I residue 199 ASP Chi-restraints excluded: chain J residue 26 SER Chi-restraints excluded: chain J residue 42 LEU Chi-restraints excluded: chain J residue 46 GLN Chi-restraints excluded: chain J residue 102 VAL Chi-restraints excluded: chain J residue 199 ASP Chi-restraints excluded: chain J residue 257 VAL Chi-restraints excluded: chain J residue 293 THR Chi-restraints excluded: chain J residue 297 SER Chi-restraints excluded: chain K residue 12 LEU Chi-restraints excluded: chain K residue 20 LEU Chi-restraints excluded: chain K residue 26 SER Chi-restraints excluded: chain K residue 102 VAL Chi-restraints excluded: chain K residue 199 ASP Chi-restraints excluded: chain K residue 257 VAL Chi-restraints excluded: chain L residue 20 LEU Chi-restraints excluded: chain L residue 26 SER Chi-restraints excluded: chain L residue 42 LEU Chi-restraints excluded: chain L residue 102 VAL Chi-restraints excluded: chain L residue 240 THR Chi-restraints excluded: chain L residue 257 VAL Chi-restraints excluded: chain M residue 20 LEU Chi-restraints excluded: chain M residue 26 SER Chi-restraints excluded: chain M residue 102 VAL Chi-restraints excluded: chain M residue 240 THR Chi-restraints excluded: chain M residue 257 VAL Chi-restraints excluded: chain N residue 20 LEU Chi-restraints excluded: chain N residue 26 SER Chi-restraints excluded: chain N residue 42 LEU Chi-restraints excluded: chain N residue 102 VAL Chi-restraints excluded: chain N residue 240 THR Chi-restraints excluded: chain O residue 20 LEU Chi-restraints excluded: chain O residue 102 VAL Chi-restraints excluded: chain O residue 225 PHE Chi-restraints excluded: chain O residue 257 VAL Chi-restraints excluded: chain P residue 20 LEU Chi-restraints excluded: chain P residue 74 LEU Chi-restraints excluded: chain P residue 102 VAL Chi-restraints excluded: chain P residue 104 CYS Chi-restraints excluded: chain P residue 199 ASP Chi-restraints excluded: chain P residue 216 VAL Chi-restraints excluded: chain P residue 262 GLN Chi-restraints excluded: chain P residue 297 SER Chi-restraints excluded: chain Q residue 20 LEU Chi-restraints excluded: chain R residue 20 LEU Chi-restraints excluded: chain R residue 42 LEU Chi-restraints excluded: chain R residue 225 PHE Chi-restraints excluded: chain S residue 20 LEU Chi-restraints excluded: chain S residue 23 THR Chi-restraints excluded: chain S residue 82 VAL Chi-restraints excluded: chain S residue 83 LEU Chi-restraints excluded: chain S residue 102 VAL Chi-restraints excluded: chain S residue 108 SER Chi-restraints excluded: chain S residue 126 LEU Chi-restraints excluded: chain T residue 20 LEU Chi-restraints excluded: chain T residue 42 LEU Chi-restraints excluded: chain T residue 82 VAL Chi-restraints excluded: chain T residue 102 VAL Chi-restraints excluded: chain T residue 108 SER Chi-restraints excluded: chain T residue 225 PHE Chi-restraints excluded: chain U residue 20 LEU Chi-restraints excluded: chain U residue 42 LEU Chi-restraints excluded: chain U residue 46 GLN Chi-restraints excluded: chain U residue 102 VAL Chi-restraints excluded: chain U residue 238 VAL Chi-restraints excluded: chain U residue 297 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 504 random chunks: chunk 405 optimal weight: 1.9990 chunk 276 optimal weight: 2.9990 chunk 7 optimal weight: 7.9990 chunk 362 optimal weight: 2.9990 chunk 201 optimal weight: 7.9990 chunk 415 optimal weight: 7.9990 chunk 336 optimal weight: 2.9990 chunk 0 optimal weight: 10.0000 chunk 248 optimal weight: 4.9990 chunk 437 optimal weight: 20.0000 chunk 122 optimal weight: 6.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 264 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 264 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 81 GLN ** E 264 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 46 GLN I 118 HIS J 46 GLN ** M 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 219 ASN O 46 GLN ** P 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 273 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 280 GLN S 121 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7809 moved from start: 0.4299 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.081 39837 Z= 0.196 Angle : 0.624 10.963 54663 Z= 0.322 Chirality : 0.046 0.173 6552 Planarity : 0.003 0.027 6909 Dihedral : 5.243 49.702 5346 Min Nonbonded Distance : 2.127 Molprobity Statistics. All-atom Clashscore : 9.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.56 % Favored : 95.44 % Rotamer: Outliers : 3.60 % Allowed : 19.16 % Favored : 77.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.50 (0.12), residues: 4998 helix: 2.91 (0.19), residues: 714 sheet: 0.63 (0.12), residues: 1764 loop : -0.65 (0.12), residues: 2520 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP J 211 HIS 0.005 0.001 HIS O 105 PHE 0.017 0.001 PHE S 237 TYR 0.027 0.001 TYR S 98 ARG 0.002 0.000 ARG R 67 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9996 Ramachandran restraints generated. 4998 Oldfield, 0 Emsley, 4998 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9996 Ramachandran restraints generated. 4998 Oldfield, 0 Emsley, 4998 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1015 residues out of total 4305 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 155 poor density : 860 time to evaluate : 4.297 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: A 233 LYS cc_start: 0.8211 (mttt) cc_final: 0.7657 (mmmm) REVERT: A 239 ASN cc_start: 0.8937 (m-40) cc_final: 0.8369 (p0) REVERT: A 286 MET cc_start: 0.9074 (mtt) cc_final: 0.8843 (mtp) REVERT: B 63 ASP cc_start: 0.8660 (m-30) cc_final: 0.8266 (t70) REVERT: B 81 GLN cc_start: 0.7850 (tm-30) cc_final: 0.7630 (pm20) REVERT: B 233 LYS cc_start: 0.8364 (mttt) cc_final: 0.7841 (mmmm) REVERT: B 239 ASN cc_start: 0.8997 (m-40) cc_final: 0.8552 (p0) REVERT: B 279 MET cc_start: 0.8424 (mtt) cc_final: 0.7877 (mtt) REVERT: C 279 MET cc_start: 0.8309 (mtt) cc_final: 0.7313 (mtt) REVERT: D 115 ASP cc_start: 0.8731 (t0) cc_final: 0.8429 (t0) REVERT: D 201 TYR cc_start: 0.8880 (m-10) cc_final: 0.8627 (m-10) REVERT: D 233 LYS cc_start: 0.8039 (mttt) cc_final: 0.7747 (mmmm) REVERT: D 236 ARG cc_start: 0.7398 (ttm-80) cc_final: 0.7154 (ttm-80) REVERT: D 239 ASN cc_start: 0.8907 (m110) cc_final: 0.8267 (p0) REVERT: D 279 MET cc_start: 0.8287 (mtt) cc_final: 0.7361 (mtm) REVERT: E 115 ASP cc_start: 0.8851 (t0) cc_final: 0.8470 (t0) REVERT: E 233 LYS cc_start: 0.7895 (mttt) cc_final: 0.7408 (mmmm) REVERT: E 239 ASN cc_start: 0.8798 (m-40) cc_final: 0.8117 (p0) REVERT: F 198 ASP cc_start: 0.8673 (t0) cc_final: 0.7660 (p0) REVERT: F 201 TYR cc_start: 0.8887 (m-80) cc_final: 0.8570 (m-80) REVERT: F 233 LYS cc_start: 0.8207 (mttt) cc_final: 0.7876 (mmmm) REVERT: F 239 ASN cc_start: 0.9043 (m-40) cc_final: 0.8196 (p0) REVERT: F 267 VAL cc_start: 0.8955 (t) cc_final: 0.8714 (m) REVERT: F 279 MET cc_start: 0.8200 (mtt) cc_final: 0.7908 (mtt) REVERT: G 62 LYS cc_start: 0.8411 (pttp) cc_final: 0.8146 (mttt) REVERT: G 114 ASP cc_start: 0.8752 (t70) cc_final: 0.8426 (t0) REVERT: G 115 ASP cc_start: 0.8883 (t0) cc_final: 0.8486 (t0) REVERT: G 233 LYS cc_start: 0.8259 (mttt) cc_final: 0.7829 (mmmm) REVERT: H 114 ASP cc_start: 0.8796 (t0) cc_final: 0.8453 (t0) REVERT: H 233 LYS cc_start: 0.8146 (mttt) cc_final: 0.7705 (mmmm) REVERT: H 239 ASN cc_start: 0.9011 (m-40) cc_final: 0.8430 (p0) REVERT: I 62 LYS cc_start: 0.8125 (pttp) cc_final: 0.7793 (mttt) REVERT: I 201 TYR cc_start: 0.8951 (m-80) cc_final: 0.8558 (m-80) REVERT: I 233 LYS cc_start: 0.7880 (mttt) cc_final: 0.7599 (mmmm) REVERT: J 62 LYS cc_start: 0.8459 (pttp) cc_final: 0.8147 (mttp) REVERT: J 63 ASP cc_start: 0.8635 (m-30) cc_final: 0.8425 (t70) REVERT: J 117 TYR cc_start: 0.7850 (t80) cc_final: 0.7589 (t80) REVERT: J 233 LYS cc_start: 0.8231 (mttt) cc_final: 0.7679 (mmmm) REVERT: J 239 ASN cc_start: 0.9112 (m-40) cc_final: 0.8491 (p0) REVERT: J 267 VAL cc_start: 0.8901 (t) cc_final: 0.8691 (m) REVERT: J 279 MET cc_start: 0.8326 (mtt) cc_final: 0.7915 (mtt) REVERT: K 62 LYS cc_start: 0.8383 (pttp) cc_final: 0.7929 (mttt) REVERT: K 63 ASP cc_start: 0.8540 (m-30) cc_final: 0.8270 (t70) REVERT: K 198 ASP cc_start: 0.8384 (t70) cc_final: 0.7903 (p0) REVERT: K 201 TYR cc_start: 0.8889 (m-80) cc_final: 0.8119 (m-80) REVERT: K 233 LYS cc_start: 0.8132 (mttt) cc_final: 0.7759 (mmmm) REVERT: K 239 ASN cc_start: 0.8403 (m110) cc_final: 0.7754 (p0) REVERT: K 267 VAL cc_start: 0.9194 (t) cc_final: 0.8932 (m) REVERT: K 279 MET cc_start: 0.8067 (mtt) cc_final: 0.7625 (mtt) REVERT: L 62 LYS cc_start: 0.8641 (pttp) cc_final: 0.8112 (mttp) REVERT: L 107 ASP cc_start: 0.7575 (p0) cc_final: 0.7009 (t0) REVERT: L 114 ASP cc_start: 0.8844 (t0) cc_final: 0.8637 (t70) REVERT: L 233 LYS cc_start: 0.8224 (mttt) cc_final: 0.7642 (mmmm) REVERT: L 262 GLN cc_start: 0.8285 (pm20) cc_final: 0.7361 (pm20) REVERT: M 46 GLN cc_start: 0.8436 (pt0) cc_final: 0.8225 (pm20) REVERT: M 233 LYS cc_start: 0.8321 (mttt) cc_final: 0.7778 (mmmm) REVERT: M 279 MET cc_start: 0.8227 (mtt) cc_final: 0.7561 (mtt) REVERT: N 21 LEU cc_start: 0.9304 (tt) cc_final: 0.8968 (tp) REVERT: N 62 LYS cc_start: 0.8165 (pttp) cc_final: 0.7853 (mttp) REVERT: N 233 LYS cc_start: 0.8019 (mttt) cc_final: 0.7386 (mmmm) REVERT: N 279 MET cc_start: 0.8003 (mtt) cc_final: 0.7224 (mtt) REVERT: N 285 LYS cc_start: 0.8881 (tttt) cc_final: 0.8638 (tttt) REVERT: O 62 LYS cc_start: 0.8440 (pttp) cc_final: 0.8115 (mttp) REVERT: O 94 ILE cc_start: 0.9300 (mt) cc_final: 0.9093 (tt) REVERT: O 214 ASN cc_start: 0.8627 (t0) cc_final: 0.7815 (p0) REVERT: O 236 ARG cc_start: 0.4040 (tpt170) cc_final: 0.3372 (tpt170) REVERT: O 279 MET cc_start: 0.7559 (mtt) cc_final: 0.6780 (mtt) REVERT: P 198 ASP cc_start: 0.8666 (t0) cc_final: 0.8394 (t0) REVERT: P 201 TYR cc_start: 0.8944 (m-80) cc_final: 0.8592 (m-80) REVERT: P 233 LYS cc_start: 0.7950 (mttt) cc_final: 0.7485 (mmmm) REVERT: P 262 GLN cc_start: 0.8148 (OUTLIER) cc_final: 0.7715 (pp30) REVERT: Q 116 LYS cc_start: 0.8857 (mttt) cc_final: 0.8514 (pttt) REVERT: R 62 LYS cc_start: 0.8767 (pttp) cc_final: 0.8004 (mttp) REVERT: R 63 ASP cc_start: 0.8650 (t70) cc_final: 0.8343 (t70) REVERT: R 225 PHE cc_start: 0.8648 (OUTLIER) cc_final: 0.8359 (t80) REVERT: R 239 ASN cc_start: 0.8838 (m-40) cc_final: 0.8392 (p0) REVERT: S 62 LYS cc_start: 0.8140 (pttp) cc_final: 0.7617 (mttp) REVERT: S 290 ASP cc_start: 0.8585 (p0) cc_final: 0.8344 (p0) REVERT: T 62 LYS cc_start: 0.8220 (pttp) cc_final: 0.7914 (mttp) REVERT: T 63 ASP cc_start: 0.8719 (t70) cc_final: 0.8500 (t70) REVERT: T 225 PHE cc_start: 0.8663 (OUTLIER) cc_final: 0.8378 (t80) REVERT: T 233 LYS cc_start: 0.7726 (mmmm) cc_final: 0.7496 (mmmm) REVERT: T 275 ASN cc_start: 0.8553 (t0) cc_final: 0.8267 (t0) REVERT: T 279 MET cc_start: 0.8310 (mtt) cc_final: 0.7842 (mtt) REVERT: U 89 ILE cc_start: 0.8288 (mm) cc_final: 0.8081 (mt) REVERT: U 115 ASP cc_start: 0.8757 (t0) cc_final: 0.8418 (t0) REVERT: U 116 LYS cc_start: 0.8927 (mttt) cc_final: 0.8471 (pttt) outliers start: 155 outliers final: 132 residues processed: 969 average time/residue: 0.4713 time to fit residues: 763.2016 Evaluate side-chains 954 residues out of total 4305 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 135 poor density : 819 time to evaluate : 4.233 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 VAL Chi-restraints excluded: chain A residue 20 LEU Chi-restraints excluded: chain A residue 26 SER Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 42 LEU Chi-restraints excluded: chain A residue 104 CYS Chi-restraints excluded: chain A residue 257 VAL Chi-restraints excluded: chain A residue 293 THR Chi-restraints excluded: chain B residue 26 SER Chi-restraints excluded: chain B residue 37 VAL Chi-restraints excluded: chain B residue 42 LEU Chi-restraints excluded: chain B residue 257 VAL Chi-restraints excluded: chain B residue 293 THR Chi-restraints excluded: chain C residue 20 LEU Chi-restraints excluded: chain C residue 26 SER Chi-restraints excluded: chain C residue 42 LEU Chi-restraints excluded: chain D residue 1 VAL Chi-restraints excluded: chain D residue 12 LEU Chi-restraints excluded: chain D residue 26 SER Chi-restraints excluded: chain D residue 42 LEU Chi-restraints excluded: chain D residue 104 CYS Chi-restraints excluded: chain D residue 246 THR Chi-restraints excluded: chain E residue 1 VAL Chi-restraints excluded: chain E residue 26 SER Chi-restraints excluded: chain E residue 42 LEU Chi-restraints excluded: chain E residue 97 LEU Chi-restraints excluded: chain E residue 102 VAL Chi-restraints excluded: chain E residue 257 VAL Chi-restraints excluded: chain F residue 1 VAL Chi-restraints excluded: chain F residue 12 LEU Chi-restraints excluded: chain F residue 26 SER Chi-restraints excluded: chain F residue 37 VAL Chi-restraints excluded: chain F residue 42 LEU Chi-restraints excluded: chain F residue 102 VAL Chi-restraints excluded: chain F residue 115 ASP Chi-restraints excluded: chain F residue 199 ASP Chi-restraints excluded: chain F residue 293 THR Chi-restraints excluded: chain F residue 297 SER Chi-restraints excluded: chain G residue 20 LEU Chi-restraints excluded: chain G residue 26 SER Chi-restraints excluded: chain G residue 102 VAL Chi-restraints excluded: chain G residue 199 ASP Chi-restraints excluded: chain G residue 240 THR Chi-restraints excluded: chain G residue 257 VAL Chi-restraints excluded: chain H residue 1 VAL Chi-restraints excluded: chain H residue 12 LEU Chi-restraints excluded: chain H residue 26 SER Chi-restraints excluded: chain H residue 42 LEU Chi-restraints excluded: chain H residue 115 ASP Chi-restraints excluded: chain H residue 199 ASP Chi-restraints excluded: chain H residue 225 PHE Chi-restraints excluded: chain H residue 240 THR Chi-restraints excluded: chain H residue 293 THR Chi-restraints excluded: chain I residue 26 SER Chi-restraints excluded: chain I residue 42 LEU Chi-restraints excluded: chain I residue 102 VAL Chi-restraints excluded: chain I residue 199 ASP Chi-restraints excluded: chain J residue 26 SER Chi-restraints excluded: chain J residue 42 LEU Chi-restraints excluded: chain J residue 102 VAL Chi-restraints excluded: chain J residue 199 ASP Chi-restraints excluded: chain J residue 240 THR Chi-restraints excluded: chain J residue 257 VAL Chi-restraints excluded: chain J residue 297 SER Chi-restraints excluded: chain K residue 12 LEU Chi-restraints excluded: chain K residue 20 LEU Chi-restraints excluded: chain K residue 26 SER Chi-restraints excluded: chain K residue 102 VAL Chi-restraints excluded: chain K residue 199 ASP Chi-restraints excluded: chain K residue 240 THR Chi-restraints excluded: chain K residue 257 VAL Chi-restraints excluded: chain L residue 20 LEU Chi-restraints excluded: chain L residue 26 SER Chi-restraints excluded: chain L residue 32 VAL Chi-restraints excluded: chain L residue 42 LEU Chi-restraints excluded: chain L residue 102 VAL Chi-restraints excluded: chain L residue 240 THR Chi-restraints excluded: chain L residue 257 VAL Chi-restraints excluded: chain M residue 20 LEU Chi-restraints excluded: chain M residue 26 SER Chi-restraints excluded: chain M residue 42 LEU Chi-restraints excluded: chain M residue 102 VAL Chi-restraints excluded: chain M residue 240 THR Chi-restraints excluded: chain M residue 297 SER Chi-restraints excluded: chain N residue 20 LEU Chi-restraints excluded: chain N residue 26 SER Chi-restraints excluded: chain N residue 42 LEU Chi-restraints excluded: chain N residue 102 VAL Chi-restraints excluded: chain N residue 257 VAL Chi-restraints excluded: chain O residue 20 LEU Chi-restraints excluded: chain O residue 46 GLN Chi-restraints excluded: chain O residue 102 VAL Chi-restraints excluded: chain O residue 199 ASP Chi-restraints excluded: chain O residue 225 PHE Chi-restraints excluded: chain O residue 257 VAL Chi-restraints excluded: chain P residue 20 LEU Chi-restraints excluded: chain P residue 26 SER Chi-restraints excluded: chain P residue 102 VAL Chi-restraints excluded: chain P residue 199 ASP Chi-restraints excluded: chain P residue 216 VAL Chi-restraints excluded: chain P residue 240 THR Chi-restraints excluded: chain P residue 262 GLN Chi-restraints excluded: chain P residue 293 THR Chi-restraints excluded: chain P residue 297 SER Chi-restraints excluded: chain Q residue 20 LEU Chi-restraints excluded: chain R residue 20 LEU Chi-restraints excluded: chain R residue 23 THR Chi-restraints excluded: chain R residue 42 LEU Chi-restraints excluded: chain R residue 82 VAL Chi-restraints excluded: chain R residue 225 PHE Chi-restraints excluded: chain R residue 257 VAL Chi-restraints excluded: chain S residue 20 LEU Chi-restraints excluded: chain S residue 23 THR Chi-restraints excluded: chain S residue 82 VAL Chi-restraints excluded: chain S residue 83 LEU Chi-restraints excluded: chain S residue 102 VAL Chi-restraints excluded: chain S residue 108 SER Chi-restraints excluded: chain S residue 126 LEU Chi-restraints excluded: chain S residue 297 SER Chi-restraints excluded: chain T residue 13 ILE Chi-restraints excluded: chain T residue 20 LEU Chi-restraints excluded: chain T residue 42 LEU Chi-restraints excluded: chain T residue 82 VAL Chi-restraints excluded: chain T residue 102 VAL Chi-restraints excluded: chain T residue 108 SER Chi-restraints excluded: chain T residue 122 THR Chi-restraints excluded: chain T residue 225 PHE Chi-restraints excluded: chain T residue 238 VAL Chi-restraints excluded: chain U residue 20 LEU Chi-restraints excluded: chain U residue 23 THR Chi-restraints excluded: chain U residue 42 LEU Chi-restraints excluded: chain U residue 102 VAL Chi-restraints excluded: chain U residue 108 SER Chi-restraints excluded: chain U residue 122 THR Chi-restraints excluded: chain U residue 297 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 504 random chunks: chunk 163 optimal weight: 20.0000 chunk 438 optimal weight: 6.9990 chunk 96 optimal weight: 6.9990 chunk 286 optimal weight: 6.9990 chunk 120 optimal weight: 6.9990 chunk 487 optimal weight: 5.9990 chunk 404 optimal weight: 9.9990 chunk 225 optimal weight: 9.9990 chunk 40 optimal weight: 6.9990 chunk 161 optimal weight: 7.9990 chunk 256 optimal weight: 0.5980 overall best weight: 5.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 264 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 264 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 264 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 46 GLN M 46 GLN ** M 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 46 GLN O 46 GLN O 200 GLN ** P 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 273 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 46 GLN S 121 GLN U 46 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7846 moved from start: 0.4469 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.080 39837 Z= 0.265 Angle : 0.649 10.843 54663 Z= 0.338 Chirality : 0.046 0.197 6552 Planarity : 0.003 0.041 6909 Dihedral : 5.314 51.013 5342 Min Nonbonded Distance : 2.134 Molprobity Statistics. All-atom Clashscore : 10.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.54 % Favored : 95.46 % Rotamer: Outliers : 4.27 % Allowed : 19.72 % Favored : 76.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.32 (0.12), residues: 4998 helix: 2.77 (0.19), residues: 714 sheet: 0.49 (0.12), residues: 1806 loop : -0.76 (0.12), residues: 2478 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP O 211 HIS 0.005 0.001 HIS O 105 PHE 0.014 0.001 PHE S 237 TYR 0.027 0.002 TYR S 98 ARG 0.003 0.001 ARG A 226 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9996 Ramachandran restraints generated. 4998 Oldfield, 0 Emsley, 4998 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9996 Ramachandran restraints generated. 4998 Oldfield, 0 Emsley, 4998 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1007 residues out of total 4305 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 184 poor density : 823 time to evaluate : 4.330 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: A 233 LYS cc_start: 0.8296 (mttt) cc_final: 0.7903 (mmmm) REVERT: A 239 ASN cc_start: 0.8895 (m-40) cc_final: 0.8273 (p0) REVERT: A 286 MET cc_start: 0.9031 (mtt) cc_final: 0.8783 (mtp) REVERT: B 233 LYS cc_start: 0.8419 (mttt) cc_final: 0.7860 (mmmm) REVERT: B 239 ASN cc_start: 0.8967 (m-40) cc_final: 0.8427 (p0) REVERT: B 279 MET cc_start: 0.8455 (mtt) cc_final: 0.7859 (mtt) REVERT: C 279 MET cc_start: 0.8327 (mtt) cc_final: 0.7358 (mtt) REVERT: D 111 MET cc_start: 0.8305 (ttm) cc_final: 0.7968 (ttm) REVERT: D 115 ASP cc_start: 0.8805 (t0) cc_final: 0.8502 (t0) REVERT: D 201 TYR cc_start: 0.8901 (m-10) cc_final: 0.8614 (m-10) REVERT: D 233 LYS cc_start: 0.8061 (mttt) cc_final: 0.7751 (mmmm) REVERT: D 236 ARG cc_start: 0.7490 (ttm-80) cc_final: 0.7225 (ttm-80) REVERT: E 115 ASP cc_start: 0.8812 (t0) cc_final: 0.8440 (t0) REVERT: E 212 GLU cc_start: 0.7349 (mt-10) cc_final: 0.7112 (mt-10) REVERT: E 233 LYS cc_start: 0.7936 (mttt) cc_final: 0.7423 (mmmm) REVERT: E 239 ASN cc_start: 0.8796 (m-40) cc_final: 0.8091 (p0) REVERT: F 198 ASP cc_start: 0.8613 (t0) cc_final: 0.7805 (p0) REVERT: F 201 TYR cc_start: 0.8900 (m-80) cc_final: 0.8559 (m-80) REVERT: F 212 GLU cc_start: 0.7582 (mt-10) cc_final: 0.7300 (mt-10) REVERT: F 233 LYS cc_start: 0.8230 (mttt) cc_final: 0.7849 (mmmm) REVERT: F 239 ASN cc_start: 0.9014 (m-40) cc_final: 0.8182 (p0) REVERT: F 267 VAL cc_start: 0.8978 (t) cc_final: 0.8726 (m) REVERT: G 114 ASP cc_start: 0.8816 (t70) cc_final: 0.8473 (t0) REVERT: G 115 ASP cc_start: 0.9002 (t0) cc_final: 0.8622 (t0) REVERT: G 201 TYR cc_start: 0.9152 (m-80) cc_final: 0.8558 (m-80) REVERT: G 233 LYS cc_start: 0.8301 (mttt) cc_final: 0.7823 (mmmm) REVERT: H 114 ASP cc_start: 0.8789 (t0) cc_final: 0.8436 (t0) REVERT: H 233 LYS cc_start: 0.8295 (mttt) cc_final: 0.7823 (mmmm) REVERT: H 239 ASN cc_start: 0.9024 (m-40) cc_final: 0.8437 (p0) REVERT: I 62 LYS cc_start: 0.8161 (pttp) cc_final: 0.7824 (mttt) REVERT: I 201 TYR cc_start: 0.8926 (m-80) cc_final: 0.8522 (m-80) REVERT: I 233 LYS cc_start: 0.7953 (mttt) cc_final: 0.7629 (mmmm) REVERT: J 62 LYS cc_start: 0.8519 (pttp) cc_final: 0.8264 (mttp) REVERT: J 115 ASP cc_start: 0.8983 (t0) cc_final: 0.8640 (t0) REVERT: J 233 LYS cc_start: 0.8220 (mttt) cc_final: 0.7650 (mmmm) REVERT: J 239 ASN cc_start: 0.9122 (m-40) cc_final: 0.8459 (p0) REVERT: J 267 VAL cc_start: 0.8861 (t) cc_final: 0.8654 (m) REVERT: J 279 MET cc_start: 0.8376 (mtt) cc_final: 0.7851 (mtt) REVERT: K 62 LYS cc_start: 0.8394 (pttp) cc_final: 0.7958 (mttt) REVERT: K 63 ASP cc_start: 0.8556 (m-30) cc_final: 0.8327 (t70) REVERT: K 198 ASP cc_start: 0.8398 (t70) cc_final: 0.7814 (p0) REVERT: K 201 TYR cc_start: 0.8932 (m-80) cc_final: 0.8143 (m-80) REVERT: K 233 LYS cc_start: 0.8145 (mttt) cc_final: 0.7756 (mmmm) REVERT: K 239 ASN cc_start: 0.8409 (m110) cc_final: 0.7699 (p0) REVERT: K 267 VAL cc_start: 0.9219 (t) cc_final: 0.8934 (m) REVERT: K 279 MET cc_start: 0.8028 (mtt) cc_final: 0.7634 (mtt) REVERT: L 62 LYS cc_start: 0.8845 (pttp) cc_final: 0.8123 (mttp) REVERT: L 114 ASP cc_start: 0.8830 (t0) cc_final: 0.8605 (t70) REVERT: L 233 LYS cc_start: 0.8264 (mttt) cc_final: 0.7656 (mmmm) REVERT: L 236 ARG cc_start: 0.7315 (ttm170) cc_final: 0.7018 (ttm170) REVERT: M 46 GLN cc_start: 0.8576 (OUTLIER) cc_final: 0.8269 (pm20) REVERT: M 233 LYS cc_start: 0.8338 (mttt) cc_final: 0.7800 (mmmm) REVERT: N 62 LYS cc_start: 0.8173 (pttp) cc_final: 0.7853 (mttp) REVERT: N 233 LYS cc_start: 0.8094 (mttt) cc_final: 0.7414 (mmmm) REVERT: N 279 MET cc_start: 0.8080 (mtt) cc_final: 0.7497 (mtt) REVERT: N 285 LYS cc_start: 0.8903 (tttt) cc_final: 0.8662 (tttt) REVERT: O 62 LYS cc_start: 0.8471 (pttp) cc_final: 0.8159 (mttp) REVERT: O 94 ILE cc_start: 0.9303 (mt) cc_final: 0.9090 (tt) REVERT: O 214 ASN cc_start: 0.8697 (t0) cc_final: 0.7939 (p0) REVERT: O 236 ARG cc_start: 0.3969 (tpt170) cc_final: 0.3261 (tpt170) REVERT: O 279 MET cc_start: 0.7579 (mtt) cc_final: 0.6900 (mtt) REVERT: P 198 ASP cc_start: 0.8636 (t0) cc_final: 0.8403 (t0) REVERT: P 201 TYR cc_start: 0.8986 (m-80) cc_final: 0.8591 (m-80) REVERT: P 233 LYS cc_start: 0.8025 (mttt) cc_final: 0.7528 (mmmm) REVERT: P 262 GLN cc_start: 0.8134 (OUTLIER) cc_final: 0.7758 (pp30) REVERT: Q 116 LYS cc_start: 0.8941 (mttt) cc_final: 0.8573 (pttt) REVERT: Q 236 ARG cc_start: 0.4568 (tpt170) cc_final: 0.4093 (tpp-160) REVERT: R 62 LYS cc_start: 0.8921 (pttp) cc_final: 0.8051 (mttp) REVERT: R 63 ASP cc_start: 0.8711 (t70) cc_final: 0.8411 (t70) REVERT: R 225 PHE cc_start: 0.8697 (OUTLIER) cc_final: 0.8430 (t80) REVERT: R 239 ASN cc_start: 0.8842 (m-40) cc_final: 0.8393 (p0) REVERT: S 62 LYS cc_start: 0.8368 (pttp) cc_final: 0.7713 (mttp) REVERT: S 290 ASP cc_start: 0.8600 (p0) cc_final: 0.8355 (p0) REVERT: T 62 LYS cc_start: 0.8209 (pttp) cc_final: 0.7933 (mttp) REVERT: T 63 ASP cc_start: 0.8751 (t70) cc_final: 0.8519 (t70) REVERT: T 225 PHE cc_start: 0.8702 (OUTLIER) cc_final: 0.8431 (t80) REVERT: T 233 LYS cc_start: 0.7791 (mmmm) cc_final: 0.7503 (mmmm) REVERT: T 275 ASN cc_start: 0.8609 (t0) cc_final: 0.8323 (t0) REVERT: T 279 MET cc_start: 0.8443 (mtt) cc_final: 0.8068 (mtt) REVERT: U 115 ASP cc_start: 0.8843 (t0) cc_final: 0.8485 (t0) REVERT: U 116 LYS cc_start: 0.9074 (mttt) cc_final: 0.8600 (pttt) outliers start: 184 outliers final: 156 residues processed: 942 average time/residue: 0.4601 time to fit residues: 724.5583 Evaluate side-chains 957 residues out of total 4305 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 160 poor density : 797 time to evaluate : 4.667 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 VAL Chi-restraints excluded: chain A residue 20 LEU Chi-restraints excluded: chain A residue 26 SER Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 42 LEU Chi-restraints excluded: chain A residue 104 CYS Chi-restraints excluded: chain A residue 293 THR Chi-restraints excluded: chain B residue 26 SER Chi-restraints excluded: chain B residue 37 VAL Chi-restraints excluded: chain B residue 42 LEU Chi-restraints excluded: chain B residue 95 ASP Chi-restraints excluded: chain B residue 108 SER Chi-restraints excluded: chain B residue 293 THR Chi-restraints excluded: chain C residue 20 LEU Chi-restraints excluded: chain C residue 26 SER Chi-restraints excluded: chain C residue 37 VAL Chi-restraints excluded: chain C residue 42 LEU Chi-restraints excluded: chain C residue 240 THR Chi-restraints excluded: chain D residue 1 VAL Chi-restraints excluded: chain D residue 12 LEU Chi-restraints excluded: chain D residue 26 SER Chi-restraints excluded: chain D residue 42 LEU Chi-restraints excluded: chain D residue 104 CYS Chi-restraints excluded: chain D residue 246 THR Chi-restraints excluded: chain E residue 1 VAL Chi-restraints excluded: chain E residue 26 SER Chi-restraints excluded: chain E residue 42 LEU Chi-restraints excluded: chain E residue 44 LEU Chi-restraints excluded: chain E residue 102 VAL Chi-restraints excluded: chain E residue 293 THR Chi-restraints excluded: chain F residue 12 LEU Chi-restraints excluded: chain F residue 20 LEU Chi-restraints excluded: chain F residue 26 SER Chi-restraints excluded: chain F residue 37 VAL Chi-restraints excluded: chain F residue 42 LEU Chi-restraints excluded: chain F residue 102 VAL Chi-restraints excluded: chain F residue 115 ASP Chi-restraints excluded: chain F residue 199 ASP Chi-restraints excluded: chain F residue 282 VAL Chi-restraints excluded: chain F residue 293 THR Chi-restraints excluded: chain F residue 297 SER Chi-restraints excluded: chain G residue 20 LEU Chi-restraints excluded: chain G residue 26 SER Chi-restraints excluded: chain G residue 95 ASP Chi-restraints excluded: chain G residue 102 VAL Chi-restraints excluded: chain G residue 199 ASP Chi-restraints excluded: chain G residue 240 THR Chi-restraints excluded: chain G residue 257 VAL Chi-restraints excluded: chain G residue 297 SER Chi-restraints excluded: chain H residue 1 VAL Chi-restraints excluded: chain H residue 12 LEU Chi-restraints excluded: chain H residue 26 SER Chi-restraints excluded: chain H residue 115 ASP Chi-restraints excluded: chain H residue 198 ASP Chi-restraints excluded: chain H residue 199 ASP Chi-restraints excluded: chain H residue 225 PHE Chi-restraints excluded: chain H residue 240 THR Chi-restraints excluded: chain H residue 293 THR Chi-restraints excluded: chain I residue 1 VAL Chi-restraints excluded: chain I residue 26 SER Chi-restraints excluded: chain I residue 42 LEU Chi-restraints excluded: chain I residue 102 VAL Chi-restraints excluded: chain I residue 240 THR Chi-restraints excluded: chain I residue 297 SER Chi-restraints excluded: chain J residue 1 VAL Chi-restraints excluded: chain J residue 26 SER Chi-restraints excluded: chain J residue 42 LEU Chi-restraints excluded: chain J residue 102 VAL Chi-restraints excluded: chain J residue 199 ASP Chi-restraints excluded: chain J residue 240 THR Chi-restraints excluded: chain J residue 257 VAL Chi-restraints excluded: chain J residue 297 SER Chi-restraints excluded: chain K residue 12 LEU Chi-restraints excluded: chain K residue 20 LEU Chi-restraints excluded: chain K residue 26 SER Chi-restraints excluded: chain K residue 102 VAL Chi-restraints excluded: chain K residue 199 ASP Chi-restraints excluded: chain K residue 240 THR Chi-restraints excluded: chain K residue 262 GLN Chi-restraints excluded: chain L residue 20 LEU Chi-restraints excluded: chain L residue 26 SER Chi-restraints excluded: chain L residue 42 LEU Chi-restraints excluded: chain L residue 45 ILE Chi-restraints excluded: chain L residue 95 ASP Chi-restraints excluded: chain L residue 102 VAL Chi-restraints excluded: chain L residue 115 ASP Chi-restraints excluded: chain L residue 240 THR Chi-restraints excluded: chain L residue 293 THR Chi-restraints excluded: chain M residue 20 LEU Chi-restraints excluded: chain M residue 26 SER Chi-restraints excluded: chain M residue 42 LEU Chi-restraints excluded: chain M residue 46 GLN Chi-restraints excluded: chain M residue 97 LEU Chi-restraints excluded: chain M residue 102 VAL Chi-restraints excluded: chain M residue 240 THR Chi-restraints excluded: chain M residue 297 SER Chi-restraints excluded: chain N residue 20 LEU Chi-restraints excluded: chain N residue 26 SER Chi-restraints excluded: chain N residue 42 LEU Chi-restraints excluded: chain N residue 46 GLN Chi-restraints excluded: chain N residue 102 VAL Chi-restraints excluded: chain N residue 257 VAL Chi-restraints excluded: chain O residue 20 LEU Chi-restraints excluded: chain O residue 102 VAL Chi-restraints excluded: chain O residue 199 ASP Chi-restraints excluded: chain O residue 225 PHE Chi-restraints excluded: chain O residue 257 VAL Chi-restraints excluded: chain O residue 293 THR Chi-restraints excluded: chain P residue 20 LEU Chi-restraints excluded: chain P residue 26 SER Chi-restraints excluded: chain P residue 91 ILE Chi-restraints excluded: chain P residue 102 VAL Chi-restraints excluded: chain P residue 199 ASP Chi-restraints excluded: chain P residue 216 VAL Chi-restraints excluded: chain P residue 240 THR Chi-restraints excluded: chain P residue 262 GLN Chi-restraints excluded: chain P residue 293 THR Chi-restraints excluded: chain P residue 297 SER Chi-restraints excluded: chain Q residue 20 LEU Chi-restraints excluded: chain Q residue 23 THR Chi-restraints excluded: chain Q residue 95 ASP Chi-restraints excluded: chain Q residue 257 VAL Chi-restraints excluded: chain R residue 20 LEU Chi-restraints excluded: chain R residue 23 THR Chi-restraints excluded: chain R residue 26 SER Chi-restraints excluded: chain R residue 46 GLN Chi-restraints excluded: chain R residue 82 VAL Chi-restraints excluded: chain R residue 225 PHE Chi-restraints excluded: chain R residue 293 THR Chi-restraints excluded: chain S residue 1 VAL Chi-restraints excluded: chain S residue 20 LEU Chi-restraints excluded: chain S residue 23 THR Chi-restraints excluded: chain S residue 82 VAL Chi-restraints excluded: chain S residue 83 LEU Chi-restraints excluded: chain S residue 108 SER Chi-restraints excluded: chain S residue 121 GLN Chi-restraints excluded: chain S residue 126 LEU Chi-restraints excluded: chain S residue 293 THR Chi-restraints excluded: chain S residue 297 SER Chi-restraints excluded: chain T residue 13 ILE Chi-restraints excluded: chain T residue 20 LEU Chi-restraints excluded: chain T residue 23 THR Chi-restraints excluded: chain T residue 42 LEU Chi-restraints excluded: chain T residue 82 VAL Chi-restraints excluded: chain T residue 102 VAL Chi-restraints excluded: chain T residue 108 SER Chi-restraints excluded: chain T residue 122 THR Chi-restraints excluded: chain T residue 225 PHE Chi-restraints excluded: chain T residue 238 VAL Chi-restraints excluded: chain T residue 240 THR Chi-restraints excluded: chain T residue 277 ASN Chi-restraints excluded: chain U residue 20 LEU Chi-restraints excluded: chain U residue 23 THR Chi-restraints excluded: chain U residue 42 LEU Chi-restraints excluded: chain U residue 46 GLN Chi-restraints excluded: chain U residue 102 VAL Chi-restraints excluded: chain U residue 108 SER Chi-restraints excluded: chain U residue 122 THR Chi-restraints excluded: chain U residue 293 THR Chi-restraints excluded: chain U residue 297 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 504 random chunks: chunk 470 optimal weight: 10.0000 chunk 54 optimal weight: 20.0000 chunk 277 optimal weight: 0.0020 chunk 356 optimal weight: 6.9990 chunk 275 optimal weight: 7.9990 chunk 410 optimal weight: 7.9990 chunk 272 optimal weight: 0.9980 chunk 485 optimal weight: 20.0000 chunk 304 optimal weight: 0.0040 chunk 296 optimal weight: 9.9990 chunk 224 optimal weight: 0.0370 overall best weight: 1.6080 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 264 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 264 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 46 GLN K 219 ASN L 219 ASN L 239 ASN ** M 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 273 ASN ** Q 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 219 ASN U 84 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7801 moved from start: 0.4639 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.081 39837 Z= 0.170 Angle : 0.622 11.712 54663 Z= 0.315 Chirality : 0.046 0.222 6552 Planarity : 0.003 0.037 6909 Dihedral : 5.034 47.612 5342 Min Nonbonded Distance : 2.125 Molprobity Statistics. All-atom Clashscore : 9.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.38 % Favored : 95.62 % Rotamer: Outliers : 2.93 % Allowed : 21.05 % Favored : 76.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.44 (0.12), residues: 4998 helix: 2.84 (0.19), residues: 714 sheet: 0.69 (0.12), residues: 1701 loop : -0.73 (0.12), residues: 2583 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP O 211 HIS 0.004 0.001 HIS O 105 PHE 0.017 0.001 PHE S 237 TYR 0.025 0.001 TYR I 98 ARG 0.002 0.000 ARG L 236 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9996 Ramachandran restraints generated. 4998 Oldfield, 0 Emsley, 4998 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9996 Ramachandran restraints generated. 4998 Oldfield, 0 Emsley, 4998 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 952 residues out of total 4305 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 126 poor density : 826 time to evaluate : 6.766 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: A 233 LYS cc_start: 0.8265 (mttt) cc_final: 0.7877 (mmmm) REVERT: A 239 ASN cc_start: 0.8882 (m-40) cc_final: 0.8288 (p0) REVERT: A 286 MET cc_start: 0.9015 (mtt) cc_final: 0.8786 (mtp) REVERT: B 233 LYS cc_start: 0.8355 (mttt) cc_final: 0.7812 (mmmm) REVERT: B 239 ASN cc_start: 0.8936 (m-40) cc_final: 0.8407 (p0) REVERT: B 279 MET cc_start: 0.8381 (mtt) cc_final: 0.7841 (mtt) REVERT: C 279 MET cc_start: 0.8226 (mtt) cc_final: 0.7323 (mtt) REVERT: D 115 ASP cc_start: 0.8707 (t0) cc_final: 0.8398 (t0) REVERT: D 201 TYR cc_start: 0.8845 (m-10) cc_final: 0.8626 (m-10) REVERT: D 233 LYS cc_start: 0.7984 (mttt) cc_final: 0.7706 (mmmm) REVERT: D 236 ARG cc_start: 0.7445 (ttm-80) cc_final: 0.7198 (ttm-80) REVERT: D 239 ASN cc_start: 0.8865 (m110) cc_final: 0.8246 (p0) REVERT: E 212 GLU cc_start: 0.7247 (mt-10) cc_final: 0.7035 (mt-10) REVERT: E 233 LYS cc_start: 0.7891 (mttt) cc_final: 0.7425 (mmmm) REVERT: E 239 ASN cc_start: 0.8772 (m-40) cc_final: 0.8065 (p0) REVERT: F 198 ASP cc_start: 0.8604 (t0) cc_final: 0.7973 (p0) REVERT: F 201 TYR cc_start: 0.8854 (m-80) cc_final: 0.8621 (m-80) REVERT: F 212 GLU cc_start: 0.7626 (mt-10) cc_final: 0.7395 (mt-10) REVERT: F 233 LYS cc_start: 0.8181 (mttt) cc_final: 0.7831 (mmmm) REVERT: F 239 ASN cc_start: 0.8982 (m-40) cc_final: 0.8163 (p0) REVERT: F 267 VAL cc_start: 0.8960 (t) cc_final: 0.8735 (m) REVERT: G 114 ASP cc_start: 0.8793 (t70) cc_final: 0.8471 (t0) REVERT: G 115 ASP cc_start: 0.8912 (t0) cc_final: 0.8533 (t0) REVERT: G 201 TYR cc_start: 0.9153 (m-80) cc_final: 0.8607 (m-80) REVERT: G 233 LYS cc_start: 0.8263 (mttt) cc_final: 0.7818 (mmmm) REVERT: H 114 ASP cc_start: 0.8757 (t0) cc_final: 0.8411 (t0) REVERT: H 233 LYS cc_start: 0.8249 (mttt) cc_final: 0.7796 (mmmm) REVERT: H 239 ASN cc_start: 0.8988 (m-40) cc_final: 0.8432 (p0) REVERT: I 62 LYS cc_start: 0.8166 (pttp) cc_final: 0.7816 (mttt) REVERT: I 201 TYR cc_start: 0.8877 (m-80) cc_final: 0.8499 (m-80) REVERT: I 233 LYS cc_start: 0.7861 (mttt) cc_final: 0.7586 (mmmm) REVERT: I 239 ASN cc_start: 0.8563 (m110) cc_final: 0.7897 (p0) REVERT: J 46 GLN cc_start: 0.8747 (pt0) cc_final: 0.8417 (pm20) REVERT: J 115 ASP cc_start: 0.8875 (t0) cc_final: 0.8603 (t70) REVERT: J 117 TYR cc_start: 0.7858 (t80) cc_final: 0.7573 (t80) REVERT: J 233 LYS cc_start: 0.8138 (mttt) cc_final: 0.7539 (mmmm) REVERT: J 239 ASN cc_start: 0.9020 (m-40) cc_final: 0.8435 (p0) REVERT: K 62 LYS cc_start: 0.8376 (pttp) cc_final: 0.7944 (mttt) REVERT: K 63 ASP cc_start: 0.8604 (m-30) cc_final: 0.8275 (t70) REVERT: K 107 ASP cc_start: 0.7263 (p0) cc_final: 0.6989 (t0) REVERT: K 198 ASP cc_start: 0.8402 (t70) cc_final: 0.7908 (p0) REVERT: K 201 TYR cc_start: 0.8876 (m-80) cc_final: 0.8126 (m-80) REVERT: K 233 LYS cc_start: 0.8096 (mttt) cc_final: 0.7739 (mmmm) REVERT: K 239 ASN cc_start: 0.8344 (m110) cc_final: 0.7674 (p0) REVERT: K 267 VAL cc_start: 0.9203 (t) cc_final: 0.8959 (m) REVERT: K 279 MET cc_start: 0.8010 (mtt) cc_final: 0.7651 (mtt) REVERT: L 62 LYS cc_start: 0.8764 (pttp) cc_final: 0.8059 (mttp) REVERT: L 107 ASP cc_start: 0.7287 (p0) cc_final: 0.6940 (t0) REVERT: L 114 ASP cc_start: 0.8781 (t0) cc_final: 0.8560 (t70) REVERT: L 233 LYS cc_start: 0.8231 (mttt) cc_final: 0.7657 (mmmm) REVERT: M 107 ASP cc_start: 0.7376 (p0) cc_final: 0.7125 (t0) REVERT: M 233 LYS cc_start: 0.8306 (mttt) cc_final: 0.7799 (mmmm) REVERT: M 279 MET cc_start: 0.8388 (mtt) cc_final: 0.7727 (mtt) REVERT: N 21 LEU cc_start: 0.9244 (tt) cc_final: 0.8958 (tp) REVERT: N 62 LYS cc_start: 0.8191 (pttp) cc_final: 0.7881 (mttp) REVERT: N 233 LYS cc_start: 0.8067 (mttt) cc_final: 0.7411 (mmmm) REVERT: N 279 MET cc_start: 0.8064 (mtt) cc_final: 0.7377 (mtt) REVERT: N 285 LYS cc_start: 0.8848 (tttt) cc_final: 0.8599 (tttt) REVERT: O 62 LYS cc_start: 0.8563 (pttp) cc_final: 0.8160 (mttt) REVERT: O 111 MET cc_start: 0.8008 (ttt) cc_final: 0.7796 (ttm) REVERT: O 214 ASN cc_start: 0.8629 (t0) cc_final: 0.8041 (p0) REVERT: O 236 ARG cc_start: 0.4063 (tpt170) cc_final: 0.3360 (tpt170) REVERT: O 279 MET cc_start: 0.7592 (mtt) cc_final: 0.6787 (mtt) REVERT: O 300 LEU cc_start: 0.8893 (tp) cc_final: 0.8533 (tt) REVERT: P 198 ASP cc_start: 0.8604 (t0) cc_final: 0.7931 (p0) REVERT: P 201 TYR cc_start: 0.8933 (m-80) cc_final: 0.8293 (m-80) REVERT: P 233 LYS cc_start: 0.7955 (mttt) cc_final: 0.7492 (mmmm) REVERT: P 262 GLN cc_start: 0.8074 (OUTLIER) cc_final: 0.7692 (pp30) REVERT: P 279 MET cc_start: 0.8321 (mtt) cc_final: 0.8104 (mtp) REVERT: Q 116 LYS cc_start: 0.8903 (mttt) cc_final: 0.8536 (pttt) REVERT: Q 236 ARG cc_start: 0.4470 (tpt170) cc_final: 0.4000 (tpp-160) REVERT: R 62 LYS cc_start: 0.8779 (pttp) cc_final: 0.8001 (mttp) REVERT: R 63 ASP cc_start: 0.8646 (t70) cc_final: 0.8363 (t70) REVERT: R 225 PHE cc_start: 0.8760 (OUTLIER) cc_final: 0.8448 (t80) REVERT: R 239 ASN cc_start: 0.8791 (m-40) cc_final: 0.8360 (p0) REVERT: S 62 LYS cc_start: 0.8366 (pttp) cc_final: 0.7705 (mttp) REVERT: S 290 ASP cc_start: 0.8575 (p0) cc_final: 0.8307 (p0) REVERT: T 62 LYS cc_start: 0.8206 (pttp) cc_final: 0.7886 (mttp) REVERT: T 63 ASP cc_start: 0.8670 (t70) cc_final: 0.8468 (t70) REVERT: T 225 PHE cc_start: 0.8684 (OUTLIER) cc_final: 0.8374 (t80) REVERT: T 233 LYS cc_start: 0.7785 (mmmm) cc_final: 0.7546 (mmmm) REVERT: U 115 ASP cc_start: 0.8822 (t0) cc_final: 0.8441 (t0) REVERT: U 116 LYS cc_start: 0.9043 (mttt) cc_final: 0.8579 (pttt) outliers start: 126 outliers final: 106 residues processed: 919 average time/residue: 0.4659 time to fit residues: 713.9428 Evaluate side-chains 909 residues out of total 4305 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 109 poor density : 800 time to evaluate : 4.596 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 VAL Chi-restraints excluded: chain A residue 20 LEU Chi-restraints excluded: chain A residue 26 SER Chi-restraints excluded: chain A residue 42 LEU Chi-restraints excluded: chain A residue 104 CYS Chi-restraints excluded: chain A residue 293 THR Chi-restraints excluded: chain B residue 26 SER Chi-restraints excluded: chain B residue 42 LEU Chi-restraints excluded: chain B residue 257 VAL Chi-restraints excluded: chain B residue 293 THR Chi-restraints excluded: chain C residue 20 LEU Chi-restraints excluded: chain C residue 26 SER Chi-restraints excluded: chain C residue 42 LEU Chi-restraints excluded: chain C residue 240 THR Chi-restraints excluded: chain D residue 1 VAL Chi-restraints excluded: chain D residue 26 SER Chi-restraints excluded: chain D residue 42 LEU Chi-restraints excluded: chain D residue 104 CYS Chi-restraints excluded: chain E residue 1 VAL Chi-restraints excluded: chain E residue 26 SER Chi-restraints excluded: chain E residue 42 LEU Chi-restraints excluded: chain E residue 102 VAL Chi-restraints excluded: chain E residue 293 THR Chi-restraints excluded: chain F residue 12 LEU Chi-restraints excluded: chain F residue 20 LEU Chi-restraints excluded: chain F residue 26 SER Chi-restraints excluded: chain F residue 42 LEU Chi-restraints excluded: chain F residue 102 VAL Chi-restraints excluded: chain F residue 115 ASP Chi-restraints excluded: chain F residue 199 ASP Chi-restraints excluded: chain F residue 282 VAL Chi-restraints excluded: chain F residue 293 THR Chi-restraints excluded: chain G residue 20 LEU Chi-restraints excluded: chain G residue 26 SER Chi-restraints excluded: chain G residue 102 VAL Chi-restraints excluded: chain G residue 199 ASP Chi-restraints excluded: chain G residue 240 THR Chi-restraints excluded: chain G residue 257 VAL Chi-restraints excluded: chain H residue 12 LEU Chi-restraints excluded: chain H residue 26 SER Chi-restraints excluded: chain H residue 115 ASP Chi-restraints excluded: chain H residue 199 ASP Chi-restraints excluded: chain H residue 225 PHE Chi-restraints excluded: chain H residue 240 THR Chi-restraints excluded: chain I residue 1 VAL Chi-restraints excluded: chain I residue 26 SER Chi-restraints excluded: chain I residue 42 LEU Chi-restraints excluded: chain I residue 46 GLN Chi-restraints excluded: chain I residue 102 VAL Chi-restraints excluded: chain I residue 199 ASP Chi-restraints excluded: chain I residue 240 THR Chi-restraints excluded: chain I residue 297 SER Chi-restraints excluded: chain J residue 1 VAL Chi-restraints excluded: chain J residue 26 SER Chi-restraints excluded: chain J residue 42 LEU Chi-restraints excluded: chain J residue 102 VAL Chi-restraints excluded: chain J residue 199 ASP Chi-restraints excluded: chain J residue 240 THR Chi-restraints excluded: chain J residue 257 VAL Chi-restraints excluded: chain K residue 20 LEU Chi-restraints excluded: chain K residue 26 SER Chi-restraints excluded: chain K residue 102 VAL Chi-restraints excluded: chain K residue 199 ASP Chi-restraints excluded: chain K residue 240 THR Chi-restraints excluded: chain K residue 262 GLN Chi-restraints excluded: chain L residue 20 LEU Chi-restraints excluded: chain L residue 26 SER Chi-restraints excluded: chain L residue 42 LEU Chi-restraints excluded: chain L residue 102 VAL Chi-restraints excluded: chain L residue 257 VAL Chi-restraints excluded: chain M residue 20 LEU Chi-restraints excluded: chain M residue 26 SER Chi-restraints excluded: chain M residue 102 VAL Chi-restraints excluded: chain M residue 297 SER Chi-restraints excluded: chain N residue 20 LEU Chi-restraints excluded: chain N residue 26 SER Chi-restraints excluded: chain N residue 42 LEU Chi-restraints excluded: chain N residue 102 VAL Chi-restraints excluded: chain N residue 257 VAL Chi-restraints excluded: chain O residue 20 LEU Chi-restraints excluded: chain O residue 102 VAL Chi-restraints excluded: chain O residue 199 ASP Chi-restraints excluded: chain O residue 225 PHE Chi-restraints excluded: chain P residue 20 LEU Chi-restraints excluded: chain P residue 26 SER Chi-restraints excluded: chain P residue 102 VAL Chi-restraints excluded: chain P residue 199 ASP Chi-restraints excluded: chain P residue 262 GLN Chi-restraints excluded: chain Q residue 20 LEU Chi-restraints excluded: chain R residue 20 LEU Chi-restraints excluded: chain R residue 26 SER Chi-restraints excluded: chain R residue 225 PHE Chi-restraints excluded: chain S residue 20 LEU Chi-restraints excluded: chain S residue 82 VAL Chi-restraints excluded: chain S residue 83 LEU Chi-restraints excluded: chain S residue 108 SER Chi-restraints excluded: chain S residue 126 LEU Chi-restraints excluded: chain T residue 20 LEU Chi-restraints excluded: chain T residue 42 LEU Chi-restraints excluded: chain T residue 82 VAL Chi-restraints excluded: chain T residue 102 VAL Chi-restraints excluded: chain T residue 108 SER Chi-restraints excluded: chain T residue 122 THR Chi-restraints excluded: chain T residue 225 PHE Chi-restraints excluded: chain T residue 238 VAL Chi-restraints excluded: chain U residue 20 LEU Chi-restraints excluded: chain U residue 42 LEU Chi-restraints excluded: chain U residue 102 VAL Chi-restraints excluded: chain U residue 122 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 504 random chunks: chunk 300 optimal weight: 4.9990 chunk 193 optimal weight: 5.9990 chunk 290 optimal weight: 5.9990 chunk 146 optimal weight: 7.9990 chunk 95 optimal weight: 4.9990 chunk 94 optimal weight: 5.9990 chunk 308 optimal weight: 20.0000 chunk 330 optimal weight: 0.9990 chunk 240 optimal weight: 0.7980 chunk 45 optimal weight: 0.0370 chunk 381 optimal weight: 9.9990 overall best weight: 2.3664 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 264 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 46 GLN ** E 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 264 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 46 GLN ** M 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 46 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7797 moved from start: 0.4770 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 39837 Z= 0.175 Angle : 0.629 13.518 54663 Z= 0.315 Chirality : 0.046 0.233 6552 Planarity : 0.003 0.039 6909 Dihedral : 4.882 44.913 5340 Min Nonbonded Distance : 2.119 Molprobity Statistics. All-atom Clashscore : 9.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.18 % Favored : 95.82 % Rotamer: Outliers : 3.00 % Allowed : 21.23 % Favored : 75.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.44 (0.12), residues: 4998 helix: 2.78 (0.19), residues: 714 sheet: 0.70 (0.12), residues: 1701 loop : -0.72 (0.12), residues: 2583 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP O 211 HIS 0.005 0.001 HIS O 105 PHE 0.016 0.001 PHE S 237 TYR 0.033 0.001 TYR C 22 ARG 0.002 0.000 ARG F 101 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9996 Ramachandran restraints generated. 4998 Oldfield, 0 Emsley, 4998 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9996 Ramachandran restraints generated. 4998 Oldfield, 0 Emsley, 4998 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 938 residues out of total 4305 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 129 poor density : 809 time to evaluate : 4.600 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 233 LYS cc_start: 0.8321 (mttt) cc_final: 0.7945 (mmmm) REVERT: A 239 ASN cc_start: 0.8895 (m-40) cc_final: 0.8256 (p0) REVERT: A 286 MET cc_start: 0.9016 (mtt) cc_final: 0.8793 (mtp) REVERT: B 233 LYS cc_start: 0.8341 (mttt) cc_final: 0.7820 (mmmm) REVERT: B 239 ASN cc_start: 0.8955 (m-40) cc_final: 0.8375 (p0) REVERT: B 279 MET cc_start: 0.8387 (mtt) cc_final: 0.7773 (mtt) REVERT: C 279 MET cc_start: 0.8127 (mtt) cc_final: 0.7206 (mtt) REVERT: D 115 ASP cc_start: 0.8632 (t0) cc_final: 0.8330 (t0) REVERT: D 201 TYR cc_start: 0.8858 (m-10) cc_final: 0.8626 (m-10) REVERT: D 233 LYS cc_start: 0.7968 (mttt) cc_final: 0.7700 (mmmm) REVERT: D 236 ARG cc_start: 0.7458 (ttm-80) cc_final: 0.7223 (ttm-80) REVERT: D 239 ASN cc_start: 0.8853 (m110) cc_final: 0.8257 (p0) REVERT: E 233 LYS cc_start: 0.7919 (mttt) cc_final: 0.7398 (mmmm) REVERT: E 239 ASN cc_start: 0.8819 (m-40) cc_final: 0.8082 (p0) REVERT: F 198 ASP cc_start: 0.8534 (t0) cc_final: 0.7895 (p0) REVERT: F 201 TYR cc_start: 0.8834 (m-80) cc_final: 0.8610 (m-80) REVERT: F 212 GLU cc_start: 0.7614 (mt-10) cc_final: 0.7411 (mt-10) REVERT: F 233 LYS cc_start: 0.8159 (mttt) cc_final: 0.7818 (mmmm) REVERT: F 239 ASN cc_start: 0.8979 (m-40) cc_final: 0.8143 (p0) REVERT: F 267 VAL cc_start: 0.8967 (t) cc_final: 0.8766 (m) REVERT: F 279 MET cc_start: 0.8142 (mtt) cc_final: 0.7869 (mtp) REVERT: G 81 GLN cc_start: 0.7619 (tm-30) cc_final: 0.7377 (tm-30) REVERT: G 114 ASP cc_start: 0.8775 (t70) cc_final: 0.8437 (t0) REVERT: G 115 ASP cc_start: 0.8918 (t0) cc_final: 0.8541 (t0) REVERT: G 201 TYR cc_start: 0.9169 (m-80) cc_final: 0.8612 (m-80) REVERT: G 233 LYS cc_start: 0.8250 (mttt) cc_final: 0.7817 (mmmm) REVERT: H 114 ASP cc_start: 0.8780 (t0) cc_final: 0.8357 (t0) REVERT: H 233 LYS cc_start: 0.8288 (mttt) cc_final: 0.7849 (mmmm) REVERT: H 239 ASN cc_start: 0.8986 (m-40) cc_final: 0.8411 (p0) REVERT: I 62 LYS cc_start: 0.8157 (pttp) cc_final: 0.7824 (mttt) REVERT: I 121 GLN cc_start: 0.7124 (mt0) cc_final: 0.6919 (mt0) REVERT: I 200 GLN cc_start: 0.8008 (mp10) cc_final: 0.7786 (mp10) REVERT: I 201 TYR cc_start: 0.8859 (m-80) cc_final: 0.8576 (m-80) REVERT: I 233 LYS cc_start: 0.7885 (mttt) cc_final: 0.7640 (mmmm) REVERT: I 239 ASN cc_start: 0.8554 (m110) cc_final: 0.7943 (p0) REVERT: J 115 ASP cc_start: 0.8871 (t0) cc_final: 0.8662 (t70) REVERT: J 117 TYR cc_start: 0.7811 (t80) cc_final: 0.7502 (t80) REVERT: J 233 LYS cc_start: 0.8152 (mttt) cc_final: 0.7741 (mmmm) REVERT: J 239 ASN cc_start: 0.8946 (m-40) cc_final: 0.8430 (p0) REVERT: J 275 ASN cc_start: 0.8345 (t0) cc_final: 0.7836 (t0) REVERT: J 279 MET cc_start: 0.8298 (mtt) cc_final: 0.7735 (mtt) REVERT: K 62 LYS cc_start: 0.8372 (pttp) cc_final: 0.7958 (mttt) REVERT: K 63 ASP cc_start: 0.8584 (m-30) cc_final: 0.8301 (t70) REVERT: K 198 ASP cc_start: 0.8353 (t70) cc_final: 0.7838 (p0) REVERT: K 201 TYR cc_start: 0.8873 (m-80) cc_final: 0.8136 (m-80) REVERT: K 233 LYS cc_start: 0.8075 (mttt) cc_final: 0.7749 (mmmm) REVERT: K 239 ASN cc_start: 0.8334 (m110) cc_final: 0.7677 (p0) REVERT: K 267 VAL cc_start: 0.9212 (t) cc_final: 0.8979 (m) REVERT: K 279 MET cc_start: 0.8087 (mtt) cc_final: 0.7838 (mtm) REVERT: L 62 LYS cc_start: 0.8766 (pttp) cc_final: 0.8032 (mttp) REVERT: L 107 ASP cc_start: 0.7379 (p0) cc_final: 0.7024 (t0) REVERT: L 114 ASP cc_start: 0.8777 (t0) cc_final: 0.8561 (t70) REVERT: L 233 LYS cc_start: 0.8223 (mttt) cc_final: 0.7661 (mmmm) REVERT: L 286 MET cc_start: 0.9045 (mtm) cc_final: 0.8817 (mtm) REVERT: M 46 GLN cc_start: 0.8457 (pt0) cc_final: 0.8257 (pm20) REVERT: M 107 ASP cc_start: 0.7366 (p0) cc_final: 0.7151 (t0) REVERT: M 233 LYS cc_start: 0.8272 (mttt) cc_final: 0.7791 (mmmm) REVERT: M 279 MET cc_start: 0.8422 (mtt) cc_final: 0.7915 (mtt) REVERT: N 62 LYS cc_start: 0.8215 (pttp) cc_final: 0.7894 (mttp) REVERT: N 233 LYS cc_start: 0.8049 (mttt) cc_final: 0.7401 (mmmm) REVERT: N 279 MET cc_start: 0.8085 (mtt) cc_final: 0.7555 (mtt) REVERT: N 285 LYS cc_start: 0.8844 (tttt) cc_final: 0.8595 (tttt) REVERT: O 62 LYS cc_start: 0.8576 (pttp) cc_final: 0.8172 (mttt) REVERT: O 111 MET cc_start: 0.7996 (ttt) cc_final: 0.7781 (ttm) REVERT: O 214 ASN cc_start: 0.8647 (t0) cc_final: 0.8132 (p0) REVERT: O 236 ARG cc_start: 0.4025 (tpt170) cc_final: 0.3301 (tpt170) REVERT: O 279 MET cc_start: 0.7703 (mtt) cc_final: 0.6848 (mtt) REVERT: O 300 LEU cc_start: 0.8933 (tp) cc_final: 0.8586 (tt) REVERT: P 198 ASP cc_start: 0.8594 (t0) cc_final: 0.8336 (t0) REVERT: P 201 TYR cc_start: 0.8914 (m-80) cc_final: 0.8577 (m-80) REVERT: P 233 LYS cc_start: 0.7960 (mttt) cc_final: 0.7491 (mmmm) REVERT: P 262 GLN cc_start: 0.8075 (OUTLIER) cc_final: 0.7663 (pp30) REVERT: Q 116 LYS cc_start: 0.8900 (mttt) cc_final: 0.8498 (pttt) REVERT: Q 236 ARG cc_start: 0.4538 (tpt170) cc_final: 0.4083 (tpp-160) REVERT: R 62 LYS cc_start: 0.8782 (pttp) cc_final: 0.8009 (mttp) REVERT: R 63 ASP cc_start: 0.8689 (t70) cc_final: 0.8414 (t70) REVERT: R 225 PHE cc_start: 0.8753 (OUTLIER) cc_final: 0.8435 (t80) REVERT: R 239 ASN cc_start: 0.8767 (m-40) cc_final: 0.8344 (p0) REVERT: S 62 LYS cc_start: 0.8370 (pttp) cc_final: 0.7704 (mttp) REVERT: S 126 LEU cc_start: 0.8127 (OUTLIER) cc_final: 0.7839 (tp) REVERT: S 290 ASP cc_start: 0.8562 (p0) cc_final: 0.8287 (p0) REVERT: T 62 LYS cc_start: 0.8213 (pttp) cc_final: 0.7888 (mttp) REVERT: T 63 ASP cc_start: 0.8684 (t70) cc_final: 0.8480 (t70) REVERT: T 225 PHE cc_start: 0.8647 (OUTLIER) cc_final: 0.8312 (t80) REVERT: T 233 LYS cc_start: 0.7819 (mmmm) cc_final: 0.7555 (mmmm) REVERT: U 115 ASP cc_start: 0.8762 (t0) cc_final: 0.8419 (t0) REVERT: U 116 LYS cc_start: 0.9014 (mttt) cc_final: 0.8546 (pttt) outliers start: 129 outliers final: 112 residues processed: 899 average time/residue: 0.4729 time to fit residues: 706.9673 Evaluate side-chains 898 residues out of total 4305 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 116 poor density : 782 time to evaluate : 4.614 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 VAL Chi-restraints excluded: chain A residue 26 SER Chi-restraints excluded: chain A residue 104 CYS Chi-restraints excluded: chain A residue 293 THR Chi-restraints excluded: chain B residue 26 SER Chi-restraints excluded: chain B residue 95 ASP Chi-restraints excluded: chain B residue 108 SER Chi-restraints excluded: chain B residue 257 VAL Chi-restraints excluded: chain B residue 293 THR Chi-restraints excluded: chain C residue 20 LEU Chi-restraints excluded: chain C residue 26 SER Chi-restraints excluded: chain C residue 42 LEU Chi-restraints excluded: chain C residue 240 THR Chi-restraints excluded: chain D residue 1 VAL Chi-restraints excluded: chain D residue 26 SER Chi-restraints excluded: chain D residue 42 LEU Chi-restraints excluded: chain D residue 46 GLN Chi-restraints excluded: chain D residue 104 CYS Chi-restraints excluded: chain E residue 1 VAL Chi-restraints excluded: chain E residue 26 SER Chi-restraints excluded: chain E residue 42 LEU Chi-restraints excluded: chain E residue 102 VAL Chi-restraints excluded: chain E residue 293 THR Chi-restraints excluded: chain F residue 12 LEU Chi-restraints excluded: chain F residue 20 LEU Chi-restraints excluded: chain F residue 26 SER Chi-restraints excluded: chain F residue 42 LEU Chi-restraints excluded: chain F residue 102 VAL Chi-restraints excluded: chain F residue 115 ASP Chi-restraints excluded: chain F residue 199 ASP Chi-restraints excluded: chain F residue 293 THR Chi-restraints excluded: chain G residue 20 LEU Chi-restraints excluded: chain G residue 26 SER Chi-restraints excluded: chain G residue 102 VAL Chi-restraints excluded: chain G residue 199 ASP Chi-restraints excluded: chain G residue 240 THR Chi-restraints excluded: chain G residue 257 VAL Chi-restraints excluded: chain H residue 12 LEU Chi-restraints excluded: chain H residue 26 SER Chi-restraints excluded: chain H residue 102 VAL Chi-restraints excluded: chain H residue 115 ASP Chi-restraints excluded: chain H residue 199 ASP Chi-restraints excluded: chain H residue 225 PHE Chi-restraints excluded: chain H residue 240 THR Chi-restraints excluded: chain I residue 1 VAL Chi-restraints excluded: chain I residue 26 SER Chi-restraints excluded: chain I residue 42 LEU Chi-restraints excluded: chain I residue 102 VAL Chi-restraints excluded: chain I residue 199 ASP Chi-restraints excluded: chain I residue 240 THR Chi-restraints excluded: chain J residue 1 VAL Chi-restraints excluded: chain J residue 26 SER Chi-restraints excluded: chain J residue 42 LEU Chi-restraints excluded: chain J residue 102 VAL Chi-restraints excluded: chain J residue 199 ASP Chi-restraints excluded: chain J residue 240 THR Chi-restraints excluded: chain J residue 257 VAL Chi-restraints excluded: chain K residue 12 LEU Chi-restraints excluded: chain K residue 20 LEU Chi-restraints excluded: chain K residue 26 SER Chi-restraints excluded: chain K residue 102 VAL Chi-restraints excluded: chain K residue 199 ASP Chi-restraints excluded: chain K residue 240 THR Chi-restraints excluded: chain K residue 262 GLN Chi-restraints excluded: chain L residue 20 LEU Chi-restraints excluded: chain L residue 26 SER Chi-restraints excluded: chain L residue 42 LEU Chi-restraints excluded: chain L residue 102 VAL Chi-restraints excluded: chain L residue 115 ASP Chi-restraints excluded: chain L residue 240 THR Chi-restraints excluded: chain L residue 257 VAL Chi-restraints excluded: chain M residue 20 LEU Chi-restraints excluded: chain M residue 26 SER Chi-restraints excluded: chain M residue 102 VAL Chi-restraints excluded: chain M residue 297 SER Chi-restraints excluded: chain N residue 20 LEU Chi-restraints excluded: chain N residue 26 SER Chi-restraints excluded: chain N residue 42 LEU Chi-restraints excluded: chain N residue 102 VAL Chi-restraints excluded: chain N residue 257 VAL Chi-restraints excluded: chain O residue 20 LEU Chi-restraints excluded: chain O residue 95 ASP Chi-restraints excluded: chain O residue 102 VAL Chi-restraints excluded: chain O residue 199 ASP Chi-restraints excluded: chain O residue 225 PHE Chi-restraints excluded: chain O residue 257 VAL Chi-restraints excluded: chain P residue 20 LEU Chi-restraints excluded: chain P residue 26 SER Chi-restraints excluded: chain P residue 102 VAL Chi-restraints excluded: chain P residue 199 ASP Chi-restraints excluded: chain P residue 240 THR Chi-restraints excluded: chain P residue 262 GLN Chi-restraints excluded: chain Q residue 20 LEU Chi-restraints excluded: chain Q residue 102 VAL Chi-restraints excluded: chain R residue 20 LEU Chi-restraints excluded: chain R residue 26 SER Chi-restraints excluded: chain R residue 82 VAL Chi-restraints excluded: chain R residue 225 PHE Chi-restraints excluded: chain S residue 20 LEU Chi-restraints excluded: chain S residue 82 VAL Chi-restraints excluded: chain S residue 83 LEU Chi-restraints excluded: chain S residue 108 SER Chi-restraints excluded: chain S residue 126 LEU Chi-restraints excluded: chain T residue 20 LEU Chi-restraints excluded: chain T residue 42 LEU Chi-restraints excluded: chain T residue 102 VAL Chi-restraints excluded: chain T residue 108 SER Chi-restraints excluded: chain T residue 122 THR Chi-restraints excluded: chain T residue 225 PHE Chi-restraints excluded: chain T residue 238 VAL Chi-restraints excluded: chain T residue 293 THR Chi-restraints excluded: chain U residue 20 LEU Chi-restraints excluded: chain U residue 42 LEU Chi-restraints excluded: chain U residue 46 GLN Chi-restraints excluded: chain U residue 102 VAL Chi-restraints excluded: chain U residue 122 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 504 random chunks: chunk 441 optimal weight: 10.0000 chunk 465 optimal weight: 5.9990 chunk 424 optimal weight: 20.0000 chunk 452 optimal weight: 20.0000 chunk 272 optimal weight: 8.9990 chunk 197 optimal weight: 2.9990 chunk 355 optimal weight: 8.9990 chunk 138 optimal weight: 0.0870 chunk 409 optimal weight: 0.8980 chunk 428 optimal weight: 9.9990 chunk 451 optimal weight: 1.9990 overall best weight: 2.3964 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 264 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 264 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 46 GLN ** J 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 46 GLN ** P 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 121 GLN P 200 GLN ** Q 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7792 moved from start: 0.4882 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.072 39837 Z= 0.176 Angle : 0.632 12.648 54663 Z= 0.315 Chirality : 0.046 0.240 6552 Planarity : 0.003 0.039 6909 Dihedral : 4.751 44.674 5336 Min Nonbonded Distance : 2.118 Molprobity Statistics. All-atom Clashscore : 10.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.44 % Favored : 95.56 % Rotamer: Outliers : 2.81 % Allowed : 21.63 % Favored : 75.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.43 (0.12), residues: 4998 helix: 2.75 (0.19), residues: 714 sheet: 0.69 (0.12), residues: 1701 loop : -0.71 (0.12), residues: 2583 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP U 211 HIS 0.004 0.001 HIS G 105 PHE 0.016 0.001 PHE S 237 TYR 0.033 0.001 TYR C 22 ARG 0.003 0.000 ARG M 101 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9996 Ramachandran restraints generated. 4998 Oldfield, 0 Emsley, 4998 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9996 Ramachandran restraints generated. 4998 Oldfield, 0 Emsley, 4998 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 919 residues out of total 4305 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 121 poor density : 798 time to evaluate : 4.264 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 233 LYS cc_start: 0.8291 (mttt) cc_final: 0.7919 (mmmm) REVERT: A 239 ASN cc_start: 0.8901 (m-40) cc_final: 0.8276 (p0) REVERT: A 286 MET cc_start: 0.9020 (mtt) cc_final: 0.8806 (mtp) REVERT: B 233 LYS cc_start: 0.8343 (mttt) cc_final: 0.7852 (mmmm) REVERT: B 239 ASN cc_start: 0.8943 (m-40) cc_final: 0.8356 (p0) REVERT: B 279 MET cc_start: 0.8342 (mtt) cc_final: 0.7754 (mtt) REVERT: C 279 MET cc_start: 0.8121 (mtt) cc_final: 0.7232 (mtt) REVERT: C 294 TRP cc_start: 0.8188 (t-100) cc_final: 0.7754 (t60) REVERT: D 115 ASP cc_start: 0.8625 (t0) cc_final: 0.8301 (t0) REVERT: D 233 LYS cc_start: 0.7954 (mttt) cc_final: 0.7732 (mmmm) REVERT: D 236 ARG cc_start: 0.7440 (ttm-80) cc_final: 0.7201 (ttm-80) REVERT: D 239 ASN cc_start: 0.8836 (m110) cc_final: 0.8255 (p0) REVERT: E 233 LYS cc_start: 0.7910 (mttt) cc_final: 0.7401 (mmmm) REVERT: E 239 ASN cc_start: 0.8832 (m-40) cc_final: 0.8090 (p0) REVERT: F 26 SER cc_start: 0.8957 (OUTLIER) cc_final: 0.8342 (p) REVERT: F 198 ASP cc_start: 0.8525 (t0) cc_final: 0.7900 (p0) REVERT: F 233 LYS cc_start: 0.8127 (mttt) cc_final: 0.7789 (mmmm) REVERT: F 239 ASN cc_start: 0.8972 (m-40) cc_final: 0.8136 (p0) REVERT: F 267 VAL cc_start: 0.8967 (t) cc_final: 0.8765 (m) REVERT: F 279 MET cc_start: 0.8202 (mtt) cc_final: 0.7957 (mtp) REVERT: G 107 ASP cc_start: 0.7836 (p0) cc_final: 0.7443 (t0) REVERT: G 114 ASP cc_start: 0.8783 (t70) cc_final: 0.8439 (t0) REVERT: G 115 ASP cc_start: 0.8919 (t0) cc_final: 0.8546 (t0) REVERT: G 233 LYS cc_start: 0.8183 (mttt) cc_final: 0.7757 (mmmm) REVERT: G 239 ASN cc_start: 0.8724 (m-40) cc_final: 0.8522 (m-40) REVERT: H 114 ASP cc_start: 0.8767 (t0) cc_final: 0.8364 (t0) REVERT: H 233 LYS cc_start: 0.8296 (mttt) cc_final: 0.7853 (mmmm) REVERT: H 239 ASN cc_start: 0.8985 (m-40) cc_final: 0.8426 (p0) REVERT: I 62 LYS cc_start: 0.8149 (pttp) cc_final: 0.7809 (mttt) REVERT: I 201 TYR cc_start: 0.8840 (m-80) cc_final: 0.8538 (m-80) REVERT: I 233 LYS cc_start: 0.7865 (mttt) cc_final: 0.7627 (mmmm) REVERT: I 239 ASN cc_start: 0.8536 (m110) cc_final: 0.7941 (p0) REVERT: J 115 ASP cc_start: 0.8906 (t0) cc_final: 0.8681 (t70) REVERT: J 117 TYR cc_start: 0.7779 (t80) cc_final: 0.7498 (t80) REVERT: J 233 LYS cc_start: 0.8092 (mttt) cc_final: 0.7559 (mmmm) REVERT: J 239 ASN cc_start: 0.8938 (m-40) cc_final: 0.8426 (p0) REVERT: J 279 MET cc_start: 0.8345 (mtt) cc_final: 0.7747 (mtt) REVERT: K 26 SER cc_start: 0.9186 (OUTLIER) cc_final: 0.8686 (p) REVERT: K 62 LYS cc_start: 0.8361 (pttp) cc_final: 0.7938 (mttt) REVERT: K 198 ASP cc_start: 0.8348 (t70) cc_final: 0.7804 (p0) REVERT: K 201 TYR cc_start: 0.8865 (m-80) cc_final: 0.8100 (m-80) REVERT: K 233 LYS cc_start: 0.8034 (mttt) cc_final: 0.7717 (mmmm) REVERT: K 239 ASN cc_start: 0.8313 (m110) cc_final: 0.7672 (p0) REVERT: K 267 VAL cc_start: 0.9212 (t) cc_final: 0.8966 (m) REVERT: K 279 MET cc_start: 0.8246 (mtt) cc_final: 0.7879 (mtt) REVERT: L 62 LYS cc_start: 0.8746 (pttp) cc_final: 0.7999 (mttp) REVERT: L 107 ASP cc_start: 0.7348 (p0) cc_final: 0.6965 (t0) REVERT: L 114 ASP cc_start: 0.8768 (t0) cc_final: 0.8544 (t70) REVERT: L 233 LYS cc_start: 0.8223 (mttt) cc_final: 0.7671 (mmmm) REVERT: L 286 MET cc_start: 0.9041 (mtm) cc_final: 0.8820 (mtm) REVERT: M 46 GLN cc_start: 0.8477 (pt0) cc_final: 0.8275 (pm20) REVERT: M 233 LYS cc_start: 0.8251 (mttt) cc_final: 0.7786 (mmmm) REVERT: M 279 MET cc_start: 0.8246 (mtt) cc_final: 0.7580 (mtt) REVERT: N 62 LYS cc_start: 0.8181 (pttp) cc_final: 0.7844 (mttp) REVERT: N 233 LYS cc_start: 0.8028 (mttt) cc_final: 0.7392 (mmmm) REVERT: N 279 MET cc_start: 0.8030 (mtt) cc_final: 0.7524 (mtt) REVERT: N 285 LYS cc_start: 0.8841 (tttt) cc_final: 0.8582 (tttt) REVERT: O 62 LYS cc_start: 0.8556 (pttp) cc_final: 0.8152 (mttt) REVERT: O 214 ASN cc_start: 0.8627 (t0) cc_final: 0.8149 (p0) REVERT: O 236 ARG cc_start: 0.3879 (tpt170) cc_final: 0.3166 (tpt170) REVERT: O 279 MET cc_start: 0.7708 (mtt) cc_final: 0.6853 (mtt) REVERT: O 300 LEU cc_start: 0.9047 (tp) cc_final: 0.8742 (tt) REVERT: P 233 LYS cc_start: 0.7972 (mttt) cc_final: 0.7494 (mmmm) REVERT: P 262 GLN cc_start: 0.8012 (OUTLIER) cc_final: 0.7581 (pp30) REVERT: Q 116 LYS cc_start: 0.8885 (mttt) cc_final: 0.8487 (pttt) REVERT: Q 236 ARG cc_start: 0.4572 (tpt170) cc_final: 0.4130 (tpp-160) REVERT: R 62 LYS cc_start: 0.8781 (pttp) cc_final: 0.8007 (mttp) REVERT: R 63 ASP cc_start: 0.8702 (t70) cc_final: 0.8439 (t70) REVERT: R 225 PHE cc_start: 0.8768 (OUTLIER) cc_final: 0.8473 (t80) REVERT: R 239 ASN cc_start: 0.8764 (m-40) cc_final: 0.8265 (p0) REVERT: S 62 LYS cc_start: 0.8372 (pttp) cc_final: 0.7723 (mttp) REVERT: S 126 LEU cc_start: 0.8118 (OUTLIER) cc_final: 0.7844 (tp) REVERT: S 290 ASP cc_start: 0.8560 (p0) cc_final: 0.8296 (p0) REVERT: T 62 LYS cc_start: 0.8213 (pttp) cc_final: 0.7884 (mttp) REVERT: T 63 ASP cc_start: 0.8687 (t70) cc_final: 0.8485 (t70) REVERT: T 225 PHE cc_start: 0.8640 (OUTLIER) cc_final: 0.8260 (t80) REVERT: T 233 LYS cc_start: 0.7823 (mmmm) cc_final: 0.7559 (mmmm) REVERT: U 115 ASP cc_start: 0.8796 (t0) cc_final: 0.8448 (t0) REVERT: U 116 LYS cc_start: 0.9029 (mttt) cc_final: 0.8552 (pttt) outliers start: 121 outliers final: 104 residues processed: 882 average time/residue: 0.4681 time to fit residues: 687.2998 Evaluate side-chains 888 residues out of total 4305 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 110 poor density : 778 time to evaluate : 4.403 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 VAL Chi-restraints excluded: chain A residue 104 CYS Chi-restraints excluded: chain A residue 293 THR Chi-restraints excluded: chain B residue 26 SER Chi-restraints excluded: chain B residue 108 SER Chi-restraints excluded: chain B residue 257 VAL Chi-restraints excluded: chain B residue 293 THR Chi-restraints excluded: chain C residue 20 LEU Chi-restraints excluded: chain C residue 26 SER Chi-restraints excluded: chain C residue 240 THR Chi-restraints excluded: chain D residue 1 VAL Chi-restraints excluded: chain D residue 26 SER Chi-restraints excluded: chain D residue 42 LEU Chi-restraints excluded: chain E residue 1 VAL Chi-restraints excluded: chain E residue 26 SER Chi-restraints excluded: chain E residue 42 LEU Chi-restraints excluded: chain E residue 97 LEU Chi-restraints excluded: chain E residue 102 VAL Chi-restraints excluded: chain E residue 293 THR Chi-restraints excluded: chain F residue 20 LEU Chi-restraints excluded: chain F residue 26 SER Chi-restraints excluded: chain F residue 42 LEU Chi-restraints excluded: chain F residue 102 VAL Chi-restraints excluded: chain F residue 115 ASP Chi-restraints excluded: chain F residue 199 ASP Chi-restraints excluded: chain F residue 293 THR Chi-restraints excluded: chain G residue 20 LEU Chi-restraints excluded: chain G residue 102 VAL Chi-restraints excluded: chain G residue 199 ASP Chi-restraints excluded: chain G residue 240 THR Chi-restraints excluded: chain G residue 257 VAL Chi-restraints excluded: chain H residue 12 LEU Chi-restraints excluded: chain H residue 26 SER Chi-restraints excluded: chain H residue 102 VAL Chi-restraints excluded: chain H residue 115 ASP Chi-restraints excluded: chain H residue 199 ASP Chi-restraints excluded: chain H residue 225 PHE Chi-restraints excluded: chain H residue 240 THR Chi-restraints excluded: chain I residue 1 VAL Chi-restraints excluded: chain I residue 26 SER Chi-restraints excluded: chain I residue 42 LEU Chi-restraints excluded: chain I residue 102 VAL Chi-restraints excluded: chain I residue 199 ASP Chi-restraints excluded: chain I residue 240 THR Chi-restraints excluded: chain J residue 1 VAL Chi-restraints excluded: chain J residue 26 SER Chi-restraints excluded: chain J residue 42 LEU Chi-restraints excluded: chain J residue 102 VAL Chi-restraints excluded: chain J residue 199 ASP Chi-restraints excluded: chain J residue 240 THR Chi-restraints excluded: chain J residue 257 VAL Chi-restraints excluded: chain K residue 12 LEU Chi-restraints excluded: chain K residue 20 LEU Chi-restraints excluded: chain K residue 26 SER Chi-restraints excluded: chain K residue 102 VAL Chi-restraints excluded: chain K residue 199 ASP Chi-restraints excluded: chain K residue 240 THR Chi-restraints excluded: chain K residue 262 GLN Chi-restraints excluded: chain L residue 20 LEU Chi-restraints excluded: chain L residue 26 SER Chi-restraints excluded: chain L residue 42 LEU Chi-restraints excluded: chain L residue 102 VAL Chi-restraints excluded: chain L residue 115 ASP Chi-restraints excluded: chain L residue 240 THR Chi-restraints excluded: chain L residue 257 VAL Chi-restraints excluded: chain M residue 20 LEU Chi-restraints excluded: chain M residue 26 SER Chi-restraints excluded: chain M residue 42 LEU Chi-restraints excluded: chain M residue 102 VAL Chi-restraints excluded: chain M residue 297 SER Chi-restraints excluded: chain N residue 20 LEU Chi-restraints excluded: chain N residue 26 SER Chi-restraints excluded: chain N residue 42 LEU Chi-restraints excluded: chain N residue 102 VAL Chi-restraints excluded: chain N residue 257 VAL Chi-restraints excluded: chain O residue 20 LEU Chi-restraints excluded: chain O residue 46 GLN Chi-restraints excluded: chain O residue 102 VAL Chi-restraints excluded: chain O residue 199 ASP Chi-restraints excluded: chain O residue 225 PHE Chi-restraints excluded: chain P residue 20 LEU Chi-restraints excluded: chain P residue 26 SER Chi-restraints excluded: chain P residue 102 VAL Chi-restraints excluded: chain P residue 121 GLN Chi-restraints excluded: chain P residue 199 ASP Chi-restraints excluded: chain P residue 240 THR Chi-restraints excluded: chain P residue 262 GLN Chi-restraints excluded: chain Q residue 20 LEU Chi-restraints excluded: chain Q residue 102 VAL Chi-restraints excluded: chain R residue 20 LEU Chi-restraints excluded: chain R residue 26 SER Chi-restraints excluded: chain R residue 82 VAL Chi-restraints excluded: chain R residue 225 PHE Chi-restraints excluded: chain S residue 20 LEU Chi-restraints excluded: chain S residue 82 VAL Chi-restraints excluded: chain S residue 83 LEU Chi-restraints excluded: chain S residue 108 SER Chi-restraints excluded: chain S residue 126 LEU Chi-restraints excluded: chain T residue 20 LEU Chi-restraints excluded: chain T residue 102 VAL Chi-restraints excluded: chain T residue 108 SER Chi-restraints excluded: chain T residue 122 THR Chi-restraints excluded: chain T residue 225 PHE Chi-restraints excluded: chain T residue 238 VAL Chi-restraints excluded: chain T residue 240 THR Chi-restraints excluded: chain T residue 285 LYS Chi-restraints excluded: chain T residue 293 THR Chi-restraints excluded: chain U residue 20 LEU Chi-restraints excluded: chain U residue 102 VAL Chi-restraints excluded: chain U residue 122 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 504 random chunks: chunk 297 optimal weight: 3.9990 chunk 478 optimal weight: 5.9990 chunk 292 optimal weight: 0.0980 chunk 227 optimal weight: 8.9990 chunk 332 optimal weight: 20.0000 chunk 502 optimal weight: 6.9990 chunk 462 optimal weight: 9.9990 chunk 399 optimal weight: 8.9990 chunk 41 optimal weight: 20.0000 chunk 308 optimal weight: 9.9990 chunk 245 optimal weight: 8.9990 overall best weight: 5.2188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 264 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 264 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 84 GLN ** J 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 46 GLN ** M 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 46 GLN ** N 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 46 GLN ** P 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 84 GLN Q 46 GLN ** Q 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 46 GLN U 200 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7830 moved from start: 0.4896 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.082 39837 Z= 0.259 Angle : 0.665 12.357 54663 Z= 0.339 Chirality : 0.047 0.241 6552 Planarity : 0.003 0.042 6909 Dihedral : 4.780 42.492 5330 Min Nonbonded Distance : 2.115 Molprobity Statistics. All-atom Clashscore : 10.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.80 % Favored : 95.20 % Rotamer: Outliers : 2.90 % Allowed : 21.93 % Favored : 75.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.30 (0.12), residues: 4998 helix: 2.61 (0.19), residues: 714 sheet: 0.62 (0.12), residues: 1701 loop : -0.81 (0.12), residues: 2583 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP O 294 HIS 0.004 0.001 HIS H 105 PHE 0.014 0.001 PHE S 237 TYR 0.034 0.002 TYR C 22 ARG 0.003 0.000 ARG C 226 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9996 Ramachandran restraints generated. 4998 Oldfield, 0 Emsley, 4998 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9996 Ramachandran restraints generated. 4998 Oldfield, 0 Emsley, 4998 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 910 residues out of total 4305 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 125 poor density : 785 time to evaluate : 4.797 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 233 LYS cc_start: 0.8411 (mttt) cc_final: 0.8032 (mmmm) REVERT: A 239 ASN cc_start: 0.8937 (m-40) cc_final: 0.8114 (p0) REVERT: A 286 MET cc_start: 0.9018 (mtt) cc_final: 0.8801 (mtp) REVERT: B 233 LYS cc_start: 0.8382 (mttt) cc_final: 0.7857 (mmmm) REVERT: B 239 ASN cc_start: 0.9000 (m-40) cc_final: 0.8353 (p0) REVERT: B 279 MET cc_start: 0.8418 (mtt) cc_final: 0.7774 (mtt) REVERT: C 279 MET cc_start: 0.8200 (mtt) cc_final: 0.7278 (mtt) REVERT: D 111 MET cc_start: 0.8198 (ttm) cc_final: 0.7845 (ttm) REVERT: D 115 ASP cc_start: 0.8734 (t0) cc_final: 0.8421 (t0) REVERT: D 233 LYS cc_start: 0.7999 (mttt) cc_final: 0.7734 (mmmm) REVERT: D 236 ARG cc_start: 0.7561 (ttm-80) cc_final: 0.7287 (ttm-80) REVERT: D 239 ASN cc_start: 0.8857 (m110) cc_final: 0.8271 (p0) REVERT: E 233 LYS cc_start: 0.7968 (mttt) cc_final: 0.7419 (mmmm) REVERT: E 239 ASN cc_start: 0.8871 (m-40) cc_final: 0.8148 (p0) REVERT: F 233 LYS cc_start: 0.8171 (mttt) cc_final: 0.7822 (mmmm) REVERT: F 239 ASN cc_start: 0.8997 (m-40) cc_final: 0.8254 (p0) REVERT: F 267 VAL cc_start: 0.8970 (t) cc_final: 0.8750 (m) REVERT: F 279 MET cc_start: 0.8256 (mtt) cc_final: 0.7925 (mtp) REVERT: F 286 MET cc_start: 0.8939 (mtm) cc_final: 0.8736 (mtm) REVERT: G 114 ASP cc_start: 0.8866 (t70) cc_final: 0.8523 (t0) REVERT: G 115 ASP cc_start: 0.9002 (t0) cc_final: 0.8640 (t0) REVERT: G 233 LYS cc_start: 0.8270 (mttt) cc_final: 0.7805 (mmmm) REVERT: H 114 ASP cc_start: 0.8801 (t0) cc_final: 0.8379 (t0) REVERT: H 233 LYS cc_start: 0.8306 (mttt) cc_final: 0.7859 (mmmm) REVERT: H 239 ASN cc_start: 0.9020 (m-40) cc_final: 0.8435 (p0) REVERT: I 62 LYS cc_start: 0.8176 (pttp) cc_final: 0.7824 (mttt) REVERT: I 201 TYR cc_start: 0.8890 (m-80) cc_final: 0.8576 (m-80) REVERT: I 233 LYS cc_start: 0.7976 (mttt) cc_final: 0.7703 (mmmm) REVERT: I 239 ASN cc_start: 0.8581 (m110) cc_final: 0.7933 (p0) REVERT: J 233 LYS cc_start: 0.8096 (mttt) cc_final: 0.7653 (mmmm) REVERT: J 239 ASN cc_start: 0.8962 (m-40) cc_final: 0.8387 (p0) REVERT: J 279 MET cc_start: 0.8437 (mtt) cc_final: 0.7884 (mtt) REVERT: K 26 SER cc_start: 0.9236 (OUTLIER) cc_final: 0.8760 (p) REVERT: K 62 LYS cc_start: 0.8326 (pttp) cc_final: 0.7936 (mttt) REVERT: K 233 LYS cc_start: 0.8043 (mttt) cc_final: 0.7718 (mmmm) REVERT: K 239 ASN cc_start: 0.8367 (m110) cc_final: 0.7748 (p0) REVERT: K 267 VAL cc_start: 0.9229 (t) cc_final: 0.8952 (m) REVERT: L 62 LYS cc_start: 0.8737 (pttp) cc_final: 0.7907 (mttt) REVERT: L 114 ASP cc_start: 0.8803 (t0) cc_final: 0.8576 (t70) REVERT: L 233 LYS cc_start: 0.8316 (mttt) cc_final: 0.7745 (mmmm) REVERT: L 286 MET cc_start: 0.9039 (mtm) cc_final: 0.8828 (mtm) REVERT: M 233 LYS cc_start: 0.8248 (mttt) cc_final: 0.7791 (mmmm) REVERT: M 279 MET cc_start: 0.8494 (mtt) cc_final: 0.7796 (mtt) REVERT: N 233 LYS cc_start: 0.8069 (mttt) cc_final: 0.7401 (mmmm) REVERT: N 285 LYS cc_start: 0.8875 (tttt) cc_final: 0.8639 (tttt) REVERT: O 62 LYS cc_start: 0.8583 (pttp) cc_final: 0.8160 (mttt) REVERT: O 214 ASN cc_start: 0.8622 (t0) cc_final: 0.8102 (p0) REVERT: O 236 ARG cc_start: 0.3900 (tpt170) cc_final: 0.3163 (tpt170) REVERT: P 233 LYS cc_start: 0.7973 (mttt) cc_final: 0.7467 (mmmm) REVERT: P 262 GLN cc_start: 0.8103 (OUTLIER) cc_final: 0.7624 (pp30) REVERT: P 279 MET cc_start: 0.8574 (mtt) cc_final: 0.8240 (mtm) REVERT: Q 116 LYS cc_start: 0.8927 (mttt) cc_final: 0.8500 (pttt) REVERT: Q 236 ARG cc_start: 0.4671 (tpt170) cc_final: 0.4232 (tpp-160) REVERT: R 62 LYS cc_start: 0.8810 (pttp) cc_final: 0.8019 (mttp) REVERT: R 63 ASP cc_start: 0.8736 (t70) cc_final: 0.8451 (t70) REVERT: R 225 PHE cc_start: 0.8782 (OUTLIER) cc_final: 0.8507 (t80) REVERT: R 239 ASN cc_start: 0.8795 (m-40) cc_final: 0.8311 (p0) REVERT: S 62 LYS cc_start: 0.8403 (pttp) cc_final: 0.7759 (mttp) REVERT: S 126 LEU cc_start: 0.8176 (OUTLIER) cc_final: 0.7886 (tp) REVERT: S 290 ASP cc_start: 0.8571 (p0) cc_final: 0.8328 (p0) REVERT: T 62 LYS cc_start: 0.8225 (pttp) cc_final: 0.7934 (mttp) REVERT: T 63 ASP cc_start: 0.8740 (t70) cc_final: 0.8526 (t70) REVERT: T 225 PHE cc_start: 0.8678 (OUTLIER) cc_final: 0.8333 (t80) REVERT: T 233 LYS cc_start: 0.7857 (mmmm) cc_final: 0.7567 (mmmm) REVERT: U 116 LYS cc_start: 0.9117 (mttt) cc_final: 0.8606 (pttt) outliers start: 125 outliers final: 110 residues processed: 873 average time/residue: 0.4670 time to fit residues: 681.0637 Evaluate side-chains 876 residues out of total 4305 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 115 poor density : 761 time to evaluate : 4.398 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 VAL Chi-restraints excluded: chain A residue 26 SER Chi-restraints excluded: chain A residue 104 CYS Chi-restraints excluded: chain A residue 293 THR Chi-restraints excluded: chain B residue 26 SER Chi-restraints excluded: chain B residue 95 ASP Chi-restraints excluded: chain B residue 108 SER Chi-restraints excluded: chain B residue 257 VAL Chi-restraints excluded: chain B residue 293 THR Chi-restraints excluded: chain C residue 20 LEU Chi-restraints excluded: chain C residue 26 SER Chi-restraints excluded: chain C residue 240 THR Chi-restraints excluded: chain D residue 1 VAL Chi-restraints excluded: chain D residue 26 SER Chi-restraints excluded: chain D residue 42 LEU Chi-restraints excluded: chain D residue 104 CYS Chi-restraints excluded: chain E residue 1 VAL Chi-restraints excluded: chain E residue 26 SER Chi-restraints excluded: chain E residue 42 LEU Chi-restraints excluded: chain E residue 97 LEU Chi-restraints excluded: chain E residue 102 VAL Chi-restraints excluded: chain E residue 293 THR Chi-restraints excluded: chain F residue 20 LEU Chi-restraints excluded: chain F residue 26 SER Chi-restraints excluded: chain F residue 37 VAL Chi-restraints excluded: chain F residue 42 LEU Chi-restraints excluded: chain F residue 102 VAL Chi-restraints excluded: chain F residue 199 ASP Chi-restraints excluded: chain F residue 293 THR Chi-restraints excluded: chain G residue 20 LEU Chi-restraints excluded: chain G residue 102 VAL Chi-restraints excluded: chain G residue 199 ASP Chi-restraints excluded: chain G residue 240 THR Chi-restraints excluded: chain G residue 257 VAL Chi-restraints excluded: chain H residue 12 LEU Chi-restraints excluded: chain H residue 26 SER Chi-restraints excluded: chain H residue 95 ASP Chi-restraints excluded: chain H residue 102 VAL Chi-restraints excluded: chain H residue 115 ASP Chi-restraints excluded: chain H residue 199 ASP Chi-restraints excluded: chain H residue 240 THR Chi-restraints excluded: chain I residue 26 SER Chi-restraints excluded: chain I residue 42 LEU Chi-restraints excluded: chain I residue 102 VAL Chi-restraints excluded: chain I residue 199 ASP Chi-restraints excluded: chain I residue 240 THR Chi-restraints excluded: chain I residue 297 SER Chi-restraints excluded: chain J residue 1 VAL Chi-restraints excluded: chain J residue 26 SER Chi-restraints excluded: chain J residue 42 LEU Chi-restraints excluded: chain J residue 102 VAL Chi-restraints excluded: chain J residue 199 ASP Chi-restraints excluded: chain J residue 240 THR Chi-restraints excluded: chain J residue 257 VAL Chi-restraints excluded: chain K residue 12 LEU Chi-restraints excluded: chain K residue 26 SER Chi-restraints excluded: chain K residue 102 VAL Chi-restraints excluded: chain K residue 199 ASP Chi-restraints excluded: chain K residue 240 THR Chi-restraints excluded: chain K residue 262 GLN Chi-restraints excluded: chain L residue 20 LEU Chi-restraints excluded: chain L residue 26 SER Chi-restraints excluded: chain L residue 42 LEU Chi-restraints excluded: chain L residue 74 LEU Chi-restraints excluded: chain L residue 102 VAL Chi-restraints excluded: chain L residue 115 ASP Chi-restraints excluded: chain L residue 240 THR Chi-restraints excluded: chain M residue 1 VAL Chi-restraints excluded: chain M residue 20 LEU Chi-restraints excluded: chain M residue 26 SER Chi-restraints excluded: chain M residue 42 LEU Chi-restraints excluded: chain M residue 102 VAL Chi-restraints excluded: chain M residue 297 SER Chi-restraints excluded: chain N residue 20 LEU Chi-restraints excluded: chain N residue 26 SER Chi-restraints excluded: chain N residue 42 LEU Chi-restraints excluded: chain N residue 102 VAL Chi-restraints excluded: chain N residue 257 VAL Chi-restraints excluded: chain O residue 20 LEU Chi-restraints excluded: chain O residue 46 GLN Chi-restraints excluded: chain O residue 102 VAL Chi-restraints excluded: chain O residue 199 ASP Chi-restraints excluded: chain O residue 225 PHE Chi-restraints excluded: chain O residue 257 VAL Chi-restraints excluded: chain P residue 20 LEU Chi-restraints excluded: chain P residue 26 SER Chi-restraints excluded: chain P residue 102 VAL Chi-restraints excluded: chain P residue 199 ASP Chi-restraints excluded: chain P residue 240 THR Chi-restraints excluded: chain P residue 262 GLN Chi-restraints excluded: chain P residue 293 THR Chi-restraints excluded: chain Q residue 20 LEU Chi-restraints excluded: chain Q residue 102 VAL Chi-restraints excluded: chain R residue 20 LEU Chi-restraints excluded: chain R residue 26 SER Chi-restraints excluded: chain R residue 82 VAL Chi-restraints excluded: chain R residue 115 ASP Chi-restraints excluded: chain R residue 225 PHE Chi-restraints excluded: chain S residue 20 LEU Chi-restraints excluded: chain S residue 82 VAL Chi-restraints excluded: chain S residue 83 LEU Chi-restraints excluded: chain S residue 108 SER Chi-restraints excluded: chain S residue 126 LEU Chi-restraints excluded: chain T residue 13 ILE Chi-restraints excluded: chain T residue 20 LEU Chi-restraints excluded: chain T residue 102 VAL Chi-restraints excluded: chain T residue 108 SER Chi-restraints excluded: chain T residue 122 THR Chi-restraints excluded: chain T residue 225 PHE Chi-restraints excluded: chain T residue 238 VAL Chi-restraints excluded: chain T residue 293 THR Chi-restraints excluded: chain U residue 20 LEU Chi-restraints excluded: chain U residue 46 GLN Chi-restraints excluded: chain U residue 102 VAL Chi-restraints excluded: chain U residue 122 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 504 random chunks: chunk 317 optimal weight: 8.9990 chunk 425 optimal weight: 7.9990 chunk 122 optimal weight: 7.9990 chunk 368 optimal weight: 0.0470 chunk 59 optimal weight: 4.9990 chunk 111 optimal weight: 4.9990 chunk 400 optimal weight: 7.9990 chunk 167 optimal weight: 8.9990 chunk 411 optimal weight: 8.9990 chunk 50 optimal weight: 8.9990 chunk 73 optimal weight: 9.9990 overall best weight: 5.2086 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 264 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 264 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 46 GLN ** J 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 46 GLN ** N 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 121 GLN ** Q 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.110472 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3236 r_free = 0.3236 target = 0.103126 restraints weight = 96419.915| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.105141 restraints weight = 55248.130| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 21)----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.106325 restraints weight = 33120.692| |-----------------------------------------------------------------------------| r_work (final): 0.3290 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7859 moved from start: 0.4971 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.081 39837 Z= 0.256 Angle : 0.671 12.268 54663 Z= 0.342 Chirality : 0.047 0.249 6552 Planarity : 0.003 0.041 6909 Dihedral : 4.854 42.988 5330 Min Nonbonded Distance : 2.087 Molprobity Statistics. All-atom Clashscore : 10.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.22 % Favored : 94.78 % Rotamer: Outliers : 3.02 % Allowed : 22.14 % Favored : 74.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.23 (0.12), residues: 4998 helix: 2.56 (0.19), residues: 714 sheet: 0.58 (0.12), residues: 1701 loop : -0.85 (0.12), residues: 2583 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.002 TRP C 294 HIS 0.005 0.001 HIS S 118 PHE 0.014 0.001 PHE S 237 TYR 0.034 0.002 TYR C 22 ARG 0.003 0.000 ARG N 226 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11553.73 seconds wall clock time: 207 minutes 59.61 seconds (12479.61 seconds total)