Starting phenix.real_space_refine (version: 1.21rc1) on Fri Aug 25 07:36:20 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5n6w_3595/08_2023/5n6w_3595.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5n6w_3595/08_2023/5n6w_3595.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5n6w_3595/08_2023/5n6w_3595.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5n6w_3595/08_2023/5n6w_3595.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5n6w_3595/08_2023/5n6w_3595.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5n6w_3595/08_2023/5n6w_3595.pdb" } resolution = 4.2 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs 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= 0.004 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: 5 Type Number sf(0) Gaussians S 112 5.16 5 C 13216 2.51 5 N 3600 2.21 5 O 3792 1.98 5 H 20032 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 71": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 93": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 108": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ASP 118": "OD1" <-> "OD2" Residue "A TYR 151": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 155": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ARG 160": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A TYR 166": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 176": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ARG 209": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B PHE 71": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B TYR 93": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 108": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B ASP 118": "OD1" <-> "OD2" Residue "B TYR 151": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B TYR 155": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B ARG 160": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B TYR 166": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 176": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B ARG 209": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C PHE 71": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C TYR 93": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C PHE 108": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C ASP 118": "OD1" <-> "OD2" Residue "C TYR 151": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C TYR 155": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C ARG 160": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C TYR 166": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C PHE 176": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C ARG 209": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D PHE 71": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D TYR 93": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D PHE 108": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D ASP 118": "OD1" <-> "OD2" Residue "D TYR 151": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D TYR 155": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D ARG 160": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D TYR 166": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D PHE 176": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D ARG 209": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "E PHE 71": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E TYR 93": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E PHE 108": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E ASP 118": "OD1" <-> "OD2" Residue "E TYR 151": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E TYR 155": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E ARG 160": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "E TYR 166": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E PHE 176": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E ARG 209": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "F PHE 71": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F TYR 93": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F PHE 108": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F ASP 118": "OD1" <-> "OD2" Residue "F TYR 151": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F TYR 155": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F ARG 160": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "F TYR 166": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F PHE 176": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F ARG 209": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "G PHE 71": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "G TYR 93": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "G PHE 108": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "G ASP 118": "OD1" <-> "OD2" Residue "G TYR 151": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "G TYR 155": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "G ARG 160": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "G TYR 166": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "G PHE 176": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "G ARG 209": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "H PHE 71": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "H TYR 93": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "H PHE 108": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "H ASP 118": "OD1" <-> "OD2" Residue "H TYR 151": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "H TYR 155": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "H ARG 160": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "H TYR 166": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "H PHE 176": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "H ARG 209": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "I PHE 71": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "I TYR 93": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "I PHE 108": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "I ASP 118": "OD1" <-> "OD2" Residue "I TYR 151": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "I TYR 155": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "I ARG 160": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "I TYR 166": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "I PHE 176": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "I ARG 209": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "J PHE 71": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "J TYR 93": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "J PHE 108": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "J ASP 118": "OD1" <-> "OD2" Residue "J TYR 151": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "J TYR 155": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "J ARG 160": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "J TYR 166": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "J PHE 176": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "J ARG 209": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "K PHE 71": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "K TYR 93": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "K PHE 108": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "K ASP 118": "OD1" <-> "OD2" Residue "K TYR 151": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "K TYR 155": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "K ARG 160": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "K TYR 166": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "K PHE 176": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "K ARG 209": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "L PHE 71": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "L TYR 93": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "L PHE 108": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "L ASP 118": "OD1" <-> "OD2" Residue "L TYR 151": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "L TYR 155": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "L ARG 160": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "L TYR 166": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "L PHE 176": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "L ARG 209": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "M PHE 71": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "M TYR 93": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "M PHE 108": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "M ASP 118": "OD1" <-> "OD2" Residue "M TYR 151": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "M TYR 155": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "M ARG 160": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "M TYR 166": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "M PHE 176": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "M ARG 209": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "N PHE 71": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "N TYR 93": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "N PHE 108": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "N ASP 118": "OD1" <-> "OD2" Residue "N TYR 151": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "N TYR 155": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "N ARG 160": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "N TYR 166": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "N PHE 176": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "N ARG 209": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "O PHE 71": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "O TYR 93": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "O PHE 108": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "O ASP 118": "OD1" <-> "OD2" Residue "O TYR 151": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "O TYR 155": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "O ARG 160": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "O TYR 166": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "O PHE 176": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "O ARG 209": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "P PHE 71": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "P TYR 93": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "P PHE 108": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "P ASP 118": "OD1" <-> "OD2" Residue "P TYR 151": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "P TYR 155": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "P ARG 160": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "P TYR 166": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "P PHE 176": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "P ARG 209": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Time to flip residues: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5044/modules/chem_data/mon_lib" Total number of atoms: 40752 Number of models: 1 Model: "" Number of chains: 16 Chain: "A" Number of atoms: 2547 Number of conformers: 1 Conformer: "" Number of residues, atoms: 157, 2547 Classifications: {'peptide': 157} Link IDs: {'PTRANS': 7, 'TRANS': 149} Chain: "B" Number of atoms: 2547 Number of conformers: 1 Conformer: "" Number of residues, atoms: 157, 2547 Classifications: {'peptide': 157} Link IDs: {'PTRANS': 7, 'TRANS': 149} Chain: "C" Number of atoms: 2547 Number of conformers: 1 Conformer: "" Number of residues, atoms: 157, 2547 Classifications: {'peptide': 157} Link IDs: {'PTRANS': 7, 'TRANS': 149} Chain: "D" Number of atoms: 2547 Number of conformers: 1 Conformer: "" Number of residues, atoms: 157, 2547 Classifications: {'peptide': 157} Link IDs: {'PTRANS': 7, 'TRANS': 149} Chain: "E" Number of atoms: 2547 Number of conformers: 1 Conformer: "" Number of residues, atoms: 157, 2547 Classifications: {'peptide': 157} Link IDs: {'PTRANS': 7, 'TRANS': 149} Chain: "F" Number of atoms: 2547 Number of conformers: 1 Conformer: "" Number of residues, atoms: 157, 2547 Classifications: {'peptide': 157} Link IDs: {'PTRANS': 7, 'TRANS': 149} Chain: "G" Number of atoms: 2547 Number of conformers: 1 Conformer: "" Number of residues, atoms: 157, 2547 Classifications: {'peptide': 157} Link IDs: {'PTRANS': 7, 'TRANS': 149} Chain: "H" Number of atoms: 2547 Number of conformers: 1 Conformer: "" Number of residues, atoms: 157, 2547 Classifications: {'peptide': 157} Link IDs: {'PTRANS': 7, 'TRANS': 149} Chain: "I" Number of atoms: 2547 Number of conformers: 1 Conformer: "" Number of residues, atoms: 157, 2547 Classifications: {'peptide': 157} Link IDs: {'PTRANS': 7, 'TRANS': 149} Chain: "J" Number of atoms: 2547 Number of conformers: 1 Conformer: "" Number of residues, atoms: 157, 2547 Classifications: {'peptide': 157} Link IDs: {'PTRANS': 7, 'TRANS': 149} Chain: "K" Number of atoms: 2547 Number of conformers: 1 Conformer: "" Number of residues, atoms: 157, 2547 Classifications: {'peptide': 157} Link IDs: {'PTRANS': 7, 'TRANS': 149} Chain: "L" Number of atoms: 2547 Number of conformers: 1 Conformer: "" Number of residues, atoms: 157, 2547 Classifications: {'peptide': 157} Link IDs: {'PTRANS': 7, 'TRANS': 149} Chain: "M" Number of atoms: 2547 Number of conformers: 1 Conformer: "" Number of residues, atoms: 157, 2547 Classifications: {'peptide': 157} Link IDs: {'PTRANS': 7, 'TRANS': 149} Chain: "N" Number of atoms: 2547 Number of conformers: 1 Conformer: "" Number of residues, atoms: 157, 2547 Classifications: {'peptide': 157} Link IDs: {'PTRANS': 7, 'TRANS': 149} Chain: "O" Number of atoms: 2547 Number of conformers: 1 Conformer: "" Number of residues, atoms: 157, 2547 Classifications: {'peptide': 157} Link IDs: {'PTRANS': 7, 'TRANS': 149} Chain: "P" Number of atoms: 2547 Number of conformers: 1 Conformer: "" Number of residues, atoms: 157, 2547 Classifications: {'peptide': 157} Link IDs: {'PTRANS': 7, 'TRANS': 149} Time building chain proxies: 16.41, per 1000 atoms: 0.40 Number of scatterers: 40752 At special positions: 0 Unit cell: (145.77, 145.77, 86.43, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 112 16.00 O 3792 8.00 N 3600 7.00 C 13216 6.00 H 20032 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=16, symmetry=0 Simple disulfide: pdb=" SG CYS A 63 " - pdb=" SG CYS A 219 " distance=2.03 Simple disulfide: pdb=" SG CYS B 63 " - pdb=" SG CYS B 219 " distance=2.03 Simple disulfide: pdb=" SG CYS C 63 " - pdb=" SG CYS C 219 " distance=2.03 Simple disulfide: pdb=" SG CYS D 63 " - pdb=" SG CYS D 219 " distance=2.03 Simple disulfide: pdb=" SG CYS E 63 " - pdb=" SG CYS E 219 " distance=2.03 Simple disulfide: pdb=" SG CYS F 63 " - pdb=" SG CYS F 219 " distance=2.03 Simple disulfide: pdb=" SG CYS G 63 " - pdb=" SG CYS G 219 " distance=2.03 Simple disulfide: pdb=" SG CYS H 63 " - pdb=" SG CYS H 219 " distance=2.03 Simple disulfide: pdb=" SG CYS I 63 " - pdb=" SG CYS I 219 " distance=2.03 Simple disulfide: pdb=" SG CYS J 63 " - pdb=" SG CYS J 219 " distance=2.03 Simple disulfide: pdb=" SG CYS K 63 " - pdb=" SG CYS K 219 " distance=2.03 Simple disulfide: pdb=" SG CYS L 63 " - pdb=" SG CYS L 219 " distance=2.03 Simple disulfide: pdb=" SG CYS M 63 " - pdb=" SG CYS M 219 " distance=2.03 Simple disulfide: pdb=" SG CYS N 63 " - pdb=" SG CYS N 219 " distance=2.03 Simple disulfide: pdb=" SG CYS O 63 " - pdb=" SG CYS O 219 " distance=2.03 Simple disulfide: pdb=" SG CYS P 63 " - pdb=" SG CYS P 219 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 29.51 Conformation dependent library (CDL) restraints added in 3.2 seconds 4960 Ramachandran restraints generated. 2480 Oldfield, 0 Emsley, 2480 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4704 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 32 sheets defined 0.0% alpha, 10.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.50 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'A' and resid 194 through 196 removed outlier: 3.922A pdb=" N ILE A 194 " --> pdb=" O ILE A 133 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N SER A 196 " --> pdb=" O LYS A 131 " (cutoff:3.500A) removed outlier: 4.967A pdb=" N LEU A 217 " --> pdb=" O SER A 134 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 163 through 164 removed outlier: 3.889A pdb=" N TRP A 163 " --> pdb=" O TYR A 155 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N TYR A 155 " --> pdb=" O TRP A 163 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N ARG A 200 " --> pdb=" O GLN A 154 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N ARG A 156 " --> pdb=" O PHE A 198 " (cutoff:3.500A) removed outlier: 4.368A pdb=" N PHE A 198 " --> pdb=" O ARG A 156 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 194 through 196 removed outlier: 3.921A pdb=" N ILE B 194 " --> pdb=" O ILE B 133 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N SER B 196 " --> pdb=" O LYS B 131 " (cutoff:3.500A) removed outlier: 4.967A pdb=" N LEU B 217 " --> pdb=" O SER B 134 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 163 through 164 removed outlier: 3.890A pdb=" N TRP B 163 " --> pdb=" O TYR B 155 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N TYR B 155 " --> pdb=" O TRP B 163 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N ARG B 200 " --> pdb=" O GLN B 154 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N ARG B 156 " --> pdb=" O PHE B 198 " (cutoff:3.500A) removed outlier: 4.369A pdb=" N PHE B 198 " --> pdb=" O ARG B 156 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 194 through 196 removed outlier: 3.920A pdb=" N ILE C 194 " --> pdb=" O ILE C 133 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N SER C 196 " --> pdb=" O LYS C 131 " (cutoff:3.500A) removed outlier: 4.967A pdb=" N LEU C 217 " --> pdb=" O SER C 134 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 163 through 164 removed outlier: 3.890A pdb=" N TRP C 163 " --> pdb=" O TYR C 155 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N TYR C 155 " --> pdb=" O TRP C 163 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N ARG C 200 " --> pdb=" O GLN C 154 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N ARG C 156 " --> pdb=" O PHE C 198 " (cutoff:3.500A) removed outlier: 4.369A pdb=" N PHE C 198 " --> pdb=" O ARG C 156 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 194 through 196 removed outlier: 3.921A pdb=" N ILE D 194 " --> pdb=" O ILE D 133 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N SER D 196 " --> pdb=" O LYS D 131 " (cutoff:3.500A) removed outlier: 4.968A pdb=" N LEU D 217 " --> pdb=" O SER D 134 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 163 through 164 removed outlier: 3.891A pdb=" N TRP D 163 " --> pdb=" O TYR D 155 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N TYR D 155 " --> pdb=" O TRP D 163 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N ARG D 200 " --> pdb=" O GLN D 154 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N ARG D 156 " --> pdb=" O PHE D 198 " (cutoff:3.500A) removed outlier: 4.371A pdb=" N PHE D 198 " --> pdb=" O ARG D 156 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 194 through 196 removed outlier: 3.927A pdb=" N ILE E 194 " --> pdb=" O ILE E 133 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N SER E 196 " --> pdb=" O LYS E 131 " (cutoff:3.500A) removed outlier: 4.970A pdb=" N LEU E 217 " --> pdb=" O SER E 134 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 163 through 164 removed outlier: 3.886A pdb=" N TRP E 163 " --> pdb=" O TYR E 155 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N TYR E 155 " --> pdb=" O TRP E 163 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N ARG E 200 " --> pdb=" O GLN E 154 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N ARG E 156 " --> pdb=" O PHE E 198 " (cutoff:3.500A) removed outlier: 4.367A pdb=" N PHE E 198 " --> pdb=" O ARG E 156 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'F' and resid 194 through 196 removed outlier: 3.921A pdb=" N ILE F 194 " --> pdb=" O ILE F 133 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N SER F 196 " --> pdb=" O LYS F 131 " (cutoff:3.500A) removed outlier: 4.968A pdb=" N LEU F 217 " --> pdb=" O SER F 134 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'F' and resid 163 through 164 removed outlier: 3.905A pdb=" N TRP F 163 " --> pdb=" O TYR F 155 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N TYR F 155 " --> pdb=" O TRP F 163 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N ARG F 200 " --> pdb=" O GLN F 154 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N ARG F 156 " --> pdb=" O PHE F 198 " (cutoff:3.500A) removed outlier: 4.372A pdb=" N PHE F 198 " --> pdb=" O ARG F 156 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'G' and resid 194 through 196 removed outlier: 3.923A pdb=" N ILE G 194 " --> pdb=" O ILE G 133 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N SER G 196 " --> pdb=" O LYS G 131 " (cutoff:3.500A) removed outlier: 4.966A pdb=" N LEU G 217 " --> pdb=" O SER G 134 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'G' and resid 163 through 164 removed outlier: 3.891A pdb=" N TRP G 163 " --> pdb=" O TYR G 155 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N TYR G 155 " --> pdb=" O TRP G 163 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N ARG G 200 " --> pdb=" O GLN G 154 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N ARG G 156 " --> pdb=" O PHE G 198 " (cutoff:3.500A) removed outlier: 4.372A pdb=" N PHE G 198 " --> pdb=" O ARG G 156 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'H' and resid 194 through 196 removed outlier: 3.923A pdb=" N ILE H 194 " --> pdb=" O ILE H 133 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N SER H 196 " --> pdb=" O LYS H 131 " (cutoff:3.500A) removed outlier: 4.970A pdb=" N LEU H 217 " --> pdb=" O SER H 134 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'H' and resid 163 through 164 removed outlier: 3.890A pdb=" N TRP H 163 " --> pdb=" O TYR H 155 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N TYR H 155 " --> pdb=" O TRP H 163 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N ARG H 200 " --> pdb=" O GLN H 154 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N ARG H 156 " --> pdb=" O PHE H 198 " (cutoff:3.500A) removed outlier: 4.368A pdb=" N PHE H 198 " --> pdb=" O ARG H 156 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'I' and resid 194 through 196 removed outlier: 3.920A pdb=" N ILE I 194 " --> pdb=" O ILE I 133 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N SER I 196 " --> pdb=" O LYS I 131 " (cutoff:3.500A) removed outlier: 4.967A pdb=" N LEU I 217 " --> pdb=" O SER I 134 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'I' and resid 163 through 164 removed outlier: 3.889A pdb=" N TRP I 163 " --> pdb=" O TYR I 155 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N TYR I 155 " --> pdb=" O TRP I 163 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N ARG I 200 " --> pdb=" O GLN I 154 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N ARG I 156 " --> pdb=" O PHE I 198 " (cutoff:3.500A) removed outlier: 4.368A pdb=" N PHE I 198 " --> pdb=" O ARG I 156 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'J' and resid 194 through 196 removed outlier: 3.921A pdb=" N ILE J 194 " --> pdb=" O ILE J 133 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N SER J 196 " --> pdb=" O LYS J 131 " (cutoff:3.500A) removed outlier: 4.967A pdb=" N LEU J 217 " --> pdb=" O SER J 134 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'J' and resid 163 through 164 removed outlier: 3.893A pdb=" N TRP J 163 " --> pdb=" O TYR J 155 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N TYR J 155 " --> pdb=" O TRP J 163 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N ARG J 200 " --> pdb=" O GLN J 154 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N ARG J 156 " --> pdb=" O PHE J 198 " (cutoff:3.500A) removed outlier: 4.370A pdb=" N PHE J 198 " --> pdb=" O ARG J 156 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'K' and resid 194 through 196 removed outlier: 3.921A pdb=" N ILE K 194 " --> pdb=" O ILE K 133 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N SER K 196 " --> pdb=" O LYS K 131 " (cutoff:3.500A) removed outlier: 4.968A pdb=" N LEU K 217 " --> pdb=" O SER K 134 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'K' and resid 163 through 164 removed outlier: 3.890A pdb=" N TRP K 163 " --> pdb=" O TYR K 155 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N TYR K 155 " --> pdb=" O TRP K 163 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N ARG K 200 " --> pdb=" O GLN K 154 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N ARG K 156 " --> pdb=" O PHE K 198 " (cutoff:3.500A) removed outlier: 4.368A pdb=" N PHE K 198 " --> pdb=" O ARG K 156 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'L' and resid 194 through 196 removed outlier: 3.921A pdb=" N ILE L 194 " --> pdb=" O ILE L 133 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N SER L 196 " --> pdb=" O LYS L 131 " (cutoff:3.500A) removed outlier: 4.967A pdb=" N LEU L 217 " --> pdb=" O SER L 134 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'L' and resid 163 through 164 removed outlier: 3.889A pdb=" N TRP L 163 " --> pdb=" O TYR L 155 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N TYR L 155 " --> pdb=" O TRP L 163 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N ARG L 200 " --> pdb=" O GLN L 154 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N ARG L 156 " --> pdb=" O PHE L 198 " (cutoff:3.500A) removed outlier: 4.371A pdb=" N PHE L 198 " --> pdb=" O ARG L 156 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'M' and resid 194 through 196 removed outlier: 3.922A pdb=" N ILE M 194 " --> pdb=" O ILE M 133 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N SER M 196 " --> pdb=" O LYS M 131 " (cutoff:3.500A) removed outlier: 4.967A pdb=" N LEU M 217 " --> pdb=" O SER M 134 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'M' and resid 163 through 164 removed outlier: 3.905A pdb=" N TRP M 163 " --> pdb=" O TYR M 155 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N TYR M 155 " --> pdb=" O TRP M 163 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N ARG M 200 " --> pdb=" O GLN M 154 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N ARG M 156 " --> pdb=" O PHE M 198 " (cutoff:3.500A) removed outlier: 4.372A pdb=" N PHE M 198 " --> pdb=" O ARG M 156 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'N' and resid 194 through 196 removed outlier: 3.923A pdb=" N ILE N 194 " --> pdb=" O ILE N 133 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N SER N 196 " --> pdb=" O LYS N 131 " (cutoff:3.500A) removed outlier: 4.966A pdb=" N LEU N 217 " --> pdb=" O SER N 134 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'N' and resid 163 through 164 removed outlier: 3.906A pdb=" N TRP N 163 " --> pdb=" O TYR N 155 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N TYR N 155 " --> pdb=" O TRP N 163 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N ARG N 200 " --> pdb=" O GLN N 154 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N ARG N 156 " --> pdb=" O PHE N 198 " (cutoff:3.500A) removed outlier: 4.373A pdb=" N PHE N 198 " --> pdb=" O ARG N 156 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'O' and resid 194 through 196 removed outlier: 3.921A pdb=" N ILE O 194 " --> pdb=" O ILE O 133 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N SER O 196 " --> pdb=" O LYS O 131 " (cutoff:3.500A) removed outlier: 4.966A pdb=" N LEU O 217 " --> pdb=" O SER O 134 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'O' and resid 163 through 164 removed outlier: 3.890A pdb=" N TRP O 163 " --> pdb=" O TYR O 155 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N TYR O 155 " --> pdb=" O TRP O 163 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N ARG O 200 " --> pdb=" O GLN O 154 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N ARG O 156 " --> pdb=" O PHE O 198 " (cutoff:3.500A) removed outlier: 4.370A pdb=" N PHE O 198 " --> pdb=" O ARG O 156 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'P' and resid 194 through 196 removed outlier: 3.918A pdb=" N ILE P 194 " --> pdb=" O ILE P 133 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N SER P 196 " --> pdb=" O LYS P 131 " (cutoff:3.500A) removed outlier: 4.968A pdb=" N LEU P 217 " --> pdb=" O SER P 134 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'P' and resid 163 through 164 removed outlier: 3.897A pdb=" N TRP P 163 " --> pdb=" O TYR P 155 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N TYR P 155 " --> pdb=" O TRP P 163 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N ARG P 200 " --> pdb=" O GLN P 154 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N ARG P 156 " --> pdb=" O PHE P 198 " (cutoff:3.500A) removed outlier: 4.369A pdb=" N PHE P 198 " --> pdb=" O ARG P 156 " (cutoff:3.500A) 64 hydrogen bonds defined for protein. 144 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: 11.75 Time building geometry restraints manager: 30.80 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 19984 1.03 - 1.23: 80 1.23 - 1.42: 9376 1.42 - 1.62: 11744 1.62 - 1.81: 144 Bond restraints: 41328 Sorted by residual: bond pdb=" N GLY I 140 " pdb=" CA GLY I 140 " ideal model delta sigma weight residual 1.445 1.452 -0.007 8.30e-03 1.45e+04 7.43e-01 bond pdb=" N GLY H 140 " pdb=" CA GLY H 140 " ideal model delta sigma weight residual 1.445 1.452 -0.007 8.30e-03 1.45e+04 7.33e-01 bond pdb=" N GLY N 140 " pdb=" CA GLY N 140 " ideal model delta sigma weight residual 1.445 1.452 -0.007 8.30e-03 1.45e+04 7.09e-01 bond pdb=" N GLY P 140 " pdb=" CA GLY P 140 " ideal model delta sigma weight residual 1.445 1.451 -0.007 8.30e-03 1.45e+04 6.62e-01 bond pdb=" N GLY M 140 " pdb=" CA GLY M 140 " ideal model delta sigma weight residual 1.445 1.451 -0.007 8.30e-03 1.45e+04 6.47e-01 ... (remaining 41323 not shown) Histogram of bond angle deviations from ideal: 100.84 - 107.46: 1428 107.46 - 114.09: 47955 114.09 - 120.72: 12753 120.72 - 127.35: 11768 127.35 - 133.97: 384 Bond angle restraints: 74288 Sorted by residual: angle pdb=" N TRP C 92 " pdb=" CA TRP C 92 " pdb=" C TRP C 92 " ideal model delta sigma weight residual 114.56 110.93 3.63 1.27e+00 6.20e-01 8.15e+00 angle pdb=" N TRP E 92 " pdb=" CA TRP E 92 " pdb=" C TRP E 92 " ideal model delta sigma weight residual 114.56 110.93 3.63 1.27e+00 6.20e-01 8.15e+00 angle pdb=" N TRP H 92 " pdb=" CA TRP H 92 " pdb=" C TRP H 92 " ideal model delta sigma weight residual 114.56 110.94 3.62 1.27e+00 6.20e-01 8.14e+00 angle pdb=" N TRP L 92 " pdb=" CA TRP L 92 " pdb=" C TRP L 92 " ideal model delta sigma weight residual 114.56 110.96 3.60 1.27e+00 6.20e-01 8.03e+00 angle pdb=" N TRP P 92 " pdb=" CA TRP P 92 " pdb=" C TRP P 92 " ideal model delta sigma weight residual 114.56 110.97 3.59 1.27e+00 6.20e-01 8.00e+00 ... (remaining 74283 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 8.93: 15946 8.93 - 17.86: 584 17.86 - 26.79: 158 26.79 - 35.73: 96 35.73 - 44.66: 16 Dihedral angle restraints: 16800 sinusoidal: 7744 harmonic: 9056 Sorted by residual: dihedral pdb=" SG CYS H 63 " pdb=" CB CYS H 219 " pdb=" SG CYS H 219 " pdb=" CA CYS H 219 " ideal model delta sinusoidal sigma weight residual -73.00 -117.66 44.66 1 2.00e+01 2.50e-03 6.93e+00 dihedral pdb=" SG CYS E 63 " pdb=" CB CYS E 219 " pdb=" SG CYS E 219 " pdb=" CA CYS E 219 " ideal model delta sinusoidal sigma weight residual -73.00 -117.65 44.65 1 2.00e+01 2.50e-03 6.93e+00 dihedral pdb=" SG CYS A 63 " pdb=" CB CYS A 219 " pdb=" SG CYS A 219 " pdb=" CA CYS A 219 " ideal model delta sinusoidal sigma weight residual -73.00 -117.64 44.64 1 2.00e+01 2.50e-03 6.92e+00 ... (remaining 16797 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.026: 1919 0.026 - 0.052: 717 0.052 - 0.079: 68 0.079 - 0.105: 172 0.105 - 0.131: 148 Chirality restraints: 3024 Sorted by residual: chirality pdb=" CA ILE E 125 " pdb=" N ILE E 125 " pdb=" C ILE E 125 " pdb=" CB ILE E 125 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.29e-01 chirality pdb=" CA ILE D 125 " pdb=" N ILE D 125 " pdb=" C ILE D 125 " pdb=" CB ILE D 125 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.29e-01 chirality pdb=" CA ILE O 125 " pdb=" N ILE O 125 " pdb=" C ILE O 125 " pdb=" CB ILE O 125 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.24e-01 ... (remaining 3021 not shown) Planarity restraints: 6064 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CG GLN G 187 " 0.142 2.00e-02 2.50e+03 1.59e-01 3.81e+02 pdb=" CD GLN G 187 " -0.008 2.00e-02 2.50e+03 pdb=" OE1 GLN G 187 " -0.139 2.00e-02 2.50e+03 pdb=" NE2 GLN G 187 " 0.002 2.00e-02 2.50e+03 pdb="HE21 GLN G 187 " -0.236 2.00e-02 2.50e+03 pdb="HE22 GLN G 187 " 0.239 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLN L 187 " 0.142 2.00e-02 2.50e+03 1.59e-01 3.80e+02 pdb=" CD GLN L 187 " -0.009 2.00e-02 2.50e+03 pdb=" OE1 GLN L 187 " -0.139 2.00e-02 2.50e+03 pdb=" NE2 GLN L 187 " 0.002 2.00e-02 2.50e+03 pdb="HE21 GLN L 187 " -0.236 2.00e-02 2.50e+03 pdb="HE22 GLN L 187 " 0.239 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLN D 187 " 0.142 2.00e-02 2.50e+03 1.59e-01 3.80e+02 pdb=" CD GLN D 187 " -0.008 2.00e-02 2.50e+03 pdb=" OE1 GLN D 187 " -0.139 2.00e-02 2.50e+03 pdb=" NE2 GLN D 187 " 0.002 2.00e-02 2.50e+03 pdb="HE21 GLN D 187 " -0.236 2.00e-02 2.50e+03 pdb="HE22 GLN D 187 " 0.239 2.00e-02 2.50e+03 ... (remaining 6061 not shown) Histogram of nonbonded interaction distances: 1.72 - 2.30: 6348 2.30 - 2.87: 91425 2.87 - 3.45: 91171 3.45 - 4.02: 124081 4.02 - 4.60: 190048 Nonbonded interactions: 503073 Sorted by model distance: nonbonded pdb=" O ALA E 98 " pdb=" HE ARG E 102 " model vdw 1.720 1.850 nonbonded pdb=" O ALA H 98 " pdb=" HE ARG H 102 " model vdw 1.721 1.850 nonbonded pdb=" O ALA M 98 " pdb=" HE ARG M 102 " model vdw 1.721 1.850 nonbonded pdb=" O ALA C 98 " pdb=" HE ARG C 102 " model vdw 1.721 1.850 nonbonded pdb=" O ALA P 98 " pdb=" HE ARG P 102 " model vdw 1.721 1.850 ... (remaining 503068 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' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.310 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: 0.600 Extract box with map and model: 7.600 Check model and map are aligned: 0.620 Set scattering table: 0.360 Process input model: 111.250 Find NCS groups from input model: 1.900 Set up NCS constraints: 0.230 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.070 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 126.940 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.2845 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 : 0.001 0.013 21296 Z= 0.099 Angle : 0.360 3.625 28928 Z= 0.217 Chirality : 0.041 0.131 3024 Planarity : 0.001 0.011 3680 Dihedral : 4.916 31.060 7792 Min Nonbonded Distance : 2.309 Molprobity Statistics. All-atom Clashscore : 3.73 Ramachandran Plot: Outliers : 2.58 % Allowed : 17.70 % Favored : 79.72 % Rotamer Outliers : 0.00 % 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: -5.61 (0.12), residues: 2480 helix: None (None), residues: 0 sheet: -4.79 (0.17), residues: 160 loop : -4.14 (0.10), residues: 2320 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4960 Ramachandran restraints generated. 2480 Oldfield, 0 Emsley, 2480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4960 Ramachandran restraints generated. 2480 Oldfield, 0 Emsley, 2480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 177 is missing expected H atoms. Skipping. Residue TYR 177 is missing expected H atoms. Skipping. Residue TYR 177 is missing expected H atoms. Skipping. Residue TYR 177 is missing expected H atoms. Skipping. Residue TYR 177 is missing expected H atoms. Skipping. Residue TYR 177 is missing expected H atoms. Skipping. Residue TYR 177 is missing expected H atoms. Skipping. Residue TYR 177 is missing expected H atoms. Skipping. Residue TYR 177 is missing expected H atoms. Skipping. Residue TYR 177 is missing expected H atoms. Skipping. Residue TYR 177 is missing expected H atoms. Skipping. Residue TYR 177 is missing expected H atoms. Skipping. Residue TYR 177 is missing expected H atoms. Skipping. Residue TYR 177 is missing expected H atoms. Skipping. Residue TYR 177 is missing expected H atoms. Skipping. Residue TYR 177 is missing expected H atoms. Skipping. Evaluate side-chains 782 residues out of total 2288 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 782 time to evaluate : 3.575 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 782 average time/residue: 0.9197 time to fit residues: 1023.0130 Evaluate side-chains 534 residues out of total 2288 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 534 time to evaluate : 3.360 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 4.2402 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 202 optimal weight: 4.9990 chunk 181 optimal weight: 9.9990 chunk 100 optimal weight: 8.9990 chunk 62 optimal weight: 4.9990 chunk 122 optimal weight: 5.9990 chunk 97 optimal weight: 3.9990 chunk 188 optimal weight: 6.9990 chunk 72 optimal weight: 5.9990 chunk 114 optimal weight: 0.9990 chunk 140 optimal weight: 5.9990 chunk 217 optimal weight: 7.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 85 ASN A 187 GLN B 187 GLN C 187 GLN D 187 GLN E 187 GLN F 187 GLN G 85 ASN G 187 GLN H 187 GLN I 187 GLN J 121 GLN J 187 GLN K 187 GLN L 187 GLN M 187 GLN N 187 GLN O 187 GLN P 187 GLN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4085 moved from start: 0.6452 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.068 21296 Z= 0.425 Angle : 0.849 10.151 28928 Z= 0.446 Chirality : 0.047 0.189 3024 Planarity : 0.008 0.120 3680 Dihedral : 4.937 22.413 2784 Min Nonbonded Distance : 1.864 Molprobity Statistics. All-atom Clashscore : 26.86 Ramachandran Plot: Outliers : 1.29 % Allowed : 13.15 % Favored : 85.56 % Rotamer Outliers : 0.00 % 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: -4.82 (0.13), residues: 2480 helix: None (None), residues: 0 sheet: -2.53 (0.18), residues: 160 loop : -3.69 (0.11), residues: 2320 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4960 Ramachandran restraints generated. 2480 Oldfield, 0 Emsley, 2480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4960 Ramachandran restraints generated. 2480 Oldfield, 0 Emsley, 2480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 177 is missing expected H atoms. Skipping. Residue TYR 177 is missing expected H atoms. Skipping. Residue TYR 177 is missing expected H atoms. Skipping. Residue TYR 177 is missing expected H atoms. Skipping. Residue TYR 177 is missing expected H atoms. Skipping. Residue TYR 177 is missing expected H atoms. Skipping. Residue TYR 177 is missing expected H atoms. Skipping. Residue TYR 177 is missing expected H atoms. Skipping. Residue TYR 177 is missing expected H atoms. Skipping. Residue TYR 177 is missing expected H atoms. Skipping. Residue TYR 177 is missing expected H atoms. Skipping. Residue TYR 177 is missing expected H atoms. Skipping. Residue TYR 177 is missing expected H atoms. Skipping. Residue TYR 177 is missing expected H atoms. Skipping. Residue TYR 177 is missing expected H atoms. Skipping. Residue TYR 177 is missing expected H atoms. Skipping. Evaluate side-chains 680 residues out of total 2288 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 680 time to evaluate : 3.728 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 680 average time/residue: 0.8923 time to fit residues: 878.8633 Evaluate side-chains 512 residues out of total 2288 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 512 time to evaluate : 3.364 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 4.3021 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 121 optimal weight: 8.9990 chunk 67 optimal weight: 0.8980 chunk 181 optimal weight: 7.9990 chunk 148 optimal weight: 4.9990 chunk 60 optimal weight: 7.9990 chunk 218 optimal weight: 8.9990 chunk 235 optimal weight: 6.9990 chunk 194 optimal weight: 5.9990 chunk 216 optimal weight: 4.9990 chunk 74 optimal weight: 0.9980 chunk 175 optimal weight: 6.9990 overall best weight: 3.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 85 ASN ** B 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 85 ASN ** E 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 85 ASN K 124 GLN M 85 ASN N 85 ASN N 124 GLN O 85 ASN O 124 GLN P 85 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4526 moved from start: 0.8939 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.100 21296 Z= 0.337 Angle : 0.655 7.906 28928 Z= 0.348 Chirality : 0.043 0.206 3024 Planarity : 0.006 0.107 3680 Dihedral : 4.972 18.428 2784 Min Nonbonded Distance : 1.827 Molprobity Statistics. All-atom Clashscore : 22.22 Ramachandran Plot: Outliers : 0.89 % Allowed : 14.76 % Favored : 84.35 % Rotamer Outliers : 0.00 % 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: -4.53 (0.13), residues: 2480 helix: None (None), residues: 0 sheet: -1.99 (0.19), residues: 192 loop : -3.51 (0.11), residues: 2288 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4960 Ramachandran restraints generated. 2480 Oldfield, 0 Emsley, 2480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4960 Ramachandran restraints generated. 2480 Oldfield, 0 Emsley, 2480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 177 is missing expected H atoms. Skipping. Residue TYR 177 is missing expected H atoms. Skipping. Residue TYR 177 is missing expected H atoms. Skipping. Residue TYR 177 is missing expected H atoms. Skipping. Residue TYR 177 is missing expected H atoms. Skipping. Residue TYR 177 is missing expected H atoms. Skipping. Residue TYR 177 is missing expected H atoms. Skipping. Residue TYR 177 is missing expected H atoms. Skipping. Residue TYR 177 is missing expected H atoms. Skipping. Residue TYR 177 is missing expected H atoms. Skipping. Residue TYR 177 is missing expected H atoms. Skipping. Residue TYR 177 is missing expected H atoms. Skipping. Residue TYR 177 is missing expected H atoms. Skipping. Residue TYR 177 is missing expected H atoms. Skipping. Residue TYR 177 is missing expected H atoms. Skipping. Residue TYR 177 is missing expected H atoms. Skipping. Evaluate side-chains 659 residues out of total 2288 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 659 time to evaluate : 3.424 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 659 average time/residue: 0.8222 time to fit residues: 799.9564 Evaluate side-chains 531 residues out of total 2288 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 531 time to evaluate : 3.426 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 4.2844 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 215 optimal weight: 6.9990 chunk 164 optimal weight: 2.9990 chunk 113 optimal weight: 6.9990 chunk 24 optimal weight: 7.9990 chunk 104 optimal weight: 0.5980 chunk 146 optimal weight: 0.9980 chunk 219 optimal weight: 8.9990 chunk 231 optimal weight: 4.9990 chunk 114 optimal weight: 0.8980 chunk 207 optimal weight: 6.9990 chunk 62 optimal weight: 0.9980 overall best weight: 1.2982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 99 ASN ** B 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 207 HIS F 207 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4480 moved from start: 0.9464 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.027 21296 Z= 0.162 Angle : 0.475 4.348 28928 Z= 0.241 Chirality : 0.041 0.149 3024 Planarity : 0.004 0.048 3680 Dihedral : 4.217 16.612 2784 Min Nonbonded Distance : 1.974 Molprobity Statistics. All-atom Clashscore : 13.22 Ramachandran Plot: Outliers : 0.65 % Allowed : 8.02 % Favored : 91.33 % Rotamer Outliers : 0.00 % 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: -4.16 (0.14), residues: 2480 helix: None (None), residues: 0 sheet: -1.08 (0.22), residues: 224 loop : -3.33 (0.11), residues: 2256 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4960 Ramachandran restraints generated. 2480 Oldfield, 0 Emsley, 2480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4960 Ramachandran restraints generated. 2480 Oldfield, 0 Emsley, 2480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 177 is missing expected H atoms. Skipping. Residue TYR 177 is missing expected H atoms. Skipping. Residue TYR 177 is missing expected H atoms. Skipping. Residue TYR 177 is missing expected H atoms. Skipping. Residue TYR 177 is missing expected H atoms. Skipping. Residue TYR 177 is missing expected H atoms. Skipping. Residue TYR 177 is missing expected H atoms. Skipping. Residue TYR 177 is missing expected H atoms. Skipping. Residue TYR 177 is missing expected H atoms. Skipping. Residue TYR 177 is missing expected H atoms. Skipping. Residue TYR 177 is missing expected H atoms. Skipping. Residue TYR 177 is missing expected H atoms. Skipping. Residue TYR 177 is missing expected H atoms. Skipping. Residue TYR 177 is missing expected H atoms. Skipping. Residue TYR 177 is missing expected H atoms. Skipping. Residue TYR 177 is missing expected H atoms. Skipping. Evaluate side-chains 652 residues out of total 2288 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 652 time to evaluate : 3.535 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 652 average time/residue: 0.7960 time to fit residues: 768.5553 Evaluate side-chains 538 residues out of total 2288 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 538 time to evaluate : 3.241 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.9161 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 193 optimal weight: 0.9990 chunk 131 optimal weight: 10.0000 chunk 3 optimal weight: 4.9990 chunk 172 optimal weight: 8.9990 chunk 95 optimal weight: 10.0000 chunk 197 optimal weight: 6.9990 chunk 160 optimal weight: 0.8980 chunk 0 optimal weight: 7.9990 chunk 118 optimal weight: 5.9990 chunk 208 optimal weight: 6.9990 chunk 58 optimal weight: 4.9990 overall best weight: 3.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 85 ASN ** H 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 85 ASN ** J 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 85 ASN K 104 ASN L 104 ASN ** M 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 85 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5020 moved from start: 1.1542 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.097 21296 Z= 0.350 Angle : 0.692 5.745 28928 Z= 0.364 Chirality : 0.044 0.152 3024 Planarity : 0.005 0.054 3680 Dihedral : 5.608 21.449 2784 Min Nonbonded Distance : 1.767 Molprobity Statistics. All-atom Clashscore : 28.55 Ramachandran Plot: Outliers : 0.65 % Allowed : 16.77 % Favored : 82.58 % Rotamer Outliers : 0.00 % 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: -4.40 (0.14), residues: 2480 helix: None (None), residues: 0 sheet: -3.48 (0.20), residues: 496 loop : -3.04 (0.12), residues: 1984 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4960 Ramachandran restraints generated. 2480 Oldfield, 0 Emsley, 2480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4960 Ramachandran restraints generated. 2480 Oldfield, 0 Emsley, 2480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 177 is missing expected H atoms. Skipping. Residue TYR 177 is missing expected H atoms. Skipping. Residue TYR 177 is missing expected H atoms. Skipping. Residue TYR 177 is missing expected H atoms. Skipping. Residue TYR 177 is missing expected H atoms. Skipping. Residue TYR 177 is missing expected H atoms. Skipping. Residue TYR 177 is missing expected H atoms. Skipping. Residue TYR 177 is missing expected H atoms. Skipping. Residue TYR 177 is missing expected H atoms. Skipping. Residue TYR 177 is missing expected H atoms. Skipping. Residue TYR 177 is missing expected H atoms. Skipping. Residue TYR 177 is missing expected H atoms. Skipping. Residue TYR 177 is missing expected H atoms. Skipping. Residue TYR 177 is missing expected H atoms. Skipping. Residue TYR 177 is missing expected H atoms. Skipping. Residue TYR 177 is missing expected H atoms. Skipping. Evaluate side-chains 646 residues out of total 2288 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 646 time to evaluate : 3.423 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 646 average time/residue: 0.7834 time to fit residues: 752.5765 Evaluate side-chains 531 residues out of total 2288 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 531 time to evaluate : 3.608 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 4.2674 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 78 optimal weight: 5.9990 chunk 208 optimal weight: 5.9990 chunk 45 optimal weight: 4.9990 chunk 136 optimal weight: 0.8980 chunk 57 optimal weight: 8.9990 chunk 232 optimal weight: 0.9990 chunk 192 optimal weight: 2.9990 chunk 107 optimal weight: 7.9990 chunk 19 optimal weight: 7.9990 chunk 76 optimal weight: 3.9990 chunk 121 optimal weight: 10.0000 overall best weight: 2.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 85 ASN A 162 ASN ** B 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 85 ASN ** C 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 207 HIS G 85 ASN H 85 ASN H 207 HIS J 104 ASN J 162 ASN K 104 ASN ** K 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 85 ASN M 104 ASN N 104 ASN ** N 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 124 GLN ** O 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 85 ASN P 162 ASN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5030 moved from start: 1.2317 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.048 21296 Z= 0.252 Angle : 0.562 4.538 28928 Z= 0.294 Chirality : 0.043 0.151 3024 Planarity : 0.005 0.051 3680 Dihedral : 5.249 19.167 2784 Min Nonbonded Distance : 1.894 Molprobity Statistics. All-atom Clashscore : 19.65 Ramachandran Plot: Outliers : 0.65 % Allowed : 13.83 % Favored : 85.52 % Rotamer Outliers : 0.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.32 (0.15), residues: 2480 helix: None (None), residues: 0 sheet: -3.11 (0.18), residues: 624 loop : -3.01 (0.12), residues: 1856 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4960 Ramachandran restraints generated. 2480 Oldfield, 0 Emsley, 2480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4960 Ramachandran restraints generated. 2480 Oldfield, 0 Emsley, 2480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 177 is missing expected H atoms. Skipping. Residue TYR 177 is missing expected H atoms. Skipping. Residue TYR 177 is missing expected H atoms. Skipping. Residue TYR 177 is missing expected H atoms. Skipping. Residue TYR 177 is missing expected H atoms. Skipping. Residue TYR 177 is missing expected H atoms. Skipping. Residue TYR 177 is missing expected H atoms. Skipping. Residue TYR 177 is missing expected H atoms. Skipping. Residue TYR 177 is missing expected H atoms. Skipping. Residue TYR 177 is missing expected H atoms. Skipping. Residue TYR 177 is missing expected H atoms. Skipping. Residue TYR 177 is missing expected H atoms. Skipping. Residue TYR 177 is missing expected H atoms. Skipping. Residue TYR 177 is missing expected H atoms. Skipping. Residue TYR 177 is missing expected H atoms. Skipping. Residue TYR 177 is missing expected H atoms. Skipping. Evaluate side-chains 651 residues out of total 2288 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 648 time to evaluate : 3.924 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 3 outliers final: 1 residues processed: 648 average time/residue: 0.8126 time to fit residues: 785.0286 Evaluate side-chains 533 residues out of total 2288 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 532 time to evaluate : 3.328 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.4414 time to fit residues: 5.0255 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 223 optimal weight: 3.9990 chunk 26 optimal weight: 1.9990 chunk 132 optimal weight: 8.9990 chunk 169 optimal weight: 4.9990 chunk 131 optimal weight: 4.9990 chunk 195 optimal weight: 0.7980 chunk 129 optimal weight: 1.9990 chunk 231 optimal weight: 2.9990 chunk 144 optimal weight: 3.9990 chunk 141 optimal weight: 0.9990 chunk 106 optimal weight: 7.9990 overall best weight: 1.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 162 ASN ** C 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 207 HIS J 104 ASN M 124 GLN O 104 ASN P 104 ASN ** P 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5037 moved from start: 1.2720 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.039 21296 Z= 0.196 Angle : 0.515 4.807 28928 Z= 0.266 Chirality : 0.042 0.146 3024 Planarity : 0.005 0.062 3680 Dihedral : 4.730 17.058 2784 Min Nonbonded Distance : 1.885 Molprobity Statistics. All-atom Clashscore : 15.55 Ramachandran Plot: Outliers : 0.65 % Allowed : 14.03 % Favored : 85.32 % Rotamer Outliers : 0.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.15 (0.15), residues: 2480 helix: None (None), residues: 0 sheet: -2.78 (0.21), residues: 544 loop : -3.01 (0.12), residues: 1936 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4960 Ramachandran restraints generated. 2480 Oldfield, 0 Emsley, 2480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4960 Ramachandran restraints generated. 2480 Oldfield, 0 Emsley, 2480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 177 is missing expected H atoms. Skipping. Residue TYR 177 is missing expected H atoms. Skipping. Residue TYR 177 is missing expected H atoms. Skipping. Residue TYR 177 is missing expected H atoms. Skipping. Residue TYR 177 is missing expected H atoms. Skipping. Residue TYR 177 is missing expected H atoms. Skipping. Residue TYR 177 is missing expected H atoms. Skipping. Residue TYR 177 is missing expected H atoms. Skipping. Residue TYR 177 is missing expected H atoms. Skipping. Residue TYR 177 is missing expected H atoms. Skipping. Residue TYR 177 is missing expected H atoms. Skipping. Residue TYR 177 is missing expected H atoms. Skipping. Residue TYR 177 is missing expected H atoms. Skipping. Residue TYR 177 is missing expected H atoms. Skipping. Residue TYR 177 is missing expected H atoms. Skipping. Residue TYR 177 is missing expected H atoms. Skipping. Evaluate side-chains 627 residues out of total 2288 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 626 time to evaluate : 3.560 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 626 average time/residue: 0.7846 time to fit residues: 739.1518 Evaluate side-chains 515 residues out of total 2288 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 515 time to evaluate : 3.428 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 4.3725 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 143 optimal weight: 5.9990 chunk 92 optimal weight: 9.9990 chunk 138 optimal weight: 20.0000 chunk 69 optimal weight: 7.9990 chunk 45 optimal weight: 5.9990 chunk 44 optimal weight: 0.0470 chunk 147 optimal weight: 4.9990 chunk 157 optimal weight: 6.9990 chunk 114 optimal weight: 0.8980 chunk 21 optimal weight: 4.9990 chunk 181 optimal weight: 0.9990 overall best weight: 2.3884 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 66 HIS ** B 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 104 ASN I 104 ASN ** I 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 104 ASN K 104 ASN ** K 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 104 ASN M 104 ASN M 124 GLN ** M 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 104 ASN ** N 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 104 ASN ** O 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 66 HIS P 104 ASN ** P 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5202 moved from start: 1.3571 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.037 21296 Z= 0.241 Angle : 0.558 4.855 28928 Z= 0.292 Chirality : 0.042 0.141 3024 Planarity : 0.005 0.066 3680 Dihedral : 5.059 18.940 2784 Min Nonbonded Distance : 1.826 Molprobity Statistics. All-atom Clashscore : 18.84 Ramachandran Plot: Outliers : 0.65 % Allowed : 15.00 % Favored : 84.35 % Rotamer Outliers : 0.00 % 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: -4.09 (0.15), residues: 2480 helix: None (None), residues: 0 sheet: -2.58 (0.21), residues: 544 loop : -3.02 (0.12), residues: 1936 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4960 Ramachandran restraints generated. 2480 Oldfield, 0 Emsley, 2480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4960 Ramachandran restraints generated. 2480 Oldfield, 0 Emsley, 2480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 177 is missing expected H atoms. Skipping. Residue TYR 177 is missing expected H atoms. Skipping. Residue TYR 177 is missing expected H atoms. Skipping. Residue TYR 177 is missing expected H atoms. Skipping. Residue TYR 177 is missing expected H atoms. Skipping. Residue TYR 177 is missing expected H atoms. Skipping. Residue TYR 177 is missing expected H atoms. Skipping. Residue TYR 177 is missing expected H atoms. Skipping. Residue TYR 177 is missing expected H atoms. Skipping. Residue TYR 177 is missing expected H atoms. Skipping. Residue TYR 177 is missing expected H atoms. Skipping. Residue TYR 177 is missing expected H atoms. Skipping. Residue TYR 177 is missing expected H atoms. Skipping. Residue TYR 177 is missing expected H atoms. Skipping. Residue TYR 177 is missing expected H atoms. Skipping. Residue TYR 177 is missing expected H atoms. Skipping. Evaluate side-chains 637 residues out of total 2288 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 637 time to evaluate : 3.524 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 637 average time/residue: 0.7820 time to fit residues: 751.6731 Evaluate side-chains 513 residues out of total 2288 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 513 time to evaluate : 3.533 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 4.3666 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 210 optimal weight: 4.9990 chunk 221 optimal weight: 9.9990 chunk 202 optimal weight: 7.9990 chunk 215 optimal weight: 2.9990 chunk 129 optimal weight: 4.9990 chunk 93 optimal weight: 20.0000 chunk 169 optimal weight: 5.9990 chunk 66 optimal weight: 0.9980 chunk 194 optimal weight: 4.9990 chunk 203 optimal weight: 4.9990 chunk 214 optimal weight: 5.9990 overall best weight: 3.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 85 ASN ** A 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 187 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 85 ASN ** B 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 187 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 85 ASN ** G 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 66 HIS I 104 ASN ** I 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 66 HIS J 85 ASN ** J 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 66 HIS ** K 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 207 HIS L 66 HIS L 104 ASN ** L 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 104 ASN ** M 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 104 ASN ** N 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5454 moved from start: 1.4980 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.065 21296 Z= 0.348 Angle : 0.681 7.699 28928 Z= 0.363 Chirality : 0.044 0.179 3024 Planarity : 0.006 0.070 3680 Dihedral : 5.933 25.763 2784 Min Nonbonded Distance : 1.861 Molprobity Statistics. All-atom Clashscore : 31.03 Ramachandran Plot: Outliers : 0.65 % Allowed : 19.23 % Favored : 80.12 % Rotamer Outliers : 0.00 % 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: -4.20 (0.15), residues: 2480 helix: None (None), residues: 0 sheet: -2.80 (0.21), residues: 576 loop : -3.04 (0.12), residues: 1904 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4960 Ramachandran restraints generated. 2480 Oldfield, 0 Emsley, 2480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4960 Ramachandran restraints generated. 2480 Oldfield, 0 Emsley, 2480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 177 is missing expected H atoms. Skipping. Residue TYR 177 is missing expected H atoms. Skipping. Residue TYR 177 is missing expected H atoms. Skipping. Residue TYR 177 is missing expected H atoms. Skipping. Residue TYR 177 is missing expected H atoms. Skipping. Residue TYR 177 is missing expected H atoms. Skipping. Residue TYR 177 is missing expected H atoms. Skipping. Residue TYR 177 is missing expected H atoms. Skipping. Residue TYR 177 is missing expected H atoms. Skipping. Residue TYR 177 is missing expected H atoms. Skipping. Residue TYR 177 is missing expected H atoms. Skipping. Residue TYR 177 is missing expected H atoms. Skipping. Residue TYR 177 is missing expected H atoms. Skipping. Residue TYR 177 is missing expected H atoms. Skipping. Residue TYR 177 is missing expected H atoms. Skipping. Residue TYR 177 is missing expected H atoms. Skipping. Evaluate side-chains 634 residues out of total 2288 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 634 time to evaluate : 3.513 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 634 average time/residue: 0.7623 time to fit residues: 730.2620 Evaluate side-chains 485 residues out of total 2288 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 485 time to evaluate : 3.480 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 4.3720 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 141 optimal weight: 0.8980 chunk 227 optimal weight: 0.4980 chunk 139 optimal weight: 0.8980 chunk 108 optimal weight: 7.9990 chunk 158 optimal weight: 0.6980 chunk 239 optimal weight: 3.9990 chunk 220 optimal weight: 4.9990 chunk 190 optimal weight: 2.9990 chunk 19 optimal weight: 2.9990 chunk 147 optimal weight: 1.9990 chunk 116 optimal weight: 8.9990 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 85 ASN B 85 ASN ** B 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 207 HIS C 104 ASN ** C 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 207 HIS E 207 HIS ** F 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 85 ASN G 104 ASN ** G 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 207 HIS J 162 ASN K 104 ASN ** K 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 104 ASN ** N 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 104 ASN ** O 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5271 moved from start: 1.4962 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.026 21296 Z= 0.176 Angle : 0.538 8.614 28928 Z= 0.276 Chirality : 0.043 0.163 3024 Planarity : 0.005 0.052 3680 Dihedral : 5.156 17.695 2784 Min Nonbonded Distance : 1.891 Molprobity Statistics. All-atom Clashscore : 16.36 Ramachandran Plot: Outliers : 0.69 % Allowed : 12.26 % Favored : 87.06 % Rotamer Outliers : 0.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.99 (0.15), residues: 2480 helix: None (None), residues: 0 sheet: -2.27 (0.22), residues: 544 loop : -3.03 (0.12), residues: 1936 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4960 Ramachandran restraints generated. 2480 Oldfield, 0 Emsley, 2480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4960 Ramachandran restraints generated. 2480 Oldfield, 0 Emsley, 2480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 177 is missing expected H atoms. Skipping. Residue TYR 177 is missing expected H atoms. Skipping. Residue TYR 177 is missing expected H atoms. Skipping. Residue TYR 177 is missing expected H atoms. Skipping. Residue TYR 177 is missing expected H atoms. Skipping. Residue TYR 177 is missing expected H atoms. Skipping. Residue TYR 177 is missing expected H atoms. Skipping. Residue TYR 177 is missing expected H atoms. Skipping. Residue TYR 177 is missing expected H atoms. Skipping. Residue TYR 177 is missing expected H atoms. Skipping. Residue TYR 177 is missing expected H atoms. Skipping. Residue TYR 177 is missing expected H atoms. Skipping. Residue TYR 177 is missing expected H atoms. Skipping. Residue TYR 177 is missing expected H atoms. Skipping. Residue TYR 177 is missing expected H atoms. Skipping. Residue TYR 177 is missing expected H atoms. Skipping. Evaluate side-chains 664 residues out of total 2288 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 663 time to evaluate : 3.425 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 663 average time/residue: 0.7189 time to fit residues: 729.3732 Evaluate side-chains 509 residues out of total 2288 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 509 time to evaluate : 3.480 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 4.2376 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 151 optimal weight: 0.5980 chunk 202 optimal weight: 7.9990 chunk 58 optimal weight: 2.9990 chunk 175 optimal weight: 6.9990 chunk 28 optimal weight: 0.5980 chunk 52 optimal weight: 0.9980 chunk 190 optimal weight: 1.9990 chunk 79 optimal weight: 5.9990 chunk 195 optimal weight: 0.7980 chunk 24 optimal weight: 0.8980 chunk 35 optimal weight: 5.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 207 HIS D 162 ASN F 162 ASN G 104 ASN ** G 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 162 ASN I 104 ASN I 207 HIS K 85 ASN ** L 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 104 ASN M 124 GLN ** M 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 104 ASN P 104 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4622 r_free = 0.4622 target = 0.174808 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4280 r_free = 0.4280 target = 0.140562 restraints weight = 171934.221| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.4327 r_free = 0.4327 target = 0.145070 restraints weight = 119858.547| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.4358 r_free = 0.4358 target = 0.148231 restraints weight = 91712.759| |-----------------------------------------------------------------------------| r_work (final): 0.4356 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7264 moved from start: 1.4953 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.028 21296 Z= 0.159 Angle : 0.521 5.419 28928 Z= 0.267 Chirality : 0.043 0.163 3024 Planarity : 0.005 0.071 3680 Dihedral : 4.721 16.152 2784 Min Nonbonded Distance : 1.946 Molprobity Statistics. All-atom Clashscore : 14.55 Ramachandran Plot: Outliers : 0.65 % Allowed : 11.90 % Favored : 87.46 % Rotamer Outliers : 0.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.87 (0.15), residues: 2480 helix: None (None), residues: 0 sheet: -2.18 (0.22), residues: 544 loop : -2.95 (0.12), residues: 1936 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 12225.17 seconds wall clock time: 216 minutes 9.89 seconds (12969.89 seconds total)