Starting phenix.real_space_refine on Sun Mar 24 20:17:13 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rgi_24450/03_2024/7rgi_24450_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rgi_24450/03_2024/7rgi_24450.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rgi_24450/03_2024/7rgi_24450.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rgi_24450/03_2024/7rgi_24450.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rgi_24450/03_2024/7rgi_24450_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rgi_24450/03_2024/7rgi_24450_trim_updated.pdb" } resolution = 3.6 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= 0.198 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: 6 Type Number sf(0) Gaussians P 24 5.49 5 S 144 5.16 5 C 13776 2.51 5 N 3768 2.21 5 O 4248 1.98 5 H 21752 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 12": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ASP 16": "OD1" <-> "OD2" Residue "A PHE 24": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ASP 28": "OD1" <-> "OD2" Residue "A ASP 34": "OD1" <-> "OD2" Residue "A PHE 41": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 44": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A GLU 48": "OE1" <-> "OE2" Residue "A ARG 57": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A PHE 90": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A GLU 103": "OE1" <-> "OE2" Residue "A ARG 105": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 224": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 253": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A TYR 289": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 294": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 353": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ARG 355": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ASP 364": "OD1" <-> "OD2" Residue "A GLU 395": "OE1" <-> "OE2" Residue "A ARG 474": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A TYR 484": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 490": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 509": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B TYR 12": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B ASP 16": "OD1" <-> "OD2" Residue "B PHE 24": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B ASP 28": "OD1" <-> "OD2" Residue "B ASP 34": "OD1" <-> "OD2" Residue "B PHE 41": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 44": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B GLU 48": "OE1" <-> "OE2" Residue "B ARG 57": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B PHE 90": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B ARG 105": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 224": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 253": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B TYR 289": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B TYR 294": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B TYR 353": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B ARG 355": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ASP 364": "OD1" <-> "OD2" Residue "B ARG 474": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B TYR 484": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 490": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B TYR 509": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C TYR 12": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C ASP 16": "OD1" <-> "OD2" Residue "C PHE 24": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C ASP 28": "OD1" <-> "OD2" Residue "C ASP 34": "OD1" <-> "OD2" Residue "C PHE 41": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C PHE 44": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C GLU 48": "OE1" <-> "OE2" Residue "C ARG 57": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C PHE 90": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C ARG 105": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C ARG 224": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C ARG 253": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C TYR 289": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C TYR 294": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C TYR 353": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C ARG 355": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C ASP 364": "OD1" <-> "OD2" Residue "C ARG 474": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C TYR 484": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C PHE 490": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C TYR 509": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D TYR 12": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D ASP 16": "OD1" <-> "OD2" Residue "D PHE 24": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D ASP 34": "OD1" <-> "OD2" Residue "D PHE 35": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D PHE 41": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D PHE 44": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D GLU 48": "OE1" <-> "OE2" Residue "D ARG 57": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D PHE 90": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D ARG 105": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D ARG 224": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D ARG 253": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D TYR 289": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D TYR 294": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D TYR 353": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D ARG 355": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D ASP 364": "OD1" <-> "OD2" Residue "D GLU 395": "OE1" <-> "OE2" Residue "D ARG 474": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D TYR 484": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E TYR 12": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E ASP 16": "OD1" <-> "OD2" Residue "E PHE 24": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E ASP 34": "OD1" <-> "OD2" Residue "E PHE 41": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E PHE 44": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E GLU 48": "OE1" <-> "OE2" Residue "E ARG 57": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "E PHE 90": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E ARG 105": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "E ARG 224": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "E ARG 253": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "E TYR 289": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E TYR 294": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E TYR 353": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E ARG 355": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "E ASP 364": "OD1" <-> "OD2" Residue "E ARG 474": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "E TYR 484": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E PHE 490": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E TYR 509": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F TYR 12": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F ASP 16": "OD1" <-> "OD2" Residue "F PHE 24": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F ASP 28": "OD1" <-> "OD2" Residue "F ASP 34": "OD1" <-> "OD2" Residue "F PHE 41": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F PHE 44": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F GLU 48": "OE1" <-> "OE2" Residue "F ARG 57": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "F PHE 90": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F ARG 105": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "F ARG 224": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "F ARG 253": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "F TYR 289": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F TYR 294": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F TYR 353": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F ARG 355": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "F ASP 364": "OD1" <-> "OD2" Residue "F ARG 474": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "F TYR 484": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F PHE 490": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F TYR 509": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "G TYR 12": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "G ASP 16": "OD1" <-> "OD2" Residue "G PHE 24": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "G ASP 28": "OD1" <-> "OD2" Residue "G PHE 41": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "G PHE 44": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "G GLU 48": "OE1" <-> "OE2" Residue "G ARG 57": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "G PHE 90": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "G ARG 105": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "G ARG 224": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "G ARG 253": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "G TYR 289": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "G TYR 294": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "G TYR 353": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "G ARG 355": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "G ASP 364": "OD1" <-> "OD2" Residue "G ARG 474": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "G TYR 484": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "G PHE 490": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "H TYR 12": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "H ASP 16": "OD1" <-> "OD2" Residue "H PHE 24": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "H ASP 34": "OD1" <-> "OD2" Residue "H PHE 35": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "H PHE 41": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "H PHE 44": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "H GLU 48": "OE1" <-> "OE2" Residue "H ARG 57": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "H PHE 90": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "H ARG 105": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "H ARG 224": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "H ARG 253": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "H TYR 289": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "H TYR 294": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "H TYR 353": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "H ARG 355": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "H ASP 364": "OD1" <-> "OD2" Residue "H ARG 474": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "H TYR 484": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "H TYR 509": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Time to flip residues: 0.10s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 43712 Number of models: 1 Model: "" Number of chains: 16 Chain: "A" Number of atoms: 5397 Number of conformers: 1 Conformer: "" Number of residues, atoms: 357, 5397 Classifications: {'peptide': 357} Link IDs: {'PTRANS': 12, 'TRANS': 344} Chain breaks: 2 Chain: "B" Number of atoms: 5397 Number of conformers: 1 Conformer: "" Number of residues, atoms: 357, 5397 Classifications: {'peptide': 357} Link IDs: {'PTRANS': 12, 'TRANS': 344} Chain breaks: 2 Chain: "C" Number of atoms: 5397 Number of conformers: 1 Conformer: "" Number of residues, atoms: 357, 5397 Classifications: {'peptide': 357} Link IDs: {'PTRANS': 12, 'TRANS': 344} Chain breaks: 2 Chain: "D" Number of atoms: 5397 Number of conformers: 1 Conformer: "" Number of residues, atoms: 357, 5397 Classifications: {'peptide': 357} Link IDs: {'PTRANS': 12, 'TRANS': 344} Chain breaks: 2 Chain: "E" Number of atoms: 5397 Number of conformers: 1 Conformer: "" Number of residues, atoms: 357, 5397 Classifications: {'peptide': 357} Link IDs: {'PTRANS': 12, 'TRANS': 344} Chain breaks: 2 Chain: "F" Number of atoms: 5397 Number of conformers: 1 Conformer: "" Number of residues, atoms: 357, 5397 Classifications: {'peptide': 357} Link IDs: {'PTRANS': 12, 'TRANS': 344} Chain breaks: 2 Chain: "G" Number of atoms: 5397 Number of conformers: 1 Conformer: "" Number of residues, atoms: 357, 5397 Classifications: {'peptide': 357} Link IDs: {'PTRANS': 12, 'TRANS': 344} Chain breaks: 2 Chain: "H" Number of atoms: 5397 Number of conformers: 1 Conformer: "" Number of residues, atoms: 357, 5397 Classifications: {'peptide': 357} Link IDs: {'PTRANS': 12, 'TRANS': 344} Chain breaks: 2 Chain: "A" Number of atoms: 67 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 67 Unusual residues: {'NAD': 1} Classifications: {'RNA': 1, 'undetermined': 1} Modifications used: {'rna2p': 1} Link IDs: {None: 1} Chain: "B" Number of atoms: 67 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 67 Unusual residues: {'NAD': 1} Classifications: {'RNA': 1, 'undetermined': 1} Modifications used: {'rna3p': 1} Link IDs: {None: 1} Chain: "C" Number of atoms: 67 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 67 Unusual residues: {'NAD': 1} Classifications: {'RNA': 1, 'undetermined': 1} Modifications used: {'rna3p': 1} Link IDs: {None: 1} Chain: "D" Number of atoms: 67 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 67 Unusual residues: {'NAD': 1} Classifications: {'RNA': 1, 'undetermined': 1} Modifications used: {'rna3p': 1} Link IDs: {None: 1} Chain: "E" Number of atoms: 67 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 67 Unusual residues: {'NAD': 1} Classifications: {'RNA': 1, 'undetermined': 1} Modifications used: {'rna3p': 1} Link IDs: {None: 1} Chain: "F" Number of atoms: 67 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 67 Unusual residues: {'NAD': 1} Classifications: {'RNA': 1, 'undetermined': 1} Modifications used: {'rna3p': 1} Link IDs: {None: 1} Chain: "G" Number of atoms: 67 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 67 Unusual residues: {'NAD': 1} Classifications: {'RNA': 1, 'undetermined': 1} Modifications used: {'rna3p': 1} Link IDs: {None: 1} Chain: "H" Number of atoms: 67 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 67 Unusual residues: {'NAD': 1} Classifications: {'RNA': 1, 'undetermined': 1} Modifications used: {'rna3p': 1} Link IDs: {None: 1} Time building chain proxies: 19.33, per 1000 atoms: 0.44 Number of scatterers: 43712 At special positions: 0 Unit cell: (142.68, 142.68, 107.88, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 144 16.00 P 24 15.00 O 4248 8.00 N 3768 7.00 C 13776 6.00 H 21752 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 34.12 Conformation dependent library (CDL) restraints added in 5.0 seconds 5616 Ramachandran restraints generated. 2808 Oldfield, 0 Emsley, 2808 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5120 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 113 helices and 31 sheets defined 36.5% alpha, 8.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 6.91 Creating SS restraints... Processing helix chain 'A' and resid 20 through 24 removed outlier: 3.741A pdb=" N PHE A 24 " --> pdb=" O ALA A 20 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 20 through 24' Processing helix chain 'A' and resid 32 through 34 No H-bonds generated for 'chain 'A' and resid 32 through 34' Processing helix chain 'A' and resid 76 through 84 Processing helix chain 'A' and resid 97 through 110 removed outlier: 4.209A pdb=" N PHE A 110 " --> pdb=" O LYS A 106 " (cutoff:3.500A) Processing helix chain 'A' and resid 225 through 232 Processing helix chain 'A' and resid 254 through 265 Processing helix chain 'A' and resid 281 through 293 Processing helix chain 'A' and resid 307 through 316 removed outlier: 4.939A pdb=" N ASN A 312 " --> pdb=" O ALA A 308 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N LEU A 313 " --> pdb=" O GLN A 309 " (cutoff:3.500A) Processing helix chain 'A' and resid 333 through 337 removed outlier: 3.784A pdb=" N MET A 337 " --> pdb=" O GLN A 334 " (cutoff:3.500A) Processing helix chain 'A' and resid 343 through 357 removed outlier: 3.894A pdb=" N TYR A 348 " --> pdb=" O GLY A 344 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N TYR A 353 " --> pdb=" O LYS A 349 " (cutoff:3.500A) removed outlier: 4.755A pdb=" N ARG A 356 " --> pdb=" O GLU A 352 " (cutoff:3.500A) removed outlier: 4.440A pdb=" N PHE A 357 " --> pdb=" O TYR A 353 " (cutoff:3.500A) Processing helix chain 'A' and resid 370 through 379 Processing helix chain 'A' and resid 453 through 471 Proline residue: A 458 - end of helix Processing helix chain 'A' and resid 476 through 484 Processing helix chain 'A' and resid 495 through 497 No H-bonds generated for 'chain 'A' and resid 495 through 497' Processing helix chain 'B' and resid 20 through 24 removed outlier: 3.707A pdb=" N PHE B 24 " --> pdb=" O ALA B 20 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 20 through 24' Processing helix chain 'B' and resid 32 through 34 No H-bonds generated for 'chain 'B' and resid 32 through 34' Processing helix chain 'B' and resid 78 through 84 Processing helix chain 'B' and resid 97 through 110 removed outlier: 4.202A pdb=" N PHE B 110 " --> pdb=" O LYS B 106 " (cutoff:3.500A) Processing helix chain 'B' and resid 225 through 232 Processing helix chain 'B' and resid 254 through 265 Processing helix chain 'B' and resid 281 through 293 Processing helix chain 'B' and resid 307 through 316 removed outlier: 4.897A pdb=" N ASN B 312 " --> pdb=" O ALA B 308 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N LEU B 313 " --> pdb=" O GLN B 309 " (cutoff:3.500A) Processing helix chain 'B' and resid 333 through 337 Processing helix chain 'B' and resid 343 through 356 removed outlier: 3.893A pdb=" N TYR B 348 " --> pdb=" O GLY B 344 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N TYR B 353 " --> pdb=" O LYS B 349 " (cutoff:3.500A) removed outlier: 4.735A pdb=" N ARG B 356 " --> pdb=" O GLU B 352 " (cutoff:3.500A) Processing helix chain 'B' and resid 370 through 379 Processing helix chain 'B' and resid 457 through 471 Processing helix chain 'B' and resid 476 through 484 Processing helix chain 'B' and resid 495 through 497 No H-bonds generated for 'chain 'B' and resid 495 through 497' Processing helix chain 'C' and resid 20 through 24 removed outlier: 3.861A pdb=" N PHE C 24 " --> pdb=" O ALA C 20 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 20 through 24' Processing helix chain 'C' and resid 32 through 34 No H-bonds generated for 'chain 'C' and resid 32 through 34' Processing helix chain 'C' and resid 78 through 84 Processing helix chain 'C' and resid 97 through 110 removed outlier: 4.214A pdb=" N PHE C 110 " --> pdb=" O LYS C 106 " (cutoff:3.500A) Processing helix chain 'C' and resid 225 through 232 Processing helix chain 'C' and resid 254 through 265 Processing helix chain 'C' and resid 281 through 293 Processing helix chain 'C' and resid 307 through 316 removed outlier: 5.008A pdb=" N ASN C 312 " --> pdb=" O ALA C 308 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N LEU C 313 " --> pdb=" O GLN C 309 " (cutoff:3.500A) Processing helix chain 'C' and resid 334 through 337 No H-bonds generated for 'chain 'C' and resid 334 through 337' Processing helix chain 'C' and resid 343 through 357 removed outlier: 3.796A pdb=" N TYR C 348 " --> pdb=" O GLY C 344 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N TYR C 353 " --> pdb=" O LYS C 349 " (cutoff:3.500A) removed outlier: 4.795A pdb=" N ARG C 356 " --> pdb=" O GLU C 352 " (cutoff:3.500A) removed outlier: 4.486A pdb=" N PHE C 357 " --> pdb=" O TYR C 353 " (cutoff:3.500A) Processing helix chain 'C' and resid 370 through 379 Processing helix chain 'C' and resid 453 through 471 Proline residue: C 458 - end of helix Processing helix chain 'C' and resid 476 through 484 Processing helix chain 'C' and resid 496 through 498 No H-bonds generated for 'chain 'C' and resid 496 through 498' Processing helix chain 'D' and resid 20 through 25 removed outlier: 4.091A pdb=" N PHE D 24 " --> pdb=" O ALA D 20 " (cutoff:3.500A) Processing helix chain 'D' and resid 32 through 34 No H-bonds generated for 'chain 'D' and resid 32 through 34' Processing helix chain 'D' and resid 78 through 84 Processing helix chain 'D' and resid 97 through 110 removed outlier: 4.283A pdb=" N PHE D 110 " --> pdb=" O LYS D 106 " (cutoff:3.500A) Processing helix chain 'D' and resid 225 through 232 Processing helix chain 'D' and resid 254 through 265 Processing helix chain 'D' and resid 281 through 293 Processing helix chain 'D' and resid 307 through 316 removed outlier: 4.925A pdb=" N ASN D 312 " --> pdb=" O ALA D 308 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N LEU D 313 " --> pdb=" O GLN D 309 " (cutoff:3.500A) Processing helix chain 'D' and resid 333 through 337 Processing helix chain 'D' and resid 343 through 356 removed outlier: 3.895A pdb=" N TYR D 348 " --> pdb=" O GLY D 344 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N TYR D 353 " --> pdb=" O LYS D 349 " (cutoff:3.500A) removed outlier: 4.627A pdb=" N ARG D 356 " --> pdb=" O GLU D 352 " (cutoff:3.500A) Processing helix chain 'D' and resid 370 through 377 Processing helix chain 'D' and resid 453 through 455 No H-bonds generated for 'chain 'D' and resid 453 through 455' Processing helix chain 'D' and resid 457 through 471 Processing helix chain 'D' and resid 476 through 484 Processing helix chain 'D' and resid 496 through 498 No H-bonds generated for 'chain 'D' and resid 496 through 498' Processing helix chain 'E' and resid 20 through 25 removed outlier: 4.083A pdb=" N PHE E 24 " --> pdb=" O ALA E 20 " (cutoff:3.500A) Processing helix chain 'E' and resid 32 through 34 No H-bonds generated for 'chain 'E' and resid 32 through 34' Processing helix chain 'E' and resid 78 through 84 Processing helix chain 'E' and resid 97 through 110 removed outlier: 4.270A pdb=" N PHE E 110 " --> pdb=" O LYS E 106 " (cutoff:3.500A) Processing helix chain 'E' and resid 225 through 232 Processing helix chain 'E' and resid 254 through 265 Processing helix chain 'E' and resid 281 through 293 Processing helix chain 'E' and resid 307 through 316 removed outlier: 4.914A pdb=" N ASN E 312 " --> pdb=" O ALA E 308 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N LEU E 313 " --> pdb=" O GLN E 309 " (cutoff:3.500A) Processing helix chain 'E' and resid 333 through 337 Processing helix chain 'E' and resid 343 through 356 removed outlier: 3.909A pdb=" N TYR E 348 " --> pdb=" O GLY E 344 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N TYR E 353 " --> pdb=" O LYS E 349 " (cutoff:3.500A) removed outlier: 4.627A pdb=" N ARG E 356 " --> pdb=" O GLU E 352 " (cutoff:3.500A) Processing helix chain 'E' and resid 370 through 379 Processing helix chain 'E' and resid 457 through 471 Processing helix chain 'E' and resid 476 through 484 Processing helix chain 'E' and resid 495 through 497 No H-bonds generated for 'chain 'E' and resid 495 through 497' Processing helix chain 'F' and resid 20 through 24 removed outlier: 3.858A pdb=" N PHE F 24 " --> pdb=" O ALA F 20 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 20 through 24' Processing helix chain 'F' and resid 32 through 34 No H-bonds generated for 'chain 'F' and resid 32 through 34' Processing helix chain 'F' and resid 78 through 84 Processing helix chain 'F' and resid 97 through 110 removed outlier: 4.264A pdb=" N PHE F 110 " --> pdb=" O LYS F 106 " (cutoff:3.500A) Processing helix chain 'F' and resid 225 through 232 Processing helix chain 'F' and resid 254 through 265 Processing helix chain 'F' and resid 281 through 293 Processing helix chain 'F' and resid 307 through 316 removed outlier: 5.013A pdb=" N ASN F 312 " --> pdb=" O ALA F 308 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N LEU F 313 " --> pdb=" O GLN F 309 " (cutoff:3.500A) Processing helix chain 'F' and resid 333 through 337 Processing helix chain 'F' and resid 343 through 357 removed outlier: 3.768A pdb=" N TYR F 348 " --> pdb=" O GLY F 344 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N TYR F 353 " --> pdb=" O LYS F 349 " (cutoff:3.500A) removed outlier: 4.627A pdb=" N ARG F 356 " --> pdb=" O GLU F 352 " (cutoff:3.500A) removed outlier: 4.442A pdb=" N PHE F 357 " --> pdb=" O TYR F 353 " (cutoff:3.500A) Processing helix chain 'F' and resid 370 through 379 Processing helix chain 'F' and resid 457 through 471 Processing helix chain 'F' and resid 476 through 484 Processing helix chain 'F' and resid 495 through 498 Processing helix chain 'G' and resid 20 through 24 removed outlier: 3.744A pdb=" N PHE G 24 " --> pdb=" O ALA G 20 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 20 through 24' Processing helix chain 'G' and resid 32 through 34 No H-bonds generated for 'chain 'G' and resid 32 through 34' Processing helix chain 'G' and resid 78 through 84 Processing helix chain 'G' and resid 97 through 110 removed outlier: 4.287A pdb=" N PHE G 110 " --> pdb=" O LYS G 106 " (cutoff:3.500A) Processing helix chain 'G' and resid 225 through 232 Processing helix chain 'G' and resid 254 through 265 Processing helix chain 'G' and resid 281 through 293 Processing helix chain 'G' and resid 307 through 316 removed outlier: 4.963A pdb=" N ASN G 312 " --> pdb=" O ALA G 308 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N LEU G 313 " --> pdb=" O GLN G 309 " (cutoff:3.500A) Processing helix chain 'G' and resid 333 through 337 Processing helix chain 'G' and resid 343 through 356 removed outlier: 3.796A pdb=" N TYR G 348 " --> pdb=" O GLY G 344 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N TYR G 353 " --> pdb=" O LYS G 349 " (cutoff:3.500A) removed outlier: 4.627A pdb=" N ARG G 356 " --> pdb=" O GLU G 352 " (cutoff:3.500A) Processing helix chain 'G' and resid 370 through 379 Processing helix chain 'G' and resid 457 through 471 Processing helix chain 'G' and resid 476 through 484 Processing helix chain 'G' and resid 495 through 498 Processing helix chain 'H' and resid 20 through 25 removed outlier: 4.091A pdb=" N PHE H 24 " --> pdb=" O ALA H 20 " (cutoff:3.500A) Processing helix chain 'H' and resid 32 through 34 No H-bonds generated for 'chain 'H' and resid 32 through 34' Processing helix chain 'H' and resid 78 through 84 Processing helix chain 'H' and resid 97 through 110 removed outlier: 4.187A pdb=" N PHE H 110 " --> pdb=" O LYS H 106 " (cutoff:3.500A) Processing helix chain 'H' and resid 225 through 232 Processing helix chain 'H' and resid 254 through 265 Processing helix chain 'H' and resid 281 through 293 Processing helix chain 'H' and resid 307 through 316 removed outlier: 5.122A pdb=" N ASN H 312 " --> pdb=" O ALA H 308 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N LEU H 313 " --> pdb=" O GLN H 309 " (cutoff:3.500A) Processing helix chain 'H' and resid 333 through 337 Processing helix chain 'H' and resid 343 through 357 removed outlier: 3.895A pdb=" N TYR H 348 " --> pdb=" O GLY H 344 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N TYR H 353 " --> pdb=" O LYS H 349 " (cutoff:3.500A) removed outlier: 4.627A pdb=" N ARG H 356 " --> pdb=" O GLU H 352 " (cutoff:3.500A) removed outlier: 4.435A pdb=" N PHE H 357 " --> pdb=" O TYR H 353 " (cutoff:3.500A) Processing helix chain 'H' and resid 370 through 377 Processing helix chain 'H' and resid 457 through 471 Processing helix chain 'H' and resid 476 through 484 Processing helix chain 'H' and resid 495 through 498 Processing sheet with id= A, first strand: chain 'A' and resid 35 through 37 Processing sheet with id= B, first strand: chain 'A' and resid 65 through 67 removed outlier: 6.436A pdb=" N VAL A 384 " --> pdb=" O ILE A 66 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N THR A 383 " --> pdb=" O ILE A 361 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 247 through 250 removed outlier: 6.685A pdb=" N VAL A 270 " --> pdb=" O ALA A 248 " (cutoff:3.500A) removed outlier: 7.427A pdb=" N VAL A 250 " --> pdb=" O VAL A 270 " (cutoff:3.500A) removed outlier: 6.146A pdb=" N VAL A 272 " --> pdb=" O VAL A 250 " (cutoff:3.500A) removed outlier: 6.708A pdb=" N GLN A 298 " --> pdb=" O ILE A 271 " (cutoff:3.500A) removed outlier: 7.785A pdb=" N LEU A 273 " --> pdb=" O GLN A 298 " (cutoff:3.500A) removed outlier: 6.817A pdb=" N ILE A 300 " --> pdb=" O LEU A 273 " (cutoff:3.500A) No H-bonds generated for sheet with id= C Processing sheet with id= D, first strand: chain 'A' and resid 53 through 56 removed outlier: 6.776A pdb=" N ILE A 59 " --> pdb=" O LEU A 55 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 35 through 37 Processing sheet with id= F, first strand: chain 'B' and resid 65 through 67 removed outlier: 6.235A pdb=" N VAL B 384 " --> pdb=" O ILE B 66 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N THR B 383 " --> pdb=" O ILE B 361 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 247 through 250 removed outlier: 6.731A pdb=" N VAL B 270 " --> pdb=" O ALA B 248 " (cutoff:3.500A) removed outlier: 7.444A pdb=" N VAL B 250 " --> pdb=" O VAL B 270 " (cutoff:3.500A) removed outlier: 6.151A pdb=" N VAL B 272 " --> pdb=" O VAL B 250 " (cutoff:3.500A) removed outlier: 6.703A pdb=" N GLN B 298 " --> pdb=" O ILE B 271 " (cutoff:3.500A) removed outlier: 7.762A pdb=" N LEU B 273 " --> pdb=" O GLN B 298 " (cutoff:3.500A) removed outlier: 6.821A pdb=" N ILE B 300 " --> pdb=" O LEU B 273 " (cutoff:3.500A) No H-bonds generated for sheet with id= G Processing sheet with id= H, first strand: chain 'B' and resid 53 through 56 removed outlier: 6.744A pdb=" N ILE B 59 " --> pdb=" O LEU B 55 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'C' and resid 35 through 37 Processing sheet with id= J, first strand: chain 'C' and resid 65 through 67 removed outlier: 6.174A pdb=" N VAL C 384 " --> pdb=" O ILE C 66 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N THR C 383 " --> pdb=" O ILE C 361 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'C' and resid 247 through 250 removed outlier: 6.668A pdb=" N VAL C 270 " --> pdb=" O ALA C 248 " (cutoff:3.500A) removed outlier: 7.410A pdb=" N VAL C 250 " --> pdb=" O VAL C 270 " (cutoff:3.500A) removed outlier: 6.083A pdb=" N VAL C 272 " --> pdb=" O VAL C 250 " (cutoff:3.500A) removed outlier: 6.729A pdb=" N GLN C 298 " --> pdb=" O ILE C 271 " (cutoff:3.500A) removed outlier: 7.826A pdb=" N LEU C 273 " --> pdb=" O GLN C 298 " (cutoff:3.500A) removed outlier: 6.929A pdb=" N ILE C 300 " --> pdb=" O LEU C 273 " (cutoff:3.500A) No H-bonds generated for sheet with id= K Processing sheet with id= L, first strand: chain 'C' and resid 53 through 56 removed outlier: 6.703A pdb=" N ILE C 59 " --> pdb=" O LEU C 55 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'D' and resid 35 through 37 Processing sheet with id= N, first strand: chain 'D' and resid 65 through 67 removed outlier: 6.338A pdb=" N VAL D 384 " --> pdb=" O ILE D 66 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N THR D 383 " --> pdb=" O ILE D 361 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'D' and resid 247 through 250 removed outlier: 6.728A pdb=" N VAL D 270 " --> pdb=" O ALA D 248 " (cutoff:3.500A) removed outlier: 7.425A pdb=" N VAL D 250 " --> pdb=" O VAL D 270 " (cutoff:3.500A) removed outlier: 6.078A pdb=" N VAL D 272 " --> pdb=" O VAL D 250 " (cutoff:3.500A) removed outlier: 6.768A pdb=" N GLN D 298 " --> pdb=" O ILE D 271 " (cutoff:3.500A) removed outlier: 7.857A pdb=" N LEU D 273 " --> pdb=" O GLN D 298 " (cutoff:3.500A) removed outlier: 6.945A pdb=" N ILE D 300 " --> pdb=" O LEU D 273 " (cutoff:3.500A) No H-bonds generated for sheet with id= O Processing sheet with id= P, first strand: chain 'D' and resid 53 through 56 removed outlier: 6.812A pdb=" N ILE D 59 " --> pdb=" O LEU D 55 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'E' and resid 35 through 37 Processing sheet with id= R, first strand: chain 'E' and resid 65 through 67 removed outlier: 6.235A pdb=" N VAL E 384 " --> pdb=" O ILE E 66 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N THR E 383 " --> pdb=" O ILE E 361 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'E' and resid 247 through 250 removed outlier: 6.693A pdb=" N VAL E 270 " --> pdb=" O ALA E 248 " (cutoff:3.500A) removed outlier: 7.366A pdb=" N VAL E 250 " --> pdb=" O VAL E 270 " (cutoff:3.500A) removed outlier: 6.064A pdb=" N VAL E 272 " --> pdb=" O VAL E 250 " (cutoff:3.500A) removed outlier: 6.679A pdb=" N GLN E 298 " --> pdb=" O ILE E 271 " (cutoff:3.500A) removed outlier: 7.843A pdb=" N LEU E 273 " --> pdb=" O GLN E 298 " (cutoff:3.500A) removed outlier: 6.942A pdb=" N ILE E 300 " --> pdb=" O LEU E 273 " (cutoff:3.500A) No H-bonds generated for sheet with id= S Processing sheet with id= T, first strand: chain 'E' and resid 53 through 56 removed outlier: 6.798A pdb=" N ILE E 59 " --> pdb=" O LEU E 55 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'F' and resid 35 through 37 Processing sheet with id= V, first strand: chain 'F' and resid 65 through 67 removed outlier: 6.166A pdb=" N VAL F 384 " --> pdb=" O ILE F 66 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N THR F 383 " --> pdb=" O ILE F 361 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'F' and resid 247 through 250 removed outlier: 6.664A pdb=" N VAL F 270 " --> pdb=" O ALA F 248 " (cutoff:3.500A) removed outlier: 7.381A pdb=" N VAL F 250 " --> pdb=" O VAL F 270 " (cutoff:3.500A) removed outlier: 6.193A pdb=" N VAL F 272 " --> pdb=" O VAL F 250 " (cutoff:3.500A) removed outlier: 6.777A pdb=" N GLN F 298 " --> pdb=" O ILE F 271 " (cutoff:3.500A) removed outlier: 7.868A pdb=" N LEU F 273 " --> pdb=" O GLN F 298 " (cutoff:3.500A) removed outlier: 6.918A pdb=" N ILE F 300 " --> pdb=" O LEU F 273 " (cutoff:3.500A) No H-bonds generated for sheet with id= W Processing sheet with id= X, first strand: chain 'F' and resid 53 through 56 removed outlier: 6.713A pdb=" N ILE F 59 " --> pdb=" O LEU F 55 " (cutoff:3.500A) Processing sheet with id= Y, first strand: chain 'G' and resid 35 through 37 Processing sheet with id= Z, first strand: chain 'G' and resid 65 through 67 removed outlier: 6.236A pdb=" N VAL G 384 " --> pdb=" O ILE G 66 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N THR G 383 " --> pdb=" O ILE G 361 " (cutoff:3.500A) Processing sheet with id= AA, first strand: chain 'G' and resid 247 through 250 removed outlier: 6.724A pdb=" N VAL G 270 " --> pdb=" O ALA G 248 " (cutoff:3.500A) removed outlier: 7.420A pdb=" N VAL G 250 " --> pdb=" O VAL G 270 " (cutoff:3.500A) removed outlier: 6.172A pdb=" N VAL G 272 " --> pdb=" O VAL G 250 " (cutoff:3.500A) removed outlier: 6.741A pdb=" N GLN G 298 " --> pdb=" O ILE G 271 " (cutoff:3.500A) removed outlier: 7.869A pdb=" N LEU G 273 " --> pdb=" O GLN G 298 " (cutoff:3.500A) removed outlier: 6.941A pdb=" N ILE G 300 " --> pdb=" O LEU G 273 " (cutoff:3.500A) No H-bonds generated for sheet with id= AA Processing sheet with id= AB, first strand: chain 'G' and resid 53 through 56 removed outlier: 6.783A pdb=" N ILE G 59 " --> pdb=" O LEU G 55 " (cutoff:3.500A) Processing sheet with id= AC, first strand: chain 'H' and resid 65 through 67 removed outlier: 6.234A pdb=" N VAL H 384 " --> pdb=" O ILE H 66 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N THR H 383 " --> pdb=" O ILE H 361 " (cutoff:3.500A) Processing sheet with id= AD, first strand: chain 'H' and resid 247 through 250 removed outlier: 6.731A pdb=" N VAL H 270 " --> pdb=" O ALA H 248 " (cutoff:3.500A) removed outlier: 7.431A pdb=" N VAL H 250 " --> pdb=" O VAL H 270 " (cutoff:3.500A) removed outlier: 6.159A pdb=" N VAL H 272 " --> pdb=" O VAL H 250 " (cutoff:3.500A) removed outlier: 6.744A pdb=" N GLN H 298 " --> pdb=" O ILE H 271 " (cutoff:3.500A) removed outlier: 7.838A pdb=" N LEU H 273 " --> pdb=" O GLN H 298 " (cutoff:3.500A) removed outlier: 6.953A pdb=" N ILE H 300 " --> pdb=" O LEU H 273 " (cutoff:3.500A) No H-bonds generated for sheet with id= AD Processing sheet with id= AE, first strand: chain 'H' and resid 53 through 56 removed outlier: 6.772A pdb=" N ILE H 59 " --> pdb=" O LEU H 55 " (cutoff:3.500A) 635 hydrogen bonds defined for protein. 1653 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: 17.42 Time building geometry restraints manager: 35.38 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.95 - 1.12: 21704 1.12 - 1.30: 3729 1.30 - 1.47: 7946 1.47 - 1.64: 10461 1.64 - 1.82: 240 Bond restraints: 44080 Sorted by residual: bond pdb=" N ALA H 497 " pdb=" H ALA H 497 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.72e+01 bond pdb=" NH2 ARG G 259 " pdb="HH21 ARG G 259 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.71e+01 bond pdb=" CD2 PHE F 490 " pdb=" HD2 PHE F 490 " ideal model delta sigma weight residual 0.930 1.081 -0.151 2.00e-02 2.50e+03 5.70e+01 bond pdb=" N SER G 496 " pdb=" H SER G 496 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.70e+01 bond pdb=" N CYS B 339 " pdb=" H CYS B 339 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.70e+01 ... (remaining 44075 not shown) Histogram of bond angle deviations from ideal: 94.68 - 102.78: 261 102.78 - 110.88: 46091 110.88 - 118.97: 16418 118.97 - 127.07: 16696 127.07 - 135.17: 198 Bond angle restraints: 79664 Sorted by residual: angle pdb=" CA ASP B 239 " pdb=" CB ASP B 239 " pdb=" CG ASP B 239 " ideal model delta sigma weight residual 112.60 119.63 -7.03 1.00e+00 1.00e+00 4.95e+01 angle pdb=" OE1 GLN G 465 " pdb=" CD GLN G 465 " pdb=" NE2 GLN G 465 " ideal model delta sigma weight residual 122.60 116.23 6.37 1.00e+00 1.00e+00 4.06e+01 angle pdb=" CA ASN H 230 " pdb=" CB ASN H 230 " pdb=" CG ASN H 230 " ideal model delta sigma weight residual 112.60 118.59 -5.99 1.00e+00 1.00e+00 3.59e+01 angle pdb=" CA ASN E 230 " pdb=" CB ASN E 230 " pdb=" CG ASN E 230 " ideal model delta sigma weight residual 112.60 118.52 -5.92 1.00e+00 1.00e+00 3.51e+01 angle pdb=" CA ASN F 230 " pdb=" CB ASN F 230 " pdb=" CG ASN F 230 " ideal model delta sigma weight residual 112.60 118.42 -5.82 1.00e+00 1.00e+00 3.38e+01 ... (remaining 79659 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 26.70: 19300 26.70 - 53.41: 1094 53.41 - 80.11: 458 80.11 - 106.82: 15 106.82 - 133.52: 5 Dihedral angle restraints: 20872 sinusoidal: 11800 harmonic: 9072 Sorted by residual: dihedral pdb=" C5' IMP E 601 " pdb=" O5' IMP E 601 " pdb=" P IMP E 601 " pdb=" O2P IMP E 601 " ideal model delta sinusoidal sigma weight residual 191.93 58.41 133.52 1 2.00e+01 2.50e-03 4.05e+01 dihedral pdb=" C5' IMP G 601 " pdb=" O5' IMP G 601 " pdb=" P IMP G 601 " pdb=" O2P IMP G 601 " ideal model delta sinusoidal sigma weight residual 191.93 58.56 133.37 1 2.00e+01 2.50e-03 4.05e+01 dihedral pdb=" C5' IMP H 601 " pdb=" O5' IMP H 601 " pdb=" P IMP H 601 " pdb=" O2P IMP H 601 " ideal model delta sinusoidal sigma weight residual 191.93 58.59 133.35 1 2.00e+01 2.50e-03 4.05e+01 ... (remaining 20869 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.084: 2515 0.084 - 0.167: 794 0.167 - 0.251: 167 0.251 - 0.334: 32 0.334 - 0.418: 4 Chirality restraints: 3512 Sorted by residual: chirality pdb=" CA GLU A 395 " pdb=" N GLU A 395 " pdb=" C GLU A 395 " pdb=" CB GLU A 395 " both_signs ideal model delta sigma weight residual False 2.51 2.09 0.42 2.00e-01 2.50e+01 4.36e+00 chirality pdb=" CA LYS A 106 " pdb=" N LYS A 106 " pdb=" C LYS A 106 " pdb=" CB LYS A 106 " both_signs ideal model delta sigma weight residual False 2.51 2.13 0.38 2.00e-01 2.50e+01 3.55e+00 chirality pdb=" CA ALA B 338 " pdb=" N ALA B 338 " pdb=" C ALA B 338 " pdb=" CB ALA B 338 " both_signs ideal model delta sigma weight residual False 2.48 2.14 0.34 2.00e-01 2.50e+01 2.90e+00 ... (remaining 3509 not shown) Planarity restraints: 6552 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG A 322 " -0.162 9.50e-02 1.11e+02 1.17e-01 2.44e+02 pdb=" NE ARG A 322 " -0.039 2.00e-02 2.50e+03 pdb=" CZ ARG A 322 " -0.035 2.00e-02 2.50e+03 pdb=" NH1 ARG A 322 " -0.068 2.00e-02 2.50e+03 pdb=" NH2 ARG A 322 " -0.007 2.00e-02 2.50e+03 pdb="HH11 ARG A 322 " 0.016 2.00e-02 2.50e+03 pdb="HH12 ARG A 322 " 0.158 2.00e-02 2.50e+03 pdb="HH21 ARG A 322 " 0.170 2.00e-02 2.50e+03 pdb="HH22 ARG A 322 " -0.187 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1B NAD G 600 " -0.173 2.00e-02 2.50e+03 7.48e-02 1.54e+02 pdb=" C2A NAD G 600 " 0.038 2.00e-02 2.50e+03 pdb=" C4A NAD G 600 " 0.049 2.00e-02 2.50e+03 pdb=" C5A NAD G 600 " 0.028 2.00e-02 2.50e+03 pdb=" C6A NAD G 600 " -0.023 2.00e-02 2.50e+03 pdb=" C8A NAD G 600 " 0.061 2.00e-02 2.50e+03 pdb=" N1A NAD G 600 " 0.005 2.00e-02 2.50e+03 pdb=" N3A NAD G 600 " 0.052 2.00e-02 2.50e+03 pdb=" N6A NAD G 600 " -0.125 2.00e-02 2.50e+03 pdb=" N7A NAD G 600 " 0.061 2.00e-02 2.50e+03 pdb=" N9A NAD G 600 " 0.027 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR F 348 " -0.144 2.00e-02 2.50e+03 6.14e-02 1.13e+02 pdb=" CG TYR F 348 " 0.035 2.00e-02 2.50e+03 pdb=" CD1 TYR F 348 " 0.057 2.00e-02 2.50e+03 pdb=" CD2 TYR F 348 " 0.037 2.00e-02 2.50e+03 pdb=" CE1 TYR F 348 " 0.026 2.00e-02 2.50e+03 pdb=" CE2 TYR F 348 " 0.044 2.00e-02 2.50e+03 pdb=" CZ TYR F 348 " 0.010 2.00e-02 2.50e+03 pdb=" OH TYR F 348 " -0.115 2.00e-02 2.50e+03 pdb=" HD1 TYR F 348 " 0.044 2.00e-02 2.50e+03 pdb=" HD2 TYR F 348 " 0.002 2.00e-02 2.50e+03 pdb=" HE1 TYR F 348 " -0.017 2.00e-02 2.50e+03 pdb=" HE2 TYR F 348 " 0.022 2.00e-02 2.50e+03 ... (remaining 6549 not shown) Histogram of nonbonded interaction distances: 1.51 - 2.13: 2267 2.13 - 2.75: 72830 2.75 - 3.37: 125889 3.37 - 3.98: 168025 3.98 - 4.60: 251182 Nonbonded interactions: 620193 Sorted by model distance: nonbonded pdb=" HB2 GLU B 75 " pdb=" HG3 PRO B 397 " model vdw 1.514 2.440 nonbonded pdb=" HB2 GLU C 75 " pdb=" HG3 PRO C 397 " model vdw 1.515 2.440 nonbonded pdb=" HB2 GLU E 75 " pdb=" HG3 PRO E 397 " model vdw 1.515 2.440 nonbonded pdb=" HB2 GLU H 75 " pdb=" HG3 PRO H 397 " model vdw 1.515 2.440 nonbonded pdb=" HB2 GLU G 75 " pdb=" HG3 PRO G 397 " model vdw 1.515 2.440 ... (remaining 620188 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' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.680 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.720 Extract box with map and model: 9.430 Check model and map are aligned: 0.700 Set scattering table: 0.410 Process input model: 139.720 Find NCS groups from input model: 1.780 Set up NCS constraints: 0.220 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.130 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 158.800 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7699 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.011 0.101 22328 Z= 0.753 Angle : 1.780 13.832 30248 Z= 1.143 Chirality : 0.087 0.418 3512 Planarity : 0.013 0.284 3816 Dihedral : 15.121 133.519 8496 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 1.57 Ramachandran Plot: Outliers : 0.14 % Allowed : 6.09 % Favored : 93.77 % Rotamer: Outliers : 1.84 % Allowed : 6.36 % Favored : 91.80 % Cbeta Deviations : 0.16 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.07 (0.15), residues: 2808 helix: -1.53 (0.14), residues: 1144 sheet: -1.42 (0.26), residues: 296 loop : -1.07 (0.16), residues: 1368 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.015 0.003 HIS F 92 PHE 0.045 0.008 PHE C 90 TYR 0.131 0.014 TYR F 348 ARG 0.007 0.001 ARG A 341 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5616 Ramachandran restraints generated. 2808 Oldfield, 0 Emsley, 2808 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5616 Ramachandran restraints generated. 2808 Oldfield, 0 Emsley, 2808 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 701 residues out of total 2280 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 659 time to evaluate : 3.614 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: A 28 ASP cc_start: 0.6799 (m-30) cc_final: 0.6369 (m-30) REVERT: A 82 MET cc_start: 0.8216 (mmm) cc_final: 0.7867 (mmm) REVERT: A 298 GLN cc_start: 0.7550 (mm110) cc_final: 0.7282 (mm-40) REVERT: A 319 ASP cc_start: 0.7787 (m-30) cc_final: 0.7541 (m-30) REVERT: A 492 LYS cc_start: 0.9029 (mtpp) cc_final: 0.8653 (ttmt) REVERT: B 28 ASP cc_start: 0.6395 (m-30) cc_final: 0.5690 (m-30) REVERT: B 298 GLN cc_start: 0.7525 (mm110) cc_final: 0.7309 (mm-40) REVERT: B 482 MET cc_start: 0.8502 (mtp) cc_final: 0.8098 (mtp) REVERT: B 492 LYS cc_start: 0.8877 (mtpp) cc_final: 0.8359 (mtpt) REVERT: C 15 GLU cc_start: 0.6561 (mt-10) cc_final: 0.6242 (mt-10) REVERT: C 16 ASP cc_start: 0.8120 (OUTLIER) cc_final: 0.7884 (m-30) REVERT: C 58 LYS cc_start: 0.8127 (tttm) cc_final: 0.7922 (mtpp) REVERT: C 482 MET cc_start: 0.8563 (mtp) cc_final: 0.8341 (mtp) REVERT: C 492 LYS cc_start: 0.8956 (mtpp) cc_final: 0.8636 (ttmt) REVERT: D 16 ASP cc_start: 0.8076 (OUTLIER) cc_final: 0.7807 (m-30) REVERT: D 34 ASP cc_start: 0.8926 (t0) cc_final: 0.8633 (t0) REVERT: D 298 GLN cc_start: 0.7601 (mm110) cc_final: 0.7295 (mm-40) REVERT: D 319 ASP cc_start: 0.7804 (m-30) cc_final: 0.7528 (m-30) REVERT: D 492 LYS cc_start: 0.8891 (mtpp) cc_final: 0.8495 (ttmt) REVERT: E 15 GLU cc_start: 0.6639 (mt-10) cc_final: 0.6367 (mt-10) REVERT: E 34 ASP cc_start: 0.8825 (t0) cc_final: 0.8618 (t0) REVERT: E 298 GLN cc_start: 0.7777 (mm110) cc_final: 0.7559 (mm110) REVERT: E 319 ASP cc_start: 0.7744 (m-30) cc_final: 0.7522 (m-30) REVERT: E 482 MET cc_start: 0.8553 (mtp) cc_final: 0.8328 (mtp) REVERT: E 492 LYS cc_start: 0.8989 (mtpp) cc_final: 0.8630 (mtpt) REVERT: F 275 SER cc_start: 0.8876 (p) cc_final: 0.8579 (m) REVERT: F 298 GLN cc_start: 0.7715 (mm110) cc_final: 0.7409 (mm-40) REVERT: F 319 ASP cc_start: 0.7815 (m-30) cc_final: 0.7456 (m-30) REVERT: F 492 LYS cc_start: 0.8876 (mtpp) cc_final: 0.8385 (mtpt) REVERT: G 15 GLU cc_start: 0.6693 (mt-10) cc_final: 0.6391 (mt-10) REVERT: G 238 LYS cc_start: 0.7450 (mtmp) cc_final: 0.7242 (mtmt) REVERT: G 298 GLN cc_start: 0.7619 (mm110) cc_final: 0.7295 (mm-40) REVERT: G 319 ASP cc_start: 0.7744 (m-30) cc_final: 0.7446 (m-30) REVERT: G 482 MET cc_start: 0.8589 (mtp) cc_final: 0.8378 (mtp) REVERT: H 15 GLU cc_start: 0.6973 (mt-10) cc_final: 0.6617 (mt-10) REVERT: H 298 GLN cc_start: 0.7596 (mm110) cc_final: 0.7349 (mm-40) REVERT: H 319 ASP cc_start: 0.7792 (m-30) cc_final: 0.7455 (m-30) REVERT: H 482 MET cc_start: 0.8587 (mtp) cc_final: 0.8370 (mtp) REVERT: H 492 LYS cc_start: 0.8953 (mtpp) cc_final: 0.8497 (ttmt) outliers start: 42 outliers final: 18 residues processed: 678 average time/residue: 0.8551 time to fit residues: 858.8529 Evaluate side-chains 554 residues out of total 2280 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 534 time to evaluate : 3.324 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 465 GLN Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 465 GLN Chi-restraints excluded: chain C residue 16 ASP Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 453 ILE Chi-restraints excluded: chain C residue 465 GLN Chi-restraints excluded: chain C residue 470 ASP Chi-restraints excluded: chain D residue 16 ASP Chi-restraints excluded: chain D residue 63 THR Chi-restraints excluded: chain D residue 465 GLN Chi-restraints excluded: chain E residue 63 THR Chi-restraints excluded: chain E residue 465 GLN Chi-restraints excluded: chain F residue 63 THR Chi-restraints excluded: chain F residue 465 GLN Chi-restraints excluded: chain G residue 63 THR Chi-restraints excluded: chain G residue 465 GLN Chi-restraints excluded: chain H residue 63 THR Chi-restraints excluded: chain H residue 465 GLN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 280 random chunks: chunk 236 optimal weight: 0.6980 chunk 212 optimal weight: 0.5980 chunk 117 optimal weight: 0.9990 chunk 72 optimal weight: 0.6980 chunk 143 optimal weight: 0.9980 chunk 113 optimal weight: 0.9980 chunk 219 optimal weight: 1.9990 chunk 84 optimal weight: 0.9980 chunk 133 optimal weight: 0.7980 chunk 163 optimal weight: 0.6980 chunk 254 optimal weight: 0.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 465 GLN B 465 GLN C 465 GLN ** C 466 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 498 GLN D 230 ASN D 465 GLN ** D 466 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 465 GLN F 465 GLN F 498 GLN G 21 GLN G 465 GLN H 230 ASN H 465 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7762 moved from start: 0.2375 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 22328 Z= 0.230 Angle : 0.611 7.555 30248 Z= 0.324 Chirality : 0.042 0.155 3512 Planarity : 0.004 0.049 3816 Dihedral : 9.834 113.123 3592 Min Nonbonded Distance : 2.100 Molprobity Statistics. All-atom Clashscore : 4.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.17 % Favored : 95.83 % Rotamer: Outliers : 1.10 % Allowed : 11.32 % Favored : 87.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.25 (0.15), residues: 2808 helix: -0.56 (0.15), residues: 1144 sheet: -1.17 (0.28), residues: 264 loop : -0.87 (0.17), residues: 1400 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.008 0.002 HIS H 466 PHE 0.012 0.002 PHE A 490 TYR 0.015 0.001 TYR C 32 ARG 0.003 0.000 ARG A 341 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5616 Ramachandran restraints generated. 2808 Oldfield, 0 Emsley, 2808 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5616 Ramachandran restraints generated. 2808 Oldfield, 0 Emsley, 2808 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 574 residues out of total 2280 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 549 time to evaluate : 3.611 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 28 ASP cc_start: 0.6790 (m-30) cc_final: 0.6514 (m-30) REVERT: A 47 ASP cc_start: 0.8212 (p0) cc_final: 0.7969 (p0) REVERT: A 298 GLN cc_start: 0.7261 (mm110) cc_final: 0.7049 (mm-40) REVERT: A 319 ASP cc_start: 0.7873 (m-30) cc_final: 0.7444 (m-30) REVERT: A 322 ARG cc_start: 0.7989 (ttp80) cc_final: 0.7771 (ttp80) REVERT: B 28 ASP cc_start: 0.6494 (m-30) cc_final: 0.5981 (m-30) REVERT: B 298 GLN cc_start: 0.7134 (mm110) cc_final: 0.6925 (mm-40) REVERT: B 453 ILE cc_start: 0.7566 (tt) cc_final: 0.7067 (mm) REVERT: B 482 MET cc_start: 0.8536 (mtp) cc_final: 0.8242 (mtp) REVERT: C 15 GLU cc_start: 0.6543 (mt-10) cc_final: 0.6251 (mt-10) REVERT: C 82 MET cc_start: 0.7756 (mmm) cc_final: 0.7472 (mmm) REVERT: C 482 MET cc_start: 0.8551 (mtp) cc_final: 0.8336 (mtp) REVERT: D 16 ASP cc_start: 0.7890 (OUTLIER) cc_final: 0.7475 (m-30) REVERT: D 319 ASP cc_start: 0.7881 (m-30) cc_final: 0.7625 (m-30) REVERT: D 491 GLU cc_start: 0.7621 (OUTLIER) cc_final: 0.7057 (mm-30) REVERT: E 15 GLU cc_start: 0.6556 (mt-10) cc_final: 0.6269 (mt-10) REVERT: E 337 MET cc_start: 0.6463 (ttt) cc_final: 0.6240 (ttt) REVERT: E 453 ILE cc_start: 0.7483 (tt) cc_final: 0.7184 (mm) REVERT: E 482 MET cc_start: 0.8608 (mtp) cc_final: 0.8318 (mtp) REVERT: G 15 GLU cc_start: 0.6478 (mt-10) cc_final: 0.6171 (mt-10) REVERT: G 319 ASP cc_start: 0.7767 (m-30) cc_final: 0.7373 (m-30) REVERT: G 482 MET cc_start: 0.8592 (mtp) cc_final: 0.8389 (mtp) REVERT: G 494 THR cc_start: 0.8574 (OUTLIER) cc_final: 0.8368 (p) REVERT: H 15 GLU cc_start: 0.6850 (mt-10) cc_final: 0.6489 (mt-10) REVERT: H 319 ASP cc_start: 0.7774 (m-30) cc_final: 0.7330 (m-30) REVERT: H 470 ASP cc_start: 0.7492 (t0) cc_final: 0.7232 (t0) outliers start: 25 outliers final: 17 residues processed: 555 average time/residue: 0.8065 time to fit residues: 678.2202 Evaluate side-chains 525 residues out of total 2280 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 505 time to evaluate : 3.395 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 LEU Chi-restraints excluded: chain A residue 245 LEU Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 245 LEU Chi-restraints excluded: chain C residue 61 LEU Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 245 LEU Chi-restraints excluded: chain C residue 393 THR Chi-restraints excluded: chain C residue 453 ILE Chi-restraints excluded: chain D residue 16 ASP Chi-restraints excluded: chain D residue 245 LEU Chi-restraints excluded: chain D residue 393 THR Chi-restraints excluded: chain D residue 491 GLU Chi-restraints excluded: chain E residue 63 THR Chi-restraints excluded: chain E residue 245 LEU Chi-restraints excluded: chain F residue 61 LEU Chi-restraints excluded: chain G residue 43 ASP Chi-restraints excluded: chain G residue 494 THR Chi-restraints excluded: chain H residue 61 LEU Chi-restraints excluded: chain H residue 245 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 280 random chunks: chunk 141 optimal weight: 0.9980 chunk 78 optimal weight: 2.9990 chunk 211 optimal weight: 1.9990 chunk 173 optimal weight: 0.9980 chunk 70 optimal weight: 1.9990 chunk 254 optimal weight: 3.9990 chunk 275 optimal weight: 1.9990 chunk 226 optimal weight: 1.9990 chunk 252 optimal weight: 1.9990 chunk 86 optimal weight: 1.9990 chunk 204 optimal weight: 0.6980 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 498 GLN B 241 GLN B 265 GLN C 265 GLN D 265 GLN E 265 GLN F 265 GLN F 298 GLN ** G 292 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 466 HIS H 265 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7822 moved from start: 0.2801 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.059 22328 Z= 0.313 Angle : 0.593 6.599 30248 Z= 0.313 Chirality : 0.043 0.175 3512 Planarity : 0.004 0.056 3816 Dihedral : 8.461 76.618 3559 Min Nonbonded Distance : 2.066 Molprobity Statistics. All-atom Clashscore : 7.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.55 % Favored : 93.45 % Rotamer: Outliers : 2.68 % Allowed : 12.32 % Favored : 85.00 % 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: -1.18 (0.16), residues: 2808 helix: -0.35 (0.16), residues: 1120 sheet: -0.96 (0.34), residues: 184 loop : -1.04 (0.16), residues: 1504 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.007 0.002 HIS F 466 PHE 0.016 0.002 PHE A 490 TYR 0.013 0.001 TYR F 32 ARG 0.002 0.000 ARG A 253 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5616 Ramachandran restraints generated. 2808 Oldfield, 0 Emsley, 2808 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5616 Ramachandran restraints generated. 2808 Oldfield, 0 Emsley, 2808 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 585 residues out of total 2280 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 524 time to evaluate : 3.426 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 28 ASP cc_start: 0.6665 (m-30) cc_final: 0.6321 (m-30) REVERT: A 103 GLU cc_start: 0.7989 (tp30) cc_final: 0.7686 (mm-30) REVERT: B 28 ASP cc_start: 0.6535 (m-30) cc_final: 0.6009 (m-30) REVERT: B 241 GLN cc_start: 0.7888 (OUTLIER) cc_final: 0.7410 (mp10) REVERT: C 15 GLU cc_start: 0.6564 (mt-10) cc_final: 0.6281 (mt-10) REVERT: C 82 MET cc_start: 0.7733 (mmm) cc_final: 0.7459 (mmm) REVERT: D 16 ASP cc_start: 0.7787 (OUTLIER) cc_final: 0.7427 (m-30) REVERT: D 491 GLU cc_start: 0.7737 (OUTLIER) cc_final: 0.7274 (mm-30) REVERT: G 15 GLU cc_start: 0.6576 (mt-10) cc_final: 0.6219 (mt-10) REVERT: H 15 GLU cc_start: 0.6830 (mt-10) cc_final: 0.6421 (mt-10) REVERT: H 470 ASP cc_start: 0.7458 (t0) cc_final: 0.7187 (t0) outliers start: 61 outliers final: 54 residues processed: 546 average time/residue: 0.8038 time to fit residues: 660.0308 Evaluate side-chains 558 residues out of total 2280 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 501 time to evaluate : 3.335 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 ASP Chi-restraints excluded: chain A residue 51 LEU Chi-restraints excluded: chain A residue 245 LEU Chi-restraints excluded: chain A residue 272 VAL Chi-restraints excluded: chain B residue 241 GLN Chi-restraints excluded: chain B residue 272 VAL Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 319 ASP Chi-restraints excluded: chain B residue 369 THR Chi-restraints excluded: chain C residue 51 LEU Chi-restraints excluded: chain C residue 61 LEU Chi-restraints excluded: chain C residue 239 ASP Chi-restraints excluded: chain C residue 245 LEU Chi-restraints excluded: chain C residue 272 VAL Chi-restraints excluded: chain C residue 275 SER Chi-restraints excluded: chain C residue 315 ASP Chi-restraints excluded: chain C residue 393 THR Chi-restraints excluded: chain C residue 453 ILE Chi-restraints excluded: chain D residue 16 ASP Chi-restraints excluded: chain D residue 18 LEU Chi-restraints excluded: chain D residue 51 LEU Chi-restraints excluded: chain D residue 63 THR Chi-restraints excluded: chain D residue 272 VAL Chi-restraints excluded: chain D residue 275 SER Chi-restraints excluded: chain D residue 315 ASP Chi-restraints excluded: chain D residue 393 THR Chi-restraints excluded: chain D residue 491 GLU Chi-restraints excluded: chain E residue 51 LEU Chi-restraints excluded: chain E residue 245 LEU Chi-restraints excluded: chain E residue 272 VAL Chi-restraints excluded: chain E residue 275 SER Chi-restraints excluded: chain E residue 319 ASP Chi-restraints excluded: chain E residue 369 THR Chi-restraints excluded: chain F residue 43 ASP Chi-restraints excluded: chain F residue 61 LEU Chi-restraints excluded: chain F residue 63 THR Chi-restraints excluded: chain F residue 272 VAL Chi-restraints excluded: chain F residue 275 SER Chi-restraints excluded: chain F residue 315 ASP Chi-restraints excluded: chain F residue 319 ASP Chi-restraints excluded: chain F residue 369 THR Chi-restraints excluded: chain F residue 370 VAL Chi-restraints excluded: chain G residue 43 ASP Chi-restraints excluded: chain G residue 272 VAL Chi-restraints excluded: chain G residue 275 SER Chi-restraints excluded: chain G residue 315 ASP Chi-restraints excluded: chain G residue 369 THR Chi-restraints excluded: chain G residue 370 VAL Chi-restraints excluded: chain G residue 495 MET Chi-restraints excluded: chain H residue 51 LEU Chi-restraints excluded: chain H residue 63 THR Chi-restraints excluded: chain H residue 245 LEU Chi-restraints excluded: chain H residue 272 VAL Chi-restraints excluded: chain H residue 275 SER Chi-restraints excluded: chain H residue 315 ASP Chi-restraints excluded: chain H residue 369 THR Chi-restraints excluded: chain H residue 370 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 280 random chunks: chunk 251 optimal weight: 1.9990 chunk 191 optimal weight: 1.9990 chunk 132 optimal weight: 1.9990 chunk 28 optimal weight: 0.0170 chunk 121 optimal weight: 2.9990 chunk 171 optimal weight: 0.9980 chunk 255 optimal weight: 2.9990 chunk 270 optimal weight: 0.0870 chunk 133 optimal weight: 0.9990 chunk 242 optimal weight: 1.9990 chunk 72 optimal weight: 0.9980 overall best weight: 0.6198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 466 HIS H 498 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7786 moved from start: 0.3109 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 22328 Z= 0.181 Angle : 0.519 5.565 30248 Z= 0.271 Chirality : 0.041 0.175 3512 Planarity : 0.004 0.047 3816 Dihedral : 7.858 75.601 3556 Min Nonbonded Distance : 2.135 Molprobity Statistics. All-atom Clashscore : 7.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.41 % Favored : 94.59 % Rotamer: Outliers : 1.36 % Allowed : 14.96 % Favored : 83.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.03 (0.16), residues: 2808 helix: -0.13 (0.16), residues: 1120 sheet: -0.79 (0.35), residues: 184 loop : -1.06 (0.16), residues: 1504 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.007 0.001 HIS H 466 PHE 0.015 0.001 PHE D 99 TYR 0.009 0.001 TYR B 348 ARG 0.001 0.000 ARG A 322 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5616 Ramachandran restraints generated. 2808 Oldfield, 0 Emsley, 2808 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5616 Ramachandran restraints generated. 2808 Oldfield, 0 Emsley, 2808 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 539 residues out of total 2280 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 508 time to evaluate : 3.304 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 28 ASP cc_start: 0.6785 (m-30) cc_final: 0.6473 (m-30) REVERT: A 82 MET cc_start: 0.8270 (mmm) cc_final: 0.7962 (mmt) REVERT: A 103 GLU cc_start: 0.7953 (tp30) cc_final: 0.7616 (mm-30) REVERT: B 28 ASP cc_start: 0.6689 (m-30) cc_final: 0.6226 (m-30) REVERT: C 15 GLU cc_start: 0.6455 (mt-10) cc_final: 0.6155 (mt-10) REVERT: C 82 MET cc_start: 0.7703 (mmm) cc_final: 0.7383 (mmm) REVERT: D 453 ILE cc_start: 0.7817 (tt) cc_final: 0.7542 (mm) REVERT: D 491 GLU cc_start: 0.7735 (OUTLIER) cc_final: 0.7234 (mm-30) REVERT: E 15 GLU cc_start: 0.6525 (mt-10) cc_final: 0.6258 (mt-10) REVERT: G 15 GLU cc_start: 0.6451 (mt-10) cc_final: 0.6117 (mt-10) REVERT: H 15 GLU cc_start: 0.6849 (mt-10) cc_final: 0.6418 (mt-10) outliers start: 31 outliers final: 27 residues processed: 521 average time/residue: 0.8270 time to fit residues: 659.2058 Evaluate side-chains 513 residues out of total 2280 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 485 time to evaluate : 3.343 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 ASP Chi-restraints excluded: chain A residue 51 LEU Chi-restraints excluded: chain A residue 272 VAL Chi-restraints excluded: chain B residue 272 VAL Chi-restraints excluded: chain C residue 51 LEU Chi-restraints excluded: chain C residue 61 LEU Chi-restraints excluded: chain C residue 245 LEU Chi-restraints excluded: chain C residue 272 VAL Chi-restraints excluded: chain C residue 393 THR Chi-restraints excluded: chain C residue 453 ILE Chi-restraints excluded: chain D residue 51 LEU Chi-restraints excluded: chain D residue 272 VAL Chi-restraints excluded: chain D residue 296 HIS Chi-restraints excluded: chain D residue 393 THR Chi-restraints excluded: chain D residue 491 GLU Chi-restraints excluded: chain E residue 51 LEU Chi-restraints excluded: chain E residue 272 VAL Chi-restraints excluded: chain F residue 61 LEU Chi-restraints excluded: chain F residue 272 VAL Chi-restraints excluded: chain G residue 43 ASP Chi-restraints excluded: chain G residue 272 VAL Chi-restraints excluded: chain G residue 315 ASP Chi-restraints excluded: chain G residue 369 THR Chi-restraints excluded: chain G residue 466 HIS Chi-restraints excluded: chain H residue 18 LEU Chi-restraints excluded: chain H residue 51 LEU Chi-restraints excluded: chain H residue 272 VAL Chi-restraints excluded: chain H residue 315 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 280 random chunks: chunk 225 optimal weight: 2.9990 chunk 153 optimal weight: 2.9990 chunk 3 optimal weight: 1.9990 chunk 201 optimal weight: 0.9990 chunk 111 optimal weight: 0.5980 chunk 230 optimal weight: 1.9990 chunk 187 optimal weight: 4.9990 chunk 0 optimal weight: 1.9990 chunk 138 optimal weight: 1.9990 chunk 242 optimal weight: 0.7980 chunk 68 optimal weight: 0.9990 overall best weight: 1.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 466 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7825 moved from start: 0.3272 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 22328 Z= 0.265 Angle : 0.535 5.662 30248 Z= 0.282 Chirality : 0.042 0.182 3512 Planarity : 0.004 0.049 3816 Dihedral : 7.789 75.633 3554 Min Nonbonded Distance : 2.113 Molprobity Statistics. All-atom Clashscore : 8.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.94 % Favored : 93.06 % Rotamer: Outliers : 2.76 % Allowed : 14.61 % Favored : 82.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.09 (0.16), residues: 2808 helix: -0.12 (0.16), residues: 1120 sheet: -0.94 (0.35), residues: 184 loop : -1.14 (0.16), residues: 1504 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.007 0.001 HIS H 466 PHE 0.012 0.001 PHE A 490 TYR 0.009 0.001 TYR G 32 ARG 0.004 0.000 ARG F 493 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5616 Ramachandran restraints generated. 2808 Oldfield, 0 Emsley, 2808 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5616 Ramachandran restraints generated. 2808 Oldfield, 0 Emsley, 2808 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 542 residues out of total 2280 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 479 time to evaluate : 2.942 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 28 ASP cc_start: 0.6788 (m-30) cc_final: 0.6480 (m-30) REVERT: A 103 GLU cc_start: 0.7942 (tp30) cc_final: 0.7573 (mm-30) REVERT: A 491 GLU cc_start: 0.7731 (OUTLIER) cc_final: 0.6979 (mm-30) REVERT: B 28 ASP cc_start: 0.6829 (m-30) cc_final: 0.6457 (m-30) REVERT: C 15 GLU cc_start: 0.6468 (mt-10) cc_final: 0.6175 (mt-10) REVERT: C 82 MET cc_start: 0.7769 (mmm) cc_final: 0.7456 (mmm) REVERT: D 453 ILE cc_start: 0.7903 (tt) cc_final: 0.7634 (mm) REVERT: D 491 GLU cc_start: 0.7732 (OUTLIER) cc_final: 0.7237 (mm-30) REVERT: F 491 GLU cc_start: 0.7589 (OUTLIER) cc_final: 0.7005 (mm-30) REVERT: G 15 GLU cc_start: 0.6481 (mt-10) cc_final: 0.6136 (mt-10) REVERT: G 491 GLU cc_start: 0.7573 (OUTLIER) cc_final: 0.7031 (mm-30) REVERT: H 15 GLU cc_start: 0.6777 (mt-10) cc_final: 0.6375 (mt-10) outliers start: 63 outliers final: 54 residues processed: 507 average time/residue: 0.8109 time to fit residues: 625.8956 Evaluate side-chains 536 residues out of total 2280 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 478 time to evaluate : 3.253 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 ASP Chi-restraints excluded: chain A residue 51 LEU Chi-restraints excluded: chain A residue 272 VAL Chi-restraints excluded: chain A residue 275 SER Chi-restraints excluded: chain A residue 319 ASP Chi-restraints excluded: chain A residue 491 GLU Chi-restraints excluded: chain B residue 272 VAL Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 369 THR Chi-restraints excluded: chain B residue 491 GLU Chi-restraints excluded: chain C residue 51 LEU Chi-restraints excluded: chain C residue 61 LEU Chi-restraints excluded: chain C residue 239 ASP Chi-restraints excluded: chain C residue 272 VAL Chi-restraints excluded: chain C residue 275 SER Chi-restraints excluded: chain C residue 315 ASP Chi-restraints excluded: chain C residue 393 THR Chi-restraints excluded: chain C residue 395 GLU Chi-restraints excluded: chain C residue 453 ILE Chi-restraints excluded: chain C residue 491 GLU Chi-restraints excluded: chain D residue 18 LEU Chi-restraints excluded: chain D residue 51 LEU Chi-restraints excluded: chain D residue 268 VAL Chi-restraints excluded: chain D residue 272 VAL Chi-restraints excluded: chain D residue 275 SER Chi-restraints excluded: chain D residue 315 ASP Chi-restraints excluded: chain D residue 319 ASP Chi-restraints excluded: chain D residue 393 THR Chi-restraints excluded: chain D residue 491 GLU Chi-restraints excluded: chain E residue 51 LEU Chi-restraints excluded: chain E residue 270 VAL Chi-restraints excluded: chain E residue 272 VAL Chi-restraints excluded: chain E residue 275 SER Chi-restraints excluded: chain E residue 319 ASP Chi-restraints excluded: chain E residue 369 THR Chi-restraints excluded: chain E residue 491 GLU Chi-restraints excluded: chain F residue 43 ASP Chi-restraints excluded: chain F residue 61 LEU Chi-restraints excluded: chain F residue 272 VAL Chi-restraints excluded: chain F residue 275 SER Chi-restraints excluded: chain F residue 315 ASP Chi-restraints excluded: chain F residue 319 ASP Chi-restraints excluded: chain F residue 370 VAL Chi-restraints excluded: chain F residue 491 GLU Chi-restraints excluded: chain G residue 43 ASP Chi-restraints excluded: chain G residue 272 VAL Chi-restraints excluded: chain G residue 275 SER Chi-restraints excluded: chain G residue 315 ASP Chi-restraints excluded: chain G residue 369 THR Chi-restraints excluded: chain G residue 370 VAL Chi-restraints excluded: chain G residue 491 GLU Chi-restraints excluded: chain H residue 18 LEU Chi-restraints excluded: chain H residue 51 LEU Chi-restraints excluded: chain H residue 272 VAL Chi-restraints excluded: chain H residue 315 ASP Chi-restraints excluded: chain H residue 369 THR Chi-restraints excluded: chain H residue 370 VAL Chi-restraints excluded: chain H residue 491 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 280 random chunks: chunk 91 optimal weight: 2.9990 chunk 243 optimal weight: 1.9990 chunk 53 optimal weight: 0.9990 chunk 158 optimal weight: 1.9990 chunk 66 optimal weight: 1.9990 chunk 270 optimal weight: 0.9990 chunk 224 optimal weight: 3.9990 chunk 125 optimal weight: 0.9990 chunk 22 optimal weight: 2.9990 chunk 89 optimal weight: 0.4980 chunk 142 optimal weight: 0.9980 overall best weight: 0.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 241 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7816 moved from start: 0.3454 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 22328 Z= 0.223 Angle : 0.513 4.705 30248 Z= 0.268 Chirality : 0.041 0.187 3512 Planarity : 0.004 0.048 3816 Dihedral : 7.593 75.532 3554 Min Nonbonded Distance : 2.133 Molprobity Statistics. All-atom Clashscore : 8.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.05 % Favored : 93.95 % Rotamer: Outliers : 2.63 % Allowed : 14.82 % Favored : 82.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.02 (0.16), residues: 2808 helix: -0.03 (0.16), residues: 1120 sheet: -0.96 (0.35), residues: 184 loop : -1.11 (0.16), residues: 1504 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.007 0.001 HIS H 466 PHE 0.010 0.001 PHE A 490 TYR 0.008 0.001 TYR A 32 ARG 0.003 0.000 ARG F 493 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5616 Ramachandran restraints generated. 2808 Oldfield, 0 Emsley, 2808 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5616 Ramachandran restraints generated. 2808 Oldfield, 0 Emsley, 2808 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 545 residues out of total 2280 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 485 time to evaluate : 3.619 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 28 ASP cc_start: 0.6909 (m-30) cc_final: 0.6612 (m-30) REVERT: A 78 MET cc_start: 0.8302 (tpp) cc_final: 0.7840 (tpt) REVERT: A 103 GLU cc_start: 0.7907 (tp30) cc_final: 0.7533 (mm-30) REVERT: B 28 ASP cc_start: 0.6774 (m-30) cc_final: 0.6371 (m-30) REVERT: B 309 GLN cc_start: 0.8962 (OUTLIER) cc_final: 0.8718 (pt0) REVERT: B 491 GLU cc_start: 0.7582 (OUTLIER) cc_final: 0.7063 (mm-30) REVERT: C 15 GLU cc_start: 0.6416 (mt-10) cc_final: 0.6115 (mt-10) REVERT: D 453 ILE cc_start: 0.7878 (tt) cc_final: 0.7662 (mm) REVERT: D 491 GLU cc_start: 0.7714 (OUTLIER) cc_final: 0.7229 (mm-30) REVERT: F 491 GLU cc_start: 0.7593 (OUTLIER) cc_final: 0.6959 (mm-30) REVERT: G 15 GLU cc_start: 0.6501 (mt-10) cc_final: 0.6154 (mt-10) REVERT: G 298 GLN cc_start: 0.7078 (mm110) cc_final: 0.6739 (mm-40) REVERT: G 309 GLN cc_start: 0.8996 (OUTLIER) cc_final: 0.8743 (pt0) REVERT: G 491 GLU cc_start: 0.7703 (OUTLIER) cc_final: 0.7151 (mm-30) REVERT: H 15 GLU cc_start: 0.6778 (mt-10) cc_final: 0.6376 (mt-10) outliers start: 60 outliers final: 46 residues processed: 512 average time/residue: 0.8040 time to fit residues: 624.4015 Evaluate side-chains 529 residues out of total 2280 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 477 time to evaluate : 2.697 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 ASP Chi-restraints excluded: chain A residue 51 LEU Chi-restraints excluded: chain A residue 272 VAL Chi-restraints excluded: chain A residue 296 HIS Chi-restraints excluded: chain A residue 319 ASP Chi-restraints excluded: chain B residue 272 VAL Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 309 GLN Chi-restraints excluded: chain B residue 491 GLU Chi-restraints excluded: chain C residue 51 LEU Chi-restraints excluded: chain C residue 61 LEU Chi-restraints excluded: chain C residue 239 ASP Chi-restraints excluded: chain C residue 245 LEU Chi-restraints excluded: chain C residue 272 VAL Chi-restraints excluded: chain C residue 315 ASP Chi-restraints excluded: chain C residue 393 THR Chi-restraints excluded: chain C residue 453 ILE Chi-restraints excluded: chain C residue 491 GLU Chi-restraints excluded: chain D residue 51 LEU Chi-restraints excluded: chain D residue 70 MET Chi-restraints excluded: chain D residue 268 VAL Chi-restraints excluded: chain D residue 272 VAL Chi-restraints excluded: chain D residue 275 SER Chi-restraints excluded: chain D residue 296 HIS Chi-restraints excluded: chain D residue 315 ASP Chi-restraints excluded: chain D residue 393 THR Chi-restraints excluded: chain D residue 491 GLU Chi-restraints excluded: chain E residue 51 LEU Chi-restraints excluded: chain E residue 272 VAL Chi-restraints excluded: chain E residue 275 SER Chi-restraints excluded: chain F residue 43 ASP Chi-restraints excluded: chain F residue 49 VAL Chi-restraints excluded: chain F residue 61 LEU Chi-restraints excluded: chain F residue 272 VAL Chi-restraints excluded: chain F residue 275 SER Chi-restraints excluded: chain F residue 315 ASP Chi-restraints excluded: chain F residue 370 VAL Chi-restraints excluded: chain F residue 491 GLU Chi-restraints excluded: chain G residue 43 ASP Chi-restraints excluded: chain G residue 51 LEU Chi-restraints excluded: chain G residue 272 VAL Chi-restraints excluded: chain G residue 296 HIS Chi-restraints excluded: chain G residue 309 GLN Chi-restraints excluded: chain G residue 315 ASP Chi-restraints excluded: chain G residue 370 VAL Chi-restraints excluded: chain G residue 491 GLU Chi-restraints excluded: chain H residue 18 LEU Chi-restraints excluded: chain H residue 51 LEU Chi-restraints excluded: chain H residue 272 VAL Chi-restraints excluded: chain H residue 315 ASP Chi-restraints excluded: chain H residue 370 VAL Chi-restraints excluded: chain H residue 491 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 280 random chunks: chunk 261 optimal weight: 1.9990 chunk 30 optimal weight: 0.8980 chunk 154 optimal weight: 1.9990 chunk 197 optimal weight: 3.9990 chunk 153 optimal weight: 2.9990 chunk 228 optimal weight: 0.9980 chunk 151 optimal weight: 1.9990 chunk 269 optimal weight: 1.9990 chunk 168 optimal weight: 0.3980 chunk 164 optimal weight: 0.9990 chunk 124 optimal weight: 0.4980 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 334 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7812 moved from start: 0.3559 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 22328 Z= 0.201 Angle : 0.504 4.546 30248 Z= 0.263 Chirality : 0.041 0.183 3512 Planarity : 0.004 0.046 3816 Dihedral : 7.364 76.260 3554 Min Nonbonded Distance : 2.011 Molprobity Statistics. All-atom Clashscore : 8.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.45 % Favored : 93.55 % Rotamer: Outliers : 2.72 % Allowed : 15.48 % Favored : 81.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.92 (0.16), residues: 2808 helix: 0.11 (0.16), residues: 1128 sheet: -1.01 (0.35), residues: 184 loop : -1.10 (0.16), residues: 1496 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.008 0.001 HIS E 466 PHE 0.009 0.001 PHE A 490 TYR 0.008 0.001 TYR C 348 ARG 0.002 0.000 ARG F 493 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5616 Ramachandran restraints generated. 2808 Oldfield, 0 Emsley, 2808 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5616 Ramachandran restraints generated. 2808 Oldfield, 0 Emsley, 2808 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 547 residues out of total 2280 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 485 time to evaluate : 3.683 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 78 MET cc_start: 0.8145 (tpp) cc_final: 0.7778 (tpt) REVERT: B 28 ASP cc_start: 0.6774 (m-30) cc_final: 0.6387 (m-30) REVERT: B 491 GLU cc_start: 0.7578 (OUTLIER) cc_final: 0.7058 (mm-30) REVERT: C 15 GLU cc_start: 0.6379 (mt-10) cc_final: 0.6107 (mt-10) REVERT: C 82 MET cc_start: 0.7751 (mmm) cc_final: 0.7354 (mmm) REVERT: D 453 ILE cc_start: 0.7877 (tt) cc_final: 0.7662 (mm) REVERT: D 491 GLU cc_start: 0.7710 (OUTLIER) cc_final: 0.7206 (mm-30) REVERT: E 15 GLU cc_start: 0.6436 (mt-10) cc_final: 0.6176 (mt-10) REVERT: E 109 LYS cc_start: 0.6987 (pttt) cc_final: 0.6345 (ptmm) REVERT: F 491 GLU cc_start: 0.7612 (OUTLIER) cc_final: 0.6963 (mm-30) REVERT: G 15 GLU cc_start: 0.6413 (mt-10) cc_final: 0.6056 (mt-10) REVERT: G 298 GLN cc_start: 0.7154 (mm110) cc_final: 0.6889 (mm-40) REVERT: G 309 GLN cc_start: 0.8999 (OUTLIER) cc_final: 0.8739 (pt0) REVERT: G 491 GLU cc_start: 0.7684 (OUTLIER) cc_final: 0.7115 (mm-30) REVERT: H 15 GLU cc_start: 0.6756 (mt-10) cc_final: 0.6357 (mt-10) REVERT: H 298 GLN cc_start: 0.7098 (mm110) cc_final: 0.6766 (mm-40) outliers start: 62 outliers final: 51 residues processed: 519 average time/residue: 0.8012 time to fit residues: 635.4415 Evaluate side-chains 533 residues out of total 2280 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 477 time to evaluate : 3.297 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 ASP Chi-restraints excluded: chain A residue 51 LEU Chi-restraints excluded: chain A residue 272 VAL Chi-restraints excluded: chain A residue 275 SER Chi-restraints excluded: chain A residue 296 HIS Chi-restraints excluded: chain A residue 309 GLN Chi-restraints excluded: chain A residue 319 ASP Chi-restraints excluded: chain A residue 491 GLU Chi-restraints excluded: chain B residue 51 LEU Chi-restraints excluded: chain B residue 272 VAL Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 370 VAL Chi-restraints excluded: chain B residue 491 GLU Chi-restraints excluded: chain C residue 51 LEU Chi-restraints excluded: chain C residue 61 LEU Chi-restraints excluded: chain C residue 70 MET Chi-restraints excluded: chain C residue 239 ASP Chi-restraints excluded: chain C residue 272 VAL Chi-restraints excluded: chain C residue 309 GLN Chi-restraints excluded: chain C residue 315 ASP Chi-restraints excluded: chain C residue 491 GLU Chi-restraints excluded: chain D residue 51 LEU Chi-restraints excluded: chain D residue 268 VAL Chi-restraints excluded: chain D residue 272 VAL Chi-restraints excluded: chain D residue 275 SER Chi-restraints excluded: chain D residue 315 ASP Chi-restraints excluded: chain D residue 393 THR Chi-restraints excluded: chain D residue 491 GLU Chi-restraints excluded: chain E residue 51 LEU Chi-restraints excluded: chain E residue 272 VAL Chi-restraints excluded: chain E residue 275 SER Chi-restraints excluded: chain E residue 491 GLU Chi-restraints excluded: chain F residue 43 ASP Chi-restraints excluded: chain F residue 61 LEU Chi-restraints excluded: chain F residue 272 VAL Chi-restraints excluded: chain F residue 315 ASP Chi-restraints excluded: chain F residue 370 VAL Chi-restraints excluded: chain F residue 491 GLU Chi-restraints excluded: chain G residue 43 ASP Chi-restraints excluded: chain G residue 51 LEU Chi-restraints excluded: chain G residue 272 VAL Chi-restraints excluded: chain G residue 275 SER Chi-restraints excluded: chain G residue 296 HIS Chi-restraints excluded: chain G residue 306 THR Chi-restraints excluded: chain G residue 309 GLN Chi-restraints excluded: chain G residue 315 ASP Chi-restraints excluded: chain G residue 370 VAL Chi-restraints excluded: chain G residue 491 GLU Chi-restraints excluded: chain H residue 18 LEU Chi-restraints excluded: chain H residue 51 LEU Chi-restraints excluded: chain H residue 239 ASP Chi-restraints excluded: chain H residue 272 VAL Chi-restraints excluded: chain H residue 275 SER Chi-restraints excluded: chain H residue 315 ASP Chi-restraints excluded: chain H residue 370 VAL Chi-restraints excluded: chain H residue 491 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 280 random chunks: chunk 166 optimal weight: 0.9990 chunk 107 optimal weight: 0.0070 chunk 161 optimal weight: 2.9990 chunk 81 optimal weight: 4.9990 chunk 53 optimal weight: 1.9990 chunk 52 optimal weight: 0.7980 chunk 171 optimal weight: 1.9990 chunk 183 optimal weight: 2.9990 chunk 133 optimal weight: 2.9990 chunk 25 optimal weight: 1.9990 chunk 212 optimal weight: 0.9980 overall best weight: 0.9602 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7826 moved from start: 0.3661 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 22328 Z= 0.241 Angle : 0.521 5.561 30248 Z= 0.272 Chirality : 0.042 0.186 3512 Planarity : 0.004 0.044 3816 Dihedral : 7.354 76.620 3552 Min Nonbonded Distance : 2.008 Molprobity Statistics. All-atom Clashscore : 9.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.55 % Favored : 93.45 % Rotamer: Outliers : 2.94 % Allowed : 16.54 % Favored : 80.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.94 (0.16), residues: 2808 helix: 0.12 (0.16), residues: 1128 sheet: -1.18 (0.34), residues: 184 loop : -1.10 (0.16), residues: 1496 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.009 0.001 HIS E 466 PHE 0.025 0.001 PHE A 99 TYR 0.008 0.001 TYR D 348 ARG 0.002 0.000 ARG F 493 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5616 Ramachandran restraints generated. 2808 Oldfield, 0 Emsley, 2808 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5616 Ramachandran restraints generated. 2808 Oldfield, 0 Emsley, 2808 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 547 residues out of total 2280 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 480 time to evaluate : 3.142 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 103 GLU cc_start: 0.7805 (tp30) cc_final: 0.7535 (mm-30) REVERT: B 309 GLN cc_start: 0.8996 (OUTLIER) cc_final: 0.8761 (pt0) REVERT: B 491 GLU cc_start: 0.7536 (OUTLIER) cc_final: 0.6991 (mm-30) REVERT: C 337 MET cc_start: 0.6611 (ttt) cc_final: 0.6366 (ttt) REVERT: D 491 GLU cc_start: 0.7691 (OUTLIER) cc_final: 0.7195 (mm-30) REVERT: E 15 GLU cc_start: 0.6494 (mt-10) cc_final: 0.6228 (mt-10) REVERT: E 109 LYS cc_start: 0.6962 (pttt) cc_final: 0.6302 (ptmm) REVERT: F 491 GLU cc_start: 0.7620 (OUTLIER) cc_final: 0.6954 (mm-30) REVERT: G 109 LYS cc_start: 0.6992 (pttt) cc_final: 0.6255 (ptmm) REVERT: G 298 GLN cc_start: 0.7135 (mm110) cc_final: 0.6882 (mm-40) REVERT: G 309 GLN cc_start: 0.9029 (OUTLIER) cc_final: 0.8776 (pt0) REVERT: G 491 GLU cc_start: 0.7643 (OUTLIER) cc_final: 0.7069 (mm-30) REVERT: H 15 GLU cc_start: 0.6799 (mt-10) cc_final: 0.6421 (mt-10) REVERT: H 298 GLN cc_start: 0.7067 (mm110) cc_final: 0.6743 (mm-40) outliers start: 67 outliers final: 56 residues processed: 520 average time/residue: 0.8464 time to fit residues: 675.6114 Evaluate side-chains 530 residues out of total 2280 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 468 time to evaluate : 3.353 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 ASP Chi-restraints excluded: chain A residue 51 LEU Chi-restraints excluded: chain A residue 272 VAL Chi-restraints excluded: chain A residue 275 SER Chi-restraints excluded: chain A residue 306 THR Chi-restraints excluded: chain A residue 309 GLN Chi-restraints excluded: chain A residue 319 ASP Chi-restraints excluded: chain A residue 491 GLU Chi-restraints excluded: chain B residue 51 LEU Chi-restraints excluded: chain B residue 272 VAL Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 309 GLN Chi-restraints excluded: chain B residue 370 VAL Chi-restraints excluded: chain B residue 491 GLU Chi-restraints excluded: chain C residue 51 LEU Chi-restraints excluded: chain C residue 61 LEU Chi-restraints excluded: chain C residue 70 MET Chi-restraints excluded: chain C residue 239 ASP Chi-restraints excluded: chain C residue 272 VAL Chi-restraints excluded: chain C residue 275 SER Chi-restraints excluded: chain C residue 309 GLN Chi-restraints excluded: chain C residue 315 ASP Chi-restraints excluded: chain C residue 491 GLU Chi-restraints excluded: chain D residue 51 LEU Chi-restraints excluded: chain D residue 70 MET Chi-restraints excluded: chain D residue 268 VAL Chi-restraints excluded: chain D residue 272 VAL Chi-restraints excluded: chain D residue 275 SER Chi-restraints excluded: chain D residue 296 HIS Chi-restraints excluded: chain D residue 315 ASP Chi-restraints excluded: chain D residue 393 THR Chi-restraints excluded: chain D residue 491 GLU Chi-restraints excluded: chain E residue 51 LEU Chi-restraints excluded: chain E residue 272 VAL Chi-restraints excluded: chain E residue 275 SER Chi-restraints excluded: chain E residue 370 VAL Chi-restraints excluded: chain E residue 491 GLU Chi-restraints excluded: chain F residue 43 ASP Chi-restraints excluded: chain F residue 49 VAL Chi-restraints excluded: chain F residue 61 LEU Chi-restraints excluded: chain F residue 272 VAL Chi-restraints excluded: chain F residue 315 ASP Chi-restraints excluded: chain F residue 370 VAL Chi-restraints excluded: chain F residue 491 GLU Chi-restraints excluded: chain G residue 43 ASP Chi-restraints excluded: chain G residue 51 LEU Chi-restraints excluded: chain G residue 272 VAL Chi-restraints excluded: chain G residue 275 SER Chi-restraints excluded: chain G residue 296 HIS Chi-restraints excluded: chain G residue 306 THR Chi-restraints excluded: chain G residue 309 GLN Chi-restraints excluded: chain G residue 315 ASP Chi-restraints excluded: chain G residue 370 VAL Chi-restraints excluded: chain G residue 491 GLU Chi-restraints excluded: chain H residue 18 LEU Chi-restraints excluded: chain H residue 51 LEU Chi-restraints excluded: chain H residue 239 ASP Chi-restraints excluded: chain H residue 272 VAL Chi-restraints excluded: chain H residue 275 SER Chi-restraints excluded: chain H residue 315 ASP Chi-restraints excluded: chain H residue 370 VAL Chi-restraints excluded: chain H residue 491 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 280 random chunks: chunk 245 optimal weight: 0.4980 chunk 258 optimal weight: 2.9990 chunk 235 optimal weight: 1.9990 chunk 251 optimal weight: 2.9990 chunk 151 optimal weight: 4.9990 chunk 109 optimal weight: 0.0970 chunk 197 optimal weight: 1.9990 chunk 77 optimal weight: 1.9990 chunk 227 optimal weight: 0.9990 chunk 237 optimal weight: 1.9990 chunk 250 optimal weight: 0.9990 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 466 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 334 GLN ** E 466 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 498 GLN F 334 GLN ** F 466 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 465 GLN ** H 466 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7827 moved from start: 0.3763 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 22328 Z= 0.231 Angle : 0.517 5.503 30248 Z= 0.270 Chirality : 0.042 0.182 3512 Planarity : 0.004 0.044 3816 Dihedral : 7.292 76.835 3552 Min Nonbonded Distance : 2.029 Molprobity Statistics. All-atom Clashscore : 9.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.73 % Favored : 93.27 % Rotamer: Outliers : 2.85 % Allowed : 16.40 % Favored : 80.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.93 (0.16), residues: 2808 helix: 0.14 (0.16), residues: 1128 sheet: -1.29 (0.34), residues: 184 loop : -1.09 (0.16), residues: 1496 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.009 0.001 HIS E 466 PHE 0.018 0.001 PHE A 99 TYR 0.008 0.001 TYR A 348 ARG 0.002 0.000 ARG F 493 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5616 Ramachandran restraints generated. 2808 Oldfield, 0 Emsley, 2808 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5616 Ramachandran restraints generated. 2808 Oldfield, 0 Emsley, 2808 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 544 residues out of total 2280 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 479 time to evaluate : 3.214 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 78 MET cc_start: 0.8118 (tpp) cc_final: 0.7808 (tpt) REVERT: B 109 LYS cc_start: 0.6974 (pttt) cc_final: 0.6559 (ptpt) REVERT: B 298 GLN cc_start: 0.7133 (mm110) cc_final: 0.6893 (mm110) REVERT: B 309 GLN cc_start: 0.8999 (OUTLIER) cc_final: 0.8756 (pt0) REVERT: B 491 GLU cc_start: 0.7536 (OUTLIER) cc_final: 0.6995 (mm-30) REVERT: C 15 GLU cc_start: 0.6355 (mt-10) cc_final: 0.6085 (mt-10) REVERT: C 109 LYS cc_start: 0.7009 (pttt) cc_final: 0.6326 (ptmm) REVERT: D 491 GLU cc_start: 0.7681 (OUTLIER) cc_final: 0.7193 (mm-30) REVERT: E 15 GLU cc_start: 0.6393 (mt-10) cc_final: 0.6132 (mt-10) REVERT: E 109 LYS cc_start: 0.6917 (pttt) cc_final: 0.6249 (ptmm) REVERT: F 491 GLU cc_start: 0.7628 (OUTLIER) cc_final: 0.6982 (mm-30) REVERT: G 109 LYS cc_start: 0.7082 (pttt) cc_final: 0.6321 (ptmm) REVERT: G 298 GLN cc_start: 0.7119 (mm110) cc_final: 0.6872 (mm-40) REVERT: G 309 GLN cc_start: 0.9028 (OUTLIER) cc_final: 0.8781 (pt0) REVERT: G 491 GLU cc_start: 0.7642 (OUTLIER) cc_final: 0.7066 (mm-30) REVERT: H 15 GLU cc_start: 0.6738 (mt-10) cc_final: 0.6365 (mt-10) REVERT: H 482 MET cc_start: 0.8595 (mtp) cc_final: 0.8369 (mtp) outliers start: 65 outliers final: 58 residues processed: 516 average time/residue: 0.7969 time to fit residues: 623.3480 Evaluate side-chains 536 residues out of total 2280 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 472 time to evaluate : 3.256 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 ASP Chi-restraints excluded: chain A residue 51 LEU Chi-restraints excluded: chain A residue 272 VAL Chi-restraints excluded: chain A residue 275 SER Chi-restraints excluded: chain A residue 306 THR Chi-restraints excluded: chain A residue 309 GLN Chi-restraints excluded: chain A residue 319 ASP Chi-restraints excluded: chain A residue 491 GLU Chi-restraints excluded: chain B residue 51 LEU Chi-restraints excluded: chain B residue 272 VAL Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 306 THR Chi-restraints excluded: chain B residue 309 GLN Chi-restraints excluded: chain B residue 370 VAL Chi-restraints excluded: chain B residue 491 GLU Chi-restraints excluded: chain C residue 51 LEU Chi-restraints excluded: chain C residue 70 MET Chi-restraints excluded: chain C residue 239 ASP Chi-restraints excluded: chain C residue 272 VAL Chi-restraints excluded: chain C residue 275 SER Chi-restraints excluded: chain C residue 309 GLN Chi-restraints excluded: chain C residue 315 ASP Chi-restraints excluded: chain C residue 491 GLU Chi-restraints excluded: chain D residue 51 LEU Chi-restraints excluded: chain D residue 268 VAL Chi-restraints excluded: chain D residue 272 VAL Chi-restraints excluded: chain D residue 275 SER Chi-restraints excluded: chain D residue 296 HIS Chi-restraints excluded: chain D residue 315 ASP Chi-restraints excluded: chain D residue 491 GLU Chi-restraints excluded: chain E residue 51 LEU Chi-restraints excluded: chain E residue 270 VAL Chi-restraints excluded: chain E residue 272 VAL Chi-restraints excluded: chain E residue 275 SER Chi-restraints excluded: chain E residue 370 VAL Chi-restraints excluded: chain E residue 491 GLU Chi-restraints excluded: chain E residue 498 GLN Chi-restraints excluded: chain F residue 43 ASP Chi-restraints excluded: chain F residue 49 VAL Chi-restraints excluded: chain F residue 61 LEU Chi-restraints excluded: chain F residue 272 VAL Chi-restraints excluded: chain F residue 275 SER Chi-restraints excluded: chain F residue 315 ASP Chi-restraints excluded: chain F residue 370 VAL Chi-restraints excluded: chain F residue 491 GLU Chi-restraints excluded: chain G residue 43 ASP Chi-restraints excluded: chain G residue 51 LEU Chi-restraints excluded: chain G residue 272 VAL Chi-restraints excluded: chain G residue 275 SER Chi-restraints excluded: chain G residue 296 HIS Chi-restraints excluded: chain G residue 306 THR Chi-restraints excluded: chain G residue 309 GLN Chi-restraints excluded: chain G residue 315 ASP Chi-restraints excluded: chain G residue 370 VAL Chi-restraints excluded: chain G residue 491 GLU Chi-restraints excluded: chain H residue 18 LEU Chi-restraints excluded: chain H residue 51 LEU Chi-restraints excluded: chain H residue 239 ASP Chi-restraints excluded: chain H residue 272 VAL Chi-restraints excluded: chain H residue 275 SER Chi-restraints excluded: chain H residue 309 GLN Chi-restraints excluded: chain H residue 315 ASP Chi-restraints excluded: chain H residue 370 VAL Chi-restraints excluded: chain H residue 491 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 280 random chunks: chunk 165 optimal weight: 1.9990 chunk 265 optimal weight: 0.9990 chunk 162 optimal weight: 0.9990 chunk 126 optimal weight: 0.9980 chunk 184 optimal weight: 0.6980 chunk 278 optimal weight: 1.9990 chunk 256 optimal weight: 4.9990 chunk 222 optimal weight: 2.9990 chunk 23 optimal weight: 0.9980 chunk 171 optimal weight: 0.9990 chunk 136 optimal weight: 0.9980 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 466 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 466 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 466 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 466 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 466 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7827 moved from start: 0.3779 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.129 22328 Z= 0.249 Angle : 0.671 59.200 30248 Z= 0.374 Chirality : 0.042 0.191 3512 Planarity : 0.004 0.044 3816 Dihedral : 7.291 76.807 3552 Min Nonbonded Distance : 2.032 Molprobity Statistics. All-atom Clashscore : 10.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.70 % Favored : 93.30 % Rotamer: Outliers : 2.85 % Allowed : 16.93 % Favored : 80.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.93 (0.16), residues: 2808 helix: 0.14 (0.16), residues: 1128 sheet: -1.30 (0.34), residues: 184 loop : -1.09 (0.16), residues: 1496 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.008 0.001 HIS E 466 PHE 0.015 0.001 PHE E 99 TYR 0.008 0.001 TYR A 348 ARG 0.002 0.000 ARG F 493 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5616 Ramachandran restraints generated. 2808 Oldfield, 0 Emsley, 2808 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5616 Ramachandran restraints generated. 2808 Oldfield, 0 Emsley, 2808 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 537 residues out of total 2280 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 472 time to evaluate : 3.195 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: A 78 MET cc_start: 0.8115 (tpp) cc_final: 0.7808 (tpt) REVERT: B 109 LYS cc_start: 0.6976 (pttt) cc_final: 0.6559 (ptpt) REVERT: B 298 GLN cc_start: 0.7139 (mm110) cc_final: 0.6895 (mm110) REVERT: B 309 GLN cc_start: 0.8999 (OUTLIER) cc_final: 0.8757 (pt0) REVERT: B 491 GLU cc_start: 0.7544 (OUTLIER) cc_final: 0.6991 (mm-30) REVERT: C 15 GLU cc_start: 0.6354 (mt-10) cc_final: 0.6086 (mt-10) REVERT: C 109 LYS cc_start: 0.7027 (pttt) cc_final: 0.6337 (ptmm) REVERT: D 491 GLU cc_start: 0.7682 (OUTLIER) cc_final: 0.7193 (mm-30) REVERT: E 15 GLU cc_start: 0.6393 (mt-10) cc_final: 0.6130 (mt-10) REVERT: E 109 LYS cc_start: 0.6914 (pttt) cc_final: 0.6252 (ptmm) REVERT: F 491 GLU cc_start: 0.7626 (OUTLIER) cc_final: 0.6980 (mm-30) REVERT: G 109 LYS cc_start: 0.7083 (pttt) cc_final: 0.6320 (ptmm) REVERT: G 298 GLN cc_start: 0.7121 (mm110) cc_final: 0.6876 (mm-40) REVERT: G 309 GLN cc_start: 0.9030 (OUTLIER) cc_final: 0.8782 (pt0) REVERT: G 491 GLU cc_start: 0.7643 (OUTLIER) cc_final: 0.7065 (mm-30) REVERT: H 15 GLU cc_start: 0.6736 (mt-10) cc_final: 0.6365 (mt-10) REVERT: H 482 MET cc_start: 0.8589 (mtp) cc_final: 0.8362 (mtp) outliers start: 65 outliers final: 59 residues processed: 509 average time/residue: 0.7784 time to fit residues: 600.7562 Evaluate side-chains 535 residues out of total 2280 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 470 time to evaluate : 3.308 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 ASP Chi-restraints excluded: chain A residue 51 LEU Chi-restraints excluded: chain A residue 272 VAL Chi-restraints excluded: chain A residue 275 SER Chi-restraints excluded: chain A residue 306 THR Chi-restraints excluded: chain A residue 309 GLN Chi-restraints excluded: chain A residue 319 ASP Chi-restraints excluded: chain A residue 491 GLU Chi-restraints excluded: chain B residue 28 ASP Chi-restraints excluded: chain B residue 51 LEU Chi-restraints excluded: chain B residue 272 VAL Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 306 THR Chi-restraints excluded: chain B residue 309 GLN Chi-restraints excluded: chain B residue 370 VAL Chi-restraints excluded: chain B residue 491 GLU Chi-restraints excluded: chain C residue 51 LEU Chi-restraints excluded: chain C residue 70 MET Chi-restraints excluded: chain C residue 239 ASP Chi-restraints excluded: chain C residue 272 VAL Chi-restraints excluded: chain C residue 275 SER Chi-restraints excluded: chain C residue 306 THR Chi-restraints excluded: chain C residue 309 GLN Chi-restraints excluded: chain C residue 315 ASP Chi-restraints excluded: chain C residue 491 GLU Chi-restraints excluded: chain D residue 51 LEU Chi-restraints excluded: chain D residue 268 VAL Chi-restraints excluded: chain D residue 272 VAL Chi-restraints excluded: chain D residue 275 SER Chi-restraints excluded: chain D residue 296 HIS Chi-restraints excluded: chain D residue 309 GLN Chi-restraints excluded: chain D residue 315 ASP Chi-restraints excluded: chain D residue 491 GLU Chi-restraints excluded: chain E residue 51 LEU Chi-restraints excluded: chain E residue 270 VAL Chi-restraints excluded: chain E residue 272 VAL Chi-restraints excluded: chain E residue 275 SER Chi-restraints excluded: chain E residue 370 VAL Chi-restraints excluded: chain E residue 491 GLU Chi-restraints excluded: chain F residue 43 ASP Chi-restraints excluded: chain F residue 61 LEU Chi-restraints excluded: chain F residue 272 VAL Chi-restraints excluded: chain F residue 275 SER Chi-restraints excluded: chain F residue 315 ASP Chi-restraints excluded: chain F residue 370 VAL Chi-restraints excluded: chain F residue 491 GLU Chi-restraints excluded: chain G residue 43 ASP Chi-restraints excluded: chain G residue 51 LEU Chi-restraints excluded: chain G residue 272 VAL Chi-restraints excluded: chain G residue 275 SER Chi-restraints excluded: chain G residue 296 HIS Chi-restraints excluded: chain G residue 306 THR Chi-restraints excluded: chain G residue 309 GLN Chi-restraints excluded: chain G residue 315 ASP Chi-restraints excluded: chain G residue 370 VAL Chi-restraints excluded: chain G residue 491 GLU Chi-restraints excluded: chain H residue 18 LEU Chi-restraints excluded: chain H residue 51 LEU Chi-restraints excluded: chain H residue 239 ASP Chi-restraints excluded: chain H residue 272 VAL Chi-restraints excluded: chain H residue 275 SER Chi-restraints excluded: chain H residue 309 GLN Chi-restraints excluded: chain H residue 315 ASP Chi-restraints excluded: chain H residue 370 VAL Chi-restraints excluded: chain H residue 491 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 280 random chunks: chunk 176 optimal weight: 1.9990 chunk 236 optimal weight: 0.7980 chunk 68 optimal weight: 0.9990 chunk 204 optimal weight: 1.9990 chunk 32 optimal weight: 1.9990 chunk 61 optimal weight: 0.9980 chunk 222 optimal weight: 2.9990 chunk 93 optimal weight: 0.9980 chunk 228 optimal weight: 0.0070 chunk 28 optimal weight: 1.9990 chunk 40 optimal weight: 1.9990 overall best weight: 0.7600 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 465 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 466 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 466 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 465 GLN ** E 466 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 465 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 466 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 466 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3584 r_free = 0.3584 target = 0.153220 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3224 r_free = 0.3224 target = 0.122229 restraints weight = 75379.364| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.126986 restraints weight = 39805.976| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.130086 restraints weight = 26930.095| |-----------------------------------------------------------------------------| r_work (final): 0.3300 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7640 moved from start: 0.3778 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.129 22328 Z= 0.249 Angle : 0.671 59.193 30248 Z= 0.374 Chirality : 0.042 0.191 3512 Planarity : 0.004 0.044 3816 Dihedral : 7.291 76.807 3552 Min Nonbonded Distance : 2.032 Molprobity Statistics. All-atom Clashscore : 10.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.70 % Favored : 93.30 % Rotamer: Outliers : 2.85 % Allowed : 16.75 % Favored : 80.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.93 (0.16), residues: 2808 helix: 0.14 (0.16), residues: 1128 sheet: -1.30 (0.34), residues: 184 loop : -1.09 (0.16), residues: 1496 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.008 0.001 HIS E 466 PHE 0.015 0.001 PHE E 99 TYR 0.008 0.001 TYR A 348 ARG 0.002 0.000 ARG F 493 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11359.26 seconds wall clock time: 200 minutes 10.07 seconds (12010.07 seconds total)