Starting phenix.real_space_refine (version: dev) on Fri Dec 23 04:59:39 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rfi_24443/12_2022/7rfi_24443_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rfi_24443/12_2022/7rfi_24443.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rfi_24443/12_2022/7rfi_24443.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rfi_24443/12_2022/7rfi_24443.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rfi_24443/12_2022/7rfi_24443_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rfi_24443/12_2022/7rfi_24443_trim_updated.pdb" } resolution = 2.6 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.217 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 Convert atoms to be neutral Process input model Symmetric amino acids flipped Residue "A ASP 3": "OD1" <-> "OD2" Residue "A TYR 4": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 12": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 24": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ASP 34": "OD1" <-> "OD2" Residue "A GLU 48": "OE1" <-> "OE2" Residue "A ASP 50": "OD1" <-> "OD2" 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 PHE 110": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 114": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A GLU 196": "OE1" <-> "OE2" Residue "A TYR 233": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ARG 253": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ASP 255": "OD1" <-> "OD2" Residue "A ASP 256": "OD1" <-> "OD2" 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 GLU 352": "OE1" <-> "OE2" Residue "A ARG 355": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A GLU 399": "OE1" <-> "OE2" Residue "A PHE 401": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 402": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ASP 404": "OD1" <-> "OD2" Residue "A ARG 407": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" 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 GLU 491": "OE1" <-> "OE2" Residue "A PHE 514": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B GLU -19": "OE1" <-> "OE2" Residue "B ASP 3": "OD1" <-> "OD2" Residue "B TYR 4": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B TYR 12": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B GLU 15": "OE1" <-> "OE2" Residue "B PHE 24": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B ASP 34": "OD1" <-> "OD2" Residue "B ARG 57": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B PHE 90": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B GLU 103": "OE1" <-> "OE2" Residue "B ARG 105": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B PHE 110": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 114": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B GLU 196": "OE1" <-> "OE2" Residue "B TYR 233": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B ARG 253": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ASP 255": "OD1" <-> "OD2" Residue "B ASP 256": "OD1" <-> "OD2" 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 GLU 352": "OE1" <-> "OE2" Residue "B ARG 355": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B PHE 401": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B ARG 407": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ASP 418": "OD1" <-> "OD2" Residue "B ASP 470": "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 GLU 491": "OE1" <-> "OE2" Residue "B GLU 500": "OE1" <-> "OE2" Residue "B PHE 514": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C ASP 3": "OD1" <-> "OD2" Residue "C TYR 4": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C TYR 12": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C GLU 15": "OE1" <-> "OE2" Residue "C PHE 24": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C ASP 34": "OD1" <-> "OD2" 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 GLU 103": "OE1" <-> "OE2" Residue "C ARG 105": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C PHE 110": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C PHE 114": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C GLU 196": "OE1" <-> "OE2" Residue "C TYR 233": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C ARG 253": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C GLU 254": "OE1" <-> "OE2" Residue "C ASP 255": "OD1" <-> "OD2" Residue "C ASP 256": "OD1" <-> "OD2" 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 GLU 352": "OE1" <-> "OE2" Residue "C ARG 355": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C PHE 401": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C ARG 407": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C ASP 418": "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 GLU 491": "OE1" <-> "OE2" Residue "C GLU 500": "OE1" <-> "OE2" Residue "C PHE 514": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D ASP 3": "OD1" <-> "OD2" Residue "D TYR 4": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D TYR 12": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D PHE 24": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D ASP 34": "OD1" <-> "OD2" 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 GLU 103": "OE1" <-> "OE2" Residue "D ARG 105": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D PHE 114": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D TYR 233": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D ARG 253": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D GLU 254": "OE1" <-> "OE2" Residue "D ASP 255": "OD1" <-> "OD2" Residue "D ASP 256": "OD1" <-> "OD2" 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 GLU 352": "OE1" <-> "OE2" Residue "D ARG 355": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D PHE 357": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D PHE 401": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D PHE 402": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D ARG 407": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D ARG 474": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D TYR 484": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D PHE 490": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D GLU 491": "OE1" <-> "OE2" Residue "D GLU 500": "OE1" <-> "OE2" Residue "D PHE 514": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E ASP 3": "OD1" <-> "OD2" Residue "E TYR 4": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E TYR 12": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E GLU 15": "OE1" <-> "OE2" Residue "E PHE 24": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E ASP 34": "OD1" <-> "OD2" Residue "E GLU 48": "OE1" <-> "OE2" Residue "E ARG 57": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "E ASP 77": "OD1" <-> "OD2" Residue "E PHE 90": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E GLU 103": "OE1" <-> "OE2" Residue "E ARG 105": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "E PHE 110": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E PHE 114": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E GLU 196": "OE1" <-> "OE2" Residue "E TYR 233": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E ARG 253": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "E ASP 255": "OD1" <-> "OD2" Residue "E ASP 256": "OD1" <-> "OD2" 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 GLU 352": "OE1" <-> "OE2" Residue "E ARG 355": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "E PHE 401": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E PHE 402": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E ARG 407": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" 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 GLU 491": "OE1" <-> "OE2" Residue "E GLU 500": "OE1" <-> "OE2" Residue "E PHE 514": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F GLU -19": "OE1" <-> "OE2" Residue "F TYR 4": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F TYR 12": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F GLU 15": "OE1" <-> "OE2" Residue "F PHE 24": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F ASP 34": "OD1" <-> "OD2" Residue "F GLU 48": "OE1" <-> "OE2" Residue "F ARG 57": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "F ASP 77": "OD1" <-> "OD2" Residue "F PHE 90": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F GLU 103": "OE1" <-> "OE2" Residue "F ARG 105": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "F PHE 110": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F PHE 114": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F GLU 196": "OE1" <-> "OE2" Residue "F TYR 233": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F ARG 253": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "F ASP 255": "OD1" <-> "OD2" Residue "F ASP 256": "OD1" <-> "OD2" 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 GLU 352": "OE1" <-> "OE2" Residue "F ARG 355": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "F PHE 401": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F ARG 407": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "F ASP 418": "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 GLU 491": "OE1" <-> "OE2" Residue "F GLU 500": "OE1" <-> "OE2" Residue "F PHE 514": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "G ASP 3": "OD1" <-> "OD2" Residue "G TYR 4": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "G TYR 12": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "G PHE 24": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "G ASP 34": "OD1" <-> "OD2" Residue "G GLU 48": "OE1" <-> "OE2" Residue "G ARG 57": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "G ASP 77": "OD1" <-> "OD2" Residue "G PHE 90": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "G GLU 103": "OE1" <-> "OE2" Residue "G ARG 105": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "G PHE 114": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "G TYR 233": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "G ARG 253": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "G ASP 255": "OD1" <-> "OD2" Residue "G ASP 256": "OD1" <-> "OD2" 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 GLU 352": "OE1" <-> "OE2" Residue "G ARG 355": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "G PHE 401": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "G ARG 407": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "G ASP 418": "OD1" <-> "OD2" Residue "G ASP 470": "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 "G GLU 491": "OE1" <-> "OE2" Residue "G GLU 500": "OE1" <-> "OE2" Residue "G PHE 514": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "H ASP 3": "OD1" <-> "OD2" Residue "H TYR 4": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "H TYR 12": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "H PHE 24": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "H ASP 34": "OD1" <-> "OD2" 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 GLU 103": "OE1" <-> "OE2" Residue "H ARG 105": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "H PHE 110": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "H PHE 114": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "H GLU 196": "OE1" <-> "OE2" Residue "H TYR 233": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "H ARG 253": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "H ASP 255": "OD1" <-> "OD2" Residue "H ASP 256": "OD1" <-> "OD2" 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 GLU 352": "OE1" <-> "OE2" Residue "H ARG 355": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "H PHE 401": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "H PHE 402": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "H ARG 407": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "H ASP 418": "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 PHE 490": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "H GLU 491": "OE1" <-> "OE2" Residue "H GLU 500": "OE1" <-> "OE2" Residue "H PHE 514": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Time to flip residues: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/chem_data/mon_lib" Total number of atoms: 52194 Number of models: 1 Model: "" Number of chains: 16 Chain: "A" Number of atoms: 6393 Number of conformers: 1 Conformer: "" Number of residues, atoms: 422, 6393 Classifications: {'peptide': 422} Link IDs: {'PTRANS': 13, 'TRANS': 408} Chain breaks: 4 Chain: "B" Number of atoms: 6393 Number of conformers: 1 Conformer: "" Number of residues, atoms: 422, 6393 Classifications: {'peptide': 422} Link IDs: {'PTRANS': 13, 'TRANS': 408} Chain breaks: 4 Chain: "C" Number of atoms: 6393 Number of conformers: 1 Conformer: "" Number of residues, atoms: 422, 6393 Classifications: {'peptide': 422} Link IDs: {'PTRANS': 13, 'TRANS': 408} Chain breaks: 4 Chain: "D" Number of atoms: 6393 Number of conformers: 1 Conformer: "" Number of residues, atoms: 422, 6393 Classifications: {'peptide': 422} Link IDs: {'PTRANS': 13, 'TRANS': 408} Chain breaks: 4 Chain: "E" Number of atoms: 6393 Number of conformers: 1 Conformer: "" Number of residues, atoms: 422, 6393 Classifications: {'peptide': 422} Link IDs: {'PTRANS': 13, 'TRANS': 408} Chain breaks: 4 Chain: "F" Number of atoms: 6394 Number of conformers: 1 Conformer: "" Number of residues, atoms: 422, 6394 Classifications: {'peptide': 422} Link IDs: {'PTRANS': 13, 'TRANS': 408} Chain breaks: 4 Chain: "G" Number of atoms: 6394 Number of conformers: 1 Conformer: "" Number of residues, atoms: 422, 6394 Classifications: {'peptide': 422} Link IDs: {'PTRANS': 13, 'TRANS': 408} Chain breaks: 4 Chain: "H" Number of atoms: 6393 Number of conformers: 1 Conformer: "" Number of residues, atoms: 422, 6393 Classifications: {'peptide': 422} Link IDs: {'PTRANS': 13, 'TRANS': 408} Chain breaks: 4 Chain: "A" Number of atoms: 131 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 131 Unusual residues: {'GTP': 2, 'NAD': 1} Classifications: {'RNA': 1, 'undetermined': 3} Modifications used: {'rna3p': 1} Link IDs: {None: 3} Chain: "B" Number of atoms: 131 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 131 Unusual residues: {'GTP': 2, 'NAD': 1} Classifications: {'RNA': 1, 'undetermined': 3} Modifications used: {'rna3p': 1} Link IDs: {None: 3} Chain: "C" Number of atoms: 131 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 131 Unusual residues: {'GTP': 2, 'NAD': 1} Classifications: {'RNA': 1, 'undetermined': 3} Modifications used: {'rna3p': 1} Link IDs: {None: 3} Chain: "D" Number of atoms: 131 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 131 Unusual residues: {'GTP': 2, 'NAD': 1} Classifications: {'RNA': 1, 'undetermined': 3} Modifications used: {'rna3p': 1} Link IDs: {None: 3} Chain: "E" Number of atoms: 131 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 131 Unusual residues: {'GTP': 2, 'NAD': 1} Classifications: {'RNA': 1, 'undetermined': 3} Modifications used: {'rna3p': 1} Link IDs: {None: 3} Chain: "F" Number of atoms: 131 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 131 Unusual residues: {'GTP': 2, 'NAD': 1} Classifications: {'RNA': 1, 'undetermined': 3} Modifications used: {'rna3p': 1} Link IDs: {None: 3} Chain: "G" Number of atoms: 131 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 131 Unusual residues: {'GTP': 2, 'NAD': 1} Classifications: {'RNA': 1, 'undetermined': 3} Modifications used: {'rna3p': 1} Link IDs: {None: 3} Chain: "H" Number of atoms: 131 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 131 Unusual residues: {'GTP': 2, 'NAD': 1} Classifications: {'RNA': 1, 'undetermined': 3} Modifications used: {'rna3p': 1} Link IDs: {None: 3} Time building chain proxies: 16.41, per 1000 atoms: 0.31 Number of scatterers: 52194 At special positions: 0 Unit cell: (137.409, 137.409, 120.549, 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 160 16.00 P 72 15.00 O 5224 8.00 N 4536 7.00 C 16504 6.00 H 25698 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: 31.65 Conformation dependent library (CDL) restraints added in 3.2 seconds 6592 Ramachandran restraints generated. 3296 Oldfield, 0 Emsley, 3296 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6032 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 144 helices and 32 sheets defined 39.0% alpha, 6.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.39 Creating SS restraints... Processing helix chain 'A' and resid -17 through -8 Processing helix chain 'A' and resid 2 through 7 removed outlier: 3.521A pdb=" N SER A 7 " --> pdb=" O ASP A 3 " (cutoff:3.500A) Processing helix chain 'A' and resid 20 through 25 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 46 through 48 No H-bonds generated for 'chain 'A' and resid 46 through 48' Processing helix chain 'A' and resid 76 through 84 Processing helix chain 'A' and resid 97 through 110 Processing helix chain 'A' and resid 194 through 197 Processing helix chain 'A' and resid 224 through 232 Processing helix chain 'A' and resid 254 through 266 removed outlier: 3.622A pdb=" N LEU A 260 " --> pdb=" O LYS A 257 " (cutoff:3.500A) Processing helix chain 'A' and resid 281 through 293 Processing helix chain 'A' and resid 307 through 316 removed outlier: 3.752A pdb=" N ASN A 312 " --> pdb=" O ALA A 308 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N LEU A 313 " --> pdb=" O GLN A 309 " (cutoff:3.500A) Processing helix chain 'A' and resid 333 through 337 Processing helix chain 'A' and resid 343 through 357 removed outlier: 4.451A pdb=" N ARG A 356 " --> pdb=" O GLU A 352 " (cutoff:3.500A) removed outlier: 4.342A pdb=" N PHE A 357 " --> pdb=" O TYR A 353 " (cutoff:3.500A) Processing helix chain 'A' and resid 370 through 378 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 501 Processing helix chain 'B' and resid -17 through -8 Processing helix chain 'B' and resid 2 through 7 Processing helix chain 'B' and resid 20 through 25 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 46 through 48 No H-bonds generated for 'chain 'B' and resid 46 through 48' Processing helix chain 'B' and resid 76 through 84 Processing helix chain 'B' and resid 97 through 110 Processing helix chain 'B' and resid 194 through 197 Processing helix chain 'B' and resid 224 through 232 Processing helix chain 'B' and resid 254 through 266 removed outlier: 3.508A pdb=" N LEU B 260 " --> pdb=" O LYS B 257 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N LEU B 263 " --> pdb=" O LEU B 260 " (cutoff:3.500A) Processing helix chain 'B' and resid 281 through 293 Processing helix chain 'B' and resid 307 through 316 removed outlier: 3.747A pdb=" N ASN B 312 " --> pdb=" O ALA B 308 " (cutoff:3.500A) removed outlier: 3.539A 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 357 removed outlier: 4.515A pdb=" N ARG B 356 " --> pdb=" O GLU B 352 " (cutoff:3.500A) removed outlier: 4.334A pdb=" N PHE B 357 " --> pdb=" O TYR B 353 " (cutoff:3.500A) Processing helix chain 'B' and resid 370 through 378 Processing helix chain 'B' and resid 453 through 471 Proline residue: B 458 - end of helix Processing helix chain 'B' and resid 476 through 484 Processing helix chain 'B' and resid 495 through 501 Processing helix chain 'C' and resid -17 through -8 Processing helix chain 'C' and resid 2 through 7 Processing helix chain 'C' and resid 20 through 25 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 46 through 48 No H-bonds generated for 'chain 'C' and resid 46 through 48' Processing helix chain 'C' and resid 76 through 85 Processing helix chain 'C' and resid 97 through 110 Processing helix chain 'C' and resid 194 through 197 Processing helix chain 'C' and resid 224 through 232 Processing helix chain 'C' and resid 254 through 266 removed outlier: 3.669A pdb=" N LEU C 260 " --> pdb=" O LYS C 257 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N LEU C 263 " --> pdb=" O LEU C 260 " (cutoff:3.500A) Processing helix chain 'C' and resid 281 through 293 Processing helix chain 'C' and resid 307 through 316 removed outlier: 3.738A pdb=" N ASN C 312 " --> pdb=" O ALA C 308 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N LEU C 313 " --> pdb=" O GLN C 309 " (cutoff:3.500A) Processing helix chain 'C' and resid 333 through 337 Processing helix chain 'C' and resid 343 through 357 removed outlier: 4.355A pdb=" N ARG C 356 " --> pdb=" O GLU C 352 " (cutoff:3.500A) removed outlier: 4.352A pdb=" N PHE C 357 " --> pdb=" O TYR C 353 " (cutoff:3.500A) Processing helix chain 'C' and resid 370 through 378 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 495 through 501 Processing helix chain 'D' and resid -17 through -8 Processing helix chain 'D' and resid 2 through 7 Processing helix chain 'D' and resid 20 through 25 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 46 through 48 No H-bonds generated for 'chain 'D' and resid 46 through 48' Processing helix chain 'D' and resid 76 through 85 Processing helix chain 'D' and resid 97 through 110 Processing helix chain 'D' and resid 194 through 197 Processing helix chain 'D' and resid 224 through 232 Processing helix chain 'D' and resid 254 through 266 removed outlier: 3.601A pdb=" N LEU D 260 " --> pdb=" O LYS D 257 " (cutoff:3.500A) Processing helix chain 'D' and resid 281 through 293 Processing helix chain 'D' and resid 307 through 316 removed outlier: 3.757A pdb=" N ASN D 312 " --> pdb=" O ALA D 308 " (cutoff:3.500A) removed outlier: 3.552A 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 357 removed outlier: 4.171A pdb=" N ARG D 356 " --> pdb=" O GLU D 352 " (cutoff:3.500A) removed outlier: 4.365A pdb=" N PHE D 357 " --> pdb=" O TYR D 353 " (cutoff:3.500A) Processing helix chain 'D' and resid 370 through 378 Processing helix chain 'D' and resid 453 through 471 Proline residue: D 458 - end of helix Processing helix chain 'D' and resid 476 through 484 Processing helix chain 'D' and resid 495 through 501 Processing helix chain 'E' and resid -17 through -8 Processing helix chain 'E' and resid 2 through 7 Processing helix chain 'E' and resid 20 through 25 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 46 through 48 No H-bonds generated for 'chain 'E' and resid 46 through 48' Processing helix chain 'E' and resid 76 through 85 Processing helix chain 'E' and resid 97 through 109 Processing helix chain 'E' and resid 194 through 197 Processing helix chain 'E' and resid 224 through 232 Processing helix chain 'E' and resid 254 through 266 removed outlier: 3.639A pdb=" N TYR E 258 " --> pdb=" O ASP E 255 " (cutoff:3.500A) Processing helix chain 'E' and resid 281 through 293 Processing helix chain 'E' and resid 307 through 316 removed outlier: 3.747A pdb=" N ASN E 312 " --> pdb=" O ALA E 308 " (cutoff:3.500A) removed outlier: 3.516A 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 357 removed outlier: 4.350A pdb=" N ARG E 356 " --> pdb=" O GLU E 352 " (cutoff:3.500A) removed outlier: 4.351A pdb=" N PHE E 357 " --> pdb=" O TYR E 353 " (cutoff:3.500A) Processing helix chain 'E' and resid 370 through 378 Processing helix chain 'E' and resid 453 through 471 Proline residue: E 458 - end of helix Processing helix chain 'E' and resid 476 through 484 Processing helix chain 'E' and resid 495 through 501 Processing helix chain 'F' and resid -17 through -8 Processing helix chain 'F' and resid 2 through 7 removed outlier: 3.538A pdb=" N SER F 7 " --> pdb=" O ASP F 3 " (cutoff:3.500A) Processing helix chain 'F' and resid 20 through 25 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 46 through 48 No H-bonds generated for 'chain 'F' and resid 46 through 48' Processing helix chain 'F' and resid 76 through 85 Processing helix chain 'F' and resid 97 through 109 Processing helix chain 'F' and resid 194 through 197 Processing helix chain 'F' and resid 224 through 232 Processing helix chain 'F' and resid 254 through 266 removed outlier: 3.783A pdb=" N TYR F 258 " --> pdb=" O ASP F 255 " (cutoff:3.500A) Processing helix chain 'F' and resid 281 through 293 Processing helix chain 'F' and resid 307 through 316 removed outlier: 3.732A pdb=" N ASN F 312 " --> pdb=" O ALA F 308 " (cutoff:3.500A) removed outlier: 3.510A 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: 4.528A pdb=" N ARG F 356 " --> pdb=" O GLU F 352 " (cutoff:3.500A) removed outlier: 4.350A pdb=" N PHE F 357 " --> pdb=" O TYR F 353 " (cutoff:3.500A) Processing helix chain 'F' and resid 370 through 378 Processing helix chain 'F' and resid 453 through 471 Proline residue: F 458 - end of helix Processing helix chain 'F' and resid 476 through 484 Processing helix chain 'F' and resid 495 through 501 Processing helix chain 'G' and resid -17 through -8 Processing helix chain 'G' and resid 2 through 7 removed outlier: 3.566A pdb=" N SER G 7 " --> pdb=" O ASP G 3 " (cutoff:3.500A) Processing helix chain 'G' and resid 20 through 25 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 46 through 48 No H-bonds generated for 'chain 'G' and resid 46 through 48' Processing helix chain 'G' and resid 76 through 85 Processing helix chain 'G' and resid 97 through 109 Processing helix chain 'G' and resid 194 through 197 Processing helix chain 'G' and resid 224 through 232 Processing helix chain 'G' and resid 254 through 266 removed outlier: 3.637A pdb=" N TYR G 258 " --> pdb=" O ASP G 255 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N LEU G 260 " --> pdb=" O LYS G 257 " (cutoff:3.500A) Processing helix chain 'G' and resid 281 through 293 Processing helix chain 'G' and resid 307 through 316 removed outlier: 3.766A pdb=" N ASN G 312 " --> pdb=" O ALA G 308 " (cutoff:3.500A) removed outlier: 3.513A 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 357 removed outlier: 4.524A pdb=" N ARG G 356 " --> pdb=" O GLU G 352 " (cutoff:3.500A) removed outlier: 4.390A pdb=" N PHE G 357 " --> pdb=" O TYR G 353 " (cutoff:3.500A) Processing helix chain 'G' and resid 370 through 378 Processing helix chain 'G' and resid 453 through 471 Proline residue: G 458 - end of helix Processing helix chain 'G' and resid 476 through 484 Processing helix chain 'G' and resid 495 through 501 Processing helix chain 'H' and resid -17 through -8 Processing helix chain 'H' and resid 2 through 7 Processing helix chain 'H' and resid 20 through 25 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 46 through 48 No H-bonds generated for 'chain 'H' and resid 46 through 48' Processing helix chain 'H' and resid 76 through 85 Processing helix chain 'H' and resid 97 through 110 Processing helix chain 'H' and resid 194 through 197 Processing helix chain 'H' and resid 224 through 232 Processing helix chain 'H' and resid 254 through 266 removed outlier: 3.791A pdb=" N TYR H 258 " --> pdb=" O ASP H 255 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N LEU H 260 " --> pdb=" O LYS H 257 " (cutoff:3.500A) Processing helix chain 'H' and resid 281 through 293 Processing helix chain 'H' and resid 307 through 316 removed outlier: 3.748A pdb=" N ASN H 312 " --> pdb=" O ALA H 308 " (cutoff:3.500A) removed outlier: 3.542A 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: 4.350A pdb=" N ARG H 356 " --> pdb=" O GLU H 352 " (cutoff:3.500A) removed outlier: 4.360A pdb=" N PHE H 357 " --> pdb=" O TYR H 353 " (cutoff:3.500A) Processing helix chain 'H' and resid 370 through 378 Processing helix chain 'H' and resid 453 through 471 Proline residue: H 458 - end of helix Processing helix chain 'H' and resid 476 through 484 Processing helix chain 'H' and resid 495 through 501 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: 6.431A pdb=" N VAL A 384 " --> pdb=" O ILE A 66 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 247 through 249 removed outlier: 6.633A pdb=" N VAL A 270 " --> pdb=" O ALA A 248 " (cutoff:3.500A) removed outlier: 6.691A pdb=" N GLN A 298 " --> pdb=" O ILE A 271 " (cutoff:3.500A) No H-bonds generated for sheet with id= C Processing sheet with id= D, first strand: chain 'A' and resid 408 through 411 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: 6.460A pdb=" N VAL B 384 " --> pdb=" O ILE B 66 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 247 through 249 removed outlier: 6.635A pdb=" N VAL B 270 " --> pdb=" O ALA B 248 " (cutoff:3.500A) removed outlier: 6.755A pdb=" N GLN B 298 " --> pdb=" O ILE B 271 " (cutoff:3.500A) No H-bonds generated for sheet with id= G Processing sheet with id= H, first strand: chain 'B' and resid 408 through 411 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: 6.461A pdb=" N VAL C 384 " --> pdb=" O ILE C 66 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'C' and resid 247 through 249 removed outlier: 6.637A pdb=" N VAL C 270 " --> pdb=" O ALA C 248 " (cutoff:3.500A) removed outlier: 6.766A pdb=" N GLN C 298 " --> pdb=" O ILE C 271 " (cutoff:3.500A) No H-bonds generated for sheet with id= K Processing sheet with id= L, first strand: chain 'C' and resid 408 through 411 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: 6.333A pdb=" N VAL D 384 " --> pdb=" O ILE D 66 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'D' and resid 247 through 249 removed outlier: 6.639A pdb=" N VAL D 270 " --> pdb=" O ALA D 248 " (cutoff:3.500A) removed outlier: 6.744A pdb=" N GLN D 298 " --> pdb=" O ILE D 271 " (cutoff:3.500A) No H-bonds generated for sheet with id= O Processing sheet with id= P, first strand: chain 'D' and resid 408 through 411 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: 6.445A pdb=" N VAL E 384 " --> pdb=" O ILE E 66 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'E' and resid 247 through 249 removed outlier: 6.649A pdb=" N VAL E 270 " --> pdb=" O ALA E 248 " (cutoff:3.500A) removed outlier: 6.684A pdb=" N GLN E 298 " --> pdb=" O ILE E 271 " (cutoff:3.500A) No H-bonds generated for sheet with id= S Processing sheet with id= T, first strand: chain 'E' and resid 408 through 411 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: 6.470A pdb=" N VAL F 384 " --> pdb=" O ILE F 66 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'F' and resid 247 through 250 removed outlier: 6.639A pdb=" N VAL F 270 " --> pdb=" O ALA F 248 " (cutoff:3.500A) removed outlier: 7.711A pdb=" N VAL F 250 " --> pdb=" O VAL F 270 " (cutoff:3.500A) removed outlier: 6.292A pdb=" N VAL F 272 " --> pdb=" O VAL F 250 " (cutoff:3.500A) removed outlier: 6.626A pdb=" N GLN F 298 " --> pdb=" O ILE F 271 " (cutoff:3.500A) removed outlier: 7.553A pdb=" N LEU F 273 " --> pdb=" O GLN F 298 " (cutoff:3.500A) removed outlier: 7.051A 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 408 through 411 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: 6.450A pdb=" N VAL G 384 " --> pdb=" O ILE G 66 " (cutoff:3.500A) Processing sheet with id= AA, first strand: chain 'G' and resid 247 through 249 removed outlier: 6.636A pdb=" N VAL G 270 " --> pdb=" O ALA G 248 " (cutoff:3.500A) removed outlier: 6.773A pdb=" N GLN G 298 " --> pdb=" O ILE G 271 " (cutoff:3.500A) No H-bonds generated for sheet with id= AA Processing sheet with id= AB, first strand: chain 'G' and resid 408 through 411 Processing sheet with id= AC, first strand: chain 'H' and resid 35 through 37 Processing sheet with id= AD, first strand: chain 'H' and resid 65 through 67 removed outlier: 6.459A pdb=" N VAL H 384 " --> pdb=" O ILE H 66 " (cutoff:3.500A) Processing sheet with id= AE, first strand: chain 'H' and resid 247 through 249 removed outlier: 6.623A pdb=" N VAL H 270 " --> pdb=" O ALA H 248 " (cutoff:3.500A) removed outlier: 6.697A pdb=" N GLN H 298 " --> pdb=" O ILE H 271 " (cutoff:3.500A) No H-bonds generated for sheet with id= AE Processing sheet with id= AF, first strand: chain 'H' and resid 408 through 411 804 hydrogen bonds defined for protein. 2136 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 15.46 Time building geometry restraints manager: 33.34 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.94 - 1.12: 25650 1.12 - 1.29: 4388 1.29 - 1.47: 9901 1.47 - 1.65: 12451 1.65 - 1.82: 276 Bond restraints: 52666 Sorted by residual: bond pdb=" C3' GTP C 602 " pdb=" C4' GTP C 602 " ideal model delta sigma weight residual 1.524 1.297 0.227 2.00e-02 2.50e+03 1.29e+02 bond pdb=" C3' GTP H 602 " pdb=" C4' GTP H 602 " ideal model delta sigma weight residual 1.524 1.299 0.225 2.00e-02 2.50e+03 1.27e+02 bond pdb=" C3' GTP D 602 " pdb=" C4' GTP D 602 " ideal model delta sigma weight residual 1.524 1.299 0.225 2.00e-02 2.50e+03 1.27e+02 bond pdb=" C4' GTP H 602 " pdb=" O4' GTP H 602 " ideal model delta sigma weight residual 1.410 1.613 -0.203 2.00e-02 2.50e+03 1.03e+02 bond pdb=" C4' GTP D 602 " pdb=" O4' GTP D 602 " ideal model delta sigma weight residual 1.410 1.613 -0.203 2.00e-02 2.50e+03 1.03e+02 ... (remaining 52661 not shown) Histogram of bond angle deviations from ideal: 93.46 - 101.81: 188 101.81 - 110.17: 48556 110.17 - 118.52: 23313 118.52 - 126.87: 22479 126.87 - 135.23: 356 Bond angle restraints: 94892 Sorted by residual: angle pdb=" O3A GTP G 602 " pdb=" PB GTP G 602 " pdb=" O3B GTP G 602 " ideal model delta sigma weight residual 102.60 121.60 -19.00 3.00e+00 1.11e-01 4.01e+01 angle pdb=" O3A GTP E 602 " pdb=" PB GTP E 602 " pdb=" O3B GTP E 602 " ideal model delta sigma weight residual 102.60 121.56 -18.96 3.00e+00 1.11e-01 4.00e+01 angle pdb=" O3A GTP B 602 " pdb=" PB GTP B 602 " pdb=" O3B GTP B 602 " ideal model delta sigma weight residual 102.60 121.17 -18.57 3.00e+00 1.11e-01 3.83e+01 angle pdb=" CA HIS H 504 " pdb=" CB HIS H 504 " pdb=" CG HIS H 504 " ideal model delta sigma weight residual 113.80 119.93 -6.13 1.00e+00 1.00e+00 3.76e+01 angle pdb=" OE1 GLN H 100 " pdb=" CD GLN H 100 " pdb=" NE2 GLN H 100 " ideal model delta sigma weight residual 122.60 116.57 6.03 1.00e+00 1.00e+00 3.64e+01 ... (remaining 94887 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.98: 19662 35.98 - 71.97: 877 71.97 - 107.95: 87 107.95 - 143.93: 36 143.93 - 179.92: 20 Dihedral angle restraints: 20682 sinusoidal: 9816 harmonic: 10866 Sorted by residual: dihedral pdb=" C8 GTP E 602 " pdb=" C1' GTP E 602 " pdb=" N9 GTP E 602 " pdb=" O4' GTP E 602 " ideal model delta sinusoidal sigma weight residual 104.59 -75.32 179.92 1 2.00e+01 2.50e-03 4.80e+01 dihedral pdb=" C8 GTP G 602 " pdb=" C1' GTP G 602 " pdb=" N9 GTP G 602 " pdb=" O4' GTP G 602 " ideal model delta sinusoidal sigma weight residual 104.59 -73.64 178.23 1 2.00e+01 2.50e-03 4.80e+01 dihedral pdb=" O5' GTP B 602 " pdb=" O3A GTP B 602 " pdb=" PA GTP B 602 " pdb=" PB GTP B 602 " ideal model delta sinusoidal sigma weight residual -85.88 91.32 -177.19 1 2.00e+01 2.50e-03 4.80e+01 ... (remaining 20679 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.161: 3840 0.161 - 0.321: 259 0.321 - 0.482: 23 0.482 - 0.642: 14 0.642 - 0.803: 16 Chirality restraints: 4152 Sorted by residual: chirality pdb=" CG LEU C -8 " pdb=" CB LEU C -8 " pdb=" CD1 LEU C -8 " pdb=" CD2 LEU C -8 " both_signs ideal model delta sigma weight residual False -2.59 -1.79 -0.80 2.00e-01 2.50e+01 1.61e+01 chirality pdb=" CG LEU D -8 " pdb=" CB LEU D -8 " pdb=" CD1 LEU D -8 " pdb=" CD2 LEU D -8 " both_signs ideal model delta sigma weight residual False -2.59 -1.81 -0.78 2.00e-01 2.50e+01 1.51e+01 chirality pdb=" CG LEU F -8 " pdb=" CB LEU F -8 " pdb=" CD1 LEU F -8 " pdb=" CD2 LEU F -8 " both_signs ideal model delta sigma weight residual False -2.59 -1.82 -0.77 2.00e-01 2.50e+01 1.48e+01 ... (remaining 4149 not shown) Planarity restraints: 7760 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' GTP F 602 " 0.231 2.00e-02 2.50e+03 9.80e-02 2.88e+02 pdb=" C2 GTP F 602 " -0.043 2.00e-02 2.50e+03 pdb=" C4 GTP F 602 " -0.096 2.00e-02 2.50e+03 pdb=" C5 GTP F 602 " -0.072 2.00e-02 2.50e+03 pdb=" C6 GTP F 602 " 0.015 2.00e-02 2.50e+03 pdb=" C8 GTP F 602 " -0.058 2.00e-02 2.50e+03 pdb=" N1 GTP F 602 " 0.021 2.00e-02 2.50e+03 pdb=" N2 GTP F 602 " 0.012 2.00e-02 2.50e+03 pdb=" N3 GTP F 602 " -0.085 2.00e-02 2.50e+03 pdb=" N7 GTP F 602 " -0.069 2.00e-02 2.50e+03 pdb=" N9 GTP F 602 " -0.027 2.00e-02 2.50e+03 pdb=" O6 GTP F 602 " 0.169 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLN B 283 " 0.110 2.00e-02 2.50e+03 9.97e-02 1.49e+02 pdb=" CD GLN B 283 " -0.059 2.00e-02 2.50e+03 pdb=" OE1 GLN B 283 " -0.049 2.00e-02 2.50e+03 pdb=" NE2 GLN B 283 " -0.101 2.00e-02 2.50e+03 pdb="HE21 GLN B 283 " -0.066 2.00e-02 2.50e+03 pdb="HE22 GLN B 283 " 0.165 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' GTP A 602 " -0.157 2.00e-02 2.50e+03 6.79e-02 1.38e+02 pdb=" C2 GTP A 602 " 0.011 2.00e-02 2.50e+03 pdb=" C4 GTP A 602 " 0.042 2.00e-02 2.50e+03 pdb=" C5 GTP A 602 " 0.025 2.00e-02 2.50e+03 pdb=" C6 GTP A 602 " -0.030 2.00e-02 2.50e+03 pdb=" C8 GTP A 602 " 0.076 2.00e-02 2.50e+03 pdb=" N1 GTP A 602 " -0.068 2.00e-02 2.50e+03 pdb=" N2 GTP A 602 " 0.054 2.00e-02 2.50e+03 pdb=" N3 GTP A 602 " 0.059 2.00e-02 2.50e+03 pdb=" N7 GTP A 602 " 0.066 2.00e-02 2.50e+03 pdb=" N9 GTP A 602 " 0.000 2.00e-02 2.50e+03 pdb=" O6 GTP A 602 " -0.078 2.00e-02 2.50e+03 ... (remaining 7757 not shown) Histogram of nonbonded interaction distances: 1.39 - 2.03: 1640 2.03 - 2.67: 67883 2.67 - 3.32: 160975 3.32 - 3.96: 219537 3.96 - 4.60: 325503 Nonbonded interactions: 775538 Sorted by model distance: nonbonded pdb=" HB3 LYS D 228 " pdb=" HE2 LYS D 228 " model vdw 1.388 2.440 nonbonded pdb=" HB3 LYS G 195 " pdb=" HE3 LYS G 195 " model vdw 1.506 2.440 nonbonded pdb=" HB3 LYS H 228 " pdb=" HE3 LYS H 228 " model vdw 1.512 2.440 nonbonded pdb=" HB3 LYS A 228 " pdb=" HE3 LYS A 228 " model vdw 1.518 2.440 nonbonded pdb=" HB3 LYS E 228 " pdb=" HE3 LYS E 228 " model vdw 1.523 2.440 ... (remaining 775533 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' and (resid -21 or (resid -20 and (name N or name CA or name C or name \ O or name CB or name CG or name ND1 or name CD2 or name CE1 or name NE2 or name \ H or name HA or name HB2 or name HB3 or name HD2 or name HE1 or name HE2)) or r \ esid -19 through 516 or resid 601 through 604)) selection = (chain 'G' and (resid -21 or (resid -20 and (name N or name CA or name C or name \ O or name CB or name CG or name ND1 or name CD2 or name CE1 or name NE2 or name \ H or name HA or name HB2 or name HB3 or name HD2 or name HE1 or name HE2)) or r \ esid -19 through 516 or resid 601 through 604)) selection = chain 'H' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 72 5.49 5 S 160 5.16 5 C 16504 2.51 5 N 4536 2.21 5 O 5224 1.98 5 H 25698 0.53 5 sf(0) = scattering factor at diffraction angle 0. 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.140 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: 0.560 Extract box with map and model: 15.020 Check model and map are aligned: 0.570 Convert atoms to be neutral: 0.330 Process input model: 115.320 Find NCS groups from input model: 1.930 Set up NCS constraints: 0.230 Set refine NCS operators: 0.000 Set scattering table: 0.010 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:8.750 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 145.870 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8707 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.014 0.227 26968 Z= 0.943 Angle : 1.868 19.005 36592 Z= 1.150 Chirality : 0.105 0.803 4152 Planarity : 0.013 0.123 4528 Dihedral : 19.440 179.917 9784 Min Nonbonded Distance : 2.335 Molprobity Statistics. All-atom Clashscore : 3.63 Ramachandran Plot: Outliers : 0.39 % Allowed : 3.97 % Favored : 95.63 % Rotamer Outliers : 1.61 % Cbeta Deviations : 0.27 % 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: -1.71 (0.12), residues: 3296 helix: -1.03 (0.12), residues: 1352 sheet: -0.95 (0.30), residues: 264 loop : -1.15 (0.13), residues: 1680 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6592 Ramachandran restraints generated. 3296 Oldfield, 0 Emsley, 3296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6592 Ramachandran restraints generated. 3296 Oldfield, 0 Emsley, 3296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 683 residues out of total 2672 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 640 time to evaluate : 2.624 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 outliers start: 43 outliers final: 20 residues processed: 670 average time/residue: 1.9730 time to fit residues: 1557.4171 Evaluate side-chains 558 residues out of total 2672 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 538 time to evaluate : 2.632 Switching outliers to nearest non-outliers outliers start: 20 outliers final: 16 residues processed: 4 average time/residue: 0.4234 time to fit residues: 6.3084 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 283 optimal weight: 0.8980 chunk 254 optimal weight: 0.9980 chunk 141 optimal weight: 0.9990 chunk 86 optimal weight: 0.7980 chunk 171 optimal weight: 2.9990 chunk 136 optimal weight: 0.9990 chunk 263 optimal weight: 0.8980 chunk 101 optimal weight: 1.9990 chunk 160 optimal weight: 0.9990 chunk 196 optimal weight: 0.8980 chunk 305 optimal weight: 2.9990 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 33 ASN A 100 GLN A 230 ASN A 312 ASN A 498 GLN B 33 ASN B 100 GLN B 312 ASN B 498 GLN C 100 GLN C 230 ASN C 312 ASN D 100 GLN D 230 ASN D 303 ASN D 312 ASN E 33 ASN E 100 GLN E 265 GLN E 283 GLN E 312 ASN E 498 GLN F 100 GLN ** F 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 312 ASN G 100 GLN ** G 303 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 312 ASN G 498 GLN H 33 ASN H 100 GLN H 230 ASN H 312 ASN H 498 GLN Total number of N/Q/H flips: 32 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8743 moved from start: 0.2370 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.024 26968 Z= 0.208 Angle : 0.609 7.669 36592 Z= 0.303 Chirality : 0.043 0.164 4152 Planarity : 0.004 0.046 4528 Dihedral : 18.926 179.671 3952 Min Nonbonded Distance : 1.999 Molprobity Statistics. All-atom Clashscore : 3.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Rotamer Outliers : 1.76 % 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: -0.51 (0.14), residues: 3296 helix: 0.37 (0.14), residues: 1352 sheet: -0.14 (0.33), residues: 296 loop : -0.94 (0.14), residues: 1648 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6592 Ramachandran restraints generated. 3296 Oldfield, 0 Emsley, 3296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6592 Ramachandran restraints generated. 3296 Oldfield, 0 Emsley, 3296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 598 residues out of total 2672 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 551 time to evaluate : 2.669 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 outliers start: 47 outliers final: 33 residues processed: 589 average time/residue: 1.9031 time to fit residues: 1322.2403 Evaluate side-chains 548 residues out of total 2672 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 515 time to evaluate : 2.476 Switching outliers to nearest non-outliers outliers start: 33 outliers final: 30 residues processed: 3 average time/residue: 0.3936 time to fit residues: 5.2500 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 169 optimal weight: 5.9990 chunk 94 optimal weight: 2.9990 chunk 253 optimal weight: 5.9990 chunk 207 optimal weight: 1.9990 chunk 84 optimal weight: 2.9990 chunk 305 optimal weight: 0.9980 chunk 330 optimal weight: 0.9990 chunk 272 optimal weight: 1.9990 chunk 303 optimal weight: 2.9990 chunk 104 optimal weight: 1.9990 chunk 245 optimal weight: 5.9990 overall best weight: 1.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 498 GLN B 498 GLN C 33 ASN ** C 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 441 GLN D 33 ASN D 283 GLN E 241 GLN E 283 GLN E 441 GLN E 498 GLN F 33 ASN ** F 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 33 ASN ** G 303 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 498 GLN H 498 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8783 moved from start: 0.2794 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.032 26968 Z= 0.293 Angle : 0.607 6.863 36592 Z= 0.303 Chirality : 0.045 0.164 4152 Planarity : 0.004 0.049 4528 Dihedral : 17.272 179.167 3952 Min Nonbonded Distance : 1.995 Molprobity Statistics. All-atom Clashscore : 3.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.58 % Favored : 96.42 % Rotamer Outliers : 2.40 % 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: -0.37 (0.14), residues: 3296 helix: 0.55 (0.14), residues: 1352 sheet: -0.29 (0.31), residues: 296 loop : -0.87 (0.14), residues: 1648 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6592 Ramachandran restraints generated. 3296 Oldfield, 0 Emsley, 3296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6592 Ramachandran restraints generated. 3296 Oldfield, 0 Emsley, 3296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 597 residues out of total 2672 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 533 time to evaluate : 2.490 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 outliers start: 64 outliers final: 36 residues processed: 575 average time/residue: 1.8920 time to fit residues: 1273.9501 Evaluate side-chains 552 residues out of total 2672 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 516 time to evaluate : 2.460 Switching outliers to nearest non-outliers outliers start: 36 outliers final: 32 residues processed: 4 average time/residue: 0.6128 time to fit residues: 6.7962 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 302 optimal weight: 0.9990 chunk 229 optimal weight: 1.9990 chunk 158 optimal weight: 2.9990 chunk 33 optimal weight: 3.9990 chunk 145 optimal weight: 1.9990 chunk 205 optimal weight: 1.9990 chunk 306 optimal weight: 1.9990 chunk 324 optimal weight: 1.9990 chunk 160 optimal weight: 3.9990 chunk 290 optimal weight: 1.9990 chunk 87 optimal weight: 0.8980 overall best weight: 1.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 498 GLN B 441 GLN B 498 GLN ** C 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 230 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 241 GLN ** E 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 498 GLN ** F 230 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 507 HIS ** G 230 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 303 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 498 GLN H 498 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8785 moved from start: 0.2972 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.030 26968 Z= 0.280 Angle : 0.581 7.049 36592 Z= 0.287 Chirality : 0.044 0.146 4152 Planarity : 0.004 0.048 4528 Dihedral : 16.714 178.546 3952 Min Nonbonded Distance : 1.966 Molprobity Statistics. All-atom Clashscore : 4.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.67 % Favored : 96.33 % Rotamer Outliers : 2.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.32 (0.14), residues: 3296 helix: 0.63 (0.14), residues: 1352 sheet: -0.39 (0.29), residues: 296 loop : -0.85 (0.14), residues: 1648 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6592 Ramachandran restraints generated. 3296 Oldfield, 0 Emsley, 3296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6592 Ramachandran restraints generated. 3296 Oldfield, 0 Emsley, 3296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 608 residues out of total 2672 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 533 time to evaluate : 2.522 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 outliers start: 75 outliers final: 46 residues processed: 583 average time/residue: 1.9218 time to fit residues: 1318.3406 Evaluate side-chains 566 residues out of total 2672 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 520 time to evaluate : 2.526 Switching outliers to nearest non-outliers outliers start: 46 outliers final: 36 residues processed: 10 average time/residue: 0.5114 time to fit residues: 11.5711 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 270 optimal weight: 0.9990 chunk 184 optimal weight: 2.9990 chunk 4 optimal weight: 2.9990 chunk 241 optimal weight: 2.9990 chunk 134 optimal weight: 1.9990 chunk 277 optimal weight: 3.9990 chunk 224 optimal weight: 7.9990 chunk 0 optimal weight: 4.9990 chunk 165 optimal weight: 1.9990 chunk 291 optimal weight: 1.9990 chunk 81 optimal weight: 1.9990 overall best weight: 1.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 498 GLN ** B 230 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 441 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 498 GLN ** C 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 230 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 265 GLN ** E 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 498 GLN ** F 230 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 441 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 507 HIS ** G 230 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 303 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 498 GLN H 498 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8795 moved from start: 0.3085 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.033 26968 Z= 0.323 Angle : 0.600 7.188 36592 Z= 0.298 Chirality : 0.045 0.147 4152 Planarity : 0.004 0.048 4528 Dihedral : 16.360 179.930 3952 Min Nonbonded Distance : 1.980 Molprobity Statistics. All-atom Clashscore : 4.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.13 % Favored : 95.87 % Rotamer Outliers : 2.92 % 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: -0.41 (0.14), residues: 3296 helix: 0.54 (0.14), residues: 1352 sheet: -0.55 (0.28), residues: 312 loop : -0.87 (0.14), residues: 1632 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6592 Ramachandran restraints generated. 3296 Oldfield, 0 Emsley, 3296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6592 Ramachandran restraints generated. 3296 Oldfield, 0 Emsley, 3296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 600 residues out of total 2672 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 78 poor density : 522 time to evaluate : 2.481 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 outliers start: 78 outliers final: 48 residues processed: 570 average time/residue: 1.8908 time to fit residues: 1271.5059 Evaluate side-chains 571 residues out of total 2672 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 523 time to evaluate : 2.456 Switching outliers to nearest non-outliers outliers start: 48 outliers final: 37 residues processed: 11 average time/residue: 0.5303 time to fit residues: 12.5295 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 109 optimal weight: 3.9990 chunk 292 optimal weight: 3.9990 chunk 64 optimal weight: 1.9990 chunk 190 optimal weight: 1.9990 chunk 80 optimal weight: 0.9980 chunk 325 optimal weight: 3.9990 chunk 269 optimal weight: 0.8980 chunk 150 optimal weight: 2.9990 chunk 27 optimal weight: 1.9990 chunk 107 optimal weight: 1.9990 chunk 170 optimal weight: 1.9990 overall best weight: 1.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 441 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 498 GLN ** B 230 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 265 GLN ** B 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 498 GLN C 265 GLN ** C 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 441 GLN ** E 230 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 265 GLN ** E 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 441 GLN E 498 GLN ** F 230 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 441 GLN ** G 230 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 303 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 498 GLN H 498 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8788 moved from start: 0.3157 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.030 26968 Z= 0.282 Angle : 0.578 7.182 36592 Z= 0.285 Chirality : 0.044 0.146 4152 Planarity : 0.004 0.047 4528 Dihedral : 15.988 177.075 3952 Min Nonbonded Distance : 1.988 Molprobity Statistics. All-atom Clashscore : 4.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.73 % Favored : 96.27 % Rotamer Outliers : 2.51 % 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: -0.33 (0.14), residues: 3296 helix: 0.63 (0.14), residues: 1352 sheet: -0.58 (0.28), residues: 312 loop : -0.83 (0.14), residues: 1632 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6592 Ramachandran restraints generated. 3296 Oldfield, 0 Emsley, 3296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6592 Ramachandran restraints generated. 3296 Oldfield, 0 Emsley, 3296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 590 residues out of total 2672 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 523 time to evaluate : 2.486 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 outliers start: 67 outliers final: 50 residues processed: 572 average time/residue: 1.8440 time to fit residues: 1235.0207 Evaluate side-chains 566 residues out of total 2672 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 516 time to evaluate : 2.443 Switching outliers to nearest non-outliers outliers start: 50 outliers final: 40 residues processed: 10 average time/residue: 0.6436 time to fit residues: 12.5572 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 313 optimal weight: 1.9990 chunk 36 optimal weight: 1.9990 chunk 185 optimal weight: 0.6980 chunk 237 optimal weight: 1.9990 chunk 183 optimal weight: 1.9990 chunk 273 optimal weight: 1.9990 chunk 181 optimal weight: 2.9990 chunk 323 optimal weight: 0.7980 chunk 202 optimal weight: 0.9990 chunk 197 optimal weight: 0.0060 chunk 149 optimal weight: 1.9990 overall best weight: 0.9000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 441 GLN A 498 GLN ** B 230 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 265 GLN ** B 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 498 GLN C 265 GLN ** C 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 441 GLN E 230 ASN E 265 GLN ** E 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 441 GLN E 498 GLN ** F 230 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 230 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 303 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 498 GLN H 441 GLN H 498 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8768 moved from start: 0.3249 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.023 26968 Z= 0.181 Angle : 0.534 7.118 36592 Z= 0.259 Chirality : 0.043 0.146 4152 Planarity : 0.003 0.046 4528 Dihedral : 15.634 177.056 3952 Min Nonbonded Distance : 2.038 Molprobity Statistics. All-atom Clashscore : 3.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.58 % Favored : 96.42 % Rotamer Outliers : 2.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.03 (0.14), residues: 3296 helix: 0.93 (0.15), residues: 1352 sheet: -0.53 (0.27), residues: 312 loop : -0.68 (0.14), residues: 1632 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6592 Ramachandran restraints generated. 3296 Oldfield, 0 Emsley, 3296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6592 Ramachandran restraints generated. 3296 Oldfield, 0 Emsley, 3296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 573 residues out of total 2672 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 515 time to evaluate : 2.508 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 outliers start: 58 outliers final: 36 residues processed: 563 average time/residue: 1.9072 time to fit residues: 1264.3770 Evaluate side-chains 552 residues out of total 2672 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 516 time to evaluate : 2.455 Switching outliers to nearest non-outliers outliers start: 36 outliers final: 33 residues processed: 3 average time/residue: 1.5416 time to fit residues: 8.6943 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 200 optimal weight: 3.9990 chunk 129 optimal weight: 0.8980 chunk 193 optimal weight: 3.9990 chunk 97 optimal weight: 0.5980 chunk 63 optimal weight: 1.9990 chunk 62 optimal weight: 0.7980 chunk 205 optimal weight: 1.9990 chunk 220 optimal weight: 1.9990 chunk 160 optimal weight: 3.9990 chunk 30 optimal weight: 2.9990 chunk 254 optimal weight: 3.9990 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 498 GLN ** B 230 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 265 GLN ** B 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 334 GLN B 498 GLN C 265 GLN ** C 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 441 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 265 GLN ** E 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 498 GLN ** F 230 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 441 GLN ** G 230 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 265 GLN ** G 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 303 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8780 moved from start: 0.3277 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.027 26968 Z= 0.240 Angle : 0.557 7.109 36592 Z= 0.272 Chirality : 0.044 0.144 4152 Planarity : 0.004 0.047 4528 Dihedral : 15.589 176.909 3952 Min Nonbonded Distance : 2.003 Molprobity Statistics. All-atom Clashscore : 4.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.79 % Favored : 96.21 % Rotamer Outliers : 1.61 % 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: -0.08 (0.14), residues: 3296 helix: 0.85 (0.14), residues: 1352 sheet: -0.54 (0.27), residues: 312 loop : -0.67 (0.14), residues: 1632 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6592 Ramachandran restraints generated. 3296 Oldfield, 0 Emsley, 3296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6592 Ramachandran restraints generated. 3296 Oldfield, 0 Emsley, 3296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 562 residues out of total 2672 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 519 time to evaluate : 2.459 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 43 outliers final: 34 residues processed: 558 average time/residue: 1.8796 time to fit residues: 1225.8264 Evaluate side-chains 552 residues out of total 2672 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 518 time to evaluate : 2.463 Switching outliers to nearest non-outliers outliers start: 34 outliers final: 32 residues processed: 2 average time/residue: 1.5503 time to fit residues: 6.7834 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 294 optimal weight: 3.9990 chunk 310 optimal weight: 0.9980 chunk 283 optimal weight: 3.9990 chunk 301 optimal weight: 0.8980 chunk 181 optimal weight: 4.9990 chunk 131 optimal weight: 1.9990 chunk 236 optimal weight: 1.9990 chunk 92 optimal weight: 0.5980 chunk 272 optimal weight: 1.9990 chunk 285 optimal weight: 2.9990 chunk 300 optimal weight: 0.5980 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 441 GLN A 498 GLN ** B 230 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 265 GLN ** B 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 498 GLN C 265 GLN ** C 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 265 GLN ** E 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 441 GLN E 498 GLN ** F 230 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 230 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 265 GLN ** G 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 303 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 441 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8770 moved from start: 0.3333 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.024 26968 Z= 0.200 Angle : 0.537 7.038 36592 Z= 0.261 Chirality : 0.043 0.145 4152 Planarity : 0.003 0.047 4528 Dihedral : 15.301 177.317 3952 Min Nonbonded Distance : 2.033 Molprobity Statistics. All-atom Clashscore : 4.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.52 % Favored : 96.48 % Rotamer Outliers : 1.53 % 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: 0.04 (0.14), residues: 3296 helix: 0.97 (0.15), residues: 1352 sheet: -0.56 (0.27), residues: 312 loop : -0.60 (0.14), residues: 1632 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6592 Ramachandran restraints generated. 3296 Oldfield, 0 Emsley, 3296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6592 Ramachandran restraints generated. 3296 Oldfield, 0 Emsley, 3296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 560 residues out of total 2672 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 519 time to evaluate : 2.473 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 outliers start: 41 outliers final: 36 residues processed: 555 average time/residue: 1.9063 time to fit residues: 1246.6131 Evaluate side-chains 555 residues out of total 2672 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 519 time to evaluate : 2.460 Switching outliers to nearest non-outliers outliers start: 36 outliers final: 32 residues processed: 4 average time/residue: 1.2240 time to fit residues: 9.2658 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 198 optimal weight: 2.9990 chunk 319 optimal weight: 2.9990 chunk 194 optimal weight: 1.9990 chunk 151 optimal weight: 0.9990 chunk 221 optimal weight: 0.4980 chunk 334 optimal weight: 0.9990 chunk 308 optimal weight: 7.9990 chunk 266 optimal weight: 0.9990 chunk 27 optimal weight: 1.9990 chunk 205 optimal weight: 1.9990 chunk 163 optimal weight: 2.9990 overall best weight: 1.0988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 498 GLN ** B 230 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 265 GLN ** B 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 498 GLN C 265 GLN ** C 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 441 GLN E 265 GLN ** E 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 498 GLN ** F 230 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 441 GLN ** G 230 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 265 GLN ** G 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 303 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8774 moved from start: 0.3353 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.025 26968 Z= 0.214 Angle : 0.543 7.072 36592 Z= 0.264 Chirality : 0.043 0.144 4152 Planarity : 0.003 0.047 4528 Dihedral : 15.221 178.853 3952 Min Nonbonded Distance : 2.019 Molprobity Statistics. All-atom Clashscore : 4.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.88 % Favored : 96.12 % Rotamer Outliers : 1.46 % 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: 0.04 (0.14), residues: 3296 helix: 0.95 (0.15), residues: 1352 sheet: -0.50 (0.27), residues: 312 loop : -0.59 (0.14), residues: 1632 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6592 Ramachandran restraints generated. 3296 Oldfield, 0 Emsley, 3296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6592 Ramachandran restraints generated. 3296 Oldfield, 0 Emsley, 3296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 557 residues out of total 2672 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 518 time to evaluate : 2.494 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 39 outliers final: 34 residues processed: 552 average time/residue: 1.9597 time to fit residues: 1280.3281 Evaluate side-chains 548 residues out of total 2672 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 514 time to evaluate : 2.490 Switching outliers to nearest non-outliers outliers start: 34 outliers final: 30 residues processed: 4 average time/residue: 1.4184 time to fit residues: 10.1653 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 211 optimal weight: 4.9990 chunk 283 optimal weight: 3.9990 chunk 81 optimal weight: 0.9990 chunk 245 optimal weight: 5.9990 chunk 39 optimal weight: 1.9990 chunk 74 optimal weight: 0.0970 chunk 266 optimal weight: 0.0670 chunk 111 optimal weight: 1.9990 chunk 274 optimal weight: 2.9990 chunk 33 optimal weight: 3.9990 chunk 49 optimal weight: 1.9990 overall best weight: 1.0322 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 498 GLN ** B 230 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 265 GLN ** B 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 498 GLN C 265 GLN ** C 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 441 GLN E 265 GLN ** E 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 498 GLN F 230 ASN ** F 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 230 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 265 GLN ** G 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 303 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 441 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3552 r_free = 0.3552 target = 0.139083 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3150 r_free = 0.3150 target = 0.106888 restraints weight = 78168.264| |-----------------------------------------------------------------------------| r_work (start): 0.3122 rms_B_bonded: 1.58 r_work: 0.3005 rms_B_bonded: 2.12 restraints_weight: 0.5000 r_work: 0.2882 rms_B_bonded: 3.45 restraints_weight: 0.2500 r_work (final): 0.2882 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8834 moved from start: 0.3379 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.024 26968 Z= 0.202 Angle : 0.535 6.996 36592 Z= 0.260 Chirality : 0.043 0.144 4152 Planarity : 0.003 0.047 4528 Dihedral : 15.149 178.498 3952 Min Nonbonded Distance : 2.030 Molprobity Statistics. All-atom Clashscore : 4.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.34 % Favored : 96.66 % Rotamer Outliers : 1.35 % 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: 0.08 (0.14), residues: 3296 helix: 0.98 (0.15), residues: 1352 sheet: -0.53 (0.27), residues: 312 loop : -0.56 (0.14), residues: 1632 =============================================================================== Job complete usr+sys time: 17396.88 seconds wall clock time: 297 minutes 20.53 seconds (17840.53 seconds total)