Starting phenix.real_space_refine (version: dev) on Thu Dec 15 04:51:24 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nfy_12306/12_2022/7nfy_12306_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nfy_12306/12_2022/7nfy_12306.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nfy_12306/12_2022/7nfy_12306.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nfy_12306/12_2022/7nfy_12306.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nfy_12306/12_2022/7nfy_12306_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nfy_12306/12_2022/7nfy_12306_trim_updated.pdb" } resolution = 3.9 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= 0.004 sd= 0.065 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 ARG 131": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 137": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 154": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 155": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 158": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 170": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A GLU 175": "OE1" <-> "OE2" Residue "A ARG 205": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 212": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 218": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A PHE 283": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ARG 301": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A TYR 310": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ARG 311": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 323": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A TYR 360": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ARG 381": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 424": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 459": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 534": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 542": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 562": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 597": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 650": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 652": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 672": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 710": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A GLU 733": "OE1" <-> "OE2" Residue "A ARG 785": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 786": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 815": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 822": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 131": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B PHE 135": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B ARG 137": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 154": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 155": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 158": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 170": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ASP 177": "OD1" <-> "OD2" Residue "B ASP 183": "OD1" <-> "OD2" Residue "B PHE 191": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B ARG 205": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 212": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 218": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B PHE 283": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B ARG 301": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 311": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B GLU 312": "OE1" <-> "OE2" Residue "B ARG 323": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 381": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ASP 412": "OD1" <-> "OD2" Residue "B ARG 459": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 482": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 534": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 542": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 562": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B GLU 609": "OE1" <-> "OE2" Residue "B ARG 652": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 672": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B PHE 745": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B ARG 785": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 786": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B GLU 801": "OE1" <-> "OE2" Residue "B ARG 815": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 822": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C ARG 131": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C ARG 137": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C ARG 154": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C ARG 155": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C ARG 158": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C TYR 163": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C ARG 170": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C ARG 205": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C ARG 212": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C ARG 218": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C PHE 283": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C ARG 301": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C ARG 311": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C ARG 323": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C TYR 360": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C ARG 381": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C GLU 382": "OE1" <-> "OE2" Residue "C ARG 424": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C ARG 459": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C ARG 482": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C GLU 503": "OE1" <-> "OE2" Residue "C ARG 534": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C ARG 538": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C ARG 542": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C GLU 686": "OE1" <-> "OE2" Residue "C ARG 705": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C ARG 785": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C ARG 786": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C ARG 815": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C ARG 822": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D ARG 131": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D ARG 137": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D ARG 154": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D ARG 155": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D ARG 158": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D ARG 170": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D ARG 205": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D ARG 212": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D ARG 218": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D PHE 283": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D ARG 301": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D ARG 311": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D ARG 323": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D ARG 381": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D GLU 441": "OE1" <-> "OE2" Residue "D GLU 476": "OE1" <-> "OE2" Residue "D GLU 583": "OE1" <-> "OE2" Residue "D ASP 629": "OD1" <-> "OD2" Residue "D ARG 785": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D ARG 786": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D ARG 815": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D ARG 822": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D GLU 897": "OE1" <-> "OE2" Residue "D ASP 919": "OD1" <-> "OD2" Residue "D ASP 944": "OD1" <-> "OD2" Residue "E ARG 131": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "E ARG 137": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "E ARG 154": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "E ARG 155": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "E ARG 158": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "E ARG 170": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "E ARG 205": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "E ARG 212": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "E ARG 218": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "E PHE 283": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E ARG 301": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "E TYR 310": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E ARG 311": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "E ARG 323": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "E ARG 381": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "E GLU 406": "OE1" <-> "OE2" Residue "E ASP 413": "OD1" <-> "OD2" Residue "E ARG 511": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "E ARG 597": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "E ARG 672": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "E ARG 705": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "E ARG 755": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "E GLU 781": "OE1" <-> "OE2" Residue "E ARG 785": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "E ARG 786": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "E ARG 815": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "E ARG 822": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "E GLU 882": "OE1" <-> "OE2" Residue "F ARG 131": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "F PHE 135": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F ARG 137": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "F ARG 154": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "F ARG 155": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "F ARG 158": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "F ARG 170": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "F ASP 183": "OD1" <-> "OD2" Residue "F ARG 205": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "F ARG 212": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "F ARG 218": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "F PHE 283": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F ARG 301": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "F ASP 302": "OD1" <-> "OD2" Residue "F TYR 310": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F ARG 311": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "F ARG 323": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "F ARG 381": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "F ASP 412": "OD1" <-> "OD2" Residue "F ARG 511": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "F ARG 542": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "F ARG 650": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "F ARG 652": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "F ARG 672": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "F ARG 705": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "F ARG 710": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "F ARG 721": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "F GLU 733": "OE1" <-> "OE2" Residue "F ARG 755": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "F ARG 785": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "F ARG 786": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "F ARG 815": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "F ARG 822": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "F PHE 926": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Time to flip residues: 0.11s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/chem_data/mon_lib" Total number of atoms: 74644 Number of models: 1 Model: "" Number of chains: 13 Chain: "A" Number of atoms: 12392 Number of conformers: 1 Conformer: "" Number of residues, atoms: 776, 12392 Classifications: {'peptide': 776} Link IDs: {'PTRANS': 32, 'TRANS': 743} Chain breaks: 1 Chain: "B" Number of atoms: 12369 Number of conformers: 1 Conformer: "" Number of residues, atoms: 776, 12369 Classifications: {'peptide': 776} Link IDs: {'PTRANS': 32, 'TRANS': 743} Chain breaks: 1 Chain: "C" Number of atoms: 12394 Number of conformers: 1 Conformer: "" Number of residues, atoms: 776, 12394 Classifications: {'peptide': 776} Link IDs: {'PTRANS': 32, 'TRANS': 743} Chain breaks: 1 Chain: "D" Number of atoms: 12394 Number of conformers: 1 Conformer: "" Number of residues, atoms: 776, 12394 Classifications: {'peptide': 776} Link IDs: {'PTRANS': 32, 'TRANS': 743} Chain breaks: 1 Chain: "E" Number of atoms: 12394 Number of conformers: 1 Conformer: "" Number of residues, atoms: 776, 12394 Classifications: {'peptide': 776} Link IDs: {'PTRANS': 32, 'TRANS': 743} Chain breaks: 1 Chain: "F" Number of atoms: 12394 Number of conformers: 1 Conformer: "" Number of residues, atoms: 776, 12394 Classifications: {'peptide': 776} Link IDs: {'PTRANS': 32, 'TRANS': 743} Chain breaks: 1 Chain: "G" Number of atoms: 120 Number of conformers: 1 Conformer: "" Number of residues, atoms: 24, 120 Classifications: {'peptide': 24} Incomplete info: {'truncation_to_alanine': 24} Link IDs: {'TRANS': 23} Unresolved non-hydrogen bonds: 48 Unresolved non-hydrogen angles: 72 Unresolved non-hydrogen dihedrals: 24 Planarities with less than four sites: {'UNK:plan-1': 24} Unresolved non-hydrogen planarities: 24 Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'AGS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'AGS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'AGS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'AGS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "F" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'AGS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 25.27, per 1000 atoms: 0.34 Number of scatterers: 74644 At special positions: 0 Unit cell: (141.772, 134.366, 230.644, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) S 167 16.00 P 17 15.00 Mg 5 11.99 O 7006 8.00 N 6450 7.00 C 23514 6.00 H 37485 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: 52.26 Conformation dependent library (CDL) restraints added in 4.6 seconds 9264 Ramachandran restraints generated. 4632 Oldfield, 0 Emsley, 4632 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8784 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 189 helices and 29 sheets defined 43.5% alpha, 4.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.08 Creating SS restraints... Processing helix chain 'A' and resid 148 through 155 removed outlier: 3.785A pdb=" N LEU A 152 " --> pdb=" O LYS A 148 " (cutoff:3.500A) Processing helix chain 'A' and resid 175 through 180 Processing helix chain 'A' and resid 289 through 306 removed outlier: 3.740A pdb=" N LEU A 292 " --> pdb=" O VAL A 289 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N ILE A 304 " --> pdb=" O ARG A 301 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N LEU A 306 " --> pdb=" O ILE A 303 " (cutoff:3.500A) Processing helix chain 'A' and resid 313 through 317 Processing helix chain 'A' and resid 328 through 338 removed outlier: 3.670A pdb=" N LEU A 338 " --> pdb=" O MET A 334 " (cutoff:3.500A) Processing helix chain 'A' and resid 343 through 351 Processing helix chain 'A' and resid 355 through 406 removed outlier: 3.687A pdb=" N LEU A 372 " --> pdb=" O LYS A 368 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N LYS A 393 " --> pdb=" O GLN A 389 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N TYR A 394 " --> pdb=" O THR A 390 " (cutoff:3.500A) Processing helix chain 'A' and resid 413 through 426 Processing helix chain 'A' and resid 432 through 447 Processing helix chain 'A' and resid 453 through 467 Processing helix chain 'A' and resid 480 through 489 Processing helix chain 'A' and resid 495 through 510 Processing helix chain 'A' and resid 533 through 540 Processing helix chain 'A' and resid 555 through 558 Processing helix chain 'A' and resid 572 through 580 Processing helix chain 'A' and resid 592 through 594 No H-bonds generated for 'chain 'A' and resid 592 through 594' Processing helix chain 'A' and resid 603 through 611 Processing helix chain 'A' and resid 615 through 618 Processing helix chain 'A' and resid 647 through 652 removed outlier: 4.337A pdb=" N ARG A 652 " --> pdb=" O PRO A 648 " (cutoff:3.500A) Processing helix chain 'A' and resid 663 through 672 Processing helix chain 'A' and resid 674 through 682 Processing helix chain 'A' and resid 693 through 702 Processing helix chain 'A' and resid 710 through 728 Processing helix chain 'A' and resid 739 through 744 removed outlier: 4.127A pdb=" N GLN A 743 " --> pdb=" O GLU A 740 " (cutoff:3.500A) Processing helix chain 'A' and resid 808 through 828 removed outlier: 3.656A pdb=" N GLU A 812 " --> pdb=" O GLU A 808 " (cutoff:3.500A) Processing helix chain 'A' and resid 850 through 869 Proline residue: A 854 - end of helix removed outlier: 4.110A pdb=" N CYS A 858 " --> pdb=" O SER A 855 " (cutoff:3.500A) Processing helix chain 'A' and resid 895 through 905 Processing helix chain 'A' and resid 914 through 921 removed outlier: 4.443A pdb=" N LYS A 918 " --> pdb=" O GLU A 915 " (cutoff:3.500A) Processing helix chain 'A' and resid 925 through 927 No H-bonds generated for 'chain 'A' and resid 925 through 927' Processing helix chain 'A' and resid 939 through 946 removed outlier: 4.214A pdb=" N ALA A 946 " --> pdb=" O PHE A 943 " (cutoff:3.500A) Processing helix chain 'B' and resid 148 through 155 removed outlier: 3.709A pdb=" N LEU B 152 " --> pdb=" O LYS B 148 " (cutoff:3.500A) Processing helix chain 'B' and resid 175 through 180 Processing helix chain 'B' and resid 293 through 306 removed outlier: 4.312A pdb=" N LYS B 298 " --> pdb=" O ALA B 294 " (cutoff:3.500A) Processing helix chain 'B' and resid 313 through 317 Processing helix chain 'B' and resid 328 through 337 Processing helix chain 'B' and resid 343 through 351 Processing helix chain 'B' and resid 355 through 388 Processing helix chain 'B' and resid 392 through 403 Processing helix chain 'B' and resid 414 through 426 removed outlier: 3.596A pdb=" N ARG B 422 " --> pdb=" O GLU B 418 " (cutoff:3.500A) Processing helix chain 'B' and resid 432 through 447 removed outlier: 3.887A pdb=" N ASP B 436 " --> pdb=" O LYS B 432 " (cutoff:3.500A) removed outlier: 4.336A pdb=" N VAL B 437 " --> pdb=" O HIS B 433 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N ASP B 439 " --> pdb=" O MET B 435 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N GLU B 440 " --> pdb=" O ASP B 436 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N GLU B 441 " --> pdb=" O VAL B 437 " (cutoff:3.500A) Processing helix chain 'B' and resid 453 through 465 removed outlier: 3.750A pdb=" N ASN B 456 " --> pdb=" O SER B 453 " (cutoff:3.500A) removed outlier: 4.336A pdb=" N ARG B 459 " --> pdb=" O ASN B 456 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N LEU B 462 " --> pdb=" O ARG B 459 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N TRP B 464 " --> pdb=" O TYR B 461 " (cutoff:3.500A) Processing helix chain 'B' and resid 480 through 488 removed outlier: 4.044A pdb=" N ALA B 485 " --> pdb=" O ALA B 481 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N VAL B 486 " --> pdb=" O ARG B 482 " (cutoff:3.500A) Processing helix chain 'B' and resid 495 through 510 Processing helix chain 'B' and resid 533 through 540 Processing helix chain 'B' and resid 555 through 559 Processing helix chain 'B' and resid 572 through 579 Processing helix chain 'B' and resid 592 through 594 No H-bonds generated for 'chain 'B' and resid 592 through 594' Processing helix chain 'B' and resid 603 through 611 removed outlier: 3.577A pdb=" N LEU B 607 " --> pdb=" O SER B 604 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N LEU B 608 " --> pdb=" O SER B 605 " (cutoff:3.500A) Processing helix chain 'B' and resid 615 through 618 Processing helix chain 'B' and resid 647 through 651 Processing helix chain 'B' and resid 663 through 672 removed outlier: 3.574A pdb=" N ARG B 672 " --> pdb=" O ALA B 668 " (cutoff:3.500A) Processing helix chain 'B' and resid 674 through 682 removed outlier: 3.574A pdb=" N LEU B 681 " --> pdb=" O GLN B 677 " (cutoff:3.500A) Processing helix chain 'B' and resid 693 through 702 removed outlier: 3.531A pdb=" N ILE B 700 " --> pdb=" O LEU B 696 " (cutoff:3.500A) Processing helix chain 'B' and resid 711 through 728 removed outlier: 3.966A pdb=" N LEU B 720 " --> pdb=" O VAL B 716 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N SER B 723 " --> pdb=" O VAL B 719 " (cutoff:3.500A) Processing helix chain 'B' and resid 739 through 745 removed outlier: 4.818A pdb=" N GLN B 743 " --> pdb=" O GLU B 740 " (cutoff:3.500A) Processing helix chain 'B' and resid 808 through 828 removed outlier: 3.817A pdb=" N GLU B 812 " --> pdb=" O GLU B 808 " (cutoff:3.500A) Processing helix chain 'B' and resid 850 through 869 Proline residue: B 854 - end of helix removed outlier: 4.120A pdb=" N CYS B 858 " --> pdb=" O SER B 855 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N LEU B 865 " --> pdb=" O THR B 862 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N MET B 869 " --> pdb=" O SER B 866 " (cutoff:3.500A) Processing helix chain 'B' and resid 895 through 905 removed outlier: 3.645A pdb=" N ILE B 900 " --> pdb=" O LYS B 896 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N ALA B 905 " --> pdb=" O ALA B 901 " (cutoff:3.500A) Processing helix chain 'B' and resid 917 through 921 removed outlier: 3.786A pdb=" N TYR B 921 " --> pdb=" O LYS B 918 " (cutoff:3.500A) Processing helix chain 'B' and resid 925 through 928 Processing helix chain 'B' and resid 939 through 946 Processing helix chain 'C' and resid 148 through 155 removed outlier: 3.965A pdb=" N LEU C 152 " --> pdb=" O LYS C 148 " (cutoff:3.500A) Processing helix chain 'C' and resid 175 through 180 removed outlier: 3.632A pdb=" N VAL C 179 " --> pdb=" O GLU C 175 " (cutoff:3.500A) Processing helix chain 'C' and resid 291 through 306 removed outlier: 3.717A pdb=" N GLU C 295 " --> pdb=" O ALA C 291 " (cutoff:3.500A) Processing helix chain 'C' and resid 313 through 317 Processing helix chain 'C' and resid 320 through 322 No H-bonds generated for 'chain 'C' and resid 320 through 322' Processing helix chain 'C' and resid 328 through 337 Processing helix chain 'C' and resid 343 through 351 Processing helix chain 'C' and resid 355 through 407 removed outlier: 3.699A pdb=" N LYS C 393 " --> pdb=" O GLN C 389 " (cutoff:3.500A) Processing helix chain 'C' and resid 414 through 424 Processing helix chain 'C' and resid 432 through 447 removed outlier: 3.771A pdb=" N ASP C 436 " --> pdb=" O LYS C 432 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N VAL C 437 " --> pdb=" O HIS C 433 " (cutoff:3.500A) Processing helix chain 'C' and resid 453 through 467 Processing helix chain 'C' and resid 481 through 488 removed outlier: 3.717A pdb=" N VAL C 486 " --> pdb=" O ARG C 482 " (cutoff:3.500A) Processing helix chain 'C' and resid 495 through 510 removed outlier: 3.729A pdb=" N LEU C 502 " --> pdb=" O LYS C 498 " (cutoff:3.500A) Processing helix chain 'C' and resid 532 through 540 Processing helix chain 'C' and resid 555 through 558 Processing helix chain 'C' and resid 572 through 579 removed outlier: 3.510A pdb=" N LYS C 579 " --> pdb=" O GLN C 575 " (cutoff:3.500A) Processing helix chain 'C' and resid 592 through 594 No H-bonds generated for 'chain 'C' and resid 592 through 594' Processing helix chain 'C' and resid 603 through 611 removed outlier: 3.579A pdb=" N LEU C 607 " --> pdb=" O SER C 604 " (cutoff:3.500A) removed outlier: 4.286A pdb=" N LEU C 608 " --> pdb=" O SER C 605 " (cutoff:3.500A) Processing helix chain 'C' and resid 615 through 618 Processing helix chain 'C' and resid 647 through 651 Processing helix chain 'C' and resid 663 through 672 removed outlier: 4.579A pdb=" N ALA C 668 " --> pdb=" O GLN C 664 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N ARG C 672 " --> pdb=" O ALA C 668 " (cutoff:3.500A) Processing helix chain 'C' and resid 674 through 682 Processing helix chain 'C' and resid 687 through 689 No H-bonds generated for 'chain 'C' and resid 687 through 689' Processing helix chain 'C' and resid 693 through 703 removed outlier: 3.711A pdb=" N THR C 697 " --> pdb=" O SER C 693 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N LEU C 698 " --> pdb=" O ASP C 694 " (cutoff:3.500A) Processing helix chain 'C' and resid 710 through 728 removed outlier: 3.532A pdb=" N SER C 723 " --> pdb=" O VAL C 719 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N LYS C 726 " --> pdb=" O LYS C 722 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N ILE C 727 " --> pdb=" O SER C 723 " (cutoff:3.500A) Processing helix chain 'C' and resid 739 through 745 removed outlier: 4.200A pdb=" N GLN C 743 " --> pdb=" O GLU C 740 " (cutoff:3.500A) Processing helix chain 'C' and resid 808 through 828 removed outlier: 4.022A pdb=" N MET C 826 " --> pdb=" O ARG C 822 " (cutoff:3.500A) Processing helix chain 'C' and resid 850 through 869 Proline residue: C 854 - end of helix removed outlier: 3.662A pdb=" N GLY C 857 " --> pdb=" O GLY C 853 " (cutoff:3.500A) removed outlier: 4.290A pdb=" N CYS C 858 " --> pdb=" O PRO C 854 " (cutoff:3.500A) removed outlier: 5.665A pdb=" N THR C 859 " --> pdb=" O SER C 855 " (cutoff:3.500A) removed outlier: 4.067A pdb=" N ILE C 860 " --> pdb=" O ALA C 856 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N VAL C 861 " --> pdb=" O GLY C 857 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N THR C 862 " --> pdb=" O CYS C 858 " (cutoff:3.500A) Processing helix chain 'C' and resid 895 through 905 Processing helix chain 'C' and resid 914 through 921 removed outlier: 5.224A pdb=" N LYS C 918 " --> pdb=" O GLU C 915 " (cutoff:3.500A) Processing helix chain 'C' and resid 939 through 946 removed outlier: 4.057A pdb=" N ALA C 946 " --> pdb=" O PHE C 943 " (cutoff:3.500A) Processing helix chain 'D' and resid 148 through 155 removed outlier: 3.586A pdb=" N LEU D 152 " --> pdb=" O LYS D 148 " (cutoff:3.500A) Processing helix chain 'D' and resid 175 through 180 Processing helix chain 'D' and resid 291 through 306 removed outlier: 3.706A pdb=" N GLU D 295 " --> pdb=" O ALA D 291 " (cutoff:3.500A) Processing helix chain 'D' and resid 313 through 317 Processing helix chain 'D' and resid 320 through 322 No H-bonds generated for 'chain 'D' and resid 320 through 322' Processing helix chain 'D' and resid 328 through 336 Processing helix chain 'D' and resid 343 through 351 Processing helix chain 'D' and resid 355 through 388 Processing helix chain 'D' and resid 392 through 409 Processing helix chain 'D' and resid 414 through 426 removed outlier: 3.679A pdb=" N LYS D 420 " --> pdb=" O ILE D 417 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N GLU D 423 " --> pdb=" O LYS D 420 " (cutoff:3.500A) Processing helix chain 'D' and resid 432 through 435 No H-bonds generated for 'chain 'D' and resid 432 through 435' Processing helix chain 'D' and resid 437 through 447 removed outlier: 3.743A pdb=" N GLU D 441 " --> pdb=" O VAL D 437 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N GLY D 446 " --> pdb=" O LEU D 442 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N LEU D 447 " --> pdb=" O SER D 443 " (cutoff:3.500A) Processing helix chain 'D' and resid 453 through 466 Processing helix chain 'D' and resid 480 through 488 removed outlier: 3.660A pdb=" N ALA D 485 " --> pdb=" O ALA D 481 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N VAL D 486 " --> pdb=" O ARG D 482 " (cutoff:3.500A) Processing helix chain 'D' and resid 495 through 508 Processing helix chain 'D' and resid 530 through 540 removed outlier: 4.087A pdb=" N ARG D 534 " --> pdb=" O SER D 531 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N LEU D 540 " --> pdb=" O ALA D 537 " (cutoff:3.500A) Processing helix chain 'D' and resid 555 through 559 Processing helix chain 'D' and resid 572 through 580 Processing helix chain 'D' and resid 592 through 594 No H-bonds generated for 'chain 'D' and resid 592 through 594' Processing helix chain 'D' and resid 603 through 611 removed outlier: 4.152A pdb=" N LEU D 608 " --> pdb=" O SER D 604 " (cutoff:3.500A) removed outlier: 4.642A pdb=" N GLU D 609 " --> pdb=" O SER D 605 " (cutoff:3.500A) removed outlier: 4.236A pdb=" N LEU D 610 " --> pdb=" O ALA D 606 " (cutoff:3.500A) Processing helix chain 'D' and resid 615 through 618 removed outlier: 3.893A pdb=" N ASN D 618 " --> pdb=" O GLN D 615 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 615 through 618' Processing helix chain 'D' and resid 647 through 650 No H-bonds generated for 'chain 'D' and resid 647 through 650' Processing helix chain 'D' and resid 665 through 670 Processing helix chain 'D' and resid 675 through 681 Processing helix chain 'D' and resid 686 through 688 No H-bonds generated for 'chain 'D' and resid 686 through 688' Processing helix chain 'D' and resid 693 through 702 Processing helix chain 'D' and resid 710 through 728 removed outlier: 3.561A pdb=" N GLU D 717 " --> pdb=" O GLN D 713 " (cutoff:3.500A) Processing helix chain 'D' and resid 742 through 746 Processing helix chain 'D' and resid 808 through 828 removed outlier: 3.706A pdb=" N MET D 826 " --> pdb=" O ARG D 822 " (cutoff:3.500A) Processing helix chain 'D' and resid 850 through 869 Proline residue: D 854 - end of helix removed outlier: 4.495A pdb=" N CYS D 858 " --> pdb=" O SER D 855 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N VAL D 861 " --> pdb=" O CYS D 858 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N LEU D 865 " --> pdb=" O THR D 862 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N MET D 869 " --> pdb=" O SER D 866 " (cutoff:3.500A) Processing helix chain 'D' and resid 895 through 904 removed outlier: 3.564A pdb=" N ILE D 900 " --> pdb=" O LYS D 896 " (cutoff:3.500A) Processing helix chain 'D' and resid 914 through 916 No H-bonds generated for 'chain 'D' and resid 914 through 916' Processing helix chain 'D' and resid 919 through 922 Processing helix chain 'D' and resid 925 through 928 No H-bonds generated for 'chain 'D' and resid 925 through 928' Processing helix chain 'D' and resid 939 through 944 Processing helix chain 'E' and resid 148 through 155 removed outlier: 3.548A pdb=" N LEU E 152 " --> pdb=" O LYS E 148 " (cutoff:3.500A) Processing helix chain 'E' and resid 175 through 180 Processing helix chain 'E' and resid 291 through 306 removed outlier: 3.774A pdb=" N GLU E 295 " --> pdb=" O ALA E 291 " (cutoff:3.500A) Processing helix chain 'E' and resid 313 through 317 Processing helix chain 'E' and resid 320 through 322 No H-bonds generated for 'chain 'E' and resid 320 through 322' Processing helix chain 'E' and resid 328 through 337 Processing helix chain 'E' and resid 343 through 351 Processing helix chain 'E' and resid 355 through 403 removed outlier: 3.965A pdb=" N LEU E 372 " --> pdb=" O LYS E 368 " (cutoff:3.500A) Processing helix chain 'E' and resid 417 through 424 Processing helix chain 'E' and resid 432 through 447 removed outlier: 3.692A pdb=" N VAL E 437 " --> pdb=" O HIS E 433 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N GLY E 446 " --> pdb=" O LEU E 442 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N LEU E 447 " --> pdb=" O SER E 443 " (cutoff:3.500A) Processing helix chain 'E' and resid 453 through 466 Processing helix chain 'E' and resid 480 through 490 removed outlier: 3.545A pdb=" N ALA E 485 " --> pdb=" O ALA E 481 " (cutoff:3.500A) Processing helix chain 'E' and resid 495 through 508 Processing helix chain 'E' and resid 529 through 540 removed outlier: 3.842A pdb=" N ALA E 533 " --> pdb=" O LYS E 529 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N ARG E 534 " --> pdb=" O THR E 530 " (cutoff:3.500A) Processing helix chain 'E' and resid 556 through 559 No H-bonds generated for 'chain 'E' and resid 556 through 559' Processing helix chain 'E' and resid 572 through 579 Processing helix chain 'E' and resid 603 through 611 removed outlier: 3.745A pdb=" N GLU E 609 " --> pdb=" O SER E 605 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N LEU E 610 " --> pdb=" O ALA E 606 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N LEU E 611 " --> pdb=" O LEU E 607 " (cutoff:3.500A) Processing helix chain 'E' and resid 613 through 618 removed outlier: 4.483A pdb=" N ASN E 618 " --> pdb=" O GLU E 614 " (cutoff:3.500A) Processing helix chain 'E' and resid 647 through 651 Processing helix chain 'E' and resid 665 through 670 Processing helix chain 'E' and resid 674 through 682 removed outlier: 3.570A pdb=" N ALA E 680 " --> pdb=" O PRO E 676 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N LEU E 681 " --> pdb=" O GLN E 677 " (cutoff:3.500A) Processing helix chain 'E' and resid 693 through 701 removed outlier: 3.613A pdb=" N THR E 697 " --> pdb=" O SER E 693 " (cutoff:3.500A) Processing helix chain 'E' and resid 710 through 728 removed outlier: 4.003A pdb=" N VAL E 719 " --> pdb=" O GLN E 715 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N LYS E 726 " --> pdb=" O LYS E 722 " (cutoff:3.500A) removed outlier: 4.113A pdb=" N ILE E 727 " --> pdb=" O SER E 723 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N VAL E 728 " --> pdb=" O ALA E 724 " (cutoff:3.500A) Processing helix chain 'E' and resid 741 through 746 Processing helix chain 'E' and resid 808 through 828 removed outlier: 3.631A pdb=" N MET E 826 " --> pdb=" O ARG E 822 " (cutoff:3.500A) Processing helix chain 'E' and resid 853 through 869 removed outlier: 4.346A pdb=" N CYS E 858 " --> pdb=" O SER E 855 " (cutoff:3.500A) removed outlier: 4.149A pdb=" N SER E 866 " --> pdb=" O ALA E 863 " (cutoff:3.500A) Processing helix chain 'E' and resid 895 through 904 Processing helix chain 'E' and resid 914 through 922 removed outlier: 5.058A pdb=" N LYS E 918 " --> pdb=" O GLU E 915 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N TYR E 921 " --> pdb=" O LYS E 918 " (cutoff:3.500A) Processing helix chain 'E' and resid 925 through 928 No H-bonds generated for 'chain 'E' and resid 925 through 928' Processing helix chain 'E' and resid 940 through 946 removed outlier: 3.562A pdb=" N ASP E 944 " --> pdb=" O ARG E 940 " (cutoff:3.500A) Processing helix chain 'F' and resid 148 through 155 Processing helix chain 'F' and resid 175 through 180 Processing helix chain 'F' and resid 289 through 306 removed outlier: 3.548A pdb=" N ALA F 294 " --> pdb=" O ALA F 291 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N ILE F 304 " --> pdb=" O ARG F 301 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N LEU F 306 " --> pdb=" O ILE F 303 " (cutoff:3.500A) Processing helix chain 'F' and resid 313 through 317 Processing helix chain 'F' and resid 320 through 322 No H-bonds generated for 'chain 'F' and resid 320 through 322' Processing helix chain 'F' and resid 328 through 337 Processing helix chain 'F' and resid 343 through 351 Processing helix chain 'F' and resid 355 through 388 Processing helix chain 'F' and resid 393 through 404 Processing helix chain 'F' and resid 412 through 426 removed outlier: 4.223A pdb=" N ILE F 417 " --> pdb=" O ASP F 413 " (cutoff:3.500A) Processing helix chain 'F' and resid 432 through 447 removed outlier: 4.029A pdb=" N ASP F 436 " --> pdb=" O LYS F 432 " (cutoff:3.500A) removed outlier: 4.353A pdb=" N VAL F 437 " --> pdb=" O HIS F 433 " (cutoff:3.500A) Processing helix chain 'F' and resid 453 through 467 removed outlier: 3.755A pdb=" N LEU F 465 " --> pdb=" O TYR F 461 " (cutoff:3.500A) Processing helix chain 'F' and resid 480 through 487 removed outlier: 3.762A pdb=" N VAL F 486 " --> pdb=" O ARG F 482 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N LEU F 487 " --> pdb=" O ALA F 483 " (cutoff:3.500A) Processing helix chain 'F' and resid 495 through 510 removed outlier: 3.676A pdb=" N LEU F 502 " --> pdb=" O LYS F 498 " (cutoff:3.500A) Processing helix chain 'F' and resid 529 through 540 removed outlier: 3.748A pdb=" N ARG F 534 " --> pdb=" O THR F 530 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N SER F 535 " --> pdb=" O SER F 531 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N ARG F 538 " --> pdb=" O ARG F 534 " (cutoff:3.500A) Processing helix chain 'F' and resid 556 through 559 No H-bonds generated for 'chain 'F' and resid 556 through 559' Processing helix chain 'F' and resid 572 through 579 removed outlier: 3.670A pdb=" N CYS F 576 " --> pdb=" O LYS F 572 " (cutoff:3.500A) Processing helix chain 'F' and resid 592 through 594 No H-bonds generated for 'chain 'F' and resid 592 through 594' Processing helix chain 'F' and resid 604 through 611 Processing helix chain 'F' and resid 647 through 650 No H-bonds generated for 'chain 'F' and resid 647 through 650' Processing helix chain 'F' and resid 663 through 670 removed outlier: 4.053A pdb=" N LEU F 667 " --> pdb=" O ALA F 663 " (cutoff:3.500A) removed outlier: 5.052A pdb=" N ALA F 668 " --> pdb=" O GLN F 664 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N ILE F 669 " --> pdb=" O GLU F 665 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N ALA F 670 " --> pdb=" O LYS F 666 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 663 through 670' Processing helix chain 'F' and resid 674 through 682 removed outlier: 3.516A pdb=" N ALA F 680 " --> pdb=" O PRO F 676 " (cutoff:3.500A) Processing helix chain 'F' and resid 693 through 703 Processing helix chain 'F' and resid 710 through 728 removed outlier: 3.522A pdb=" N GLN F 715 " --> pdb=" O ASN F 711 " (cutoff:3.500A) Processing helix chain 'F' and resid 741 through 746 removed outlier: 3.704A pdb=" N VAL F 746 " --> pdb=" O GLN F 743 " (cutoff:3.500A) Processing helix chain 'F' and resid 808 through 828 removed outlier: 3.697A pdb=" N SER F 813 " --> pdb=" O VAL F 809 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N ARG F 815 " --> pdb=" O LYS F 811 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N MET F 826 " --> pdb=" O ARG F 822 " (cutoff:3.500A) Processing helix chain 'F' and resid 850 through 852 No H-bonds generated for 'chain 'F' and resid 850 through 852' Processing helix chain 'F' and resid 854 through 869 removed outlier: 4.756A pdb=" N CYS F 858 " --> pdb=" O SER F 855 " (cutoff:3.500A) removed outlier: 4.301A pdb=" N LEU F 864 " --> pdb=" O VAL F 861 " (cutoff:3.500A) Processing helix chain 'F' and resid 895 through 905 removed outlier: 3.664A pdb=" N ARG F 904 " --> pdb=" O ILE F 900 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N ALA F 905 " --> pdb=" O ALA F 901 " (cutoff:3.500A) Processing helix chain 'F' and resid 914 through 921 removed outlier: 3.953A pdb=" N LYS F 917 " --> pdb=" O ALA F 914 " (cutoff:3.500A) removed outlier: 5.357A pdb=" N LYS F 918 " --> pdb=" O GLU F 915 " (cutoff:3.500A) Processing helix chain 'F' and resid 925 through 928 No H-bonds generated for 'chain 'F' and resid 925 through 928' Processing helix chain 'F' and resid 939 through 946 removed outlier: 3.551A pdb=" N PHE F 943 " --> pdb=" O ARG F 940 " (cutoff:3.500A) removed outlier: 4.203A pdb=" N ALA F 946 " --> pdb=" O PHE F 943 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 140 through 142 Processing sheet with id= B, first strand: chain 'A' and resid 188 through 191 Processing sheet with id= C, first strand: chain 'A' and resid 520 through 522 removed outlier: 6.153A pdb=" N CYS A 637 " --> pdb=" O PHE A 521 " (cutoff:3.500A) No H-bonds generated for sheet with id= C Processing sheet with id= D, first strand: chain 'A' and resid 544 through 546 removed outlier: 5.840A pdb=" N LEU A 586 " --> pdb=" O PHE A 545 " (cutoff:3.500A) No H-bonds generated for sheet with id= D Processing sheet with id= E, first strand: chain 'A' and resid 764 through 769 removed outlier: 6.779A pdb=" N GLU A 801 " --> pdb=" O LEU A 842 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'A' and resid 911 through 913 removed outlier: 6.508A pdb=" N HIS A 934 " --> pdb=" O LEU A 912 " (cutoff:3.500A) No H-bonds generated for sheet with id= F Processing sheet with id= G, first strand: chain 'B' and resid 140 through 142 Processing sheet with id= H, first strand: chain 'B' and resid 188 through 191 Processing sheet with id= I, first strand: chain 'B' and resid 765 through 769 removed outlier: 3.654A pdb=" N VAL B 765 " --> pdb=" O VAL B 780 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N VAL B 780 " --> pdb=" O VAL B 765 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N ALA B 769 " --> pdb=" O SER B 776 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'B' and resid 781 through 783 Processing sheet with id= K, first strand: chain 'C' and resid 140 through 142 Processing sheet with id= L, first strand: chain 'C' and resid 188 through 191 Processing sheet with id= M, first strand: chain 'C' and resid 767 through 769 Processing sheet with id= N, first strand: chain 'C' and resid 780 through 784 Processing sheet with id= O, first strand: chain 'D' and resid 140 through 142 Processing sheet with id= P, first strand: chain 'D' and resid 188 through 191 Processing sheet with id= Q, first strand: chain 'D' and resid 544 through 548 removed outlier: 6.348A pdb=" N LEU D 586 " --> pdb=" O PHE D 545 " (cutoff:3.500A) removed outlier: 7.274A pdb=" N PHE D 547 " --> pdb=" O LEU D 586 " (cutoff:3.500A) removed outlier: 5.966A pdb=" N LEU D 588 " --> pdb=" O PHE D 547 " (cutoff:3.500A) No H-bonds generated for sheet with id= Q Processing sheet with id= R, first strand: chain 'D' and resid 764 through 766 Processing sheet with id= S, first strand: chain 'E' and resid 140 through 142 Processing sheet with id= T, first strand: chain 'E' and resid 188 through 191 Processing sheet with id= U, first strand: chain 'E' and resid 544 through 548 removed outlier: 5.914A pdb=" N LEU E 586 " --> pdb=" O PHE E 545 " (cutoff:3.500A) removed outlier: 7.761A pdb=" N PHE E 547 " --> pdb=" O LEU E 586 " (cutoff:3.500A) removed outlier: 6.490A pdb=" N LEU E 588 " --> pdb=" O PHE E 547 " (cutoff:3.500A) No H-bonds generated for sheet with id= U Processing sheet with id= V, first strand: chain 'E' and resid 767 through 769 Processing sheet with id= W, first strand: chain 'E' and resid 780 through 784 removed outlier: 3.645A pdb=" N GLU E 781 " --> pdb=" O HIS E 843 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain 'E' and resid 911 through 913 removed outlier: 6.364A pdb=" N HIS E 934 " --> pdb=" O LEU E 912 " (cutoff:3.500A) No H-bonds generated for sheet with id= X Processing sheet with id= Y, first strand: chain 'F' and resid 140 through 142 Processing sheet with id= Z, first strand: chain 'F' and resid 164 through 167 Processing sheet with id= AA, first strand: chain 'F' and resid 689 through 691 removed outlier: 6.884A pdb=" N VAL F 735 " --> pdb=" O LYS F 690 " (cutoff:3.500A) No H-bonds generated for sheet with id= AA Processing sheet with id= AB, first strand: chain 'F' and resid 764 through 766 removed outlier: 3.556A pdb=" N GLU F 781 " --> pdb=" O HIS F 843 " (cutoff:3.500A) Processing sheet with id= AC, first strand: chain 'F' and resid 909 through 913 removed outlier: 6.514A pdb=" N GLU F 932 " --> pdb=" O ILE F 910 " (cutoff:3.500A) removed outlier: 8.122A pdb=" N LEU F 912 " --> pdb=" O GLU F 932 " (cutoff:3.500A) removed outlier: 6.240A pdb=" N HIS F 934 " --> pdb=" O LEU F 912 " (cutoff:3.500A) No H-bonds generated for sheet with id= AC 1263 hydrogen bonds defined for protein. 3219 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: 23.99 Time building geometry restraints manager: 54.87 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.80 - 1.03: 37443 1.03 - 1.25: 6383 1.25 - 1.48: 14743 1.48 - 1.71: 16406 1.71 - 1.94: 287 Bond restraints: 75262 Sorted by residual: bond pdb=" NE2 GLN C 389 " pdb="HE22 GLN C 389 " ideal model delta sigma weight residual 0.860 0.800 0.060 2.00e-02 2.50e+03 9.08e+00 bond pdb=" CD1 TYR D 492 " pdb=" CE1 TYR D 492 " ideal model delta sigma weight residual 1.382 1.292 0.090 3.00e-02 1.11e+03 8.98e+00 bond pdb=" CB TRP D 464 " pdb=" CG TRP D 464 " ideal model delta sigma weight residual 1.498 1.406 0.092 3.10e-02 1.04e+03 8.86e+00 bond pdb=" C LYS F 290 " pdb=" N ALA F 291 " ideal model delta sigma weight residual 1.335 1.373 -0.038 1.32e-02 5.74e+03 8.20e+00 bond pdb=" CB GLU E 882 " pdb=" CG GLU E 882 " ideal model delta sigma weight residual 1.520 1.435 0.085 3.00e-02 1.11e+03 7.99e+00 ... (remaining 75257 not shown) Histogram of bond angle deviations from ideal: 74.42 - 87.20: 19 87.20 - 99.98: 33 99.98 - 112.76: 89766 112.76 - 125.54: 44732 125.54 - 138.32: 2075 Bond angle restraints: 136625 Sorted by residual: angle pdb=" HE1 MET E 209 " pdb=" CE MET E 209 " pdb=" HE2 MET E 209 " ideal model delta sigma weight residual 110.00 75.00 35.00 3.00e+00 1.11e-01 1.36e+02 angle pdb=" SD MET E 209 " pdb=" CE MET E 209 " pdb=" HE2 MET E 209 " ideal model delta sigma weight residual 109.00 74.42 34.58 3.00e+00 1.11e-01 1.33e+02 angle pdb="HG11 VAL B 753 " pdb=" CG1 VAL B 753 " pdb="HG12 VAL B 753 " ideal model delta sigma weight residual 110.00 75.61 34.39 3.00e+00 1.11e-01 1.31e+02 angle pdb="HG11 VAL C 753 " pdb=" CG1 VAL C 753 " pdb="HG12 VAL C 753 " ideal model delta sigma weight residual 110.00 75.66 34.34 3.00e+00 1.11e-01 1.31e+02 angle pdb="HG11 VAL C 753 " pdb=" CG1 VAL C 753 " pdb="HG13 VAL C 753 " ideal model delta sigma weight residual 110.00 77.53 32.47 3.00e+00 1.11e-01 1.17e+02 ... (remaining 136620 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.97: 28373 21.97 - 43.94: 1295 43.94 - 65.92: 178 65.92 - 87.89: 39 87.89 - 109.86: 11 Dihedral angle restraints: 29896 sinusoidal: 14585 harmonic: 15311 Sorted by residual: dihedral pdb=" C GLU B 288 " pdb=" N GLU B 288 " pdb=" CA GLU B 288 " pdb=" CB GLU B 288 " ideal model delta harmonic sigma weight residual -122.60 -107.39 -15.21 0 2.50e+00 1.60e-01 3.70e+01 dihedral pdb=" O1B ADP E1001 " pdb=" O3A ADP E1001 " pdb=" PB ADP E1001 " pdb=" PA ADP E1001 " ideal model delta sinusoidal sigma weight residual -60.00 49.86 -109.86 1 2.00e+01 2.50e-03 3.22e+01 dihedral pdb=" N GLU B 288 " pdb=" C GLU B 288 " pdb=" CA GLU B 288 " pdb=" CB GLU B 288 " ideal model delta harmonic sigma weight residual 122.80 110.12 12.68 0 2.50e+00 1.60e-01 2.57e+01 ... (remaining 29893 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.357: 5862 0.357 - 0.714: 2 0.714 - 1.071: 0 1.071 - 1.428: 0 1.428 - 1.785: 2 Chirality restraints: 5866 Sorted by residual: chirality pdb=" CG LEU D 425 " pdb=" CB LEU D 425 " pdb=" CD1 LEU D 425 " pdb=" CD2 LEU D 425 " both_signs ideal model delta sigma weight residual False -2.59 -0.80 -1.79 2.00e-01 2.50e+01 7.97e+01 chirality pdb=" CG LEU F 400 " pdb=" CB LEU F 400 " pdb=" CD1 LEU F 400 " pdb=" CD2 LEU F 400 " both_signs ideal model delta sigma weight residual False -2.59 -1.11 -1.48 2.00e-01 2.50e+01 5.46e+01 chirality pdb=" CG LEU C 153 " pdb=" CB LEU C 153 " pdb=" CD1 LEU C 153 " pdb=" CD2 LEU C 153 " both_signs ideal model delta sigma weight residual False -2.59 -2.20 -0.39 2.00e-01 2.50e+01 3.79e+00 ... (remaining 5863 not shown) Planarity restraints: 10969 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CG GLN A 377 " 0.047 2.00e-02 2.50e+03 9.83e-02 1.45e+02 pdb=" CD GLN A 377 " -0.114 2.00e-02 2.50e+03 pdb=" OE1 GLN A 377 " -0.011 2.00e-02 2.50e+03 pdb=" NE2 GLN A 377 " 0.163 2.00e-02 2.50e+03 pdb="HE21 GLN A 377 " 0.036 2.00e-02 2.50e+03 pdb="HE22 GLN A 377 " -0.121 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLN C 389 " 0.061 2.00e-02 2.50e+03 9.57e-02 1.37e+02 pdb=" CD GLN C 389 " -0.023 2.00e-02 2.50e+03 pdb=" OE1 GLN C 389 " -0.001 2.00e-02 2.50e+03 pdb=" NE2 GLN C 389 " -0.161 2.00e-02 2.50e+03 pdb="HE21 GLN C 389 " -0.030 2.00e-02 2.50e+03 pdb="HE22 GLN C 389 " 0.154 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASP F 302 " 0.032 2.00e-02 2.50e+03 6.39e-02 4.08e+01 pdb=" C ASP F 302 " -0.111 2.00e-02 2.50e+03 pdb=" O ASP F 302 " 0.041 2.00e-02 2.50e+03 pdb=" N ILE F 303 " 0.038 2.00e-02 2.50e+03 ... (remaining 10966 not shown) Histogram of nonbonded interaction distances: 1.63 - 2.22: 6780 2.22 - 2.82: 161445 2.82 - 3.41: 193430 3.41 - 4.01: 243937 4.01 - 4.60: 384170 Nonbonded interactions: 989762 Sorted by model distance: nonbonded pdb=" O GLU D 557 " pdb=" H LYS D 572 " model vdw 1.630 1.850 nonbonded pdb=" O ALA A 556 " pdb=" H GLY A 560 " model vdw 1.640 1.850 nonbonded pdb=" O ASP C 694 " pdb=" HG1 THR C 697 " model vdw 1.641 1.850 nonbonded pdb=" O ALA D 556 " pdb=" H GLY D 560 " model vdw 1.642 1.850 nonbonded pdb=" H ALA E 914 " pdb=" O VAL E 936 " model vdw 1.651 1.850 ... (remaining 989757 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' and (resid 123 through 405 or (resid 406 and (name N or name CA or na \ me C or name O or name CB or name CG or name CD or name OE1 or name OE2)) or (re \ sid 407 and (name N or name CA or name C or name O or name CB or name CG or name \ CD1 or name CD2)) or resid 408 through 411 or (resid 412 through 413 and (name \ N or name CA or name C or name O or name CB or name CG or name OD1 or name OD2)) \ or resid 414 through 948)) selection = (chain 'B' and (resid 123 through 720 or (resid 721 and (name N or name CA or na \ me C or name O or name CB or name CG or name CD or name NE or name CZ or name NH \ 1 or name NH2 or name H or name HA or name HB2 or name HB3 or name HG2 or name H \ G3 or name HD2 or name HD3 or name HE or name HH21 or name HH22)) or resid 722 t \ hrough 948)) selection = (chain 'C' and (resid 123 through 405 or (resid 406 and (name N or name CA or na \ me C or name O or name CB or name CG or name CD or name OE1 or name OE2)) or (re \ sid 407 and (name N or name CA or name C or name O or name CB or name CG or name \ CD1 or name CD2)) or resid 408 through 411 or (resid 412 through 413 and (name \ N or name CA or name C or name O or name CB or name CG or name OD1 or name OD2)) \ or resid 414 through 720 or (resid 721 and (name N or name CA or name C or name \ O or name CB or name CG or name CD or name NE or name CZ or name NH1 or name NH \ 2 or name H or name HA or name HB2 or name HB3 or name HG2 or name HG3 or name H \ D2 or name HD3 or name HE or name HH21 or name HH22)) or resid 722 through 948)) \ selection = (chain 'D' and (resid 123 through 405 or (resid 406 and (name N or name CA or na \ me C or name O or name CB or name CG or name CD or name OE1 or name OE2)) or (re \ sid 407 and (name N or name CA or name C or name O or name CB or name CG or name \ CD1 or name CD2)) or resid 408 through 411 or (resid 412 through 413 and (name \ N or name CA or name C or name O or name CB or name CG or name OD1 or name OD2)) \ or resid 414 through 720 or (resid 721 and (name N or name CA or name C or name \ O or name CB or name CG or name CD or name NE or name CZ or name NH1 or name NH \ 2 or name H or name HA or name HB2 or name HB3 or name HG2 or name HG3 or name H \ D2 or name HD3 or name HE or name HH21 or name HH22)) or resid 722 through 948)) \ selection = (chain 'E' and (resid 123 through 405 or (resid 406 and (name N or name CA or na \ me C or name O or name CB or name CG or name CD or name OE1 or name OE2)) or (re \ sid 407 and (name N or name CA or name C or name O or name CB or name CG or name \ CD1 or name CD2)) or resid 408 through 411 or (resid 412 through 413 and (name \ N or name CA or name C or name O or name CB or name CG or name OD1 or name OD2)) \ or resid 414 through 720 or (resid 721 and (name N or name CA or name C or name \ O or name CB or name CG or name CD or name NE or name CZ or name NH1 or name NH \ 2 or name H or name HA or name HB2 or name HB3 or name HG2 or name HG3 or name H \ D2 or name HD3 or name HE or name HH21 or name HH22)) or resid 722 through 948)) \ selection = (chain 'F' and (resid 123 through 405 or (resid 406 and (name N or name CA or na \ me C or name O or name CB or name CG or name CD or name OE1 or name OE2)) or (re \ sid 407 and (name N or name CA or name C or name O or name CB or name CG or name \ CD1 or name CD2)) or resid 408 through 411 or (resid 412 through 413 and (name \ N or name CA or name C or name O or name CB or name CG or name OD1 or name OD2)) \ or resid 414 through 720 or (resid 721 and (name N or name CA or name C or name \ O or name CB or name CG or name CD or name NE or name CZ or name NH1 or name NH \ 2 or name H or name HA or name HB2 or name HB3 or name HG2 or name HG3 or name H \ D2 or name HD3 or name HE or name HH21 or name HH22)) or resid 722 through 948)) \ } 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: 7 Type Number sf(0) Gaussians P 17 5.49 5 Mg 5 5.21 5 S 167 5.16 5 C 23514 2.51 5 N 6450 2.21 5 O 7006 1.98 5 H 37485 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=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.230 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.790 Extract box with map and model: 16.930 Check model and map are aligned: 0.820 Convert atoms to be neutral: 0.490 Process input model: 182.550 Find NCS groups from input model: 3.620 Set up NCS constraints: 0.190 Set refine NCS operators: 0.000 Set scattering table: 0.040 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.970 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 211.650 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7922 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.011 0.110 37777 Z= 0.756 Angle : 1.265 14.598 51044 Z= 0.694 Chirality : 0.071 1.785 5866 Planarity : 0.009 0.078 6545 Dihedral : 12.766 109.862 14473 Min Nonbonded Distance : 2.011 Molprobity Statistics. All-atom Clashscore : 5.80 Ramachandran Plot: Outliers : 0.02 % Allowed : 8.48 % Favored : 91.49 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.02 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.41 (0.12), residues: 4632 helix: -2.22 (0.08), residues: 2005 sheet: -3.86 (0.18), residues: 538 loop : 0.04 (0.15), residues: 2089 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9264 Ramachandran restraints generated. 4632 Oldfield, 0 Emsley, 4632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9264 Ramachandran restraints generated. 4632 Oldfield, 0 Emsley, 4632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 530 is missing expected H atoms. Skipping. Residue THR 530 is missing expected H atoms. Skipping. Residue THR 530 is missing expected H atoms. Skipping. Residue THR 530 is missing expected H atoms. Skipping. Residue THR 530 is missing expected H atoms. Skipping. Residue THR 530 is missing expected H atoms. Skipping. Evaluate side-chains 162 residues out of total 4050 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 162 time to evaluate : 4.762 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 162 average time/residue: 0.9229 time to fit residues: 245.9529 Evaluate side-chains 146 residues out of total 4050 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 146 time to evaluate : 4.515 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 5.9546 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 464 random chunks: chunk 391 optimal weight: 20.0000 chunk 351 optimal weight: 0.9990 chunk 195 optimal weight: 0.6980 chunk 120 optimal weight: 0.9990 chunk 237 optimal weight: 20.0000 chunk 187 optimal weight: 0.9990 chunk 363 optimal weight: 0.8980 chunk 140 optimal weight: 9.9990 chunk 221 optimal weight: 3.9990 chunk 270 optimal weight: 0.5980 chunk 421 optimal weight: 2.9990 overall best weight: 0.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7859 moved from start: 0.0868 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.058 37777 Z= 0.169 Angle : 0.598 10.981 51044 Z= 0.311 Chirality : 0.049 1.686 5866 Planarity : 0.004 0.053 6545 Dihedral : 6.542 113.100 5137 Min Nonbonded Distance : 1.860 Molprobity Statistics. All-atom Clashscore : 8.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.38 % Favored : 95.62 % Rotamer Outliers : 0.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.59 (0.12), residues: 4632 helix: -0.85 (0.10), residues: 1998 sheet: -3.54 (0.19), residues: 528 loop : -0.32 (0.15), residues: 2106 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9264 Ramachandran restraints generated. 4632 Oldfield, 0 Emsley, 4632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9264 Ramachandran restraints generated. 4632 Oldfield, 0 Emsley, 4632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 530 is missing expected H atoms. Skipping. Residue THR 530 is missing expected H atoms. Skipping. Residue THR 530 is missing expected H atoms. Skipping. Residue THR 530 is missing expected H atoms. Skipping. Residue THR 530 is missing expected H atoms. Skipping. Residue THR 530 is missing expected H atoms. Skipping. Evaluate side-chains 157 residues out of total 4050 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 152 time to evaluate : 4.589 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: 5 outliers final: 3 residues processed: 152 average time/residue: 0.8963 time to fit residues: 228.8929 Evaluate side-chains 151 residues out of total 4050 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 148 time to evaluate : 4.523 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.6792 time to fit residues: 9.6379 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 464 random chunks: chunk 234 optimal weight: 20.0000 chunk 130 optimal weight: 5.9990 chunk 350 optimal weight: 7.9990 chunk 286 optimal weight: 4.9990 chunk 116 optimal weight: 5.9990 chunk 422 optimal weight: 6.9990 chunk 456 optimal weight: 4.9990 chunk 375 optimal weight: 0.4980 chunk 418 optimal weight: 3.9990 chunk 143 optimal weight: 9.9990 chunk 338 optimal weight: 0.9980 overall best weight: 3.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 376 GLN E 284 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7895 moved from start: 0.1086 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.041 37777 Z= 0.294 Angle : 0.591 10.878 51044 Z= 0.306 Chirality : 0.049 1.680 5866 Planarity : 0.004 0.051 6545 Dihedral : 6.397 106.460 5137 Min Nonbonded Distance : 1.619 Molprobity Statistics. All-atom Clashscore : 10.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.61 % Favored : 94.39 % Rotamer Outliers : 0.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.42 (0.12), residues: 4632 helix: -0.43 (0.11), residues: 1994 sheet: -3.48 (0.19), residues: 534 loop : -0.54 (0.14), residues: 2104 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9264 Ramachandran restraints generated. 4632 Oldfield, 0 Emsley, 4632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9264 Ramachandran restraints generated. 4632 Oldfield, 0 Emsley, 4632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 530 is missing expected H atoms. Skipping. Residue THR 530 is missing expected H atoms. Skipping. Residue THR 530 is missing expected H atoms. Skipping. Residue THR 530 is missing expected H atoms. Skipping. Residue THR 530 is missing expected H atoms. Skipping. Residue THR 530 is missing expected H atoms. Skipping. Evaluate side-chains 159 residues out of total 4050 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 147 time to evaluate : 4.677 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 outliers start: 12 outliers final: 8 residues processed: 153 average time/residue: 0.9010 time to fit residues: 231.9612 Evaluate side-chains 154 residues out of total 4050 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 146 time to evaluate : 4.531 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.8561 time to fit residues: 17.2539 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 464 random chunks: chunk 417 optimal weight: 3.9990 chunk 317 optimal weight: 30.0000 chunk 219 optimal weight: 5.9990 chunk 46 optimal weight: 3.9990 chunk 201 optimal weight: 2.9990 chunk 283 optimal weight: 0.8980 chunk 423 optimal weight: 1.9990 chunk 448 optimal weight: 5.9990 chunk 221 optimal weight: 0.6980 chunk 401 optimal weight: 40.0000 chunk 120 optimal weight: 2.9990 overall best weight: 1.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 456 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7869 moved from start: 0.1268 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.030 37777 Z= 0.182 Angle : 0.524 10.669 51044 Z= 0.269 Chirality : 0.049 1.716 5866 Planarity : 0.003 0.046 6545 Dihedral : 6.071 102.523 5137 Min Nonbonded Distance : 1.750 Molprobity Statistics. All-atom Clashscore : 9.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.17 % Favored : 95.83 % Rotamer Outliers : 0.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.17 (0.12), residues: 4632 helix: -0.08 (0.11), residues: 1994 sheet: -3.30 (0.19), residues: 547 loop : -0.56 (0.14), residues: 2091 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9264 Ramachandran restraints generated. 4632 Oldfield, 0 Emsley, 4632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9264 Ramachandran restraints generated. 4632 Oldfield, 0 Emsley, 4632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 530 is missing expected H atoms. Skipping. Residue THR 530 is missing expected H atoms. Skipping. Residue THR 530 is missing expected H atoms. Skipping. Residue THR 530 is missing expected H atoms. Skipping. Residue THR 530 is missing expected H atoms. Skipping. Residue THR 530 is missing expected H atoms. Skipping. Evaluate side-chains 156 residues out of total 4050 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 150 time to evaluate : 4.530 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 outliers start: 6 outliers final: 2 residues processed: 156 average time/residue: 0.8743 time to fit residues: 229.7541 Evaluate side-chains 150 residues out of total 4050 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 148 time to evaluate : 4.458 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.6935 time to fit residues: 8.3510 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 464 random chunks: chunk 373 optimal weight: 3.9990 chunk 254 optimal weight: 6.9990 chunk 6 optimal weight: 20.0000 chunk 333 optimal weight: 3.9990 chunk 185 optimal weight: 4.9990 chunk 382 optimal weight: 2.9990 chunk 310 optimal weight: 20.0000 chunk 0 optimal weight: 20.0000 chunk 229 optimal weight: 6.9990 chunk 402 optimal weight: 20.0000 chunk 113 optimal weight: 2.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 541 ASN ** E 450 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7905 moved from start: 0.1431 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.043 37777 Z= 0.322 Angle : 0.578 10.575 51044 Z= 0.300 Chirality : 0.049 1.683 5866 Planarity : 0.004 0.046 6545 Dihedral : 6.143 96.789 5137 Min Nonbonded Distance : 1.637 Molprobity Statistics. All-atom Clashscore : 11.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.87 % Favored : 94.13 % Rotamer Outliers : 0.35 % 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: -1.33 (0.12), residues: 4632 helix: -0.12 (0.11), residues: 2003 sheet: -3.20 (0.20), residues: 545 loop : -0.82 (0.14), residues: 2084 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9264 Ramachandran restraints generated. 4632 Oldfield, 0 Emsley, 4632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9264 Ramachandran restraints generated. 4632 Oldfield, 0 Emsley, 4632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 530 is missing expected H atoms. Skipping. Residue THR 530 is missing expected H atoms. Skipping. Residue THR 530 is missing expected H atoms. Skipping. Residue THR 530 is missing expected H atoms. Skipping. Residue THR 530 is missing expected H atoms. Skipping. Residue THR 530 is missing expected H atoms. Skipping. Evaluate side-chains 163 residues out of total 4050 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 149 time to evaluate : 4.530 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 outliers start: 14 outliers final: 8 residues processed: 158 average time/residue: 0.8628 time to fit residues: 230.3086 Evaluate side-chains 156 residues out of total 4050 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 148 time to evaluate : 4.477 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.6544 time to fit residues: 15.6031 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 464 random chunks: chunk 150 optimal weight: 10.0000 chunk 403 optimal weight: 5.9990 chunk 88 optimal weight: 0.0980 chunk 263 optimal weight: 2.9990 chunk 110 optimal weight: 2.9990 chunk 448 optimal weight: 5.9990 chunk 372 optimal weight: 4.9990 chunk 207 optimal weight: 3.9990 chunk 37 optimal weight: 2.9990 chunk 148 optimal weight: 6.9990 chunk 235 optimal weight: 20.0000 overall best weight: 2.6188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 541 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7885 moved from start: 0.1540 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.033 37777 Z= 0.223 Angle : 0.527 10.432 51044 Z= 0.271 Chirality : 0.048 1.682 5866 Planarity : 0.003 0.043 6545 Dihedral : 5.905 91.707 5137 Min Nonbonded Distance : 1.713 Molprobity Statistics. All-atom Clashscore : 10.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.53 % Favored : 95.47 % Rotamer Outliers : 0.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.13 (0.13), residues: 4632 helix: 0.13 (0.12), residues: 1992 sheet: -3.10 (0.20), residues: 551 loop : -0.80 (0.14), residues: 2089 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9264 Ramachandran restraints generated. 4632 Oldfield, 0 Emsley, 4632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9264 Ramachandran restraints generated. 4632 Oldfield, 0 Emsley, 4632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 530 is missing expected H atoms. Skipping. Residue THR 530 is missing expected H atoms. Skipping. Residue THR 530 is missing expected H atoms. Skipping. Residue THR 530 is missing expected H atoms. Skipping. Residue THR 530 is missing expected H atoms. Skipping. Residue THR 530 is missing expected H atoms. Skipping. Evaluate side-chains 163 residues out of total 4050 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 150 time to evaluate : 4.539 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 outliers start: 13 outliers final: 7 residues processed: 160 average time/residue: 0.9203 time to fit residues: 246.8441 Evaluate side-chains 155 residues out of total 4050 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 148 time to evaluate : 4.536 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 7 outliers final: 1 residues processed: 7 average time/residue: 0.8598 time to fit residues: 15.7617 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 464 random chunks: chunk 432 optimal weight: 6.9990 chunk 50 optimal weight: 1.9990 chunk 255 optimal weight: 0.0980 chunk 327 optimal weight: 9.9990 chunk 254 optimal weight: 5.9990 chunk 377 optimal weight: 3.9990 chunk 250 optimal weight: 9.9990 chunk 447 optimal weight: 8.9990 chunk 279 optimal weight: 2.9990 chunk 272 optimal weight: 3.9990 chunk 206 optimal weight: 2.9990 overall best weight: 2.4188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 541 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7884 moved from start: 0.1653 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.036 37777 Z= 0.221 Angle : 0.520 10.410 51044 Z= 0.266 Chirality : 0.048 1.695 5866 Planarity : 0.003 0.040 6545 Dihedral : 5.761 85.391 5137 Min Nonbonded Distance : 1.712 Molprobity Statistics. All-atom Clashscore : 10.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.31 % Favored : 94.69 % Rotamer Outliers : 0.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.04 (0.13), residues: 4632 helix: 0.26 (0.12), residues: 1998 sheet: -3.00 (0.20), residues: 551 loop : -0.83 (0.14), residues: 2083 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9264 Ramachandran restraints generated. 4632 Oldfield, 0 Emsley, 4632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9264 Ramachandran restraints generated. 4632 Oldfield, 0 Emsley, 4632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 530 is missing expected H atoms. Skipping. Residue THR 530 is missing expected H atoms. Skipping. Residue THR 530 is missing expected H atoms. Skipping. Residue THR 530 is missing expected H atoms. Skipping. Residue THR 530 is missing expected H atoms. Skipping. Residue THR 530 is missing expected H atoms. Skipping. Evaluate side-chains 161 residues out of total 4050 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 150 time to evaluate : 4.652 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 outliers start: 11 outliers final: 10 residues processed: 159 average time/residue: 0.9125 time to fit residues: 244.6143 Evaluate side-chains 160 residues out of total 4050 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 150 time to evaluate : 4.526 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 10 outliers final: 1 residues processed: 10 average time/residue: 0.7737 time to fit residues: 19.2364 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 464 random chunks: chunk 276 optimal weight: 0.0270 chunk 178 optimal weight: 7.9990 chunk 267 optimal weight: 0.6980 chunk 134 optimal weight: 5.9990 chunk 87 optimal weight: 7.9990 chunk 86 optimal weight: 6.9990 chunk 284 optimal weight: 3.9990 chunk 304 optimal weight: 3.9990 chunk 221 optimal weight: 4.9990 chunk 41 optimal weight: 2.9990 chunk 351 optimal weight: 0.1980 overall best weight: 1.5842 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 541 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7864 moved from start: 0.1753 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.030 37777 Z= 0.162 Angle : 0.497 10.351 51044 Z= 0.252 Chirality : 0.048 1.693 5866 Planarity : 0.003 0.038 6545 Dihedral : 5.557 80.268 5137 Min Nonbonded Distance : 1.756 Molprobity Statistics. All-atom Clashscore : 9.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.93 % Favored : 96.07 % Rotamer Outliers : 0.17 % 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: -0.83 (0.13), residues: 4632 helix: 0.45 (0.12), residues: 2002 sheet: -2.89 (0.20), residues: 551 loop : -0.75 (0.14), residues: 2079 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9264 Ramachandran restraints generated. 4632 Oldfield, 0 Emsley, 4632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9264 Ramachandran restraints generated. 4632 Oldfield, 0 Emsley, 4632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 530 is missing expected H atoms. Skipping. Residue THR 530 is missing expected H atoms. Skipping. Residue THR 530 is missing expected H atoms. Skipping. Residue THR 530 is missing expected H atoms. Skipping. Residue THR 530 is missing expected H atoms. Skipping. Residue THR 530 is missing expected H atoms. Skipping. Evaluate side-chains 157 residues out of total 4050 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 150 time to evaluate : 4.612 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: 7 outliers final: 4 residues processed: 157 average time/residue: 0.9356 time to fit residues: 248.5740 Evaluate side-chains 152 residues out of total 4050 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 148 time to evaluate : 4.586 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 4 outliers final: 1 residues processed: 4 average time/residue: 1.1200 time to fit residues: 14.1424 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 464 random chunks: chunk 406 optimal weight: 20.0000 chunk 428 optimal weight: 4.9990 chunk 390 optimal weight: 3.9990 chunk 416 optimal weight: 4.9990 chunk 250 optimal weight: 9.9990 chunk 181 optimal weight: 6.9990 chunk 327 optimal weight: 20.0000 chunk 127 optimal weight: 0.8980 chunk 376 optimal weight: 3.9990 chunk 394 optimal weight: 30.0000 chunk 415 optimal weight: 0.5980 overall best weight: 2.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7886 moved from start: 0.1809 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.045 37777 Z= 0.247 Angle : 0.524 10.326 51044 Z= 0.267 Chirality : 0.048 1.700 5866 Planarity : 0.003 0.039 6545 Dihedral : 5.608 86.328 5137 Min Nonbonded Distance : 1.685 Molprobity Statistics. All-atom Clashscore : 10.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.42 % Favored : 94.58 % Rotamer Outliers : 0.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.92 (0.13), residues: 4632 helix: 0.41 (0.12), residues: 1996 sheet: -2.90 (0.21), residues: 548 loop : -0.86 (0.14), residues: 2088 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9264 Ramachandran restraints generated. 4632 Oldfield, 0 Emsley, 4632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9264 Ramachandran restraints generated. 4632 Oldfield, 0 Emsley, 4632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 530 is missing expected H atoms. Skipping. Residue THR 530 is missing expected H atoms. Skipping. Residue THR 530 is missing expected H atoms. Skipping. Residue THR 530 is missing expected H atoms. Skipping. Residue THR 530 is missing expected H atoms. Skipping. Residue THR 530 is missing expected H atoms. Skipping. Evaluate side-chains 159 residues out of total 4050 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 150 time to evaluate : 4.576 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: 9 outliers final: 4 residues processed: 157 average time/residue: 0.9258 time to fit residues: 244.3345 Evaluate side-chains 153 residues out of total 4050 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 149 time to evaluate : 4.713 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 4 outliers final: 1 residues processed: 4 average time/residue: 1.0750 time to fit residues: 12.4992 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 464 random chunks: chunk 273 optimal weight: 6.9990 chunk 440 optimal weight: 6.9990 chunk 268 optimal weight: 0.7980 chunk 209 optimal weight: 2.9990 chunk 306 optimal weight: 6.9990 chunk 462 optimal weight: 30.0000 chunk 425 optimal weight: 2.9990 chunk 368 optimal weight: 3.9990 chunk 38 optimal weight: 4.9990 chunk 284 optimal weight: 3.9990 chunk 225 optimal weight: 5.9990 overall best weight: 2.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 541 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7888 moved from start: 0.1886 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.040 37777 Z= 0.250 Angle : 0.533 10.274 51044 Z= 0.271 Chirality : 0.048 1.697 5866 Planarity : 0.003 0.040 6545 Dihedral : 5.602 93.161 5137 Min Nonbonded Distance : 1.694 Molprobity Statistics. All-atom Clashscore : 10.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.25 % Favored : 94.75 % Rotamer Outliers : 0.10 % 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: -0.97 (0.13), residues: 4632 helix: 0.38 (0.12), residues: 2002 sheet: -2.87 (0.21), residues: 548 loop : -0.91 (0.14), residues: 2082 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9264 Ramachandran restraints generated. 4632 Oldfield, 0 Emsley, 4632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9264 Ramachandran restraints generated. 4632 Oldfield, 0 Emsley, 4632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 530 is missing expected H atoms. Skipping. Residue THR 530 is missing expected H atoms. Skipping. Residue THR 530 is missing expected H atoms. Skipping. Residue THR 530 is missing expected H atoms. Skipping. Residue THR 530 is missing expected H atoms. Skipping. Residue THR 530 is missing expected H atoms. Skipping. Evaluate side-chains 154 residues out of total 4050 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 150 time to evaluate : 5.580 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: 4 outliers final: 4 residues processed: 153 average time/residue: 0.8985 time to fit residues: 229.9616 Evaluate side-chains 153 residues out of total 4050 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 149 time to evaluate : 4.515 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 4 outliers final: 1 residues processed: 4 average time/residue: 1.0222 time to fit residues: 12.2626 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 464 random chunks: chunk 292 optimal weight: 0.3980 chunk 392 optimal weight: 20.0000 chunk 112 optimal weight: 2.9990 chunk 339 optimal weight: 2.9990 chunk 54 optimal weight: 3.9990 chunk 102 optimal weight: 2.9990 chunk 368 optimal weight: 2.9990 chunk 154 optimal weight: 20.0000 chunk 378 optimal weight: 0.8980 chunk 46 optimal weight: 3.9990 chunk 67 optimal weight: 2.9990 overall best weight: 2.0586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4019 r_free = 0.4019 target = 0.095888 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.065926 restraints weight = 470683.958| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.068015 restraints weight = 192846.348| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.068530 restraints weight = 97944.474| |-----------------------------------------------------------------------------| r_work (final): 0.3300 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7871 moved from start: 0.1951 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.030 37777 Z= 0.190 Angle : 0.501 10.287 51044 Z= 0.254 Chirality : 0.048 1.689 5866 Planarity : 0.003 0.039 6545 Dihedral : 5.447 96.643 5137 Min Nonbonded Distance : 1.741 Molprobity Statistics. All-atom Clashscore : 10.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.92 % Favored : 95.08 % Rotamer Outliers : 0.07 % 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: -0.82 (0.13), residues: 4632 helix: 0.54 (0.12), residues: 1998 sheet: -2.79 (0.21), residues: 555 loop : -0.85 (0.14), residues: 2079 =============================================================================== Job complete usr+sys time: 7537.25 seconds wall clock time: 134 minutes 10.36 seconds (8050.36 seconds total)