Starting phenix.real_space_refine (version: 1.21rc1) on Wed Jul 12 09:59:15 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ng5_12308/07_2023/7ng5_12308_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ng5_12308/07_2023/7ng5_12308.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ng5_12308/07_2023/7ng5_12308.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ng5_12308/07_2023/7ng5_12308.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ng5_12308/07_2023/7ng5_12308_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ng5_12308/07_2023/7ng5_12308_trim_updated.pdb" } resolution = 3.8 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= 0.003 sd= 0.046 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians P 17 5.49 5 Mg 5 5.21 5 S 162 5.16 5 C 23475 2.51 5 N 6437 2.21 5 O 6998 1.98 5 H 37485 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 131": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A PHE 135": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" 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 PHE 191": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" 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 GLU 281": "OE1" <-> "OE2" Residue "A PHE 283": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ARG 301": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 311": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 323": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A GLU 342": "OE1" <-> "OE2" Residue "A ARG 381": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 424": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A PHE 455": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ARG 459": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A TYR 461": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A GLU 488": "OE1" <-> "OE2" Residue "A GLU 503": "OE1" <-> "OE2" Residue "A ARG 534": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 542": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A TYR 544": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 547": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ARG 562": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A GLU 591": "OE1" <-> "OE2" Residue "A ARG 597": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A TYR 599": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 619": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ASP 621": "OD1" <-> "OD2" Residue "A ARG 650": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 652": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A GLU 671": "OE1" <-> "OE2" Residue "A ARG 672": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 710": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A TYR 757": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" 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 "A GLU 882": "OE1" <-> "OE2" Residue "A PHE 920": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 939": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" 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 GLU 180": "OE1" <-> "OE2" 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 GLU 295": "OE1" <-> "OE2" Residue "B ARG 301": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 311": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 323": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ASP 348": "OD1" <-> "OD2" Residue "B ARG 381": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B GLU 382": "OE1" <-> "OE2" Residue "B ASP 436": "OD1" <-> "OD2" Residue "B ARG 459": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 482": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B GLU 495": "OE1" <-> "OE2" Residue "B ARG 534": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 542": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B TYR 544": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B GLU 557": "OE1" <-> "OE2" Residue "B ARG 562": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B GLU 591": "OE1" <-> "OE2" Residue "B GLU 609": "OE1" <-> "OE2" Residue "B PHE 635": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B ARG 652": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B TYR 661": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B ARG 672": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 785": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 786": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 815": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 822": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B PHE 943": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" 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 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 GLU 312": "OE1" <-> "OE2" Residue "C ARG 323": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C ARG 381": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C ASP 413": "OD1" <-> "OD2" 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 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 591": "OE1" <-> "OE2" Residue "C ASP 593": "OD1" <-> "OD2" Residue "C GLU 609": "OE1" <-> "OE2" Residue "C ARG 705": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C GLU 781": "OE1" <-> "OE2" 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 "C TYR 834": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C ASP 919": "OD1" <-> "OD2" Residue "C PHE 926": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C TYR 939": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D ARG 131": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D PHE 135": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" 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 GLU 175": "OE1" <-> "OE2" 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 TYR 394": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D GLU 419": "OE1" <-> "OE2" Residue "D ASP 439": "OD1" <-> "OD2" Residue "D GLU 476": "OE1" <-> "OE2" Residue "D GLU 489": "OE1" <-> "OE2" Residue "D GLU 543": "OE1" <-> "OE2" Residue "D PHE 545": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D GLU 583": "OE1" <-> "OE2" Residue "D TYR 757": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" 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 TYR 818": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D ARG 822": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D TYR 939": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D PHE 943": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" 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 GLU 175": "OE1" <-> "OE2" Residue "E GLU 180": "OE1" <-> "OE2" 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 GLU 221": "OE1" <-> "OE2" Residue "E PHE 283": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E ARG 301": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "E ARG 311": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "E ARG 323": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "E GLU 342": "OE1" <-> "OE2" Residue "E ARG 381": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "E ASP 412": "OD1" <-> "OD2" Residue "E ARG 511": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "E TYR 522": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E PHE 547": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E GLU 591": "OE1" <-> "OE2" 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 TYR 834": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E ASP 852": "OD1" <-> "OD2" Residue "E PHE 920": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E GLU 929": "OE1" <-> "OE2" Residue "E TYR 939": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F ARG 131": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" 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 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 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 GLU 385": "OE1" <-> "OE2" Residue "F TYR 461": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F TYR 492": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F GLU 495": "OE1" <-> "OE2" Residue "F PHE 504": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F ARG 511": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "F ARG 542": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "F TYR 544": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F GLU 591": "OE1" <-> "OE2" Residue "F TYR 623": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F ASP 629": "OD1" <-> "OD2" Residue "F ARG 650": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "F ARG 652": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "F TYR 661": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F ARG 672": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "F TYR 673": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F ASP 685": "OD1" <-> "OD2" Residue "F GLU 686": "OE1" <-> "OE2" Residue "F ARG 705": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "F ARG 710": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "F GLU 717": "OE1" <-> "OE2" Residue "F ARG 721": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "F PHE 751": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" 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 GLU 812": "OE1" <-> "OE2" Residue "F ARG 815": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "F ARG 822": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "F ASP 852": "OD1" <-> "OD2" Time to flip residues: 0.10s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5013/modules/chem_data/mon_lib" Total number of atoms: 74579 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: 55 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 55 Classifications: {'peptide': 11} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'TRANS': 10} Unresolved non-hydrogen bonds: 22 Unresolved non-hydrogen angles: 33 Unresolved non-hydrogen dihedrals: 11 Planarities with less than four sites: {'UNK:plan-1': 11} Unresolved non-hydrogen planarities: 11 Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 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, 'ATP': 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, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 22.03, per 1000 atoms: 0.30 Number of scatterers: 74579 At special positions: 0 Unit cell: (137.946, 145.425, 230.187, 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 162 16.00 P 17 15.00 Mg 5 11.99 O 6998 8.00 N 6437 7.00 C 23475 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: 45.27 Conformation dependent library (CDL) restraints added in 5.6 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: 8758 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 189 helices and 31 sheets defined 44.2% alpha, 4.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.34 Creating SS restraints... Processing helix chain 'A' and resid 148 through 156 removed outlier: 3.686A 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 288 through 306 removed outlier: 3.808A pdb=" N LEU A 292 " --> pdb=" O VAL A 289 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N VAL A 297 " --> pdb=" O ALA A 294 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N THR A 299 " --> pdb=" O ILE A 296 " (cutoff:3.500A) removed outlier: 3.890A 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 320 through 322 No H-bonds generated for 'chain 'A' and resid 320 through 322' Processing helix chain 'A' and resid 328 through 337 Processing helix chain 'A' and resid 343 through 351 Processing helix chain 'A' and resid 355 through 405 removed outlier: 4.401A pdb=" N LYS A 393 " --> pdb=" O GLN A 389 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N TYR A 394 " --> pdb=" O THR A 390 " (cutoff:3.500A) Processing helix chain 'A' and resid 413 through 424 Processing helix chain 'A' and resid 432 through 447 Processing helix chain 'A' and resid 453 through 466 Processing helix chain 'A' and resid 480 through 488 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 559 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: 4.176A 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 686 through 688 No H-bonds generated for 'chain 'A' and resid 686 through 688' Processing helix chain 'A' and resid 693 through 702 Processing helix chain 'A' and resid 710 through 729 removed outlier: 3.682A pdb=" N SER A 729 " --> pdb=" O TYR A 725 " (cutoff:3.500A) Processing helix chain 'A' and resid 742 through 746 removed outlier: 3.946A pdb=" N VAL A 746 " --> pdb=" O GLN A 743 " (cutoff:3.500A) Processing helix chain 'A' and resid 809 through 828 Processing helix chain 'A' and resid 850 through 869 Proline residue: A 854 - end of helix removed outlier: 3.857A 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 922 removed outlier: 4.896A pdb=" N LYS A 918 " --> pdb=" O GLU A 915 " (cutoff:3.500A) Processing helix chain 'A' and resid 925 through 928 Processing helix chain 'A' and resid 939 through 946 removed outlier: 4.373A pdb=" N ALA A 946 " --> pdb=" O PHE A 943 " (cutoff:3.500A) Processing helix chain 'B' and resid 148 through 156 Processing helix chain 'B' and resid 175 through 180 Processing helix chain 'B' and resid 289 through 306 removed outlier: 3.686A pdb=" N LEU B 292 " --> pdb=" O VAL B 289 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N VAL B 297 " --> pdb=" O ALA B 294 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N ILE B 304 " --> pdb=" O ARG B 301 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N LEU B 306 " --> pdb=" O ILE B 303 " (cutoff:3.500A) Processing helix chain 'B' and resid 313 through 317 Processing helix chain 'B' and resid 320 through 322 No H-bonds generated for 'chain 'B' and resid 320 through 322' Processing helix chain 'B' and resid 328 through 338 removed outlier: 3.907A pdb=" N LEU B 338 " --> pdb=" O MET B 334 " (cutoff:3.500A) 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 407 Processing helix chain 'B' and resid 413 through 424 removed outlier: 4.071A pdb=" N ARG B 422 " --> pdb=" O GLU B 418 " (cutoff:3.500A) Processing helix chain 'B' and resid 432 through 447 removed outlier: 3.920A pdb=" N ASP B 436 " --> pdb=" O LYS B 432 " (cutoff:3.500A) removed outlier: 4.217A pdb=" N VAL B 437 " --> pdb=" O HIS B 433 " (cutoff:3.500A) Processing helix chain 'B' and resid 455 through 465 Processing helix chain 'B' and resid 480 through 488 removed outlier: 4.079A pdb=" N ALA B 485 " --> pdb=" O ALA B 481 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N VAL B 486 " --> pdb=" O ARG B 482 " (cutoff:3.500A) Processing helix chain 'B' and resid 495 through 511 Processing helix chain 'B' and resid 532 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 609 removed outlier: 3.789A pdb=" N LEU B 607 " --> pdb=" O SER B 604 " (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 Processing helix chain 'B' and resid 674 through 682 Processing helix chain 'B' and resid 693 through 702 Processing helix chain 'B' and resid 711 through 728 removed outlier: 3.909A pdb=" N LEU B 720 " --> pdb=" O VAL B 716 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N SER B 723 " --> pdb=" O VAL B 719 " (cutoff:3.500A) Processing helix chain 'B' and resid 739 through 746 removed outlier: 4.648A pdb=" N GLN B 743 " --> pdb=" O GLU B 740 " (cutoff:3.500A) removed outlier: 4.274A pdb=" N VAL B 746 " --> pdb=" O GLN B 743 " (cutoff:3.500A) Processing helix chain 'B' and resid 808 through 828 removed outlier: 3.661A 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: 4.366A pdb=" N CYS B 858 " --> pdb=" O SER B 855 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N VAL B 861 " --> pdb=" O CYS B 858 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N LEU B 865 " --> pdb=" O THR B 862 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N MET B 869 " --> pdb=" O SER B 866 " (cutoff:3.500A) Processing helix chain 'B' and resid 895 through 904 removed outlier: 3.946A pdb=" N ILE B 900 " --> pdb=" O LYS B 896 " (cutoff:3.500A) Processing helix chain 'B' and resid 914 through 921 removed outlier: 5.125A pdb=" N LYS B 918 " --> pdb=" O GLU B 915 " (cutoff:3.500A) removed outlier: 4.271A pdb=" N TYR B 921 " --> pdb=" O LYS B 918 " (cutoff:3.500A) Processing helix chain 'B' and resid 925 through 928 No H-bonds generated for '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: 3.755A pdb=" N LEU C 152 " --> pdb=" O LYS C 148 " (cutoff:3.500A) Processing helix chain 'C' and resid 175 through 180 Processing helix chain 'C' and resid 291 through 306 removed outlier: 3.932A 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 328 through 338 removed outlier: 3.761A pdb=" N LEU C 338 " --> pdb=" O MET C 334 " (cutoff:3.500A) Processing helix chain 'C' and resid 343 through 350 Processing helix chain 'C' and resid 355 through 406 removed outlier: 3.826A pdb=" N LEU C 372 " --> pdb=" O LYS C 368 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N LYS C 393 " --> pdb=" O GLN C 389 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N TYR C 394 " --> pdb=" O THR C 390 " (cutoff:3.500A) Processing helix chain 'C' and resid 415 through 424 Processing helix chain 'C' and resid 433 through 447 removed outlier: 4.168A pdb=" N VAL C 437 " --> pdb=" O HIS C 433 " (cutoff:3.500A) Processing helix chain 'C' and resid 453 through 467 removed outlier: 3.626A pdb=" N VAL C 457 " --> pdb=" O SER C 453 " (cutoff:3.500A) Processing helix chain 'C' and resid 481 through 488 removed outlier: 3.786A pdb=" N VAL C 486 " --> pdb=" O ARG C 482 " (cutoff:3.500A) Processing helix chain 'C' and resid 495 through 510 removed outlier: 3.645A pdb=" N LEU C 502 " --> pdb=" O LYS C 498 " (cutoff:3.500A) Processing helix chain 'C' and resid 532 through 539 Processing helix chain 'C' and resid 555 through 558 Processing helix chain 'C' and resid 572 through 579 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: 4.336A 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 650 No H-bonds generated for 'chain 'C' and resid 647 through 650' Processing helix chain 'C' and resid 663 through 670 removed outlier: 4.284A pdb=" N ALA C 668 " --> pdb=" O GLN C 664 " (cutoff:3.500A) Processing helix chain 'C' and resid 674 through 682 Processing helix chain 'C' and resid 693 through 703 Processing helix chain 'C' and resid 710 through 728 Processing helix chain 'C' and resid 739 through 746 removed outlier: 4.294A pdb=" N GLN C 743 " --> pdb=" O GLU C 740 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N VAL C 746 " --> pdb=" O GLN C 743 " (cutoff:3.500A) Processing helix chain 'C' and resid 809 through 828 removed outlier: 3.656A pdb=" N MET C 826 " --> pdb=" O ARG C 822 " (cutoff:3.500A) Processing helix chain 'C' and resid 835 through 837 No H-bonds generated for 'chain 'C' and resid 835 through 837' Processing helix chain 'C' and resid 850 through 869 Proline residue: C 854 - end of helix removed outlier: 4.476A pdb=" N CYS C 858 " --> pdb=" O SER C 855 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N VAL C 861 " --> pdb=" O CYS C 858 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N MET C 869 " --> pdb=" O SER C 866 " (cutoff:3.500A) Processing helix chain 'C' and resid 895 through 905 Processing helix chain 'C' and resid 914 through 921 removed outlier: 4.712A pdb=" N LYS C 918 " --> pdb=" O GLU C 915 " (cutoff:3.500A) Processing helix chain 'C' and resid 939 through 946 removed outlier: 4.138A pdb=" N ALA C 946 " --> pdb=" O PHE C 943 " (cutoff:3.500A) Processing helix chain 'D' and resid 148 through 156 removed outlier: 3.652A 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 289 through 306 removed outlier: 3.790A pdb=" N LEU D 292 " --> pdb=" O VAL D 289 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N LYS D 298 " --> pdb=" O GLU D 295 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N ILE D 304 " --> pdb=" O ARG D 301 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N LEU D 306 " --> pdb=" O ILE D 303 " (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 406 removed outlier: 3.620A pdb=" N LYS D 404 " --> pdb=" O LEU D 400 " (cutoff:3.500A) Processing helix chain 'D' and resid 414 through 425 removed outlier: 3.796A pdb=" N PHE D 421 " --> pdb=" O ILE D 417 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ARG D 422 " --> pdb=" O GLU D 418 " (cutoff:3.500A) Processing helix chain 'D' and resid 432 through 447 removed outlier: 3.801A pdb=" N ASP D 436 " --> pdb=" O LYS D 432 " (cutoff:3.500A) removed outlier: 4.303A pdb=" N VAL D 437 " --> pdb=" O HIS D 433 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N VAL D 438 " --> pdb=" O VAL D 434 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N ASP D 439 " --> pdb=" O MET D 435 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N GLY D 446 " --> pdb=" O LEU D 442 " (cutoff:3.500A) removed outlier: 4.285A 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 Processing helix chain 'D' and resid 495 through 510 removed outlier: 3.545A pdb=" N LEU D 510 " --> pdb=" O ALA D 506 " (cutoff:3.500A) Processing helix chain 'D' and resid 531 through 540 Processing helix chain 'D' and resid 555 through 558 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 605 No H-bonds generated for 'chain 'D' and resid 603 through 605' Processing helix chain 'D' and resid 607 through 611 Processing helix chain 'D' and resid 616 through 618 No H-bonds generated for 'chain 'D' and resid 616 through 618' Processing helix chain 'D' and resid 647 through 651 Processing helix chain 'D' and resid 665 through 673 removed outlier: 3.581A pdb=" N GLU D 671 " --> pdb=" O LEU D 667 " (cutoff:3.500A) removed outlier: 4.411A pdb=" N ARG D 672 " --> pdb=" O ALA D 668 " (cutoff:3.500A) Processing helix chain 'D' and resid 675 through 682 Processing helix chain 'D' and resid 693 through 702 Processing helix chain 'D' and resid 710 through 728 Processing helix chain 'D' and resid 739 through 746 removed outlier: 4.393A pdb=" N GLN D 743 " --> pdb=" O GLU D 740 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N VAL D 746 " --> pdb=" O GLN D 743 " (cutoff:3.500A) Processing helix chain 'D' and resid 808 through 828 removed outlier: 3.863A 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: 4.403A pdb=" N CYS D 858 " --> pdb=" O SER D 855 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N VAL D 861 " --> pdb=" O CYS D 858 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N LEU D 865 " --> pdb=" O THR D 862 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N MET D 869 " --> pdb=" O SER D 866 " (cutoff:3.500A) Processing helix chain 'D' and resid 895 through 904 Processing helix chain 'D' and resid 914 through 922 removed outlier: 4.587A pdb=" N LYS D 918 " --> pdb=" O GLU D 915 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N PHE D 920 " --> pdb=" O LYS D 917 " (cutoff:3.500A) 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 946 removed outlier: 4.426A pdb=" N ALA D 946 " --> pdb=" O PHE D 943 " (cutoff:3.500A) Processing helix chain 'E' and resid 148 through 156 Processing helix chain 'E' and resid 175 through 178 No H-bonds generated for 'chain 'E' and resid 175 through 178' Processing helix chain 'E' and resid 288 through 306 removed outlier: 4.109A pdb=" N LEU E 292 " --> pdb=" O VAL E 289 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N VAL E 297 " --> pdb=" O ALA E 294 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N THR E 299 " --> pdb=" O ILE E 296 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N LEU E 306 " --> pdb=" O ILE E 303 " (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 406 removed outlier: 3.617A pdb=" N LEU E 372 " --> pdb=" O LYS E 368 " (cutoff:3.500A) removed outlier: 4.179A pdb=" N LYS E 393 " --> pdb=" O GLN E 389 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N TYR E 394 " --> pdb=" O THR E 390 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N ILE E 402 " --> pdb=" O GLU E 398 " (cutoff:3.500A) Processing helix chain 'E' and resid 415 through 424 Processing helix chain 'E' and resid 432 through 447 removed outlier: 3.556A pdb=" N VAL E 437 " --> pdb=" O HIS E 433 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N LEU E 447 " --> pdb=" O SER E 443 " (cutoff:3.500A) Processing helix chain 'E' and resid 453 through 467 removed outlier: 3.629A pdb=" N SER E 467 " --> pdb=" O ASP E 463 " (cutoff:3.500A) Processing helix chain 'E' and resid 480 through 488 removed outlier: 3.912A pdb=" N ALA E 485 " --> pdb=" O ALA E 481 " (cutoff:3.500A) Processing helix chain 'E' and resid 495 through 510 Processing helix chain 'E' and resid 531 through 540 Processing helix chain 'E' and resid 556 through 558 No H-bonds generated for 'chain 'E' and resid 556 through 558' Processing helix chain 'E' and resid 572 through 579 Processing helix chain 'E' and resid 603 through 611 Processing helix chain 'E' and resid 613 through 618 removed outlier: 5.346A pdb=" N ASN E 618 " --> pdb=" O GLU E 614 " (cutoff:3.500A) Processing helix chain 'E' and resid 642 through 644 No H-bonds generated for 'chain 'E' and resid 642 through 644' Processing helix chain 'E' and resid 647 through 652 removed outlier: 4.196A pdb=" N ARG E 652 " --> pdb=" O PRO E 648 " (cutoff:3.500A) Processing helix chain 'E' and resid 665 through 673 removed outlier: 3.666A pdb=" N ARG E 672 " --> pdb=" O ALA E 668 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N TYR E 673 " --> pdb=" O ILE E 669 " (cutoff:3.500A) Processing helix chain 'E' and resid 675 through 682 Processing helix chain 'E' and resid 693 through 701 Processing helix chain 'E' and resid 711 through 728 removed outlier: 3.862A pdb=" N LYS E 726 " --> pdb=" O LYS E 722 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N ILE E 727 " --> pdb=" O SER E 723 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N VAL E 728 " --> pdb=" O ALA E 724 " (cutoff:3.500A) Processing helix chain 'E' and resid 739 through 746 removed outlier: 3.530A pdb=" N LEU E 742 " --> pdb=" O PRO E 739 " (cutoff:3.500A) removed outlier: 4.415A pdb=" N GLN E 743 " --> pdb=" O GLU E 740 " (cutoff:3.500A) Processing helix chain 'E' and resid 808 through 828 removed outlier: 3.730A pdb=" N MET E 826 " --> pdb=" O ARG E 822 " (cutoff:3.500A) Processing helix chain 'E' and resid 850 through 869 Proline residue: E 854 - end of helix removed outlier: 3.977A pdb=" N CYS E 858 " --> pdb=" O SER E 855 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N LEU E 865 " --> pdb=" O THR E 862 " (cutoff:3.500A) Processing helix chain 'E' and resid 895 through 904 Processing helix chain 'E' and resid 914 through 922 removed outlier: 4.278A pdb=" N LYS E 918 " --> pdb=" O GLU E 915 " (cutoff:3.500A) removed outlier: 4.091A pdb=" N TYR E 921 " --> pdb=" O LYS E 918 " (cutoff:3.500A) Processing helix chain 'E' and resid 939 through 946 removed outlier: 3.830A pdb=" N PHE E 943 " --> pdb=" O ARG E 940 " (cutoff:3.500A) removed outlier: 4.116A pdb=" N ALA E 946 " --> pdb=" O PHE E 943 " (cutoff:3.500A) Processing helix chain 'F' and resid 148 through 156 removed outlier: 3.657A pdb=" N LEU F 152 " --> pdb=" O LYS F 148 " (cutoff:3.500A) Processing helix chain 'F' and resid 175 through 180 Processing helix chain 'F' and resid 291 through 306 removed outlier: 3.721A pdb=" N GLU F 295 " --> pdb=" O ALA F 291 " (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 392 through 404 Processing helix chain 'F' and resid 412 through 424 removed outlier: 4.266A pdb=" N GLU F 419 " --> pdb=" O ALA F 416 " (cutoff:3.500A) Processing helix chain 'F' and resid 432 through 447 removed outlier: 4.077A pdb=" N ASP F 436 " --> pdb=" O LYS F 432 " (cutoff:3.500A) removed outlier: 4.713A pdb=" N VAL F 437 " --> pdb=" O HIS F 433 " (cutoff:3.500A) Processing helix chain 'F' and resid 453 through 467 Processing helix chain 'F' and resid 480 through 489 removed outlier: 3.538A pdb=" N LEU F 487 " --> pdb=" O ALA F 483 " (cutoff:3.500A) Processing helix chain 'F' and resid 495 through 510 Processing helix chain 'F' and resid 529 through 540 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 580 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 613 through 618 removed outlier: 5.559A pdb=" N ASN F 618 " --> pdb=" O GLU F 614 " (cutoff:3.500A) Processing helix chain 'F' and resid 647 through 652 removed outlier: 3.942A pdb=" N ARG F 652 " --> pdb=" O PRO F 648 " (cutoff:3.500A) Processing helix chain 'F' and resid 666 through 672 removed outlier: 3.680A pdb=" N ARG F 672 " --> pdb=" O ALA F 668 " (cutoff:3.500A) Processing helix chain 'F' and resid 674 through 682 removed outlier: 3.565A pdb=" N ALA F 680 " --> pdb=" O PRO F 676 " (cutoff:3.500A) Processing helix chain 'F' and resid 693 through 702 Processing helix chain 'F' and resid 710 through 728 removed outlier: 3.857A pdb=" N LYS F 714 " --> pdb=" O ARG F 710 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N GLN F 715 " --> pdb=" O ASN F 711 " (cutoff:3.500A) Processing helix chain 'F' and resid 742 through 746 Processing helix chain 'F' and resid 808 through 828 removed outlier: 3.663A pdb=" N MET F 826 " --> pdb=" O ARG F 822 " (cutoff:3.500A) Processing helix chain 'F' and resid 850 through 869 Proline residue: F 854 - end of helix removed outlier: 4.483A pdb=" N CYS F 858 " --> pdb=" O SER F 855 " (cutoff:3.500A) removed outlier: 4.277A pdb=" N LEU F 864 " --> pdb=" O VAL F 861 " (cutoff:3.500A) Processing helix chain 'F' and resid 895 through 905 removed outlier: 4.329A pdb=" N ARG F 904 " --> pdb=" O ILE F 900 " (cutoff:3.500A) removed outlier: 4.137A pdb=" N ALA F 905 " --> pdb=" O ALA F 901 " (cutoff:3.500A) Processing helix chain 'F' and resid 914 through 921 removed outlier: 3.598A pdb=" N LYS F 917 " --> pdb=" O ALA F 914 " (cutoff:3.500A) removed outlier: 5.453A 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: 3.720A pdb=" N PHE F 943 " --> pdb=" O ARG F 940 " (cutoff:3.500A) removed outlier: 4.222A 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 544 through 548 removed outlier: 6.021A pdb=" N LEU A 586 " --> pdb=" O PHE A 545 " (cutoff:3.500A) removed outlier: 7.224A pdb=" N PHE A 547 " --> pdb=" O LEU A 586 " (cutoff:3.500A) removed outlier: 6.047A pdb=" N LEU A 588 " --> pdb=" O PHE A 547 " (cutoff:3.500A) No H-bonds generated for sheet with id= C Processing sheet with id= D, first strand: chain 'A' and resid 764 through 769 removed outlier: 6.920A pdb=" N GLU A 801 " --> pdb=" O LEU A 842 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 140 through 142 Processing sheet with id= F, first strand: chain 'B' and resid 163 through 167 Processing sheet with id= G, first strand: chain 'B' and resid 765 through 770 Processing sheet with id= H, first strand: chain 'B' and resid 781 through 783 Processing sheet with id= I, first strand: chain 'C' and resid 140 through 142 Processing sheet with id= J, first strand: chain 'C' and resid 188 through 191 Processing sheet with id= K, first strand: chain 'C' and resid 544 through 548 removed outlier: 5.657A pdb=" N LEU C 586 " --> pdb=" O PHE C 545 " (cutoff:3.500A) removed outlier: 7.482A pdb=" N PHE C 547 " --> pdb=" O LEU C 586 " (cutoff:3.500A) removed outlier: 6.194A pdb=" N LEU C 588 " --> pdb=" O PHE C 547 " (cutoff:3.500A) No H-bonds generated for sheet with id= K Processing sheet with id= L, first strand: chain 'C' and resid 767 through 769 Processing sheet with id= M, first strand: chain 'C' and resid 780 through 784 Processing sheet with id= N, first strand: chain 'D' and resid 140 through 142 Processing sheet with id= O, first strand: chain 'D' and resid 188 through 191 Processing sheet with id= P, first strand: chain 'D' and resid 544 through 548 removed outlier: 6.282A pdb=" N LEU D 586 " --> pdb=" O PHE D 545 " (cutoff:3.500A) removed outlier: 7.506A pdb=" N PHE D 547 " --> pdb=" O LEU D 586 " (cutoff:3.500A) removed outlier: 5.947A pdb=" N LEU D 588 " --> pdb=" O PHE D 547 " (cutoff:3.500A) No H-bonds generated for sheet with id= P Processing sheet with id= Q, first strand: chain 'D' and resid 689 through 691 removed outlier: 7.370A pdb=" N VAL D 735 " --> pdb=" O LYS D 690 " (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 'D' and resid 910 through 913 Processing sheet with id= T, first strand: chain 'E' and resid 140 through 142 Processing sheet with id= U, first strand: chain 'E' and resid 188 through 191 Processing sheet with id= V, first strand: chain 'E' and resid 544 through 548 removed outlier: 6.163A pdb=" N LEU E 586 " --> pdb=" O PHE E 545 " (cutoff:3.500A) removed outlier: 7.987A pdb=" N PHE E 547 " --> pdb=" O LEU E 586 " (cutoff:3.500A) removed outlier: 6.616A pdb=" N LEU E 588 " --> pdb=" O PHE E 547 " (cutoff:3.500A) No H-bonds generated for sheet with id= V Processing sheet with id= W, first strand: chain 'E' and resid 689 through 691 removed outlier: 6.786A pdb=" N VAL E 735 " --> pdb=" O LYS E 690 " (cutoff:3.500A) No H-bonds generated for sheet with id= W Processing sheet with id= X, first strand: chain 'E' and resid 764 through 769 removed outlier: 3.696A pdb=" N VAL E 765 " --> pdb=" O VAL E 780 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N VAL E 780 " --> pdb=" O VAL E 765 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N VAL E 844 " --> pdb=" O THR E 803 " (cutoff:3.500A) Processing sheet with id= Y, first strand: chain 'E' and resid 911 through 913 removed outlier: 6.617A pdb=" N HIS E 934 " --> pdb=" O LEU E 912 " (cutoff:3.500A) No H-bonds generated for sheet with id= Y Processing sheet with id= Z, first strand: chain 'F' and resid 140 through 142 Processing sheet with id= AA, first strand: chain 'F' and resid 164 through 166 Processing sheet with id= AB, first strand: chain 'F' and resid 520 through 522 removed outlier: 6.757A pdb=" N CYS F 637 " --> pdb=" O PHE F 521 " (cutoff:3.500A) No H-bonds generated for sheet with id= AB Processing sheet with id= AC, first strand: chain 'F' and resid 544 through 548 removed outlier: 6.372A pdb=" N LEU F 586 " --> pdb=" O PHE F 545 " (cutoff:3.500A) removed outlier: 7.291A pdb=" N PHE F 547 " --> pdb=" O LEU F 586 " (cutoff:3.500A) removed outlier: 5.848A pdb=" N LEU F 588 " --> pdb=" O PHE F 547 " (cutoff:3.500A) No H-bonds generated for sheet with id= AC Processing sheet with id= AD, first strand: chain 'F' and resid 764 through 766 Processing sheet with id= AE, first strand: chain 'F' and resid 909 through 913 removed outlier: 6.596A pdb=" N GLU F 932 " --> pdb=" O ILE F 910 " (cutoff:3.500A) removed outlier: 8.284A pdb=" N LEU F 912 " --> pdb=" O GLU F 932 " (cutoff:3.500A) removed outlier: 6.621A pdb=" N HIS F 934 " --> pdb=" O LEU F 912 " (cutoff:3.500A) No H-bonds generated for sheet with id= AE 1328 hydrogen bonds defined for protein. 3279 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: 25.27 Time building geometry restraints manager: 48.14 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.83 - 1.03: 37443 1.03 - 1.23: 371 1.23 - 1.42: 14781 1.42 - 1.62: 22320 1.62 - 1.82: 282 Bond restraints: 75197 Sorted by residual: bond pdb=" C4 ATP F1001 " pdb=" C5 ATP F1001 " ideal model delta sigma weight residual 1.388 1.465 -0.077 1.00e-02 1.00e+04 5.95e+01 bond pdb=" C4 ATP B1001 " pdb=" N9 ATP B1001 " ideal model delta sigma weight residual 1.374 1.297 0.077 1.00e-02 1.00e+04 5.87e+01 bond pdb=" C5 ATP E1001 " pdb=" N7 ATP E1001 " ideal model delta sigma weight residual 1.387 1.310 0.077 1.00e-02 1.00e+04 5.86e+01 bond pdb=" C5 ATP A1001 " pdb=" N7 ATP A1001 " ideal model delta sigma weight residual 1.387 1.316 0.071 1.00e-02 1.00e+04 5.03e+01 bond pdb=" C4 ATP E1001 " pdb=" N9 ATP E1001 " ideal model delta sigma weight residual 1.374 1.304 0.070 1.00e-02 1.00e+04 4.90e+01 ... (remaining 75192 not shown) Histogram of bond angle deviations from ideal: 76.58 - 88.67: 12 88.67 - 100.76: 48 100.76 - 112.86: 89924 112.86 - 124.95: 43117 124.95 - 137.04: 3433 Bond angle restraints: 136534 Sorted by residual: angle pdb=" PB ATP A1001 " pdb=" O3B ATP A1001 " pdb=" PG ATP A1001 " ideal model delta sigma weight residual 139.87 111.24 28.63 1.00e+00 1.00e+00 8.20e+02 angle pdb=" PB ATP F1001 " pdb=" O3B ATP F1001 " pdb=" PG ATP F1001 " ideal model delta sigma weight residual 139.87 113.74 26.13 1.00e+00 1.00e+00 6.83e+02 angle pdb=" PA ATP E1001 " pdb=" O3A ATP E1001 " pdb=" PB ATP E1001 " ideal model delta sigma weight residual 136.83 111.62 25.21 1.00e+00 1.00e+00 6.36e+02 angle pdb=" PA ATP C1001 " pdb=" O3A ATP C1001 " pdb=" PB ATP C1001 " ideal model delta sigma weight residual 136.83 112.19 24.64 1.00e+00 1.00e+00 6.07e+02 angle pdb=" PA ATP A1001 " pdb=" O3A ATP A1001 " pdb=" PB ATP A1001 " ideal model delta sigma weight residual 136.83 112.49 24.34 1.00e+00 1.00e+00 5.92e+02 ... (remaining 136529 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 19.67: 27650 19.67 - 39.34: 1868 39.34 - 59.01: 245 59.01 - 78.68: 43 78.68 - 98.35: 21 Dihedral angle restraints: 29827 sinusoidal: 14555 harmonic: 15272 Sorted by residual: dihedral pdb=" CA PRO E 762 " pdb=" C PRO E 762 " pdb=" N GLY E 763 " pdb=" CA GLY E 763 " ideal model delta harmonic sigma weight residual -180.00 -149.45 -30.55 0 5.00e+00 4.00e-02 3.73e+01 dihedral pdb=" O1B ADP D1001 " pdb=" O3A ADP D1001 " pdb=" PB ADP D1001 " pdb=" PA ADP D1001 " ideal model delta sinusoidal sigma weight residual -60.00 38.35 -98.35 1 2.00e+01 2.50e-03 2.75e+01 dihedral pdb=" CA ILE D 727 " pdb=" C ILE D 727 " pdb=" N VAL D 728 " pdb=" CA VAL D 728 " ideal model delta harmonic sigma weight residual 180.00 -154.60 -25.40 0 5.00e+00 4.00e-02 2.58e+01 ... (remaining 29824 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.056: 3697 0.056 - 0.113: 1638 0.113 - 0.169: 420 0.169 - 0.226: 75 0.226 - 0.282: 13 Chirality restraints: 5843 Sorted by residual: chirality pdb=" CB VAL C 907 " pdb=" CA VAL C 907 " pdb=" CG1 VAL C 907 " pdb=" CG2 VAL C 907 " both_signs ideal model delta sigma weight residual False -2.63 -2.35 -0.28 2.00e-01 2.50e+01 1.99e+00 chirality pdb=" C2' ATP A1001 " pdb=" C1' ATP A1001 " pdb=" C3' ATP A1001 " pdb=" O2' ATP A1001 " both_signs ideal model delta sigma weight residual False -2.68 -2.42 -0.26 2.00e-01 2.50e+01 1.73e+00 chirality pdb=" C2' ATP C1001 " pdb=" C1' ATP C1001 " pdb=" C3' ATP C1001 " pdb=" O2' ATP C1001 " both_signs ideal model delta sigma weight residual False -2.68 -2.42 -0.26 2.00e-01 2.50e+01 1.73e+00 ... (remaining 5840 not shown) Planarity restraints: 10956 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASP F 302 " 0.027 2.00e-02 2.50e+03 5.38e-02 2.90e+01 pdb=" C ASP F 302 " -0.093 2.00e-02 2.50e+03 pdb=" O ASP F 302 " 0.034 2.00e-02 2.50e+03 pdb=" N ILE F 303 " 0.032 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU D 608 " -0.025 2.00e-02 2.50e+03 5.07e-02 2.57e+01 pdb=" C LEU D 608 " 0.088 2.00e-02 2.50e+03 pdb=" O LEU D 608 " -0.033 2.00e-02 2.50e+03 pdb=" N GLU D 609 " -0.030 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ARG A 301 " 0.025 2.00e-02 2.50e+03 5.05e-02 2.55e+01 pdb=" C ARG A 301 " -0.087 2.00e-02 2.50e+03 pdb=" O ARG A 301 " 0.032 2.00e-02 2.50e+03 pdb=" N ASP A 302 " 0.030 2.00e-02 2.50e+03 ... (remaining 10953 not shown) Histogram of nonbonded interaction distances: 1.66 - 2.25: 8547 2.25 - 2.83: 163708 2.83 - 3.42: 184484 3.42 - 4.01: 235489 4.01 - 4.60: 369501 Nonbonded interactions: 961729 Sorted by model distance: nonbonded pdb="HH22 ARG C 822 " pdb=" O VAL C 836 " model vdw 1.657 1.850 nonbonded pdb=" OD1 ASP E 629 " pdb=" H SER E 631 " model vdw 1.660 1.850 nonbonded pdb=" H GLY E 471 " pdb=" OE1 GLU E 583 " model vdw 1.671 1.850 nonbonded pdb=" OE1 GLU E 557 " pdb=" H GLU E 557 " model vdw 1.679 1.850 nonbonded pdb=" O GLN F 743 " pdb=" H GLY F 747 " model vdw 1.679 1.850 ... (remaining 961724 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 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: 5.860 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: 0.830 Extract box with map and model: 17.780 Check model and map are aligned: 0.820 Set scattering table: 0.490 Process input model: 171.680 Find NCS groups from input model: 3.230 Set up NCS constraints: 0.230 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.020 Load rotamer database and sin/cos tables:2.280 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 203.230 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7992 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 : 0.013 0.125 37712 Z= 0.822 Angle : 1.313 28.627 50953 Z= 0.784 Chirality : 0.066 0.282 5843 Planarity : 0.009 0.093 6532 Dihedral : 13.351 98.354 14430 Min Nonbonded Distance : 1.977 Molprobity Statistics. All-atom Clashscore : 5.18 Ramachandran Plot: Outliers : 0.02 % Allowed : 7.56 % Favored : 92.42 % Rotamer Outliers : 0.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % 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: -2.18 (0.12), residues: 4632 helix: -1.97 (0.08), residues: 2034 sheet: -3.79 (0.19), residues: 493 loop : 0.05 (0.15), residues: 2105 *********************** 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 197 residues out of total 4050 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 191 time to evaluate : 4.317 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: 6 outliers final: 0 residues processed: 197 average time/residue: 0.8892 time to fit residues: 295.6696 Evaluate side-chains 164 residues out of total 4050 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 164 time to evaluate : 4.281 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 5.7007 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 463 random chunks: chunk 390 optimal weight: 8.9990 chunk 350 optimal weight: 3.9990 chunk 194 optimal weight: 0.5980 chunk 119 optimal weight: 0.6980 chunk 236 optimal weight: 10.0000 chunk 187 optimal weight: 0.9990 chunk 362 optimal weight: 0.6980 chunk 140 optimal weight: 10.0000 chunk 220 optimal weight: 2.9990 chunk 270 optimal weight: 2.9990 chunk 420 optimal weight: 0.6980 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 433 HIS B 541 ASN ** B 788 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 600 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 805 GLN ** F 399 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7906 moved from start: 0.0850 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.052 37712 Z= 0.166 Angle : 0.597 7.768 50953 Z= 0.313 Chirality : 0.039 0.154 5843 Planarity : 0.004 0.045 6532 Dihedral : 6.360 102.891 5094 Min Nonbonded Distance : 2.009 Molprobity Statistics. All-atom Clashscore : 7.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.79 % Favored : 95.21 % 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: -1.31 (0.12), residues: 4632 helix: -0.59 (0.10), residues: 2036 sheet: -3.52 (0.19), residues: 503 loop : -0.20 (0.15), residues: 2093 *********************** 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 177 residues out of total 4050 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 166 time to evaluate : 4.423 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 11 outliers final: 6 residues processed: 173 average time/residue: 0.9160 time to fit residues: 271.5659 Evaluate side-chains 161 residues out of total 4050 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 155 time to evaluate : 4.286 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.6868 time to fit residues: 13.3516 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 463 random chunks: chunk 233 optimal weight: 9.9990 chunk 130 optimal weight: 5.9990 chunk 349 optimal weight: 2.9990 chunk 286 optimal weight: 7.9990 chunk 115 optimal weight: 3.9990 chunk 421 optimal weight: 6.9990 chunk 455 optimal weight: 5.9990 chunk 375 optimal weight: 4.9990 chunk 417 optimal weight: 1.9990 chunk 143 optimal weight: 8.9990 chunk 337 optimal weight: 8.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 433 HIS B 433 HIS B 541 ASN ** B 788 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 600 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 399 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7950 moved from start: 0.1065 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.062 37712 Z= 0.338 Angle : 0.585 6.657 50953 Z= 0.311 Chirality : 0.040 0.141 5843 Planarity : 0.004 0.045 6532 Dihedral : 6.058 98.428 5094 Min Nonbonded Distance : 1.665 Molprobity Statistics. All-atom Clashscore : 9.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.63 % Favored : 94.37 % 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: -1.24 (0.12), residues: 4632 helix: -0.18 (0.11), residues: 2031 sheet: -3.43 (0.20), residues: 492 loop : -0.62 (0.14), residues: 2109 *********************** 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 172 residues out of total 4050 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 160 time to evaluate : 4.408 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: 12 outliers final: 7 residues processed: 170 average time/residue: 0.9111 time to fit residues: 268.6918 Evaluate side-chains 163 residues out of total 4050 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 156 time to evaluate : 4.336 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.6737 time to fit residues: 14.5617 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 463 random chunks: chunk 416 optimal weight: 0.5980 chunk 316 optimal weight: 6.9990 chunk 218 optimal weight: 5.9990 chunk 46 optimal weight: 2.9990 chunk 201 optimal weight: 3.9990 chunk 282 optimal weight: 4.9990 chunk 422 optimal weight: 7.9990 chunk 447 optimal weight: 9.9990 chunk 220 optimal weight: 3.9990 chunk 400 optimal weight: 0.0670 chunk 120 optimal weight: 2.9990 overall best weight: 2.1324 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 541 ASN ** B 788 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 600 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 399 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7917 moved from start: 0.1246 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.032 37712 Z= 0.185 Angle : 0.522 8.591 50953 Z= 0.270 Chirality : 0.038 0.147 5843 Planarity : 0.003 0.037 6532 Dihedral : 5.705 99.879 5094 Min Nonbonded Distance : 1.715 Molprobity Statistics. All-atom Clashscore : 8.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.25 % Favored : 95.75 % 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: -0.94 (0.13), residues: 4632 helix: 0.21 (0.11), residues: 2028 sheet: -3.27 (0.20), residues: 513 loop : -0.60 (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 169 residues out of total 4050 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 163 time to evaluate : 4.503 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: 6 outliers final: 3 residues processed: 168 average time/residue: 0.8808 time to fit residues: 254.2060 Evaluate side-chains 162 residues out of total 4050 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 159 time to evaluate : 4.297 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.6744 time to fit residues: 9.3656 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 463 random chunks: chunk 372 optimal weight: 4.9990 chunk 254 optimal weight: 10.0000 chunk 6 optimal weight: 20.0000 chunk 333 optimal weight: 9.9990 chunk 184 optimal weight: 6.9990 chunk 381 optimal weight: 4.9990 chunk 309 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 chunk 228 optimal weight: 1.9990 chunk 401 optimal weight: 20.0000 chunk 112 optimal weight: 3.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 541 ASN ** B 788 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 600 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 399 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7964 moved from start: 0.1410 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.073 37712 Z= 0.372 Angle : 0.579 7.642 50953 Z= 0.307 Chirality : 0.040 0.140 5843 Planarity : 0.004 0.042 6532 Dihedral : 5.747 98.075 5094 Min Nonbonded Distance : 1.652 Molprobity Statistics. All-atom Clashscore : 10.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.33 % Favored : 93.67 % 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: -1.20 (0.12), residues: 4632 helix: 0.15 (0.11), residues: 2020 sheet: -3.27 (0.21), residues: 522 loop : -0.94 (0.14), residues: 2090 *********************** 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 170 residues out of total 4050 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 161 time to evaluate : 4.305 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: 9 outliers final: 3 residues processed: 170 average time/residue: 0.9054 time to fit residues: 261.9842 Evaluate side-chains 160 residues out of total 4050 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 157 time to evaluate : 4.269 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.6799 time to fit residues: 9.4752 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 463 random chunks: chunk 150 optimal weight: 9.9990 chunk 403 optimal weight: 9.9990 chunk 88 optimal weight: 4.9990 chunk 262 optimal weight: 6.9990 chunk 110 optimal weight: 0.8980 chunk 447 optimal weight: 7.9990 chunk 371 optimal weight: 1.9990 chunk 207 optimal weight: 4.9990 chunk 37 optimal weight: 1.9990 chunk 148 optimal weight: 9.9990 chunk 235 optimal weight: 7.9990 overall best weight: 2.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 541 ASN ** B 788 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 600 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 399 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7939 moved from start: 0.1524 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.038 37712 Z= 0.237 Angle : 0.520 7.774 50953 Z= 0.271 Chirality : 0.038 0.145 5843 Planarity : 0.003 0.038 6532 Dihedral : 5.570 98.955 5094 Min Nonbonded Distance : 1.691 Molprobity Statistics. All-atom Clashscore : 9.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.94 % Favored : 95.06 % Rotamer Outliers : 0.25 % 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: -0.96 (0.13), residues: 4632 helix: 0.40 (0.12), residues: 2011 sheet: -3.15 (0.21), residues: 505 loop : -0.89 (0.14), residues: 2116 *********************** 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 170 residues out of total 4050 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 160 time to evaluate : 5.413 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: 10 outliers final: 4 residues processed: 170 average time/residue: 0.8674 time to fit residues: 254.6782 Evaluate side-chains 159 residues out of total 4050 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 155 time to evaluate : 4.348 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.6691 time to fit residues: 10.6747 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 463 random chunks: chunk 431 optimal weight: 3.9990 chunk 50 optimal weight: 0.6980 chunk 255 optimal weight: 6.9990 chunk 327 optimal weight: 8.9990 chunk 253 optimal weight: 10.0000 chunk 377 optimal weight: 2.9990 chunk 250 optimal weight: 30.0000 chunk 446 optimal weight: 4.9990 chunk 279 optimal weight: 3.9990 chunk 272 optimal weight: 2.9990 chunk 206 optimal weight: 1.9990 overall best weight: 2.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 541 ASN ** B 788 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 600 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 399 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7934 moved from start: 0.1628 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.039 37712 Z= 0.218 Angle : 0.507 9.608 50953 Z= 0.262 Chirality : 0.038 0.145 5843 Planarity : 0.003 0.037 6532 Dihedral : 5.396 97.769 5094 Min Nonbonded Distance : 1.718 Molprobity Statistics. All-atom Clashscore : 9.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.53 % Favored : 94.47 % Rotamer Outliers : 0.05 % 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: 0.52 (0.12), residues: 2014 sheet: -3.05 (0.21), residues: 496 loop : -0.87 (0.14), residues: 2122 *********************** 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 165 residues out of total 4050 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 163 time to evaluate : 4.369 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: 2 outliers final: 1 residues processed: 165 average time/residue: 0.8821 time to fit residues: 250.2780 Evaluate side-chains 160 residues out of total 4050 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 159 time to evaluate : 4.288 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.6410 time to fit residues: 6.9900 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 463 random chunks: chunk 276 optimal weight: 0.0980 chunk 178 optimal weight: 5.9990 chunk 266 optimal weight: 3.9990 chunk 134 optimal weight: 4.9990 chunk 87 optimal weight: 0.0370 chunk 86 optimal weight: 6.9990 chunk 283 optimal weight: 2.9990 chunk 304 optimal weight: 3.9990 chunk 220 optimal weight: 3.9990 chunk 41 optimal weight: 2.9990 chunk 350 optimal weight: 0.9990 overall best weight: 1.4264 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 541 ASN ** B 788 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 399 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7909 moved from start: 0.1728 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.028 37712 Z= 0.148 Angle : 0.484 9.784 50953 Z= 0.247 Chirality : 0.038 0.149 5843 Planarity : 0.003 0.035 6532 Dihedral : 5.199 97.035 5094 Min Nonbonded Distance : 1.774 Molprobity Statistics. All-atom Clashscore : 8.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.02 % Favored : 95.98 % 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: -0.62 (0.13), residues: 4632 helix: 0.74 (0.12), residues: 2011 sheet: -3.00 (0.21), residues: 505 loop : -0.78 (0.14), residues: 2116 *********************** 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 168 residues out of total 4050 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 164 time to evaluate : 4.328 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: 4 outliers final: 3 residues processed: 168 average time/residue: 0.8528 time to fit residues: 246.7472 Evaluate side-chains 161 residues out of total 4050 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 158 time to evaluate : 4.260 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.6664 time to fit residues: 9.3474 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 463 random chunks: chunk 405 optimal weight: 6.9990 chunk 427 optimal weight: 6.9990 chunk 390 optimal weight: 30.0000 chunk 415 optimal weight: 9.9990 chunk 250 optimal weight: 30.0000 chunk 181 optimal weight: 1.9990 chunk 326 optimal weight: 10.0000 chunk 127 optimal weight: 2.9990 chunk 375 optimal weight: 0.9990 chunk 393 optimal weight: 4.9990 chunk 414 optimal weight: 5.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 541 ASN ** B 788 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 805 GLN ** F 399 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7939 moved from start: 0.1774 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.048 37712 Z= 0.274 Angle : 0.515 10.514 50953 Z= 0.267 Chirality : 0.038 0.143 5843 Planarity : 0.003 0.036 6532 Dihedral : 5.195 95.763 5094 Min Nonbonded Distance : 1.704 Molprobity Statistics. All-atom Clashscore : 9.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.59 % Favored : 94.41 % 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: -0.72 (0.13), residues: 4632 helix: 0.68 (0.12), residues: 2015 sheet: -2.89 (0.22), residues: 504 loop : -0.90 (0.14), residues: 2113 *********************** 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 161 residues out of total 4050 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 158 time to evaluate : 4.455 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: 3 outliers final: 1 residues processed: 161 average time/residue: 0.9096 time to fit residues: 251.9266 Evaluate side-chains 157 residues out of total 4050 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 156 time to evaluate : 4.344 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.6778 time to fit residues: 7.0898 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 463 random chunks: chunk 273 optimal weight: 3.9990 chunk 439 optimal weight: 2.9990 chunk 268 optimal weight: 3.9990 chunk 208 optimal weight: 1.9990 chunk 305 optimal weight: 0.5980 chunk 461 optimal weight: 2.9990 chunk 424 optimal weight: 4.9990 chunk 367 optimal weight: 5.9990 chunk 38 optimal weight: 4.9990 chunk 283 optimal weight: 1.9990 chunk 225 optimal weight: 5.9990 overall best weight: 2.1188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 541 ASN ** B 788 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 399 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 433 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7920 moved from start: 0.1838 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.032 37712 Z= 0.184 Angle : 0.489 10.946 50953 Z= 0.251 Chirality : 0.038 0.146 5843 Planarity : 0.003 0.035 6532 Dihedral : 5.083 95.973 5094 Min Nonbonded Distance : 1.726 Molprobity Statistics. All-atom Clashscore : 9.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.47 % Favored : 95.53 % Rotamer Outliers : 0.05 % 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: -0.60 (0.13), residues: 4632 helix: 0.80 (0.12), residues: 2013 sheet: -2.91 (0.22), residues: 508 loop : -0.83 (0.14), residues: 2111 ********************** 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 161 residues out of total 4050 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 159 time to evaluate : 4.402 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 outliers start: 2 outliers final: 1 residues processed: 161 average time/residue: 0.8774 time to fit residues: 242.4622 Evaluate side-chains 157 residues out of total 4050 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 156 time to evaluate : 4.312 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.7825 time to fit residues: 7.0178 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 463 random chunks: chunk 291 optimal weight: 3.9990 chunk 391 optimal weight: 20.0000 chunk 112 optimal weight: 2.9990 chunk 338 optimal weight: 10.0000 chunk 54 optimal weight: 2.9990 chunk 102 optimal weight: 2.9990 chunk 367 optimal weight: 5.9990 chunk 153 optimal weight: 0.9980 chunk 377 optimal weight: 1.9990 chunk 46 optimal weight: 0.9980 chunk 67 optimal weight: 2.9990 overall best weight: 1.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 541 ASN ** B 788 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 399 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4154 r_free = 0.4154 target = 0.137311 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.089063 restraints weight = 275252.690| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.093161 restraints weight = 129397.266| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.093947 restraints weight = 64104.899| |-----------------------------------------------------------------------------| r_work (final): 0.3375 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7959 moved from start: 0.1922 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.033 37712 Z= 0.184 Angle : 0.483 10.930 50953 Z= 0.247 Chirality : 0.038 0.147 5843 Planarity : 0.003 0.035 6532 Dihedral : 4.941 94.490 5094 Min Nonbonded Distance : 1.730 Molprobity Statistics. All-atom Clashscore : 8.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.18 % Favored : 94.82 % Rotamer Outliers : 0.05 % 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: -0.52 (0.13), residues: 4632 helix: 0.89 (0.12), residues: 2015 sheet: -2.80 (0.22), residues: 510 loop : -0.83 (0.14), residues: 2107 =============================================================================== Job complete usr+sys time: 7967.58 seconds wall clock time: 141 minutes 20.86 seconds (8480.86 seconds total)