Starting phenix.real_space_refine on Sat Mar 16 20:31:35 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ng4_12307/03_2024/7ng4_12307_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ng4_12307/03_2024/7ng4_12307.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ng4_12307/03_2024/7ng4_12307.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ng4_12307/03_2024/7ng4_12307.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ng4_12307/03_2024/7ng4_12307_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ng4_12307/03_2024/7ng4_12307_trim_updated.pdb" } resolution = 4.4 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.004 sd= 0.051 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 16 5.49 5 Mg 4 5.21 5 S 162 5.16 5 C 23505 2.51 5 N 6447 2.21 5 O 7005 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 ARG 205": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 212": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 218": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A PHE 283": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ARG 301": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A TYR 310": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ARG 311": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 323": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A 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 ARG 205": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 212": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 218": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B PHE 283": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B ARG 301": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B TYR 310": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B ARG 311": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 323": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 381": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B GLU 406": "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 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 PHE 135": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" 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 TYR 310": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C ARG 311": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C ARG 323": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C ARG 381": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" 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 ARG 137": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D ARG 154": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D ARG 155": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D ARG 158": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D ARG 170": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D ARG 205": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D ARG 212": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D ARG 218": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D PHE 283": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D ARG 301": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D ARG 311": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D ARG 323": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D ARG 381": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D GLU 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 PHE 135": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E ARG 137": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "E ARG 154": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "E ARG 155": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "E ARG 158": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "E ARG 170": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "E ARG 205": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "E ARG 212": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "E ARG 218": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "E ARG 301": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "E TYR 310": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E ARG 311": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "E ARG 323": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "E TYR 360": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E ARG 381": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "E ASP 415": "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 PHE 135": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F ARG 137": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "F ARG 154": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "F ARG 155": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "F ARG 158": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "F ARG 170": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "F 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 GLU 295": "OE1" <-> "OE2" 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 410": "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: 0.13s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 74624 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: 105 Number of conformers: 1 Conformer: "" Number of residues, atoms: 21, 105 Classifications: {'peptide': 21} Incomplete info: {'truncation_to_alanine': 21} Link IDs: {'TRANS': 20} Unresolved non-hydrogen bonds: 42 Unresolved non-hydrogen angles: 63 Unresolved non-hydrogen dihedrals: 21 Planarities with less than four sites: {'UNK:plan-1': 21} Unresolved non-hydrogen planarities: 21 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: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "F" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 25.35, per 1000 atoms: 0.34 Number of scatterers: 74624 At special positions: 0 Unit cell: (136.284, 143.763, 226.032, 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 16 15.00 Mg 4 11.99 O 7005 8.00 N 6447 7.00 C 23505 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: 45.70 Conformation dependent library (CDL) restraints added in 5.9 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: 8778 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 190 helices and 30 sheets defined 44.5% alpha, 4.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 9.67 Creating SS restraints... Processing helix chain 'A' and resid 148 through 155 Processing helix chain 'A' and resid 175 through 180 Processing helix chain 'A' and resid 291 through 306 removed outlier: 3.848A pdb=" N GLU A 295 " --> pdb=" O ALA A 291 " (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 338 removed outlier: 3.866A pdb=" N LEU A 338 " --> pdb=" O MET A 334 " (cutoff:3.500A) Processing helix chain 'A' and resid 343 through 351 Processing helix chain 'A' and resid 355 through 407 removed outlier: 3.743A pdb=" N LEU A 372 " --> pdb=" O LYS A 368 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N LEU A 407 " --> pdb=" O ILE A 403 " (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: 4.263A 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: 3.615A pdb=" N SER A 729 " --> pdb=" O TYR A 725 " (cutoff:3.500A) Processing helix chain 'A' and resid 742 through 746 removed outlier: 3.952A 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: 3.875A 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: 4.714A 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: 4.226A pdb=" N ALA A 946 " --> pdb=" O PHE A 943 " (cutoff:3.500A) Processing helix chain 'B' and resid 148 through 155 removed outlier: 3.841A pdb=" N LEU B 152 " --> pdb=" O LYS B 148 " (cutoff:3.500A) Processing helix chain 'B' and resid 175 through 180 Processing helix chain 'B' and resid 291 through 306 removed outlier: 3.548A pdb=" N GLU B 295 " --> pdb=" O ALA B 291 " (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 337 Processing helix chain 'B' and resid 343 through 351 Processing helix chain 'B' and resid 355 through 388 Processing helix chain 'B' and resid 392 through 406 Processing helix chain 'B' and resid 413 through 424 Processing helix chain 'B' and resid 432 through 447 removed outlier: 3.594A pdb=" N ASP B 436 " --> pdb=" O LYS B 432 " (cutoff:3.500A) removed outlier: 4.449A 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: 3.926A pdb=" N ALA B 485 " --> pdb=" O ALA B 481 " (cutoff:3.500A) removed outlier: 3.715A 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 611 removed outlier: 3.571A pdb=" N LEU B 607 " --> pdb=" O SER B 604 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N LEU B 611 " --> pdb=" O LEU B 608 " (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: 3.743A pdb=" N LEU B 720 " --> pdb=" O VAL B 716 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N SER B 723 " --> pdb=" O VAL B 719 " (cutoff:3.500A) Processing helix chain 'B' and resid 739 through 745 removed outlier: 4.672A pdb=" N GLN B 743 " --> pdb=" O GLU B 740 " (cutoff:3.500A) Processing helix chain 'B' and resid 808 through 828 removed outlier: 3.621A pdb=" N GLU B 812 " --> pdb=" O GLU B 808 " (cutoff:3.500A) Processing helix chain 'B' and resid 834 through 837 No H-bonds generated for 'chain 'B' and resid 834 through 837' Processing helix chain 'B' and resid 850 through 869 Proline residue: B 854 - end of helix removed outlier: 4.319A pdb=" N CYS B 858 " --> pdb=" O SER B 855 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N VAL B 861 " --> pdb=" O CYS B 858 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N LEU B 865 " --> pdb=" O THR B 862 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N MET B 869 " --> pdb=" O SER B 866 " (cutoff:3.500A) Processing helix chain 'B' and resid 895 through 904 removed outlier: 4.025A pdb=" N ILE B 900 " --> pdb=" O LYS B 896 " (cutoff:3.500A) Processing helix chain 'B' and resid 914 through 921 removed outlier: 5.176A pdb=" N LYS B 918 " --> pdb=" O GLU B 915 " (cutoff:3.500A) removed outlier: 4.041A 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 157 removed outlier: 3.560A pdb=" N LEU C 152 " --> pdb=" O LYS C 148 " (cutoff:3.500A) Processing helix chain 'C' and resid 175 through 178 No H-bonds generated for 'chain 'C' and resid 175 through 178' Processing helix chain 'C' and resid 290 through 306 removed outlier: 3.765A pdb=" N VAL C 297 " --> pdb=" O ALA C 294 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N ILE C 304 " --> pdb=" O ARG C 301 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N ALA C 305 " --> pdb=" O ASP C 302 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N LEU C 306 " --> pdb=" O ILE C 303 " (cutoff:3.500A) Processing helix chain 'C' and resid 313 through 317 Processing helix chain 'C' and resid 328 through 336 Processing helix chain 'C' and resid 343 through 351 Processing helix chain 'C' and resid 355 through 406 removed outlier: 3.643A pdb=" N LEU C 372 " --> pdb=" O LYS C 368 " (cutoff:3.500A) Processing helix chain 'C' and resid 414 through 424 removed outlier: 3.653A pdb=" N GLU C 418 " --> pdb=" O LYS C 414 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N GLU C 419 " --> pdb=" O ASP C 415 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N PHE C 421 " --> pdb=" O ILE C 417 " (cutoff:3.500A) Processing helix chain 'C' and resid 432 through 447 removed outlier: 3.992A pdb=" N ASP C 436 " --> pdb=" O LYS C 432 " (cutoff:3.500A) removed outlier: 4.265A pdb=" N VAL C 437 " --> pdb=" O HIS C 433 " (cutoff:3.500A) Processing helix chain 'C' and resid 453 through 467 Processing helix chain 'C' and resid 481 through 488 removed outlier: 3.679A pdb=" N VAL C 486 " --> pdb=" O ARG C 482 " (cutoff:3.500A) Processing helix chain 'C' and resid 495 through 510 removed outlier: 3.688A pdb=" N LEU C 502 " --> pdb=" O LYS C 498 " (cutoff:3.500A) Processing helix chain 'C' and resid 532 through 540 Processing helix chain 'C' and resid 555 through 558 Processing helix chain 'C' and resid 572 through 579 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: 4.219A 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 652 removed outlier: 4.140A pdb=" N ARG C 652 " --> pdb=" O PRO C 648 " (cutoff:3.500A) Processing helix chain 'C' and resid 663 through 670 removed outlier: 3.932A 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: 4.148A pdb=" N GLN C 743 " --> pdb=" O GLU C 740 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N VAL C 746 " --> pdb=" O GLN C 743 " (cutoff:3.500A) Processing helix chain 'C' and resid 809 through 828 Processing helix chain 'C' and resid 850 through 869 Proline residue: C 854 - end of helix removed outlier: 4.415A pdb=" N CYS C 858 " --> pdb=" O SER C 855 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N VAL C 861 " --> pdb=" O CYS C 858 " (cutoff:3.500A) removed outlier: 3.796A 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: 4.591A pdb=" N LYS C 918 " --> pdb=" O GLU C 915 " (cutoff:3.500A) Processing helix chain 'C' and resid 939 through 946 removed outlier: 3.788A pdb=" N ALA C 946 " --> pdb=" O PHE C 943 " (cutoff:3.500A) Processing helix chain 'D' and resid 148 through 156 Processing helix chain 'D' and resid 175 through 180 Processing helix chain 'D' and resid 288 through 306 removed outlier: 4.096A pdb=" N LEU D 292 " --> pdb=" O VAL D 289 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N VAL D 297 " --> pdb=" O ALA D 294 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N ILE D 304 " --> pdb=" O ARG D 301 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N ALA D 305 " --> pdb=" O ASP D 302 " (cutoff:3.500A) removed outlier: 4.013A 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 328 through 337 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 407 removed outlier: 3.605A pdb=" N LEU D 407 " --> pdb=" O ILE D 403 " (cutoff:3.500A) Processing helix chain 'D' and resid 414 through 425 Processing helix chain 'D' and resid 432 through 435 No H-bonds generated for 'chain 'D' and resid 432 through 435' Processing helix chain 'D' and resid 437 through 447 removed outlier: 3.927A 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 511 removed outlier: 3.702A pdb=" N ARG D 511 " --> pdb=" O VAL D 507 " (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 611 removed outlier: 3.756A pdb=" N LEU D 607 " --> pdb=" O SER D 604 " (cutoff:3.500A) removed outlier: 4.241A pdb=" N LEU D 608 " --> pdb=" O SER D 605 " (cutoff:3.500A) Processing helix chain 'D' and resid 615 through 618 removed outlier: 3.762A pdb=" N ASN D 618 " --> pdb=" O GLN D 615 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 615 through 618' Processing helix chain 'D' and resid 647 through 651 Processing helix chain 'D' and resid 663 through 673 removed outlier: 3.917A pdb=" N LEU D 667 " --> pdb=" O ALA D 663 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N ALA D 668 " --> pdb=" O GLN D 664 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N GLU D 671 " --> pdb=" O LEU D 667 " (cutoff:3.500A) removed outlier: 4.356A 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: 4.359A pdb=" N GLN D 743 " --> pdb=" O GLU D 740 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N VAL D 746 " --> pdb=" O GLN D 743 " (cutoff:3.500A) Processing helix chain 'D' and resid 808 through 828 removed outlier: 3.612A 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: 4.212A pdb=" N CYS D 858 " --> pdb=" O SER D 855 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N VAL D 861 " --> pdb=" O CYS D 858 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N LEU D 865 " --> pdb=" O THR D 862 " (cutoff:3.500A) removed outlier: 3.967A 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: 4.465A pdb=" N LYS D 918 " --> pdb=" O GLU D 915 " (cutoff:3.500A) removed outlier: 3.687A 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: 4.387A pdb=" N ALA D 946 " --> pdb=" O PHE D 943 " (cutoff:3.500A) Processing helix chain 'E' and resid 148 through 157 removed outlier: 3.528A pdb=" N LEU E 152 " --> pdb=" O LYS E 148 " (cutoff:3.500A) Processing helix chain 'E' and resid 175 through 180 removed outlier: 3.662A pdb=" N VAL E 179 " --> pdb=" O GLU E 175 " (cutoff:3.500A) Processing helix chain 'E' and resid 291 through 306 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 338 removed outlier: 3.757A pdb=" N LEU E 338 " --> pdb=" O MET E 334 " (cutoff:3.500A) Processing helix chain 'E' and resid 343 through 351 Processing helix chain 'E' and resid 355 through 402 removed outlier: 3.523A pdb=" N LEU E 372 " --> pdb=" O LYS E 368 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N LYS E 393 " --> pdb=" O GLN E 389 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N TYR E 394 " --> pdb=" O THR E 390 " (cutoff:3.500A) Processing helix chain 'E' and resid 415 through 424 Processing helix chain 'E' and resid 432 through 447 removed outlier: 3.546A pdb=" N VAL E 437 " --> pdb=" O HIS E 433 " (cutoff:3.500A) removed outlier: 4.127A pdb=" N LEU E 447 " --> pdb=" O SER E 443 " (cutoff:3.500A) Processing helix chain 'E' and resid 453 through 467 Processing helix chain 'E' and resid 480 through 488 removed outlier: 3.985A 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 592 through 594 No H-bonds generated for 'chain 'E' and resid 592 through 594' Processing helix chain 'E' and resid 603 through 611 Processing helix chain 'E' and resid 613 through 618 removed outlier: 4.789A 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: 3.768A pdb=" N ARG E 652 " --> pdb=" O PRO E 648 " (cutoff:3.500A) Processing helix chain 'E' and resid 666 through 673 Processing helix chain 'E' and resid 675 through 682 Processing helix chain 'E' and resid 693 through 702 Processing helix chain 'E' and resid 711 through 728 removed outlier: 3.690A pdb=" N LYS E 726 " --> pdb=" O LYS E 722 " (cutoff:3.500A) Processing helix chain 'E' and resid 739 through 746 removed outlier: 3.522A pdb=" N LEU E 742 " --> pdb=" O PRO E 739 " (cutoff:3.500A) removed outlier: 4.472A pdb=" N GLN E 743 " --> pdb=" O GLU E 740 " (cutoff:3.500A) Processing helix chain 'E' and resid 808 through 828 removed outlier: 3.576A 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: 4.101A pdb=" N CYS E 858 " --> pdb=" O SER E 855 " (cutoff:3.500A) removed outlier: 4.004A 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: 4.160A pdb=" N LYS E 918 " --> pdb=" O GLU E 915 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N TYR E 921 " --> pdb=" O LYS E 918 " (cutoff:3.500A) Processing helix chain 'E' and resid 939 through 946 removed outlier: 3.741A pdb=" N PHE E 943 " --> pdb=" O ARG E 940 " (cutoff:3.500A) removed outlier: 4.106A pdb=" N ALA E 946 " --> pdb=" O PHE E 943 " (cutoff:3.500A) Processing helix chain 'F' and resid 148 through 155 Processing helix chain 'F' and resid 175 through 180 Processing helix chain 'F' and resid 291 through 306 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 336 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 425 removed outlier: 3.850A pdb=" N LYS F 420 " --> pdb=" O ALA F 416 " (cutoff:3.500A) Processing helix chain 'F' and resid 432 through 447 removed outlier: 3.632A pdb=" N ASP F 436 " --> pdb=" O LYS F 432 " (cutoff:3.500A) removed outlier: 4.693A 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 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: 5.353A pdb=" N ASN F 618 " --> pdb=" O GLU F 614 " (cutoff:3.500A) Processing helix chain 'F' and resid 647 through 652 removed outlier: 3.610A pdb=" N ARG F 652 " --> pdb=" O PRO F 648 " (cutoff:3.500A) Processing helix chain 'F' and resid 663 through 672 removed outlier: 4.043A pdb=" N LEU F 667 " --> pdb=" O ALA F 663 " (cutoff:3.500A) removed outlier: 5.254A pdb=" N ALA F 668 " --> pdb=" O GLN F 664 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N ILE F 669 " --> pdb=" O GLU F 665 " (cutoff:3.500A) Processing helix chain 'F' and resid 674 through 682 Processing helix chain 'F' and resid 686 through 688 No H-bonds generated for 'chain 'F' and resid 686 through 688' Processing helix chain 'F' and resid 693 through 703 Processing helix chain 'F' and resid 710 through 728 removed outlier: 3.930A pdb=" N LYS F 714 " --> pdb=" O ARG F 710 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N GLN F 715 " --> pdb=" O ASN F 711 " (cutoff:3.500A) Processing helix chain 'F' and resid 739 through 746 removed outlier: 4.211A pdb=" N GLN F 743 " --> pdb=" O PRO F 739 " (cutoff:3.500A) removed outlier: 5.514A pdb=" N ASP F 744 " --> pdb=" O GLU F 740 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N PHE F 745 " --> pdb=" O ASN F 741 " (cutoff:3.500A) Processing helix chain 'F' and resid 808 through 828 removed outlier: 3.626A 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: 4.475A pdb=" N CYS F 858 " --> pdb=" O SER F 855 " (cutoff:3.500A) removed outlier: 4.180A pdb=" N LEU F 864 " --> pdb=" O VAL F 861 " (cutoff:3.500A) Processing helix chain 'F' and resid 895 through 905 removed outlier: 4.197A pdb=" N ARG F 904 " --> pdb=" O ILE F 900 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N ALA F 905 " --> pdb=" O ALA F 901 " (cutoff:3.500A) Processing helix chain 'F' and resid 914 through 921 removed outlier: 5.487A 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: 3.715A pdb=" N PHE F 943 " --> pdb=" O ARG F 940 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N ALA F 946 " --> pdb=" O PHE F 943 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 140 through 142 Processing sheet with id= B, first strand: chain 'A' and resid 188 through 191 Processing sheet with id= C, first strand: chain 'A' and resid 520 through 522 removed outlier: 6.389A pdb=" N CYS A 637 " --> pdb=" O PHE A 521 " (cutoff:3.500A) No H-bonds generated for sheet with id= C Processing sheet with id= D, first strand: chain 'A' and resid 544 through 548 removed outlier: 5.916A pdb=" N LEU A 586 " --> pdb=" O PHE A 545 " (cutoff:3.500A) removed outlier: 7.024A pdb=" N PHE A 547 " --> pdb=" O LEU A 586 " (cutoff:3.500A) removed outlier: 6.027A pdb=" N LEU A 588 " --> pdb=" O PHE A 547 " (cutoff:3.500A) No H-bonds generated for sheet with id= D Processing sheet with id= E, first strand: chain 'A' and resid 764 through 769 removed outlier: 3.708A pdb=" N LEU A 842 " --> pdb=" O GLU A 801 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 140 through 142 Processing sheet with id= G, first strand: chain 'B' and resid 188 through 191 Processing sheet with id= H, first strand: chain 'B' and resid 517 through 520 removed outlier: 3.557A pdb=" N PHE B 635 " --> pdb=" O LYS B 517 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N LEU B 519 " --> pdb=" O PHE B 635 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'B' and resid 765 through 770 Processing sheet with id= J, first strand: chain 'B' and resid 781 through 783 Processing sheet with id= K, first strand: chain 'C' and resid 140 through 142 Processing sheet with id= L, first strand: chain 'C' and resid 188 through 191 Processing sheet with id= M, first strand: chain 'C' and resid 767 through 769 Processing sheet with id= N, first strand: chain 'C' and resid 780 through 784 Processing sheet with id= O, first strand: chain 'D' and resid 140 through 142 Processing sheet with id= P, first strand: chain 'D' and resid 163 through 166 Processing sheet with id= Q, first strand: chain 'D' and resid 544 through 548 removed outlier: 6.444A pdb=" N LEU D 586 " --> pdb=" O PHE D 545 " (cutoff:3.500A) removed outlier: 7.567A 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= 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 764 through 769 removed outlier: 3.768A pdb=" N VAL E 765 " --> pdb=" O VAL E 780 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N VAL E 780 " --> pdb=" O VAL E 765 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'E' and resid 911 through 913 removed outlier: 6.476A pdb=" N HIS E 934 " --> pdb=" O LEU E 912 " (cutoff:3.500A) No H-bonds generated for sheet with id= W Processing sheet with id= X, first strand: chain 'F' and resid 140 through 142 Processing sheet with id= Y, first strand: chain 'F' and resid 164 through 167 Processing sheet with id= Z, first strand: chain 'F' and resid 520 through 522 removed outlier: 6.989A pdb=" N CYS F 637 " --> pdb=" O PHE F 521 " (cutoff:3.500A) No H-bonds generated for sheet with id= Z Processing sheet with id= AA, first strand: chain 'F' and resid 544 through 548 removed outlier: 6.428A pdb=" N LEU F 586 " --> pdb=" O PHE F 545 " (cutoff:3.500A) removed outlier: 7.431A pdb=" N PHE F 547 " --> pdb=" O LEU F 586 " (cutoff:3.500A) removed outlier: 5.976A pdb=" N LEU F 588 " --> pdb=" O PHE F 547 " (cutoff:3.500A) No H-bonds generated for sheet with id= AA Processing sheet with id= AB, first strand: chain 'F' and resid 689 through 691 removed outlier: 7.209A pdb=" N VAL F 735 " --> pdb=" O LYS F 690 " (cutoff:3.500A) No H-bonds generated for sheet with id= AB Processing sheet with id= AC, first strand: chain 'F' and resid 764 through 766 Processing sheet with id= AD, first strand: chain 'F' and resid 909 through 913 removed outlier: 6.139A pdb=" N GLU F 932 " --> pdb=" O ILE F 910 " (cutoff:3.500A) removed outlier: 7.717A pdb=" N LEU F 912 " --> pdb=" O GLU F 932 " (cutoff:3.500A) removed outlier: 6.003A pdb=" N HIS F 934 " --> pdb=" O LEU F 912 " (cutoff:3.500A) No H-bonds generated for sheet with id= AD 1350 hydrogen bonds defined for protein. 3453 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: 25.60 Time building geometry restraints manager: 48.25 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.82 - 1.02: 37443 1.02 - 1.22: 90 1.22 - 1.42: 14990 1.42 - 1.63: 22438 1.63 - 1.83: 282 Bond restraints: 75243 Sorted by residual: bond pdb=" C4 ATP F1001 " pdb=" C5 ATP F1001 " ideal model delta sigma weight residual 1.388 1.463 -0.075 1.00e-02 1.00e+04 5.67e+01 bond pdb=" C4 ATP A1001 " pdb=" C5 ATP A1001 " ideal model delta sigma weight residual 1.388 1.460 -0.072 1.00e-02 1.00e+04 5.13e+01 bond pdb=" C5 ATP F1001 " pdb=" C6 ATP F1001 " ideal model delta sigma weight residual 1.409 1.479 -0.070 1.00e-02 1.00e+04 4.88e+01 bond pdb=" C4 ATP C1001 " pdb=" C5 ATP C1001 " ideal model delta sigma weight residual 1.388 1.450 -0.062 1.00e-02 1.00e+04 3.87e+01 bond pdb=" C5 ATP A1001 " pdb=" C6 ATP A1001 " ideal model delta sigma weight residual 1.409 1.471 -0.062 1.00e-02 1.00e+04 3.85e+01 ... (remaining 75238 not shown) Histogram of bond angle deviations from ideal: 76.88 - 89.09: 12 89.09 - 101.31: 90 101.31 - 113.52: 92294 113.52 - 125.74: 42474 125.74 - 137.95: 1727 Bond angle restraints: 136597 Sorted by residual: angle pdb=" PA ATP C1001 " pdb=" O3A ATP C1001 " pdb=" PB ATP C1001 " ideal model delta sigma weight residual 136.83 110.91 25.92 1.00e+00 1.00e+00 6.72e+02 angle pdb=" PB ATP B1001 " pdb=" O3B ATP B1001 " pdb=" PG ATP B1001 " ideal model delta sigma weight residual 139.87 114.66 25.21 1.00e+00 1.00e+00 6.36e+02 angle pdb=" PA ATP B1001 " pdb=" O3A ATP B1001 " pdb=" PB ATP B1001 " ideal model delta sigma weight residual 136.83 112.06 24.77 1.00e+00 1.00e+00 6.14e+02 angle pdb=" PA ATP A1001 " pdb=" O3A ATP A1001 " pdb=" PB ATP A1001 " ideal model delta sigma weight residual 136.83 112.78 24.05 1.00e+00 1.00e+00 5.79e+02 angle pdb=" PB ATP A1001 " pdb=" O3B ATP A1001 " pdb=" PG ATP A1001 " ideal model delta sigma weight residual 139.87 115.97 23.90 1.00e+00 1.00e+00 5.71e+02 ... (remaining 136592 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 27.34: 33389 27.34 - 54.68: 1427 54.68 - 82.02: 158 82.02 - 109.36: 20 109.36 - 136.70: 1 Dihedral angle restraints: 34995 sinusoidal: 19693 harmonic: 15302 Sorted by residual: dihedral pdb=" O2A ADP D1001 " pdb=" O3A ADP D1001 " pdb=" PA ADP D1001 " pdb=" PB ADP D1001 " ideal model delta sinusoidal sigma weight residual -60.00 76.70 -136.70 1 2.00e+01 2.50e-03 4.15e+01 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 -150.89 -29.11 0 5.00e+00 4.00e-02 3.39e+01 dihedral pdb=" CA LYS E 404 " pdb=" C LYS E 404 " pdb=" N LYS E 405 " pdb=" CA LYS E 405 " ideal model delta harmonic sigma weight residual 180.00 152.09 27.91 0 5.00e+00 4.00e-02 3.12e+01 ... (remaining 34992 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.090: 4921 0.090 - 0.181: 877 0.181 - 0.271: 50 0.271 - 0.362: 4 0.362 - 0.452: 1 Chirality restraints: 5853 Sorted by residual: chirality pdb=" CG LEU A 395 " pdb=" CB LEU A 395 " pdb=" CD1 LEU A 395 " pdb=" CD2 LEU A 395 " both_signs ideal model delta sigma weight residual False -2.59 -2.14 -0.45 2.00e-01 2.50e+01 5.11e+00 chirality pdb=" CB THR F 299 " pdb=" CA THR F 299 " pdb=" OG1 THR F 299 " pdb=" CG2 THR F 299 " both_signs ideal model delta sigma weight residual False 2.55 2.25 0.31 2.00e-01 2.50e+01 2.35e+00 chirality pdb=" CB ILE E 402 " pdb=" CA ILE E 402 " pdb=" CG1 ILE E 402 " pdb=" CG2 ILE E 402 " both_signs ideal model delta sigma weight residual False 2.64 2.93 -0.29 2.00e-01 2.50e+01 2.08e+00 ... (remaining 5850 not shown) Planarity restraints: 10966 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ARG E 301 " -0.028 2.00e-02 2.50e+03 5.61e-02 3.15e+01 pdb=" C ARG E 301 " 0.097 2.00e-02 2.50e+03 pdb=" O ARG E 301 " -0.036 2.00e-02 2.50e+03 pdb=" N ASP E 302 " -0.033 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR E 803 " 0.027 2.00e-02 2.50e+03 5.47e-02 2.99e+01 pdb=" C THR E 803 " -0.095 2.00e-02 2.50e+03 pdb=" O THR E 803 " 0.036 2.00e-02 2.50e+03 pdb=" N GLY E 804 " 0.032 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LYS A 298 " 0.025 2.00e-02 2.50e+03 5.09e-02 2.59e+01 pdb=" C LYS A 298 " -0.088 2.00e-02 2.50e+03 pdb=" O LYS A 298 " 0.033 2.00e-02 2.50e+03 pdb=" N THR A 299 " 0.030 2.00e-02 2.50e+03 ... (remaining 10963 not shown) Histogram of nonbonded interaction distances: 1.63 - 2.22: 6763 2.22 - 2.82: 160760 2.82 - 3.41: 194805 3.41 - 4.01: 244171 4.01 - 4.60: 385284 Nonbonded interactions: 991783 Sorted by model distance: nonbonded pdb=" H ILE A 889 " pdb=" O GLU A 937 " model vdw 1.628 1.850 nonbonded pdb=" O VAL E 166 " pdb=" H THR E 190 " model vdw 1.631 1.850 nonbonded pdb=" O LEU D 168 " pdb=" H TYR D 186 " model vdw 1.640 1.850 nonbonded pdb=" H CYS B 858 " pdb=" O GLY B 881 " model vdw 1.641 1.850 nonbonded pdb=" O ALA E 856 " pdb=" HG1 THR E 859 " model vdw 1.646 1.850 ... (remaining 991778 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: 3.950 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.020 Construct map_model_manager: 0.860 Extract box with map and model: 19.820 Check model and map are aligned: 0.860 Set scattering table: 0.530 Process input model: 184.650 Find NCS groups from input model: 3.400 Set up NCS constraints: 0.200 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: 216.590 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7969 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 : 0.010 0.105 37758 Z= 0.684 Angle : 1.367 25.922 51016 Z= 0.809 Chirality : 0.065 0.452 5853 Planarity : 0.009 0.064 6542 Dihedral : 13.477 136.701 14572 Min Nonbonded Distance : 1.977 Molprobity Statistics. All-atom Clashscore : 6.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.28 % Favored : 92.72 % Rotamer: Outliers : 0.12 % Allowed : 0.94 % Favored : 98.94 % 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: -2.19 (0.12), residues: 4632 helix: -1.86 (0.09), residues: 2065 sheet: -3.87 (0.18), residues: 537 loop : 0.06 (0.15), residues: 2030 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.003 TRP B 470 HIS 0.027 0.005 HIS B 839 PHE 0.046 0.005 PHE C 943 TYR 0.057 0.005 TYR A 673 ARG 0.018 0.002 ARG F 786 *********************** 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 154 residues out of total 4050 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 149 time to evaluate : 4.766 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 334 MET cc_start: 0.0048 (mtp) cc_final: -0.0322 (tpp) REVERT: A 643 ASP cc_start: 0.9105 (m-30) cc_final: 0.8761 (p0) REVERT: A 756 MET cc_start: 0.8672 (tpp) cc_final: 0.8036 (tpp) REVERT: A 766 MET cc_start: 0.5411 (ptm) cc_final: 0.5194 (ppp) REVERT: B 494 MET cc_start: 0.8662 (mtm) cc_final: 0.8289 (mtt) REVERT: B 810 MET cc_start: 0.9317 (mtt) cc_final: 0.8790 (tpp) REVERT: C 272 MET cc_start: 0.3908 (ptm) cc_final: 0.1811 (ppp) REVERT: C 317 MET cc_start: -0.3901 (tmm) cc_final: -0.4164 (ttt) REVERT: C 773 MET cc_start: 0.9125 (mmp) cc_final: 0.8888 (tmm) REVERT: C 879 MET cc_start: 0.8324 (ptm) cc_final: 0.7516 (ppp) REVERT: D 197 MET cc_start: 0.1570 (mmt) cc_final: 0.1182 (pmm) REVERT: D 206 MET cc_start: -0.1635 (ppp) cc_final: -0.2248 (tpt) REVERT: D 569 MET cc_start: 0.9226 (ptp) cc_final: 0.8807 (pmm) REVERT: E 272 MET cc_start: 0.4485 (ppp) cc_final: 0.4165 (tmm) REVERT: F 318 MET cc_start: -0.3479 (ptt) cc_final: -0.4219 (ttt) outliers start: 5 outliers final: 2 residues processed: 154 average time/residue: 1.0239 time to fit residues: 261.4982 Evaluate side-chains 135 residues out of total 4050 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 133 time to evaluate : 4.709 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 464 random chunks: chunk 391 optimal weight: 3.9990 chunk 351 optimal weight: 0.9980 chunk 195 optimal weight: 0.4980 chunk 120 optimal weight: 5.9990 chunk 237 optimal weight: 7.9990 chunk 187 optimal weight: 5.9990 chunk 363 optimal weight: 7.9990 chunk 140 optimal weight: 9.9990 chunk 221 optimal weight: 5.9990 chunk 270 optimal weight: 0.9990 chunk 421 optimal weight: 10.0000 overall best weight: 2.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7922 moved from start: 0.0913 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 37758 Z= 0.172 Angle : 0.603 7.136 51016 Z= 0.319 Chirality : 0.039 0.159 5853 Planarity : 0.004 0.052 6542 Dihedral : 8.079 128.118 5236 Min Nonbonded Distance : 1.829 Molprobity Statistics. All-atom Clashscore : 9.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.40 % Favored : 95.60 % Rotamer: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.36 (0.12), residues: 4632 helix: -0.54 (0.11), residues: 2064 sheet: -3.55 (0.19), residues: 555 loop : -0.23 (0.15), residues: 2013 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 470 HIS 0.009 0.001 HIS C 622 PHE 0.015 0.001 PHE C 370 TYR 0.013 0.001 TYR D 703 ARG 0.005 0.000 ARG D 874 *********************** 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 139 residues out of total 4050 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 139 time to evaluate : 4.851 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 334 MET cc_start: 0.0017 (mtp) cc_final: -0.0300 (tpp) REVERT: A 643 ASP cc_start: 0.9104 (m-30) cc_final: 0.8748 (p0) REVERT: A 756 MET cc_start: 0.8614 (tpp) cc_final: 0.8082 (tpp) REVERT: B 494 MET cc_start: 0.8587 (mtm) cc_final: 0.8263 (mtt) REVERT: C 272 MET cc_start: 0.3863 (ptm) cc_final: 0.1694 (ppp) REVERT: C 317 MET cc_start: -0.3931 (tmm) cc_final: -0.4155 (ttt) REVERT: C 773 MET cc_start: 0.9120 (mmp) cc_final: 0.8905 (tmm) REVERT: D 569 MET cc_start: 0.9216 (ptp) cc_final: 0.8753 (pmm) REVERT: E 272 MET cc_start: 0.4283 (ppp) cc_final: 0.4025 (ppp) REVERT: E 879 MET cc_start: 0.9096 (ptp) cc_final: 0.8884 (ptp) REVERT: F 318 MET cc_start: -0.3688 (ptt) cc_final: -0.4404 (ttt) outliers start: 0 outliers final: 0 residues processed: 139 average time/residue: 0.9053 time to fit residues: 211.9897 Evaluate side-chains 132 residues out of total 4050 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 132 time to evaluate : 4.688 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 464 random chunks: chunk 234 optimal weight: 20.0000 chunk 130 optimal weight: 10.0000 chunk 350 optimal weight: 20.0000 chunk 286 optimal weight: 7.9990 chunk 116 optimal weight: 10.0000 chunk 422 optimal weight: 10.0000 chunk 456 optimal weight: 10.0000 chunk 375 optimal weight: 0.6980 chunk 418 optimal weight: 8.9990 chunk 143 optimal weight: 5.9990 chunk 338 optimal weight: 9.9990 overall best weight: 6.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 491 HIS ** C 841 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 509 GLN E 215 HIS E 491 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7966 moved from start: 0.1420 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.086 37758 Z= 0.295 Angle : 0.606 8.146 51016 Z= 0.324 Chirality : 0.038 0.145 5853 Planarity : 0.004 0.059 6542 Dihedral : 7.759 120.887 5236 Min Nonbonded Distance : 1.689 Molprobity Statistics. All-atom Clashscore : 12.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.40 % Favored : 94.60 % Rotamer: Outliers : 0.00 % Allowed : 1.90 % Favored : 98.10 % 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: -1.30 (0.12), residues: 4632 helix: -0.19 (0.11), residues: 2058 sheet: -3.47 (0.19), residues: 571 loop : -0.56 (0.15), residues: 2003 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 470 HIS 0.008 0.001 HIS C 843 PHE 0.017 0.001 PHE D 824 TYR 0.015 0.001 TYR B 623 ARG 0.011 0.000 ARG F 482 *********************** 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 136 residues out of total 4050 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 136 time to evaluate : 4.740 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 318 MET cc_start: -0.6732 (ttt) cc_final: -0.6971 (ttt) REVERT: A 334 MET cc_start: 0.0058 (mtp) cc_final: -0.0206 (tpp) REVERT: A 643 ASP cc_start: 0.9147 (m-30) cc_final: 0.8758 (p0) REVERT: A 756 MET cc_start: 0.8597 (tpp) cc_final: 0.8154 (tpp) REVERT: B 494 MET cc_start: 0.8660 (mtm) cc_final: 0.8368 (mtt) REVERT: C 206 MET cc_start: -0.5278 (ttt) cc_final: -0.5516 (ttt) REVERT: C 272 MET cc_start: 0.4025 (ptm) cc_final: 0.1747 (ppp) REVERT: C 317 MET cc_start: -0.3894 (tmm) cc_final: -0.4138 (ttt) REVERT: C 773 MET cc_start: 0.9164 (mmp) cc_final: 0.8947 (tmm) REVERT: C 869 MET cc_start: 0.9539 (mtm) cc_final: 0.9288 (ptp) REVERT: D 569 MET cc_start: 0.9233 (ptp) cc_final: 0.8890 (pmm) REVERT: E 197 MET cc_start: 0.3151 (mmt) cc_final: 0.2397 (mmm) REVERT: E 272 MET cc_start: 0.4388 (ppp) cc_final: 0.4047 (ppp) REVERT: E 879 MET cc_start: 0.9193 (ptp) cc_final: 0.8979 (ptp) REVERT: F 318 MET cc_start: -0.4340 (ptt) cc_final: -0.4807 (ttt) outliers start: 0 outliers final: 0 residues processed: 136 average time/residue: 0.8960 time to fit residues: 209.8018 Evaluate side-chains 130 residues out of total 4050 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 130 time to evaluate : 4.749 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 464 random chunks: chunk 417 optimal weight: 4.9990 chunk 317 optimal weight: 20.0000 chunk 219 optimal weight: 10.0000 chunk 46 optimal weight: 0.6980 chunk 201 optimal weight: 4.9990 chunk 283 optimal weight: 7.9990 chunk 423 optimal weight: 20.0000 chunk 448 optimal weight: 9.9990 chunk 221 optimal weight: 3.9990 chunk 401 optimal weight: 50.0000 chunk 120 optimal weight: 0.0060 overall best weight: 2.9402 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7934 moved from start: 0.1609 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 37758 Z= 0.159 Angle : 0.518 6.224 51016 Z= 0.272 Chirality : 0.038 0.145 5853 Planarity : 0.004 0.070 6542 Dihedral : 7.352 115.247 5236 Min Nonbonded Distance : 1.823 Molprobity Statistics. All-atom Clashscore : 10.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.97 % Favored : 96.03 % Rotamer: Outliers : 0.00 % Allowed : 1.21 % Favored : 98.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.02 (0.12), residues: 4632 helix: 0.13 (0.11), residues: 2071 sheet: -3.32 (0.19), residues: 573 loop : -0.53 (0.15), residues: 1988 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 770 HIS 0.005 0.001 HIS B 843 PHE 0.018 0.001 PHE C 779 TYR 0.013 0.001 TYR E 394 ARG 0.005 0.000 ARG D 218 *********************** 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 135 residues out of total 4050 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 135 time to evaluate : 4.681 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 318 MET cc_start: -0.6730 (ttt) cc_final: -0.6953 (ttt) REVERT: A 334 MET cc_start: -0.0066 (mtp) cc_final: -0.0287 (tpp) REVERT: A 643 ASP cc_start: 0.9176 (m-30) cc_final: 0.8802 (p0) REVERT: A 756 MET cc_start: 0.8569 (tpp) cc_final: 0.8141 (tpp) REVERT: B 494 MET cc_start: 0.8599 (mtm) cc_final: 0.8312 (mtt) REVERT: C 206 MET cc_start: -0.5324 (ttt) cc_final: -0.5890 (ttt) REVERT: C 272 MET cc_start: 0.4018 (ptm) cc_final: 0.1711 (ppp) REVERT: C 317 MET cc_start: -0.3841 (tmm) cc_final: -0.4076 (ttt) REVERT: D 569 MET cc_start: 0.9207 (ptp) cc_final: 0.8877 (pmm) REVERT: E 197 MET cc_start: 0.2597 (mmt) cc_final: 0.2265 (mmm) REVERT: E 272 MET cc_start: 0.4252 (ppp) cc_final: 0.3886 (ppp) REVERT: E 879 MET cc_start: 0.9216 (ptp) cc_final: 0.8997 (ptp) REVERT: F 318 MET cc_start: -0.4380 (ptt) cc_final: -0.4769 (ttt) outliers start: 0 outliers final: 0 residues processed: 135 average time/residue: 0.8827 time to fit residues: 204.6287 Evaluate side-chains 128 residues out of total 4050 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 128 time to evaluate : 4.696 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 464 random chunks: chunk 373 optimal weight: 0.9980 chunk 254 optimal weight: 8.9990 chunk 6 optimal weight: 10.0000 chunk 333 optimal weight: 8.9990 chunk 185 optimal weight: 8.9990 chunk 382 optimal weight: 7.9990 chunk 310 optimal weight: 30.0000 chunk 0 optimal weight: 20.0000 chunk 229 optimal weight: 9.9990 chunk 402 optimal weight: 20.0000 chunk 113 optimal weight: 6.9990 overall best weight: 6.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 433 HIS C 622 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7973 moved from start: 0.1927 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 37758 Z= 0.296 Angle : 0.579 7.316 51016 Z= 0.309 Chirality : 0.038 0.172 5853 Planarity : 0.004 0.065 6542 Dihedral : 7.273 112.855 5236 Min Nonbonded Distance : 1.778 Molprobity Statistics. All-atom Clashscore : 13.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.87 % Favored : 94.13 % Rotamer: Outliers : 0.02 % Allowed : 1.31 % Favored : 98.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.25 (0.12), residues: 4632 helix: 0.01 (0.11), residues: 2061 sheet: -3.28 (0.19), residues: 562 loop : -0.80 (0.14), residues: 2009 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 464 HIS 0.009 0.001 HIS C 843 PHE 0.018 0.001 PHE D 824 TYR 0.015 0.001 TYR B 725 ARG 0.005 0.000 ARG C 652 *********************** 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 135 residues out of total 4050 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 134 time to evaluate : 4.847 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 643 ASP cc_start: 0.9212 (m-30) cc_final: 0.8976 (p0) REVERT: B 494 MET cc_start: 0.8737 (mtm) cc_final: 0.8495 (mtt) REVERT: B 552 MET cc_start: 0.8471 (tpp) cc_final: 0.8236 (tpp) REVERT: C 206 MET cc_start: -0.5132 (ttt) cc_final: -0.5718 (ttt) REVERT: C 272 MET cc_start: 0.3935 (ptm) cc_final: 0.1671 (ppp) REVERT: C 879 MET cc_start: 0.8295 (ptm) cc_final: 0.7543 (ptm) REVERT: D 569 MET cc_start: 0.9215 (ptp) cc_final: 0.8914 (pmm) REVERT: D 879 MET cc_start: 0.8772 (ptp) cc_final: 0.8449 (ptm) REVERT: E 197 MET cc_start: 0.3079 (mmt) cc_final: 0.2360 (mmm) REVERT: E 272 MET cc_start: 0.4310 (ppp) cc_final: 0.3934 (ppp) REVERT: E 879 MET cc_start: 0.9204 (ptp) cc_final: 0.8987 (ptp) REVERT: F 318 MET cc_start: -0.4348 (ptt) cc_final: -0.4803 (ttt) outliers start: 1 outliers final: 1 residues processed: 135 average time/residue: 0.9034 time to fit residues: 209.9897 Evaluate side-chains 130 residues out of total 4050 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 129 time to evaluate : 4.666 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 464 random chunks: chunk 150 optimal weight: 30.0000 chunk 403 optimal weight: 20.0000 chunk 88 optimal weight: 0.7980 chunk 263 optimal weight: 2.9990 chunk 110 optimal weight: 7.9990 chunk 448 optimal weight: 3.9990 chunk 372 optimal weight: 8.9990 chunk 207 optimal weight: 10.0000 chunk 37 optimal weight: 9.9990 chunk 148 optimal weight: 1.9990 chunk 235 optimal weight: 1.9990 overall best weight: 2.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7935 moved from start: 0.2018 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.048 37758 Z= 0.149 Angle : 0.505 10.121 51016 Z= 0.262 Chirality : 0.038 0.152 5853 Planarity : 0.004 0.091 6542 Dihedral : 7.024 107.700 5236 Min Nonbonded Distance : 1.814 Molprobity Statistics. All-atom Clashscore : 10.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.78 % Favored : 96.22 % Rotamer: Outliers : 0.00 % Allowed : 0.74 % Favored : 99.26 % 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: -0.89 (0.13), residues: 4632 helix: 0.37 (0.11), residues: 2054 sheet: -3.16 (0.20), residues: 558 loop : -0.67 (0.14), residues: 2020 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 770 HIS 0.005 0.001 HIS B 843 PHE 0.011 0.001 PHE D 920 TYR 0.018 0.001 TYR D 492 ARG 0.004 0.000 ARG B 482 *********************** 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 135 residues out of total 4050 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 135 time to evaluate : 5.073 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 643 ASP cc_start: 0.9210 (m-30) cc_final: 0.8957 (p0) REVERT: A 756 MET cc_start: 0.8166 (tpp) cc_final: 0.7907 (mmm) REVERT: B 552 MET cc_start: 0.8634 (tpp) cc_final: 0.8401 (tpp) REVERT: C 272 MET cc_start: 0.3947 (ptm) cc_final: 0.1666 (ppp) REVERT: C 879 MET cc_start: 0.8312 (ptm) cc_final: 0.7522 (ptm) REVERT: D 569 MET cc_start: 0.9186 (ptp) cc_final: 0.8904 (pmm) REVERT: E 197 MET cc_start: 0.3109 (mmt) cc_final: 0.2548 (mmm) REVERT: E 879 MET cc_start: 0.9226 (ptp) cc_final: 0.9009 (ptp) REVERT: F 318 MET cc_start: -0.4325 (ptt) cc_final: -0.4716 (ttt) outliers start: 0 outliers final: 0 residues processed: 135 average time/residue: 0.8932 time to fit residues: 209.0567 Evaluate side-chains 130 residues out of total 4050 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 130 time to evaluate : 4.705 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 464 random chunks: chunk 432 optimal weight: 7.9990 chunk 50 optimal weight: 8.9990 chunk 255 optimal weight: 7.9990 chunk 327 optimal weight: 40.0000 chunk 254 optimal weight: 8.9990 chunk 377 optimal weight: 6.9990 chunk 250 optimal weight: 30.0000 chunk 447 optimal weight: 10.0000 chunk 279 optimal weight: 0.9980 chunk 272 optimal weight: 6.9990 chunk 206 optimal weight: 5.9990 overall best weight: 5.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 460 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 399 GLN ** F 876 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7969 moved from start: 0.2227 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 37758 Z= 0.258 Angle : 0.543 8.538 51016 Z= 0.287 Chirality : 0.037 0.136 5853 Planarity : 0.004 0.041 6542 Dihedral : 6.993 105.375 5236 Min Nonbonded Distance : 1.749 Molprobity Statistics. All-atom Clashscore : 13.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.35 % Favored : 94.65 % Rotamer: Outliers : 0.00 % Allowed : 0.91 % Favored : 99.09 % 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: -1.11 (0.12), residues: 4632 helix: 0.21 (0.11), residues: 2071 sheet: -3.11 (0.20), residues: 569 loop : -0.86 (0.14), residues: 1992 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP C 464 HIS 0.008 0.001 HIS C 843 PHE 0.019 0.001 PHE F 935 TYR 0.012 0.001 TYR D 492 ARG 0.004 0.000 ARG E 755 *********************** 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 133 residues out of total 4050 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 133 time to evaluate : 4.832 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 552 MET cc_start: 0.8647 (tpp) cc_final: 0.8355 (tpp) REVERT: C 206 MET cc_start: -0.5487 (ttt) cc_final: -0.6125 (ttt) REVERT: C 272 MET cc_start: 0.4202 (ptm) cc_final: 0.2272 (ppp) REVERT: C 879 MET cc_start: 0.8353 (ptm) cc_final: 0.7557 (ptm) REVERT: D 569 MET cc_start: 0.9192 (ptp) cc_final: 0.8904 (pmm) REVERT: E 879 MET cc_start: 0.9234 (ptp) cc_final: 0.9023 (ptp) REVERT: F 318 MET cc_start: -0.4284 (ptt) cc_final: -0.4733 (ttt) outliers start: 0 outliers final: 0 residues processed: 133 average time/residue: 0.9171 time to fit residues: 209.3366 Evaluate side-chains 127 residues out of total 4050 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 127 time to evaluate : 4.854 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 464 random chunks: chunk 276 optimal weight: 5.9990 chunk 178 optimal weight: 10.0000 chunk 267 optimal weight: 2.9990 chunk 134 optimal weight: 7.9990 chunk 87 optimal weight: 30.0000 chunk 86 optimal weight: 20.0000 chunk 284 optimal weight: 10.0000 chunk 304 optimal weight: 2.9990 chunk 221 optimal weight: 9.9990 chunk 41 optimal weight: 5.9990 chunk 351 optimal weight: 6.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 460 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 876 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7962 moved from start: 0.2363 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 37758 Z= 0.214 Angle : 0.521 6.626 51016 Z= 0.276 Chirality : 0.037 0.138 5853 Planarity : 0.004 0.054 6542 Dihedral : 6.874 104.987 5236 Min Nonbonded Distance : 1.785 Molprobity Statistics. All-atom Clashscore : 12.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.73 % Favored : 95.27 % Rotamer: Outliers : 0.00 % Allowed : 0.74 % Favored : 99.26 % 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: -1.05 (0.12), residues: 4632 helix: 0.27 (0.11), residues: 2073 sheet: -3.03 (0.20), residues: 542 loop : -0.91 (0.14), residues: 2017 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 770 HIS 0.007 0.001 HIS C 843 PHE 0.016 0.001 PHE D 824 TYR 0.019 0.001 TYR A 703 ARG 0.003 0.000 ARG B 786 *********************** 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 133 residues out of total 4050 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 133 time to evaluate : 4.776 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 756 MET cc_start: 0.8695 (mmm) cc_final: 0.8382 (tpp) REVERT: B 552 MET cc_start: 0.8604 (tpp) cc_final: 0.8353 (tpp) REVERT: C 206 MET cc_start: -0.5466 (ttt) cc_final: -0.6315 (ttt) REVERT: C 272 MET cc_start: 0.4251 (ptm) cc_final: 0.2653 (ppp) REVERT: C 879 MET cc_start: 0.8368 (ptm) cc_final: 0.7569 (ptm) REVERT: D 569 MET cc_start: 0.9178 (ptp) cc_final: 0.8904 (pmm) REVERT: E 197 MET cc_start: 0.3087 (mmt) cc_final: 0.2619 (mmm) REVERT: E 879 MET cc_start: 0.9255 (ptp) cc_final: 0.9039 (ptp) REVERT: F 318 MET cc_start: -0.4325 (ptt) cc_final: -0.4750 (ttt) outliers start: 0 outliers final: 0 residues processed: 133 average time/residue: 0.8968 time to fit residues: 204.7926 Evaluate side-chains 126 residues out of total 4050 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 126 time to evaluate : 4.726 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 464 random chunks: chunk 406 optimal weight: 20.0000 chunk 428 optimal weight: 9.9990 chunk 390 optimal weight: 10.0000 chunk 416 optimal weight: 0.6980 chunk 250 optimal weight: 10.0000 chunk 181 optimal weight: 2.9990 chunk 327 optimal weight: 40.0000 chunk 127 optimal weight: 7.9990 chunk 376 optimal weight: 7.9990 chunk 394 optimal weight: 10.0000 chunk 415 optimal weight: 20.0000 overall best weight: 5.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 460 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 876 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7972 moved from start: 0.2499 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 37758 Z= 0.254 Angle : 0.540 7.048 51016 Z= 0.288 Chirality : 0.037 0.137 5853 Planarity : 0.004 0.048 6542 Dihedral : 6.869 104.724 5236 Min Nonbonded Distance : 1.727 Molprobity Statistics. All-atom Clashscore : 13.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.59 % Favored : 94.41 % Rotamer: Outliers : 0.00 % Allowed : 0.32 % Favored : 99.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.18 (0.12), residues: 4632 helix: 0.17 (0.11), residues: 2074 sheet: -2.99 (0.20), residues: 556 loop : -0.99 (0.14), residues: 2002 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 770 HIS 0.008 0.001 HIS C 843 PHE 0.018 0.001 PHE D 824 TYR 0.020 0.001 TYR B 703 ARG 0.003 0.000 ARG A 679 *********************** 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 135 residues out of total 4050 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 135 time to evaluate : 4.815 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 756 MET cc_start: 0.8682 (mmm) cc_final: 0.8411 (tpp) REVERT: B 552 MET cc_start: 0.8590 (tpp) cc_final: 0.8308 (tpp) REVERT: C 206 MET cc_start: -0.5416 (ttt) cc_final: -0.6275 (ttt) REVERT: C 272 MET cc_start: 0.4333 (ptm) cc_final: 0.2733 (ppp) REVERT: C 879 MET cc_start: 0.8383 (ptm) cc_final: 0.7577 (ptm) REVERT: D 334 MET cc_start: 0.1284 (mtt) cc_final: 0.0444 (ttp) REVERT: D 569 MET cc_start: 0.9178 (ptp) cc_final: 0.8790 (pmm) REVERT: E 879 MET cc_start: 0.9262 (ptp) cc_final: 0.9047 (ptp) REVERT: F 318 MET cc_start: -0.4256 (ptt) cc_final: -0.4734 (ttt) outliers start: 0 outliers final: 0 residues processed: 135 average time/residue: 0.9126 time to fit residues: 211.4079 Evaluate side-chains 127 residues out of total 4050 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 127 time to evaluate : 4.717 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 464 random chunks: chunk 273 optimal weight: 9.9990 chunk 440 optimal weight: 10.0000 chunk 268 optimal weight: 3.9990 chunk 209 optimal weight: 1.9990 chunk 306 optimal weight: 9.9990 chunk 462 optimal weight: 50.0000 chunk 425 optimal weight: 7.9990 chunk 368 optimal weight: 8.9990 chunk 38 optimal weight: 9.9990 chunk 284 optimal weight: 9.9990 chunk 225 optimal weight: 4.9990 overall best weight: 5.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 839 HIS ** E 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 876 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7970 moved from start: 0.2646 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 37758 Z= 0.238 Angle : 0.538 7.133 51016 Z= 0.285 Chirality : 0.037 0.161 5853 Planarity : 0.004 0.044 6542 Dihedral : 6.857 104.074 5236 Min Nonbonded Distance : 1.726 Molprobity Statistics. All-atom Clashscore : 13.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.12 % Favored : 94.88 % Rotamer: Outliers : 0.00 % Allowed : 0.15 % Favored : 99.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.18 (0.12), residues: 4632 helix: 0.19 (0.11), residues: 2086 sheet: -2.92 (0.21), residues: 559 loop : -1.05 (0.14), residues: 1987 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 770 HIS 0.008 0.001 HIS C 843 PHE 0.018 0.001 PHE D 824 TYR 0.014 0.001 TYR B 703 ARG 0.007 0.000 ARG E 154 ********************** 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 133 residues out of total 4050 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 133 time to evaluate : 4.746 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 756 MET cc_start: 0.8691 (mmm) cc_final: 0.8423 (tpp) REVERT: B 494 MET cc_start: 0.8784 (mtm) cc_final: 0.8430 (mtt) REVERT: B 552 MET cc_start: 0.8597 (tpp) cc_final: 0.8321 (tpp) REVERT: C 206 MET cc_start: -0.5425 (ttt) cc_final: -0.6343 (ttt) REVERT: C 272 MET cc_start: 0.4544 (ptm) cc_final: 0.2973 (ppp) REVERT: C 879 MET cc_start: 0.8372 (ptm) cc_final: 0.7554 (ptm) REVERT: D 569 MET cc_start: 0.9171 (ptp) cc_final: 0.8796 (pmm) REVERT: E 197 MET cc_start: 0.2724 (mmt) cc_final: 0.2365 (mmm) REVERT: E 879 MET cc_start: 0.9278 (ptp) cc_final: 0.9063 (ptp) REVERT: F 318 MET cc_start: -0.4273 (ptt) cc_final: -0.4751 (ttt) outliers start: 0 outliers final: 0 residues processed: 133 average time/residue: 0.9540 time to fit residues: 216.5433 Evaluate side-chains 127 residues out of total 4050 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 127 time to evaluate : 4.741 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 464 random chunks: chunk 292 optimal weight: 1.9990 chunk 392 optimal weight: 30.0000 chunk 112 optimal weight: 0.0040 chunk 339 optimal weight: 7.9990 chunk 54 optimal weight: 8.9990 chunk 102 optimal weight: 6.9990 chunk 368 optimal weight: 7.9990 chunk 154 optimal weight: 40.0000 chunk 378 optimal weight: 6.9990 chunk 46 optimal weight: 9.9990 chunk 67 optimal weight: 20.0000 overall best weight: 4.8000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 376 GLN ** E 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 876 ASN ** 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 = 0.3872 r_free = 0.3872 target = 0.055262 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.039157 restraints weight = 1177500.774| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.039635 restraints weight = 725599.436| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 50)----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.040411 restraints weight = 477769.180| |-----------------------------------------------------------------------------| r_work (final): 0.3357 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8104 moved from start: 0.2737 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 37758 Z= 0.218 Angle : 0.526 12.191 51016 Z= 0.277 Chirality : 0.037 0.140 5853 Planarity : 0.004 0.038 6542 Dihedral : 6.807 102.472 5236 Min Nonbonded Distance : 1.735 Molprobity Statistics. All-atom Clashscore : 13.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.40 % Favored : 94.60 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.11 (0.12), residues: 4632 helix: 0.26 (0.11), residues: 2089 sheet: -2.88 (0.21), residues: 567 loop : -1.01 (0.14), residues: 1976 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 770 HIS 0.007 0.001 HIS C 843 PHE 0.018 0.001 PHE C 779 TYR 0.012 0.001 TYR B 703 ARG 0.003 0.000 ARG E 940 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8261.13 seconds wall clock time: 146 minutes 59.67 seconds (8819.67 seconds total)