Starting phenix.real_space_refine on Sun Mar 17 20:38:26 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zqm_11368/03_2024/6zqm_11368_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zqm_11368/03_2024/6zqm_11368.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.29 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zqm_11368/03_2024/6zqm_11368.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zqm_11368/03_2024/6zqm_11368.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zqm_11368/03_2024/6zqm_11368_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zqm_11368/03_2024/6zqm_11368_trim_updated.pdb" } resolution = 3.29 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= 0.015 sd= 1.097 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 23 5.49 5 Mg 5 5.21 5 S 150 5.16 5 C 25548 2.51 5 N 6742 2.21 5 O 7534 1.98 5 H 40460 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 27": "OE1" <-> "OE2" Residue "A ASP 36": "OD1" <-> "OD2" Residue "A GLU 51": "OE1" <-> "OE2" Residue "A PHE 76": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ASP 79": "OD1" <-> "OD2" Residue "A ASP 96": "OD1" <-> "OD2" Residue "A GLU 102": "OE1" <-> "OE2" Residue "A ARG 143": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ASP 181": "OD1" <-> "OD2" Residue "A PHE 189": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 200": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ASP 224": "OD1" <-> "OD2" Residue "A TYR 248": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 257": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 268": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ASP 269": "OD1" <-> "OD2" Residue "A ARG 286": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 287": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 291": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A TYR 294": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 299": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ASP 314": "OD1" <-> "OD2" Residue "A GLU 328": "OE1" <-> "OE2" Residue "A ASP 333": "OD1" <-> "OD2" Residue "A TYR 337": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ASP 347": "OD1" <-> "OD2" Residue "A GLU 355": "OE1" <-> "OE2" Residue "A PHE 357": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A GLU 399": "OE1" <-> "OE2" Residue "A PHE 406": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ASP 454": "OD1" <-> "OD2" Residue "A PHE 464": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A GLU 465": "OE1" <-> "OE2" Residue "A GLU 499": "OE1" <-> "OE2" Residue "B GLU 50": "OE1" <-> "OE2" Residue "B GLU 51": "OE1" <-> "OE2" Residue "B GLU 101": "OE1" <-> "OE2" Residue "B ASP 109": "OD1" <-> "OD2" Residue "B ASP 116": "OD1" <-> "OD2" Residue "B PHE 189": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B ASP 194": "OD1" <-> "OD2" Residue "B GLU 195": "OE1" <-> "OE2" Residue "B TYR 200": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B ARG 219": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ASP 224": "OD1" <-> "OD2" Residue "B TYR 228": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B TYR 248": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B GLU 255": "OE1" <-> "OE2" Residue "B PHE 257": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B ASP 259": "OD1" <-> "OD2" Residue "B ARG 291": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B TYR 294": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B ASP 314": "OD1" <-> "OD2" Residue "B PHE 316": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B ASP 333": "OD1" <-> "OD2" Residue "B PHE 351": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B GLU 353": "OE1" <-> "OE2" Residue "B GLU 355": "OE1" <-> "OE2" Residue "B ARG 362": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 373": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B PHE 403": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B GLU 426": "OE1" <-> "OE2" Residue "B TYR 433": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B GLU 440": "OE1" <-> "OE2" Residue "B TYR 452": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B GLU 465": "OE1" <-> "OE2" Residue "B ARG 484": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ASP 486": "OD1" <-> "OD2" Residue "B PHE 504": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 508": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C GLU 14": "OE1" <-> "OE2" Residue "C ASP 24": "OD1" <-> "OD2" Residue "C ASP 36": "OD1" <-> "OD2" Residue "C ARG 45": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C GLU 54": "OE1" <-> "OE2" Residue "C PHE 55": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C ASP 69": "OD1" <-> "OD2" Residue "C PHE 76": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C ASP 86": "OD1" <-> "OD2" Residue "C ASP 96": "OD1" <-> "OD2" Residue "C ASP 154": "OD1" <-> "OD2" Residue "C PHE 189": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C ASP 194": "OD1" <-> "OD2" Residue "C GLU 195": "OE1" <-> "OE2" Residue "C TYR 248": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C GLU 255": "OE1" <-> "OE2" Residue "C TYR 268": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C ARG 291": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C TYR 294": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C PHE 299": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C GLU 307": "OE1" <-> "OE2" Residue "C ASP 314": "OD1" <-> "OD2" Residue "C GLU 328": "OE1" <-> "OE2" Residue "C ASP 333": "OD1" <-> "OD2" Residue "C PHE 351": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C PHE 357": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C TYR 358": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C ARG 381": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C GLU 393": "OE1" <-> "OE2" Residue "C PHE 403": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C ASP 411": "OD1" <-> "OD2" Residue "C TYR 433": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C ASP 454": "OD1" <-> "OD2" Residue "C GLU 457": "OE1" <-> "OE2" Residue "C ASP 494": "OD1" <-> "OD2" Residue "C GLU 499": "OE1" <-> "OE2" Residue "C PHE 504": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C PHE 508": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C GLU 509": "OE1" <-> "OE2" Residue "D ARG 12": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D GLU 37": "OE1" <-> "OE2" Residue "D ASP 77": "OD1" <-> "OD2" Residue "D GLU 104": "OE1" <-> "OE2" Residue "D PHE 113": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D GLU 122": "OE1" <-> "OE2" Residue "D PHE 123": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D GLU 125": "OE1" <-> "OE2" Residue "D TYR 180": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D PHE 183": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D GLU 199": "OE1" <-> "OE2" Residue "D TYR 219": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D TYR 242": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D PHE 243": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D ASP 245": "OD1" <-> "OD2" Residue "D GLU 267": "OE1" <-> "OE2" Residue "D TYR 281": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D GLU 294": "OE1" <-> "OE2" Residue "D GLU 341": "OE1" <-> "OE2" Residue "D ASP 359": "OD1" <-> "OD2" Residue "D TYR 368": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D ASP 369": "OD1" <-> "OD2" Residue "D GLU 398": "OE1" <-> "OE2" Residue "D GLU 399": "OE1" <-> "OE2" Residue "D PHE 413": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D PHE 424": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D PHE 441": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D TYR 449": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D ASP 450": "OD1" <-> "OD2" Residue "D PHE 457": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D GLU 464": "OE1" <-> "OE2" Residue "D GLU 465": "OE1" <-> "OE2" Residue "D ASP 471": "OD1" <-> "OD2" Residue "D GLU 475": "OE1" <-> "OE2" Residue "E GLU 67": "OE1" <-> "OE2" Residue "E PHE 113": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E GLU 122": "OE1" <-> "OE2" Residue "E PHE 123": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E TYR 180": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E GLU 241": "OE1" <-> "OE2" Residue "E TYR 242": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E PHE 243": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E GLU 247": "OE1" <-> "OE2" Residue "E ASP 256": "OD1" <-> "OD2" Residue "E PHE 259": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E TYR 281": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E PHE 326": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E ASP 349": "OD1" <-> "OD2" Residue "E ASP 394": "OD1" <-> "OD2" Residue "E PHE 413": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E PHE 441": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E GLU 448": "OE1" <-> "OE2" Residue "E TYR 449": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E PHE 457": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E GLU 464": "OE1" <-> "OE2" Residue "E GLU 465": "OE1" <-> "OE2" Residue "E ASP 471": "OD1" <-> "OD2" Residue "F GLU 37": "OE1" <-> "OE2" Residue "F GLU 48": "OE1" <-> "OE2" Residue "F GLU 55": "OE1" <-> "OE2" Residue "F GLU 67": "OE1" <-> "OE2" Residue "F GLU 89": "OE1" <-> "OE2" Residue "F GLU 122": "OE1" <-> "OE2" Residue "F GLU 131": "OE1" <-> "OE2" Residue "F GLU 168": "OE1" <-> "OE2" Residue "F TYR 180": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F PHE 183": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F TYR 197": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F GLU 224": "OE1" <-> "OE2" Residue "F GLU 241": "OE1" <-> "OE2" Residue "F TYR 242": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F PHE 243": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F GLU 267": "OE1" <-> "OE2" Residue "F TYR 281": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F ASP 288": "OD1" <-> "OD2" Residue "F ASP 316": "OD1" <-> "OD2" Residue "F GLU 341": "OE1" <-> "OE2" Residue "F TYR 345": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F ASP 349": "OD1" <-> "OD2" Residue "F ASP 359": "OD1" <-> "OD2" Residue "F GLU 366": "OE1" <-> "OE2" Residue "F ASP 380": "OD1" <-> "OD2" Residue "F GLU 399": "OE1" <-> "OE2" Residue "F PHE 413": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F PHE 418": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F PHE 424": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F PHE 441": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F GLU 448": "OE1" <-> "OE2" Residue "F ASP 450": "OD1" <-> "OD2" Residue "F PHE 457": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F GLU 465": "OE1" <-> "OE2" Residue "F ASP 471": "OD1" <-> "OD2" Residue "G GLU 37": "OE1" <-> "OE2" Residue "G TYR 44": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "G ASP 74": "OD1" <-> "OD2" Residue "G ARG 75": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "G GLU 102": "OE1" <-> "OE2" Residue "G ARG 118": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "G TYR 153": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "G PHE 155": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "G GLU 157": "OE1" <-> "OE2" Residue "G PHE 165": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "G ARG 166": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "G GLU 175": "OE1" <-> "OE2" Residue "G TYR 193": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "G ASP 197": "OD1" <-> "OD2" Residue "G ASP 199": "OD1" <-> "OD2" Residue "G TYR 204": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "G TYR 207": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "G GLU 219": "OE1" <-> "OE2" Residue "G GLU 241": "OE1" <-> "OE2" Residue "G ASP 244": "OD1" <-> "OD2" Residue "G PHE 250": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "G GLU 261": "OE1" <-> "OE2" Residue "G GLU 264": "OE1" <-> "OE2" Residue "H PHE 18": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "H PHE 27": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "H PHE 28": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "H ASP 37": "OD1" <-> "OD2" Residue "H PHE 45": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "H PHE 76": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "H GLU 95": "OE1" <-> "OE2" Residue "H ASP 101": "OD1" <-> "OD2" Residue "H ASP 124": "OD1" <-> "OD2" Residue "H GLU 125": "OE1" <-> "OE2" Residue "H GLU 130": "OE1" <-> "OE2" Residue "I ARG 5": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "I ARG 13": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "I TYR 14": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "J ARG 25": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "J TYR 33": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "K ARG 38": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "K GLU 58": "OE1" <-> "OE2" Residue "L ASP 1": "OD1" <-> "OD2" Residue "L PHE 8": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "L PHE 29": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "L TYR 36": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "L ARG 38": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "M ASP 1": "OD1" <-> "OD2" Residue "M PHE 47": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "M PHE 73": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "N PHE 8": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "N PHE 29": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "N TYR 36": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "N ARG 38": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "N PHE 63": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "O ASP 1": "OD1" <-> "OD2" Residue "O PHE 29": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "O PHE 54": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "O GLU 58": "OE1" <-> "OE2" Residue "O PHE 69": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "P PHE 29": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "P ARG 38": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "P PHE 47": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "P GLU 58": "OE1" <-> "OE2" Residue "P PHE 63": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "P PHE 73": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "Q PHE 29": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "Q ARG 38": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "Q PHE 47": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "Q GLU 58": "OE1" <-> "OE2" Residue "Q PHE 73": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "R PHE 29": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "R GLU 58": "OE1" <-> "OE2" Residue "R PHE 63": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "S PHE 1": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "S TYR 23": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "S GLU 36": "OE1" <-> "OE2" Residue "S TYR 59": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "S GLU 91": "OE1" <-> "OE2" Residue "S ARG 94": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "S PHE 105": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "S GLU 115": "OE1" <-> "OE2" Residue "S GLU 128": "OE1" <-> "OE2" Residue "S GLU 133": "OE1" <-> "OE2" Residue "S ASP 155": "OD1" <-> "OD2" Residue "S ARG 165": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "S TYR 170": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "8 PHE 21": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "a PHE 26": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "a ARG 36": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "a PHE 42": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "a ARG 159": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "a ASP 224": "OD1" <-> "OD2" Residue "d ASP 11": "OD1" <-> "OD2" Residue "d ASP 52": "OD1" <-> "OD2" Residue "d GLU 102": "OE1" <-> "OE2" Residue "d TYR 114": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "d GLU 137": "OE1" <-> "OE2" Residue "d ARG 155": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "f ARG 39": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "f TYR 71": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "f ARG 73": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "f ARG 84": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "f TYR 86": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "g TYR 21": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "g ARG 25": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "g PHE 64": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "g GLU 90": "OE1" <-> "OE2" Residue "g ARG 95": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "j TYR 16": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "j TYR 17": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "j TYR 33": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "j ASP 42": "OD1" <-> "OD2" Residue "b ARG 13": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "b PHE 24": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "b TYR 26": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "b TYR 35": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "b GLU 80": "OE1" <-> "OE2" Residue "b PHE 81": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "b ARG 121": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "b ARG 129": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "b TYR 140": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "b ARG 141": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "b TYR 157": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "h PHE 11": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "h GLU 42": "OE1" <-> "OE2" Residue "k PHE 18": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "k TYR 34": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "e TYR 24": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Time to flip residues: 0.11s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 80462 Number of models: 1 Model: "" Number of chains: 42 Chain: "A" Number of atoms: 7519 Number of conformers: 1 Conformer: "" Number of residues, atoms: 486, 7519 Classifications: {'peptide': 486} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 16, 'TRANS': 467} Chain: "B" Number of atoms: 7657 Number of conformers: 1 Conformer: "" Number of residues, atoms: 495, 7657 Classifications: {'peptide': 495} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 16, 'TRANS': 476} Chain breaks: 1 Chain: "C" Number of atoms: 7741 Number of conformers: 1 Conformer: "" Number of residues, atoms: 501, 7741 Classifications: {'peptide': 501} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 16, 'TRANS': 482} Chain breaks: 1 Chain: "D" Number of atoms: 7163 Number of conformers: 1 Conformer: "" Number of residues, atoms: 469, 7163 Classifications: {'peptide': 469} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 22, 'TRANS': 444} Chain: "E" Number of atoms: 7132 Number of conformers: 1 Conformer: "" Number of residues, atoms: 467, 7132 Classifications: {'peptide': 467} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 22, 'TRANS': 442} Chain: "F" Number of atoms: 7131 Number of conformers: 1 Conformer: "" Number of residues, atoms: 467, 7131 Classifications: {'peptide': 467} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 22, 'TRANS': 442} Chain: "G" Number of atoms: 4300 Number of conformers: 1 Conformer: "" Number of residues, atoms: 272, 4300 Classifications: {'peptide': 272} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 5, 'TRANS': 266} Chain: "H" Number of atoms: 1957 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 1957 Classifications: {'peptide': 132} Link IDs: {'PTRANS': 4, 'TRANS': 127} Chain: "I" Number of atoms: 764 Number of conformers: 1 Conformer: "" Number of residues, atoms: 47, 764 Classifications: {'peptide': 47} Modifications used: {'NH3': 1} Link IDs: {'TRANS': 46} Chain: "J" Number of atoms: 731 Number of conformers: 1 Conformer: "" Number of residues, atoms: 47, 731 Classifications: {'peptide': 47} Link IDs: {'TRANS': 46} Chain: "K" Number of atoms: 1060 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 1060 Classifications: {'peptide': 74} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 1, 'TRANS': 72} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'M3L:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "L" Number of atoms: 1077 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 1077 Classifications: {'peptide': 75} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 1, 'TRANS': 73} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'M3L:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "M" Number of atoms: 1060 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 1060 Classifications: {'peptide': 74} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 1, 'TRANS': 72} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'M3L:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "N" Number of atoms: 1060 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 1060 Classifications: {'peptide': 74} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 1, 'TRANS': 72} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'M3L:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "O" Number of atoms: 1060 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 1060 Classifications: {'peptide': 74} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 1, 'TRANS': 72} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'M3L:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "P" Number of atoms: 1060 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 1060 Classifications: {'peptide': 74} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 1, 'TRANS': 72} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'M3L:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "Q" Number of atoms: 1060 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 1060 Classifications: {'peptide': 74} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 1, 'TRANS': 72} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'M3L:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "R" Number of atoms: 1060 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 1060 Classifications: {'peptide': 74} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 1, 'TRANS': 72} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'M3L:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "S" Number of atoms: 3004 Number of conformers: 1 Conformer: "" Number of residues, atoms: 188, 3004 Classifications: {'peptide': 188} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 8, 'TRANS': 179} Chain: "8" Number of atoms: 649 Number of conformers: 1 Conformer: "" Number of residues, atoms: 38, 649 Classifications: {'peptide': 38} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 2, 'TRANS': 35} Chain: "a" Number of atoms: 3611 Number of conformers: 1 Conformer: "" Number of residues, atoms: 226, 3611 Classifications: {'peptide': 226} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 12, 'TRANS': 213} Chain: "d" Number of atoms: 2534 Number of conformers: 1 Conformer: "" Number of residues, atoms: 154, 2534 Classifications: {'peptide': 154} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 142} Chain: "f" Number of atoms: 1411 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 1411 Classifications: {'peptide': 83} Link IDs: {'PTRANS': 2, 'TRANS': 80} Chain: "g" Number of atoms: 1291 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 1291 Classifications: {'peptide': 79} Link IDs: {'PTRANS': 5, 'TRANS': 73} Chain: "j" Number of atoms: 828 Number of conformers: 1 Conformer: "" Number of residues, atoms: 48, 828 Classifications: {'peptide': 48} Link IDs: {'PTRANS': 2, 'TRANS': 45} Chain: "b" Number of atoms: 3457 Number of conformers: 1 Conformer: "" Number of residues, atoms: 209, 3457 Classifications: {'peptide': 209} Modifications used: {'NH2': 1} Link IDs: {'PTRANS': 7, 'TRANS': 201} Chain: "h" Number of atoms: 1009 Number of conformers: 1 Conformer: "" Number of residues, atoms: 62, 1009 Classifications: {'peptide': 62} Link IDs: {'PTRANS': 5, 'TRANS': 56} Chain: "k" Number of atoms: 596 Number of conformers: 1 Conformer: "" Number of residues, atoms: 36, 596 Classifications: {'peptide': 36} Link IDs: {'TRANS': 35} Chain: "e" Number of atoms: 951 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 951 Classifications: {'peptide': 56} Link IDs: {'PTRANS': 3, 'TRANS': 52} 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: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "f" Number of atoms: 201 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 201 Unusual residues: {'CDL': 2, 'LHG': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 48 Unresolved non-hydrogen angles: 48 Unresolved non-hydrogen dihedrals: 48 Chain: "b" Number of atoms: 132 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 132 Unusual residues: {'CDL': 1, 'LHG': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 17 Unresolved non-hydrogen dihedrals: 17 Chain: "A" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "C" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "D" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Classifications: {'water': 4} Link IDs: {None: 3} Chain: "F" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Classifications: {'water': 4} Link IDs: {None: 3} Time building chain proxies: 26.06, per 1000 atoms: 0.32 Number of scatterers: 80462 At special positions: 0 Unit cell: (153.008, 139.384, 253.616, 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 150 16.00 P 23 15.00 Mg 5 11.99 O 7534 8.00 N 6742 7.00 C 25548 6.00 H 40460 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 Atom "HETATM80259 OA2 CDL f 102 .*. O " rejected from bonding due to valence issues. Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 55.78 Conformation dependent library (CDL) restraints added in 6.7 seconds 10138 Ramachandran restraints generated. 5069 Oldfield, 0 Emsley, 5069 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 9418 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 194 helices and 23 sheets defined 53.6% alpha, 8.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 8.88 Creating SS restraints... Processing helix chain 'A' and resid 79 through 81 No H-bonds generated for 'chain 'A' and resid 79 through 81' Processing helix chain 'A' and resid 151 through 156 Processing helix chain 'A' and resid 175 through 190 removed outlier: 3.568A pdb=" N GLN A 186 " --> pdb=" O THR A 182 " (cutoff:3.500A) removed outlier: 4.428A pdb=" N LYS A 187 " --> pdb=" O ILE A 183 " (cutoff:3.500A) removed outlier: 4.960A pdb=" N ARG A 188 " --> pdb=" O ILE A 184 " (cutoff:3.500A) removed outlier: 4.576A pdb=" N PHE A 189 " --> pdb=" O ASN A 185 " (cutoff:3.500A) Processing helix chain 'A' and resid 210 through 222 Processing helix chain 'A' and resid 240 through 260 Proline residue: A 247 - end of helix removed outlier: 3.996A pdb=" N PHE A 257 " --> pdb=" O MET A 253 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N ASN A 260 " --> pdb=" O TYR A 256 " (cutoff:3.500A) Processing helix chain 'A' and resid 272 through 285 Processing helix chain 'A' and resid 291 through 293 No H-bonds generated for 'chain 'A' and resid 291 through 293' Processing helix chain 'A' and resid 300 through 308 removed outlier: 3.648A pdb=" N LEU A 305 " --> pdb=" O LEU A 301 " (cutoff:3.500A) removed outlier: 5.157A pdb=" N ARG A 308 " --> pdb=" O ARG A 304 " (cutoff:3.500A) Processing helix chain 'A' and resid 314 through 316 No H-bonds generated for 'chain 'A' and resid 314 through 316' Processing helix chain 'A' and resid 330 through 332 No H-bonds generated for 'chain 'A' and resid 330 through 332' Processing helix chain 'A' and resid 337 through 343 Processing helix chain 'A' and resid 354 through 358 Processing helix chain 'A' and resid 375 through 378 removed outlier: 3.637A pdb=" N ALA A 378 " --> pdb=" O GLY A 375 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 375 through 378' Processing helix chain 'A' and resid 381 through 399 removed outlier: 4.557A pdb=" N THR A 389 " --> pdb=" O GLN A 385 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N LEU A 392 " --> pdb=" O GLY A 388 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N GLU A 399 " --> pdb=" O ALA A 395 " (cutoff:3.500A) Processing helix chain 'A' and resid 402 through 405 removed outlier: 3.653A pdb=" N GLN A 405 " --> pdb=" O ALA A 402 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 402 through 405' Processing helix chain 'A' and resid 412 through 427 removed outlier: 3.724A pdb=" N VAL A 422 " --> pdb=" O LEU A 418 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N ARG A 423 " --> pdb=" O SER A 419 " (cutoff:3.500A) Processing helix chain 'A' and resid 438 through 450 Processing helix chain 'A' and resid 458 through 475 removed outlier: 4.373A pdb=" N THR A 462 " --> pdb=" O SER A 459 " (cutoff:3.500A) removed outlier: 4.575A pdb=" N LEU A 469 " --> pdb=" O ASN A 466 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N GLN A 475 " --> pdb=" O VAL A 472 " (cutoff:3.500A) Processing helix chain 'A' and resid 477 through 486 Processing helix chain 'A' and resid 491 through 506 Processing helix chain 'B' and resid 10 through 16 Processing helix chain 'B' and resid 79 through 81 No H-bonds generated for 'chain 'B' and resid 79 through 81' Processing helix chain 'B' and resid 101 through 103 No H-bonds generated for 'chain 'B' and resid 101 through 103' Processing helix chain 'B' and resid 151 through 155 Processing helix chain 'B' and resid 175 through 187 removed outlier: 3.654A pdb=" N GLN B 186 " --> pdb=" O THR B 182 " (cutoff:3.500A) removed outlier: 4.509A pdb=" N LYS B 187 " --> pdb=" O ILE B 183 " (cutoff:3.500A) Processing helix chain 'B' and resid 189 through 191 No H-bonds generated for 'chain 'B' and resid 189 through 191' Processing helix chain 'B' and resid 210 through 222 Processing helix chain 'B' and resid 240 through 260 removed outlier: 3.693A pdb=" N LEU B 245 " --> pdb=" O PRO B 241 " (cutoff:3.500A) Proline residue: B 247 - end of helix removed outlier: 4.133A pdb=" N PHE B 257 " --> pdb=" O MET B 253 " (cutoff:3.500A) Processing helix chain 'B' and resid 275 through 285 Processing helix chain 'B' and resid 291 through 293 No H-bonds generated for 'chain 'B' and resid 291 through 293' Processing helix chain 'B' and resid 296 through 298 No H-bonds generated for 'chain 'B' and resid 296 through 298' Processing helix chain 'B' and resid 300 through 308 removed outlier: 3.693A pdb=" N LEU B 305 " --> pdb=" O LEU B 301 " (cutoff:3.500A) removed outlier: 4.296A pdb=" N ARG B 308 " --> pdb=" O ARG B 304 " (cutoff:3.500A) Processing helix chain 'B' and resid 314 through 316 No H-bonds generated for 'chain 'B' and resid 314 through 316' Processing helix chain 'B' and resid 330 through 332 No H-bonds generated for 'chain 'B' and resid 330 through 332' Processing helix chain 'B' and resid 337 through 343 Processing helix chain 'B' and resid 354 through 359 removed outlier: 3.518A pdb=" N TYR B 358 " --> pdb=" O THR B 354 " (cutoff:3.500A) Processing helix chain 'B' and resid 381 through 400 removed outlier: 4.239A pdb=" N THR B 389 " --> pdb=" O GLN B 385 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N MET B 390 " --> pdb=" O VAL B 386 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N VAL B 400 " --> pdb=" O GLN B 396 " (cutoff:3.500A) Processing helix chain 'B' and resid 412 through 428 Processing helix chain 'B' and resid 438 through 449 Processing helix chain 'B' and resid 458 through 475 removed outlier: 4.410A pdb=" N THR B 462 " --> pdb=" O SER B 459 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N PHE B 464 " --> pdb=" O ILE B 461 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N ILE B 473 " --> pdb=" O SER B 470 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N GLN B 475 " --> pdb=" O VAL B 472 " (cutoff:3.500A) Processing helix chain 'B' and resid 477 through 485 Processing helix chain 'B' and resid 491 through 506 Processing helix chain 'C' and resid 9 through 16 removed outlier: 3.934A pdb=" N GLU C 14 " --> pdb=" O SER C 10 " (cutoff:3.500A) Processing helix chain 'C' and resid 20 through 22 No H-bonds generated for 'chain 'C' and resid 20 through 22' Processing helix chain 'C' and resid 151 through 156 Processing helix chain 'C' and resid 175 through 190 removed outlier: 3.664A pdb=" N GLN C 186 " --> pdb=" O THR C 182 " (cutoff:3.500A) removed outlier: 4.420A pdb=" N LYS C 187 " --> pdb=" O ILE C 183 " (cutoff:3.500A) removed outlier: 4.931A pdb=" N ARG C 188 " --> pdb=" O ILE C 184 " (cutoff:3.500A) removed outlier: 4.672A pdb=" N PHE C 189 " --> pdb=" O ASN C 185 " (cutoff:3.500A) Processing helix chain 'C' and resid 210 through 222 Processing helix chain 'C' and resid 240 through 260 Proline residue: C 247 - end of helix removed outlier: 3.870A pdb=" N PHE C 257 " --> pdb=" O MET C 253 " (cutoff:3.500A) Processing helix chain 'C' and resid 271 through 285 removed outlier: 3.610A pdb=" N VAL C 276 " --> pdb=" O SER C 272 " (cutoff:3.500A) Processing helix chain 'C' and resid 291 through 293 No H-bonds generated for 'chain 'C' and resid 291 through 293' Processing helix chain 'C' and resid 298 through 308 removed outlier: 3.963A pdb=" N HIS C 302 " --> pdb=" O VAL C 298 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N LEU C 305 " --> pdb=" O LEU C 301 " (cutoff:3.500A) removed outlier: 4.520A pdb=" N ARG C 308 " --> pdb=" O ARG C 304 " (cutoff:3.500A) Processing helix chain 'C' and resid 314 through 316 No H-bonds generated for 'chain 'C' and resid 314 through 316' Processing helix chain 'C' and resid 337 through 343 Processing helix chain 'C' and resid 375 through 378 Processing helix chain 'C' and resid 381 through 399 removed outlier: 3.918A pdb=" N THR C 389 " --> pdb=" O GLN C 385 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N LEU C 392 " --> pdb=" O GLY C 388 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N GLU C 399 " --> pdb=" O ALA C 395 " (cutoff:3.500A) Processing helix chain 'C' and resid 413 through 428 Processing helix chain 'C' and resid 438 through 450 Processing helix chain 'C' and resid 458 through 475 removed outlier: 4.039A pdb=" N THR C 462 " --> pdb=" O PRO C 458 " (cutoff:3.500A) removed outlier: 4.730A pdb=" N LYS C 463 " --> pdb=" O SER C 459 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N ASN C 466 " --> pdb=" O THR C 462 " (cutoff:3.500A) Processing helix chain 'C' and resid 477 through 486 Processing helix chain 'C' and resid 491 through 506 Processing helix chain 'D' and resid 123 through 125 No H-bonds generated for 'chain 'D' and resid 123 through 125' Processing helix chain 'D' and resid 138 through 143 Processing helix chain 'D' and resid 162 through 176 removed outlier: 3.788A pdb=" N LYS D 175 " --> pdb=" O ASN D 171 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N ALA D 176 " --> pdb=" O ASN D 172 " (cutoff:3.500A) Processing helix chain 'D' and resid 190 through 203 Processing helix chain 'D' and resid 226 through 229 No H-bonds generated for 'chain 'D' and resid 226 through 229' Processing helix chain 'D' and resid 232 through 245 Processing helix chain 'D' and resid 260 through 272 removed outlier: 3.852A pdb=" N GLY D 265 " --> pdb=" O PHE D 261 " (cutoff:3.500A) removed outlier: 4.194A pdb=" N ALA D 270 " --> pdb=" O SER D 266 " (cutoff:3.500A) removed outlier: 4.971A pdb=" N LEU D 271 " --> pdb=" O GLU D 267 " (cutoff:3.500A) Processing helix chain 'D' and resid 285 through 293 removed outlier: 4.177A pdb=" N MET D 292 " --> pdb=" O ASP D 288 " (cutoff:3.500A) Processing helix chain 'D' and resid 313 through 315 No H-bonds generated for 'chain 'D' and resid 313 through 315' Processing helix chain 'D' and resid 320 through 328 removed outlier: 4.540A pdb=" N ALA D 327 " --> pdb=" O ALA D 323 " (cutoff:3.500A) removed outlier: 4.532A pdb=" N HIS D 328 " --> pdb=" O THR D 324 " (cutoff:3.500A) Processing helix chain 'D' and resid 337 through 341 Processing helix chain 'D' and resid 365 through 391 removed outlier: 3.983A pdb=" N ASP D 386 " --> pdb=" O LYS D 382 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N ILE D 387 " --> pdb=" O SER D 383 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N ILE D 390 " --> pdb=" O ASP D 386 " (cutoff:3.500A) Processing helix chain 'D' and resid 401 through 414 Processing helix chain 'D' and resid 422 through 425 No H-bonds generated for 'chain 'D' and resid 422 through 425' Processing helix chain 'D' and resid 434 through 446 Processing helix chain 'D' and resid 454 through 457 Processing helix chain 'D' and resid 463 through 476 Processing helix chain 'E' and resid 138 through 142 Processing helix chain 'E' and resid 162 through 176 Processing helix chain 'E' and resid 190 through 203 Processing helix chain 'E' and resid 226 through 229 No H-bonds generated for 'chain 'E' and resid 226 through 229' Processing helix chain 'E' and resid 232 through 245 Processing helix chain 'E' and resid 259 through 272 Processing helix chain 'E' and resid 285 through 295 removed outlier: 3.740A pdb=" N MET E 292 " --> pdb=" O ASP E 288 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N ARG E 295 " --> pdb=" O THR E 291 " (cutoff:3.500A) Processing helix chain 'E' and resid 313 through 315 No H-bonds generated for 'chain 'E' and resid 313 through 315' Processing helix chain 'E' and resid 320 through 326 Processing helix chain 'E' and resid 337 through 340 No H-bonds generated for 'chain 'E' and resid 337 through 340' Processing helix chain 'E' and resid 360 through 363 No H-bonds generated for 'chain 'E' and resid 360 through 363' Processing helix chain 'E' and resid 365 through 390 removed outlier: 3.970A pdb=" N ASP E 386 " --> pdb=" O LYS E 382 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N ILE E 387 " --> pdb=" O SER E 383 " (cutoff:3.500A) Processing helix chain 'E' and resid 393 through 395 No H-bonds generated for 'chain 'E' and resid 393 through 395' Processing helix chain 'E' and resid 398 through 414 Processing helix chain 'E' and resid 422 through 425 No H-bonds generated for 'chain 'E' and resid 422 through 425' Processing helix chain 'E' and resid 434 through 446 Processing helix chain 'E' and resid 454 through 456 No H-bonds generated for 'chain 'E' and resid 454 through 456' Processing helix chain 'E' and resid 463 through 474 removed outlier: 3.717A pdb=" N ALA E 474 " --> pdb=" O ALA E 470 " (cutoff:3.500A) Processing helix chain 'F' and resid 138 through 143 Processing helix chain 'F' and resid 162 through 176 removed outlier: 3.655A pdb=" N ALA F 176 " --> pdb=" O ASN F 172 " (cutoff:3.500A) Processing helix chain 'F' and resid 190 through 202 removed outlier: 3.680A pdb=" N GLU F 202 " --> pdb=" O HIS F 198 " (cutoff:3.500A) Processing helix chain 'F' and resid 226 through 229 No H-bonds generated for 'chain 'F' and resid 226 through 229' Processing helix chain 'F' and resid 232 through 245 removed outlier: 3.700A pdb=" N PHE F 243 " --> pdb=" O VAL F 239 " (cutoff:3.500A) Processing helix chain 'F' and resid 258 through 267 Processing helix chain 'F' and resid 285 through 293 removed outlier: 3.559A pdb=" N MET F 292 " --> pdb=" O ASP F 288 " (cutoff:3.500A) Processing helix chain 'F' and resid 313 through 315 No H-bonds generated for 'chain 'F' and resid 313 through 315' Processing helix chain 'F' and resid 320 through 327 removed outlier: 4.716A pdb=" N ALA F 327 " --> pdb=" O ALA F 323 " (cutoff:3.500A) Processing helix chain 'F' and resid 337 through 342 removed outlier: 3.645A pdb=" N LEU F 342 " --> pdb=" O ALA F 338 " (cutoff:3.500A) Processing helix chain 'F' and resid 365 through 391 removed outlier: 4.266A pdb=" N ASP F 386 " --> pdb=" O LYS F 382 " (cutoff:3.500A) removed outlier: 4.850A pdb=" N ILE F 387 " --> pdb=" O SER F 383 " (cutoff:3.500A) removed outlier: 4.158A pdb=" N ILE F 390 " --> pdb=" O ASP F 386 " (cutoff:3.500A) Processing helix chain 'F' and resid 393 through 395 No H-bonds generated for 'chain 'F' and resid 393 through 395' Processing helix chain 'F' and resid 398 through 414 Processing helix chain 'F' and resid 422 through 425 No H-bonds generated for 'chain 'F' and resid 422 through 425' Processing helix chain 'F' and resid 434 through 446 Processing helix chain 'F' and resid 454 through 457 Processing helix chain 'F' and resid 463 through 473 Processing helix chain 'G' and resid 3 through 54 removed outlier: 3.975A pdb=" N LYS G 39 " --> pdb=" O GLU G 35 " (cutoff:3.500A) Proline residue: G 40 - end of helix removed outlier: 3.509A pdb=" N VAL G 43 " --> pdb=" O LYS G 39 " (cutoff:3.500A) removed outlier: 4.393A pdb=" N LEU G 51 " --> pdb=" O GLY G 47 " (cutoff:3.500A) removed outlier: 5.144A pdb=" N TYR G 52 " --> pdb=" O SER G 48 " (cutoff:3.500A) Processing helix chain 'G' and resid 81 through 99 removed outlier: 3.860A pdb=" N ALA G 99 " --> pdb=" O ASN G 95 " (cutoff:3.500A) Processing helix chain 'G' and resid 110 through 115 Processing helix chain 'G' and resid 138 through 150 Processing helix chain 'G' and resid 181 through 185 Processing helix chain 'G' and resid 188 through 192 removed outlier: 3.930A pdb=" N ILE G 192 " --> pdb=" O SER G 189 " (cutoff:3.500A) Processing helix chain 'G' and resid 200 through 270 removed outlier: 3.873A pdb=" N LYS G 245 " --> pdb=" O GLU G 241 " (cutoff:3.500A) Processing helix chain 'H' and resid 100 through 102 No H-bonds generated for 'chain 'H' and resid 100 through 102' Processing helix chain 'H' and resid 105 through 119 Processing helix chain 'H' and resid 125 through 145 Processing helix chain 'I' and resid 3 through 7 removed outlier: 3.920A pdb=" N ALA I 7 " --> pdb=" O TYR I 3 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 3 through 7' Processing helix chain 'I' and resid 11 through 24 Processing helix chain 'I' and resid 28 through 34 removed outlier: 4.231A pdb=" N ALA I 32 " --> pdb=" O THR I 28 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N ASN I 33 " --> pdb=" O GLU I 29 " (cutoff:3.500A) Processing helix chain 'J' and resid 14 through 18 Processing helix chain 'J' and resid 21 through 53 Processing helix chain 'K' and resid 2 through 12 removed outlier: 4.746A pdb=" N PHE K 8 " --> pdb=" O THR K 4 " (cutoff:3.500A) Processing helix chain 'K' and resid 16 through 38 removed outlier: 3.587A pdb=" N GLY K 20 " --> pdb=" O GLY K 17 " (cutoff:3.500A) removed outlier: 4.337A pdb=" N LEU K 32 " --> pdb=" O PHE K 29 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N ARG K 38 " --> pdb=" O GLY K 35 " (cutoff:3.500A) Processing helix chain 'K' and resid 44 through 72 removed outlier: 5.296A pdb=" N ILE K 51 " --> pdb=" O SER K 48 " (cutoff:3.500A) Processing helix chain 'L' and resid 2 through 38 removed outlier: 4.490A pdb=" N LYS L 7 " --> pdb=" O ASP L 3 " (cutoff:3.500A) removed outlier: 4.626A pdb=" N PHE L 8 " --> pdb=" O THR L 4 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N ILE L 9 " --> pdb=" O ALA L 5 " (cutoff:3.500A) removed outlier: 4.836A pdb=" N GLY L 17 " --> pdb=" O ALA L 13 " (cutoff:3.500A) removed outlier: 4.867A pdb=" N VAL L 18 " --> pdb=" O ALA L 14 " (cutoff:3.500A) removed outlier: 4.991A pdb=" N ALA L 19 " --> pdb=" O THR L 15 " (cutoff:3.500A) removed outlier: 4.914A pdb=" N GLY L 20 " --> pdb=" O VAL L 16 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N SER L 21 " --> pdb=" O GLY L 17 " (cutoff:3.500A) Processing helix chain 'L' and resid 46 through 72 removed outlier: 3.938A pdb=" N CYS L 64 " --> pdb=" O MET L 60 " (cutoff:3.500A) Processing helix chain 'M' and resid 2 through 14 Processing helix chain 'M' and resid 19 through 38 Processing helix chain 'M' and resid 45 through 73 removed outlier: 3.884A pdb=" N LEU M 52 " --> pdb=" O SER M 48 " (cutoff:3.500A) Processing helix chain 'N' and resid 2 through 16 removed outlier: 4.376A pdb=" N VAL N 16 " --> pdb=" O GLY N 12 " (cutoff:3.500A) Processing helix chain 'N' and resid 19 through 37 Processing helix chain 'N' and resid 46 through 72 removed outlier: 4.497A pdb=" N MET N 60 " --> pdb=" O LEU N 56 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N GLY N 61 " --> pdb=" O SER N 57 " (cutoff:3.500A) Processing helix chain 'O' and resid 2 through 39 removed outlier: 3.969A pdb=" N VAL O 16 " --> pdb=" O GLY O 12 " (cutoff:3.500A) removed outlier: 4.237A pdb=" N GLY O 17 " --> pdb=" O ALA O 13 " (cutoff:3.500A) removed outlier: 5.048A pdb=" N VAL O 18 " --> pdb=" O ALA O 14 " (cutoff:3.500A) removed outlier: 5.137A pdb=" N ALA O 19 " --> pdb=" O THR O 15 " (cutoff:3.500A) removed outlier: 4.453A pdb=" N GLY O 20 " --> pdb=" O VAL O 16 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N SER O 21 " --> pdb=" O GLY O 17 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N ILE O 33 " --> pdb=" O PHE O 29 " (cutoff:3.500A) Processing helix chain 'O' and resid 46 through 72 removed outlier: 4.851A pdb=" N MET O 60 " --> pdb=" O LEU O 56 " (cutoff:3.500A) removed outlier: 4.149A pdb=" N GLY O 61 " --> pdb=" O SER O 57 " (cutoff:3.500A) Processing helix chain 'P' and resid 2 through 36 removed outlier: 3.633A pdb=" N VAL P 16 " --> pdb=" O GLY P 12 " (cutoff:3.500A) removed outlier: 5.082A pdb=" N GLY P 17 " --> pdb=" O ALA P 13 " (cutoff:3.500A) removed outlier: 5.085A pdb=" N VAL P 18 " --> pdb=" O ALA P 14 " (cutoff:3.500A) removed outlier: 4.932A pdb=" N ALA P 19 " --> pdb=" O THR P 15 " (cutoff:3.500A) removed outlier: 4.854A pdb=" N GLY P 20 " --> pdb=" O VAL P 16 " (cutoff:3.500A) removed outlier: 4.530A pdb=" N SER P 21 " --> pdb=" O GLY P 17 " (cutoff:3.500A) Processing helix chain 'P' and resid 44 through 73 removed outlier: 3.735A pdb=" N SER P 48 " --> pdb=" O GLN P 45 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N LEU P 56 " --> pdb=" O GLY P 53 " (cutoff:3.500A) removed outlier: 4.908A pdb=" N ALA P 59 " --> pdb=" O LEU P 56 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N MET P 60 " --> pdb=" O SER P 57 " (cutoff:3.500A) Processing helix chain 'Q' and resid 2 through 36 removed outlier: 3.974A pdb=" N VAL Q 16 " --> pdb=" O GLY Q 12 " (cutoff:3.500A) removed outlier: 5.234A pdb=" N GLY Q 17 " --> pdb=" O ALA Q 13 " (cutoff:3.500A) removed outlier: 4.931A pdb=" N VAL Q 18 " --> pdb=" O ALA Q 14 " (cutoff:3.500A) removed outlier: 4.787A pdb=" N ALA Q 19 " --> pdb=" O THR Q 15 " (cutoff:3.500A) removed outlier: 4.593A pdb=" N GLY Q 20 " --> pdb=" O VAL Q 16 " (cutoff:3.500A) removed outlier: 4.527A pdb=" N SER Q 21 " --> pdb=" O GLY Q 17 " (cutoff:3.500A) Processing helix chain 'Q' and resid 46 through 72 removed outlier: 3.697A pdb=" N MET Q 60 " --> pdb=" O LEU Q 56 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N GLY Q 61 " --> pdb=" O SER Q 57 " (cutoff:3.500A) Processing helix chain 'R' and resid 2 through 38 removed outlier: 4.151A pdb=" N VAL R 16 " --> pdb=" O GLY R 12 " (cutoff:3.500A) removed outlier: 4.493A pdb=" N GLY R 17 " --> pdb=" O ALA R 13 " (cutoff:3.500A) removed outlier: 5.110A pdb=" N VAL R 18 " --> pdb=" O ALA R 14 " (cutoff:3.500A) removed outlier: 4.977A pdb=" N ALA R 19 " --> pdb=" O THR R 15 " (cutoff:3.500A) removed outlier: 4.701A pdb=" N GLY R 20 " --> pdb=" O VAL R 16 " (cutoff:3.500A) removed outlier: 4.193A pdb=" N SER R 21 " --> pdb=" O GLY R 17 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N ILE R 33 " --> pdb=" O PHE R 29 " (cutoff:3.500A) Processing helix chain 'R' and resid 46 through 73 removed outlier: 5.143A pdb=" N MET R 60 " --> pdb=" O LEU R 56 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N GLY R 61 " --> pdb=" O SER R 57 " (cutoff:3.500A) Processing helix chain 'S' and resid 13 through 27 Processing helix chain 'S' and resid 32 through 46 removed outlier: 3.723A pdb=" N GLN S 44 " --> pdb=" O LEU S 40 " (cutoff:3.500A) Processing helix chain 'S' and resid 49 through 56 removed outlier: 3.598A pdb=" N LEU S 56 " --> pdb=" O ALA S 52 " (cutoff:3.500A) Processing helix chain 'S' and resid 62 through 75 Processing helix chain 'S' and resid 80 through 92 Processing helix chain 'S' and resid 95 through 113 Proline residue: S 99 - end of helix removed outlier: 3.813A pdb=" N ILE S 102 " --> pdb=" O PRO S 99 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N SER S 103 " --> pdb=" O ALA S 100 " (cutoff:3.500A) removed outlier: 4.333A pdb=" N VAL S 111 " --> pdb=" O MET S 108 " (cutoff:3.500A) Processing helix chain 'S' and resid 128 through 141 removed outlier: 3.668A pdb=" N SER S 140 " --> pdb=" O THR S 136 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N PHE S 141 " --> pdb=" O VAL S 137 " (cutoff:3.500A) Processing helix chain 'S' and resid 175 through 187 Processing helix chain '8' and resid 2 through 4 No H-bonds generated for 'chain '8' and resid 2 through 4' Processing helix chain '8' and resid 6 through 21 removed outlier: 4.732A pdb=" N LEU 8 10 " --> pdb=" O SER 8 7 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N LEU 8 14 " --> pdb=" O THR 8 11 " (cutoff:3.500A) removed outlier: 4.369A pdb=" N LEU 8 18 " --> pdb=" O SER 8 15 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N PHE 8 21 " --> pdb=" O LEU 8 18 " (cutoff:3.500A) Processing helix chain '8' and resid 24 through 28 Processing helix chain 'a' and resid 7 through 9 No H-bonds generated for 'chain 'a' and resid 7 through 9' Processing helix chain 'a' and resid 19 through 30 removed outlier: 3.618A pdb=" N PHE a 26 " --> pdb=" O ILE a 23 " (cutoff:3.500A) Proline residue: a 27 - end of helix Processing helix chain 'a' and resid 41 through 60 removed outlier: 3.897A pdb=" N SER a 59 " --> pdb=" O LYS a 55 " (cutoff:3.500A) removed outlier: 5.916A pdb=" N ILE a 60 " --> pdb=" O GLN a 56 " (cutoff:3.500A) Processing helix chain 'a' and resid 63 through 87 removed outlier: 4.737A pdb=" N LEU a 70 " --> pdb=" O GLN a 66 " (cutoff:3.500A) removed outlier: 5.220A pdb=" N MET a 71 " --> pdb=" O THR a 67 " (cutoff:3.500A) removed outlier: 4.232A pdb=" N LEU a 87 " --> pdb=" O ASN a 83 " (cutoff:3.500A) Processing helix chain 'a' and resid 94 through 96 No H-bonds generated for 'chain 'a' and resid 94 through 96' Processing helix chain 'a' and resid 98 through 119 Proline residue: a 107 - end of helix Processing helix chain 'a' and resid 121 through 128 removed outlier: 4.432A pdb=" N PHE a 128 " --> pdb=" O SER a 124 " (cutoff:3.500A) Processing helix chain 'a' and resid 135 through 137 No H-bonds generated for 'chain 'a' and resid 135 through 137' Processing helix chain 'a' and resid 139 through 183 removed outlier: 4.521A pdb=" N ILE a 144 " --> pdb=" O MET a 140 " (cutoff:3.500A) Proline residue: a 153 - end of helix removed outlier: 4.337A pdb=" N SER a 183 " --> pdb=" O LEU a 179 " (cutoff:3.500A) Processing helix chain 'a' and resid 186 through 224 Processing helix chain 'd' and resid 12 through 18 removed outlier: 4.415A pdb=" N GLU d 17 " --> pdb=" O VAL d 13 " (cutoff:3.500A) removed outlier: 4.362A pdb=" N ILE d 18 " --> pdb=" O ALA d 14 " (cutoff:3.500A) Processing helix chain 'd' and resid 21 through 43 removed outlier: 5.376A pdb=" N ALA d 25 " --> pdb=" O ASN d 22 " (cutoff:3.500A) removed outlier: 4.411A pdb=" N VAL d 26 " --> pdb=" O GLN d 23 " (cutoff:3.500A) removed outlier: 4.352A pdb=" N THR d 43 " --> pdb=" O ARG d 40 " (cutoff:3.500A) Processing helix chain 'd' and resid 53 through 59 Processing helix chain 'd' and resid 63 through 75 Processing helix chain 'd' and resid 86 through 122 removed outlier: 3.574A pdb=" N GLU d 95 " --> pdb=" O GLU d 92 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N SER d 99 " --> pdb=" O ASP d 96 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N CYS d 100 " --> pdb=" O VAL d 97 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ALA d 101 " --> pdb=" O LYS d 98 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N GLU d 102 " --> pdb=" O SER d 99 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N PHE d 103 " --> pdb=" O CYS d 100 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N LEU d 104 " --> pdb=" O ALA d 101 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N GLN d 106 " --> pdb=" O PHE d 103 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N SER d 107 " --> pdb=" O LEU d 104 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N THR d 109 " --> pdb=" O GLN d 106 " (cutoff:3.500A) Processing helix chain 'd' and resid 127 through 129 No H-bonds generated for 'chain 'd' and resid 127 through 129' Processing helix chain 'd' and resid 132 through 138 Processing helix chain 'd' and resid 140 through 142 No H-bonds generated for 'chain 'd' and resid 140 through 142' Processing helix chain 'f' and resid 16 through 25 Proline residue: f 20 - end of helix Processing helix chain 'f' and resid 30 through 48 Processing helix chain 'f' and resid 56 through 79 removed outlier: 4.857A pdb=" N MET f 61 " --> pdb=" O GLY f 58 " (cutoff:3.500A) removed outlier: 4.794A pdb=" N LYS f 76 " --> pdb=" O ARG f 73 " (cutoff:3.500A) Processing helix chain 'g' and resid 22 through 33 Processing helix chain 'g' and resid 42 through 60 Proline residue: g 46 - end of helix Processing helix chain 'g' and resid 63 through 66 Processing helix chain 'g' and resid 69 through 93 removed outlier: 3.746A pdb=" N TRP g 85 " --> pdb=" O GLU g 81 " (cutoff:3.500A) removed outlier: 4.328A pdb=" N PHE g 86 " --> pdb=" O VAL g 82 " (cutoff:3.500A) removed outlier: 4.242A pdb=" N TYR g 87 " --> pdb=" O TRP g 83 " (cutoff:3.500A) Processing helix chain 'j' and resid 3 through 12 removed outlier: 3.989A pdb=" N ILE j 11 " --> pdb=" O LYS j 7 " (cutoff:3.500A) Proline residue: j 12 - end of helix Processing helix chain 'j' and resid 14 through 18 Processing helix chain 'j' and resid 22 through 47 Processing helix chain 'b' and resid 19 through 29 Proline residue: b 27 - end of helix Processing helix chain 'b' and resid 33 through 48 Processing helix chain 'b' and resid 55 through 186 removed outlier: 5.821A pdb=" N ALA b 76 " --> pdb=" O LYS b 72 " (cutoff:3.500A) removed outlier: 5.374A pdb=" N SER b 77 " --> pdb=" O LYS b 73 " (cutoff:3.500A) removed outlier: 5.018A pdb=" N HIS b 122 " --> pdb=" O VAL b 118 " (cutoff:3.500A) removed outlier: 6.585A pdb=" N TYR b 123 " --> pdb=" O GLN b 119 " (cutoff:3.500A) removed outlier: 5.577A pdb=" N LEU b 124 " --> pdb=" O LYS b 120 " (cutoff:3.500A) removed outlier: 4.890A pdb=" N PHE b 125 " --> pdb=" O ARG b 121 " (cutoff:3.500A) removed outlier: 4.281A pdb=" N HIS b 158 " --> pdb=" O ARG b 154 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N ILE b 159 " --> pdb=" O LEU b 155 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N VAL b 161 " --> pdb=" O TYR b 157 " (cutoff:3.500A) removed outlier: 4.625A pdb=" N SER b 186 " --> pdb=" O VAL b 182 " (cutoff:3.500A) Processing helix chain 'b' and resid 190 through 208 Processing helix chain 'h' and resid 9 through 26 removed outlier: 4.063A pdb=" N GLY h 26 " --> pdb=" O ARG h 22 " (cutoff:3.500A) Processing helix chain 'h' and resid 33 through 50 Processing helix chain 'k' and resid 14 through 17 No H-bonds generated for 'chain 'k' and resid 14 through 17' Processing helix chain 'k' and resid 23 through 45 Processing helix chain 'e' and resid 8 through 56 Proline residue: e 34 - end of helix Processing sheet with id= A, first strand: chain 'A' and resid 28 through 30 removed outlier: 3.818A pdb=" N GLU A 51 " --> pdb=" O SER A 63 " (cutoff:3.500A) removed outlier: 6.232A pdb=" N GLY A 72 " --> pdb=" O LEU A 64 " (cutoff:3.500A) removed outlier: 5.876A pdb=" N HIS A 42 " --> pdb=" O VAL A 31 " (cutoff:3.500A) removed outlier: 5.268A pdb=" N VAL A 31 " --> pdb=" O HIS A 42 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 96 through 98 Processing sheet with id= C, first strand: chain 'A' and resid 349 through 352 removed outlier: 7.321A pdb=" N LEU A 166 " --> pdb=" O ILE A 350 " (cutoff:3.500A) removed outlier: 7.967A pdb=" N LEU A 352 " --> pdb=" O LEU A 166 " (cutoff:3.500A) removed outlier: 7.275A pdb=" N ILE A 168 " --> pdb=" O LEU A 352 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 229 through 234 removed outlier: 7.064A pdb=" N CYS A 201 " --> pdb=" O ILE A 230 " (cutoff:3.500A) removed outlier: 7.912A pdb=" N VAL A 232 " --> pdb=" O CYS A 201 " (cutoff:3.500A) removed outlier: 6.257A pdb=" N TYR A 203 " --> pdb=" O VAL A 232 " (cutoff:3.500A) removed outlier: 7.329A pdb=" N ALA A 234 " --> pdb=" O TYR A 203 " (cutoff:3.500A) removed outlier: 6.121A pdb=" N ALA A 205 " --> pdb=" O ALA A 234 " (cutoff:3.500A) removed outlier: 6.457A pdb=" N SER A 320 " --> pdb=" O ALA A 264 " (cutoff:3.500A) removed outlier: 7.895A pdb=" N ILE A 266 " --> pdb=" O SER A 320 " (cutoff:3.500A) removed outlier: 6.407A pdb=" N THR A 322 " --> pdb=" O ILE A 266 " (cutoff:3.500A) removed outlier: 7.731A pdb=" N TYR A 268 " --> pdb=" O THR A 322 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 28 through 30 removed outlier: 6.454A pdb=" N GLY B 72 " --> pdb=" O LEU B 64 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N ILE B 38 " --> pdb=" O GLY B 35 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N GLY B 35 " --> pdb=" O ILE B 38 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N SER B 33 " --> pdb=" O ARG B 40 " (cutoff:3.500A) removed outlier: 5.717A pdb=" N HIS B 42 " --> pdb=" O VAL B 31 " (cutoff:3.500A) removed outlier: 5.373A pdb=" N VAL B 31 " --> pdb=" O HIS B 42 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 96 through 99 removed outlier: 4.027A pdb=" N ALA B 125 " --> pdb=" O VAL B 99 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 350 through 352 removed outlier: 8.058A pdb=" N GLU B 165 " --> pdb=" O LEU B 321 " (cutoff:3.500A) removed outlier: 6.002A pdb=" N ALA B 323 " --> pdb=" O GLU B 165 " (cutoff:3.500A) removed outlier: 7.265A pdb=" N ILE B 167 " --> pdb=" O ALA B 323 " (cutoff:3.500A) removed outlier: 8.076A pdb=" N GLY B 169 " --> pdb=" O PRO B 325 " (cutoff:3.500A) removed outlier: 6.216A pdb=" N ILE B 327 " --> pdb=" O GLY B 169 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N TYR B 268 " --> pdb=" O LEU B 324 " (cutoff:3.500A) removed outlier: 6.385A pdb=" N TYR B 200 " --> pdb=" O LEU B 265 " (cutoff:3.500A) removed outlier: 8.165A pdb=" N ILE B 267 " --> pdb=" O TYR B 200 " (cutoff:3.500A) removed outlier: 7.119A pdb=" N ILE B 202 " --> pdb=" O ILE B 267 " (cutoff:3.500A) removed outlier: 8.179A pdb=" N ASP B 269 " --> pdb=" O ILE B 202 " (cutoff:3.500A) removed outlier: 6.335A pdb=" N VAL B 204 " --> pdb=" O ASP B 269 " (cutoff:3.500A) removed outlier: 6.274A pdb=" N ILE B 230 " --> pdb=" O TYR B 203 " (cutoff:3.500A) removed outlier: 7.253A pdb=" N ALA B 205 " --> pdb=" O ILE B 230 " (cutoff:3.500A) removed outlier: 6.337A pdb=" N VAL B 232 " --> pdb=" O ALA B 205 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'C' and resid 87 through 89 removed outlier: 6.718A pdb=" N ARG C 40 " --> pdb=" O LEU C 32 " (cutoff:3.500A) removed outlier: 4.611A pdb=" N ILE C 34 " --> pdb=" O ILE C 38 " (cutoff:3.500A) removed outlier: 6.736A pdb=" N ILE C 38 " --> pdb=" O ILE C 34 " (cutoff:3.500A) removed outlier: 6.910A pdb=" N VAL C 74 " --> pdb=" O SER C 63 " (cutoff:3.500A) removed outlier: 5.681A pdb=" N SER C 63 " --> pdb=" O VAL C 74 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'C' and resid 96 through 99 removed outlier: 4.061A pdb=" N ALA C 125 " --> pdb=" O VAL C 99 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'C' and resid 350 through 352 removed outlier: 8.247A pdb=" N GLU C 165 " --> pdb=" O LEU C 321 " (cutoff:3.500A) removed outlier: 6.576A pdb=" N ALA C 323 " --> pdb=" O GLU C 165 " (cutoff:3.500A) removed outlier: 7.400A pdb=" N ILE C 167 " --> pdb=" O ALA C 323 " (cutoff:3.500A) removed outlier: 8.122A pdb=" N GLY C 169 " --> pdb=" O PRO C 325 " (cutoff:3.500A) removed outlier: 6.343A pdb=" N ILE C 327 " --> pdb=" O GLY C 169 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N TYR C 268 " --> pdb=" O LEU C 324 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'D' and resid 12 through 17 removed outlier: 6.515A pdb=" N ASP D 22 " --> pdb=" O VAL D 14 " (cutoff:3.500A) removed outlier: 4.563A pdb=" N VAL D 16 " --> pdb=" O VAL D 20 " (cutoff:3.500A) removed outlier: 6.879A pdb=" N VAL D 20 " --> pdb=" O VAL D 16 " (cutoff:3.500A) removed outlier: 5.904A pdb=" N ILE D 61 " --> pdb=" O VAL D 49 " (cutoff:3.500A) removed outlier: 5.534A pdb=" N VAL D 49 " --> pdb=" O ILE D 61 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'D' and resid 83 through 86 removed outlier: 4.170A pdb=" N GLN D 112 " --> pdb=" O VAL D 86 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'D' and resid 152 through 156 removed outlier: 3.903A pdb=" N LEU D 253 " --> pdb=" O THR D 305 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'E' and resid 10 through 12 removed outlier: 6.176A pdb=" N GLN E 24 " --> pdb=" O ILE E 13 " (cutoff:3.500A) removed outlier: 5.821A pdb=" N ILE E 13 " --> pdb=" O GLN E 24 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'E' and resid 83 through 85 Processing sheet with id= P, first strand: chain 'E' and resid 331 through 334 removed outlier: 8.242A pdb=" N ILE E 152 " --> pdb=" O ILE E 304 " (cutoff:3.500A) removed outlier: 6.655A pdb=" N SER E 306 " --> pdb=" O ILE E 152 " (cutoff:3.500A) removed outlier: 7.526A pdb=" N LEU E 154 " --> pdb=" O SER E 306 " (cutoff:3.500A) removed outlier: 6.671A pdb=" N GLN E 308 " --> pdb=" O LEU E 154 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'F' and resid 10 through 12 removed outlier: 4.414A pdb=" N LYS F 74 " --> pdb=" O GLN F 39 " (cutoff:3.500A) removed outlier: 6.578A pdb=" N ARG F 59 " --> pdb=" O ALA F 50 " (cutoff:3.500A) removed outlier: 4.763A pdb=" N HIS F 52 " --> pdb=" O THR F 57 " (cutoff:3.500A) removed outlier: 6.592A pdb=" N THR F 57 " --> pdb=" O HIS F 52 " (cutoff:3.500A) removed outlier: 5.892A pdb=" N GLN F 24 " --> pdb=" O ILE F 13 " (cutoff:3.500A) removed outlier: 5.422A pdb=" N ILE F 13 " --> pdb=" O GLN F 24 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'F' and resid 83 through 85 Processing sheet with id= S, first strand: chain 'F' and resid 331 through 334 removed outlier: 6.906A pdb=" N TYR F 180 " --> pdb=" O LEU F 252 " (cutoff:3.500A) removed outlier: 8.474A pdb=" N PHE F 254 " --> pdb=" O TYR F 180 " (cutoff:3.500A) removed outlier: 6.387A pdb=" N VAL F 182 " --> pdb=" O PHE F 254 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'G' and resid 172 through 178 removed outlier: 5.319A pdb=" N ASN G 163 " --> pdb=" O VAL G 71 " (cutoff:3.500A) removed outlier: 8.096A pdb=" N GLY G 107 " --> pdb=" O LEU G 125 " (cutoff:3.500A) removed outlier: 4.404A pdb=" N THR G 127 " --> pdb=" O GLY G 107 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'H' and resid 17 through 22 Processing sheet with id= V, first strand: chain 'H' and resid 45 through 47 removed outlier: 6.960A pdb=" N HIS H 66 " --> pdb=" O ARG H 34 " (cutoff:3.500A) removed outlier: 4.435A pdb=" N VAL H 36 " --> pdb=" O VAL H 64 " (cutoff:3.500A) removed outlier: 6.372A pdb=" N VAL H 64 " --> pdb=" O VAL H 36 " (cutoff:3.500A) removed outlier: 5.719A pdb=" N VAL H 38 " --> pdb=" O LEU H 62 " (cutoff:3.500A) removed outlier: 7.541A pdb=" N LEU H 62 " --> pdb=" O VAL H 38 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'S' and resid 152 through 154 removed outlier: 7.946A pdb=" N LYS S 153 " --> pdb=" O CYS S 118 " (cutoff:3.500A) removed outlier: 6.027A pdb=" N VAL S 120 " --> pdb=" O LYS S 153 " (cutoff:3.500A) 2046 hydrogen bonds defined for protein. 5514 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: 33.04 Time building geometry restraints manager: 58.50 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 40439 1.03 - 1.23: 237 1.23 - 1.42: 15932 1.42 - 1.62: 24183 1.62 - 1.81: 294 Bond restraints: 81085 Sorted by residual: bond pdb=" C4 ATP B 600 " pdb=" C5 ATP B 600 " ideal model delta sigma weight residual 1.388 1.460 -0.072 1.00e-02 1.00e+04 5.12e+01 bond pdb=" C4 ATP C 600 " pdb=" C5 ATP C 600 " ideal model delta sigma weight residual 1.388 1.458 -0.070 1.00e-02 1.00e+04 4.86e+01 bond pdb=" C4 ATP A 600 " pdb=" C5 ATP A 600 " ideal model delta sigma weight residual 1.388 1.458 -0.070 1.00e-02 1.00e+04 4.84e+01 bond pdb=" CB7 CDL b 301 " pdb=" OB8 CDL b 301 " ideal model delta sigma weight residual 1.334 1.409 -0.075 1.10e-02 8.26e+03 4.70e+01 bond pdb=" CB7 CDL f 102 " pdb=" OB8 CDL f 102 " ideal model delta sigma weight residual 1.334 1.409 -0.075 1.10e-02 8.26e+03 4.69e+01 ... (remaining 81080 not shown) Histogram of bond angle deviations from ideal: 94.58 - 102.95: 245 102.95 - 111.32: 93272 111.32 - 119.69: 24617 119.69 - 128.06: 28481 128.06 - 136.43: 265 Bond angle restraints: 146880 Sorted by residual: angle pdb=" PB ATP B 600 " pdb=" O3B ATP B 600 " pdb=" PG ATP B 600 " ideal model delta sigma weight residual 139.87 115.14 24.73 1.00e+00 1.00e+00 6.12e+02 angle pdb=" PB ATP C 600 " pdb=" O3B ATP C 600 " pdb=" PG ATP C 600 " ideal model delta sigma weight residual 139.87 116.51 23.36 1.00e+00 1.00e+00 5.46e+02 angle pdb=" PB ATP A 600 " pdb=" O3B ATP A 600 " pdb=" PG ATP A 600 " ideal model delta sigma weight residual 139.87 121.44 18.43 1.00e+00 1.00e+00 3.40e+02 angle pdb=" PA ATP B 600 " pdb=" O3A ATP B 600 " pdb=" PB ATP B 600 " ideal model delta sigma weight residual 136.83 119.49 17.34 1.00e+00 1.00e+00 3.01e+02 angle pdb=" PA ATP A 600 " pdb=" O3A ATP A 600 " pdb=" PB ATP A 600 " ideal model delta sigma weight residual 136.83 119.73 17.10 1.00e+00 1.00e+00 2.92e+02 ... (remaining 146875 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 19.27: 33874 19.27 - 38.54: 2956 38.54 - 57.82: 974 57.82 - 77.09: 108 77.09 - 96.36: 47 Dihedral angle restraints: 37959 sinusoidal: 21250 harmonic: 16709 Sorted by residual: dihedral pdb=" CA LEU D 391 " pdb=" C LEU D 391 " pdb=" N GLY D 392 " pdb=" CA GLY D 392 " ideal model delta harmonic sigma weight residual 180.00 -152.64 -27.36 0 5.00e+00 4.00e-02 2.99e+01 dihedral pdb=" CA ARG G 202 " pdb=" C ARG G 202 " pdb=" N ASN G 203 " pdb=" CA ASN G 203 " ideal model delta harmonic sigma weight residual 180.00 153.25 26.75 0 5.00e+00 4.00e-02 2.86e+01 dihedral pdb=" O2A ADP E 600 " pdb=" O3A ADP E 600 " pdb=" PA ADP E 600 " pdb=" PB ADP E 600 " ideal model delta sinusoidal sigma weight residual -60.00 -156.36 96.36 1 2.00e+01 2.50e-03 2.67e+01 ... (remaining 37956 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.043: 4226 0.043 - 0.086: 1660 0.086 - 0.128: 393 0.128 - 0.171: 66 0.171 - 0.214: 8 Chirality restraints: 6353 Sorted by residual: chirality pdb=" CA ARG G 202 " pdb=" N ARG G 202 " pdb=" C ARG G 202 " pdb=" CB ARG G 202 " both_signs ideal model delta sigma weight residual False 2.51 2.30 0.21 2.00e-01 2.50e+01 1.15e+00 chirality pdb=" CA PHE R 54 " pdb=" N PHE R 54 " pdb=" C PHE R 54 " pdb=" CB PHE R 54 " both_signs ideal model delta sigma weight residual False 2.51 2.30 0.21 2.00e-01 2.50e+01 1.14e+00 chirality pdb=" CA GLU b 87 " pdb=" N GLU b 87 " pdb=" C GLU b 87 " pdb=" CB GLU b 87 " both_signs ideal model delta sigma weight residual False 2.51 2.32 0.19 2.00e-01 2.50e+01 9.43e-01 ... (remaining 6350 not shown) Planarity restraints: 11868 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C7 LHG f 103 " 0.073 2.00e-02 2.50e+03 4.24e-02 1.79e+01 pdb=" C8 LHG f 103 " -0.021 2.00e-02 2.50e+03 pdb=" O7 LHG f 103 " -0.023 2.00e-02 2.50e+03 pdb=" O9 LHG f 103 " -0.029 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C23 LHG f 103 " 0.068 2.00e-02 2.50e+03 3.93e-02 1.55e+01 pdb=" C24 LHG f 103 " -0.020 2.00e-02 2.50e+03 pdb=" O10 LHG f 103 " -0.025 2.00e-02 2.50e+03 pdb=" O8 LHG f 103 " -0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C7 LHG b 302 " 0.058 2.00e-02 2.50e+03 3.33e-02 1.11e+01 pdb=" C8 LHG b 302 " -0.017 2.00e-02 2.50e+03 pdb=" O7 LHG b 302 " -0.018 2.00e-02 2.50e+03 pdb=" O9 LHG b 302 " -0.023 2.00e-02 2.50e+03 ... (remaining 11865 not shown) Histogram of nonbonded interaction distances: 1.50 - 2.12: 2369 2.12 - 2.74: 153521 2.74 - 3.36: 235196 3.36 - 3.98: 303020 3.98 - 4.60: 483259 Nonbonded interactions: 1177365 Sorted by model distance: nonbonded pdb=" O PRO a 130 " pdb=" HG1 THR a 133 " model vdw 1.497 1.850 nonbonded pdb=" O LEU N 42 " pdb=" H GLN N 44 " model vdw 1.503 1.850 nonbonded pdb=" OD1 ASP d 83 " pdb=" H TYR d 85 " model vdw 1.519 1.850 nonbonded pdb="HH12 ARG f 39 " pdb=" O1 LHG f 103 " model vdw 1.525 1.850 nonbonded pdb="HH22 ARG B 139 " pdb=" O GLU B 307 " model vdw 1.531 1.850 ... (remaining 1177360 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 23 through 403 or (resid 411 and (name N or name CA or nam \ e C or name O or name CB or name CG or name OD1 or name OD2 or name HA or name H \ B2 or name HB3)) or resid 412 through 508 or resid 600 through 601)) selection = (chain 'B' and ((resid 23 and (name N or name CA or name C or name O or name CB \ or name CG1 or name CG2 or name HA or name HB or name HG11 or name HG12 or name \ HG13 or name HG21 or name HG22 or name HG23)) or resid 24 through 403 or (resid \ 411 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 name HA or name HB2 or name HB3)) or resid 412 through 508 or re \ sid 600 through 601)) selection = (chain 'C' and ((resid 23 and (name N or name CA or name C or name O or name CB \ or name CG1 or name CG2 or name HA or name HB or name HG11 or name HG12 or name \ HG13 or name HG21 or name HG22 or name HG23)) or resid 24 through 508 or resid 6 \ 00 through 601)) } ncs_group { reference = (chain 'D' and resid 9 through 475) selection = (chain 'E' and (resid 9 through 162 or (resid 163 and (name N or name CA or name \ C or name O or name CB or name OG1 or name CG2 or name H or name HA or name HB \ or name HG21 or name HG22 or name HG23)) or resid 164 through 475)) selection = (chain 'F' and resid 9 through 475) } ncs_group { reference = chain 'K' selection = (chain 'L' and resid 1 through 74) selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' } 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=0.75 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 5.450 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.900 Extract box with map and model: 27.200 Check model and map are aligned: 0.860 Set scattering table: 0.540 Process input model: 215.690 Find NCS groups from input model: 3.180 Set up NCS constraints: 0.360 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:2.790 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 257.000 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8121 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 : 0.009 0.107 40625 Z= 0.607 Angle : 0.858 24.732 54883 Z= 0.495 Chirality : 0.047 0.214 6353 Planarity : 0.004 0.071 6946 Dihedral : 15.946 96.362 15316 Min Nonbonded Distance : 1.787 Molprobity Statistics. All-atom Clashscore : 12.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.09 % Favored : 91.91 % Rotamer: Outliers : 0.00 % Allowed : 0.62 % Favored : 99.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.61 % Cis-general : 0.12 % 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: -1.08 (0.12), residues: 5069 helix: 0.15 (0.10), residues: 2660 sheet: -1.67 (0.22), residues: 579 loop : -1.56 (0.15), residues: 1830 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.054 0.002 TRP g 85 HIS 0.007 0.001 HIS G 66 PHE 0.032 0.002 PHE O 47 TYR 0.033 0.002 TYR b 140 ARG 0.013 0.001 ARG b 143 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10138 Ramachandran restraints generated. 5069 Oldfield, 0 Emsley, 5069 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10138 Ramachandran restraints generated. 5069 Oldfield, 0 Emsley, 5069 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 176 is missing expected H atoms. Skipping. Residue THR 176 is missing expected H atoms. Skipping. Residue THR 176 is missing expected H atoms. Skipping. Residue THR 163 is missing expected H atoms. Skipping. Residue THR 163 is missing expected H atoms. Skipping. Evaluate side-chains 505 residues out of total 4173 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 505 time to evaluate : 4.841 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: B 181 ASP cc_start: 0.7632 (m-30) cc_final: 0.7412 (m-30) REVERT: B 297 ASP cc_start: 0.7636 (t0) cc_final: 0.7432 (t0) REVERT: J 35 ARG cc_start: 0.8332 (mmt90) cc_final: 0.8126 (mmt90) REVERT: h 42 GLU cc_start: 0.6785 (pt0) cc_final: 0.6177 (pt0) REVERT: e 47 LYS cc_start: 0.8705 (tptt) cc_final: 0.8247 (tppt) outliers start: 0 outliers final: 0 residues processed: 505 average time/residue: 1.0486 time to fit residues: 860.7991 Evaluate side-chains 422 residues out of total 4173 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 422 time to evaluate : 4.686 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 500 random chunks: chunk 422 optimal weight: 4.9990 chunk 378 optimal weight: 0.9990 chunk 210 optimal weight: 1.9990 chunk 129 optimal weight: 0.9980 chunk 255 optimal weight: 2.9990 chunk 202 optimal weight: 1.9990 chunk 391 optimal weight: 3.9990 chunk 151 optimal weight: 2.9990 chunk 238 optimal weight: 2.9990 chunk 291 optimal weight: 0.9980 chunk 454 optimal weight: 3.9990 overall best weight: 1.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 208 GLN ** E 308 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 8 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8077 moved from start: 0.0684 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 40625 Z= 0.270 Angle : 0.560 6.871 54883 Z= 0.293 Chirality : 0.041 0.149 6353 Planarity : 0.004 0.038 6946 Dihedral : 9.915 94.233 6015 Min Nonbonded Distance : 1.703 Molprobity Statistics. All-atom Clashscore : 9.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.97 % Favored : 95.03 % Rotamer: Outliers : 0.67 % Allowed : 5.66 % Favored : 93.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.61 % Cis-general : 0.12 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.60 (0.12), residues: 5069 helix: 0.50 (0.10), residues: 2671 sheet: -1.28 (0.23), residues: 554 loop : -1.34 (0.15), residues: 1844 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP g 85 HIS 0.005 0.001 HIS G 66 PHE 0.020 0.001 PHE R 54 TYR 0.019 0.001 TYR b 157 ARG 0.004 0.000 ARG b 166 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10138 Ramachandran restraints generated. 5069 Oldfield, 0 Emsley, 5069 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10138 Ramachandran restraints generated. 5069 Oldfield, 0 Emsley, 5069 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 176 is missing expected H atoms. Skipping. Residue THR 176 is missing expected H atoms. Skipping. Residue THR 176 is missing expected H atoms. Skipping. Residue THR 163 is missing expected H atoms. Skipping. Residue THR 163 is missing expected H atoms. Skipping. Evaluate side-chains 493 residues out of total 4173 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 465 time to evaluate : 4.751 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: B 181 ASP cc_start: 0.7597 (m-30) cc_final: 0.7386 (m-30) REVERT: C 79 ASP cc_start: 0.8625 (p0) cc_final: 0.8419 (p0) REVERT: D 22 ASP cc_start: 0.7834 (m-30) cc_final: 0.7592 (m-30) REVERT: J 35 ARG cc_start: 0.8286 (mmt90) cc_final: 0.7877 (mmt90) outliers start: 28 outliers final: 25 residues processed: 482 average time/residue: 1.0744 time to fit residues: 853.6499 Evaluate side-chains 457 residues out of total 4173 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 432 time to evaluate : 4.754 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 170 ASP Chi-restraints excluded: chain A residue 409 ASP Chi-restraints excluded: chain B residue 140 ILE Chi-restraints excluded: chain C residue 270 ASP Chi-restraints excluded: chain D residue 297 THR Chi-restraints excluded: chain E residue 61 ILE Chi-restraints excluded: chain E residue 315 ASP Chi-restraints excluded: chain E residue 386 ASP Chi-restraints excluded: chain F residue 306 SER Chi-restraints excluded: chain F residue 387 ILE Chi-restraints excluded: chain F residue 431 LEU Chi-restraints excluded: chain G residue 74 ASP Chi-restraints excluded: chain G residue 202 ARG Chi-restraints excluded: chain L residue 65 LEU Chi-restraints excluded: chain N residue 67 VAL Chi-restraints excluded: chain O residue 41 SER Chi-restraints excluded: chain P residue 21 SER Chi-restraints excluded: chain Q residue 70 LEU Chi-restraints excluded: chain R residue 71 ILE Chi-restraints excluded: chain a residue 2 ASN Chi-restraints excluded: chain a residue 98 LEU Chi-restraints excluded: chain b residue 153 ASN Chi-restraints excluded: chain h residue 43 LEU Chi-restraints excluded: chain e residue 18 LEU Chi-restraints excluded: chain e residue 39 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 500 random chunks: chunk 252 optimal weight: 0.7980 chunk 140 optimal weight: 0.8980 chunk 377 optimal weight: 1.9990 chunk 309 optimal weight: 1.9990 chunk 125 optimal weight: 0.8980 chunk 454 optimal weight: 4.9990 chunk 491 optimal weight: 3.9990 chunk 405 optimal weight: 5.9990 chunk 451 optimal weight: 2.9990 chunk 155 optimal weight: 2.9990 chunk 364 optimal weight: 1.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 208 GLN E 308 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8068 moved from start: 0.0947 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 40625 Z= 0.248 Angle : 0.534 6.407 54883 Z= 0.277 Chirality : 0.040 0.144 6353 Planarity : 0.003 0.041 6946 Dihedral : 9.088 92.288 6015 Min Nonbonded Distance : 1.697 Molprobity Statistics. All-atom Clashscore : 9.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.01 % Favored : 94.99 % Rotamer: Outliers : 0.86 % Allowed : 7.40 % Favored : 91.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.61 % Cis-general : 0.12 % 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: -0.29 (0.12), residues: 5069 helix: 0.74 (0.10), residues: 2671 sheet: -1.16 (0.23), residues: 554 loop : -1.18 (0.15), residues: 1844 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP g 85 HIS 0.004 0.001 HIS G 66 PHE 0.017 0.001 PHE Q 54 TYR 0.018 0.001 TYR b 157 ARG 0.003 0.000 ARG G 202 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10138 Ramachandran restraints generated. 5069 Oldfield, 0 Emsley, 5069 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10138 Ramachandran restraints generated. 5069 Oldfield, 0 Emsley, 5069 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 176 is missing expected H atoms. Skipping. Residue THR 176 is missing expected H atoms. Skipping. Residue THR 176 is missing expected H atoms. Skipping. Residue THR 163 is missing expected H atoms. Skipping. Residue THR 163 is missing expected H atoms. Skipping. Evaluate side-chains 515 residues out of total 4173 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 479 time to evaluate : 4.930 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: B 181 ASP cc_start: 0.7588 (m-30) cc_final: 0.7365 (m-30) REVERT: C 79 ASP cc_start: 0.8613 (p0) cc_final: 0.8410 (p0) REVERT: D 22 ASP cc_start: 0.7847 (m-30) cc_final: 0.7602 (m-30) REVERT: J 35 ARG cc_start: 0.8303 (mmt90) cc_final: 0.8017 (mmt90) outliers start: 36 outliers final: 28 residues processed: 496 average time/residue: 1.1006 time to fit residues: 903.4567 Evaluate side-chains 474 residues out of total 4173 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 446 time to evaluate : 4.683 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 170 ASP Chi-restraints excluded: chain B residue 140 ILE Chi-restraints excluded: chain C residue 270 ASP Chi-restraints excluded: chain D residue 297 THR Chi-restraints excluded: chain D residue 431 LEU Chi-restraints excluded: chain E residue 61 ILE Chi-restraints excluded: chain E residue 315 ASP Chi-restraints excluded: chain E residue 386 ASP Chi-restraints excluded: chain F residue 306 SER Chi-restraints excluded: chain F residue 387 ILE Chi-restraints excluded: chain F residue 431 LEU Chi-restraints excluded: chain G residue 74 ASP Chi-restraints excluded: chain L residue 65 LEU Chi-restraints excluded: chain N residue 67 VAL Chi-restraints excluded: chain O residue 41 SER Chi-restraints excluded: chain P residue 21 SER Chi-restraints excluded: chain Q residue 70 LEU Chi-restraints excluded: chain R residue 71 ILE Chi-restraints excluded: chain a residue 98 LEU Chi-restraints excluded: chain d residue 30 LEU Chi-restraints excluded: chain d residue 104 LEU Chi-restraints excluded: chain b residue 43 LEU Chi-restraints excluded: chain b residue 126 ASP Chi-restraints excluded: chain h residue 15 ILE Chi-restraints excluded: chain h residue 43 LEU Chi-restraints excluded: chain k residue 39 LEU Chi-restraints excluded: chain e residue 18 LEU Chi-restraints excluded: chain e residue 38 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 500 random chunks: chunk 449 optimal weight: 4.9990 chunk 341 optimal weight: 4.9990 chunk 236 optimal weight: 4.9990 chunk 50 optimal weight: 1.9990 chunk 217 optimal weight: 2.9990 chunk 305 optimal weight: 1.9990 chunk 456 optimal weight: 8.9990 chunk 483 optimal weight: 0.7980 chunk 238 optimal weight: 2.9990 chunk 432 optimal weight: 5.9990 chunk 130 optimal weight: 2.9990 overall best weight: 2.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 396 GLN a 163 ASN b 209 GLN e 30 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8096 moved from start: 0.0980 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.061 40625 Z= 0.360 Angle : 0.565 8.322 54883 Z= 0.295 Chirality : 0.042 0.167 6353 Planarity : 0.004 0.042 6946 Dihedral : 8.860 95.915 6015 Min Nonbonded Distance : 1.662 Molprobity Statistics. All-atom Clashscore : 10.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.06 % Favored : 93.94 % Rotamer: Outliers : 0.93 % Allowed : 9.30 % Favored : 89.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.61 % Cis-general : 0.12 % 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: -0.38 (0.12), residues: 5069 helix: 0.68 (0.10), residues: 2669 sheet: -1.22 (0.22), residues: 572 loop : -1.22 (0.15), residues: 1828 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP g 85 HIS 0.004 0.001 HIS f 80 PHE 0.018 0.001 PHE M 29 TYR 0.018 0.001 TYR b 157 ARG 0.005 0.000 ARG J 37 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10138 Ramachandran restraints generated. 5069 Oldfield, 0 Emsley, 5069 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10138 Ramachandran restraints generated. 5069 Oldfield, 0 Emsley, 5069 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 176 is missing expected H atoms. Skipping. Residue THR 176 is missing expected H atoms. Skipping. Residue THR 176 is missing expected H atoms. Skipping. Residue THR 163 is missing expected H atoms. Skipping. Residue THR 163 is missing expected H atoms. Skipping. Evaluate side-chains 491 residues out of total 4173 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 452 time to evaluate : 4.812 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: B 181 ASP cc_start: 0.7557 (m-30) cc_final: 0.7326 (m-30) REVERT: C 79 ASP cc_start: 0.8631 (p0) cc_final: 0.8426 (p0) REVERT: D 22 ASP cc_start: 0.7840 (m-30) cc_final: 0.7612 (m-30) REVERT: J 35 ARG cc_start: 0.8307 (mmt90) cc_final: 0.7913 (mmt90) REVERT: J 37 ARG cc_start: 0.8196 (mmp80) cc_final: 0.7964 (mmp80) outliers start: 39 outliers final: 34 residues processed: 469 average time/residue: 1.0260 time to fit residues: 784.1588 Evaluate side-chains 469 residues out of total 4173 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 435 time to evaluate : 4.725 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 170 ASP Chi-restraints excluded: chain A residue 371 VAL Chi-restraints excluded: chain B residue 24 ASP Chi-restraints excluded: chain B residue 140 ILE Chi-restraints excluded: chain B residue 270 ASP Chi-restraints excluded: chain C residue 270 ASP Chi-restraints excluded: chain C residue 396 GLN Chi-restraints excluded: chain D residue 297 THR Chi-restraints excluded: chain D residue 431 LEU Chi-restraints excluded: chain E residue 61 ILE Chi-restraints excluded: chain E residue 315 ASP Chi-restraints excluded: chain E residue 386 ASP Chi-restraints excluded: chain F residue 306 SER Chi-restraints excluded: chain F residue 387 ILE Chi-restraints excluded: chain F residue 431 LEU Chi-restraints excluded: chain G residue 74 ASP Chi-restraints excluded: chain L residue 65 LEU Chi-restraints excluded: chain N residue 66 MET Chi-restraints excluded: chain N residue 67 VAL Chi-restraints excluded: chain O residue 41 SER Chi-restraints excluded: chain P residue 21 SER Chi-restraints excluded: chain Q residue 70 LEU Chi-restraints excluded: chain a residue 49 MET Chi-restraints excluded: chain a residue 98 LEU Chi-restraints excluded: chain d residue 30 LEU Chi-restraints excluded: chain d residue 105 THR Chi-restraints excluded: chain b residue 43 LEU Chi-restraints excluded: chain b residue 95 GLU Chi-restraints excluded: chain b residue 126 ASP Chi-restraints excluded: chain b residue 153 ASN Chi-restraints excluded: chain b residue 193 THR Chi-restraints excluded: chain k residue 39 LEU Chi-restraints excluded: chain e residue 18 LEU Chi-restraints excluded: chain e residue 38 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 500 random chunks: chunk 402 optimal weight: 6.9990 chunk 274 optimal weight: 1.9990 chunk 7 optimal weight: 0.7980 chunk 359 optimal weight: 1.9990 chunk 199 optimal weight: 1.9990 chunk 412 optimal weight: 0.7980 chunk 334 optimal weight: 1.9990 chunk 0 optimal weight: 3.9990 chunk 246 optimal weight: 0.9990 chunk 433 optimal weight: 7.9990 chunk 121 optimal weight: 0.9990 overall best weight: 1.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: a 163 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8065 moved from start: 0.1177 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 40625 Z= 0.215 Angle : 0.518 7.474 54883 Z= 0.267 Chirality : 0.040 0.163 6353 Planarity : 0.003 0.037 6946 Dihedral : 8.426 91.086 6015 Min Nonbonded Distance : 1.766 Molprobity Statistics. All-atom Clashscore : 8.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.52 % Favored : 95.48 % Rotamer: Outliers : 0.96 % Allowed : 10.21 % Favored : 88.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.61 % Cis-general : 0.12 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.08 (0.12), residues: 5069 helix: 0.89 (0.10), residues: 2674 sheet: -1.05 (0.23), residues: 562 loop : -1.04 (0.15), residues: 1833 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP g 85 HIS 0.003 0.001 HIS f 80 PHE 0.014 0.001 PHE M 29 TYR 0.016 0.001 TYR b 157 ARG 0.003 0.000 ARG F 412 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10138 Ramachandran restraints generated. 5069 Oldfield, 0 Emsley, 5069 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10138 Ramachandran restraints generated. 5069 Oldfield, 0 Emsley, 5069 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 176 is missing expected H atoms. Skipping. Residue THR 176 is missing expected H atoms. Skipping. Residue THR 176 is missing expected H atoms. Skipping. Residue THR 163 is missing expected H atoms. Skipping. Residue THR 163 is missing expected H atoms. Skipping. Evaluate side-chains 509 residues out of total 4173 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 469 time to evaluate : 4.796 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: B 181 ASP cc_start: 0.7570 (m-30) cc_final: 0.7363 (m-30) REVERT: D 22 ASP cc_start: 0.7793 (m-30) cc_final: 0.7569 (m-30) REVERT: J 35 ARG cc_start: 0.8257 (mmt90) cc_final: 0.7966 (mmt90) outliers start: 40 outliers final: 33 residues processed: 487 average time/residue: 1.0266 time to fit residues: 822.0266 Evaluate side-chains 477 residues out of total 4173 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 444 time to evaluate : 4.718 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 170 ASP Chi-restraints excluded: chain A residue 371 VAL Chi-restraints excluded: chain B residue 24 ASP Chi-restraints excluded: chain B residue 140 ILE Chi-restraints excluded: chain B residue 270 ASP Chi-restraints excluded: chain C residue 270 ASP Chi-restraints excluded: chain D residue 297 THR Chi-restraints excluded: chain D residue 431 LEU Chi-restraints excluded: chain E residue 386 ASP Chi-restraints excluded: chain F residue 306 SER Chi-restraints excluded: chain F residue 431 LEU Chi-restraints excluded: chain G residue 156 ASP Chi-restraints excluded: chain L residue 65 LEU Chi-restraints excluded: chain N residue 66 MET Chi-restraints excluded: chain N residue 67 VAL Chi-restraints excluded: chain O residue 41 SER Chi-restraints excluded: chain P residue 21 SER Chi-restraints excluded: chain Q residue 1 ASP Chi-restraints excluded: chain Q residue 70 LEU Chi-restraints excluded: chain R residue 56 LEU Chi-restraints excluded: chain R residue 60 MET Chi-restraints excluded: chain a residue 98 LEU Chi-restraints excluded: chain d residue 30 LEU Chi-restraints excluded: chain d residue 105 THR Chi-restraints excluded: chain f residue 25 MET Chi-restraints excluded: chain b residue 43 LEU Chi-restraints excluded: chain b residue 126 ASP Chi-restraints excluded: chain b residue 153 ASN Chi-restraints excluded: chain b residue 193 THR Chi-restraints excluded: chain h residue 43 LEU Chi-restraints excluded: chain k residue 39 LEU Chi-restraints excluded: chain e residue 18 LEU Chi-restraints excluded: chain e residue 38 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 500 random chunks: chunk 162 optimal weight: 1.9990 chunk 435 optimal weight: 3.9990 chunk 95 optimal weight: 4.9990 chunk 283 optimal weight: 2.9990 chunk 119 optimal weight: 2.9990 chunk 483 optimal weight: 4.9990 chunk 401 optimal weight: 6.9990 chunk 223 optimal weight: 1.9990 chunk 40 optimal weight: 2.9990 chunk 160 optimal weight: 0.2980 chunk 253 optimal weight: 1.9990 overall best weight: 1.8588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 396 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8086 moved from start: 0.1179 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 40625 Z= 0.315 Angle : 0.545 8.210 54883 Z= 0.283 Chirality : 0.041 0.161 6353 Planarity : 0.004 0.067 6946 Dihedral : 8.265 93.803 6015 Min Nonbonded Distance : 1.696 Molprobity Statistics. All-atom Clashscore : 9.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.52 % Favored : 94.48 % Rotamer: Outliers : 0.98 % Allowed : 11.12 % Favored : 87.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.61 % Cis-general : 0.12 % 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: -0.14 (0.12), residues: 5069 helix: 0.86 (0.10), residues: 2668 sheet: -1.08 (0.23), residues: 567 loop : -1.09 (0.15), residues: 1834 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP g 85 HIS 0.004 0.001 HIS f 80 PHE 0.017 0.001 PHE M 29 TYR 0.017 0.001 TYR b 157 ARG 0.004 0.000 ARG J 37 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10138 Ramachandran restraints generated. 5069 Oldfield, 0 Emsley, 5069 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10138 Ramachandran restraints generated. 5069 Oldfield, 0 Emsley, 5069 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 176 is missing expected H atoms. Skipping. Residue THR 176 is missing expected H atoms. Skipping. Residue THR 176 is missing expected H atoms. Skipping. Residue THR 163 is missing expected H atoms. Skipping. Residue THR 163 is missing expected H atoms. Skipping. Evaluate side-chains 490 residues out of total 4173 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 449 time to evaluate : 4.840 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: B 181 ASP cc_start: 0.7597 (m-30) cc_final: 0.7372 (m-30) REVERT: D 22 ASP cc_start: 0.7813 (m-30) cc_final: 0.7601 (m-30) REVERT: J 35 ARG cc_start: 0.8238 (mmt90) cc_final: 0.7979 (mmt90) outliers start: 41 outliers final: 38 residues processed: 469 average time/residue: 1.0463 time to fit residues: 795.4726 Evaluate side-chains 469 residues out of total 4173 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 431 time to evaluate : 4.641 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 170 ASP Chi-restraints excluded: chain A residue 371 VAL Chi-restraints excluded: chain B residue 24 ASP Chi-restraints excluded: chain B residue 140 ILE Chi-restraints excluded: chain B residue 270 ASP Chi-restraints excluded: chain B residue 374 VAL Chi-restraints excluded: chain C residue 270 ASP Chi-restraints excluded: chain D residue 297 THR Chi-restraints excluded: chain D residue 431 LEU Chi-restraints excluded: chain E residue 202 GLU Chi-restraints excluded: chain E residue 315 ASP Chi-restraints excluded: chain E residue 386 ASP Chi-restraints excluded: chain F residue 22 ASP Chi-restraints excluded: chain F residue 186 VAL Chi-restraints excluded: chain F residue 306 SER Chi-restraints excluded: chain F residue 387 ILE Chi-restraints excluded: chain F residue 431 LEU Chi-restraints excluded: chain J residue 8 VAL Chi-restraints excluded: chain K residue 47 PHE Chi-restraints excluded: chain L residue 65 LEU Chi-restraints excluded: chain N residue 66 MET Chi-restraints excluded: chain N residue 67 VAL Chi-restraints excluded: chain O residue 41 SER Chi-restraints excluded: chain P residue 21 SER Chi-restraints excluded: chain Q residue 70 LEU Chi-restraints excluded: chain R residue 15 THR Chi-restraints excluded: chain a residue 98 LEU Chi-restraints excluded: chain d residue 30 LEU Chi-restraints excluded: chain d residue 105 THR Chi-restraints excluded: chain f residue 25 MET Chi-restraints excluded: chain b residue 95 GLU Chi-restraints excluded: chain b residue 126 ASP Chi-restraints excluded: chain b residue 153 ASN Chi-restraints excluded: chain b residue 193 THR Chi-restraints excluded: chain h residue 43 LEU Chi-restraints excluded: chain k residue 37 ILE Chi-restraints excluded: chain k residue 39 LEU Chi-restraints excluded: chain e residue 18 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 500 random chunks: chunk 466 optimal weight: 0.9990 chunk 54 optimal weight: 0.9990 chunk 275 optimal weight: 1.9990 chunk 353 optimal weight: 5.9990 chunk 273 optimal weight: 0.9990 chunk 407 optimal weight: 3.9990 chunk 270 optimal weight: 0.9980 chunk 481 optimal weight: 4.9990 chunk 301 optimal weight: 1.9990 chunk 293 optimal weight: 1.9990 chunk 222 optimal weight: 2.9990 overall best weight: 1.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8065 moved from start: 0.1321 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 40625 Z= 0.223 Angle : 0.515 7.932 54883 Z= 0.265 Chirality : 0.040 0.168 6353 Planarity : 0.003 0.060 6946 Dihedral : 7.984 90.832 6015 Min Nonbonded Distance : 1.748 Molprobity Statistics. All-atom Clashscore : 8.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.24 % Favored : 95.76 % Rotamer: Outliers : 1.01 % Allowed : 11.65 % Favored : 87.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.61 % Cis-general : 0.12 % 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: 0.06 (0.12), residues: 5069 helix: 1.00 (0.10), residues: 2673 sheet: -1.02 (0.23), residues: 555 loop : -0.97 (0.15), residues: 1841 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP g 85 HIS 0.003 0.001 HIS f 80 PHE 0.015 0.001 PHE J 34 TYR 0.016 0.001 TYR b 157 ARG 0.004 0.000 ARG d 40 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10138 Ramachandran restraints generated. 5069 Oldfield, 0 Emsley, 5069 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10138 Ramachandran restraints generated. 5069 Oldfield, 0 Emsley, 5069 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 176 is missing expected H atoms. Skipping. Residue THR 176 is missing expected H atoms. Skipping. Residue THR 176 is missing expected H atoms. Skipping. Residue THR 163 is missing expected H atoms. Skipping. Residue THR 163 is missing expected H atoms. Skipping. Evaluate side-chains 505 residues out of total 4173 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 463 time to evaluate : 4.913 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: A 383 MET cc_start: 0.9194 (tpt) cc_final: 0.8894 (tpt) REVERT: B 181 ASP cc_start: 0.7581 (m-30) cc_final: 0.7366 (m-30) REVERT: D 22 ASP cc_start: 0.7778 (m-30) cc_final: 0.7549 (m-30) REVERT: J 35 ARG cc_start: 0.8271 (mmt90) cc_final: 0.7984 (mmt90) outliers start: 42 outliers final: 38 residues processed: 481 average time/residue: 1.0708 time to fit residues: 849.9329 Evaluate side-chains 483 residues out of total 4173 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 445 time to evaluate : 4.740 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 170 ASP Chi-restraints excluded: chain A residue 371 VAL Chi-restraints excluded: chain B residue 24 ASP Chi-restraints excluded: chain B residue 140 ILE Chi-restraints excluded: chain B residue 270 ASP Chi-restraints excluded: chain B residue 374 VAL Chi-restraints excluded: chain C residue 270 ASP Chi-restraints excluded: chain D residue 297 THR Chi-restraints excluded: chain D residue 431 LEU Chi-restraints excluded: chain E residue 202 GLU Chi-restraints excluded: chain E residue 386 ASP Chi-restraints excluded: chain F residue 22 ASP Chi-restraints excluded: chain F residue 306 SER Chi-restraints excluded: chain F residue 387 ILE Chi-restraints excluded: chain F residue 431 LEU Chi-restraints excluded: chain G residue 74 ASP Chi-restraints excluded: chain K residue 47 PHE Chi-restraints excluded: chain L residue 65 LEU Chi-restraints excluded: chain N residue 66 MET Chi-restraints excluded: chain N residue 67 VAL Chi-restraints excluded: chain O residue 41 SER Chi-restraints excluded: chain P residue 21 SER Chi-restraints excluded: chain Q residue 1 ASP Chi-restraints excluded: chain Q residue 70 LEU Chi-restraints excluded: chain R residue 56 LEU Chi-restraints excluded: chain 8 residue 6 THR Chi-restraints excluded: chain a residue 98 LEU Chi-restraints excluded: chain d residue 30 LEU Chi-restraints excluded: chain d residue 105 THR Chi-restraints excluded: chain f residue 25 MET Chi-restraints excluded: chain b residue 95 GLU Chi-restraints excluded: chain b residue 126 ASP Chi-restraints excluded: chain b residue 153 ASN Chi-restraints excluded: chain b residue 193 THR Chi-restraints excluded: chain k residue 37 ILE Chi-restraints excluded: chain k residue 39 LEU Chi-restraints excluded: chain e residue 18 LEU Chi-restraints excluded: chain e residue 38 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 500 random chunks: chunk 298 optimal weight: 0.7980 chunk 192 optimal weight: 1.9990 chunk 287 optimal weight: 2.9990 chunk 145 optimal weight: 3.9990 chunk 94 optimal weight: 3.9990 chunk 93 optimal weight: 4.9990 chunk 306 optimal weight: 1.9990 chunk 328 optimal weight: 1.9990 chunk 238 optimal weight: 0.6980 chunk 44 optimal weight: 0.9980 chunk 378 optimal weight: 1.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** a 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8066 moved from start: 0.1376 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 40625 Z= 0.237 Angle : 0.517 8.169 54883 Z= 0.267 Chirality : 0.040 0.164 6353 Planarity : 0.003 0.057 6946 Dihedral : 7.834 90.170 6015 Min Nonbonded Distance : 1.732 Molprobity Statistics. All-atom Clashscore : 8.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.85 % Favored : 95.15 % Rotamer: Outliers : 1.01 % Allowed : 11.96 % Favored : 87.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.61 % Cis-general : 0.12 % 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: 0.11 (0.12), residues: 5069 helix: 1.07 (0.10), residues: 2666 sheet: -0.99 (0.23), residues: 555 loop : -0.97 (0.15), residues: 1848 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP g 85 HIS 0.003 0.001 HIS f 80 PHE 0.016 0.001 PHE Q 54 TYR 0.015 0.001 TYR b 157 ARG 0.005 0.000 ARG b 149 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10138 Ramachandran restraints generated. 5069 Oldfield, 0 Emsley, 5069 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10138 Ramachandran restraints generated. 5069 Oldfield, 0 Emsley, 5069 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 176 is missing expected H atoms. Skipping. Residue THR 176 is missing expected H atoms. Skipping. Residue THR 176 is missing expected H atoms. Skipping. Residue THR 163 is missing expected H atoms. Skipping. Residue THR 163 is missing expected H atoms. Skipping. Evaluate side-chains 491 residues out of total 4173 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 449 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: B 181 ASP cc_start: 0.7586 (m-30) cc_final: 0.7369 (m-30) REVERT: D 22 ASP cc_start: 0.7764 (m-30) cc_final: 0.7540 (m-30) REVERT: J 35 ARG cc_start: 0.8187 (mmt90) cc_final: 0.7902 (mmt90) outliers start: 42 outliers final: 42 residues processed: 471 average time/residue: 1.0471 time to fit residues: 812.0163 Evaluate side-chains 482 residues out of total 4173 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 440 time to evaluate : 4.766 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 170 ASP Chi-restraints excluded: chain A residue 244 TYR Chi-restraints excluded: chain A residue 371 VAL Chi-restraints excluded: chain B residue 24 ASP Chi-restraints excluded: chain B residue 140 ILE Chi-restraints excluded: chain B residue 270 ASP Chi-restraints excluded: chain B residue 374 VAL Chi-restraints excluded: chain C residue 270 ASP Chi-restraints excluded: chain D residue 431 LEU Chi-restraints excluded: chain E residue 202 GLU Chi-restraints excluded: chain E residue 386 ASP Chi-restraints excluded: chain F residue 22 ASP Chi-restraints excluded: chain F residue 186 VAL Chi-restraints excluded: chain F residue 306 SER Chi-restraints excluded: chain F residue 387 ILE Chi-restraints excluded: chain F residue 431 LEU Chi-restraints excluded: chain G residue 74 ASP Chi-restraints excluded: chain J residue 8 VAL Chi-restraints excluded: chain K residue 47 PHE Chi-restraints excluded: chain L residue 65 LEU Chi-restraints excluded: chain N residue 66 MET Chi-restraints excluded: chain N residue 67 VAL Chi-restraints excluded: chain O residue 41 SER Chi-restraints excluded: chain P residue 21 SER Chi-restraints excluded: chain Q residue 70 LEU Chi-restraints excluded: chain R residue 15 THR Chi-restraints excluded: chain R residue 56 LEU Chi-restraints excluded: chain 8 residue 6 THR Chi-restraints excluded: chain a residue 98 LEU Chi-restraints excluded: chain d residue 30 LEU Chi-restraints excluded: chain d residue 105 THR Chi-restraints excluded: chain f residue 25 MET Chi-restraints excluded: chain b residue 43 LEU Chi-restraints excluded: chain b residue 95 GLU Chi-restraints excluded: chain b residue 126 ASP Chi-restraints excluded: chain b residue 153 ASN Chi-restraints excluded: chain b residue 193 THR Chi-restraints excluded: chain h residue 43 LEU Chi-restraints excluded: chain k residue 37 ILE Chi-restraints excluded: chain k residue 39 LEU Chi-restraints excluded: chain e residue 18 LEU Chi-restraints excluded: chain e residue 38 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 500 random chunks: chunk 438 optimal weight: 0.7980 chunk 461 optimal weight: 0.9990 chunk 421 optimal weight: 4.9990 chunk 449 optimal weight: 2.9990 chunk 270 optimal weight: 0.5980 chunk 195 optimal weight: 1.9990 chunk 352 optimal weight: 1.9990 chunk 137 optimal weight: 6.9990 chunk 405 optimal weight: 6.9990 chunk 424 optimal weight: 1.9990 chunk 447 optimal weight: 3.9990 overall best weight: 1.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: a 152 GLN d 106 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8063 moved from start: 0.1445 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 40625 Z= 0.231 Angle : 0.517 8.351 54883 Z= 0.267 Chirality : 0.040 0.167 6353 Planarity : 0.003 0.056 6946 Dihedral : 7.709 89.814 6015 Min Nonbonded Distance : 1.742 Molprobity Statistics. All-atom Clashscore : 8.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.34 % Favored : 95.66 % Rotamer: Outliers : 1.05 % Allowed : 12.08 % Favored : 86.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.61 % Cis-general : 0.12 % 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: 0.18 (0.12), residues: 5069 helix: 1.13 (0.10), residues: 2667 sheet: -0.98 (0.23), residues: 545 loop : -0.95 (0.15), residues: 1857 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP g 85 HIS 0.003 0.001 HIS f 80 PHE 0.022 0.001 PHE Q 54 TYR 0.016 0.001 TYR b 157 ARG 0.004 0.000 ARG F 412 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10138 Ramachandran restraints generated. 5069 Oldfield, 0 Emsley, 5069 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10138 Ramachandran restraints generated. 5069 Oldfield, 0 Emsley, 5069 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 176 is missing expected H atoms. Skipping. Residue THR 176 is missing expected H atoms. Skipping. Residue THR 176 is missing expected H atoms. Skipping. Residue THR 163 is missing expected H atoms. Skipping. Residue THR 163 is missing expected H atoms. Skipping. Evaluate side-chains 504 residues out of total 4173 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 460 time to evaluate : 4.940 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: B 181 ASP cc_start: 0.7586 (m-30) cc_final: 0.7360 (m-30) REVERT: D 22 ASP cc_start: 0.7757 (m-30) cc_final: 0.7552 (m-30) REVERT: J 35 ARG cc_start: 0.8251 (mmt90) cc_final: 0.7961 (mmt90) outliers start: 44 outliers final: 42 residues processed: 483 average time/residue: 1.1169 time to fit residues: 895.2231 Evaluate side-chains 492 residues out of total 4173 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 450 time to evaluate : 4.964 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 170 ASP Chi-restraints excluded: chain A residue 244 TYR Chi-restraints excluded: chain A residue 371 VAL Chi-restraints excluded: chain B residue 24 ASP Chi-restraints excluded: chain B residue 140 ILE Chi-restraints excluded: chain B residue 270 ASP Chi-restraints excluded: chain B residue 374 VAL Chi-restraints excluded: chain C residue 270 ASP Chi-restraints excluded: chain D residue 297 THR Chi-restraints excluded: chain D residue 431 LEU Chi-restraints excluded: chain E residue 202 GLU Chi-restraints excluded: chain E residue 386 ASP Chi-restraints excluded: chain F residue 22 ASP Chi-restraints excluded: chain F residue 186 VAL Chi-restraints excluded: chain F residue 306 SER Chi-restraints excluded: chain F residue 387 ILE Chi-restraints excluded: chain F residue 431 LEU Chi-restraints excluded: chain G residue 74 ASP Chi-restraints excluded: chain J residue 8 VAL Chi-restraints excluded: chain K residue 47 PHE Chi-restraints excluded: chain L residue 65 LEU Chi-restraints excluded: chain N residue 66 MET Chi-restraints excluded: chain N residue 67 VAL Chi-restraints excluded: chain O residue 41 SER Chi-restraints excluded: chain P residue 21 SER Chi-restraints excluded: chain Q residue 70 LEU Chi-restraints excluded: chain R residue 15 THR Chi-restraints excluded: chain R residue 56 LEU Chi-restraints excluded: chain R residue 65 LEU Chi-restraints excluded: chain 8 residue 6 THR Chi-restraints excluded: chain a residue 98 LEU Chi-restraints excluded: chain d residue 30 LEU Chi-restraints excluded: chain d residue 105 THR Chi-restraints excluded: chain f residue 25 MET Chi-restraints excluded: chain b residue 43 LEU Chi-restraints excluded: chain b residue 95 GLU Chi-restraints excluded: chain b residue 126 ASP Chi-restraints excluded: chain b residue 193 THR Chi-restraints excluded: chain k residue 37 ILE Chi-restraints excluded: chain k residue 39 LEU Chi-restraints excluded: chain e residue 18 LEU Chi-restraints excluded: chain e residue 38 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 500 random chunks: chunk 294 optimal weight: 6.9990 chunk 474 optimal weight: 0.9980 chunk 289 optimal weight: 0.6980 chunk 225 optimal weight: 1.9990 chunk 330 optimal weight: 4.9990 chunk 498 optimal weight: 0.7980 chunk 458 optimal weight: 2.9990 chunk 396 optimal weight: 0.7980 chunk 41 optimal weight: 2.9990 chunk 306 optimal weight: 0.9980 chunk 243 optimal weight: 2.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8046 moved from start: 0.1554 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 40625 Z= 0.178 Angle : 0.503 8.214 54883 Z= 0.258 Chirality : 0.040 0.166 6353 Planarity : 0.003 0.056 6946 Dihedral : 7.536 87.271 6015 Min Nonbonded Distance : 1.772 Molprobity Statistics. All-atom Clashscore : 8.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.12 % Favored : 95.88 % Rotamer: Outliers : 0.79 % Allowed : 12.56 % Favored : 86.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.61 % Cis-general : 0.12 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.32 (0.12), residues: 5069 helix: 1.24 (0.11), residues: 2675 sheet: -0.95 (0.23), residues: 549 loop : -0.87 (0.15), residues: 1845 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP f 22 HIS 0.002 0.001 HIS F 367 PHE 0.022 0.001 PHE Q 54 TYR 0.015 0.001 TYR b 157 ARG 0.008 0.000 ARG b 166 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10138 Ramachandran restraints generated. 5069 Oldfield, 0 Emsley, 5069 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10138 Ramachandran restraints generated. 5069 Oldfield, 0 Emsley, 5069 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 176 is missing expected H atoms. Skipping. Residue THR 176 is missing expected H atoms. Skipping. Residue THR 176 is missing expected H atoms. Skipping. Residue THR 163 is missing expected H atoms. Skipping. Residue THR 163 is missing expected H atoms. Skipping. Evaluate side-chains 504 residues out of total 4173 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 471 time to evaluate : 4.838 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 383 MET cc_start: 0.9159 (tpt) cc_final: 0.8884 (tpt) REVERT: B 181 ASP cc_start: 0.7562 (m-30) cc_final: 0.7346 (m-30) REVERT: D 22 ASP cc_start: 0.7731 (m-30) cc_final: 0.7515 (m-30) REVERT: E 294 GLU cc_start: 0.8059 (tp30) cc_final: 0.7840 (mm-30) REVERT: J 35 ARG cc_start: 0.8179 (mmt90) cc_final: 0.7896 (mmt90) REVERT: O 60 MET cc_start: 0.7735 (mmp) cc_final: 0.7449 (mmp) REVERT: R 65 LEU cc_start: 0.8707 (OUTLIER) cc_final: 0.8500 (mp) outliers start: 33 outliers final: 26 residues processed: 484 average time/residue: 1.0245 time to fit residues: 819.4635 Evaluate side-chains 479 residues out of total 4173 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 452 time to evaluate : 4.696 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 170 ASP Chi-restraints excluded: chain A residue 199 LEU Chi-restraints excluded: chain A residue 244 TYR Chi-restraints excluded: chain B residue 140 ILE Chi-restraints excluded: chain B residue 270 ASP Chi-restraints excluded: chain C residue 270 ASP Chi-restraints excluded: chain D residue 431 LEU Chi-restraints excluded: chain E residue 386 ASP Chi-restraints excluded: chain F residue 186 VAL Chi-restraints excluded: chain F residue 306 SER Chi-restraints excluded: chain F residue 431 LEU Chi-restraints excluded: chain K residue 47 PHE Chi-restraints excluded: chain L residue 65 LEU Chi-restraints excluded: chain N residue 66 MET Chi-restraints excluded: chain N residue 67 VAL Chi-restraints excluded: chain P residue 21 SER Chi-restraints excluded: chain Q residue 70 LEU Chi-restraints excluded: chain R residue 65 LEU Chi-restraints excluded: chain a residue 98 LEU Chi-restraints excluded: chain d residue 30 LEU Chi-restraints excluded: chain d residue 105 THR Chi-restraints excluded: chain b residue 126 ASP Chi-restraints excluded: chain k residue 23 LEU Chi-restraints excluded: chain k residue 37 ILE Chi-restraints excluded: chain k residue 39 LEU Chi-restraints excluded: chain e residue 18 LEU Chi-restraints excluded: chain e residue 38 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 500 random chunks: chunk 315 optimal weight: 0.9990 chunk 422 optimal weight: 0.2980 chunk 121 optimal weight: 0.7980 chunk 365 optimal weight: 1.9990 chunk 58 optimal weight: 0.1980 chunk 110 optimal weight: 1.9990 chunk 397 optimal weight: 2.9990 chunk 166 optimal weight: 0.9980 chunk 407 optimal weight: 1.9990 chunk 50 optimal weight: 2.9990 chunk 73 optimal weight: 1.9990 overall best weight: 0.6582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 411 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.117553 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3052 r_free = 0.3052 target = 0.092656 restraints weight = 208775.510| |-----------------------------------------------------------------------------| r_work (start): 0.3053 rms_B_bonded: 1.87 r_work: 0.2948 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.2835 rms_B_bonded: 3.73 restraints_weight: 0.2500 r_work (final): 0.2835 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2843 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2843 r_free = 0.2843 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.75 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2843 r_free = 0.2843 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.56 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2843 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8156 moved from start: 0.1670 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 40625 Z= 0.160 Angle : 0.497 8.617 54883 Z= 0.253 Chirality : 0.039 0.208 6353 Planarity : 0.003 0.062 6946 Dihedral : 7.361 85.739 6015 Min Nonbonded Distance : 1.783 Molprobity Statistics. All-atom Clashscore : 8.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.49 % Favored : 96.51 % Rotamer: Outliers : 0.81 % Allowed : 12.65 % Favored : 86.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.61 % Cis-general : 0.12 % 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: 0.48 (0.13), residues: 5069 helix: 1.35 (0.11), residues: 2677 sheet: -0.82 (0.23), residues: 554 loop : -0.78 (0.15), residues: 1838 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP g 85 HIS 0.003 0.000 HIS F 367 PHE 0.029 0.001 PHE Q 54 TYR 0.014 0.001 TYR b 157 ARG 0.007 0.000 ARG b 166 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 15853.65 seconds wall clock time: 276 minutes 36.10 seconds (16596.10 seconds total)