Starting phenix.real_space_refine on Mon Mar 11 00:38:50 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yeg_33772/03_2024/7yeg_33772.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yeg_33772/03_2024/7yeg_33772.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.73 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yeg_33772/03_2024/7yeg_33772.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yeg_33772/03_2024/7yeg_33772.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yeg_33772/03_2024/7yeg_33772.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yeg_33772/03_2024/7yeg_33772.pdb" } resolution = 3.73 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= 0.000 sd= 0.005 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 4497 atoms to isotropic. 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: 5 Type Number sf(0) Gaussians Zn 3 6.06 5 S 240 5.16 5 C 31752 2.51 5 N 8259 2.21 5 O 9720 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 28": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 40": "OD1" <-> "OD2" Residue "A PHE 43": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 58": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 79": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 92": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 106": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 133": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 135": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 140": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 157": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 175": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 186": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 192": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 194": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 200": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 215": "OD1" <-> "OD2" Residue "A PHE 238": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 248": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 275": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 281": "OE1" <-> "OE2" Residue "A PHE 306": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 318": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 329": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 357": "NH1" <-> "NH2" Residue "A TYR 365": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 369": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 396": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 405": "OD1" <-> "OD2" Residue "A PHE 464": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 489": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 541": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 559": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 612": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 663": "OD1" <-> "OD2" Residue "A TYR 674": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 695": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 718": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 741": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 756": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 780": "OE1" <-> "OE2" Residue "A PHE 797": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 800": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 802": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 823": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 950": "OD1" <-> "OD2" Residue "A PHE 970": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 985": "OD1" <-> "OD2" Residue "A GLU 988": "OE1" <-> "OE2" Residue "A GLU 990": "OE1" <-> "OE2" Residue "A PHE 1042": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1047": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1062": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1067": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1089": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1092": "OE1" <-> "OE2" Residue "A PHE 1095": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 1127": "OD1" <-> "OD2" Residue "A TYR 1138": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 28": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 38": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 43": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 58": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 80": "OD1" <-> "OD2" Residue "B ASP 88": "OD1" <-> "OD2" Residue "B PHE 92": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 106": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 111": "OD1" <-> "OD2" Residue "B PHE 133": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 135": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 157": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 175": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 186": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 192": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 194": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 200": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 238": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 248": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 275": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 281": "OE1" <-> "OE2" Residue "B PHE 306": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 318": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 324": "OE1" <-> "OE2" Residue "B PHE 342": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 357": "NH1" <-> "NH2" Residue "B TYR 365": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 369": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 396": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 400": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 405": "OD1" <-> "OD2" Residue "B ASP 420": "OD1" <-> "OD2" Residue "B ASP 427": "OD1" <-> "OD2" Residue "B ASP 442": "OD1" <-> "OD2" Residue "B PHE 464": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 489": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 541": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 559": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 612": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 674": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 695": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 718": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 741": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 745": "OD1" <-> "OD2" Residue "B TYR 756": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 775": "OD1" <-> "OD2" Residue "B GLU 780": "OE1" <-> "OE2" Residue "B PHE 797": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 800": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 802": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 823": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 950": "OD1" <-> "OD2" Residue "B PHE 970": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 988": "OE1" <-> "OE2" Residue "B GLU 990": "OE1" <-> "OE2" Residue "B PHE 1042": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 1047": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 1062": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 1067": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 1089": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 1092": "OE1" <-> "OE2" Residue "B PHE 1095": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 1127": "OD1" <-> "OD2" Residue "B TYR 1138": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 28": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 38": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 43": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 58": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 88": "OD1" <-> "OD2" Residue "C PHE 92": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 106": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 111": "OD1" <-> "OD2" Residue "C PHE 133": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 135": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 157": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 175": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 186": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 192": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 194": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 200": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 220": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 238": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 248": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 275": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 281": "OE1" <-> "OE2" Residue "C PHE 306": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 318": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 357": "NH1" <-> "NH2" Residue "C ASP 364": "OD1" <-> "OD2" Residue "C TYR 365": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 369": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 389": "OD1" <-> "OD2" Residue "C TYR 396": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 405": "OD1" <-> "OD2" Residue "C ASP 420": "OD1" <-> "OD2" Residue "C ASP 428": "OD1" <-> "OD2" Residue "C ASP 442": "OD1" <-> "OD2" Residue "C PHE 464": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 486": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 489": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 541": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 559": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 612": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 674": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 695": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 718": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 741": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 756": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 780": "OE1" <-> "OE2" Residue "C PHE 797": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 800": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 802": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 823": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 970": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 985": "OD1" <-> "OD2" Residue "C GLU 988": "OE1" <-> "OE2" Residue "C GLU 990": "OE1" <-> "OE2" Residue "C PHE 1042": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 1047": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 1062": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 1067": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 1089": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 1092": "OE1" <-> "OE2" Residue "C PHE 1095": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 1138": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 22": "OE1" <-> "OE2" Residue "E PHE 28": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 67": "OD1" <-> "OD2" Residue "E TYR 83": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 87": "OE1" <-> "OE2" Residue "E GLU 110": "OE1" <-> "OE2" Residue "E ARG 115": "NH1" <-> "NH2" Residue "E TYR 127": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 140": "OE1" <-> "OE2" Residue "E GLU 145": "OE1" <-> "OE2" Residue "E ASP 157": "OD1" <-> "OD2" Residue "E TYR 158": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 169": "NH1" <-> "NH2" Residue "E GLU 171": "OE1" <-> "OE2" Residue "E ARG 177": "NH1" <-> "NH2" Residue "E GLU 182": "OE1" <-> "OE2" Residue "E ARG 192": "NH1" <-> "NH2" Residue "E TYR 196": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 199": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 202": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 217": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 231": "OE1" <-> "OE2" Residue "E ARG 245": "NH1" <-> "NH2" Residue "E ARG 273": "NH1" <-> "NH2" Residue "E PHE 308": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 312": "OE1" <-> "OE2" Residue "E PHE 327": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 329": "OE1" <-> "OE2" Residue "E ASP 355": "OD1" <-> "OD2" Residue "E ARG 357": "NH1" <-> "NH2" Residue "E ASP 367": "OD1" <-> "OD2" Residue "E ASP 368": "OD1" <-> "OD2" Residue "E PHE 369": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 385": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 390": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 406": "OE1" <-> "OE2" Residue "E ASP 427": "OD1" <-> "OD2" Residue "E PHE 428": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 433": "OE1" <-> "OE2" Residue "E PHE 452": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 464": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 471": "OD1" <-> "OD2" Residue "E ASP 494": "OD1" <-> "OD2" Residue "E TYR 497": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 504": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 509": "OD1" <-> "OD2" Residue "E TYR 515": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 516": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 518": "NH1" <-> "NH2" Residue "E PHE 525": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 549": "OE1" <-> "OE2" Residue "E GLU 564": "OE1" <-> "OE2" Residue "E PHE 588": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 589": "OE1" <-> "OE2" Residue "E ASP 597": "OD1" <-> "OD2" Residue "E PHE 603": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 609": "OD1" <-> "OD2" Residue "H GLU 10": "OE1" <-> "OE2" Residue "H PHE 29": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ASP 73": "OD1" <-> "OD2" Residue "H GLU 89": "OE1" <-> "OE2" Residue "H TYR 94": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 102": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 157": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 177": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 187": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 223": "OE1" <-> "OE2" Residue "L TYR 33": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ASP 34": "OD1" <-> "OD2" Residue "L TYR 38": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 51": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ARG 56": "NH1" <-> "NH2" Residue "L ASP 84": "OD1" <-> "OD2" Residue "L TYR 88": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ASP 143": "OD1" <-> "OD2" Residue "L PHE 144": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ASP 156": "OD1" <-> "OD2" Residue "L GLU 165": "OE1" <-> "OE2" Residue "L GLU 203": "OE1" <-> "OE2" Residue "G PHE 29": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 73": "OD1" <-> "OD2" Residue "G TYR 94": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 102": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 157": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 187": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 205": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 223": "OE1" <-> "OE2" Residue "I TYR 33": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ASP 34": "OD1" <-> "OD2" Residue "I TYR 38": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 51": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ARG 56": "NH1" <-> "NH2" Residue "I ASP 62": "OD1" <-> "OD2" Residue "I ASP 84": "OD1" <-> "OD2" Residue "I TYR 88": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I GLU 128": "OE1" <-> "OE2" Residue "I PHE 144": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ASP 156": "OD1" <-> "OD2" Residue "I GLU 165": "OE1" <-> "OE2" Residue "J PHE 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 41": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 83": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ASP 111": "OD1" <-> "OD2" Residue "J ARG 115": "NH1" <-> "NH2" Residue "J TYR 158": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ARG 169": "NH1" <-> "NH2" Residue "J ARG 177": "NH1" <-> "NH2" Residue "J ARG 192": "NH1" <-> "NH2" Residue "J TYR 196": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J GLU 197": "OE1" <-> "OE2" Residue "J TYR 202": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J GLU 231": "OE1" <-> "OE2" Residue "J ARG 245": "NH1" <-> "NH2" Residue "J TYR 255": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ARG 273": "NH1" <-> "NH2" Residue "J PHE 285": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ASP 295": "OD1" <-> "OD2" Residue "J ASP 299": "OD1" <-> "OD2" Residue "J PHE 308": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J GLU 312": "OE1" <-> "OE2" Residue "J PHE 327": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ASP 350": "OD1" <-> "OD2" Residue "J PHE 356": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ARG 357": "NH1" <-> "NH2" Residue "J GLU 375": "OE1" <-> "OE2" Residue "J PHE 390": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 428": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J GLU 433": "OE1" <-> "OE2" Residue "J GLU 435": "OE1" <-> "OE2" Residue "J PHE 464": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ASP 471": "OD1" <-> "OD2" Residue "J GLU 479": "OE1" <-> "OE2" Residue "J ASP 494": "OD1" <-> "OD2" Residue "J GLU 495": "OE1" <-> "OE2" Residue "J TYR 497": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ASP 509": "OD1" <-> "OD2" Residue "J TYR 516": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ARG 518": "NH1" <-> "NH2" Residue "J PHE 523": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 525": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J GLU 549": "OE1" <-> "OE2" Residue "J TYR 587": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 588": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 603": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M PHE 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M TYR 41": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M TYR 83": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M GLU 110": "OE1" <-> "OE2" Residue "M ASP 111": "OD1" <-> "OD2" Residue "M ARG 115": "NH1" <-> "NH2" Residue "M GLU 140": "OE1" <-> "OE2" Residue "M TYR 158": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M ARG 169": "NH1" <-> "NH2" Residue "M ARG 177": "NH1" <-> "NH2" Residue "M ARG 192": "NH1" <-> "NH2" Residue "M TYR 196": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M GLU 197": "OE1" <-> "OE2" Residue "M TYR 202": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M ASP 213": "OD1" <-> "OD2" Residue "M GLU 231": "OE1" <-> "OE2" Residue "M ARG 245": "NH1" <-> "NH2" Residue "M TYR 255": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M ARG 273": "NH1" <-> "NH2" Residue "M PHE 285": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M ASP 292": "OD1" <-> "OD2" Residue "M ASP 295": "OD1" <-> "OD2" Residue "M ASP 299": "OD1" <-> "OD2" Residue "M PHE 308": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M GLU 312": "OE1" <-> "OE2" Residue "M PHE 327": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M ASP 350": "OD1" <-> "OD2" Residue "M PHE 356": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M ARG 357": "NH1" <-> "NH2" Residue "M GLU 375": "OE1" <-> "OE2" Residue "M PHE 390": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M PHE 428": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M GLU 435": "OE1" <-> "OE2" Residue "M PHE 464": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M ASP 471": "OD1" <-> "OD2" Residue "M GLU 479": "OE1" <-> "OE2" Residue "M ASP 494": "OD1" <-> "OD2" Residue "M GLU 495": "OE1" <-> "OE2" Residue "M TYR 497": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M ASP 509": "OD1" <-> "OD2" Residue "M TYR 516": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M ARG 518": "NH1" <-> "NH2" Residue "M PHE 523": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M PHE 525": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M GLU 536": "OE1" <-> "OE2" Residue "M GLU 549": "OE1" <-> "OE2" Residue "M TYR 587": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M PHE 588": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M PHE 603": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N GLU 10": "OE1" <-> "OE2" Residue "N PHE 29": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N TYR 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N TYR 80": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N TYR 94": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N TYR 102": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N ASP 155": "OD1" <-> "OD2" Residue "N PHE 157": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N PHE 177": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N TYR 187": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N ASP 219": "OD1" <-> "OD2" Residue "O TYR 33": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O ASP 34": "OD1" <-> "OD2" Residue "O TYR 38": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O TYR 51": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O ARG 56": "NH1" <-> "NH2" Residue "O ASP 62": "OD1" <-> "OD2" Residue "O ASP 84": "OD1" <-> "OD2" Residue "O TYR 88": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O ASP 143": "OD1" <-> "OD2" Residue "O PHE 144": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O ASP 156": "OD1" <-> "OD2" Residue "O GLU 165": "OE1" <-> "OE2" Residue "O GLU 203": "OE1" <-> "OE2" Time to flip residues: 0.13s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 49974 Number of models: 1 Model: "" Number of chains: 24 Chain: "A" Number of atoms: 8344 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1066, 8344 Classifications: {'peptide': 1066} Link IDs: {'PTRANS': 56, 'TRANS': 1009} Chain breaks: 5 Chain: "B" Number of atoms: 8344 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1066, 8344 Classifications: {'peptide': 1066} Link IDs: {'PTRANS': 56, 'TRANS': 1009} Chain breaks: 5 Chain: "C" Number of atoms: 8344 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1066, 8344 Classifications: {'peptide': 1066} Link IDs: {'PTRANS': 56, 'TRANS': 1009} Chain breaks: 5 Chain: "E" Number of atoms: 4865 Number of conformers: 1 Conformer: "" Number of residues, atoms: 596, 4865 Classifications: {'peptide': 596} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 26, 'TRANS': 568} Chain: "H" Number of atoms: 1667 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 227, 1661 Classifications: {'peptide': 227} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 2, 'PTRANS': 10, 'TRANS': 214} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Conformer: "B" Number of residues, atoms: 227, 1661 Classifications: {'peptide': 227} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 2, 'PTRANS': 10, 'TRANS': 214} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 bond proxies already assigned to first conformer: 1690 Chain: "L" Number of atoms: 1557 Number of conformers: 1 Conformer: "" Number of residues, atoms: 213, 1557 Classifications: {'peptide': 213} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 15, 'TRANS': 196} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "G" Number of atoms: 1667 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 227, 1661 Classifications: {'peptide': 227} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 2, 'PTRANS': 10, 'TRANS': 214} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Conformer: "B" Number of residues, atoms: 227, 1661 Classifications: {'peptide': 227} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 2, 'PTRANS': 10, 'TRANS': 214} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 bond proxies already assigned to first conformer: 1690 Chain: "I" Number of atoms: 1557 Number of conformers: 1 Conformer: "" Number of residues, atoms: 213, 1557 Classifications: {'peptide': 213} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 15, 'TRANS': 196} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "J" Number of atoms: 4865 Number of conformers: 1 Conformer: "" Number of residues, atoms: 596, 4865 Classifications: {'peptide': 596} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 26, 'TRANS': 568} Chain: "M" Number of atoms: 4865 Number of conformers: 1 Conformer: "" Number of residues, atoms: 596, 4865 Classifications: {'peptide': 596} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 26, 'TRANS': 568} Chain: "N" Number of atoms: 1667 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 227, 1661 Classifications: {'peptide': 227} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 2, 'PTRANS': 10, 'TRANS': 214} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Conformer: "B" Number of residues, atoms: 227, 1661 Classifications: {'peptide': 227} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 2, 'PTRANS': 10, 'TRANS': 214} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 bond proxies already assigned to first conformer: 1690 Chain: "O" Number of atoms: 1557 Number of conformers: 1 Conformer: "" Number of residues, atoms: 213, 1557 Classifications: {'peptide': 213} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 15, 'TRANS': 196} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "P" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "R" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 112 Unusual residues: {'NAG': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 8 Chain: "B" Number of atoms: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 112 Unusual residues: {'NAG': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 8 Chain: "C" Number of atoms: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 112 Unusual residues: {'NAG': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 8 Chain: "E" Number of atoms: 57 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 57 Unusual residues: {' ZN': 1, 'NAG': 4} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "J" Number of atoms: 57 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 57 Unusual residues: {' ZN': 1, 'NAG': 4} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "M" Number of atoms: 57 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 57 Unusual residues: {' ZN': 1, 'NAG': 4} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Time building chain proxies: 21.51, per 1000 atoms: 0.43 Number of scatterers: 49974 At special positions: 0 Unit cell: (240.768, 228.096, 216.832, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Zn 3 29.99 S 240 16.00 O 9720 8.00 N 8259 7.00 C 31752 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=66, symmetry=0 Simple disulfide: pdb=" SG CYS A 15 " - pdb=" SG CYS A 136 " distance=2.03 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.03 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.03 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.03 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.03 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.03 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.04 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.03 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.03 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.02 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.03 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.03 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.04 Simple disulfide: pdb=" SG CYS B 15 " - pdb=" SG CYS B 136 " distance=2.03 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.03 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.03 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.03 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.02 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.04 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.03 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=2.03 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.03 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.03 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 760 " distance=2.02 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.03 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.03 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.03 Simple disulfide: pdb=" SG CYS C 15 " - pdb=" SG CYS C 136 " distance=2.03 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.03 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.03 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.03 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.03 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.03 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " distance=2.03 Simple disulfide: pdb=" SG CYS C 538 " - pdb=" SG CYS C 590 " distance=2.04 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.03 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.03 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=2.02 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.03 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.03 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.03 Simple disulfide: pdb=" SG CYS E 133 " - pdb=" SG CYS E 141 " distance=2.03 Simple disulfide: pdb=" SG CYS E 344 " - pdb=" SG CYS E 361 " distance=2.03 Simple disulfide: pdb=" SG CYS E 530 " - pdb=" SG CYS E 542 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.03 Simple disulfide: pdb=" SG ACYS H 151 " - pdb=" SG ACYS H 207 " distance=2.03 Simple disulfide: pdb=" SG BCYS H 151 " - pdb=" SG BCYS H 207 " distance=2.03 Simple disulfide: pdb=" SG CYS L 22 " - pdb=" SG CYS L 90 " distance=2.03 Simple disulfide: pdb=" SG CYS L 139 " - pdb=" SG CYS L 198 " distance=2.03 Simple disulfide: pdb=" SG CYS G 22 " - pdb=" SG CYS G 96 " distance=2.03 Simple disulfide: pdb=" SG ACYS G 151 " - pdb=" SG ACYS G 207 " distance=2.03 Simple disulfide: pdb=" SG BCYS G 151 " - pdb=" SG BCYS G 207 " distance=2.03 Simple disulfide: pdb=" SG CYS I 22 " - pdb=" SG CYS I 90 " distance=2.03 Simple disulfide: pdb=" SG CYS I 139 " - pdb=" SG CYS I 198 " distance=2.03 Simple disulfide: pdb=" SG CYS J 133 " - pdb=" SG CYS J 141 " distance=2.04 Simple disulfide: pdb=" SG CYS J 344 " - pdb=" SG CYS J 361 " distance=2.03 Simple disulfide: pdb=" SG CYS J 530 " - pdb=" SG CYS J 542 " distance=2.04 Simple disulfide: pdb=" SG CYS M 133 " - pdb=" SG CYS M 141 " distance=2.04 Simple disulfide: pdb=" SG CYS M 344 " - pdb=" SG CYS M 361 " distance=2.03 Simple disulfide: pdb=" SG CYS M 530 " - pdb=" SG CYS M 542 " distance=2.04 Simple disulfide: pdb=" SG CYS N 22 " - pdb=" SG CYS N 96 " distance=2.03 Simple disulfide: pdb=" SG ACYS N 151 " - pdb=" SG ACYS N 207 " distance=2.03 Simple disulfide: pdb=" SG BCYS N 151 " - pdb=" SG BCYS N 207 " distance=2.03 Simple disulfide: pdb=" SG CYS O 22 " - pdb=" SG CYS O 90 " distance=2.03 Simple disulfide: pdb=" SG CYS O 139 " - pdb=" SG CYS O 198 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG D 1 " - " NAG D 2 " " NAG F 1 " - " NAG F 2 " " NAG K 1 " - " NAG K 2 " " NAG P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " " NAG R 1 " - " NAG R 2 " NAG-ASN " NAG A1301 " - " ASN A 282 " " NAG A1302 " - " ASN A 331 " " NAG A1303 " - " ASN A 603 " " NAG A1304 " - " ASN A 616 " " NAG A1305 " - " ASN A 657 " " NAG A1306 " - " ASN A 709 " " NAG A1307 " - " ASN A1098 " " NAG A1308 " - " ASN A1134 " " NAG B1301 " - " ASN B 282 " " NAG B1302 " - " ASN B 331 " " NAG B1303 " - " ASN B 603 " " NAG B1304 " - " ASN B 616 " " NAG B1305 " - " ASN B 657 " " NAG B1306 " - " ASN B 709 " " NAG B1307 " - " ASN B1098 " " NAG B1308 " - " ASN B1134 " " NAG C1301 " - " ASN C 282 " " NAG C1302 " - " ASN C 331 " " NAG C1303 " - " ASN C 603 " " NAG C1304 " - " ASN C 616 " " NAG C1305 " - " ASN C 657 " " NAG C1306 " - " ASN C 709 " " NAG C1307 " - " ASN C1098 " " NAG C1308 " - " ASN C1134 " " NAG D 1 " - " ASN A 717 " " NAG E 902 " - " ASN E 53 " " NAG E 903 " - " ASN E 90 " " NAG E 904 " - " ASN E 322 " " NAG E 905 " - " ASN E 546 " " NAG F 1 " - " ASN A 801 " " NAG J 902 " - " ASN J 53 " " NAG J 903 " - " ASN J 90 " " NAG J 904 " - " ASN J 322 " " NAG J 905 " - " ASN J 546 " " NAG K 1 " - " ASN B 717 " " NAG M 902 " - " ASN M 53 " " NAG M 903 " - " ASN M 90 " " NAG M 904 " - " ASN M 322 " " NAG M 905 " - " ASN M 546 " " NAG P 1 " - " ASN B 801 " " NAG Q 1 " - " ASN C 717 " " NAG R 1 " - " ASN C 801 " Time building additional restraints: 13.57 Conformation dependent library (CDL) restraints added in 7.9 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN E 901 " pdb="ZN ZN E 901 " - pdb=" NE2 HIS E 378 " pdb=" ZN J 901 " pdb="ZN ZN J 901 " - pdb=" NE2 HIS J 374 " pdb="ZN ZN J 901 " - pdb=" NE2 HIS J 378 " pdb=" ZN M 901 " pdb="ZN ZN M 901 " - pdb=" NE2 HIS M 374 " pdb="ZN ZN M 901 " - pdb=" NE2 HIS M 378 " 12516 Ramachandran restraints generated. 6258 Oldfield, 0 Emsley, 6258 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 11772 Finding SS restraints... Secondary structure from input PDB file: 142 helices and 94 sheets defined 26.5% alpha, 19.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.58 Creating SS restraints... Processing helix chain 'A' and resid 294 through 303 removed outlier: 3.551A pdb=" N LYS A 300 " --> pdb=" O LEU A 296 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N THR A 302 " --> pdb=" O GLU A 298 " (cutoff:3.500A) Processing helix chain 'A' and resid 338 through 343 removed outlier: 3.928A pdb=" N PHE A 342 " --> pdb=" O PHE A 338 " (cutoff:3.500A) Processing helix chain 'A' and resid 403 through 410 removed outlier: 3.528A pdb=" N GLU A 406 " --> pdb=" O ARG A 403 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N VAL A 407 " --> pdb=" O GLY A 404 " (cutoff:3.500A) removed outlier: 4.674A pdb=" N ARG A 408 " --> pdb=" O ASP A 405 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N ILE A 410 " --> pdb=" O VAL A 407 " (cutoff:3.500A) Processing helix chain 'A' and resid 737 through 742 removed outlier: 3.625A pdb=" N TYR A 741 " --> pdb=" O ASP A 737 " (cutoff:3.500A) Processing helix chain 'A' and resid 747 through 754 removed outlier: 3.671A pdb=" N ASN A 751 " --> pdb=" O THR A 747 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N LEU A 752 " --> pdb=" O GLU A 748 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N LEU A 754 " --> pdb=" O SER A 750 " (cutoff:3.500A) Processing helix chain 'A' and resid 756 through 777 removed outlier: 3.545A pdb=" N CYS A 760 " --> pdb=" O TYR A 756 " (cutoff:3.500A) Processing helix chain 'A' and resid 777 through 782 removed outlier: 3.592A pdb=" N VAL A 781 " --> pdb=" O ASN A 777 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 824 removed outlier: 3.647A pdb=" N ASN A 824 " --> pdb=" O ASP A 820 " (cutoff:3.500A) Processing helix chain 'A' and resid 852 through 857 removed outlier: 4.238A pdb=" N ASN A 856 " --> pdb=" O GLN A 853 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N GLY A 857 " --> pdb=" O LYS A 854 " (cutoff:3.500A) Processing helix chain 'A' and resid 866 through 884 Processing helix chain 'A' and resid 897 through 907 removed outlier: 3.555A pdb=" N TYR A 904 " --> pdb=" O MET A 900 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 939 Processing helix chain 'A' and resid 949 through 966 removed outlier: 3.828A pdb=" N ASN A 955 " --> pdb=" O VAL A 951 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N VAL A 963 " --> pdb=" O LEU A 959 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N LYS A 964 " --> pdb=" O ASN A 960 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N LEU A 966 " --> pdb=" O LEU A 962 " (cutoff:3.500A) Processing helix chain 'A' and resid 976 through 984 removed outlier: 4.181A pdb=" N ILE A 980 " --> pdb=" O VAL A 976 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N LEU A 981 " --> pdb=" O LEU A 977 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N SER A 982 " --> pdb=" O ASN A 978 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N ARG A 983 " --> pdb=" O ASP A 979 " (cutoff:3.500A) Processing helix chain 'A' and resid 989 through 1032 removed outlier: 3.579A pdb=" N SER A1003 " --> pdb=" O GLY A 999 " (cutoff:3.500A) Processing helix chain 'A' and resid 1141 through 1145 removed outlier: 3.544A pdb=" N GLU A1144 " --> pdb=" O LEU A1141 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 303 removed outlier: 3.527A pdb=" N LYS B 300 " --> pdb=" O LEU B 296 " (cutoff:3.500A) Processing helix chain 'B' and resid 338 through 342 removed outlier: 3.758A pdb=" N VAL B 341 " --> pdb=" O PHE B 338 " (cutoff:3.500A) Processing helix chain 'B' and resid 737 through 742 removed outlier: 3.576A pdb=" N TYR B 741 " --> pdb=" O ASP B 737 " (cutoff:3.500A) Processing helix chain 'B' and resid 747 through 753 removed outlier: 3.702A pdb=" N ASN B 751 " --> pdb=" O THR B 747 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N LEU B 752 " --> pdb=" O GLU B 748 " (cutoff:3.500A) Processing helix chain 'B' and resid 756 through 777 removed outlier: 3.572A pdb=" N CYS B 760 " --> pdb=" O TYR B 756 " (cutoff:3.500A) Processing helix chain 'B' and resid 777 through 782 removed outlier: 3.583A pdb=" N VAL B 781 " --> pdb=" O ASN B 777 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 824 removed outlier: 3.653A pdb=" N ASN B 824 " --> pdb=" O ASP B 820 " (cutoff:3.500A) Processing helix chain 'B' and resid 852 through 857 removed outlier: 4.191A pdb=" N ASN B 856 " --> pdb=" O GLN B 853 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N GLY B 857 " --> pdb=" O LYS B 854 " (cutoff:3.500A) Processing helix chain 'B' and resid 866 through 884 Processing helix chain 'B' and resid 897 through 907 removed outlier: 3.533A pdb=" N ARG B 905 " --> pdb=" O GLN B 901 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ASN B 907 " --> pdb=" O ALA B 903 " (cutoff:3.500A) Processing helix chain 'B' and resid 919 through 939 Processing helix chain 'B' and resid 949 through 966 removed outlier: 3.812A pdb=" N ASN B 955 " --> pdb=" O VAL B 951 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N VAL B 963 " --> pdb=" O LEU B 959 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N LEU B 966 " --> pdb=" O LEU B 962 " (cutoff:3.500A) Processing helix chain 'B' and resid 976 through 984 removed outlier: 4.175A pdb=" N ILE B 980 " --> pdb=" O VAL B 976 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N LEU B 981 " --> pdb=" O LEU B 977 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N SER B 982 " --> pdb=" O ASN B 978 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ARG B 983 " --> pdb=" O ASP B 979 " (cutoff:3.500A) Processing helix chain 'B' and resid 989 through 1032 removed outlier: 3.651A pdb=" N SER B1003 " --> pdb=" O GLY B 999 " (cutoff:3.500A) Processing helix chain 'B' and resid 1141 through 1145 Processing helix chain 'C' and resid 294 through 303 removed outlier: 3.549A pdb=" N LYS C 300 " --> pdb=" O LEU C 296 " (cutoff:3.500A) Processing helix chain 'C' and resid 737 through 742 removed outlier: 3.600A pdb=" N TYR C 741 " --> pdb=" O ASP C 737 " (cutoff:3.500A) Processing helix chain 'C' and resid 747 through 753 removed outlier: 3.681A pdb=" N ASN C 751 " --> pdb=" O THR C 747 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N LEU C 752 " --> pdb=" O GLU C 748 " (cutoff:3.500A) Processing helix chain 'C' and resid 756 through 777 removed outlier: 3.586A pdb=" N CYS C 760 " --> pdb=" O TYR C 756 " (cutoff:3.500A) Processing helix chain 'C' and resid 777 through 782 removed outlier: 3.630A pdb=" N VAL C 781 " --> pdb=" O ASN C 777 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 824 removed outlier: 3.647A pdb=" N ASN C 824 " --> pdb=" O ASP C 820 " (cutoff:3.500A) Processing helix chain 'C' and resid 852 through 857 removed outlier: 4.193A pdb=" N ASN C 856 " --> pdb=" O GLN C 853 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N GLY C 857 " --> pdb=" O LYS C 854 " (cutoff:3.500A) Processing helix chain 'C' and resid 866 through 884 Processing helix chain 'C' and resid 897 through 907 removed outlier: 3.558A pdb=" N ARG C 905 " --> pdb=" O GLN C 901 " (cutoff:3.500A) Processing helix chain 'C' and resid 919 through 939 Processing helix chain 'C' and resid 949 through 966 removed outlier: 3.816A pdb=" N ASN C 955 " --> pdb=" O VAL C 951 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N VAL C 963 " --> pdb=" O LEU C 959 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N LEU C 966 " --> pdb=" O LEU C 962 " (cutoff:3.500A) Processing helix chain 'C' and resid 976 through 984 removed outlier: 4.164A pdb=" N ILE C 980 " --> pdb=" O VAL C 976 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N LEU C 981 " --> pdb=" O LEU C 977 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N SER C 982 " --> pdb=" O ASN C 978 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N ARG C 983 " --> pdb=" O ASP C 979 " (cutoff:3.500A) Processing helix chain 'C' and resid 989 through 1032 removed outlier: 3.671A pdb=" N SER C1003 " --> pdb=" O GLY C 999 " (cutoff:3.500A) Processing helix chain 'E' and resid 21 through 53 removed outlier: 3.616A pdb=" N LYS E 26 " --> pdb=" O GLU E 22 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N THR E 27 " --> pdb=" O GLU E 23 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N PHE E 28 " --> pdb=" O GLN E 24 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N LYS E 31 " --> pdb=" O THR E 27 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N PHE E 32 " --> pdb=" O PHE E 28 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N GLU E 37 " --> pdb=" O ASN E 33 " (cutoff:3.500A) removed outlier: 4.616A pdb=" N ASP E 38 " --> pdb=" O HIS E 34 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N TYR E 41 " --> pdb=" O GLU E 37 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N THR E 52 " --> pdb=" O TRP E 48 " (cutoff:3.500A) Processing helix chain 'E' and resid 57 through 81 removed outlier: 3.695A pdb=" N THR E 78 " --> pdb=" O LYS E 74 " (cutoff:3.500A) Processing helix chain 'E' and resid 90 through 101 removed outlier: 3.829A pdb=" N LYS E 94 " --> pdb=" O ASN E 90 " (cutoff:3.500A) removed outlier: 4.127A pdb=" N GLN E 96 " --> pdb=" O THR E 92 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N GLN E 98 " --> pdb=" O LYS E 94 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N ALA E 99 " --> pdb=" O LEU E 95 " (cutoff:3.500A) Processing helix chain 'E' and resid 103 through 108 removed outlier: 3.576A pdb=" N SER E 106 " --> pdb=" O ASN E 103 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N VAL E 107 " --> pdb=" O GLY E 104 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N LEU E 108 " --> pdb=" O SER E 105 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 103 through 108' Processing helix chain 'E' and resid 109 through 127 removed outlier: 3.764A pdb=" N LYS E 114 " --> pdb=" O GLU E 110 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N LEU E 116 " --> pdb=" O LYS E 112 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N ASN E 117 " --> pdb=" O SER E 113 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N TYR E 127 " --> pdb=" O MET E 123 " (cutoff:3.500A) Processing helix chain 'E' and resid 146 through 152 removed outlier: 3.970A pdb=" N GLU E 150 " --> pdb=" O PRO E 146 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N ILE E 151 " --> pdb=" O GLY E 147 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N MET E 152 " --> pdb=" O LEU E 148 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 146 through 152' Processing helix chain 'E' and resid 157 through 169 removed outlier: 3.699A pdb=" N ARG E 161 " --> pdb=" O ASP E 157 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N TRP E 168 " --> pdb=" O ALA E 164 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N ARG E 169 " --> pdb=" O TRP E 165 " (cutoff:3.500A) Processing helix chain 'E' and resid 171 through 176 removed outlier: 4.377A pdb=" N GLN E 175 " --> pdb=" O GLU E 171 " (cutoff:3.500A) Processing helix chain 'E' and resid 176 through 193 removed outlier: 3.858A pdb=" N GLU E 182 " --> pdb=" O PRO E 178 " (cutoff:3.500A) removed outlier: 4.289A pdb=" N VAL E 185 " --> pdb=" O GLU E 181 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N LEU E 186 " --> pdb=" O GLU E 182 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N LYS E 187 " --> pdb=" O TYR E 183 " (cutoff:3.500A) Processing helix chain 'E' and resid 198 through 205 removed outlier: 3.839A pdb=" N TYR E 202 " --> pdb=" O ASP E 198 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N TRP E 203 " --> pdb=" O TYR E 199 " (cutoff:3.500A) Processing helix chain 'E' and resid 221 through 252 removed outlier: 3.787A pdb=" N VAL E 226 " --> pdb=" O LEU E 222 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N GLU E 231 " --> pdb=" O GLU E 227 " (cutoff:3.500A) removed outlier: 4.689A pdb=" N GLU E 232 " --> pdb=" O HIS E 228 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N ILE E 233 " --> pdb=" O THR E 229 " (cutoff:3.500A) Proline residue: E 235 - end of helix removed outlier: 3.618A pdb=" N MET E 249 " --> pdb=" O ARG E 245 " (cutoff:3.500A) removed outlier: 4.853A pdb=" N ASN E 250 " --> pdb=" O ALA E 246 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N ALA E 251 " --> pdb=" O LYS E 247 " (cutoff:3.500A) Processing helix chain 'E' and resid 275 through 280 removed outlier: 3.784A pdb=" N LEU E 278 " --> pdb=" O TRP E 275 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N TYR E 279 " --> pdb=" O THR E 276 " (cutoff:3.500A) removed outlier: 4.276A pdb=" N SER E 280 " --> pdb=" O ASN E 277 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 275 through 280' Processing helix chain 'E' and resid 293 through 298 removed outlier: 3.665A pdb=" N VAL E 298 " --> pdb=" O THR E 294 " (cutoff:3.500A) Processing helix chain 'E' and resid 303 through 317 removed outlier: 3.578A pdb=" N SER E 317 " --> pdb=" O LYS E 313 " (cutoff:3.500A) Processing helix chain 'E' and resid 366 through 383 removed outlier: 4.102A pdb=" N LEU E 370 " --> pdb=" O MET E 366 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N THR E 371 " --> pdb=" O ASP E 367 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N HIS E 373 " --> pdb=" O PHE E 369 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N MET E 376 " --> pdb=" O ALA E 372 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N HIS E 378 " --> pdb=" O HIS E 374 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N ILE E 379 " --> pdb=" O GLU E 375 " (cutoff:3.500A) Processing helix chain 'E' and resid 399 through 413 removed outlier: 3.579A pdb=" N ILE E 407 " --> pdb=" O ALA E 403 " (cutoff:3.500A) removed outlier: 4.687A pdb=" N MET E 408 " --> pdb=" O VAL E 404 " (cutoff:3.500A) removed outlier: 4.109A pdb=" N SER E 409 " --> pdb=" O GLY E 405 " (cutoff:3.500A) Processing helix chain 'E' and resid 414 through 421 Processing helix chain 'E' and resid 435 through 443 removed outlier: 3.779A pdb=" N LEU E 439 " --> pdb=" O GLU E 435 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N GLN E 442 " --> pdb=" O PHE E 438 " (cutoff:3.500A) Processing helix chain 'E' and resid 449 through 464 removed outlier: 3.585A pdb=" N TYR E 454 " --> pdb=" O LEU E 450 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N ARG E 460 " --> pdb=" O LEU E 456 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N PHE E 464 " --> pdb=" O ARG E 460 " (cutoff:3.500A) Processing helix chain 'E' and resid 469 through 473 removed outlier: 4.023A pdb=" N TRP E 473 " --> pdb=" O LYS E 470 " (cutoff:3.500A) Processing helix chain 'E' and resid 474 through 480 removed outlier: 3.732A pdb=" N MET E 480 " --> pdb=" O LYS E 476 " (cutoff:3.500A) Processing helix chain 'E' and resid 512 through 529 removed outlier: 4.256A pdb=" N TYR E 516 " --> pdb=" O PHE E 512 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N LEU E 520 " --> pdb=" O TYR E 516 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N GLN E 522 " --> pdb=" O ARG E 518 " (cutoff:3.500A) removed outlier: 4.594A pdb=" N PHE E 523 " --> pdb=" O THR E 519 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N GLN E 524 " --> pdb=" O LEU E 520 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N GLN E 526 " --> pdb=" O GLN E 522 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N LEU E 529 " --> pdb=" O PHE E 525 " (cutoff:3.500A) Processing helix chain 'E' and resid 538 through 542 removed outlier: 3.580A pdb=" N LYS E 541 " --> pdb=" O PRO E 538 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N CYS E 542 " --> pdb=" O LEU E 539 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 538 through 542' Processing helix chain 'E' and resid 547 through 556 removed outlier: 3.937A pdb=" N GLY E 551 " --> pdb=" O SER E 547 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N GLN E 552 " --> pdb=" O THR E 548 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N LYS E 553 " --> pdb=" O GLU E 549 " (cutoff:3.500A) Processing helix chain 'E' and resid 565 through 570 removed outlier: 3.565A pdb=" N LEU E 570 " --> pdb=" O TRP E 566 " (cutoff:3.500A) Processing helix chain 'E' and resid 581 through 588 removed outlier: 3.923A pdb=" N PHE E 588 " --> pdb=" O LEU E 584 " (cutoff:3.500A) Processing helix chain 'E' and resid 588 through 597 removed outlier: 3.793A pdb=" N LYS E 596 " --> pdb=" O PHE E 592 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N ASP E 597 " --> pdb=" O THR E 593 " (cutoff:3.500A) Processing helix chain 'E' and resid 611 through 615 removed outlier: 3.517A pdb=" N ALA E 614 " --> pdb=" O SER E 611 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N ASP E 615 " --> pdb=" O PRO E 612 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 611 through 615' Processing helix chain 'H' and resid 198 through 200 No H-bonds generated for 'chain 'H' and resid 198 through 200' Processing helix chain 'L' and resid 129 through 133 removed outlier: 3.817A pdb=" N ASN L 133 " --> pdb=" O LEU L 130 " (cutoff:3.500A) Processing helix chain 'L' and resid 186 through 191 removed outlier: 4.050A pdb=" N LYS L 191 " --> pdb=" O PRO L 187 " (cutoff:3.500A) Processing helix chain 'G' and resid 198 through 200 No H-bonds generated for 'chain 'G' and resid 198 through 200' Processing helix chain 'I' and resid 129 through 133 removed outlier: 3.749A pdb=" N ASN I 133 " --> pdb=" O LEU I 130 " (cutoff:3.500A) Processing helix chain 'I' and resid 186 through 191 removed outlier: 4.054A pdb=" N LYS I 191 " --> pdb=" O PRO I 187 " (cutoff:3.500A) Processing helix chain 'J' and resid 21 through 53 removed outlier: 3.660A pdb=" N THR J 27 " --> pdb=" O GLU J 23 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N PHE J 28 " --> pdb=" O GLN J 24 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N ASP J 30 " --> pdb=" O LYS J 26 " (cutoff:3.500A) removed outlier: 4.354A pdb=" N LYS J 31 " --> pdb=" O THR J 27 " (cutoff:3.500A) removed outlier: 4.104A pdb=" N PHE J 32 " --> pdb=" O PHE J 28 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N ASP J 38 " --> pdb=" O HIS J 34 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N TYR J 41 " --> pdb=" O GLU J 37 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N SER J 47 " --> pdb=" O SER J 43 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ASN J 49 " --> pdb=" O LEU J 45 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N ASN J 51 " --> pdb=" O SER J 47 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N THR J 52 " --> pdb=" O TRP J 48 " (cutoff:3.500A) Processing helix chain 'J' and resid 58 through 77 removed outlier: 3.648A pdb=" N LEU J 73 " --> pdb=" O TRP J 69 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N LYS J 74 " --> pdb=" O SER J 70 " (cutoff:3.500A) Processing helix chain 'J' and resid 79 through 83 removed outlier: 3.682A pdb=" N MET J 82 " --> pdb=" O LEU J 79 " (cutoff:3.500A) Processing helix chain 'J' and resid 90 through 101 removed outlier: 3.721A pdb=" N LYS J 94 " --> pdb=" O ASN J 90 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N LEU J 95 " --> pdb=" O LEU J 91 " (cutoff:3.500A) removed outlier: 4.071A pdb=" N GLN J 96 " --> pdb=" O THR J 92 " (cutoff:3.500A) Processing helix chain 'J' and resid 109 through 129 removed outlier: 3.742A pdb=" N LYS J 114 " --> pdb=" O GLU J 110 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N ARG J 115 " --> pdb=" O ASP J 111 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N LEU J 116 " --> pdb=" O LYS J 112 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N ASN J 117 " --> pdb=" O SER J 113 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N ASN J 121 " --> pdb=" O ASN J 117 " (cutoff:3.500A) Processing helix chain 'J' and resid 147 through 152 Processing helix chain 'J' and resid 158 through 169 removed outlier: 3.917A pdb=" N ARG J 169 " --> pdb=" O TRP J 165 " (cutoff:3.500A) Processing helix chain 'J' and resid 171 through 194 removed outlier: 4.127A pdb=" N GLN J 175 " --> pdb=" O GLU J 171 " (cutoff:3.500A) Proline residue: J 178 - end of helix removed outlier: 3.586A pdb=" N GLU J 182 " --> pdb=" O PRO J 178 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N VAL J 185 " --> pdb=" O GLU J 181 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N LEU J 186 " --> pdb=" O GLU J 182 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N LYS J 187 " --> pdb=" O TYR J 183 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N ALA J 193 " --> pdb=" O GLU J 189 " (cutoff:3.500A) Processing helix chain 'J' and resid 198 through 205 removed outlier: 3.675A pdb=" N TYR J 202 " --> pdb=" O ASP J 198 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N TRP J 203 " --> pdb=" O TYR J 199 " (cutoff:3.500A) Processing helix chain 'J' and resid 221 through 229 removed outlier: 3.572A pdb=" N VAL J 226 " --> pdb=" O LEU J 222 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N GLU J 227 " --> pdb=" O ILE J 223 " (cutoff:3.500A) Processing helix chain 'J' and resid 229 through 248 Proline residue: J 235 - end of helix removed outlier: 3.506A pdb=" N LEU J 240 " --> pdb=" O LEU J 236 " (cutoff:3.500A) Processing helix chain 'J' and resid 275 through 279 removed outlier: 3.752A pdb=" N LEU J 278 " --> pdb=" O TRP J 275 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N TYR J 279 " --> pdb=" O THR J 276 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 275 through 279' Processing helix chain 'J' and resid 293 through 297 Processing helix chain 'J' and resid 303 through 317 removed outlier: 3.805A pdb=" N SER J 317 " --> pdb=" O LYS J 313 " (cutoff:3.500A) Processing helix chain 'J' and resid 325 through 330 removed outlier: 3.563A pdb=" N GLU J 329 " --> pdb=" O GLN J 325 " (cutoff:3.500A) removed outlier: 4.071A pdb=" N ASN J 330 " --> pdb=" O GLY J 326 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 325 through 330' Processing helix chain 'J' and resid 366 through 371 removed outlier: 3.898A pdb=" N LEU J 370 " --> pdb=" O MET J 366 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N THR J 371 " --> pdb=" O ASP J 367 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 366 through 371' Processing helix chain 'J' and resid 371 through 385 removed outlier: 3.793A pdb=" N MET J 376 " --> pdb=" O ALA J 372 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N ALA J 384 " --> pdb=" O GLN J 380 " (cutoff:3.500A) removed outlier: 4.380A pdb=" N TYR J 385 " --> pdb=" O TYR J 381 " (cutoff:3.500A) Processing helix chain 'J' and resid 400 through 413 removed outlier: 3.847A pdb=" N VAL J 404 " --> pdb=" O PHE J 400 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N GLY J 405 " --> pdb=" O HIS J 401 " (cutoff:3.500A) removed outlier: 4.379A pdb=" N MET J 408 " --> pdb=" O VAL J 404 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N SER J 409 " --> pdb=" O GLY J 405 " (cutoff:3.500A) Processing helix chain 'J' and resid 414 through 421 removed outlier: 3.594A pdb=" N SER J 420 " --> pdb=" O LYS J 416 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N ILE J 421 " --> pdb=" O HIS J 417 " (cutoff:3.500A) Processing helix chain 'J' and resid 435 through 444 removed outlier: 3.517A pdb=" N LEU J 439 " --> pdb=" O GLU J 435 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N GLN J 442 " --> pdb=" O PHE J 438 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N LEU J 444 " --> pdb=" O LEU J 440 " (cutoff:3.500A) Processing helix chain 'J' and resid 449 through 464 removed outlier: 3.873A pdb=" N ARG J 460 " --> pdb=" O LEU J 456 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N MET J 462 " --> pdb=" O LYS J 458 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N VAL J 463 " --> pdb=" O TRP J 459 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N PHE J 464 " --> pdb=" O ARG J 460 " (cutoff:3.500A) Processing helix chain 'J' and resid 472 through 484 removed outlier: 3.565A pdb=" N LYS J 476 " --> pdb=" O GLN J 472 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N GLU J 479 " --> pdb=" O LYS J 475 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N MET J 480 " --> pdb=" O LYS J 476 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N LYS J 481 " --> pdb=" O TRP J 477 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N ARG J 482 " --> pdb=" O TRP J 478 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N GLU J 483 " --> pdb=" O GLU J 479 " (cutoff:3.500A) Processing helix chain 'J' and resid 512 through 528 removed outlier: 4.143A pdb=" N TYR J 516 " --> pdb=" O PHE J 512 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N THR J 517 " --> pdb=" O ILE J 513 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N LEU J 520 " --> pdb=" O TYR J 516 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N GLN J 522 " --> pdb=" O ARG J 518 " (cutoff:3.500A) removed outlier: 4.975A pdb=" N PHE J 523 " --> pdb=" O THR J 519 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N GLN J 526 " --> pdb=" O GLN J 522 " (cutoff:3.500A) Processing helix chain 'J' and resid 538 through 542 removed outlier: 3.585A pdb=" N LYS J 541 " --> pdb=" O PRO J 538 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N CYS J 542 " --> pdb=" O LEU J 539 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 538 through 542' Processing helix chain 'J' and resid 548 through 559 removed outlier: 3.516A pdb=" N GLN J 552 " --> pdb=" O THR J 548 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N LYS J 553 " --> pdb=" O GLU J 549 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N LEU J 554 " --> pdb=" O ALA J 550 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N ASN J 556 " --> pdb=" O GLN J 552 " (cutoff:3.500A) removed outlier: 4.431A pdb=" N MET J 557 " --> pdb=" O LYS J 553 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N LEU J 558 " --> pdb=" O LEU J 554 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N ARG J 559 " --> pdb=" O PHE J 555 " (cutoff:3.500A) Processing helix chain 'J' and resid 565 through 570 Processing helix chain 'J' and resid 570 through 575 removed outlier: 3.526A pdb=" N VAL J 574 " --> pdb=" O LEU J 570 " (cutoff:3.500A) Processing helix chain 'J' and resid 581 through 588 Processing helix chain 'J' and resid 588 through 593 Processing helix chain 'J' and resid 611 through 615 removed outlier: 3.852A pdb=" N ASP J 615 " --> pdb=" O PRO J 612 " (cutoff:3.500A) Processing helix chain 'M' and resid 21 through 53 removed outlier: 3.610A pdb=" N THR M 27 " --> pdb=" O GLU M 23 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N PHE M 28 " --> pdb=" O GLN M 24 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N ASP M 30 " --> pdb=" O LYS M 26 " (cutoff:3.500A) removed outlier: 4.432A pdb=" N LYS M 31 " --> pdb=" O THR M 27 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N PHE M 32 " --> pdb=" O PHE M 28 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N ASP M 38 " --> pdb=" O HIS M 34 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N TYR M 41 " --> pdb=" O GLU M 37 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N SER M 47 " --> pdb=" O SER M 43 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ASN M 49 " --> pdb=" O LEU M 45 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N ASN M 51 " --> pdb=" O SER M 47 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N THR M 52 " --> pdb=" O TRP M 48 " (cutoff:3.500A) Processing helix chain 'M' and resid 58 through 78 removed outlier: 3.650A pdb=" N LEU M 73 " --> pdb=" O TRP M 69 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N LYS M 74 " --> pdb=" O SER M 70 " (cutoff:3.500A) removed outlier: 4.186A pdb=" N THR M 78 " --> pdb=" O LYS M 74 " (cutoff:3.500A) Processing helix chain 'M' and resid 79 through 83 removed outlier: 3.723A pdb=" N MET M 82 " --> pdb=" O LEU M 79 " (cutoff:3.500A) Processing helix chain 'M' and resid 90 through 101 removed outlier: 3.760A pdb=" N LYS M 94 " --> pdb=" O ASN M 90 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N LEU M 95 " --> pdb=" O LEU M 91 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N GLN M 96 " --> pdb=" O THR M 92 " (cutoff:3.500A) Processing helix chain 'M' and resid 109 through 129 removed outlier: 3.686A pdb=" N LYS M 114 " --> pdb=" O GLU M 110 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N ARG M 115 " --> pdb=" O ASP M 111 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N LEU M 116 " --> pdb=" O LYS M 112 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N ASN M 117 " --> pdb=" O SER M 113 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N ASN M 121 " --> pdb=" O ASN M 117 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ILE M 126 " --> pdb=" O THR M 122 " (cutoff:3.500A) Processing helix chain 'M' and resid 147 through 152 Processing helix chain 'M' and resid 158 through 167 Processing helix chain 'M' and resid 175 through 194 removed outlier: 4.082A pdb=" N LEU M 179 " --> pdb=" O GLN M 175 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N GLU M 182 " --> pdb=" O PRO M 178 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N VAL M 185 " --> pdb=" O GLU M 181 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N LEU M 186 " --> pdb=" O GLU M 182 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N LYS M 187 " --> pdb=" O TYR M 183 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N ALA M 193 " --> pdb=" O GLU M 189 " (cutoff:3.500A) Processing helix chain 'M' and resid 198 through 205 removed outlier: 3.678A pdb=" N TYR M 202 " --> pdb=" O ASP M 198 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N TRP M 203 " --> pdb=" O TYR M 199 " (cutoff:3.500A) Processing helix chain 'M' and resid 221 through 229 removed outlier: 3.591A pdb=" N VAL M 226 " --> pdb=" O LEU M 222 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N GLU M 227 " --> pdb=" O ILE M 223 " (cutoff:3.500A) Processing helix chain 'M' and resid 229 through 248 Proline residue: M 235 - end of helix removed outlier: 3.541A pdb=" N LEU M 240 " --> pdb=" O LEU M 236 " (cutoff:3.500A) Processing helix chain 'M' and resid 275 through 279 removed outlier: 3.752A pdb=" N LEU M 278 " --> pdb=" O TRP M 275 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N TYR M 279 " --> pdb=" O THR M 276 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 275 through 279' Processing helix chain 'M' and resid 293 through 297 Processing helix chain 'M' and resid 303 through 317 removed outlier: 3.805A pdb=" N SER M 317 " --> pdb=" O LYS M 313 " (cutoff:3.500A) Processing helix chain 'M' and resid 325 through 330 removed outlier: 3.563A pdb=" N GLU M 329 " --> pdb=" O GLN M 325 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N ASN M 330 " --> pdb=" O GLY M 326 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 325 through 330' Processing helix chain 'M' and resid 366 through 371 removed outlier: 3.903A pdb=" N LEU M 370 " --> pdb=" O MET M 366 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N THR M 371 " --> pdb=" O ASP M 367 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 366 through 371' Processing helix chain 'M' and resid 371 through 385 removed outlier: 3.790A pdb=" N MET M 376 " --> pdb=" O ALA M 372 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N ALA M 384 " --> pdb=" O GLN M 380 " (cutoff:3.500A) removed outlier: 4.380A pdb=" N TYR M 385 " --> pdb=" O TYR M 381 " (cutoff:3.500A) Processing helix chain 'M' and resid 400 through 413 removed outlier: 3.847A pdb=" N VAL M 404 " --> pdb=" O PHE M 400 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N GLY M 405 " --> pdb=" O HIS M 401 " (cutoff:3.500A) removed outlier: 4.380A pdb=" N MET M 408 " --> pdb=" O VAL M 404 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N SER M 409 " --> pdb=" O GLY M 405 " (cutoff:3.500A) Processing helix chain 'M' and resid 414 through 421 removed outlier: 3.593A pdb=" N SER M 420 " --> pdb=" O LYS M 416 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N ILE M 421 " --> pdb=" O HIS M 417 " (cutoff:3.500A) Processing helix chain 'M' and resid 435 through 444 removed outlier: 3.505A pdb=" N LEU M 439 " --> pdb=" O GLU M 435 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N GLN M 442 " --> pdb=" O PHE M 438 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N LEU M 444 " --> pdb=" O LEU M 440 " (cutoff:3.500A) Processing helix chain 'M' and resid 449 through 464 removed outlier: 3.874A pdb=" N ARG M 460 " --> pdb=" O LEU M 456 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N MET M 462 " --> pdb=" O LYS M 458 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N VAL M 463 " --> pdb=" O TRP M 459 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N PHE M 464 " --> pdb=" O ARG M 460 " (cutoff:3.500A) Processing helix chain 'M' and resid 472 through 484 removed outlier: 3.614A pdb=" N LYS M 476 " --> pdb=" O GLN M 472 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N GLU M 479 " --> pdb=" O LYS M 475 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N MET M 480 " --> pdb=" O LYS M 476 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N LYS M 481 " --> pdb=" O TRP M 477 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N ARG M 482 " --> pdb=" O TRP M 478 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N GLU M 483 " --> pdb=" O GLU M 479 " (cutoff:3.500A) Processing helix chain 'M' and resid 512 through 528 removed outlier: 4.143A pdb=" N TYR M 516 " --> pdb=" O PHE M 512 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N THR M 517 " --> pdb=" O ILE M 513 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N LEU M 520 " --> pdb=" O TYR M 516 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N GLN M 522 " --> pdb=" O ARG M 518 " (cutoff:3.500A) removed outlier: 4.974A pdb=" N PHE M 523 " --> pdb=" O THR M 519 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N GLN M 526 " --> pdb=" O GLN M 522 " (cutoff:3.500A) Processing helix chain 'M' and resid 538 through 542 removed outlier: 3.599A pdb=" N LYS M 541 " --> pdb=" O PRO M 538 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N CYS M 542 " --> pdb=" O LEU M 539 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 538 through 542' Processing helix chain 'M' and resid 548 through 553 removed outlier: 3.504A pdb=" N GLN M 552 " --> pdb=" O THR M 548 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N LYS M 553 " --> pdb=" O GLU M 549 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 548 through 553' Processing helix chain 'M' and resid 554 through 559 removed outlier: 3.564A pdb=" N LEU M 558 " --> pdb=" O LEU M 554 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N ARG M 559 " --> pdb=" O PHE M 555 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 554 through 559' Processing helix chain 'M' and resid 565 through 570 Processing helix chain 'M' and resid 570 through 575 removed outlier: 3.521A pdb=" N VAL M 574 " --> pdb=" O LEU M 570 " (cutoff:3.500A) Processing helix chain 'M' and resid 581 through 588 Processing helix chain 'M' and resid 588 through 593 Processing helix chain 'M' and resid 611 through 615 removed outlier: 3.851A pdb=" N ASP M 615 " --> pdb=" O PRO M 612 " (cutoff:3.500A) Processing helix chain 'N' and resid 198 through 200 No H-bonds generated for 'chain 'N' and resid 198 through 200' Processing helix chain 'O' and resid 129 through 133 removed outlier: 3.517A pdb=" N ALA O 132 " --> pdb=" O GLU O 129 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N ASN O 133 " --> pdb=" O LEU O 130 " (cutoff:3.500A) No H-bonds generated for 'chain 'O' and resid 129 through 133' Processing helix chain 'O' and resid 186 through 191 removed outlier: 4.257A pdb=" N LYS O 191 " --> pdb=" O PRO O 187 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 27 through 30 removed outlier: 8.796A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 6.854A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N THR A 63 " --> pdb=" O VAL A 267 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N VAL A 267 " --> pdb=" O THR A 63 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N PHE A 65 " --> pdb=" O TYR A 265 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N TYR A 265 " --> pdb=" O PHE A 65 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N PHE A 194 " --> pdb=" O VAL A 90 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N GLU A 191 " --> pdb=" O LYS A 206 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N LYS A 206 " --> pdb=" O GLU A 191 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N GLU A 224 " --> pdb=" O SER A 205 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 27 through 30 removed outlier: 8.796A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 6.854A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N THR A 63 " --> pdb=" O VAL A 267 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N VAL A 267 " --> pdb=" O THR A 63 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N PHE A 65 " --> pdb=" O TYR A 265 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N TYR A 265 " --> pdb=" O PHE A 65 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N PHE A 194 " --> pdb=" O VAL A 90 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N GLU A 191 " --> pdb=" O LYS A 206 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N LYS A 206 " --> pdb=" O GLU A 191 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 42 through 43 Processing sheet with id=AA4, first strand: chain 'A' and resid 50 through 55 removed outlier: 3.688A pdb=" N THR A 51 " --> pdb=" O PHE A 275 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N PHE A 275 " --> pdb=" O THR A 51 " (cutoff:3.500A) removed outlier: 4.329A pdb=" N ASP A 53 " --> pdb=" O ARG A 273 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N ARG A 273 " --> pdb=" O ASP A 53 " (cutoff:3.500A) removed outlier: 4.374A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 84 through 85 removed outlier: 6.666A pdb=" N LEU A 141 " --> pdb=" O LEU A 244 " (cutoff:3.500A) removed outlier: 7.894A pdb=" N ARG A 246 " --> pdb=" O LEU A 141 " (cutoff:3.500A) removed outlier: 6.808A pdb=" N VAL A 143 " --> pdb=" O ARG A 246 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N ARG A 158 " --> pdb=" O PHE A 140 " (cutoff:3.500A) removed outlier: 6.261A pdb=" N TYR A 144 " --> pdb=" O GLU A 154 " (cutoff:3.500A) removed outlier: 5.170A pdb=" N GLU A 154 " --> pdb=" O TYR A 144 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 84 through 85 removed outlier: 4.358A pdb=" N GLY A 103 " --> pdb=" O LEU A 241 " (cutoff:3.500A) removed outlier: 6.893A pdb=" N ALA A 243 " --> pdb=" O ILE A 101 " (cutoff:3.500A) removed outlier: 6.189A pdb=" N ILE A 101 " --> pdb=" O ALA A 243 " (cutoff:3.500A) removed outlier: 5.580A pdb=" N ARG A 102 " --> pdb=" O ASN A 121 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N VAL A 120 " --> pdb=" O VAL A 127 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N VAL A 127 " --> pdb=" O VAL A 120 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 311 through 313 removed outlier: 4.065A pdb=" N GLY A 311 " --> pdb=" O THR A 599 " (cutoff:3.500A) removed outlier: 4.248A pdb=" N THR A 599 " --> pdb=" O GLY A 311 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N TYR A 313 " --> pdb=" O VAL A 597 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N VAL A 597 " --> pdb=" O TYR A 313 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N ALA A 609 " --> pdb=" O ILE A 598 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N VAL A 610 " --> pdb=" O ILE A 651 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 325 through 326 removed outlier: 3.668A pdb=" N THR A 588 " --> pdb=" O VAL A 551 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N GLU A 583 " --> pdb=" O ASP A 578 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N LEU A 585 " --> pdb=" O VAL A 576 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 354 through 358 removed outlier: 3.520A pdb=" N ASN A 354 " --> pdb=" O SER A 399 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N VAL A 395 " --> pdb=" O ILE A 358 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N THR A 376 " --> pdb=" O ALA A 435 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AB2, first strand: chain 'A' and resid 466 through 467 removed outlier: 3.652A pdb=" N ARG A 466 " --> pdb=" O GLY H 104 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N GLY H 104 " --> pdb=" O ARG A 466 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'A' and resid 473 through 474 removed outlier: 3.568A pdb=" N TYR A 489 " --> pdb=" O TYR A 473 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 565 through 566 removed outlier: 7.464A pdb=" N PHE A 565 " --> pdb=" O PHE B 43 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB4 Processing sheet with id=AB5, first strand: chain 'A' and resid 654 through 655 removed outlier: 6.491A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N GLN A 675 " --> pdb=" O SER A 691 " (cutoff:3.500A) removed outlier: 6.111A pdb=" N ALA A 672 " --> pdb=" O PRO A 665 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 701 through 703 removed outlier: 3.709A pdb=" N ASN A 703 " --> pdb=" O ILE B 788 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 712 through 715 removed outlier: 3.591A pdb=" N LYS A1073 " --> pdb=" O ILE A 714 " (cutoff:3.500A) removed outlier: 4.414A pdb=" N PHE A1095 " --> pdb=" O ALA A1078 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 718 through 719 removed outlier: 3.709A pdb=" N VAL A1068 " --> pdb=" O THR A 719 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'A' and resid 724 through 727 removed outlier: 3.531A pdb=" N GLU A 725 " --> pdb=" O PHE A1062 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N PHE A1062 " --> pdb=" O GLU A 725 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N ALA A1056 " --> pdb=" O GLY A1059 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N VAL A1061 " --> pdb=" O GLN A1054 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N MET A1050 " --> pdb=" O VAL A1065 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'A' and resid 733 through 735 removed outlier: 4.359A pdb=" N LYS A 733 " --> pdb=" O LEU A 861 " (cutoff:3.500A) removed outlier: 4.427A pdb=" N THR A 859 " --> pdb=" O SER A 735 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'A' and resid 787 through 789 removed outlier: 6.168A pdb=" N ILE A 788 " --> pdb=" O ASN C 703 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC2 Processing sheet with id=AC3, first strand: chain 'A' and resid 1120 through 1122 removed outlier: 3.698A pdb=" N CYS A1082 " --> pdb=" O VAL A1133 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 27 through 30 removed outlier: 8.826A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 6.863A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N THR B 63 " --> pdb=" O VAL B 267 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N VAL B 267 " --> pdb=" O THR B 63 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N PHE B 65 " --> pdb=" O TYR B 265 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N TYR B 265 " --> pdb=" O PHE B 65 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N PHE B 194 " --> pdb=" O VAL B 90 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N GLU B 191 " --> pdb=" O LYS B 206 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N LYS B 206 " --> pdb=" O GLU B 191 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 50 through 55 removed outlier: 3.673A pdb=" N THR B 51 " --> pdb=" O PHE B 275 " (cutoff:3.500A) removed outlier: 4.343A pdb=" N ASP B 53 " --> pdb=" O ARG B 273 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N ARG B 273 " --> pdb=" O ASP B 53 " (cutoff:3.500A) removed outlier: 4.550A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 84 through 85 Processing sheet with id=AC7, first strand: chain 'B' and resid 152 through 158 removed outlier: 6.720A pdb=" N GLY B 142 " --> pdb=" O SER B 155 " (cutoff:3.500A) removed outlier: 5.950A pdb=" N PHE B 157 " --> pdb=" O PHE B 140 " (cutoff:3.500A) removed outlier: 8.010A pdb=" N PHE B 140 " --> pdb=" O PHE B 157 " (cutoff:3.500A) removed outlier: 6.667A pdb=" N LEU B 141 " --> pdb=" O LEU B 244 " (cutoff:3.500A) removed outlier: 7.925A pdb=" N ARG B 246 " --> pdb=" O LEU B 141 " (cutoff:3.500A) removed outlier: 6.992A pdb=" N VAL B 143 " --> pdb=" O ARG B 246 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 311 through 317 removed outlier: 6.115A pdb=" N ILE B 312 " --> pdb=" O THR B 599 " (cutoff:3.500A) removed outlier: 7.799A pdb=" N THR B 599 " --> pdb=" O ILE B 312 " (cutoff:3.500A) removed outlier: 5.880A pdb=" N GLN B 314 " --> pdb=" O VAL B 597 " (cutoff:3.500A) removed outlier: 7.143A pdb=" N VAL B 597 " --> pdb=" O GLN B 314 " (cutoff:3.500A) removed outlier: 4.700A pdb=" N SER B 316 " --> pdb=" O VAL B 595 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ALA B 609 " --> pdb=" O ILE B 598 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N VAL B 610 " --> pdb=" O ILE B 651 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 325 through 326 removed outlier: 3.660A pdb=" N THR B 588 " --> pdb=" O VAL B 551 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N GLU B 583 " --> pdb=" O ASP B 578 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N LEU B 585 " --> pdb=" O VAL B 576 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 354 through 358 removed outlier: 4.097A pdb=" N VAL B 395 " --> pdb=" O ILE B 358 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AD3, first strand: chain 'B' and resid 466 through 467 removed outlier: 3.775A pdb=" N ARG B 466 " --> pdb=" O GLY N 104 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N GLY N 104 " --> pdb=" O ARG B 466 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD3 Processing sheet with id=AD4, first strand: chain 'B' and resid 473 through 474 removed outlier: 3.567A pdb=" N TYR B 489 " --> pdb=" O TYR B 473 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 565 through 566 removed outlier: 7.433A pdb=" N PHE B 565 " --> pdb=" O PHE C 43 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD5 Processing sheet with id=AD6, first strand: chain 'B' and resid 654 through 655 removed outlier: 6.458A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.789A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N GLN B 675 " --> pdb=" O SER B 691 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N TYR B 695 " --> pdb=" O CYS B 671 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N GLY B 667 " --> pdb=" O ILE B 670 " (cutoff:3.500A) removed outlier: 6.226A pdb=" N ALA B 672 " --> pdb=" O PRO B 665 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'B' and resid 701 through 703 removed outlier: 3.617A pdb=" N ASN B 703 " --> pdb=" O ILE C 788 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'B' and resid 712 through 715 removed outlier: 3.612A pdb=" N LYS B1073 " --> pdb=" O ILE B 714 " (cutoff:3.500A) removed outlier: 4.434A pdb=" N PHE B1095 " --> pdb=" O ALA B1078 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'B' and resid 718 through 719 removed outlier: 3.662A pdb=" N VAL B1068 " --> pdb=" O THR B 719 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'B' and resid 724 through 727 removed outlier: 3.513A pdb=" N GLU B 725 " --> pdb=" O PHE B1062 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N PHE B1062 " --> pdb=" O GLU B 725 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N ALA B1056 " --> pdb=" O GLY B1059 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N VAL B1061 " --> pdb=" O GLN B1054 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'B' and resid 734 through 735 removed outlier: 4.350A pdb=" N THR B 859 " --> pdb=" O SER B 735 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'B' and resid 1120 through 1122 Processing sheet with id=AE4, first strand: chain 'C' and resid 27 through 30 removed outlier: 8.819A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 6.862A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N THR C 63 " --> pdb=" O VAL C 267 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N VAL C 267 " --> pdb=" O THR C 63 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N PHE C 65 " --> pdb=" O TYR C 265 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N TYR C 265 " --> pdb=" O PHE C 65 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N PHE C 194 " --> pdb=" O VAL C 90 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N GLU C 191 " --> pdb=" O LYS C 206 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N LYS C 206 " --> pdb=" O GLU C 191 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N GLU C 224 " --> pdb=" O SER C 205 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 50 through 55 removed outlier: 3.652A pdb=" N THR C 51 " --> pdb=" O PHE C 275 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N PHE C 275 " --> pdb=" O THR C 51 " (cutoff:3.500A) removed outlier: 4.343A pdb=" N ASP C 53 " --> pdb=" O ARG C 273 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N ARG C 273 " --> pdb=" O ASP C 53 " (cutoff:3.500A) removed outlier: 4.755A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 84 through 85 Processing sheet with id=AE7, first strand: chain 'C' and resid 152 through 158 removed outlier: 6.725A pdb=" N GLY C 142 " --> pdb=" O SER C 155 " (cutoff:3.500A) removed outlier: 5.956A pdb=" N PHE C 157 " --> pdb=" O PHE C 140 " (cutoff:3.500A) removed outlier: 8.061A pdb=" N PHE C 140 " --> pdb=" O PHE C 157 " (cutoff:3.500A) removed outlier: 6.686A pdb=" N LEU C 141 " --> pdb=" O LEU C 244 " (cutoff:3.500A) removed outlier: 7.929A pdb=" N ARG C 246 " --> pdb=" O LEU C 141 " (cutoff:3.500A) removed outlier: 7.021A pdb=" N VAL C 143 " --> pdb=" O ARG C 246 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'C' and resid 311 through 313 removed outlier: 4.100A pdb=" N GLY C 311 " --> pdb=" O THR C 599 " (cutoff:3.500A) removed outlier: 4.274A pdb=" N THR C 599 " --> pdb=" O GLY C 311 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N TYR C 313 " --> pdb=" O VAL C 597 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N VAL C 597 " --> pdb=" O TYR C 313 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N ALA C 609 " --> pdb=" O ILE C 598 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N VAL C 610 " --> pdb=" O ILE C 651 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'C' and resid 325 through 326 removed outlier: 3.547A pdb=" N GLY C 548 " --> pdb=" O PHE C 541 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N THR C 588 " --> pdb=" O VAL C 551 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N GLU C 583 " --> pdb=" O ASP C 578 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N LEU C 585 " --> pdb=" O VAL C 576 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'C' and resid 354 through 358 removed outlier: 3.756A pdb=" N VAL C 395 " --> pdb=" O ILE C 358 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N TRP C 436 " --> pdb=" O ARG C 509 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N THR C 376 " --> pdb=" O ALA C 435 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AF3, first strand: chain 'C' and resid 466 through 467 removed outlier: 3.589A pdb=" N ARG C 466 " --> pdb=" O GLY G 104 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N GLY G 104 " --> pdb=" O ARG C 466 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF3 Processing sheet with id=AF4, first strand: chain 'C' and resid 473 through 474 Processing sheet with id=AF5, first strand: chain 'C' and resid 654 through 655 removed outlier: 6.426A pdb=" N GLU C 654 " --> pdb=" O ALA C 694 " (cutoff:3.500A) removed outlier: 8.764A pdb=" N THR C 696 " --> pdb=" O GLU C 654 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N GLN C 675 " --> pdb=" O SER C 691 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N TYR C 695 " --> pdb=" O CYS C 671 " (cutoff:3.500A) removed outlier: 7.139A pdb=" N ILE C 670 " --> pdb=" O ILE C 666 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N ILE C 666 " --> pdb=" O ILE C 670 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N ILE C 664 " --> pdb=" O ALA C 672 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'C' and resid 712 through 715 removed outlier: 3.603A pdb=" N LYS C1073 " --> pdb=" O ILE C 714 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'C' and resid 718 through 721 removed outlier: 3.733A pdb=" N VAL C1068 " --> pdb=" O THR C 719 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N SER C 721 " --> pdb=" O THR C1066 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N GLU C 725 " --> pdb=" O PHE C1062 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'C' and resid 718 through 721 removed outlier: 3.733A pdb=" N VAL C1068 " --> pdb=" O THR C 719 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N SER C 721 " --> pdb=" O THR C1066 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N ALA C1056 " --> pdb=" O GLY C1059 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N VAL C1061 " --> pdb=" O GLN C1054 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N MET C1050 " --> pdb=" O VAL C1065 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'C' and resid 733 through 735 removed outlier: 4.454A pdb=" N LYS C 733 " --> pdb=" O LEU C 861 " (cutoff:3.500A) removed outlier: 4.291A pdb=" N THR C 859 " --> pdb=" O SER C 735 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'C' and resid 1120 through 1122 Processing sheet with id=AG2, first strand: chain 'C' and resid 1094 through 1096 Processing sheet with id=AG3, first strand: chain 'E' and resid 262 through 263 removed outlier: 5.997A pdb=" N LEU E 262 " --> pdb=" O VAL E 488 " (cutoff:3.500A) No H-bonds generated for sheet with id=AG3 Processing sheet with id=AG4, first strand: chain 'E' and resid 348 through 352 removed outlier: 6.198A pdb=" N ASP E 350 " --> pdb=" O ARG E 357 " (cutoff:3.500A) removed outlier: 7.953A pdb=" N ARG E 357 " --> pdb=" O ASP E 350 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N GLY E 352 " --> pdb=" O ASP E 355 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'H' and resid 3 through 6 removed outlier: 4.206A pdb=" N GLN H 3 " --> pdb=" O SER H 25 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N LEU H 83 " --> pdb=" O VAL H 18 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N VAL H 20 " --> pdb=" O MET H 81 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'H' and resid 10 through 11 removed outlier: 3.507A pdb=" N THR H 121 " --> pdb=" O GLU H 10 " (cutoff:3.500A) removed outlier: 4.243A pdb=" N GLY H 49 " --> pdb=" O TRP H 36 " (cutoff:3.500A) removed outlier: 7.145A pdb=" N ARG H 38 " --> pdb=" O TRP H 47 " (cutoff:3.500A) removed outlier: 5.665A pdb=" N TRP H 47 " --> pdb=" O ARG H 38 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'H' and resid 10 through 11 removed outlier: 3.507A pdb=" N THR H 121 " --> pdb=" O GLU H 10 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N LEU H 113 " --> pdb=" O ARG H 98 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'H' and resid 131 through 135 removed outlier: 3.608A pdb=" N GLY H 150 " --> pdb=" O LEU H 135 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N LEU H 149 " --> pdb=" O VAL H 193 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N SER H 191 " --> pdb=" O CYS H 151 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N VAL H 153 " --> pdb=" O LEU H 189 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N ASP H 155 " --> pdb=" O TYR H 187 " (cutoff:3.500A) removed outlier: 7.385A pdb=" N TYR H 187 " --> pdb=" O ASP H 155 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N VAL H 192 " --> pdb=" O HIS H 175 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N HIS H 175 " --> pdb=" O VAL H 192 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'H' and resid 162 through 165 removed outlier: 3.753A pdb=" N THR H 162 " --> pdb=" O ASN H 210 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N ASN H 210 " --> pdb=" O THR H 162 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N CYS H 207 " --> pdb=" O LYS H 220 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N LYS H 220 " --> pdb=" O CYS H 207 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'L' and resid 17 through 22 Processing sheet with id=AH2, first strand: chain 'L' and resid 47 through 51 removed outlier: 6.879A pdb=" N LEU L 48 " --> pdb=" O GLN L 39 " (cutoff:3.500A) removed outlier: 7.207A pdb=" N GLN L 39 " --> pdb=" O LEU L 48 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N ILE L 50 " --> pdb=" O TRP L 37 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N TRP L 37 " --> pdb=" O ILE L 50 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N TYR L 38 " --> pdb=" O TYR L 89 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain 'L' and resid 47 through 51 removed outlier: 6.879A pdb=" N LEU L 48 " --> pdb=" O GLN L 39 " (cutoff:3.500A) removed outlier: 7.207A pdb=" N GLN L 39 " --> pdb=" O LEU L 48 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N ILE L 50 " --> pdb=" O TRP L 37 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N TRP L 37 " --> pdb=" O ILE L 50 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N TYR L 38 " --> pdb=" O TYR L 89 " (cutoff:3.500A) Processing sheet with id=AH4, first strand: chain 'L' and resid 119 through 123 removed outlier: 3.717A pdb=" N PHE L 123 " --> pdb=" O VAL L 138 " (cutoff:3.500A) removed outlier: 4.106A pdb=" N VAL L 138 " --> pdb=" O PHE L 123 " (cutoff:3.500A) removed outlier: 6.473A pdb=" N TYR L 177 " --> pdb=" O ASP L 143 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N ALA L 178 " --> pdb=" O SER L 170 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N SER L 170 " --> pdb=" O ALA L 178 " (cutoff:3.500A) Processing sheet with id=AH5, first strand: chain 'L' and resid 135 through 136 Processing sheet with id=AH6, first strand: chain 'L' and resid 150 through 154 removed outlier: 3.973A pdb=" N THR L 150 " --> pdb=" O THR L 201 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N THR L 201 " --> pdb=" O THR L 150 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N TYR L 196 " --> pdb=" O VAL L 211 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N CYS L 198 " --> pdb=" O LYS L 209 " (cutoff:3.500A) removed outlier: 4.554A pdb=" N LYS L 209 " --> pdb=" O CYS L 198 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N VAL L 200 " --> pdb=" O VAL L 207 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N VAL L 207 " --> pdb=" O VAL L 200 " (cutoff:3.500A) Processing sheet with id=AH7, first strand: chain 'G' and resid 3 through 6 removed outlier: 3.947A pdb=" N GLN G 3 " --> pdb=" O SER G 25 " (cutoff:3.500A) Processing sheet with id=AH8, first strand: chain 'G' and resid 10 through 12 removed outlier: 3.776A pdb=" N LYS G 12 " --> pdb=" O THR G 121 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N ALA G 33 " --> pdb=" O GLU G 99 " (cutoff:3.500A) removed outlier: 4.424A pdb=" N GLY G 49 " --> pdb=" O TRP G 36 " (cutoff:3.500A) removed outlier: 7.297A pdb=" N ARG G 38 " --> pdb=" O TRP G 47 " (cutoff:3.500A) removed outlier: 5.823A pdb=" N TRP G 47 " --> pdb=" O ARG G 38 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N ILE G 52 " --> pdb=" O ILE G 57 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N ILE G 57 " --> pdb=" O ILE G 52 " (cutoff:3.500A) Processing sheet with id=AH9, first strand: chain 'G' and resid 131 through 134 removed outlier: 3.664A pdb=" N LEU G 149 " --> pdb=" O VAL G 193 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N CYS G 151 " --> pdb=" O SER G 191 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N SER G 191 " --> pdb=" O CYS G 151 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N VAL G 153 " --> pdb=" O LEU G 189 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N LEU G 189 " --> pdb=" O VAL G 153 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N ASP G 155 " --> pdb=" O TYR G 187 " (cutoff:3.500A) removed outlier: 7.144A pdb=" N TYR G 187 " --> pdb=" O ASP G 155 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N VAL G 192 " --> pdb=" O HIS G 175 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N HIS G 175 " --> pdb=" O VAL G 192 " (cutoff:3.500A) Processing sheet with id=AI1, first strand: chain 'G' and resid 162 through 165 removed outlier: 3.872A pdb=" N THR G 162 " --> pdb=" O ASN G 210 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N CYS G 207 " --> pdb=" O LYS G 220 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N LYS G 220 " --> pdb=" O CYS G 207 " (cutoff:3.500A) Processing sheet with id=AI2, first strand: chain 'I' and resid 17 through 23 Processing sheet with id=AI3, first strand: chain 'I' and resid 47 through 51 removed outlier: 6.877A pdb=" N LEU I 48 " --> pdb=" O GLN I 39 " (cutoff:3.500A) removed outlier: 7.234A pdb=" N GLN I 39 " --> pdb=" O LEU I 48 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N ILE I 50 " --> pdb=" O TRP I 37 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N TRP I 37 " --> pdb=" O ILE I 50 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N TYR I 38 " --> pdb=" O TYR I 89 " (cutoff:3.500A) Processing sheet with id=AI4, first strand: chain 'I' and resid 47 through 51 removed outlier: 6.877A pdb=" N LEU I 48 " --> pdb=" O GLN I 39 " (cutoff:3.500A) removed outlier: 7.234A pdb=" N GLN I 39 " --> pdb=" O LEU I 48 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N ILE I 50 " --> pdb=" O TRP I 37 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N TRP I 37 " --> pdb=" O ILE I 50 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N TYR I 38 " --> pdb=" O TYR I 89 " (cutoff:3.500A) Processing sheet with id=AI5, first strand: chain 'I' and resid 119 through 123 removed outlier: 3.810A pdb=" N PHE I 123 " --> pdb=" O VAL I 138 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N VAL I 138 " --> pdb=" O PHE I 123 " (cutoff:3.500A) removed outlier: 6.454A pdb=" N TYR I 177 " --> pdb=" O ASP I 143 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N ALA I 178 " --> pdb=" O SER I 170 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N SER I 170 " --> pdb=" O ALA I 178 " (cutoff:3.500A) Processing sheet with id=AI6, first strand: chain 'I' and resid 135 through 136 Processing sheet with id=AI7, first strand: chain 'I' and resid 150 through 154 removed outlier: 4.033A pdb=" N THR I 150 " --> pdb=" O THR I 201 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N THR I 201 " --> pdb=" O THR I 150 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N TYR I 196 " --> pdb=" O VAL I 211 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N CYS I 198 " --> pdb=" O LYS I 209 " (cutoff:3.500A) removed outlier: 4.566A pdb=" N LYS I 209 " --> pdb=" O CYS I 198 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N VAL I 200 " --> pdb=" O VAL I 207 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N VAL I 207 " --> pdb=" O VAL I 200 " (cutoff:3.500A) Processing sheet with id=AI8, first strand: chain 'J' and resid 131 through 132 removed outlier: 4.065A pdb=" N VAL J 132 " --> pdb=" O LEU J 142 " (cutoff:3.500A) removed outlier: 4.274A pdb=" N LEU J 142 " --> pdb=" O VAL J 132 " (cutoff:3.500A) No H-bonds generated for sheet with id=AI8 Processing sheet with id=AI9, first strand: chain 'J' and resid 347 through 350 removed outlier: 3.671A pdb=" N THR J 347 " --> pdb=" O LEU J 359 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N LEU J 359 " --> pdb=" O THR J 347 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N TRP J 349 " --> pdb=" O ARG J 357 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N ARG J 357 " --> pdb=" O TRP J 349 " (cutoff:3.500A) No H-bonds generated for sheet with id=AI9 Processing sheet with id=AJ1, first strand: chain 'M' and resid 131 through 132 removed outlier: 3.907A pdb=" N VAL M 132 " --> pdb=" O LEU M 142 " (cutoff:3.500A) removed outlier: 4.164A pdb=" N LEU M 142 " --> pdb=" O VAL M 132 " (cutoff:3.500A) No H-bonds generated for sheet with id=AJ1 Processing sheet with id=AJ2, first strand: chain 'M' and resid 347 through 350 removed outlier: 3.577A pdb=" N THR M 347 " --> pdb=" O LEU M 359 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N LEU M 359 " --> pdb=" O THR M 347 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N TRP M 349 " --> pdb=" O ARG M 357 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N ARG M 357 " --> pdb=" O TRP M 349 " (cutoff:3.500A) No H-bonds generated for sheet with id=AJ2 Processing sheet with id=AJ3, first strand: chain 'N' and resid 3 through 6 removed outlier: 4.398A pdb=" N GLN N 3 " --> pdb=" O SER N 25 " (cutoff:3.500A) Processing sheet with id=AJ4, first strand: chain 'N' and resid 10 through 12 removed outlier: 4.364A pdb=" N GLY N 49 " --> pdb=" O TRP N 36 " (cutoff:3.500A) removed outlier: 7.200A pdb=" N ARG N 38 " --> pdb=" O TRP N 47 " (cutoff:3.500A) removed outlier: 5.699A pdb=" N TRP N 47 " --> pdb=" O ARG N 38 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N ILE N 52 " --> pdb=" O ILE N 57 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N ILE N 57 " --> pdb=" O ILE N 52 " (cutoff:3.500A) Processing sheet with id=AJ5, first strand: chain 'N' and resid 98 through 99 removed outlier: 4.478A pdb=" N LEU N 113 " --> pdb=" O ARG N 98 " (cutoff:3.500A) Processing sheet with id=AJ6, first strand: chain 'N' and resid 131 through 134 removed outlier: 3.610A pdb=" N SER N 191 " --> pdb=" O CYS N 151 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N VAL N 153 " --> pdb=" O LEU N 189 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N LEU N 189 " --> pdb=" O VAL N 153 " (cutoff:3.500A) removed outlier: 4.599A pdb=" N ASP N 155 " --> pdb=" O TYR N 187 " (cutoff:3.500A) removed outlier: 7.944A pdb=" N TYR N 187 " --> pdb=" O ASP N 155 " (cutoff:3.500A) Processing sheet with id=AJ7, first strand: chain 'N' and resid 162 through 165 removed outlier: 3.735A pdb=" N THR N 162 " --> pdb=" O ASN N 210 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N ASN N 210 " --> pdb=" O THR N 162 " (cutoff:3.500A) Processing sheet with id=AJ8, first strand: chain 'O' and resid 17 through 22 removed outlier: 3.519A pdb=" N SER O 72 " --> pdb=" O SER O 69 " (cutoff:3.500A) Processing sheet with id=AJ9, first strand: chain 'O' and resid 47 through 51 removed outlier: 6.880A pdb=" N LEU O 48 " --> pdb=" O GLN O 39 " (cutoff:3.500A) removed outlier: 7.194A pdb=" N GLN O 39 " --> pdb=" O LEU O 48 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N ILE O 50 " --> pdb=" O TRP O 37 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N TRP O 37 " --> pdb=" O ILE O 50 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N TYR O 38 " --> pdb=" O TYR O 89 " (cutoff:3.500A) Processing sheet with id=AK1, first strand: chain 'O' and resid 47 through 51 removed outlier: 6.880A pdb=" N LEU O 48 " --> pdb=" O GLN O 39 " (cutoff:3.500A) removed outlier: 7.194A pdb=" N GLN O 39 " --> pdb=" O LEU O 48 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N ILE O 50 " --> pdb=" O TRP O 37 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N TRP O 37 " --> pdb=" O ILE O 50 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N TYR O 38 " --> pdb=" O TYR O 89 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N TYR O 88 " --> pdb=" O THR O 106 " (cutoff:3.500A) Processing sheet with id=AK2, first strand: chain 'O' and resid 119 through 123 removed outlier: 3.707A pdb=" N PHE O 123 " --> pdb=" O VAL O 138 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N VAL O 138 " --> pdb=" O PHE O 123 " (cutoff:3.500A) removed outlier: 6.467A pdb=" N TYR O 177 " --> pdb=" O ASP O 143 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N ALA O 178 " --> pdb=" O SER O 170 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N SER O 170 " --> pdb=" O ALA O 178 " (cutoff:3.500A) Processing sheet with id=AK3, first strand: chain 'O' and resid 135 through 136 Processing sheet with id=AK4, first strand: chain 'O' and resid 150 through 154 removed outlier: 3.964A pdb=" N THR O 150 " --> pdb=" O THR O 201 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N THR O 201 " --> pdb=" O THR O 150 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N TYR O 196 " --> pdb=" O VAL O 211 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N CYS O 198 " --> pdb=" O LYS O 209 " (cutoff:3.500A) removed outlier: 4.568A pdb=" N LYS O 209 " --> pdb=" O CYS O 198 " (cutoff:3.500A) removed outlier: 4.058A pdb=" N VAL O 200 " --> pdb=" O VAL O 207 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N VAL O 207 " --> pdb=" O VAL O 200 " (cutoff:3.500A) 1463 hydrogen bonds defined for protein. 3969 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: 17.95 Time building geometry restraints manager: 15.13 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 16025 1.34 - 1.46: 12459 1.46 - 1.58: 22378 1.58 - 1.70: 0 1.70 - 1.82: 339 Bond restraints: 51201 Sorted by residual: bond pdb=" C GLY B 526 " pdb=" N PRO B 527 " ideal model delta sigma weight residual 1.329 1.362 -0.032 1.25e-02 6.40e+03 6.65e+00 bond pdb=" CA LYS B 528 " pdb=" C LYS B 528 " ideal model delta sigma weight residual 1.523 1.491 0.032 1.28e-02 6.10e+03 6.22e+00 bond pdb=" C GLN I 113 " pdb=" O GLN I 113 " ideal model delta sigma weight residual 1.249 1.230 0.018 8.50e-03 1.38e+04 4.67e+00 bond pdb=" C PHE B 329 " pdb=" N PRO B 330 " ideal model delta sigma weight residual 1.328 1.353 -0.025 1.25e-02 6.40e+03 4.12e+00 bond pdb=" C1 NAG B1303 " pdb=" O5 NAG B1303 " ideal model delta sigma weight residual 1.406 1.442 -0.036 2.00e-02 2.50e+03 3.23e+00 ... (remaining 51196 not shown) Histogram of bond angle deviations from ideal: 99.28 - 106.22: 1410 106.22 - 113.16: 27574 113.16 - 120.11: 17803 120.11 - 127.05: 22316 127.05 - 134.00: 593 Bond angle restraints: 69696 Sorted by residual: angle pdb=" O GLY B 526 " pdb=" C GLY B 526 " pdb=" N PRO B 527 " ideal model delta sigma weight residual 121.77 128.50 -6.73 1.00e+00 1.00e+00 4.53e+01 angle pdb=" N HIS M 378 " pdb=" CA HIS M 378 " pdb=" C HIS M 378 " ideal model delta sigma weight residual 111.07 106.12 4.95 1.07e+00 8.73e-01 2.14e+01 angle pdb=" CA GLY B 526 " pdb=" C GLY B 526 " pdb=" O GLY B 526 " ideal model delta sigma weight residual 121.52 115.16 6.36 1.43e+00 4.89e-01 1.98e+01 angle pdb=" N HIS M 378 " pdb=" CA HIS M 378 " pdb=" CB HIS M 378 " ideal model delta sigma weight residual 110.01 115.99 -5.98 1.45e+00 4.76e-01 1.70e+01 angle pdb=" N LYS B 529 " pdb=" CA LYS B 529 " pdb=" C LYS B 529 " ideal model delta sigma weight residual 110.35 115.57 -5.22 1.36e+00 5.41e-01 1.47e+01 ... (remaining 69691 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.95: 28430 17.95 - 35.91: 2122 35.91 - 53.86: 432 53.86 - 71.81: 70 71.81 - 89.77: 59 Dihedral angle restraints: 31113 sinusoidal: 12765 harmonic: 18348 Sorted by residual: dihedral pdb=" CB CYS M 344 " pdb=" SG CYS M 344 " pdb=" SG CYS M 361 " pdb=" CB CYS M 361 " ideal model delta sinusoidal sigma weight residual -86.00 -169.51 83.51 1 1.00e+01 1.00e-02 8.51e+01 dihedral pdb=" CB CYS C 538 " pdb=" SG CYS C 538 " pdb=" SG CYS C 590 " pdb=" CB CYS C 590 " ideal model delta sinusoidal sigma weight residual 93.00 10.17 82.83 1 1.00e+01 1.00e-02 8.40e+01 dihedral pdb=" CB CYS C 291 " pdb=" SG CYS C 291 " pdb=" SG CYS C 301 " pdb=" CB CYS C 301 " ideal model delta sinusoidal sigma weight residual 93.00 174.21 -81.21 1 1.00e+01 1.00e-02 8.13e+01 ... (remaining 31110 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.131: 7836 0.131 - 0.263: 16 0.263 - 0.394: 4 0.394 - 0.526: 0 0.526 - 0.657: 1 Chirality restraints: 7857 Sorted by residual: chirality pdb=" C1 NAG A1302 " pdb=" ND2 ASN A 331 " pdb=" C2 NAG A1302 " pdb=" O5 NAG A1302 " both_signs ideal model delta sigma weight residual False -2.40 -1.74 -0.66 2.00e-01 2.50e+01 1.08e+01 chirality pdb=" C1 NAG B1303 " pdb=" ND2 ASN B 603 " pdb=" C2 NAG B1303 " pdb=" O5 NAG B1303 " both_signs ideal model delta sigma weight residual False -2.40 -2.06 -0.34 2.00e-01 2.50e+01 2.83e+00 chirality pdb=" C1 NAG A1303 " pdb=" ND2 ASN A 603 " pdb=" C2 NAG A1303 " pdb=" O5 NAG A1303 " both_signs ideal model delta sigma weight residual False -2.40 -2.07 -0.33 2.00e-01 2.50e+01 2.79e+00 ... (remaining 7854 not shown) Planarity restraints: 9003 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA MET M 376 " 0.015 2.00e-02 2.50e+03 3.13e-02 9.77e+00 pdb=" C MET M 376 " -0.054 2.00e-02 2.50e+03 pdb=" O MET M 376 " 0.020 2.00e-02 2.50e+03 pdb=" N GLY M 377 " 0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PRO C 986 " -0.038 5.00e-02 4.00e+02 5.70e-02 5.21e+00 pdb=" N PRO C 987 " 0.099 5.00e-02 4.00e+02 pdb=" CA PRO C 987 " -0.028 5.00e-02 4.00e+02 pdb=" CD PRO C 987 " -0.032 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO A 986 " -0.038 5.00e-02 4.00e+02 5.64e-02 5.08e+00 pdb=" N PRO A 987 " 0.097 5.00e-02 4.00e+02 pdb=" CA PRO A 987 " -0.028 5.00e-02 4.00e+02 pdb=" CD PRO A 987 " -0.032 5.00e-02 4.00e+02 ... (remaining 9000 not shown) Histogram of nonbonded interaction distances: 2.19 - 2.73: 2706 2.73 - 3.27: 45850 3.27 - 3.82: 78178 3.82 - 4.36: 90843 4.36 - 4.90: 157152 Nonbonded interactions: 374729 Sorted by model distance: nonbonded pdb=" OD1 ASN A 331 " pdb=" N ILE A 332 " model vdw 2.191 2.520 nonbonded pdb=" OD1 ASN C 501 " pdb=" OH TYR J 41 " model vdw 2.214 2.440 nonbonded pdb=" OE1 GLU M 402 " pdb="ZN ZN M 901 " model vdw 2.223 2.230 nonbonded pdb=" O GLU J 166 " pdb=" OG SER J 170 " model vdw 2.234 2.440 nonbonded pdb=" OG1 THR B 109 " pdb=" OD1 ASP B 111 " model vdw 2.237 2.440 ... (remaining 374724 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } ncs_group { reference = chain 'D' selection = chain 'F' selection = chain 'K' selection = chain 'P' selection = chain 'Q' selection = chain 'R' } ncs_group { reference = chain 'E' selection = chain 'J' selection = chain 'M' } ncs_group { reference = (chain 'G' and (resid 2 through 150 or resid 152 through 206 or resid 208 throug \ h 228)) selection = (chain 'H' and (resid 2 through 150 or resid 152 through 206 or resid 208 throug \ h 228)) selection = (chain 'N' and (resid 2 through 150 or resid 152 through 206 or resid 208 throug \ h 228)) } ncs_group { reference = chain 'I' selection = chain 'L' selection = chain 'O' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.050 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.250 Construct map_model_manager: 0.030 Extract box with map and model: 7.710 Check model and map are aligned: 0.540 Set scattering table: 0.360 Process input model: 108.250 Find NCS groups from input model: 2.340 Set up NCS constraints: 0.400 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: 0.010 Load rotamer database and sin/cos tables:2.230 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 123.170 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5621 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 : 0.002 0.036 51201 Z= 0.156 Angle : 0.484 6.728 69696 Z= 0.260 Chirality : 0.042 0.657 7857 Planarity : 0.004 0.057 8961 Dihedral : 13.187 89.766 19143 Min Nonbonded Distance : 2.191 Molprobity Statistics. All-atom Clashscore : 5.16 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.10 % Favored : 96.85 % Rotamer: Outliers : 0.37 % Allowed : 2.60 % Favored : 97.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.60 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.62 (0.08), residues: 6258 helix: -4.70 (0.05), residues: 1464 sheet: -1.22 (0.15), residues: 1101 loop : -3.08 (0.08), residues: 3693 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.000 TRP J 473 HIS 0.008 0.000 HIS M 374 PHE 0.008 0.000 PHE M 603 TYR 0.007 0.000 TYR C 351 ARG 0.002 0.000 ARG B 765 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12516 Ramachandran restraints generated. 6258 Oldfield, 0 Emsley, 6258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12516 Ramachandran restraints generated. 6258 Oldfield, 0 Emsley, 6258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 959 residues out of total 5457 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 941 time to evaluate : 4.109 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: A 188 ASN cc_start: 0.5964 (m-40) cc_final: 0.5400 (m-40) REVERT: A 369 TYR cc_start: 0.4436 (t80) cc_final: 0.3344 (t80) REVERT: A 572 THR cc_start: 0.3595 (m) cc_final: 0.3049 (p) REVERT: A 734 THR cc_start: 0.8391 (p) cc_final: 0.7960 (t) REVERT: A 898 PHE cc_start: 0.6871 (t80) cc_final: 0.5479 (t80) REVERT: A 1073 LYS cc_start: 0.7175 (mtpt) cc_final: 0.6557 (ttpp) REVERT: B 38 TYR cc_start: 0.7287 (m-80) cc_final: 0.6981 (m-80) REVERT: B 177 MET cc_start: -0.0426 (mmt) cc_final: -0.0911 (ttt) REVERT: B 188 ASN cc_start: 0.6338 (m-40) cc_final: 0.5756 (m110) REVERT: B 197 ILE cc_start: 0.7316 (pt) cc_final: 0.6988 (tt) REVERT: B 528 LYS cc_start: 0.6771 (OUTLIER) cc_final: 0.6291 (mmmt) REVERT: B 572 THR cc_start: 0.4935 (m) cc_final: 0.4526 (p) REVERT: B 583 GLU cc_start: 0.7497 (tt0) cc_final: 0.7249 (pm20) REVERT: B 734 THR cc_start: 0.7853 (p) cc_final: 0.7600 (t) REVERT: B 748 GLU cc_start: 0.6046 (mp0) cc_final: 0.5803 (tp30) REVERT: B 859 THR cc_start: 0.5375 (p) cc_final: 0.4872 (t) REVERT: B 898 PHE cc_start: 0.6394 (t80) cc_final: 0.5599 (t80) REVERT: B 979 ASP cc_start: 0.7562 (t70) cc_final: 0.7221 (t0) REVERT: B 1101 HIS cc_start: 0.6816 (m90) cc_final: 0.6073 (m170) REVERT: B 1114 ILE cc_start: 0.7821 (mm) cc_final: 0.7564 (mm) REVERT: C 130 VAL cc_start: 0.6708 (t) cc_final: 0.6490 (m) REVERT: C 188 ASN cc_start: 0.6658 (m-40) cc_final: 0.6028 (m110) REVERT: C 197 ILE cc_start: 0.7609 (pt) cc_final: 0.7216 (tt) REVERT: C 572 THR cc_start: 0.4774 (m) cc_final: 0.4203 (p) REVERT: C 607 GLN cc_start: 0.7535 (pt0) cc_final: 0.7271 (pm20) REVERT: C 734 THR cc_start: 0.7892 (p) cc_final: 0.7597 (t) REVERT: C 950 ASP cc_start: 0.7819 (m-30) cc_final: 0.7585 (m-30) REVERT: C 969 ASN cc_start: 0.8176 (m-40) cc_final: 0.7957 (m110) REVERT: C 979 ASP cc_start: 0.7729 (t70) cc_final: 0.7197 (t0) REVERT: C 1101 HIS cc_start: 0.6257 (m90) cc_final: 0.5658 (m170) REVERT: C 1102 TRP cc_start: 0.4894 (m100) cc_final: 0.2142 (m100) REVERT: C 1122 VAL cc_start: 0.7851 (m) cc_final: 0.7638 (t) REVERT: E 26 LYS cc_start: 0.3123 (tptt) cc_final: 0.2918 (mmtt) REVERT: E 148 LEU cc_start: 0.2747 (mt) cc_final: 0.2415 (mm) REVERT: E 152 MET cc_start: 0.5066 (mmm) cc_final: 0.4316 (tpt) REVERT: E 241 HIS cc_start: 0.2573 (t-90) cc_final: 0.2157 (t-170) REVERT: E 293 VAL cc_start: 0.2097 (p) cc_final: 0.1212 (t) REVERT: E 302 TRP cc_start: 0.0208 (t60) cc_final: -0.0657 (t-100) REVERT: E 313 LYS cc_start: 0.1176 (mmmt) cc_final: 0.0949 (ptmm) REVERT: E 332 MET cc_start: 0.4425 (ttt) cc_final: 0.3308 (mtp) REVERT: E 346 PRO cc_start: 0.2649 (Cg_endo) cc_final: 0.2398 (Cg_exo) REVERT: E 366 MET cc_start: -0.0372 (mtm) cc_final: -0.0651 (tpt) REVERT: E 462 MET cc_start: 0.2480 (ptt) cc_final: 0.2153 (ptt) REVERT: E 474 MET cc_start: 0.0818 (tpp) cc_final: -0.0180 (mmp) REVERT: E 480 MET cc_start: 0.2590 (mtp) cc_final: 0.2266 (ptp) REVERT: E 518 ARG cc_start: 0.0704 (ptm160) cc_final: 0.0258 (tmt170) REVERT: E 522 GLN cc_start: 0.1046 (pt0) cc_final: 0.0343 (pp30) REVERT: E 579 MET cc_start: -0.0036 (pmm) cc_final: -0.0774 (mtm) REVERT: H 110 ASN cc_start: 0.2502 (p0) cc_final: 0.2281 (t0) REVERT: H 162 THR cc_start: 0.3947 (t) cc_final: 0.3709 (p) REVERT: L 64 PHE cc_start: -0.0146 (m-80) cc_final: -0.0955 (m-80) REVERT: G 111 PHE cc_start: 0.2482 (m-80) cc_final: 0.2274 (m-80) REVERT: G 175 HIS cc_start: 0.1273 (t-90) cc_final: 0.0744 (m-70) REVERT: J 73 LEU cc_start: 0.1365 (tt) cc_final: 0.1107 (mt) REVERT: J 75 GLU cc_start: 0.3325 (pt0) cc_final: 0.3093 (tm-30) REVERT: J 180 TYR cc_start: 0.0917 (t80) cc_final: 0.0615 (t80) REVERT: J 217 TYR cc_start: 0.2612 (t80) cc_final: 0.1571 (m-80) REVERT: J 225 ASP cc_start: 0.2948 (p0) cc_final: 0.2499 (p0) REVERT: J 241 HIS cc_start: 0.1375 (t-90) cc_final: 0.1071 (t-90) REVERT: J 270 MET cc_start: 0.0110 (tpp) cc_final: -0.1572 (tpp) REVERT: J 271 TRP cc_start: 0.1588 (m-90) cc_final: 0.0433 (t-100) REVERT: J 281 LEU cc_start: 0.3104 (tp) cc_final: 0.2768 (mp) REVERT: J 332 MET cc_start: 0.2069 (ttt) cc_final: 0.0552 (mtt) REVERT: J 356 PHE cc_start: 0.1333 (m-80) cc_final: -0.0136 (m-80) REVERT: J 374 HIS cc_start: -0.0928 (OUTLIER) cc_final: -0.1879 (t-170) REVERT: J 497 TYR cc_start: 0.3417 (m-80) cc_final: 0.3084 (m-80) REVERT: J 505 HIS cc_start: 0.1710 (m170) cc_final: 0.0791 (p-80) REVERT: J 515 TYR cc_start: 0.3138 (t80) cc_final: 0.2533 (t80) REVERT: M 26 LYS cc_start: 0.4510 (mtmm) cc_final: 0.4281 (mmpt) REVERT: M 42 GLN cc_start: 0.6722 (mt0) cc_final: 0.6209 (tp40) REVERT: M 145 GLU cc_start: 0.5324 (pp20) cc_final: 0.5102 (mm-30) REVERT: M 195 HIS cc_start: 0.5965 (t-170) cc_final: 0.5730 (m170) REVERT: M 217 TYR cc_start: 0.4061 (t80) cc_final: 0.2936 (m-80) REVERT: M 270 MET cc_start: 0.0025 (tpp) cc_final: -0.0949 (tpp) REVERT: M 271 TRP cc_start: 0.0946 (m-90) cc_final: 0.0527 (t-100) REVERT: M 297 MET cc_start: 0.0660 (mtt) cc_final: 0.0271 (ppp) REVERT: M 356 PHE cc_start: 0.1393 (m-80) cc_final: 0.0130 (m-80) REVERT: M 366 MET cc_start: -0.0817 (mtp) cc_final: -0.1292 (tpp) REVERT: M 482 ARG cc_start: 0.4140 (mtt180) cc_final: 0.3874 (ttm-80) REVERT: M 515 TYR cc_start: 0.2803 (t80) cc_final: 0.2033 (t80) REVERT: M 566 TRP cc_start: 0.2755 (p-90) cc_final: 0.2122 (p-90) REVERT: M 579 MET cc_start: 0.2391 (ptp) cc_final: 0.1511 (mtm) REVERT: N 4 LEU cc_start: 0.3343 (mp) cc_final: 0.2776 (mt) REVERT: N 81 MET cc_start: -0.0800 (ttt) cc_final: -0.1086 (ttt) REVERT: N 122 VAL cc_start: 0.0868 (p) cc_final: 0.0605 (m) REVERT: O 48 LEU cc_start: 0.5431 (tp) cc_final: 0.4892 (tp) REVERT: O 64 PHE cc_start: -0.0573 (m-80) cc_final: -0.1153 (m-10) outliers start: 18 outliers final: 5 residues processed: 954 average time/residue: 0.4988 time to fit residues: 782.2389 Evaluate side-chains 492 residues out of total 5457 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 485 time to evaluate : 4.048 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 528 LYS Chi-restraints excluded: chain B residue 528 LYS Chi-restraints excluded: chain B residue 900 MET Chi-restraints excluded: chain L residue 111 LEU Chi-restraints excluded: chain J residue 374 HIS Chi-restraints excluded: chain O residue 109 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 624 random chunks: chunk 526 optimal weight: 9.9990 chunk 472 optimal weight: 5.9990 chunk 262 optimal weight: 7.9990 chunk 161 optimal weight: 8.9990 chunk 319 optimal weight: 7.9990 chunk 252 optimal weight: 10.0000 chunk 489 optimal weight: 0.0050 chunk 189 optimal weight: 3.9990 chunk 297 optimal weight: 0.5980 chunk 364 optimal weight: 20.0000 chunk 566 optimal weight: 1.9990 overall best weight: 2.5200 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 87 ASN A 137 ASN ** A 165 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 183 GLN A 196 ASN A 207 HIS A 218 GLN A 271 GLN A 409 GLN A 474 GLN A 493 GLN A 540 ASN A 580 GLN A 613 GLN A 703 ASN A 762 GLN A 901 GLN A 926 GLN A 955 ASN A 965 GLN A 992 GLN A1023 ASN A1064 HIS A1101 HIS A1142 GLN B 87 ASN B 137 ASN B 165 ASN B 183 GLN B 196 ASN B 218 GLN B 271 GLN B 394 ASN B 460 ASN B 498 GLN B 532 ASN B 580 GLN B 613 GLN B 703 ASN B 762 GLN B 901 GLN B 913 GLN B 920 GLN B 926 GLN B 965 GLN B 992 GLN B1023 ASN B1064 HIS ** B1142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 87 ASN C 137 ASN C 165 ASN C 183 GLN C 196 ASN C 207 HIS C 218 GLN ** C 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 271 GLN C 314 GLN C 439 ASN C 474 GLN C 493 GLN C 506 GLN C 532 ASN C 580 GLN ** C 675 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 703 ASN C 762 GLN C 901 GLN C 920 GLN C 926 GLN C 965 GLN C 992 GLN C1023 ASN C1058 HIS ** C1064 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C1142 GLN E 33 ASN ** E 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 101 GLN E 134 ASN E 188 ASN E 265 HIS E 325 GLN E 345 HIS E 378 HIS E 397 ASN E 442 GLN ** E 540 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 175 HIS H 208 ASN H 210 ASN ** H 211 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 16 GLN ** L 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 193 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 39 GLN ** G 208 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 210 ASN I 55 ASN ** I 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 193 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 33 ASN J 49 ASN J 63 ASN J 188 ASN J 265 HIS J 300 GLN J 432 ASN ** J 522 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 599 ASN M 33 ASN M 49 ASN M 51 ASN M 63 ASN M 98 GLN M 101 GLN M 188 ASN ** M 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 305 GLN ** M 325 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 397 ASN M 401 HIS M 522 GLN M 556 ASN M 599 ASN N 166 ASN N 208 ASN O 16 GLN ** O 36 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 113 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6130 moved from start: 0.3430 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.066 51201 Z= 0.344 Angle : 0.696 11.811 69696 Z= 0.355 Chirality : 0.048 0.341 7857 Planarity : 0.006 0.091 8961 Dihedral : 5.585 58.958 7793 Min Nonbonded Distance : 1.898 Molprobity Statistics. All-atom Clashscore : 9.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.53 % Favored : 95.47 % Rotamer: Outliers : 1.78 % Allowed : 12.38 % Favored : 85.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.60 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.32 (0.09), residues: 6258 helix: -2.62 (0.10), residues: 1587 sheet: -0.67 (0.15), residues: 1233 loop : -2.65 (0.09), residues: 3438 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP G 114 HIS 0.039 0.003 HIS M 378 PHE 0.034 0.003 PHE M 72 TYR 0.032 0.002 TYR B 674 ARG 0.012 0.001 ARG M 460 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12516 Ramachandran restraints generated. 6258 Oldfield, 0 Emsley, 6258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12516 Ramachandran restraints generated. 6258 Oldfield, 0 Emsley, 6258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 595 residues out of total 5457 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 95 poor density : 500 time to evaluate : 4.138 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: A 177 MET cc_start: 0.0936 (OUTLIER) cc_final: 0.0732 (mtp) REVERT: A 449 TYR cc_start: 0.3437 (OUTLIER) cc_final: 0.2783 (m-80) REVERT: A 751 ASN cc_start: 0.7628 (OUTLIER) cc_final: 0.7268 (p0) REVERT: A 786 LYS cc_start: 0.7149 (mptt) cc_final: 0.6805 (mmmt) REVERT: A 814 LYS cc_start: 0.6592 (tptt) cc_final: 0.6277 (tptt) REVERT: A 823 PHE cc_start: 0.7650 (OUTLIER) cc_final: 0.7042 (t80) REVERT: A 904 TYR cc_start: 0.8010 (m-10) cc_final: 0.7347 (m-80) REVERT: A 979 ASP cc_start: 0.7719 (t70) cc_final: 0.7452 (t0) REVERT: A 1005 GLN cc_start: 0.7597 (mm-40) cc_final: 0.7391 (mt0) REVERT: A 1019 ARG cc_start: 0.6938 (tpt-90) cc_final: 0.6598 (ttm110) REVERT: A 1038 LYS cc_start: 0.7683 (tppt) cc_final: 0.7404 (tppt) REVERT: B 177 MET cc_start: 0.0201 (mmt) cc_final: -0.0541 (ttp) REVERT: B 321 GLN cc_start: 0.7553 (mm-40) cc_final: 0.7209 (tp-100) REVERT: B 737 ASP cc_start: 0.7992 (OUTLIER) cc_final: 0.7057 (p0) REVERT: B 823 PHE cc_start: 0.7703 (OUTLIER) cc_final: 0.7058 (t80) REVERT: B 1019 ARG cc_start: 0.7165 (tpt-90) cc_final: 0.6894 (ttm110) REVERT: C 572 THR cc_start: 0.4723 (m) cc_final: 0.4289 (p) REVERT: C 740 MET cc_start: 0.6854 (tpt) cc_final: 0.6352 (tpp) REVERT: C 786 LYS cc_start: 0.7533 (mptt) cc_final: 0.7121 (mmmt) REVERT: C 814 LYS cc_start: 0.6555 (tptt) cc_final: 0.6004 (tppt) REVERT: C 1005 GLN cc_start: 0.7894 (mm-40) cc_final: 0.7672 (mt0) REVERT: C 1017 GLU cc_start: 0.7273 (tt0) cc_final: 0.6669 (tm-30) REVERT: C 1019 ARG cc_start: 0.7096 (tpt-90) cc_final: 0.6782 (ttm110) REVERT: E 26 LYS cc_start: 0.3078 (tptt) cc_final: 0.2624 (mmtt) REVERT: E 91 LEU cc_start: 0.4248 (mm) cc_final: 0.4005 (tp) REVERT: E 293 VAL cc_start: 0.1711 (p) cc_final: 0.1289 (t) REVERT: E 323 MET cc_start: 0.1372 (mtt) cc_final: 0.0993 (tpp) REVERT: E 332 MET cc_start: 0.3433 (ttt) cc_final: 0.2205 (mtp) REVERT: E 366 MET cc_start: -0.0123 (mtm) cc_final: -0.0541 (tpp) REVERT: E 459 TRP cc_start: 0.0766 (OUTLIER) cc_final: -0.0012 (t60) REVERT: E 474 MET cc_start: 0.1153 (tpp) cc_final: -0.0013 (mmp) REVERT: E 515 TYR cc_start: 0.3036 (t80) cc_final: 0.2626 (t80) REVERT: E 518 ARG cc_start: 0.0830 (ptm160) cc_final: 0.0375 (tmt170) REVERT: H 110 ASN cc_start: 0.2485 (p0) cc_final: 0.2004 (t0) REVERT: L 64 PHE cc_start: -0.0402 (m-80) cc_final: -0.0882 (m-80) REVERT: J 73 LEU cc_start: 0.1143 (tt) cc_final: 0.0834 (mt) REVERT: J 75 GLU cc_start: 0.3119 (pt0) cc_final: 0.2852 (tm-30) REVERT: J 134 ASN cc_start: 0.2154 (OUTLIER) cc_final: 0.1609 (t0) REVERT: J 332 MET cc_start: 0.2040 (ttt) cc_final: 0.0791 (mtt) REVERT: J 482 ARG cc_start: 0.3375 (ttm-80) cc_final: 0.3175 (tpp-160) REVERT: J 505 HIS cc_start: 0.2469 (m170) cc_final: 0.2178 (m90) REVERT: J 546 ASN cc_start: 0.2187 (m-40) cc_final: 0.1597 (t0) REVERT: M 98 GLN cc_start: 0.1713 (mm-40) cc_final: 0.1478 (mt0) REVERT: M 195 HIS cc_start: 0.6197 (t-170) cc_final: 0.5889 (m170) REVERT: M 217 TYR cc_start: 0.3651 (t80) cc_final: 0.2814 (m-80) REVERT: M 270 MET cc_start: -0.1312 (tpp) cc_final: -0.2486 (tpp) REVERT: M 271 TRP cc_start: 0.1259 (m-90) cc_final: 0.0787 (t-100) REVERT: M 356 PHE cc_start: 0.0551 (m-80) cc_final: 0.0309 (m-80) REVERT: M 366 MET cc_start: -0.0155 (mtp) cc_final: -0.0810 (tpp) REVERT: M 401 HIS cc_start: 0.1149 (OUTLIER) cc_final: 0.0703 (m-70) REVERT: M 474 MET cc_start: 0.1037 (mmp) cc_final: 0.0808 (mmm) REVERT: M 482 ARG cc_start: 0.4441 (mtt180) cc_final: 0.4196 (ttm-80) REVERT: M 579 MET cc_start: 0.2098 (ptp) cc_final: 0.1627 (mtm) REVERT: N 81 MET cc_start: -0.1340 (ttt) cc_final: -0.1647 (ttt) REVERT: N 105 TYR cc_start: 0.4132 (m-80) cc_final: 0.3736 (m-80) REVERT: O 16 GLN cc_start: 0.0968 (OUTLIER) cc_final: 0.0493 (mm-40) REVERT: O 64 PHE cc_start: -0.0454 (m-80) cc_final: -0.0959 (m-10) outliers start: 95 outliers final: 44 residues processed: 569 average time/residue: 0.5013 time to fit residues: 475.1028 Evaluate side-chains 436 residues out of total 5457 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 382 time to evaluate : 4.119 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 177 MET Chi-restraints excluded: chain A residue 285 ILE Chi-restraints excluded: chain A residue 400 PHE Chi-restraints excluded: chain A residue 449 TYR Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 528 LYS Chi-restraints excluded: chain A residue 747 THR Chi-restraints excluded: chain A residue 751 ASN Chi-restraints excluded: chain A residue 823 PHE Chi-restraints excluded: chain A residue 1107 ARG Chi-restraints excluded: chain B residue 198 ASP Chi-restraints excluded: chain B residue 305 SER Chi-restraints excluded: chain B residue 400 PHE Chi-restraints excluded: chain B residue 737 ASP Chi-restraints excluded: chain B residue 747 THR Chi-restraints excluded: chain B residue 751 ASN Chi-restraints excluded: chain B residue 823 PHE Chi-restraints excluded: chain B residue 991 VAL Chi-restraints excluded: chain B residue 996 LEU Chi-restraints excluded: chain B residue 1001 LEU Chi-restraints excluded: chain C residue 198 ASP Chi-restraints excluded: chain C residue 238 PHE Chi-restraints excluded: chain C residue 276 LEU Chi-restraints excluded: chain C residue 285 ILE Chi-restraints excluded: chain C residue 590 CYS Chi-restraints excluded: chain C residue 670 ILE Chi-restraints excluded: chain C residue 823 PHE Chi-restraints excluded: chain C residue 996 LEU Chi-restraints excluded: chain C residue 1077 THR Chi-restraints excluded: chain E residue 144 LEU Chi-restraints excluded: chain E residue 318 VAL Chi-restraints excluded: chain E residue 459 TRP Chi-restraints excluded: chain E residue 504 PHE Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 111 PHE Chi-restraints excluded: chain H residue 118 THR Chi-restraints excluded: chain H residue 122 VAL Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 27 SER Chi-restraints excluded: chain L residue 71 THR Chi-restraints excluded: chain L residue 111 LEU Chi-restraints excluded: chain G residue 5 VAL Chi-restraints excluded: chain G residue 48 MET Chi-restraints excluded: chain I residue 5 THR Chi-restraints excluded: chain J residue 134 ASN Chi-restraints excluded: chain J residue 292 ASP Chi-restraints excluded: chain J residue 524 GLN Chi-restraints excluded: chain M residue 50 TYR Chi-restraints excluded: chain M residue 401 HIS Chi-restraints excluded: chain N residue 93 VAL Chi-restraints excluded: chain O residue 16 GLN Chi-restraints excluded: chain O residue 27 SER Chi-restraints excluded: chain O residue 71 THR Chi-restraints excluded: chain O residue 109 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 624 random chunks: chunk 314 optimal weight: 0.9980 chunk 175 optimal weight: 4.9990 chunk 471 optimal weight: 0.9990 chunk 385 optimal weight: 20.0000 chunk 156 optimal weight: 4.9990 chunk 567 optimal weight: 5.9990 chunk 613 optimal weight: 30.0000 chunk 505 optimal weight: 8.9990 chunk 562 optimal weight: 2.9990 chunk 193 optimal weight: 2.9990 chunk 455 optimal weight: 3.9990 overall best weight: 2.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 99 ASN A 165 ASN A 354 ASN A 751 ASN A 913 GLN A 955 ASN A1101 HIS A1142 GLN ** B 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 354 ASN B 487 ASN ** B 856 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1054 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1101 HIS C 66 HIS ** C 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 394 ASN C 409 GLN C 913 GLN C 965 GLN C1064 HIS C1101 HIS ** E 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 89 GLN ** E 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 378 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 211 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 6 GLN ** L 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 172 GLN ** L 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 193 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 39 GLN ** G 208 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 193 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 300 GLN ** J 325 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 374 HIS J 397 ASN ** J 401 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 508 ASN J 522 GLN M 81 GLN ** M 325 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 397 ASN M 401 HIS Total number of N/Q/H flips: 30 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6233 moved from start: 0.4335 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.078 51201 Z= 0.292 Angle : 0.596 14.850 69696 Z= 0.303 Chirality : 0.045 0.333 7857 Planarity : 0.005 0.064 8961 Dihedral : 5.076 59.234 7784 Min Nonbonded Distance : 1.859 Molprobity Statistics. All-atom Clashscore : 9.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.27 % Favored : 95.73 % Rotamer: Outliers : 2.12 % Allowed : 15.35 % Favored : 82.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.60 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.55 (0.10), residues: 6258 helix: -1.33 (0.12), residues: 1593 sheet: -0.50 (0.15), residues: 1242 loop : -2.41 (0.09), residues: 3423 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP J 271 HIS 0.071 0.002 HIS M 374 PHE 0.021 0.002 PHE A 898 TYR 0.020 0.002 TYR B 170 ARG 0.006 0.001 ARG A 905 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12516 Ramachandran restraints generated. 6258 Oldfield, 0 Emsley, 6258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12516 Ramachandran restraints generated. 6258 Oldfield, 0 Emsley, 6258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 494 residues out of total 5457 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 114 poor density : 380 time to evaluate : 4.143 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: A 105 ILE cc_start: 0.7839 (pt) cc_final: 0.7505 (mt) REVERT: A 117 LEU cc_start: 0.6184 (mp) cc_final: 0.5855 (mp) REVERT: A 153 MET cc_start: 0.5793 (pmm) cc_final: 0.5210 (pmm) REVERT: A 177 MET cc_start: 0.0946 (ttp) cc_final: 0.0734 (mtp) REVERT: A 220 PHE cc_start: 0.7385 (t80) cc_final: 0.7041 (t80) REVERT: A 347 PHE cc_start: 0.1334 (OUTLIER) cc_final: 0.1091 (m-80) REVERT: A 449 TYR cc_start: 0.3269 (OUTLIER) cc_final: 0.2615 (m-80) REVERT: A 572 THR cc_start: 0.4813 (m) cc_final: 0.4511 (p) REVERT: A 740 MET cc_start: 0.7029 (mmm) cc_final: 0.6755 (mmm) REVERT: A 751 ASN cc_start: 0.7505 (OUTLIER) cc_final: 0.7138 (p0) REVERT: A 814 LYS cc_start: 0.6461 (tptt) cc_final: 0.6134 (tptt) REVERT: A 1005 GLN cc_start: 0.7782 (mm-40) cc_final: 0.7460 (mt0) REVERT: B 177 MET cc_start: -0.0699 (mmt) cc_final: -0.1151 (ttp) REVERT: B 271 GLN cc_start: 0.7405 (mm-40) cc_final: 0.7129 (mt0) REVERT: B 321 GLN cc_start: 0.7420 (mm-40) cc_final: 0.7168 (tp40) REVERT: B 572 THR cc_start: 0.5378 (m) cc_final: 0.4966 (p) REVERT: B 737 ASP cc_start: 0.8081 (OUTLIER) cc_final: 0.7137 (p0) REVERT: B 1019 ARG cc_start: 0.7289 (tpt-90) cc_final: 0.6960 (ttm110) REVERT: C 321 GLN cc_start: 0.6965 (mm-40) cc_final: 0.6594 (tp-100) REVERT: C 347 PHE cc_start: -0.0853 (OUTLIER) cc_final: -0.1103 (m-10) REVERT: C 572 THR cc_start: 0.4818 (m) cc_final: 0.4367 (p) REVERT: C 726 ILE cc_start: 0.8424 (OUTLIER) cc_final: 0.8141 (mm) REVERT: C 814 LYS cc_start: 0.6518 (tptt) cc_final: 0.5904 (tppt) REVERT: C 1005 GLN cc_start: 0.8027 (mm-40) cc_final: 0.7593 (mt0) REVERT: C 1017 GLU cc_start: 0.7457 (tt0) cc_final: 0.6775 (tm-30) REVERT: C 1019 ARG cc_start: 0.6885 (tpt-90) cc_final: 0.6568 (ttm110) REVERT: C 1040 VAL cc_start: 0.7313 (p) cc_final: 0.6896 (m) REVERT: C 1141 LEU cc_start: 0.8131 (mt) cc_final: 0.7645 (tp) REVERT: E 26 LYS cc_start: 0.4106 (tptt) cc_final: 0.3643 (mmtt) REVERT: E 91 LEU cc_start: 0.4279 (mm) cc_final: 0.4023 (tp) REVERT: E 293 VAL cc_start: 0.1839 (p) cc_final: 0.1252 (t) REVERT: E 366 MET cc_start: 0.0070 (mtm) cc_final: -0.0385 (tpp) REVERT: E 474 MET cc_start: 0.0701 (tpp) cc_final: -0.0004 (mmp) REVERT: E 515 TYR cc_start: 0.2643 (t80) cc_final: 0.2257 (t80) REVERT: E 518 ARG cc_start: 0.0372 (ptm160) cc_final: -0.0049 (tmt170) REVERT: H 81 MET cc_start: -0.0619 (tpp) cc_final: -0.1581 (tpt) REVERT: H 110 ASN cc_start: 0.2374 (p0) cc_final: 0.1949 (t0) REVERT: L 22 CYS cc_start: 0.6729 (OUTLIER) cc_final: 0.6454 (m) REVERT: L 64 PHE cc_start: -0.0455 (m-80) cc_final: -0.0891 (m-80) REVERT: G 59 ASN cc_start: 0.4267 (t0) cc_final: 0.3687 (p0) REVERT: J 75 GLU cc_start: 0.2346 (pt0) cc_final: 0.1802 (tm-30) REVERT: J 134 ASN cc_start: 0.1832 (OUTLIER) cc_final: 0.1301 (t0) REVERT: J 270 MET cc_start: -0.0314 (tpp) cc_final: -0.1244 (tpp) REVERT: J 332 MET cc_start: 0.2499 (ttt) cc_final: 0.1340 (mtt) REVERT: J 488 VAL cc_start: 0.1690 (OUTLIER) cc_final: 0.1483 (t) REVERT: J 546 ASN cc_start: 0.2546 (m-40) cc_final: 0.1948 (t0) REVERT: M 217 TYR cc_start: 0.2840 (t80) cc_final: 0.2507 (m-80) REVERT: M 270 MET cc_start: -0.1095 (tpp) cc_final: -0.2713 (tpp) REVERT: M 366 MET cc_start: 0.0569 (mtp) cc_final: -0.0087 (tpp) REVERT: M 400 PHE cc_start: -0.0039 (m-80) cc_final: -0.0857 (t80) REVERT: M 474 MET cc_start: 0.0974 (mmp) cc_final: 0.0643 (mmm) REVERT: M 482 ARG cc_start: 0.4350 (mtt180) cc_final: 0.4094 (ttm-80) REVERT: N 57 ILE cc_start: 0.0548 (mp) cc_final: -0.0462 (mt) REVERT: N 81 MET cc_start: -0.1067 (ttt) cc_final: -0.1310 (tmm) REVERT: N 105 TYR cc_start: 0.4228 (m-80) cc_final: 0.3896 (m-80) REVERT: O 64 PHE cc_start: -0.0485 (m-80) cc_final: -0.0907 (m-10) outliers start: 114 outliers final: 74 residues processed: 469 average time/residue: 0.4766 time to fit residues: 380.3348 Evaluate side-chains 416 residues out of total 5457 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 83 poor density : 333 time to evaluate : 4.092 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 198 ASP Chi-restraints excluded: chain A residue 236 THR Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 285 ILE Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain A residue 347 PHE Chi-restraints excluded: chain A residue 400 PHE Chi-restraints excluded: chain A residue 448 ASN Chi-restraints excluded: chain A residue 449 TYR Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 660 TYR Chi-restraints excluded: chain A residue 734 THR Chi-restraints excluded: chain A residue 751 ASN Chi-restraints excluded: chain A residue 761 THR Chi-restraints excluded: chain A residue 887 THR Chi-restraints excluded: chain A residue 912 THR Chi-restraints excluded: chain A residue 1107 ARG Chi-restraints excluded: chain B residue 105 ILE Chi-restraints excluded: chain B residue 135 PHE Chi-restraints excluded: chain B residue 198 ASP Chi-restraints excluded: chain B residue 305 SER Chi-restraints excluded: chain B residue 307 THR Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 598 ILE Chi-restraints excluded: chain B residue 660 TYR Chi-restraints excluded: chain B residue 670 ILE Chi-restraints excluded: chain B residue 734 THR Chi-restraints excluded: chain B residue 737 ASP Chi-restraints excluded: chain B residue 761 THR Chi-restraints excluded: chain B residue 821 LEU Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 991 VAL Chi-restraints excluded: chain B residue 996 LEU Chi-restraints excluded: chain B residue 1001 LEU Chi-restraints excluded: chain B residue 1018 ILE Chi-restraints excluded: chain B residue 1077 THR Chi-restraints excluded: chain C residue 198 ASP Chi-restraints excluded: chain C residue 238 PHE Chi-restraints excluded: chain C residue 276 LEU Chi-restraints excluded: chain C residue 285 ILE Chi-restraints excluded: chain C residue 307 THR Chi-restraints excluded: chain C residue 347 PHE Chi-restraints excluded: chain C residue 449 TYR Chi-restraints excluded: chain C residue 660 TYR Chi-restraints excluded: chain C residue 670 ILE Chi-restraints excluded: chain C residue 726 ILE Chi-restraints excluded: chain C residue 734 THR Chi-restraints excluded: chain C residue 737 ASP Chi-restraints excluded: chain C residue 823 PHE Chi-restraints excluded: chain C residue 996 LEU Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain E residue 132 VAL Chi-restraints excluded: chain E residue 504 PHE Chi-restraints excluded: chain E residue 513 ILE Chi-restraints excluded: chain E residue 545 SER Chi-restraints excluded: chain E residue 548 THR Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 111 PHE Chi-restraints excluded: chain H residue 118 THR Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 22 CYS Chi-restraints excluded: chain L residue 27 SER Chi-restraints excluded: chain L residue 111 LEU Chi-restraints excluded: chain L residue 130 LEU Chi-restraints excluded: chain G residue 5 VAL Chi-restraints excluded: chain G residue 71 THR Chi-restraints excluded: chain G residue 111 PHE Chi-restraints excluded: chain I residue 5 THR Chi-restraints excluded: chain I residue 206 THR Chi-restraints excluded: chain J residue 132 VAL Chi-restraints excluded: chain J residue 134 ASN Chi-restraints excluded: chain J residue 292 ASP Chi-restraints excluded: chain J residue 452 PHE Chi-restraints excluded: chain J residue 488 VAL Chi-restraints excluded: chain J residue 591 LEU Chi-restraints excluded: chain M residue 50 TYR Chi-restraints excluded: chain M residue 134 ASN Chi-restraints excluded: chain M residue 162 LEU Chi-restraints excluded: chain N residue 120 VAL Chi-restraints excluded: chain N residue 122 VAL Chi-restraints excluded: chain O residue 27 SER Chi-restraints excluded: chain O residue 71 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 624 random chunks: chunk 560 optimal weight: 8.9990 chunk 426 optimal weight: 1.9990 chunk 294 optimal weight: 0.7980 chunk 62 optimal weight: 2.9990 chunk 270 optimal weight: 2.9990 chunk 381 optimal weight: 8.9990 chunk 569 optimal weight: 9.9990 chunk 603 optimal weight: 0.5980 chunk 297 optimal weight: 0.7980 chunk 539 optimal weight: 9.9990 chunk 162 optimal weight: 0.5980 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 965 GLN ** B 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 856 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 913 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 354 ASN C 675 GLN C 913 GLN ** C 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1135 ASN ** E 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 378 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 211 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 189 GLN L 193 HIS ** G 208 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 193 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 51 ASN ** J 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 325 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 397 ASN J 401 HIS J 578 ASN M 51 ASN M 195 HIS M 305 GLN M 325 GLN O 16 GLN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6217 moved from start: 0.4561 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 51201 Z= 0.164 Angle : 0.498 9.541 69696 Z= 0.249 Chirality : 0.043 0.346 7857 Planarity : 0.004 0.056 8961 Dihedral : 4.507 59.894 7779 Min Nonbonded Distance : 2.071 Molprobity Statistics. All-atom Clashscore : 9.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.06 % Favored : 95.94 % Rotamer: Outliers : 1.70 % Allowed : 16.87 % Favored : 81.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.60 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.13 (0.10), residues: 6258 helix: -0.66 (0.13), residues: 1593 sheet: -0.49 (0.15), residues: 1248 loop : -2.22 (0.09), residues: 3417 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP M 594 HIS 0.019 0.001 HIS J 239 PHE 0.023 0.001 PHE E 512 TYR 0.027 0.001 TYR N 102 ARG 0.003 0.000 ARG M 460 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12516 Ramachandran restraints generated. 6258 Oldfield, 0 Emsley, 6258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12516 Ramachandran restraints generated. 6258 Oldfield, 0 Emsley, 6258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 451 residues out of total 5457 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 91 poor density : 360 time to evaluate : 4.140 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: A 105 ILE cc_start: 0.7830 (pt) cc_final: 0.7510 (mt) REVERT: A 153 MET cc_start: 0.5763 (pmm) cc_final: 0.5190 (pmm) REVERT: A 220 PHE cc_start: 0.7320 (t80) cc_final: 0.6934 (t80) REVERT: A 449 TYR cc_start: 0.3263 (OUTLIER) cc_final: 0.2614 (m-80) REVERT: A 572 THR cc_start: 0.4804 (m) cc_final: 0.4428 (p) REVERT: A 740 MET cc_start: 0.7074 (mmm) cc_final: 0.6740 (mmm) REVERT: A 814 LYS cc_start: 0.6473 (tptt) cc_final: 0.6084 (tptt) REVERT: A 1005 GLN cc_start: 0.7974 (mm-40) cc_final: 0.7530 (mt0) REVERT: B 177 MET cc_start: 0.0118 (mmt) cc_final: -0.0637 (ttp) REVERT: B 321 GLN cc_start: 0.7434 (mm-40) cc_final: 0.7067 (tp-100) REVERT: B 572 THR cc_start: 0.5488 (m) cc_final: 0.5103 (p) REVERT: B 726 ILE cc_start: 0.8641 (OUTLIER) cc_final: 0.8342 (mm) REVERT: B 856 ASN cc_start: 0.6366 (t0) cc_final: 0.6161 (t0) REVERT: B 1019 ARG cc_start: 0.7186 (tpt-90) cc_final: 0.6820 (ttm110) REVERT: C 276 LEU cc_start: 0.7736 (OUTLIER) cc_final: 0.7469 (tt) REVERT: C 347 PHE cc_start: -0.0844 (OUTLIER) cc_final: -0.1081 (m-10) REVERT: C 377 PHE cc_start: 0.5825 (p90) cc_final: 0.5585 (p90) REVERT: C 572 THR cc_start: 0.4905 (m) cc_final: 0.4431 (p) REVERT: C 598 ILE cc_start: 0.8123 (OUTLIER) cc_final: 0.7826 (mp) REVERT: C 726 ILE cc_start: 0.8481 (OUTLIER) cc_final: 0.8218 (mm) REVERT: C 814 LYS cc_start: 0.6429 (tptt) cc_final: 0.5851 (tppt) REVERT: C 1005 GLN cc_start: 0.8049 (mm-40) cc_final: 0.7719 (mt0) REVERT: C 1017 GLU cc_start: 0.7545 (tt0) cc_final: 0.7178 (tm-30) REVERT: C 1019 ARG cc_start: 0.6858 (tpt-90) cc_final: 0.6532 (ttm110) REVERT: C 1040 VAL cc_start: 0.7732 (p) cc_final: 0.7304 (m) REVERT: C 1141 LEU cc_start: 0.8141 (mt) cc_final: 0.7669 (tp) REVERT: E 26 LYS cc_start: 0.3538 (tptt) cc_final: 0.3121 (mmtt) REVERT: E 91 LEU cc_start: 0.4561 (mm) cc_final: 0.4317 (tp) REVERT: E 474 MET cc_start: 0.0991 (tpp) cc_final: 0.0271 (mmp) REVERT: E 515 TYR cc_start: 0.2545 (t80) cc_final: 0.2292 (t80) REVERT: E 518 ARG cc_start: 0.0647 (ptm160) cc_final: 0.0289 (tmt170) REVERT: H 81 MET cc_start: -0.0647 (tpp) cc_final: -0.1557 (tpt) REVERT: H 110 ASN cc_start: 0.2374 (p0) cc_final: 0.1909 (t0) REVERT: L 48 LEU cc_start: 0.4082 (tp) cc_final: 0.3580 (tp) REVERT: L 64 PHE cc_start: -0.0459 (m-80) cc_final: -0.0893 (m-80) REVERT: G 59 ASN cc_start: 0.3849 (t0) cc_final: 0.3281 (p0) REVERT: J 75 GLU cc_start: 0.2129 (pt0) cc_final: 0.1579 (tm-30) REVERT: J 134 ASN cc_start: 0.1405 (OUTLIER) cc_final: 0.0942 (t0) REVERT: J 401 HIS cc_start: 0.0380 (OUTLIER) cc_final: 0.0123 (m90) REVERT: J 488 VAL cc_start: 0.1925 (OUTLIER) cc_final: 0.1689 (t) REVERT: J 546 ASN cc_start: 0.2600 (m-40) cc_final: 0.1940 (p0) REVERT: M 217 TYR cc_start: 0.2969 (t80) cc_final: 0.2502 (m-80) REVERT: M 366 MET cc_start: -0.0081 (mtp) cc_final: -0.0600 (tpp) REVERT: M 474 MET cc_start: 0.0930 (mmp) cc_final: 0.0677 (mmm) REVERT: M 482 ARG cc_start: 0.4348 (mtt180) cc_final: 0.4093 (ttm-80) REVERT: N 81 MET cc_start: -0.0940 (ttt) cc_final: -0.1206 (tmm) REVERT: N 105 TYR cc_start: 0.3983 (m-80) cc_final: 0.3632 (m-80) REVERT: O 16 GLN cc_start: 0.0139 (OUTLIER) cc_final: -0.0125 (mt0) REVERT: O 64 PHE cc_start: -0.0478 (m-80) cc_final: -0.0957 (m-10) outliers start: 91 outliers final: 55 residues processed: 425 average time/residue: 0.4728 time to fit residues: 344.2728 Evaluate side-chains 384 residues out of total 5457 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 319 time to evaluate : 4.100 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 198 ASP Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 449 TYR Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 660 TYR Chi-restraints excluded: chain A residue 887 THR Chi-restraints excluded: chain A residue 900 MET Chi-restraints excluded: chain A residue 912 THR Chi-restraints excluded: chain A residue 991 VAL Chi-restraints excluded: chain A residue 1107 ARG Chi-restraints excluded: chain A residue 1117 THR Chi-restraints excluded: chain A residue 1133 VAL Chi-restraints excluded: chain B residue 105 ILE Chi-restraints excluded: chain B residue 198 ASP Chi-restraints excluded: chain B residue 307 THR Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 598 ILE Chi-restraints excluded: chain B residue 660 TYR Chi-restraints excluded: chain B residue 670 ILE Chi-restraints excluded: chain B residue 726 ILE Chi-restraints excluded: chain B residue 821 LEU Chi-restraints excluded: chain B residue 996 LEU Chi-restraints excluded: chain B residue 1001 LEU Chi-restraints excluded: chain B residue 1117 THR Chi-restraints excluded: chain C residue 198 ASP Chi-restraints excluded: chain C residue 276 LEU Chi-restraints excluded: chain C residue 347 PHE Chi-restraints excluded: chain C residue 449 TYR Chi-restraints excluded: chain C residue 598 ILE Chi-restraints excluded: chain C residue 670 ILE Chi-restraints excluded: chain C residue 726 ILE Chi-restraints excluded: chain C residue 737 ASP Chi-restraints excluded: chain C residue 821 LEU Chi-restraints excluded: chain C residue 980 ILE Chi-restraints excluded: chain C residue 996 LEU Chi-restraints excluded: chain C residue 1135 ASN Chi-restraints excluded: chain E residue 145 GLU Chi-restraints excluded: chain E residue 459 TRP Chi-restraints excluded: chain E residue 499 ASP Chi-restraints excluded: chain E residue 504 PHE Chi-restraints excluded: chain E residue 513 ILE Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 111 PHE Chi-restraints excluded: chain H residue 118 THR Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 22 CYS Chi-restraints excluded: chain L residue 111 LEU Chi-restraints excluded: chain L residue 130 LEU Chi-restraints excluded: chain G residue 5 VAL Chi-restraints excluded: chain G residue 71 THR Chi-restraints excluded: chain G residue 111 PHE Chi-restraints excluded: chain J residue 132 VAL Chi-restraints excluded: chain J residue 134 ASN Chi-restraints excluded: chain J residue 275 TRP Chi-restraints excluded: chain J residue 292 ASP Chi-restraints excluded: chain J residue 343 VAL Chi-restraints excluded: chain J residue 401 HIS Chi-restraints excluded: chain J residue 408 MET Chi-restraints excluded: chain J residue 449 THR Chi-restraints excluded: chain J residue 488 VAL Chi-restraints excluded: chain J residue 506 VAL Chi-restraints excluded: chain M residue 134 ASN Chi-restraints excluded: chain N residue 48 MET Chi-restraints excluded: chain N residue 120 VAL Chi-restraints excluded: chain O residue 16 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 624 random chunks: chunk 502 optimal weight: 9.9990 chunk 342 optimal weight: 20.0000 chunk 8 optimal weight: 10.0000 chunk 449 optimal weight: 20.0000 chunk 248 optimal weight: 9.9990 chunk 514 optimal weight: 20.0000 chunk 416 optimal weight: 20.0000 chunk 0 optimal weight: 10.0000 chunk 307 optimal weight: 0.9990 chunk 541 optimal weight: 10.0000 chunk 152 optimal weight: 7.9990 overall best weight: 7.7992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 448 ASN A 450 ASN A 474 GLN ** A 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 787 GLN A 913 GLN ** A 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 965 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 99 ASN ** B 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 450 ASN ** B 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 787 GLN B 804 GLN B 856 ASN ** B 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 487 ASN C 913 GLN ** C 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 378 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 508 ASN E 524 GLN ** E 578 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 3 GLN ** H 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 182 GLN ** L 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 65 GLN G 208 ASN I 172 GLN ** I 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 277 ASN J 305 GLN J 397 ASN J 437 ASN ** M 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 175 GLN M 195 HIS M 305 GLN M 374 HIS M 397 ASN ** M 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 442 GLN ** M 505 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 508 ASN O 16 GLN ** O 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 31 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6421 moved from start: 0.7524 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.013 0.150 51201 Z= 0.819 Angle : 1.161 14.575 69696 Z= 0.591 Chirality : 0.064 0.494 7857 Planarity : 0.008 0.069 8961 Dihedral : 8.186 59.955 7779 Min Nonbonded Distance : 1.992 Molprobity Statistics. All-atom Clashscore : 23.55 Ramachandran Plot: Outliers : 0.21 % Allowed : 9.66 % Favored : 90.13 % Rotamer: Outliers : 4.84 % Allowed : 17.64 % Favored : 77.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.60 % Cis-general : 0.00 % Twisted Proline : 0.30 % Twisted General : 0.05 % 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: -3.02 (0.09), residues: 6258 helix: -1.58 (0.12), residues: 1551 sheet: -0.90 (0.15), residues: 1179 loop : -2.70 (0.09), residues: 3528 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.063 0.004 TRP G 114 HIS 0.052 0.004 HIS J 401 PHE 0.063 0.005 PHE A1042 TYR 0.043 0.004 TYR B 495 ARG 0.017 0.002 ARG A 905 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12516 Ramachandran restraints generated. 6258 Oldfield, 0 Emsley, 6258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12516 Ramachandran restraints generated. 6258 Oldfield, 0 Emsley, 6258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 640 residues out of total 5457 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 262 poor density : 378 time to evaluate : 4.148 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: A 52 GLN cc_start: 0.7311 (tm-30) cc_final: 0.7077 (tm-30) REVERT: A 129 LYS cc_start: 0.5546 (tttp) cc_final: 0.4809 (tttm) REVERT: A 134 GLN cc_start: 0.5894 (mt0) cc_final: 0.5657 (mt0) REVERT: A 138 ASP cc_start: 0.4696 (OUTLIER) cc_final: 0.2098 (t0) REVERT: A 220 PHE cc_start: 0.7704 (t80) cc_final: 0.6950 (t80) REVERT: A 238 PHE cc_start: 0.5722 (OUTLIER) cc_final: 0.5152 (p90) REVERT: A 572 THR cc_start: 0.5613 (m) cc_final: 0.5120 (p) REVERT: A 592 PHE cc_start: 0.5092 (OUTLIER) cc_final: 0.4607 (m-80) REVERT: A 745 ASP cc_start: 0.6804 (t70) cc_final: 0.6240 (t0) REVERT: A 753 LEU cc_start: 0.7973 (OUTLIER) cc_final: 0.7740 (tp) REVERT: A 814 LYS cc_start: 0.6878 (tptt) cc_final: 0.6625 (tptt) REVERT: A 823 PHE cc_start: 0.7914 (OUTLIER) cc_final: 0.7394 (t80) REVERT: A 1017 GLU cc_start: 0.7497 (tt0) cc_final: 0.6773 (tm-30) REVERT: A 1138 TYR cc_start: 0.8104 (t80) cc_final: 0.7831 (t80) REVERT: B 53 ASP cc_start: 0.6917 (OUTLIER) cc_final: 0.6456 (m-30) REVERT: B 129 LYS cc_start: 0.5640 (tttp) cc_final: 0.5383 (tttp) REVERT: B 137 ASN cc_start: 0.4349 (m-40) cc_final: 0.4110 (m110) REVERT: B 138 ASP cc_start: 0.3661 (OUTLIER) cc_final: 0.3383 (t0) REVERT: B 177 MET cc_start: -0.1005 (mmt) cc_final: -0.1234 (ttt) REVERT: B 384 PRO cc_start: 0.2515 (Cg_exo) cc_final: 0.2207 (Cg_endo) REVERT: B 505 TYR cc_start: 0.5850 (m-80) cc_final: 0.5226 (m-80) REVERT: B 528 LYS cc_start: 0.7389 (OUTLIER) cc_final: 0.7180 (mmmt) REVERT: B 572 THR cc_start: 0.6416 (m) cc_final: 0.5868 (p) REVERT: B 592 PHE cc_start: 0.4876 (OUTLIER) cc_final: 0.4438 (m-80) REVERT: B 696 THR cc_start: 0.8301 (OUTLIER) cc_final: 0.8089 (t) REVERT: B 740 MET cc_start: 0.7847 (mmm) cc_final: 0.7646 (mmm) REVERT: B 745 ASP cc_start: 0.7938 (m-30) cc_final: 0.6784 (t0) REVERT: B 916 LEU cc_start: 0.7213 (OUTLIER) cc_final: 0.7003 (tt) REVERT: B 965 GLN cc_start: 0.8983 (OUTLIER) cc_final: 0.8754 (tp40) REVERT: B 969 ASN cc_start: 0.9079 (OUTLIER) cc_final: 0.8646 (m-40) REVERT: C 347 PHE cc_start: 0.0093 (OUTLIER) cc_final: -0.0219 (m-10) REVERT: C 592 PHE cc_start: 0.5289 (OUTLIER) cc_final: 0.5024 (m-80) REVERT: C 661 GLU cc_start: 0.7851 (tp30) cc_final: 0.7525 (pm20) REVERT: C 814 LYS cc_start: 0.7042 (tptt) cc_final: 0.6305 (tppt) REVERT: C 1017 GLU cc_start: 0.7614 (tt0) cc_final: 0.7071 (tp30) REVERT: C 1119 ASN cc_start: 0.7771 (OUTLIER) cc_final: 0.7387 (p0) REVERT: C 1138 TYR cc_start: 0.7173 (t80) cc_final: 0.6786 (t80) REVERT: C 1141 LEU cc_start: 0.8308 (mt) cc_final: 0.7949 (tp) REVERT: E 26 LYS cc_start: 0.3744 (tptt) cc_final: 0.3177 (mmtt) REVERT: E 222 LEU cc_start: 0.2968 (OUTLIER) cc_final: 0.2767 (mt) REVERT: E 444 LEU cc_start: 0.3672 (tp) cc_final: 0.3063 (mt) REVERT: E 513 ILE cc_start: -0.0904 (OUTLIER) cc_final: -0.1208 (mm) REVERT: E 531 GLN cc_start: 0.4415 (OUTLIER) cc_final: 0.3683 (mm110) REVERT: E 606 TRP cc_start: 0.3401 (OUTLIER) cc_final: 0.3098 (p-90) REVERT: H 59 ASN cc_start: 0.3949 (t0) cc_final: 0.3267 (p0) REVERT: J 233 ILE cc_start: 0.1805 (OUTLIER) cc_final: 0.1455 (tt) REVERT: J 401 HIS cc_start: 0.0796 (m170) cc_final: 0.0416 (t-90) REVERT: J 437 ASN cc_start: -0.4508 (OUTLIER) cc_final: -0.4710 (p0) REVERT: J 516 TYR cc_start: 0.0799 (OUTLIER) cc_final: 0.0548 (m-80) REVERT: M 241 HIS cc_start: 0.2137 (t-90) cc_final: 0.1843 (t70) REVERT: M 332 MET cc_start: -0.2167 (ttm) cc_final: -0.2724 (ttm) REVERT: M 439 LEU cc_start: 0.2338 (OUTLIER) cc_final: 0.1998 (pp) REVERT: M 482 ARG cc_start: 0.4527 (mtt180) cc_final: 0.4266 (ttm-80) REVERT: M 514 ARG cc_start: 0.0376 (OUTLIER) cc_final: 0.0100 (ttp80) REVERT: N 81 MET cc_start: 0.0804 (ttt) cc_final: 0.0495 (tmm) outliers start: 262 outliers final: 143 residues processed: 614 average time/residue: 0.4649 time to fit residues: 489.8934 Evaluate side-chains 469 residues out of total 5457 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 168 poor density : 301 time to evaluate : 4.105 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 138 ASP Chi-restraints excluded: chain A residue 198 ASP Chi-restraints excluded: chain A residue 236 THR Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 285 ILE Chi-restraints excluded: chain A residue 297 SER Chi-restraints excluded: chain A residue 323 THR Chi-restraints excluded: chain A residue 326 ILE Chi-restraints excluded: chain A residue 331 ASN Chi-restraints excluded: chain A residue 400 PHE Chi-restraints excluded: chain A residue 402 ILE Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 439 ASN Chi-restraints excluded: chain A residue 448 ASN Chi-restraints excluded: chain A residue 478 THR Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 592 PHE Chi-restraints excluded: chain A residue 595 VAL Chi-restraints excluded: chain A residue 656 VAL Chi-restraints excluded: chain A residue 660 TYR Chi-restraints excluded: chain A residue 734 THR Chi-restraints excluded: chain A residue 753 LEU Chi-restraints excluded: chain A residue 823 PHE Chi-restraints excluded: chain A residue 873 TYR Chi-restraints excluded: chain A residue 887 THR Chi-restraints excluded: chain A residue 900 MET Chi-restraints excluded: chain A residue 991 VAL Chi-restraints excluded: chain A residue 1061 VAL Chi-restraints excluded: chain A residue 1082 CYS Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain B residue 53 ASP Chi-restraints excluded: chain B residue 105 ILE Chi-restraints excluded: chain B residue 138 ASP Chi-restraints excluded: chain B residue 198 ASP Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain B residue 285 ILE Chi-restraints excluded: chain B residue 297 SER Chi-restraints excluded: chain B residue 307 THR Chi-restraints excluded: chain B residue 400 PHE Chi-restraints excluded: chain B residue 402 ILE Chi-restraints excluded: chain B residue 445 VAL Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 528 LYS Chi-restraints excluded: chain B residue 592 PHE Chi-restraints excluded: chain B residue 598 ILE Chi-restraints excluded: chain B residue 660 TYR Chi-restraints excluded: chain B residue 670 ILE Chi-restraints excluded: chain B residue 696 THR Chi-restraints excluded: chain B residue 734 THR Chi-restraints excluded: chain B residue 823 PHE Chi-restraints excluded: chain B residue 915 VAL Chi-restraints excluded: chain B residue 916 LEU Chi-restraints excluded: chain B residue 919 ASN Chi-restraints excluded: chain B residue 929 SER Chi-restraints excluded: chain B residue 965 GLN Chi-restraints excluded: chain B residue 969 ASN Chi-restraints excluded: chain B residue 991 VAL Chi-restraints excluded: chain B residue 996 LEU Chi-restraints excluded: chain B residue 1001 LEU Chi-restraints excluded: chain B residue 1018 ILE Chi-restraints excluded: chain B residue 1077 THR Chi-restraints excluded: chain B residue 1117 THR Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 138 ASP Chi-restraints excluded: chain C residue 198 ASP Chi-restraints excluded: chain C residue 238 PHE Chi-restraints excluded: chain C residue 240 THR Chi-restraints excluded: chain C residue 276 LEU Chi-restraints excluded: chain C residue 297 SER Chi-restraints excluded: chain C residue 307 THR Chi-restraints excluded: chain C residue 323 THR Chi-restraints excluded: chain C residue 326 ILE Chi-restraints excluded: chain C residue 347 PHE Chi-restraints excluded: chain C residue 367 VAL Chi-restraints excluded: chain C residue 402 ILE Chi-restraints excluded: chain C residue 449 TYR Chi-restraints excluded: chain C residue 470 THR Chi-restraints excluded: chain C residue 547 THR Chi-restraints excluded: chain C residue 565 PHE Chi-restraints excluded: chain C residue 590 CYS Chi-restraints excluded: chain C residue 592 PHE Chi-restraints excluded: chain C residue 595 VAL Chi-restraints excluded: chain C residue 598 ILE Chi-restraints excluded: chain C residue 660 TYR Chi-restraints excluded: chain C residue 662 CYS Chi-restraints excluded: chain C residue 670 ILE Chi-restraints excluded: chain C residue 712 ILE Chi-restraints excluded: chain C residue 729 VAL Chi-restraints excluded: chain C residue 734 THR Chi-restraints excluded: chain C residue 737 ASP Chi-restraints excluded: chain C residue 794 ILE Chi-restraints excluded: chain C residue 915 VAL Chi-restraints excluded: chain C residue 963 VAL Chi-restraints excluded: chain C residue 991 VAL Chi-restraints excluded: chain C residue 996 LEU Chi-restraints excluded: chain C residue 1040 VAL Chi-restraints excluded: chain C residue 1061 VAL Chi-restraints excluded: chain C residue 1077 THR Chi-restraints excluded: chain C residue 1092 GLU Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain C residue 1117 THR Chi-restraints excluded: chain C residue 1119 ASN Chi-restraints excluded: chain C residue 1136 THR Chi-restraints excluded: chain E residue 96 GLN Chi-restraints excluded: chain E residue 132 VAL Chi-restraints excluded: chain E residue 134 ASN Chi-restraints excluded: chain E residue 150 GLU Chi-restraints excluded: chain E residue 222 LEU Chi-restraints excluded: chain E residue 274 PHE Chi-restraints excluded: chain E residue 281 LEU Chi-restraints excluded: chain E residue 459 TRP Chi-restraints excluded: chain E residue 468 ILE Chi-restraints excluded: chain E residue 499 ASP Chi-restraints excluded: chain E residue 504 PHE Chi-restraints excluded: chain E residue 513 ILE Chi-restraints excluded: chain E residue 531 GLN Chi-restraints excluded: chain E residue 548 THR Chi-restraints excluded: chain E residue 577 LYS Chi-restraints excluded: chain E residue 606 TRP Chi-restraints excluded: chain H residue 111 PHE Chi-restraints excluded: chain H residue 118 THR Chi-restraints excluded: chain H residue 122 VAL Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 22 CYS Chi-restraints excluded: chain L residue 90 CYS Chi-restraints excluded: chain L residue 111 LEU Chi-restraints excluded: chain L residue 130 LEU Chi-restraints excluded: chain G residue 5 VAL Chi-restraints excluded: chain G residue 48 MET Chi-restraints excluded: chain G residue 71 THR Chi-restraints excluded: chain G residue 111 PHE Chi-restraints excluded: chain I residue 28 ASN Chi-restraints excluded: chain I residue 206 THR Chi-restraints excluded: chain J residue 69 TRP Chi-restraints excluded: chain J residue 88 ILE Chi-restraints excluded: chain J residue 132 VAL Chi-restraints excluded: chain J residue 134 ASN Chi-restraints excluded: chain J residue 233 ILE Chi-restraints excluded: chain J residue 271 TRP Chi-restraints excluded: chain J residue 292 ASP Chi-restraints excluded: chain J residue 323 MET Chi-restraints excluded: chain J residue 343 VAL Chi-restraints excluded: chain J residue 364 VAL Chi-restraints excluded: chain J residue 437 ASN Chi-restraints excluded: chain J residue 449 THR Chi-restraints excluded: chain J residue 494 ASP Chi-restraints excluded: chain J residue 504 PHE Chi-restraints excluded: chain J residue 513 ILE Chi-restraints excluded: chain J residue 516 TYR Chi-restraints excluded: chain J residue 524 GLN Chi-restraints excluded: chain J residue 529 LEU Chi-restraints excluded: chain J residue 591 LEU Chi-restraints excluded: chain M residue 50 TYR Chi-restraints excluded: chain M residue 134 ASN Chi-restraints excluded: chain M residue 162 LEU Chi-restraints excluded: chain M residue 184 VAL Chi-restraints excluded: chain M residue 274 PHE Chi-restraints excluded: chain M residue 283 VAL Chi-restraints excluded: chain M residue 343 VAL Chi-restraints excluded: chain M residue 439 LEU Chi-restraints excluded: chain M residue 513 ILE Chi-restraints excluded: chain M residue 514 ARG Chi-restraints excluded: chain N residue 120 VAL Chi-restraints excluded: chain O residue 5 THR Chi-restraints excluded: chain O residue 28 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 624 random chunks: chunk 202 optimal weight: 0.8980 chunk 543 optimal weight: 10.0000 chunk 119 optimal weight: 9.9990 chunk 354 optimal weight: 9.9990 chunk 148 optimal weight: 0.0040 chunk 603 optimal weight: 6.9990 chunk 501 optimal weight: 9.9990 chunk 279 optimal weight: 0.9980 chunk 50 optimal weight: 9.9990 chunk 199 optimal weight: 0.6980 chunk 316 optimal weight: 0.8980 overall best weight: 0.6992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 580 GLN A 913 GLN A 953 ASN ** A1135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 474 GLN B 953 ASN ** B 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 965 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 99 ASN C 239 GLN C 487 ASN ** C 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 856 ASN C 953 ASN ** C 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1142 GLN ** E 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 378 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 508 ASN H 3 GLN L 39 GLN ** L 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 193 HIS I 189 GLN ** J 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 397 ASN ** J 401 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 437 ASN M 195 HIS ** M 378 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 401 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 437 ASN M 578 ASN ** O 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6325 moved from start: 0.7153 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.068 51201 Z= 0.192 Angle : 0.622 12.549 69696 Z= 0.314 Chirality : 0.046 0.380 7857 Planarity : 0.005 0.058 8961 Dihedral : 6.637 122.243 7779 Min Nonbonded Distance : 1.651 Molprobity Statistics. All-atom Clashscore : 12.59 Ramachandran Plot: Outliers : 0.02 % Allowed : 4.70 % Favored : 95.28 % Rotamer: Outliers : 2.14 % Allowed : 20.70 % Favored : 77.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.60 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.41 (0.10), residues: 6258 helix: -0.93 (0.13), residues: 1590 sheet: -0.70 (0.15), residues: 1218 loop : -2.33 (0.10), residues: 3450 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP G 36 HIS 0.044 0.002 HIS J 378 PHE 0.024 0.002 PHE C 541 TYR 0.020 0.002 TYR N 102 ARG 0.008 0.001 ARG A 78 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12516 Ramachandran restraints generated. 6258 Oldfield, 0 Emsley, 6258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12516 Ramachandran restraints generated. 6258 Oldfield, 0 Emsley, 6258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 469 residues out of total 5457 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 115 poor density : 354 time to evaluate : 4.170 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: A 134 GLN cc_start: 0.6217 (mt0) cc_final: 0.5926 (mt0) REVERT: A 153 MET cc_start: 0.5384 (pmm) cc_final: 0.4890 (pmm) REVERT: A 220 PHE cc_start: 0.7483 (t80) cc_final: 0.7194 (t80) REVERT: A 238 PHE cc_start: 0.6098 (OUTLIER) cc_final: 0.5681 (p90) REVERT: A 439 ASN cc_start: 0.3505 (OUTLIER) cc_final: 0.2897 (t0) REVERT: A 449 TYR cc_start: 0.3039 (OUTLIER) cc_final: 0.2416 (m-80) REVERT: A 572 THR cc_start: 0.6280 (m) cc_final: 0.5630 (p) REVERT: A 592 PHE cc_start: 0.5114 (OUTLIER) cc_final: 0.4782 (m-80) REVERT: A 745 ASP cc_start: 0.6561 (t70) cc_final: 0.5952 (t0) REVERT: A 753 LEU cc_start: 0.7960 (mt) cc_final: 0.7709 (tp) REVERT: A 814 LYS cc_start: 0.6617 (tptt) cc_final: 0.6119 (tppt) REVERT: A 1107 ARG cc_start: 0.8264 (OUTLIER) cc_final: 0.7883 (ptp90) REVERT: A 1138 TYR cc_start: 0.7894 (t80) cc_final: 0.7653 (t80) REVERT: A 1141 LEU cc_start: 0.8225 (mt) cc_final: 0.7934 (tp) REVERT: B 137 ASN cc_start: 0.4431 (m-40) cc_final: 0.4172 (p0) REVERT: B 177 MET cc_start: -0.1132 (mmt) cc_final: -0.1576 (ttt) REVERT: B 326 ILE cc_start: 0.6451 (OUTLIER) cc_final: 0.6194 (tp) REVERT: B 449 TYR cc_start: 0.5199 (p90) cc_final: 0.4801 (m-80) REVERT: B 528 LYS cc_start: 0.7164 (OUTLIER) cc_final: 0.6760 (mmmt) REVERT: B 572 THR cc_start: 0.6667 (m) cc_final: 0.6326 (p) REVERT: B 592 PHE cc_start: 0.4607 (OUTLIER) cc_final: 0.4164 (m-80) REVERT: B 670 ILE cc_start: 0.8389 (OUTLIER) cc_final: 0.8174 (mt) REVERT: B 745 ASP cc_start: 0.7577 (m-30) cc_final: 0.6517 (t0) REVERT: B 1092 GLU cc_start: 0.7871 (pm20) cc_final: 0.7647 (mt-10) REVERT: C 53 ASP cc_start: 0.6923 (m-30) cc_final: 0.6543 (m-30) REVERT: C 239 GLN cc_start: 0.6971 (OUTLIER) cc_final: 0.6731 (tm-30) REVERT: C 276 LEU cc_start: 0.7850 (OUTLIER) cc_final: 0.7488 (tt) REVERT: C 318 PHE cc_start: 0.7416 (t80) cc_final: 0.7134 (t80) REVERT: C 592 PHE cc_start: 0.5643 (OUTLIER) cc_final: 0.5378 (m-80) REVERT: C 661 GLU cc_start: 0.8006 (tp30) cc_final: 0.7535 (pm20) REVERT: C 814 LYS cc_start: 0.6614 (tptt) cc_final: 0.5930 (tppt) REVERT: C 1017 GLU cc_start: 0.7758 (tt0) cc_final: 0.7263 (tm-30) REVERT: C 1127 ASP cc_start: 0.7833 (m-30) cc_final: 0.7382 (p0) REVERT: C 1138 TYR cc_start: 0.7540 (t80) cc_final: 0.7127 (t80) REVERT: C 1141 LEU cc_start: 0.8314 (mt) cc_final: 0.7883 (tp) REVERT: E 26 LYS cc_start: 0.3233 (tptt) cc_final: 0.2683 (mmtt) REVERT: E 27 THR cc_start: 0.0602 (p) cc_final: 0.0263 (p) REVERT: H 59 ASN cc_start: 0.4586 (t0) cc_final: 0.3953 (p0) REVERT: I 189 GLN cc_start: 0.0284 (OUTLIER) cc_final: -0.0155 (tp-100) REVERT: J 75 GLU cc_start: 0.1791 (pt0) cc_final: 0.1054 (tm-30) REVERT: J 134 ASN cc_start: 0.1295 (OUTLIER) cc_final: 0.0973 (t0) REVERT: J 329 GLU cc_start: 0.4255 (OUTLIER) cc_final: 0.4040 (pp20) REVERT: J 357 ARG cc_start: 0.1846 (mtt180) cc_final: 0.1184 (ptt-90) REVERT: J 360 MET cc_start: 0.2902 (mtp) cc_final: 0.1173 (mmm) REVERT: J 401 HIS cc_start: 0.0903 (m170) cc_final: 0.0508 (t-170) REVERT: J 546 ASN cc_start: 0.2888 (m-40) cc_final: 0.2067 (p0) REVERT: M 94 LYS cc_start: 0.0676 (pptt) cc_final: 0.0269 (tppt) REVERT: M 241 HIS cc_start: 0.1829 (t-90) cc_final: 0.1505 (t70) REVERT: M 332 MET cc_start: -0.2069 (ttm) cc_final: -0.2338 (ttm) REVERT: M 400 PHE cc_start: 0.0726 (m-80) cc_final: -0.0431 (t80) REVERT: M 437 ASN cc_start: -0.4752 (OUTLIER) cc_final: -0.5004 (p0) REVERT: M 482 ARG cc_start: 0.4686 (mtt180) cc_final: 0.4386 (ttm-80) REVERT: N 48 MET cc_start: 0.0915 (ptp) cc_final: 0.0638 (ptp) REVERT: O 64 PHE cc_start: -0.0126 (m-80) cc_final: -0.0433 (m-10) outliers start: 115 outliers final: 67 residues processed: 445 average time/residue: 0.4664 time to fit residues: 355.5812 Evaluate side-chains 394 residues out of total 5457 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 83 poor density : 311 time to evaluate : 4.119 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 198 ASP Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 439 ASN Chi-restraints excluded: chain A residue 449 TYR Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 592 PHE Chi-restraints excluded: chain A residue 660 TYR Chi-restraints excluded: chain A residue 823 PHE Chi-restraints excluded: chain A residue 900 MET Chi-restraints excluded: chain A residue 1061 VAL Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain A residue 1107 ARG Chi-restraints excluded: chain B residue 45 SER Chi-restraints excluded: chain B residue 135 PHE Chi-restraints excluded: chain B residue 198 ASP Chi-restraints excluded: chain B residue 307 THR Chi-restraints excluded: chain B residue 326 ILE Chi-restraints excluded: chain B residue 341 VAL Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 528 LYS Chi-restraints excluded: chain B residue 592 PHE Chi-restraints excluded: chain B residue 598 ILE Chi-restraints excluded: chain B residue 603 ASN Chi-restraints excluded: chain B residue 660 TYR Chi-restraints excluded: chain B residue 662 CYS Chi-restraints excluded: chain B residue 670 ILE Chi-restraints excluded: chain B residue 915 VAL Chi-restraints excluded: chain B residue 929 SER Chi-restraints excluded: chain B residue 996 LEU Chi-restraints excluded: chain B residue 1018 ILE Chi-restraints excluded: chain B residue 1077 THR Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain C residue 198 ASP Chi-restraints excluded: chain C residue 238 PHE Chi-restraints excluded: chain C residue 239 GLN Chi-restraints excluded: chain C residue 276 LEU Chi-restraints excluded: chain C residue 307 THR Chi-restraints excluded: chain C residue 449 TYR Chi-restraints excluded: chain C residue 565 PHE Chi-restraints excluded: chain C residue 590 CYS Chi-restraints excluded: chain C residue 592 PHE Chi-restraints excluded: chain C residue 696 THR Chi-restraints excluded: chain C residue 737 ASP Chi-restraints excluded: chain C residue 821 LEU Chi-restraints excluded: chain C residue 969 ASN Chi-restraints excluded: chain C residue 996 LEU Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain C residue 1117 THR Chi-restraints excluded: chain E residue 88 ILE Chi-restraints excluded: chain E residue 96 GLN Chi-restraints excluded: chain E residue 132 VAL Chi-restraints excluded: chain E residue 150 GLU Chi-restraints excluded: chain E residue 274 PHE Chi-restraints excluded: chain E residue 488 VAL Chi-restraints excluded: chain E residue 504 PHE Chi-restraints excluded: chain E residue 513 ILE Chi-restraints excluded: chain H residue 111 PHE Chi-restraints excluded: chain L residue 22 CYS Chi-restraints excluded: chain L residue 27 SER Chi-restraints excluded: chain L residue 111 LEU Chi-restraints excluded: chain L residue 130 LEU Chi-restraints excluded: chain G residue 5 VAL Chi-restraints excluded: chain G residue 71 THR Chi-restraints excluded: chain G residue 111 PHE Chi-restraints excluded: chain I residue 189 GLN Chi-restraints excluded: chain J residue 132 VAL Chi-restraints excluded: chain J residue 134 ASN Chi-restraints excluded: chain J residue 196 TYR Chi-restraints excluded: chain J residue 329 GLU Chi-restraints excluded: chain J residue 447 VAL Chi-restraints excluded: chain J residue 449 THR Chi-restraints excluded: chain J residue 488 VAL Chi-restraints excluded: chain J residue 504 PHE Chi-restraints excluded: chain J residue 529 LEU Chi-restraints excluded: chain J residue 591 LEU Chi-restraints excluded: chain M residue 50 TYR Chi-restraints excluded: chain M residue 144 LEU Chi-restraints excluded: chain M residue 184 VAL Chi-restraints excluded: chain M residue 437 ASN Chi-restraints excluded: chain M residue 513 ILE Chi-restraints excluded: chain N residue 120 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 624 random chunks: chunk 582 optimal weight: 5.9990 chunk 68 optimal weight: 4.9990 chunk 343 optimal weight: 8.9990 chunk 440 optimal weight: 1.9990 chunk 341 optimal weight: 9.9990 chunk 508 optimal weight: 8.9990 chunk 337 optimal weight: 0.9990 chunk 601 optimal weight: 1.9990 chunk 376 optimal weight: 0.0770 chunk 366 optimal weight: 10.0000 chunk 277 optimal weight: 0.8980 overall best weight: 1.1944 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 580 GLN ** B 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 856 ASN ** C 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1135 ASN ** E 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 378 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 325 GLN J 397 ASN ** J 401 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 305 GLN M 378 HIS M 401 HIS M 437 ASN ** O 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 202 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6337 moved from start: 0.7159 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 51201 Z= 0.199 Angle : 0.577 12.185 69696 Z= 0.288 Chirality : 0.045 0.496 7857 Planarity : 0.004 0.067 8961 Dihedral : 6.069 121.923 7779 Min Nonbonded Distance : 2.017 Molprobity Statistics. All-atom Clashscore : 11.96 Ramachandran Plot: Outliers : 0.02 % Allowed : 5.52 % Favored : 94.47 % Rotamer: Outliers : 2.31 % Allowed : 20.97 % Favored : 76.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.60 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.10 (0.10), residues: 6258 helix: -0.51 (0.13), residues: 1578 sheet: -0.64 (0.14), residues: 1251 loop : -2.18 (0.10), residues: 3429 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP E 163 HIS 0.021 0.001 HIS M 378 PHE 0.022 0.001 PHE B 238 TYR 0.017 0.001 TYR N 102 ARG 0.007 0.000 ARG B 319 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12516 Ramachandran restraints generated. 6258 Oldfield, 0 Emsley, 6258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12516 Ramachandran restraints generated. 6258 Oldfield, 0 Emsley, 6258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 453 residues out of total 5457 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 124 poor density : 329 time to evaluate : 4.263 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: A 134 GLN cc_start: 0.6343 (mt0) cc_final: 0.6057 (mt0) REVERT: A 138 ASP cc_start: 0.4977 (OUTLIER) cc_final: 0.2765 (t0) REVERT: A 153 MET cc_start: 0.5388 (pmm) cc_final: 0.4903 (pmm) REVERT: A 220 PHE cc_start: 0.7520 (t80) cc_final: 0.7270 (t80) REVERT: A 238 PHE cc_start: 0.6111 (OUTLIER) cc_final: 0.5696 (p90) REVERT: A 369 TYR cc_start: 0.5227 (t80) cc_final: 0.3791 (t80) REVERT: A 439 ASN cc_start: 0.3083 (OUTLIER) cc_final: 0.2423 (t0) REVERT: A 449 TYR cc_start: 0.3124 (OUTLIER) cc_final: 0.2487 (m-80) REVERT: A 572 THR cc_start: 0.6198 (m) cc_final: 0.5582 (p) REVERT: A 753 LEU cc_start: 0.7887 (OUTLIER) cc_final: 0.7658 (tp) REVERT: A 814 LYS cc_start: 0.6615 (tptt) cc_final: 0.6116 (tppt) REVERT: A 1107 ARG cc_start: 0.8311 (ptt-90) cc_final: 0.8082 (ptp90) REVERT: A 1119 ASN cc_start: 0.7159 (OUTLIER) cc_final: 0.6754 (p0) REVERT: A 1141 LEU cc_start: 0.8199 (mt) cc_final: 0.7823 (tt) REVERT: B 177 MET cc_start: -0.1057 (mmt) cc_final: -0.1498 (ttt) REVERT: B 449 TYR cc_start: 0.5108 (p90) cc_final: 0.4745 (m-80) REVERT: B 528 LYS cc_start: 0.7127 (OUTLIER) cc_final: 0.6711 (mmmt) REVERT: B 572 THR cc_start: 0.6821 (m) cc_final: 0.6454 (p) REVERT: B 745 ASP cc_start: 0.7540 (m-30) cc_final: 0.6477 (t0) REVERT: B 869 MET cc_start: 0.8475 (mtm) cc_final: 0.7852 (mtm) REVERT: C 53 ASP cc_start: 0.6606 (m-30) cc_final: 0.6212 (m-30) REVERT: C 276 LEU cc_start: 0.7862 (OUTLIER) cc_final: 0.7473 (tt) REVERT: C 318 PHE cc_start: 0.7444 (t80) cc_final: 0.7214 (t80) REVERT: C 661 GLU cc_start: 0.7924 (tp30) cc_final: 0.7349 (pm20) REVERT: C 814 LYS cc_start: 0.6662 (tptt) cc_final: 0.5982 (tppt) REVERT: C 1017 GLU cc_start: 0.7607 (tt0) cc_final: 0.7187 (tm-30) REVERT: C 1127 ASP cc_start: 0.7865 (m-30) cc_final: 0.7488 (p0) REVERT: C 1138 TYR cc_start: 0.7708 (t80) cc_final: 0.7350 (t80) REVERT: C 1141 LEU cc_start: 0.8326 (mt) cc_final: 0.7907 (tp) REVERT: E 26 LYS cc_start: 0.3233 (tptt) cc_final: 0.2688 (mmtt) REVERT: E 27 THR cc_start: 0.0515 (p) cc_final: 0.0203 (p) REVERT: E 444 LEU cc_start: 0.2766 (tp) cc_final: 0.2469 (mt) REVERT: E 480 MET cc_start: -0.1527 (ptt) cc_final: -0.1932 (ptt) REVERT: E 531 GLN cc_start: 0.3902 (OUTLIER) cc_final: 0.2908 (tp40) REVERT: H 59 ASN cc_start: 0.4910 (t0) cc_final: 0.4318 (p0) REVERT: H 81 MET cc_start: -0.0596 (tpp) cc_final: -0.1203 (tpt) REVERT: L 22 CYS cc_start: 0.6004 (t) cc_final: 0.5512 (p) REVERT: J 75 GLU cc_start: 0.1702 (pt0) cc_final: 0.1006 (tm-30) REVERT: J 134 ASN cc_start: 0.0738 (OUTLIER) cc_final: 0.0529 (t0) REVERT: J 270 MET cc_start: 0.0308 (tpp) cc_final: -0.0168 (tpp) REVERT: J 329 GLU cc_start: 0.3825 (OUTLIER) cc_final: 0.3591 (pp20) REVERT: J 356 PHE cc_start: 0.2311 (m-80) cc_final: 0.1770 (m-80) REVERT: J 357 ARG cc_start: 0.1801 (mtt180) cc_final: 0.1094 (ptt-90) REVERT: J 383 MET cc_start: 0.1847 (tmm) cc_final: 0.0903 (mtt) REVERT: J 401 HIS cc_start: 0.1163 (m170) cc_final: 0.0872 (t-170) REVERT: J 546 ASN cc_start: 0.2923 (m-40) cc_final: 0.2162 (p0) REVERT: M 94 LYS cc_start: 0.0842 (pptt) cc_final: 0.0389 (tppt) REVERT: M 134 ASN cc_start: 0.1848 (OUTLIER) cc_final: 0.0973 (t0) REVERT: M 152 MET cc_start: 0.0963 (ttt) cc_final: 0.0572 (ppp) REVERT: M 241 HIS cc_start: 0.1595 (t-90) cc_final: 0.1345 (t70) REVERT: M 332 MET cc_start: -0.2018 (ttm) cc_final: -0.2304 (ttm) REVERT: M 376 MET cc_start: -0.0239 (mmm) cc_final: -0.0526 (tmm) REVERT: M 400 PHE cc_start: 0.0278 (m-80) cc_final: -0.0605 (t80) REVERT: M 482 ARG cc_start: 0.4499 (mtt180) cc_final: 0.4194 (tpp80) outliers start: 124 outliers final: 80 residues processed: 434 average time/residue: 0.4648 time to fit residues: 347.8487 Evaluate side-chains 404 residues out of total 5457 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 92 poor density : 312 time to evaluate : 4.054 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 138 ASP Chi-restraints excluded: chain A residue 198 ASP Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 439 ASN Chi-restraints excluded: chain A residue 449 TYR Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 660 TYR Chi-restraints excluded: chain A residue 751 ASN Chi-restraints excluded: chain A residue 753 LEU Chi-restraints excluded: chain A residue 873 TYR Chi-restraints excluded: chain A residue 900 MET Chi-restraints excluded: chain A residue 915 VAL Chi-restraints excluded: chain A residue 1061 VAL Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain A residue 1119 ASN Chi-restraints excluded: chain B residue 105 ILE Chi-restraints excluded: chain B residue 135 PHE Chi-restraints excluded: chain B residue 198 ASP Chi-restraints excluded: chain B residue 307 THR Chi-restraints excluded: chain B residue 478 THR Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 528 LYS Chi-restraints excluded: chain B residue 598 ILE Chi-restraints excluded: chain B residue 603 ASN Chi-restraints excluded: chain B residue 660 TYR Chi-restraints excluded: chain B residue 662 CYS Chi-restraints excluded: chain B residue 670 ILE Chi-restraints excluded: chain B residue 915 VAL Chi-restraints excluded: chain B residue 916 LEU Chi-restraints excluded: chain B residue 937 SER Chi-restraints excluded: chain B residue 996 LEU Chi-restraints excluded: chain B residue 1001 LEU Chi-restraints excluded: chain B residue 1077 THR Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain C residue 198 ASP Chi-restraints excluded: chain C residue 238 PHE Chi-restraints excluded: chain C residue 276 LEU Chi-restraints excluded: chain C residue 307 THR Chi-restraints excluded: chain C residue 449 TYR Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 565 PHE Chi-restraints excluded: chain C residue 590 CYS Chi-restraints excluded: chain C residue 602 THR Chi-restraints excluded: chain C residue 660 TYR Chi-restraints excluded: chain C residue 662 CYS Chi-restraints excluded: chain C residue 737 ASP Chi-restraints excluded: chain C residue 911 VAL Chi-restraints excluded: chain C residue 915 VAL Chi-restraints excluded: chain C residue 969 ASN Chi-restraints excluded: chain C residue 996 LEU Chi-restraints excluded: chain C residue 1061 VAL Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain C residue 1117 THR Chi-restraints excluded: chain C residue 1135 ASN Chi-restraints excluded: chain E residue 88 ILE Chi-restraints excluded: chain E residue 96 GLN Chi-restraints excluded: chain E residue 132 VAL Chi-restraints excluded: chain E residue 150 GLU Chi-restraints excluded: chain E residue 274 PHE Chi-restraints excluded: chain E residue 281 LEU Chi-restraints excluded: chain E residue 488 VAL Chi-restraints excluded: chain E residue 504 PHE Chi-restraints excluded: chain E residue 513 ILE Chi-restraints excluded: chain E residue 531 GLN Chi-restraints excluded: chain H residue 111 PHE Chi-restraints excluded: chain L residue 27 SER Chi-restraints excluded: chain L residue 111 LEU Chi-restraints excluded: chain L residue 130 LEU Chi-restraints excluded: chain L residue 136 THR Chi-restraints excluded: chain G residue 5 VAL Chi-restraints excluded: chain G residue 71 THR Chi-restraints excluded: chain G residue 111 PHE Chi-restraints excluded: chain J residue 132 VAL Chi-restraints excluded: chain J residue 134 ASN Chi-restraints excluded: chain J residue 329 GLU Chi-restraints excluded: chain J residue 447 VAL Chi-restraints excluded: chain J residue 449 THR Chi-restraints excluded: chain J residue 488 VAL Chi-restraints excluded: chain J residue 529 LEU Chi-restraints excluded: chain J residue 591 LEU Chi-restraints excluded: chain M residue 134 ASN Chi-restraints excluded: chain M residue 144 LEU Chi-restraints excluded: chain M residue 184 VAL Chi-restraints excluded: chain M residue 275 TRP Chi-restraints excluded: chain M residue 283 VAL Chi-restraints excluded: chain M residue 401 HIS Chi-restraints excluded: chain M residue 437 ASN Chi-restraints excluded: chain M residue 447 VAL Chi-restraints excluded: chain M residue 513 ILE Chi-restraints excluded: chain N residue 120 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 624 random chunks: chunk 372 optimal weight: 5.9990 chunk 240 optimal weight: 2.9990 chunk 359 optimal weight: 0.9980 chunk 181 optimal weight: 0.5980 chunk 118 optimal weight: 8.9990 chunk 116 optimal weight: 6.9990 chunk 382 optimal weight: 5.9990 chunk 409 optimal weight: 20.0000 chunk 297 optimal weight: 3.9990 chunk 56 optimal weight: 0.9990 chunk 472 optimal weight: 9.9990 overall best weight: 1.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 787 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 137 ASN B 409 GLN ** B 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 787 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 856 ASN ** C 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1135 ASN ** E 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 378 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 578 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 39 GLN ** L 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 189 GLN ** J 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 265 HIS ** J 325 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 397 ASN ** J 401 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 397 ASN ** M 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6351 moved from start: 0.7299 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 51201 Z= 0.246 Angle : 0.584 12.048 69696 Z= 0.292 Chirality : 0.045 0.371 7857 Planarity : 0.004 0.061 8961 Dihedral : 5.930 120.838 7779 Min Nonbonded Distance : 2.075 Molprobity Statistics. All-atom Clashscore : 12.57 Ramachandran Plot: Outliers : 0.02 % Allowed : 5.42 % Favored : 94.56 % Rotamer: Outliers : 2.47 % Allowed : 21.15 % Favored : 76.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.60 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.98 (0.10), residues: 6258 helix: -0.35 (0.13), residues: 1578 sheet: -0.61 (0.14), residues: 1245 loop : -2.12 (0.10), residues: 3435 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP E 163 HIS 0.041 0.002 HIS M 401 PHE 0.021 0.002 PHE B 238 TYR 0.018 0.001 TYR A1138 ARG 0.005 0.001 ARG A 319 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12516 Ramachandran restraints generated. 6258 Oldfield, 0 Emsley, 6258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12516 Ramachandran restraints generated. 6258 Oldfield, 0 Emsley, 6258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 453 residues out of total 5457 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 133 poor density : 320 time to evaluate : 4.122 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: A 134 GLN cc_start: 0.6359 (mt0) cc_final: 0.6066 (mt0) REVERT: A 138 ASP cc_start: 0.4920 (OUTLIER) cc_final: 0.2367 (t0) REVERT: A 153 MET cc_start: 0.5287 (pmm) cc_final: 0.4847 (pmm) REVERT: A 220 PHE cc_start: 0.7563 (t80) cc_final: 0.7296 (t80) REVERT: A 238 PHE cc_start: 0.6161 (OUTLIER) cc_final: 0.5724 (p90) REVERT: A 369 TYR cc_start: 0.5166 (t80) cc_final: 0.3784 (t80) REVERT: A 439 ASN cc_start: 0.3120 (OUTLIER) cc_final: 0.2531 (t0) REVERT: A 572 THR cc_start: 0.6680 (m) cc_final: 0.6022 (p) REVERT: A 814 LYS cc_start: 0.6656 (tptt) cc_final: 0.6151 (tppt) REVERT: A 1107 ARG cc_start: 0.8364 (OUTLIER) cc_final: 0.7914 (ptp90) REVERT: A 1119 ASN cc_start: 0.7132 (OUTLIER) cc_final: 0.6735 (p0) REVERT: B 177 MET cc_start: -0.1025 (mmt) cc_final: -0.1657 (ttt) REVERT: B 449 TYR cc_start: 0.5214 (p90) cc_final: 0.4806 (m-80) REVERT: B 528 LYS cc_start: 0.7127 (OUTLIER) cc_final: 0.6713 (mmmt) REVERT: B 572 THR cc_start: 0.7214 (m) cc_final: 0.6736 (p) REVERT: B 745 ASP cc_start: 0.7589 (m-30) cc_final: 0.6485 (t0) REVERT: C 53 ASP cc_start: 0.6602 (m-30) cc_final: 0.6230 (m-30) REVERT: C 276 LEU cc_start: 0.7859 (OUTLIER) cc_final: 0.7487 (tt) REVERT: C 318 PHE cc_start: 0.7458 (t80) cc_final: 0.7255 (t80) REVERT: C 661 GLU cc_start: 0.8011 (tp30) cc_final: 0.7550 (pm20) REVERT: C 814 LYS cc_start: 0.6724 (tptt) cc_final: 0.6081 (tppt) REVERT: C 1017 GLU cc_start: 0.7651 (tt0) cc_final: 0.7193 (tm-30) REVERT: C 1127 ASP cc_start: 0.7925 (m-30) cc_final: 0.7612 (p0) REVERT: C 1138 TYR cc_start: 0.7884 (t80) cc_final: 0.7554 (t80) REVERT: C 1141 LEU cc_start: 0.8350 (mt) cc_final: 0.7871 (tp) REVERT: E 26 LYS cc_start: 0.3149 (tptt) cc_final: 0.2579 (mmtt) REVERT: E 27 THR cc_start: 0.0550 (p) cc_final: 0.0249 (p) REVERT: E 444 LEU cc_start: 0.2709 (tp) cc_final: 0.2408 (mt) REVERT: E 531 GLN cc_start: 0.4044 (OUTLIER) cc_final: 0.3085 (tp40) REVERT: H 59 ASN cc_start: 0.4904 (t0) cc_final: 0.4314 (p0) REVERT: H 70 ILE cc_start: 0.1227 (mp) cc_final: 0.0880 (mt) REVERT: H 81 MET cc_start: -0.0812 (tpp) cc_final: -0.1399 (tpt) REVERT: L 22 CYS cc_start: 0.6250 (t) cc_final: 0.6031 (p) REVERT: J 75 GLU cc_start: 0.1696 (pt0) cc_final: 0.1001 (tm-30) REVERT: J 134 ASN cc_start: 0.0727 (OUTLIER) cc_final: 0.0480 (t0) REVERT: J 270 MET cc_start: 0.0566 (tpp) cc_final: 0.0297 (tpp) REVERT: J 357 ARG cc_start: 0.1796 (mtt180) cc_final: 0.1092 (ptt-90) REVERT: J 449 THR cc_start: 0.0536 (OUTLIER) cc_final: 0.0232 (t) REVERT: J 546 ASN cc_start: 0.3287 (m-40) cc_final: 0.2461 (p0) REVERT: M 134 ASN cc_start: 0.1959 (OUTLIER) cc_final: 0.1064 (t0) REVERT: M 163 TRP cc_start: -0.1162 (t60) cc_final: -0.1522 (t60) REVERT: M 241 HIS cc_start: 0.1013 (t-90) cc_final: 0.0676 (t70) REVERT: M 332 MET cc_start: -0.1756 (ttm) cc_final: -0.2096 (ttm) REVERT: M 360 MET cc_start: 0.2856 (mtp) cc_final: 0.2484 (mmm) REVERT: M 437 ASN cc_start: -0.4093 (OUTLIER) cc_final: -0.4332 (p0) REVERT: M 482 ARG cc_start: 0.4638 (mtt180) cc_final: 0.4338 (ttm-80) outliers start: 133 outliers final: 96 residues processed: 432 average time/residue: 0.4920 time to fit residues: 368.8741 Evaluate side-chains 417 residues out of total 5457 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 108 poor density : 309 time to evaluate : 4.136 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 138 ASP Chi-restraints excluded: chain A residue 198 ASP Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 439 ASN Chi-restraints excluded: chain A residue 449 TYR Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 660 TYR Chi-restraints excluded: chain A residue 662 CYS Chi-restraints excluded: chain A residue 751 ASN Chi-restraints excluded: chain A residue 856 ASN Chi-restraints excluded: chain A residue 873 TYR Chi-restraints excluded: chain A residue 887 THR Chi-restraints excluded: chain A residue 900 MET Chi-restraints excluded: chain A residue 915 VAL Chi-restraints excluded: chain A residue 1004 LEU Chi-restraints excluded: chain A residue 1061 VAL Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain A residue 1107 ARG Chi-restraints excluded: chain A residue 1119 ASN Chi-restraints excluded: chain B residue 45 SER Chi-restraints excluded: chain B residue 105 ILE Chi-restraints excluded: chain B residue 135 PHE Chi-restraints excluded: chain B residue 198 ASP Chi-restraints excluded: chain B residue 259 THR Chi-restraints excluded: chain B residue 307 THR Chi-restraints excluded: chain B residue 379 CYS Chi-restraints excluded: chain B residue 478 THR Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 528 LYS Chi-restraints excluded: chain B residue 598 ILE Chi-restraints excluded: chain B residue 603 ASN Chi-restraints excluded: chain B residue 660 TYR Chi-restraints excluded: chain B residue 662 CYS Chi-restraints excluded: chain B residue 670 ILE Chi-restraints excluded: chain B residue 915 VAL Chi-restraints excluded: chain B residue 916 LEU Chi-restraints excluded: chain B residue 937 SER Chi-restraints excluded: chain B residue 969 ASN Chi-restraints excluded: chain B residue 996 LEU Chi-restraints excluded: chain B residue 1001 LEU Chi-restraints excluded: chain B residue 1077 THR Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain B residue 1117 THR Chi-restraints excluded: chain C residue 105 ILE Chi-restraints excluded: chain C residue 198 ASP Chi-restraints excluded: chain C residue 238 PHE Chi-restraints excluded: chain C residue 276 LEU Chi-restraints excluded: chain C residue 307 THR Chi-restraints excluded: chain C residue 449 TYR Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 565 PHE Chi-restraints excluded: chain C residue 590 CYS Chi-restraints excluded: chain C residue 602 THR Chi-restraints excluded: chain C residue 660 TYR Chi-restraints excluded: chain C residue 662 CYS Chi-restraints excluded: chain C residue 737 ASP Chi-restraints excluded: chain C residue 821 LEU Chi-restraints excluded: chain C residue 911 VAL Chi-restraints excluded: chain C residue 915 VAL Chi-restraints excluded: chain C residue 969 ASN Chi-restraints excluded: chain C residue 980 ILE Chi-restraints excluded: chain C residue 996 LEU Chi-restraints excluded: chain C residue 1004 LEU Chi-restraints excluded: chain C residue 1061 VAL Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain C residue 1117 THR Chi-restraints excluded: chain E residue 88 ILE Chi-restraints excluded: chain E residue 96 GLN Chi-restraints excluded: chain E residue 132 VAL Chi-restraints excluded: chain E residue 150 GLU Chi-restraints excluded: chain E residue 274 PHE Chi-restraints excluded: chain E residue 281 LEU Chi-restraints excluded: chain E residue 488 VAL Chi-restraints excluded: chain E residue 499 ASP Chi-restraints excluded: chain E residue 504 PHE Chi-restraints excluded: chain E residue 531 GLN Chi-restraints excluded: chain E residue 606 TRP Chi-restraints excluded: chain H residue 111 PHE Chi-restraints excluded: chain H residue 212 LYS Chi-restraints excluded: chain L residue 27 SER Chi-restraints excluded: chain L residue 111 LEU Chi-restraints excluded: chain L residue 130 LEU Chi-restraints excluded: chain L residue 136 THR Chi-restraints excluded: chain G residue 5 VAL Chi-restraints excluded: chain G residue 71 THR Chi-restraints excluded: chain G residue 111 PHE Chi-restraints excluded: chain I residue 189 GLN Chi-restraints excluded: chain J residue 69 TRP Chi-restraints excluded: chain J residue 132 VAL Chi-restraints excluded: chain J residue 134 ASN Chi-restraints excluded: chain J residue 196 TYR Chi-restraints excluded: chain J residue 329 GLU Chi-restraints excluded: chain J residue 447 VAL Chi-restraints excluded: chain J residue 449 THR Chi-restraints excluded: chain J residue 529 LEU Chi-restraints excluded: chain J residue 591 LEU Chi-restraints excluded: chain M residue 50 TYR Chi-restraints excluded: chain M residue 134 ASN Chi-restraints excluded: chain M residue 184 VAL Chi-restraints excluded: chain M residue 275 TRP Chi-restraints excluded: chain M residue 283 VAL Chi-restraints excluded: chain M residue 437 ASN Chi-restraints excluded: chain M residue 447 VAL Chi-restraints excluded: chain M residue 513 ILE Chi-restraints excluded: chain N residue 37 VAL Chi-restraints excluded: chain N residue 120 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 624 random chunks: chunk 547 optimal weight: 1.9990 chunk 576 optimal weight: 0.0060 chunk 525 optimal weight: 0.9980 chunk 560 optimal weight: 3.9990 chunk 337 optimal weight: 4.9990 chunk 244 optimal weight: 9.9990 chunk 440 optimal weight: 30.0000 chunk 171 optimal weight: 0.9990 chunk 506 optimal weight: 3.9990 chunk 530 optimal weight: 20.0000 chunk 558 optimal weight: 7.9990 overall best weight: 1.6002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 787 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 137 ASN ** B 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 239 GLN C 856 ASN ** C 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 378 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 189 GLN ** J 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 325 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 378 HIS J 397 ASN M 397 ASN ** M 401 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 437 ASN ** O 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6343 moved from start: 0.7382 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.073 51201 Z= 0.217 Angle : 0.570 12.428 69696 Z= 0.283 Chirality : 0.045 0.349 7857 Planarity : 0.004 0.066 8961 Dihedral : 5.750 120.015 7779 Min Nonbonded Distance : 2.109 Molprobity Statistics. All-atom Clashscore : 12.15 Ramachandran Plot: Outliers : 0.02 % Allowed : 5.47 % Favored : 94.51 % Rotamer: Outliers : 2.40 % Allowed : 21.32 % Favored : 76.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.60 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.85 (0.10), residues: 6258 helix: -0.20 (0.13), residues: 1581 sheet: -0.55 (0.15), residues: 1206 loop : -2.03 (0.10), residues: 3471 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP E 163 HIS 0.017 0.001 HIS J 378 PHE 0.020 0.001 PHE E 327 TYR 0.016 0.001 TYR A1138 ARG 0.005 0.001 ARG A 319 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12516 Ramachandran restraints generated. 6258 Oldfield, 0 Emsley, 6258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12516 Ramachandran restraints generated. 6258 Oldfield, 0 Emsley, 6258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 447 residues out of total 5457 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 129 poor density : 318 time to evaluate : 4.149 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: A 134 GLN cc_start: 0.6412 (mt0) cc_final: 0.6012 (mt0) REVERT: A 138 ASP cc_start: 0.4762 (OUTLIER) cc_final: 0.2492 (t0) REVERT: A 220 PHE cc_start: 0.7234 (t80) cc_final: 0.7031 (t80) REVERT: A 238 PHE cc_start: 0.6187 (OUTLIER) cc_final: 0.5726 (p90) REVERT: A 369 TYR cc_start: 0.5353 (t80) cc_final: 0.4022 (t80) REVERT: A 439 ASN cc_start: 0.3223 (OUTLIER) cc_final: 0.2681 (t0) REVERT: A 814 LYS cc_start: 0.6640 (tptt) cc_final: 0.6138 (tppt) REVERT: A 969 ASN cc_start: 0.9104 (m110) cc_final: 0.8408 (m-40) REVERT: A 1107 ARG cc_start: 0.8367 (OUTLIER) cc_final: 0.7713 (ptp90) REVERT: A 1119 ASN cc_start: 0.7134 (OUTLIER) cc_final: 0.6750 (p0) REVERT: B 177 MET cc_start: -0.1023 (mmt) cc_final: -0.1698 (ttt) REVERT: B 377 PHE cc_start: 0.5938 (p90) cc_final: 0.5712 (p90) REVERT: B 572 THR cc_start: 0.7358 (m) cc_final: 0.6872 (p) REVERT: B 745 ASP cc_start: 0.7524 (m-30) cc_final: 0.6388 (t0) REVERT: C 53 ASP cc_start: 0.6526 (m-30) cc_final: 0.6129 (m-30) REVERT: C 239 GLN cc_start: 0.6621 (OUTLIER) cc_final: 0.6072 (tm-30) REVERT: C 276 LEU cc_start: 0.7850 (OUTLIER) cc_final: 0.7483 (tt) REVERT: C 326 ILE cc_start: 0.6063 (OUTLIER) cc_final: 0.5818 (tp) REVERT: C 661 GLU cc_start: 0.7970 (tp30) cc_final: 0.7566 (pm20) REVERT: C 814 LYS cc_start: 0.6711 (tptt) cc_final: 0.6077 (tppt) REVERT: C 1017 GLU cc_start: 0.7644 (tt0) cc_final: 0.7188 (tm-30) REVERT: C 1127 ASP cc_start: 0.7948 (m-30) cc_final: 0.7372 (p0) REVERT: C 1138 TYR cc_start: 0.7697 (t80) cc_final: 0.7399 (t80) REVERT: E 26 LYS cc_start: 0.3192 (tptt) cc_final: 0.2649 (mmtt) REVERT: E 27 THR cc_start: 0.0522 (p) cc_final: 0.0216 (p) REVERT: E 531 GLN cc_start: 0.4030 (OUTLIER) cc_final: 0.3065 (tp40) REVERT: H 59 ASN cc_start: 0.4922 (t0) cc_final: 0.4366 (p0) REVERT: H 70 ILE cc_start: 0.1184 (mp) cc_final: 0.0833 (mt) REVERT: H 81 MET cc_start: -0.0813 (tpp) cc_final: -0.1367 (tpt) REVERT: I 189 GLN cc_start: 0.1294 (OUTLIER) cc_final: 0.0600 (tp-100) REVERT: J 75 GLU cc_start: 0.1810 (pt0) cc_final: 0.1006 (tm-30) REVERT: J 134 ASN cc_start: 0.0738 (OUTLIER) cc_final: 0.0513 (t0) REVERT: J 270 MET cc_start: 0.0412 (tpp) cc_final: -0.0055 (tpp) REVERT: J 449 THR cc_start: 0.0559 (OUTLIER) cc_final: 0.0246 (t) REVERT: J 546 ASN cc_start: 0.3056 (m-40) cc_final: 0.2267 (p0) REVERT: M 134 ASN cc_start: 0.1961 (OUTLIER) cc_final: 0.1072 (t0) REVERT: M 332 MET cc_start: -0.1670 (ttm) cc_final: -0.2059 (ttm) REVERT: M 400 PHE cc_start: 0.0658 (m-80) cc_final: -0.0198 (t80) REVERT: M 478 TRP cc_start: -0.0278 (m100) cc_final: -0.0648 (m100) REVERT: M 482 ARG cc_start: 0.4803 (mtt180) cc_final: 0.4495 (tpp-160) outliers start: 129 outliers final: 95 residues processed: 427 average time/residue: 0.4550 time to fit residues: 336.0901 Evaluate side-chains 410 residues out of total 5457 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 108 poor density : 302 time to evaluate : 4.110 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 138 ASP Chi-restraints excluded: chain A residue 198 ASP Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 439 ASN Chi-restraints excluded: chain A residue 449 TYR Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 595 VAL Chi-restraints excluded: chain A residue 660 TYR Chi-restraints excluded: chain A residue 662 CYS Chi-restraints excluded: chain A residue 693 ILE Chi-restraints excluded: chain A residue 778 THR Chi-restraints excluded: chain A residue 856 ASN Chi-restraints excluded: chain A residue 873 TYR Chi-restraints excluded: chain A residue 900 MET Chi-restraints excluded: chain A residue 915 VAL Chi-restraints excluded: chain A residue 1061 VAL Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain A residue 1107 ARG Chi-restraints excluded: chain A residue 1119 ASN Chi-restraints excluded: chain B residue 45 SER Chi-restraints excluded: chain B residue 105 ILE Chi-restraints excluded: chain B residue 198 ASP Chi-restraints excluded: chain B residue 259 THR Chi-restraints excluded: chain B residue 307 THR Chi-restraints excluded: chain B residue 379 CYS Chi-restraints excluded: chain B residue 478 THR Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 598 ILE Chi-restraints excluded: chain B residue 603 ASN Chi-restraints excluded: chain B residue 660 TYR Chi-restraints excluded: chain B residue 662 CYS Chi-restraints excluded: chain B residue 670 ILE Chi-restraints excluded: chain B residue 915 VAL Chi-restraints excluded: chain B residue 916 LEU Chi-restraints excluded: chain B residue 931 ILE Chi-restraints excluded: chain B residue 937 SER Chi-restraints excluded: chain B residue 969 ASN Chi-restraints excluded: chain B residue 996 LEU Chi-restraints excluded: chain B residue 1001 LEU Chi-restraints excluded: chain B residue 1077 THR Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain B residue 1117 THR Chi-restraints excluded: chain C residue 198 ASP Chi-restraints excluded: chain C residue 238 PHE Chi-restraints excluded: chain C residue 239 GLN Chi-restraints excluded: chain C residue 276 LEU Chi-restraints excluded: chain C residue 307 THR Chi-restraints excluded: chain C residue 326 ILE Chi-restraints excluded: chain C residue 449 TYR Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 565 PHE Chi-restraints excluded: chain C residue 590 CYS Chi-restraints excluded: chain C residue 602 THR Chi-restraints excluded: chain C residue 660 TYR Chi-restraints excluded: chain C residue 662 CYS Chi-restraints excluded: chain C residue 737 ASP Chi-restraints excluded: chain C residue 911 VAL Chi-restraints excluded: chain C residue 915 VAL Chi-restraints excluded: chain C residue 969 ASN Chi-restraints excluded: chain C residue 996 LEU Chi-restraints excluded: chain C residue 1004 LEU Chi-restraints excluded: chain C residue 1061 VAL Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain C residue 1129 VAL Chi-restraints excluded: chain E residue 88 ILE Chi-restraints excluded: chain E residue 96 GLN Chi-restraints excluded: chain E residue 132 VAL Chi-restraints excluded: chain E residue 150 GLU Chi-restraints excluded: chain E residue 274 PHE Chi-restraints excluded: chain E residue 281 LEU Chi-restraints excluded: chain E residue 488 VAL Chi-restraints excluded: chain E residue 499 ASP Chi-restraints excluded: chain E residue 504 PHE Chi-restraints excluded: chain E residue 531 GLN Chi-restraints excluded: chain E residue 568 LEU Chi-restraints excluded: chain E residue 606 TRP Chi-restraints excluded: chain H residue 111 PHE Chi-restraints excluded: chain H residue 212 LYS Chi-restraints excluded: chain L residue 27 SER Chi-restraints excluded: chain L residue 111 LEU Chi-restraints excluded: chain L residue 130 LEU Chi-restraints excluded: chain L residue 136 THR Chi-restraints excluded: chain G residue 5 VAL Chi-restraints excluded: chain G residue 71 THR Chi-restraints excluded: chain G residue 111 PHE Chi-restraints excluded: chain I residue 189 GLN Chi-restraints excluded: chain J residue 69 TRP Chi-restraints excluded: chain J residue 107 VAL Chi-restraints excluded: chain J residue 132 VAL Chi-restraints excluded: chain J residue 134 ASN Chi-restraints excluded: chain J residue 196 TYR Chi-restraints excluded: chain J residue 329 GLU Chi-restraints excluded: chain J residue 391 LEU Chi-restraints excluded: chain J residue 447 VAL Chi-restraints excluded: chain J residue 449 THR Chi-restraints excluded: chain J residue 591 LEU Chi-restraints excluded: chain M residue 38 ASP Chi-restraints excluded: chain M residue 50 TYR Chi-restraints excluded: chain M residue 134 ASN Chi-restraints excluded: chain M residue 275 TRP Chi-restraints excluded: chain M residue 283 VAL Chi-restraints excluded: chain M residue 375 GLU Chi-restraints excluded: chain M residue 447 VAL Chi-restraints excluded: chain M residue 513 ILE Chi-restraints excluded: chain N residue 37 VAL Chi-restraints excluded: chain N residue 120 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 624 random chunks: chunk 368 optimal weight: 0.8980 chunk 592 optimal weight: 8.9990 chunk 361 optimal weight: 0.7980 chunk 281 optimal weight: 4.9990 chunk 411 optimal weight: 0.5980 chunk 621 optimal weight: 10.0000 chunk 572 optimal weight: 4.9990 chunk 495 optimal weight: 0.9980 chunk 51 optimal weight: 2.9990 chunk 382 optimal weight: 9.9990 chunk 303 optimal weight: 3.9990 overall best weight: 1.2582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 787 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 856 ASN ** B 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 965 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 239 GLN C 856 ASN ** C 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 378 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 189 GLN ** J 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 325 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 397 ASN M 397 ASN ** M 401 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6335 moved from start: 0.7418 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 51201 Z= 0.194 Angle : 0.560 12.769 69696 Z= 0.278 Chirality : 0.044 0.350 7857 Planarity : 0.004 0.065 8961 Dihedral : 5.619 119.627 7779 Min Nonbonded Distance : 2.121 Molprobity Statistics. All-atom Clashscore : 11.58 Ramachandran Plot: Outliers : 0.02 % Allowed : 4.97 % Favored : 95.01 % Rotamer: Outliers : 2.25 % Allowed : 21.47 % Favored : 76.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.60 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.73 (0.10), residues: 6258 helix: -0.07 (0.13), residues: 1581 sheet: -0.49 (0.15), residues: 1206 loop : -1.97 (0.10), residues: 3471 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP E 163 HIS 0.011 0.001 HIS J 239 PHE 0.023 0.001 PHE C 238 TYR 0.016 0.001 TYR A1138 ARG 0.005 0.000 ARG M 115 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12516 Ramachandran restraints generated. 6258 Oldfield, 0 Emsley, 6258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12516 Ramachandran restraints generated. 6258 Oldfield, 0 Emsley, 6258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 430 residues out of total 5457 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 121 poor density : 309 time to evaluate : 4.218 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: A 134 GLN cc_start: 0.6567 (mt0) cc_final: 0.6238 (mt0) REVERT: A 138 ASP cc_start: 0.4925 (OUTLIER) cc_final: 0.3037 (t0) REVERT: A 238 PHE cc_start: 0.6158 (OUTLIER) cc_final: 0.5683 (p90) REVERT: A 369 TYR cc_start: 0.5527 (t80) cc_final: 0.4173 (t80) REVERT: A 439 ASN cc_start: 0.3084 (OUTLIER) cc_final: 0.2562 (t0) REVERT: A 740 MET cc_start: 0.7508 (mmm) cc_final: 0.7148 (mmm) REVERT: A 814 LYS cc_start: 0.6634 (tptt) cc_final: 0.6134 (tppt) REVERT: A 969 ASN cc_start: 0.9111 (m110) cc_final: 0.8403 (m-40) REVERT: A 1107 ARG cc_start: 0.8275 (OUTLIER) cc_final: 0.7708 (ptp90) REVERT: A 1119 ASN cc_start: 0.7117 (OUTLIER) cc_final: 0.6749 (p0) REVERT: B 51 THR cc_start: 0.8171 (t) cc_final: 0.7963 (t) REVERT: B 177 MET cc_start: -0.1020 (mmt) cc_final: -0.1711 (ttt) REVERT: B 449 TYR cc_start: 0.5082 (p90) cc_final: 0.4693 (m-80) REVERT: B 572 THR cc_start: 0.7435 (m) cc_final: 0.6950 (p) REVERT: B 745 ASP cc_start: 0.7477 (m-30) cc_final: 0.6391 (t0) REVERT: B 1117 THR cc_start: 0.8237 (OUTLIER) cc_final: 0.8011 (p) REVERT: C 53 ASP cc_start: 0.6525 (m-30) cc_final: 0.6153 (m-30) REVERT: C 138 ASP cc_start: 0.4510 (OUTLIER) cc_final: 0.2566 (t70) REVERT: C 239 GLN cc_start: 0.6857 (OUTLIER) cc_final: 0.6346 (tm-30) REVERT: C 276 LEU cc_start: 0.7841 (OUTLIER) cc_final: 0.7473 (tt) REVERT: C 326 ILE cc_start: 0.5831 (OUTLIER) cc_final: 0.5571 (tp) REVERT: C 661 GLU cc_start: 0.7944 (tp30) cc_final: 0.7553 (pm20) REVERT: C 814 LYS cc_start: 0.6698 (tptt) cc_final: 0.6089 (tppt) REVERT: C 1017 GLU cc_start: 0.7643 (tt0) cc_final: 0.7192 (tm-30) REVERT: C 1138 TYR cc_start: 0.7705 (t80) cc_final: 0.7411 (t80) REVERT: E 26 LYS cc_start: 0.3189 (tptt) cc_final: 0.2650 (mmtt) REVERT: E 27 THR cc_start: 0.0558 (p) cc_final: 0.0255 (p) REVERT: E 323 MET cc_start: 0.1875 (tpt) cc_final: 0.1641 (tpt) REVERT: E 531 GLN cc_start: 0.4011 (OUTLIER) cc_final: 0.3041 (tp40) REVERT: H 59 ASN cc_start: 0.4745 (t0) cc_final: 0.4208 (p0) REVERT: H 70 ILE cc_start: 0.1174 (mp) cc_final: 0.0815 (mt) REVERT: H 81 MET cc_start: -0.0813 (tpp) cc_final: -0.1373 (tpt) REVERT: I 189 GLN cc_start: 0.0887 (OUTLIER) cc_final: 0.0310 (tp-100) REVERT: J 75 GLU cc_start: 0.1793 (pt0) cc_final: 0.0994 (tm-30) REVERT: J 134 ASN cc_start: 0.0719 (OUTLIER) cc_final: 0.0493 (t0) REVERT: J 270 MET cc_start: 0.0572 (tpp) cc_final: 0.0131 (tpp) REVERT: J 374 HIS cc_start: -0.1094 (OUTLIER) cc_final: -0.1418 (t-90) REVERT: J 449 THR cc_start: 0.0251 (OUTLIER) cc_final: -0.0093 (t) REVERT: J 546 ASN cc_start: 0.3020 (m-40) cc_final: 0.2180 (p0) REVERT: M 134 ASN cc_start: 0.2552 (OUTLIER) cc_final: 0.1456 (t0) REVERT: M 152 MET cc_start: 0.0183 (ppp) cc_final: -0.0188 (ppp) REVERT: M 241 HIS cc_start: 0.0785 (t70) cc_final: 0.0458 (t70) REVERT: M 332 MET cc_start: -0.1645 (ttm) cc_final: -0.2059 (ttm) REVERT: M 400 PHE cc_start: 0.0842 (m-80) cc_final: -0.0054 (t80) REVERT: M 478 TRP cc_start: -0.0240 (m100) cc_final: -0.0592 (m100) REVERT: M 482 ARG cc_start: 0.4582 (mtt180) cc_final: 0.4262 (tpp-160) outliers start: 121 outliers final: 94 residues processed: 410 average time/residue: 0.4536 time to fit residues: 322.3719 Evaluate side-chains 410 residues out of total 5457 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 110 poor density : 300 time to evaluate : 4.077 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 138 ASP Chi-restraints excluded: chain A residue 198 ASP Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 439 ASN Chi-restraints excluded: chain A residue 449 TYR Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 660 TYR Chi-restraints excluded: chain A residue 662 CYS Chi-restraints excluded: chain A residue 753 LEU Chi-restraints excluded: chain A residue 778 THR Chi-restraints excluded: chain A residue 856 ASN Chi-restraints excluded: chain A residue 873 TYR Chi-restraints excluded: chain A residue 887 THR Chi-restraints excluded: chain A residue 900 MET Chi-restraints excluded: chain A residue 915 VAL Chi-restraints excluded: chain A residue 1061 VAL Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain A residue 1107 ARG Chi-restraints excluded: chain A residue 1119 ASN Chi-restraints excluded: chain B residue 45 SER Chi-restraints excluded: chain B residue 105 ILE Chi-restraints excluded: chain B residue 198 ASP Chi-restraints excluded: chain B residue 259 THR Chi-restraints excluded: chain B residue 307 THR Chi-restraints excluded: chain B residue 379 CYS Chi-restraints excluded: chain B residue 478 THR Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 598 ILE Chi-restraints excluded: chain B residue 603 ASN Chi-restraints excluded: chain B residue 660 TYR Chi-restraints excluded: chain B residue 662 CYS Chi-restraints excluded: chain B residue 670 ILE Chi-restraints excluded: chain B residue 747 THR Chi-restraints excluded: chain B residue 915 VAL Chi-restraints excluded: chain B residue 916 LEU Chi-restraints excluded: chain B residue 937 SER Chi-restraints excluded: chain B residue 969 ASN Chi-restraints excluded: chain B residue 996 LEU Chi-restraints excluded: chain B residue 1001 LEU Chi-restraints excluded: chain B residue 1077 THR Chi-restraints excluded: chain B residue 1117 THR Chi-restraints excluded: chain C residue 138 ASP Chi-restraints excluded: chain C residue 198 ASP Chi-restraints excluded: chain C residue 238 PHE Chi-restraints excluded: chain C residue 239 GLN Chi-restraints excluded: chain C residue 276 LEU Chi-restraints excluded: chain C residue 307 THR Chi-restraints excluded: chain C residue 326 ILE Chi-restraints excluded: chain C residue 449 TYR Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 565 PHE Chi-restraints excluded: chain C residue 590 CYS Chi-restraints excluded: chain C residue 602 THR Chi-restraints excluded: chain C residue 660 TYR Chi-restraints excluded: chain C residue 662 CYS Chi-restraints excluded: chain C residue 696 THR Chi-restraints excluded: chain C residue 737 ASP Chi-restraints excluded: chain C residue 751 ASN Chi-restraints excluded: chain C residue 915 VAL Chi-restraints excluded: chain C residue 969 ASN Chi-restraints excluded: chain C residue 980 ILE Chi-restraints excluded: chain C residue 996 LEU Chi-restraints excluded: chain C residue 1004 LEU Chi-restraints excluded: chain C residue 1061 VAL Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain C residue 1117 THR Chi-restraints excluded: chain C residue 1129 VAL Chi-restraints excluded: chain E residue 88 ILE Chi-restraints excluded: chain E residue 96 GLN Chi-restraints excluded: chain E residue 132 VAL Chi-restraints excluded: chain E residue 150 GLU Chi-restraints excluded: chain E residue 274 PHE Chi-restraints excluded: chain E residue 281 LEU Chi-restraints excluded: chain E residue 488 VAL Chi-restraints excluded: chain E residue 499 ASP Chi-restraints excluded: chain E residue 504 PHE Chi-restraints excluded: chain E residue 516 TYR Chi-restraints excluded: chain E residue 531 GLN Chi-restraints excluded: chain E residue 568 LEU Chi-restraints excluded: chain E residue 606 TRP Chi-restraints excluded: chain H residue 111 PHE Chi-restraints excluded: chain H residue 212 LYS Chi-restraints excluded: chain L residue 27 SER Chi-restraints excluded: chain L residue 111 LEU Chi-restraints excluded: chain L residue 130 LEU Chi-restraints excluded: chain L residue 136 THR Chi-restraints excluded: chain G residue 71 THR Chi-restraints excluded: chain G residue 111 PHE Chi-restraints excluded: chain I residue 189 GLN Chi-restraints excluded: chain J residue 69 TRP Chi-restraints excluded: chain J residue 132 VAL Chi-restraints excluded: chain J residue 134 ASN Chi-restraints excluded: chain J residue 196 TYR Chi-restraints excluded: chain J residue 271 TRP Chi-restraints excluded: chain J residue 329 GLU Chi-restraints excluded: chain J residue 374 HIS Chi-restraints excluded: chain J residue 391 LEU Chi-restraints excluded: chain J residue 447 VAL Chi-restraints excluded: chain J residue 449 THR Chi-restraints excluded: chain J residue 591 LEU Chi-restraints excluded: chain M residue 38 ASP Chi-restraints excluded: chain M residue 50 TYR Chi-restraints excluded: chain M residue 134 ASN Chi-restraints excluded: chain M residue 275 TRP Chi-restraints excluded: chain M residue 283 VAL Chi-restraints excluded: chain M residue 447 VAL Chi-restraints excluded: chain M residue 513 ILE Chi-restraints excluded: chain N residue 120 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 624 random chunks: chunk 393 optimal weight: 0.9990 chunk 527 optimal weight: 10.0000 chunk 151 optimal weight: 20.0000 chunk 456 optimal weight: 6.9990 chunk 73 optimal weight: 3.9990 chunk 137 optimal weight: 9.9990 chunk 495 optimal weight: 1.9990 chunk 207 optimal weight: 0.9980 chunk 509 optimal weight: 8.9990 chunk 62 optimal weight: 2.9990 chunk 91 optimal weight: 0.8980 overall best weight: 1.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 787 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 965 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 856 ASN ** C 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 378 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 189 GLN ** J 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 325 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 401 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 397 ASN ** O 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4734 r_free = 0.4734 target = 0.200520 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.4577 r_free = 0.4577 target = 0.187211 restraints weight = 162253.656| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.4555 r_free = 0.4555 target = 0.185634 restraints weight = 214796.289| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.4535 r_free = 0.4535 target = 0.183986 restraints weight = 167406.881| |-----------------------------------------------------------------------------| r_work (final): 0.4574 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4574 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4574 r_free = 0.4574 target_work(ls_wunit_k1) = 0.195 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 30 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4574 r_free = 0.4574 target_work(ls_wunit_k1) = 0.195 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 33 | |-----------------------------------------------------------------------------| r_final: 0.4574 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5381 moved from start: 0.7510 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 51201 Z= 0.215 Angle : 0.571 13.512 69696 Z= 0.283 Chirality : 0.045 0.349 7857 Planarity : 0.004 0.063 8961 Dihedral : 5.590 119.032 7779 Min Nonbonded Distance : 1.594 Molprobity Statistics. All-atom Clashscore : 11.70 Ramachandran Plot: Outliers : 0.02 % Allowed : 5.44 % Favored : 94.55 % Rotamer: Outliers : 2.22 % Allowed : 21.67 % Favored : 76.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.60 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.67 (0.10), residues: 6258 helix: -0.02 (0.13), residues: 1587 sheet: -0.46 (0.15), residues: 1206 loop : -1.94 (0.10), residues: 3465 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP M 163 HIS 0.015 0.001 HIS M 378 PHE 0.020 0.001 PHE O 64 TYR 0.024 0.001 TYR M 515 ARG 0.005 0.000 ARG A 319 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8494.07 seconds wall clock time: 152 minutes 4.16 seconds (9124.16 seconds total)