Starting phenix.real_space_refine on Thu Feb 15 06:47:47 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7bkb_12206/02_2024/7bkb_12206_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7bkb_12206/02_2024/7bkb_12206.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7bkb_12206/02_2024/7bkb_12206_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7bkb_12206/02_2024/7bkb_12206_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7bkb_12206/02_2024/7bkb_12206_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7bkb_12206/02_2024/7bkb_12206.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7bkb_12206/02_2024/7bkb_12206.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7bkb_12206/02_2024/7bkb_12206_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7bkb_12206/02_2024/7bkb_12206_updated.pdb" } resolution = 3.5 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= 0.047 sd= 1.829 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 212 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: 8 Type Number sf(0) Gaussians Mo 2 10.26 5 Fe 212 7.16 5 Zn 4 6.06 5 P 16 5.49 5 S 790 5.16 5 C 40194 2.51 5 N 10932 2.21 5 O 11976 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 47": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 59": "OD1" <-> "OD2" Residue "A PHE 95": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 104": "OE1" <-> "OE2" Residue "A GLU 147": "OE1" <-> "OE2" Residue "A ARG 178": "NH1" <-> "NH2" Residue "A ARG 185": "NH1" <-> "NH2" Residue "A GLU 228": "OE1" <-> "OE2" Residue "A ASP 235": "OD1" <-> "OD2" Residue "A ARG 243": "NH1" <-> "NH2" Residue "A TYR 290": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 320": "OD1" <-> "OD2" Residue "A PHE 332": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 356": "OE1" <-> "OE2" Residue "A ASP 363": "OD1" <-> "OD2" Residue "A GLU 370": "OE1" <-> "OE2" Residue "A TYR 415": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 419": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 423": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 448": "NH1" <-> "NH2" Residue "A PHE 450": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 459": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 464": "OE1" <-> "OE2" Residue "A PHE 468": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 478": "OE1" <-> "OE2" Residue "A GLU 501": "OE1" <-> "OE2" Residue "A ASP 503": "OD1" <-> "OD2" Residue "A ASP 565": "OD1" <-> "OD2" Residue "A PHE 653": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 19": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 23": "OD1" <-> "OD2" Residue "F ASP 100": "OD1" <-> "OD2" Residue "F PHE 107": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 6": "OD1" <-> "OD2" Residue "E GLU 22": "OE1" <-> "OE2" Residue "E ASP 41": "OD1" <-> "OD2" Residue "E ASP 51": "OD1" <-> "OD2" Residue "E TYR 53": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 54": "OD1" <-> "OD2" Residue "E PHE 146": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 163": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 166": "OE1" <-> "OE2" Residue "E ASP 177": "OD1" <-> "OD2" Residue "E GLU 180": "OE1" <-> "OE2" Residue "E GLU 182": "OE1" <-> "OE2" Residue "E ARG 191": "NH1" <-> "NH2" Residue "E GLU 267": "OE1" <-> "OE2" Residue "E TYR 307": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 328": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 330": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 355": "OE1" <-> "OE2" Residue "E GLU 370": "OE1" <-> "OE2" Residue "E ASP 380": "OD1" <-> "OD2" Residue "E PHE 388": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 411": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 24": "OD1" <-> "OD2" Residue "C TYR 45": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 82": "OD1" <-> "OD2" Residue "C TYR 92": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 106": "OD1" <-> "OD2" Residue "C ASP 119": "OD1" <-> "OD2" Residue "C TYR 164": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 179": "OE1" <-> "OE2" Residue "B ARG 15": "NH1" <-> "NH2" Residue "B PHE 49": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 129": "OD1" <-> "OD2" Residue "B ASP 130": "OD1" <-> "OD2" Residue "B TYR 155": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 191": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 218": "OE1" <-> "OE2" Residue "B GLU 225": "OE1" <-> "OE2" Residue "B ASP 229": "OD1" <-> "OD2" Residue "B GLU 266": "OE1" <-> "OE2" Residue "D TYR 10": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 17": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 37": "OE1" <-> "OE2" Residue "D PHE 77": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 83": "OD1" <-> "OD2" Residue "D PHE 107": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 119": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 121": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 162": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 164": "OD1" <-> "OD2" Residue "D ASP 214": "OD1" <-> "OD2" Residue "D PHE 245": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 248": "OD1" <-> "OD2" Residue "D PHE 282": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 346": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 397": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 407": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 429": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 446": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 489": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 492": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 545": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 555": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 560": "NH1" <-> "NH2" Residue "I PHE 15": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 54": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I GLU 55": "OE1" <-> "OE2" Residue "I ARG 74": "NH1" <-> "NH2" Residue "I TYR 217": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 239": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ASP 245": "OD1" <-> "OD2" Residue "I TYR 259": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 263": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ASP 108": "OD1" <-> "OD2" Residue "L GLU 117": "OE1" <-> "OE2" Residue "L TYR 131": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ASP 132": "OD1" <-> "OD2" Residue "G PHE 78": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ARG 80": "NH1" <-> "NH2" Residue "G TYR 83": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ARG 112": "NH1" <-> "NH2" Residue "G PHE 117": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 133": "OE1" <-> "OE2" Residue "G ARG 136": "NH1" <-> "NH2" Residue "G ASP 142": "OD1" <-> "OD2" Residue "G PHE 154": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 158": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 198": "OE1" <-> "OE2" Residue "G TYR 247": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 260": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 282": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 289": "OD1" <-> "OD2" Residue "G ASP 299": "OD1" <-> "OD2" Residue "G ASP 317": "OD1" <-> "OD2" Residue "G GLU 318": "OE1" <-> "OE2" Residue "G PHE 328": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 330": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 344": "OD1" <-> "OD2" Residue "G GLU 346": "OE1" <-> "OE2" Residue "G PHE 397": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 400": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 424": "OD1" <-> "OD2" Residue "G ASP 436": "OD1" <-> "OD2" Residue "G TYR 442": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 482": "OD1" <-> "OD2" Residue "G TYR 499": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 537": "OD1" <-> "OD2" Residue "G PHE 542": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 553": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J GLU 16": "OE1" <-> "OE2" Residue "J TYR 30": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J GLU 63": "OE1" <-> "OE2" Residue "J TYR 76": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 8": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ASP 35": "OD1" <-> "OD2" Residue "K GLU 45": "OE1" <-> "OE2" Residue "K GLU 49": "OE1" <-> "OE2" Residue "K ASP 67": "OD1" <-> "OD2" Residue "K PHE 90": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K GLU 100": "OE1" <-> "OE2" Residue "K GLU 107": "OE1" <-> "OE2" Residue "K ASP 121": "OD1" <-> "OD2" Residue "K ASP 132": "OD1" <-> "OD2" Residue "K ARG 231": "NH1" <-> "NH2" Residue "H TYR 12": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ARG 21": "NH1" <-> "NH2" Residue "H ASP 26": "OD1" <-> "OD2" Residue "H ASP 30": "OD1" <-> "OD2" Residue "H GLU 43": "OE1" <-> "OE2" Residue "H ASP 148": "OD1" <-> "OD2" Residue "H ASP 201": "OD1" <-> "OD2" Residue "H ASP 211": "OD1" <-> "OD2" Residue "H PHE 218": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 253": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 257": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 258": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ASP 266": "OD1" <-> "OD2" Residue "H ASP 340": "OD1" <-> "OD2" Residue "H TYR 401": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ASP 423": "OD1" <-> "OD2" Residue "H GLU 424": "OE1" <-> "OE2" Residue "a TYR 47": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a ASP 59": "OD1" <-> "OD2" Residue "a PHE 95": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a GLU 104": "OE1" <-> "OE2" Residue "a GLU 147": "OE1" <-> "OE2" Residue "a ARG 178": "NH1" <-> "NH2" Residue "a ARG 185": "NH1" <-> "NH2" Residue "a GLU 228": "OE1" <-> "OE2" Residue "a ASP 235": "OD1" <-> "OD2" Residue "a ARG 243": "NH1" <-> "NH2" Residue "a TYR 290": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a ASP 320": "OD1" <-> "OD2" Residue "a PHE 332": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a GLU 356": "OE1" <-> "OE2" Residue "a ASP 363": "OD1" <-> "OD2" Residue "a GLU 370": "OE1" <-> "OE2" Residue "a TYR 415": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a PHE 419": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a TYR 423": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a ARG 448": "NH1" <-> "NH2" Residue "a PHE 450": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a TYR 459": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a GLU 464": "OE1" <-> "OE2" Residue "a PHE 468": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a GLU 478": "OE1" <-> "OE2" Residue "a GLU 501": "OE1" <-> "OE2" Residue "a ASP 503": "OD1" <-> "OD2" Residue "a ASP 565": "OD1" <-> "OD2" Residue "a PHE 653": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "f TYR 19": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "f ASP 23": "OD1" <-> "OD2" Residue "f ASP 100": "OD1" <-> "OD2" Residue "f PHE 107": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "e ASP 6": "OD1" <-> "OD2" Residue "e GLU 22": "OE1" <-> "OE2" Residue "e ASP 41": "OD1" <-> "OD2" Residue "e ASP 51": "OD1" <-> "OD2" Residue "e TYR 53": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "e ASP 54": "OD1" <-> "OD2" Residue "e PHE 146": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "e PHE 163": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "e GLU 166": "OE1" <-> "OE2" Residue "e ASP 177": "OD1" <-> "OD2" Residue "e GLU 180": "OE1" <-> "OE2" Residue "e GLU 182": "OE1" <-> "OE2" Residue "e ARG 191": "NH1" <-> "NH2" Residue "e GLU 267": "OE1" <-> "OE2" Residue "e TYR 307": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "e PHE 328": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "e PHE 330": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "e GLU 355": "OE1" <-> "OE2" Residue "e GLU 370": "OE1" <-> "OE2" Residue "e ASP 380": "OD1" <-> "OD2" Residue "e PHE 388": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "e PHE 411": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c ASP 24": "OD1" <-> "OD2" Residue "c TYR 45": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c ASP 82": "OD1" <-> "OD2" Residue "c TYR 92": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c ASP 106": "OD1" <-> "OD2" Residue "c ASP 119": "OD1" <-> "OD2" Residue "c TYR 164": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c GLU 179": "OE1" <-> "OE2" Residue "b ARG 15": "NH1" <-> "NH2" Residue "b PHE 49": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b ASP 129": "OD1" <-> "OD2" Residue "b ASP 130": "OD1" <-> "OD2" Residue "b TYR 155": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b TYR 191": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b GLU 218": "OE1" <-> "OE2" Residue "b GLU 225": "OE1" <-> "OE2" Residue "b ASP 229": "OD1" <-> "OD2" Residue "b GLU 266": "OE1" <-> "OE2" Residue "d TYR 10": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d TYR 17": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d GLU 37": "OE1" <-> "OE2" Residue "d PHE 77": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d ASP 83": "OD1" <-> "OD2" Residue "d PHE 107": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d TYR 119": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d PHE 121": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d PHE 162": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d ASP 164": "OD1" <-> "OD2" Residue "d ASP 214": "OD1" <-> "OD2" Residue "d PHE 245": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d ASP 248": "OD1" <-> "OD2" Residue "d PHE 282": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d TYR 346": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d TYR 397": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d TYR 407": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d PHE 429": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d PHE 446": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d PHE 489": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d PHE 492": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d PHE 545": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d PHE 555": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d ARG 560": "NH1" <-> "NH2" Residue "i PHE 15": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "i PHE 54": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "i GLU 55": "OE1" <-> "OE2" Residue "i ARG 74": "NH1" <-> "NH2" Residue "i TYR 217": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "i PHE 239": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "i ASP 245": "OD1" <-> "OD2" Residue "i TYR 259": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "i PHE 263": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "l ASP 108": "OD1" <-> "OD2" Residue "l GLU 117": "OE1" <-> "OE2" Residue "l TYR 131": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "l ASP 132": "OD1" <-> "OD2" Residue "g PHE 78": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "g ARG 80": "NH1" <-> "NH2" Residue "g TYR 83": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "g ARG 112": "NH1" <-> "NH2" Residue "g PHE 117": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "g GLU 133": "OE1" <-> "OE2" Residue "g ARG 136": "NH1" <-> "NH2" Residue "g ASP 142": "OD1" <-> "OD2" Residue "g PHE 154": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "g TYR 158": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "g GLU 198": "OE1" <-> "OE2" Residue "g TYR 247": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "g TYR 260": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "g TYR 282": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "g ASP 289": "OD1" <-> "OD2" Residue "g ASP 299": "OD1" <-> "OD2" Residue "g ASP 317": "OD1" <-> "OD2" Residue "g GLU 318": "OE1" <-> "OE2" Residue "g PHE 328": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "g TYR 330": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "g ASP 344": "OD1" <-> "OD2" Residue "g GLU 346": "OE1" <-> "OE2" Residue "g PHE 397": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "g TYR 400": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "g ASP 424": "OD1" <-> "OD2" Residue "g ASP 436": "OD1" <-> "OD2" Residue "g TYR 442": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "g ASP 482": "OD1" <-> "OD2" Residue "g TYR 499": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "g ASP 537": "OD1" <-> "OD2" Residue "g PHE 542": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "g TYR 553": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "j GLU 16": "OE1" <-> "OE2" Residue "j TYR 30": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "j GLU 63": "OE1" <-> "OE2" Residue "j TYR 76": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "k TYR 8": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "k ASP 35": "OD1" <-> "OD2" Residue "k GLU 45": "OE1" <-> "OE2" Residue "k GLU 49": "OE1" <-> "OE2" Residue "k ASP 67": "OD1" <-> "OD2" Residue "k PHE 90": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "k GLU 100": "OE1" <-> "OE2" Residue "k GLU 107": "OE1" <-> "OE2" Residue "k ASP 121": "OD1" <-> "OD2" Residue "k ASP 132": "OD1" <-> "OD2" Residue "k PHE 167": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "h TYR 12": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "h ARG 21": "NH1" <-> "NH2" Residue "h ASP 26": "OD1" <-> "OD2" Residue "h ASP 30": "OD1" <-> "OD2" Residue "h GLU 43": "OE1" <-> "OE2" Residue "h ASP 148": "OD1" <-> "OD2" Residue "h ASP 201": "OD1" <-> "OD2" Residue "h ASP 211": "OD1" <-> "OD2" Residue "h PHE 218": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "h PHE 253": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "h PHE 257": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "h PHE 258": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "h ASP 266": "OD1" <-> "OD2" Residue "h ASP 340": "OD1" <-> "OD2" Residue "h TYR 401": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "h ASP 423": "OD1" <-> "OD2" Residue "h GLU 424": "OE1" <-> "OE2" Time to flip residues: 0.15s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 64126 Number of models: 1 Model: "" Number of chains: 44 Chain: "A" Number of atoms: 5011 Number of conformers: 1 Conformer: "" Number of residues, atoms: 662, 5011 Classifications: {'peptide': 662} Link IDs: {'PCIS': 1, 'PTRANS': 33, 'TRANS': 627} Chain: "F" Number of atoms: 1073 Number of conformers: 1 Conformer: "" Number of residues, atoms: 137, 1073 Classifications: {'peptide': 137} Link IDs: {'PTRANS': 5, 'TRANS': 131} Chain: "E" Number of atoms: 3151 Number of conformers: 1 Conformer: "" Number of residues, atoms: 411, 3151 Classifications: {'peptide': 411} Link IDs: {'PTRANS': 17, 'TRANS': 393} Chain: "C" Number of atoms: 1498 Number of conformers: 1 Conformer: "" Number of residues, atoms: 189, 1498 Classifications: {'peptide': 189} Link IDs: {'PTRANS': 13, 'TRANS': 175} Chain: "B" Number of atoms: 2304 Number of conformers: 1 Conformer: "" Number of residues, atoms: 296, 2304 Classifications: {'peptide': 296} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 282} Chain: "D" Number of atoms: 4251 Number of conformers: 1 Conformer: "" Number of residues, atoms: 549, 4251 Classifications: {'peptide': 549} Link IDs: {'PTRANS': 29, 'TRANS': 519} Chain breaks: 1 Chain: "I" Number of atoms: 1996 Number of conformers: 1 Conformer: "" Number of residues, atoms: 264, 1996 Classifications: {'peptide': 264} Link IDs: {'PTRANS': 5, 'TRANS': 258} Chain: "L" Number of atoms: 576 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 576 Classifications: {'peptide': 79} Link IDs: {'PTRANS': 5, 'TRANS': 73} Chain: "G" Number of atoms: 4455 Number of conformers: 1 Conformer: "" Number of residues, atoms: 568, 4455 Classifications: {'peptide': 568} Link IDs: {'PCIS': 1, 'PTRANS': 25, 'TRANS': 541} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'KCX:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "J" Number of atoms: 1007 Number of conformers: 1 Conformer: "" Number of residues, atoms: 131, 1007 Classifications: {'peptide': 131} Link IDs: {'PTRANS': 7, 'TRANS': 123} Chain: "K" Number of atoms: 2910 Number of conformers: 1 Conformer: "" Number of residues, atoms: 386, 2910 Classifications: {'peptide': 386} Link IDs: {'PTRANS': 19, 'TRANS': 366} Chain: "H" Number of atoms: 3416 Number of conformers: 1 Conformer: "" Number of residues, atoms: 438, 3416 Classifications: {'peptide': 438} Link IDs: {'PTRANS': 22, 'TRANS': 415} Chain: "a" Number of atoms: 5011 Number of conformers: 1 Conformer: "" Number of residues, atoms: 662, 5011 Classifications: {'peptide': 662} Link IDs: {'PCIS': 1, 'PTRANS': 33, 'TRANS': 627} Chain: "f" Number of atoms: 1073 Number of conformers: 1 Conformer: "" Number of residues, atoms: 137, 1073 Classifications: {'peptide': 137} Link IDs: {'PTRANS': 5, 'TRANS': 131} Chain: "e" Number of atoms: 3151 Number of conformers: 1 Conformer: "" Number of residues, atoms: 411, 3151 Classifications: {'peptide': 411} Link IDs: {'PTRANS': 17, 'TRANS': 393} Chain: "c" Number of atoms: 1498 Number of conformers: 1 Conformer: "" Number of residues, atoms: 189, 1498 Classifications: {'peptide': 189} Link IDs: {'PTRANS': 13, 'TRANS': 175} Chain: "b" Number of atoms: 2304 Number of conformers: 1 Conformer: "" Number of residues, atoms: 296, 2304 Classifications: {'peptide': 296} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 282} Chain: "d" Number of atoms: 4251 Number of conformers: 1 Conformer: "" Number of residues, atoms: 549, 4251 Classifications: {'peptide': 549} Link IDs: {'PTRANS': 29, 'TRANS': 519} Chain breaks: 1 Chain: "i" Number of atoms: 1996 Number of conformers: 1 Conformer: "" Number of residues, atoms: 264, 1996 Classifications: {'peptide': 264} Link IDs: {'PTRANS': 5, 'TRANS': 258} Chain: "l" Number of atoms: 576 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 576 Classifications: {'peptide': 79} Link IDs: {'PTRANS': 5, 'TRANS': 73} Chain: "g" Number of atoms: 4455 Number of conformers: 1 Conformer: "" Number of residues, atoms: 568, 4455 Classifications: {'peptide': 568} Link IDs: {'PCIS': 1, 'PTRANS': 25, 'TRANS': 541} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'KCX:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "j" Number of atoms: 1007 Number of conformers: 1 Conformer: "" Number of residues, atoms: 131, 1007 Classifications: {'peptide': 131} Link IDs: {'PTRANS': 7, 'TRANS': 123} Chain: "k" Number of atoms: 2910 Number of conformers: 1 Conformer: "" Number of residues, atoms: 386, 2910 Classifications: {'peptide': 386} Link IDs: {'PTRANS': 19, 'TRANS': 366} Chain: "h" Number of atoms: 3416 Number of conformers: 1 Conformer: "" Number of residues, atoms: 438, 3416 Classifications: {'peptide': 438} Link IDs: {'PTRANS': 22, 'TRANS': 415} Chain: "A" Number of atoms: 101 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 101 Unusual residues: {'FAD': 1, 'SF4': 6} Classifications: {'undetermined': 7} Link IDs: {None: 6} Chain: "F" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 4 Unusual residues: {'FES': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 85 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 85 Unusual residues: {'FAD': 1, 'SF4': 4} Classifications: {'undetermined': 5} Link IDs: {None: 4} Chain: "C" Number of atoms: 16 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 16 Unusual residues: {'SF4': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 16 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 16 Unusual residues: {'9S8': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 8 Unusual residues: {'SF4': 1} Classifications: {'undetermined': 1} Chain: "L" Number of atoms: 16 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 16 Unusual residues: {'SF4': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "G" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "K" Number of atoms: 64 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 64 Unusual residues: {'SF4': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} Chain: "H" Number of atoms: 103 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 103 Unusual residues: {' MO': 1, 'MGD': 2, 'SF4': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "a" Number of atoms: 101 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 101 Unusual residues: {'FAD': 1, 'SF4': 6} Classifications: {'undetermined': 7} Link IDs: {None: 6} Chain: "f" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 4 Unusual residues: {'FES': 1} Classifications: {'undetermined': 1} Chain: "e" Number of atoms: 85 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 85 Unusual residues: {'FAD': 1, 'SF4': 4} Classifications: {'undetermined': 5} Link IDs: {None: 4} Chain: "c" Number of atoms: 16 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 16 Unusual residues: {'SF4': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "b" Number of atoms: 16 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 16 Unusual residues: {'9S8': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "d" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 8 Unusual residues: {'SF4': 1} Classifications: {'undetermined': 1} Chain: "l" Number of atoms: 16 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 16 Unusual residues: {'SF4': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "g" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "k" Number of atoms: 64 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 64 Unusual residues: {'SF4': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} Chain: "h" Number of atoms: 103 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 103 Unusual residues: {' MO': 1, 'MGD': 2, 'SF4': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 3141 SG CYS A 420 96.279 101.074 123.443 1.00 25.60 S ATOM 3008 SG CYS A 402 101.591 104.965 125.017 1.00 24.42 S ATOM 3147 SG CYS A 421 101.486 102.323 119.858 1.00 23.19 S ATOM 3107 SG CYS A 416 101.192 98.489 124.945 1.00 24.09 S ATOM 509 SG CYS A 74 113.212 69.123 141.383 1.00 34.55 S ATOM 61 SG CYS A 14 119.244 65.628 141.129 1.00 43.93 S ATOM 77 SG CYS A 16 119.251 70.750 139.709 1.00 43.93 S ATOM 327 SG CYS A 49 115.531 66.003 136.418 1.00 44.62 S ATOM 4595 SG CYS A 610 83.682 72.360 152.943 1.00 16.99 S ATOM 4800 SG CYS A 639 87.563 69.259 157.213 1.00 14.78 S ATOM 4783 SG CYS A 636 90.018 73.378 153.706 1.00 19.06 S ATOM 4764 SG CYS A 633 87.840 67.549 151.411 1.00 23.69 S ATOM 4533 SG CYS A 600 81.188 63.327 164.278 1.00 21.92 S ATOM 4548 SG CYS A 603 81.339 69.186 167.174 1.00 15.83 S ATOM 4566 SG CYS A 606 82.446 68.985 161.413 1.00 17.66 S ATOM 4825 SG CYS A 643 86.807 66.609 165.201 1.00 15.02 S ATOM 1949 SG CYS A 264 57.361 93.661 112.599 1.00 45.93 S ATOM 2355 SG CYS A 318 54.506 91.630 117.571 1.00 46.09 S ATOM 1967 SG CYS A 267 59.233 96.300 117.585 1.00 36.95 S ATOM 1931 SG CYS A 261 60.972 90.245 117.045 1.00 48.22 S ATOM 2328 SG CYS A 314 55.017 97.543 123.102 1.00 39.06 S ATOM 2288 SG CYS A 308 57.472 99.762 128.037 1.00 37.05 S ATOM 2310 SG CYS A 311 53.423 103.232 124.208 1.00 36.71 S ATOM 1991 SG CYS A 271 59.059 102.858 122.452 1.00 32.03 S ATOM 5101 SG CYS F 14 100.035 79.173 151.553 1.00 20.48 S ATOM 5499 SG CYS F 68 97.603 81.383 150.181 1.00 22.41 S ATOM 5319 SG CYS F 43 94.301 77.370 153.357 1.00 16.75 S ATOM 5538 SG CYS F 73 93.232 79.941 151.793 1.00 22.68 S ATOM 8414 SG CYS E 308 86.452 66.770 171.881 1.00 13.37 S ATOM 8396 SG CYS E 306 87.597 68.987 178.024 1.00 16.79 S ATOM 8437 SG CYS E 311 91.349 65.185 176.031 1.00 19.40 S ATOM 8325 SG CYS E 296 92.390 62.580 187.699 1.00 22.09 S ATOM 8759 SG CYS E 352 94.411 67.663 189.911 1.00 18.90 S ATOM 8348 SG CYS E 299 91.875 67.210 183.753 1.00 17.50 S ATOM 8302 SG CYS E 293 97.673 64.938 184.804 1.00 22.99 S ATOM 8375 SG CYS E 303 85.683 71.675 180.743 1.00 12.71 S ATOM 8708 SG CYS E 345 82.940 73.660 185.698 1.00 18.14 S ATOM 8686 SG CYS E 342 86.774 77.898 182.608 1.00 16.75 S ATOM 8727 SG CYS E 348 88.896 72.989 186.083 1.00 17.49 S ATOM 6838 SG CYS E 103 77.705 76.529 189.028 1.00 17.79 S ATOM 7043 SG CYS E 129 75.805 79.664 193.766 1.00 22.43 S ATOM 7544 SG CYS E 193 79.764 82.767 189.352 1.00 22.97 S ATOM 7516 SG CYS E 190 81.450 78.683 193.998 1.00 29.27 S ATOM 9971 SG CYS C 94 124.208 110.798 104.916 1.00 21.73 S ATOM 9650 SG CYS C 54 127.860 114.254 109.504 1.00 20.77 S ATOM 9927 SG CYS C 88 126.674 116.308 103.558 1.00 25.41 S ATOM 9947 SG CYS C 91 130.349 110.956 105.051 1.00 24.23 S ATOM 9610 SG CYS C 47 117.919 105.329 111.899 1.00 21.58 S ATOM 9627 SG CYS C 50 120.412 110.521 110.101 1.00 19.58 S ATOM 9583 SG CYS C 44 114.325 110.377 109.368 1.00 24.10 S ATOM 10003 SG CYS C 98 117.707 105.780 105.971 1.00 22.88 S ATOM 10817 SG CYS B 10 139.229 121.152 86.947 1.00 43.94 S ATOM 11047 SG CYS B 42 135.557 121.276 87.507 1.00 44.18 S ATOM 11324 SG CYS B 79 139.244 113.270 91.741 1.00 33.37 S ATOM 11342 SG CYS B 82 137.701 114.560 88.271 1.00 35.70 S ATOM 11053 SG CYS B 43 134.775 116.072 87.963 1.00 42.93 S ATOM 11342 SG CYS B 82 137.701 114.560 88.271 1.00 35.70 S ATOM 11945 SG CYS B 157 134.258 109.264 102.343 1.00 29.86 S ATOM 12278 SG CYS B 197 135.157 113.242 103.846 1.00 28.61 S ATOM 12549 SG CYS B 235 139.735 112.605 95.039 1.00 36.06 S ATOM 12573 SG CYS B 238 140.062 111.935 99.207 1.00 36.24 S ATOM 12284 SG CYS B 198 139.686 114.367 102.097 1.00 28.31 S ATOM 12573 SG CYS B 238 140.062 111.935 99.207 1.00 36.24 S ATOM 13121 SG CYS D 15 88.915 52.259 194.097 1.00 21.69 S ATOM 13167 SG CYS D 22 90.657 57.108 197.502 1.00 19.12 S ATOM 13373 SG CYS D 50 93.367 55.371 191.548 1.00 18.54 S ATOM 13146 SG CYS D 18 94.743 52.431 196.900 1.00 26.56 S ATOM 19709 SG CYS L 119 60.147 125.512 155.017 1.00 43.58 S ATOM 19724 SG CYS L 122 54.863 129.474 154.906 1.00 37.39 S ATOM 19742 SG CYS L 125 59.972 131.407 155.934 1.00 38.09 S ATOM 19435 SG CYS L 83 56.942 128.273 160.339 1.00 31.04 S ATOM 19768 SG CYS L 129 64.180 139.395 158.220 1.00 37.54 S ATOM 19371 SG CYS L 73 67.724 137.162 163.533 1.00 44.76 S ATOM 19410 SG CYS L 79 62.247 134.670 162.715 1.00 29.12 S ATOM 19388 SG CYS L 76 62.235 140.521 162.854 1.00 31.95 S ATOM 27803 SG CYS K 333 47.492 123.286 154.736 1.00 30.11 S ATOM 27477 SG CYS K 288 44.477 128.211 151.728 1.00 26.56 S ATOM 27458 SG CYS K 285 49.791 128.625 155.621 1.00 30.95 S ATOM 27437 SG CYS K 281 44.332 128.076 157.515 1.00 34.78 S ATOM 27740 SG CYS K 323 38.590 122.116 143.904 1.00 23.93 S ATOM 27505 SG CYS K 292 42.077 127.942 143.659 1.00 24.80 S ATOM 27762 SG CYS K 326 44.705 122.771 141.791 1.00 23.64 S ATOM 27777 SG CYS K 329 43.710 122.458 147.082 1.00 26.23 S ATOM 25672 SG CYS K 47 57.614 110.611 135.219 1.00 31.82 S ATOM 25915 SG CYS K 81 56.984 109.502 129.198 1.00 32.37 S ATOM 25891 SG CYS K 78 61.394 112.901 130.624 1.00 37.63 S ATOM 25932 SG CYS K 84 55.786 115.441 130.808 1.00 28.06 S ATOM 25626 SG CYS K 40 48.849 121.269 138.556 1.00 25.36 S ATOM 25961 SG CYS K 88 50.126 121.149 132.957 1.00 27.02 S ATOM 25644 SG CYS K 43 53.873 117.902 137.669 1.00 25.92 S ATOM 25609 SG CYS K 37 54.350 123.775 137.339 1.00 26.92 S ATOM 27264 SG CYS K 259 27.800 134.283 128.776 1.00 31.85 S ATOM 26248 SG CYS K 125 30.178 136.882 122.971 1.00 40.15 S ATOM 26294 SG CYS K 131 34.038 136.673 127.806 1.00 34.13 S ATOM 26272 SG CYS K 128 30.378 139.471 128.900 1.00 38.62 S ATOM 26323 SG CYS K 135 40.031 132.528 132.029 1.00 28.89 S ATOM 27187 SG CYS K 249 38.610 126.279 130.216 1.00 32.77 S ATOM 27237 SG CYS K 255 34.334 130.794 131.142 1.00 28.46 S ATOM 27206 SG CYS K 252 37.045 129.058 135.476 1.00 26.78 S ATOM 26959 SG CYS K 218 23.481 168.695 114.999 1.00 57.47 S ATOM 26938 SG CYS K 215 23.972 165.567 119.559 1.00 59.91 S ATOM 26697 SG CYS K 184 28.560 164.776 115.152 1.00 54.22 S ATOM 26920 SG CYS K 212 24.079 162.189 113.737 1.00 58.92 S ATOM 26653 SG CYS K 177 26.023 179.435 111.962 1.00 46.42 S ATOM 26984 SG CYS K 222 21.812 174.574 112.836 1.00 49.12 S ATOM 26671 SG CYS K 180 27.012 173.609 110.496 1.00 48.22 S ATOM 26631 SG CYS K 174 23.889 175.867 106.679 1.00 52.96 S ATOM 29146 SG CYS H 122 61.072 160.552 172.457 1.00 39.16 S ATOM 28344 SG CYS H 17 59.361 143.412 173.825 1.00 35.68 S ATOM 28322 SG CYS H 13 61.612 148.268 172.418 1.00 35.09 S ATOM 28505 SG CYS H 38 65.531 143.625 170.960 1.00 33.73 S ATOM 28297 SG CYS H 10 65.373 144.083 176.211 1.00 37.65 S ATOM 34789 SG CYS a 420 113.646 91.041 117.935 1.00 25.60 S ATOM 34656 SG CYS a 402 114.337 97.573 116.294 1.00 24.42 S ATOM 34795 SG CYS a 421 112.136 96.205 121.479 1.00 23.19 S ATOM 34755 SG CYS a 416 108.936 93.979 116.434 1.00 24.09 S ATOM 32157 SG CYS a 74 77.404 89.488 100.227 1.00 34.55 S ATOM 31709 SG CYS a 14 71.356 92.957 100.484 1.00 33.40 S ATOM 31725 SG CYS a 16 75.792 95.545 101.851 1.00 39.46 S ATOM 31975 SG CYS a 49 73.572 89.978 105.212 1.00 44.62 S ATOM 36243 SG CYS a 610 94.948 65.454 88.795 1.00 16.99 S ATOM 36448 SG CYS a 639 90.294 67.216 84.535 1.00 14.78 S ATOM 36431 SG CYS a 636 92.646 71.440 87.987 1.00 19.06 S ATOM 36412 SG CYS a 633 88.710 66.653 90.352 1.00 23.69 S ATOM 36181 SG CYS a 600 88.316 58.657 77.564 1.00 21.92 S ATOM 36196 SG CYS a 603 93.293 61.699 74.609 1.00 15.83 S ATOM 36214 SG CYS a 606 92.599 62.611 80.365 1.00 17.66 S ATOM 36473 SG CYS a 643 88.332 65.155 76.577 1.00 15.02 S ATOM 33597 SG CYS a 264 126.821 53.760 129.063 1.00 45.93 S ATOM 34003 SG CYS a 318 126.466 50.225 124.128 1.00 46.09 S ATOM 33615 SG CYS a 267 128.134 56.655 124.040 1.00 36.95 S ATOM 33579 SG CYS a 261 122.026 55.128 124.632 1.00 48.22 S ATOM 33976 SG CYS a 314 131.291 53.578 118.535 1.00 39.06 S ATOM 33936 SG CYS a 308 131.950 56.766 113.565 1.00 37.05 S ATOM 33958 SG CYS a 311 137.005 55.042 117.380 1.00 36.71 S ATOM 33639 SG CYS a 271 133.865 59.747 119.110 1.00 32.03 S ATOM 36749 SG CYS f 14 92.647 83.031 90.027 1.00 20.48 S ATOM 37147 SG CYS f 68 95.788 82.050 91.391 1.00 22.41 S ATOM 36967 SG CYS f 43 93.953 77.149 88.272 1.00 16.75 S ATOM 37186 SG CYS f 73 96.722 77.530 89.817 1.00 22.68 S ATOM 40062 SG CYS e 308 88.609 64.864 69.898 1.00 13.37 S ATOM 40044 SG CYS e 306 89.916 66.906 63.727 1.00 16.79 S ATOM 40085 SG CYS e 311 84.756 68.266 65.739 1.00 19.40 S ATOM 39973 SG CYS e 296 81.912 67.745 54.092 1.00 22.09 S ATOM 40407 SG CYS e 352 85.282 72.022 51.819 1.00 18.90 S ATOM 39996 SG CYS e 299 86.199 69.660 57.994 1.00 17.50 S ATOM 39950 SG CYS e 293 81.319 73.526 56.934 1.00 22.99 S ATOM 40023 SG CYS e 303 93.187 66.573 60.991 1.00 12.71 S ATOM 40356 SG CYS e 345 96.249 65.147 56.032 1.00 18.14 S ATOM 40334 SG CYS e 342 98.010 70.620 59.059 1.00 16.75 S ATOM 40375 SG CYS e 348 92.677 69.958 55.622 1.00 17.49 S ATOM 38486 SG CYS e 103 101.336 62.025 52.701 1.00 17.79 S ATOM 38691 SG CYS e 129 104.974 61.907 47.942 1.00 22.43 S ATOM 39192 SG CYS e 193 105.699 66.932 52.305 1.00 22.97 S ATOM 39164 SG CYS e 190 101.292 66.297 47.690 1.00 29.27 S ATOM 41619 SG CYS c 94 108.157 120.257 136.213 1.00 21.73 S ATOM 41298 SG CYS c 54 109.289 125.106 131.571 1.00 20.77 S ATOM 41575 SG CYS c 88 111.696 125.168 137.502 1.00 25.41 S ATOM 41595 SG CYS c 91 105.214 125.648 136.043 1.00 24.23 S ATOM 41258 SG CYS c 47 106.540 112.005 129.320 1.00 21.58 S ATOM 41275 SG CYS c 50 109.791 116.784 131.052 1.00 19.58 S ATOM 41231 SG CYS c 44 112.725 111.454 131.819 1.00 24.10 S ATOM 41651 SG CYS c 98 107.073 112.107 135.244 1.00 22.88 S ATOM 42465 SG CYS b 10 109.687 138.619 153.996 1.00 43.94 S ATOM 42695 SG CYS b 42 111.635 135.499 153.455 1.00 44.18 S ATOM 42972 SG CYS b 79 102.833 134.634 149.282 1.00 33.37 S ATOM 42990 SG CYS b 82 104.743 133.980 152.747 1.00 35.70 S ATOM 42701 SG CYS b 43 107.521 132.208 153.055 1.00 42.93 S ATOM 42990 SG CYS b 82 104.743 133.980 152.747 1.00 35.70 S ATOM 43593 SG CYS b 157 101.806 128.207 138.748 1.00 29.86 S ATOM 43926 SG CYS b 197 104.787 130.965 137.200 1.00 28.61 S ATOM 44197 SG CYS b 235 101.993 134.692 145.988 1.00 36.06 S ATOM 44221 SG CYS b 238 101.224 134.598 141.824 1.00 36.24 S ATOM 43932 SG CYS b 198 103.498 135.464 138.913 1.00 28.31 S ATOM 44221 SG CYS b 238 101.224 134.598 141.824 1.00 36.24 S ATOM 44769 SG CYS d 15 74.689 59.500 47.817 1.00 21.69 S ATOM 44815 SG CYS d 22 77.989 63.405 44.353 1.00 19.12 S ATOM 45021 SG CYS d 50 75.163 64.937 50.310 1.00 18.54 S ATOM 44794 SG CYS d 18 71.898 64.601 44.980 1.00 26.56 S ATOM 51357 SG CYS l 119 152.723 71.735 86.314 1.00 43.58 S ATOM 51372 SG CYS l 122 158.800 69.150 86.414 1.00 37.39 S ATOM 51390 SG CYS l 125 157.903 74.529 85.338 1.00 38.09 S ATOM 51083 SG CYS l 83 156.685 70.294 80.982 1.00 31.04 S ATOM 51416 SG CYS l 129 162.689 82.155 82.951 1.00 37.54 S ATOM 51019 SG CYS l 73 158.947 84.049 77.641 1.00 44.76 S ATOM 51058 SG CYS l 79 159.544 78.068 78.513 1.00 29.12 S ATOM 51036 SG CYS l 76 164.611 80.991 78.315 1.00 31.95 S ATOM 59451 SG CYS k 333 157.145 59.671 86.687 1.00 30.11 S ATOM 59125 SG CYS k 288 162.936 59.563 89.660 1.00 26.56 S ATOM 59106 SG CYS k 285 160.605 64.331 85.734 1.00 30.95 S ATOM 59085 SG CYS k 281 162.858 59.314 83.875 1.00 34.78 S ATOM 59388 SG CYS k 323 160.663 51.490 97.577 1.00 23.93 S ATOM 59153 SG CYS k 292 163.955 57.431 97.744 1.00 24.80 S ATOM 59410 SG CYS k 326 158.175 57.129 99.650 1.00 23.64 S ATOM 59425 SG CYS k 329 158.372 56.060 94.366 1.00 26.23 S ATOM 57320 SG CYS k 47 141.220 62.261 106.273 1.00 31.82 S ATOM 57563 SG CYS k 81 140.614 61.218 112.308 1.00 32.37 S ATOM 57539 SG CYS k 78 141.333 66.725 110.825 1.00 37.63 S ATOM 57580 SG CYS k 84 146.341 63.144 110.646 1.00 28.06 S ATOM 57274 SG CYS k 40 154.817 59.993 102.877 1.00 25.36 S ATOM 57609 SG CYS k 88 154.105 61.091 108.469 1.00 27.02 S ATOM 57292 SG CYS k 43 149.390 62.658 103.770 1.00 25.92 S ATOM 57257 SG CYS k 37 154.233 66.020 104.039 1.00 26.92 S ATOM 58912 SG CYS k 259 176.692 48.405 112.639 1.00 31.85 S ATOM 57896 SG CYS k 125 177.781 51.822 118.405 1.00 40.15 S ATOM 57942 SG CYS k 131 175.636 55.009 113.551 1.00 34.13 S ATOM 57920 SG CYS k 128 179.887 53.236 112.450 1.00 38.62 S ATOM 57971 SG CYS k 135 169.063 58.538 109.379 1.00 28.89 S ATOM 58835 SG CYS k 249 164.400 53.793 111.627 1.00 32.77 S ATOM 58885 SG CYS k 255 169.320 52.233 110.457 1.00 28.46 S ATOM 58841 SG CYS k 250 164.214 56.775 106.936 1.00 27.69 S ATOM 58854 SG CYS k 252 166.554 54.901 105.958 1.00 26.78 S ATOM 58607 SG CYS k 218 208.792 61.465 127.051 1.00 57.47 S ATOM 58586 SG CYS k 215 205.829 60.310 122.500 1.00 59.91 S ATOM 58345 SG CYS k 184 202.858 63.903 126.900 1.00 54.22 S ATOM 58568 SG CYS k 212 202.862 58.733 128.333 1.00 58.92 S ATOM 58301 SG CYS k 177 217.116 68.264 130.874 1.00 46.42 S ATOM 58632 SG CYS k 222 216.602 63.100 129.342 1.00 49.12 S ATOM 58319 SG CYS k 180 210.852 66.374 131.531 1.00 48.22 S ATOM 58279 SG CYS k 174 215.055 64.945 135.452 1.00 52.96 S ATOM 60794 SG CYS h 122 182.465 89.938 68.518 1.00 39.16 S ATOM 59992 SG CYS h 17 168.488 79.849 67.331 1.00 35.68 S ATOM 59970 SG CYS h 13 171.567 84.246 68.678 1.00 35.09 S ATOM 60153 SG CYS h 38 165.593 85.321 70.160 1.00 33.73 S ATOM 59945 SG CYS h 10 166.038 85.363 64.906 1.00 37.65 S Time building chain proxies: 25.63, per 1000 atoms: 0.40 Number of scatterers: 64126 At special positions: 0 Unit cell: (240.24, 221.76, 243.6, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 8 Type Number sf(0) Mo 2 41.97 Zn 4 29.99 Fe 212 26.01 S 790 16.00 P 16 15.00 O 11976 8.00 N 10932 7.00 C 40194 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS A 198 " - pdb=" SG CYS A 201 " distance=2.03 Simple disulfide: pdb=" SG CYS a 198 " - pdb=" SG CYS a 201 " 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=14, symmetry=0 Number of additional bonds: simple=14, symmetry=0 Coordination: Other bonds: Time building additional restraints: 20.30 Conformation dependent library (CDL) restraints added in 8.8 seconds Dynamic metal coordination Iron sulfur cluster coordination pdb=" FES F 201 " pdb="FE2 FES F 201 " - pdb=" SG CYS F 73 " pdb="FE2 FES F 201 " - pdb=" SG CYS F 43 " pdb="FE1 FES F 201 " - pdb=" SG CYS F 14 " pdb="FE1 FES F 201 " - pdb=" SG CYS F 68 " pdb=" FES f 201 " pdb="FE2 FES f 201 " - pdb=" SG CYS f 73 " pdb="FE2 FES f 201 " - pdb=" SG CYS f 43 " pdb="FE1 FES f 201 " - pdb=" SG CYS f 14 " pdb="FE1 FES f 201 " - pdb=" SG CYS f 68 " pdb=" SF4 A 701 " pdb="FE1 SF4 A 701 " - pdb=" SG CYS A 420 " pdb="FE3 SF4 A 701 " - pdb=" SG CYS A 421 " pdb="FE4 SF4 A 701 " - pdb=" SG CYS A 416 " pdb="FE2 SF4 A 701 " - pdb=" SG CYS A 402 " pdb=" SF4 A 703 " pdb="FE2 SF4 A 703 " - pdb=" SG CYS A 14 " pdb="FE4 SF4 A 703 " - pdb=" SG CYS A 49 " pdb="FE1 SF4 A 703 " - pdb=" SG CYS A 74 " pdb="FE3 SF4 A 703 " - pdb=" SG CYS A 16 " pdb=" SF4 A 704 " pdb="FE1 SF4 A 704 " - pdb=" SG CYS A 610 " pdb="FE3 SF4 A 704 " - pdb=" SG CYS A 636 " pdb="FE2 SF4 A 704 " - pdb=" SG CYS A 639 " pdb="FE4 SF4 A 704 " - pdb=" SG CYS A 633 " pdb=" SF4 A 705 " pdb="FE2 SF4 A 705 " - pdb=" SG CYS A 603 " pdb="FE3 SF4 A 705 " - pdb=" SG CYS A 606 " pdb="FE4 SF4 A 705 " - pdb=" SG CYS A 643 " pdb="FE1 SF4 A 705 " - pdb=" SG CYS A 600 " pdb=" SF4 A 706 " pdb="FE1 SF4 A 706 " - pdb=" SG CYS A 264 " pdb="FE4 SF4 A 706 " - pdb=" SG CYS A 261 " pdb="FE3 SF4 A 706 " - pdb=" SG CYS A 267 " pdb="FE2 SF4 A 706 " - pdb=" SG CYS A 318 " pdb=" SF4 A 707 " pdb="FE2 SF4 A 707 " - pdb=" SG CYS A 308 " pdb="FE3 SF4 A 707 " - pdb=" SG CYS A 311 " pdb="FE4 SF4 A 707 " - pdb=" SG CYS A 271 " pdb="FE1 SF4 A 707 " - pdb=" SG CYS A 314 " pdb=" SF4 C 201 " pdb="FE3 SF4 C 201 " - pdb=" SG CYS C 88 " pdb="FE2 SF4 C 201 " - pdb=" SG CYS C 54 " pdb="FE1 SF4 C 201 " - pdb=" SG CYS C 94 " pdb="FE4 SF4 C 201 " - pdb=" SG CYS C 91 " pdb=" SF4 C 202 " pdb="FE3 SF4 C 202 " - pdb=" SG CYS C 44 " pdb="FE1 SF4 C 202 " - pdb=" SG CYS C 47 " pdb="FE4 SF4 C 202 " - pdb=" SG CYS C 98 " pdb="FE2 SF4 C 202 " - pdb=" SG CYS C 50 " pdb=" SF4 D 701 " pdb="FE4 SF4 D 701 " - pdb=" SG CYS D 18 " pdb="FE3 SF4 D 701 " - pdb=" SG CYS D 50 " pdb="FE2 SF4 D 701 " - pdb=" SG CYS D 22 " pdb="FE1 SF4 D 701 " - pdb=" SG CYS D 15 " pdb=" SF4 E 501 " pdb="FE4 SF4 E 501 " - pdb=" SG CYS E 311 " pdb="FE3 SF4 E 501 " - pdb=" ND1 HIS E 337 " pdb="FE1 SF4 E 501 " - pdb=" SG CYS E 308 " pdb="FE2 SF4 E 501 " - pdb=" SG CYS E 306 " pdb=" SF4 E 502 " pdb="FE1 SF4 E 502 " - pdb=" SG CYS E 296 " pdb="FE4 SF4 E 502 " - pdb=" SG CYS E 293 " pdb="FE2 SF4 E 502 " - pdb=" SG CYS E 352 " pdb="FE3 SF4 E 502 " - pdb=" SG CYS E 299 " pdb=" SF4 E 503 " pdb="FE4 SF4 E 503 " - pdb=" SG CYS E 348 " pdb="FE3 SF4 E 503 " - pdb=" SG CYS E 342 " pdb="FE2 SF4 E 503 " - pdb=" SG CYS E 345 " pdb="FE1 SF4 E 503 " - pdb=" SG CYS E 303 " pdb=" SF4 E 504 " pdb="FE2 SF4 E 504 " - pdb=" SG CYS E 129 " pdb="FE4 SF4 E 504 " - pdb=" SG CYS E 190 " pdb="FE3 SF4 E 504 " - pdb=" SG CYS E 193 " pdb="FE1 SF4 E 504 " - pdb=" SG CYS E 103 " pdb=" SF4 H 504 " pdb="FE4 SF4 H 504 " - pdb=" SG CYS H 10 " pdb="FE3 SF4 H 504 " - pdb=" SG CYS H 38 " pdb="FE2 SF4 H 504 " - pdb=" SG CYS H 13 " pdb="FE1 SF4 H 504 " - pdb=" SG CYS H 17 " pdb=" SF4 K 401 " pdb="FE1 SF4 K 401 " - pdb=" SG CYS K 333 " pdb="FE4 SF4 K 401 " - pdb=" SG CYS K 281 " pdb="FE2 SF4 K 401 " - pdb=" SG CYS K 288 " pdb="FE3 SF4 K 401 " - pdb=" SG CYS K 285 " pdb=" SF4 K 402 " pdb="FE4 SF4 K 402 " - pdb=" SG CYS K 329 " pdb="FE1 SF4 K 402 " - pdb=" SG CYS K 323 " pdb="FE3 SF4 K 402 " - pdb=" SG CYS K 326 " pdb="FE2 SF4 K 402 " - pdb=" SG CYS K 292 " pdb=" SF4 K 403 " pdb="FE3 SF4 K 403 " - pdb=" SG CYS K 78 " pdb="FE2 SF4 K 403 " - pdb=" SG CYS K 81 " pdb="FE4 SF4 K 403 " - pdb=" SG CYS K 84 " pdb="FE1 SF4 K 403 " - pdb=" SG CYS K 47 " pdb=" SF4 K 404 " pdb="FE2 SF4 K 404 " - pdb=" SG CYS K 88 " pdb="FE1 SF4 K 404 " - pdb=" SG CYS K 40 " pdb="FE4 SF4 K 404 " - pdb=" SG CYS K 37 " pdb="FE3 SF4 K 404 " - pdb=" SG CYS K 43 " pdb=" SF4 K 405 " pdb="FE4 SF4 K 405 " - pdb=" SG CYS K 128 " pdb="FE3 SF4 K 405 " - pdb=" SG CYS K 131 " pdb="FE1 SF4 K 405 " - pdb=" SG CYS K 259 " pdb="FE2 SF4 K 405 " - pdb=" SG CYS K 125 " pdb=" SF4 K 406 " pdb="FE1 SF4 K 406 " - pdb=" SG CYS K 135 " pdb="FE2 SF4 K 406 " - pdb=" SG CYS K 249 " pdb="FE4 SF4 K 406 " - pdb=" SG CYS K 252 " pdb="FE3 SF4 K 406 " - pdb=" SG CYS K 255 " pdb=" SF4 K 407 " pdb="FE2 SF4 K 407 " - pdb=" SG CYS K 215 " pdb="FE3 SF4 K 407 " - pdb=" SG CYS K 184 " pdb="FE4 SF4 K 407 " - pdb=" SG CYS K 212 " pdb="FE1 SF4 K 407 " - pdb=" SG CYS K 218 " pdb=" SF4 K 408 " pdb="FE3 SF4 K 408 " - pdb=" SG CYS K 180 " pdb="FE2 SF4 K 408 " - pdb=" SG CYS K 222 " pdb="FE1 SF4 K 408 " - pdb=" SG CYS K 177 " pdb="FE4 SF4 K 408 " - pdb=" SG CYS K 174 " pdb=" SF4 L 201 " pdb="FE2 SF4 L 201 " - pdb=" SG CYS L 122 " pdb="FE1 SF4 L 201 " - pdb=" SG CYS L 119 " pdb="FE4 SF4 L 201 " - pdb=" SG CYS L 83 " pdb="FE3 SF4 L 201 " - pdb=" SG CYS L 125 " pdb=" SF4 L 202 " pdb="FE4 SF4 L 202 " - pdb=" SG CYS L 76 " pdb="FE2 SF4 L 202 " - pdb=" SG CYS L 73 " pdb="FE1 SF4 L 202 " - pdb=" SG CYS L 129 " pdb="FE3 SF4 L 202 " - pdb=" SG CYS L 79 " pdb=" SF4 a 701 " pdb="FE1 SF4 a 701 " - pdb=" SG CYS a 420 " pdb="FE3 SF4 a 701 " - pdb=" SG CYS a 421 " pdb="FE4 SF4 a 701 " - pdb=" SG CYS a 416 " pdb="FE2 SF4 a 701 " - pdb=" SG CYS a 402 " pdb=" SF4 a 703 " pdb="FE2 SF4 a 703 " - pdb=" SG CYS a 14 " pdb="FE4 SF4 a 703 " - pdb=" SG CYS a 49 " pdb="FE1 SF4 a 703 " - pdb=" SG CYS a 74 " pdb="FE3 SF4 a 703 " - pdb=" SG CYS a 16 " pdb=" SF4 a 704 " pdb="FE1 SF4 a 704 " - pdb=" SG CYS a 610 " pdb="FE3 SF4 a 704 " - pdb=" SG CYS a 636 " pdb="FE2 SF4 a 704 " - pdb=" SG CYS a 639 " pdb="FE4 SF4 a 704 " - pdb=" SG CYS a 633 " pdb=" SF4 a 705 " pdb="FE2 SF4 a 705 " - pdb=" SG CYS a 603 " pdb="FE3 SF4 a 705 " - pdb=" SG CYS a 606 " pdb="FE4 SF4 a 705 " - pdb=" SG CYS a 643 " pdb="FE1 SF4 a 705 " - pdb=" SG CYS a 600 " pdb=" SF4 a 706 " pdb="FE1 SF4 a 706 " - pdb=" SG CYS a 264 " pdb="FE4 SF4 a 706 " - pdb=" SG CYS a 261 " pdb="FE3 SF4 a 706 " - pdb=" SG CYS a 267 " pdb="FE2 SF4 a 706 " - pdb=" SG CYS a 318 " pdb=" SF4 a 707 " pdb="FE2 SF4 a 707 " - pdb=" SG CYS a 308 " pdb="FE3 SF4 a 707 " - pdb=" SG CYS a 311 " pdb="FE4 SF4 a 707 " - pdb=" SG CYS a 271 " pdb="FE1 SF4 a 707 " - pdb=" SG CYS a 314 " pdb=" SF4 c 201 " pdb="FE3 SF4 c 201 " - pdb=" SG CYS c 88 " pdb="FE2 SF4 c 201 " - pdb=" SG CYS c 54 " pdb="FE1 SF4 c 201 " - pdb=" SG CYS c 94 " pdb="FE4 SF4 c 201 " - pdb=" SG CYS c 91 " pdb=" SF4 c 202 " pdb="FE3 SF4 c 202 " - pdb=" SG CYS c 44 " pdb="FE1 SF4 c 202 " - pdb=" SG CYS c 47 " pdb="FE4 SF4 c 202 " - pdb=" SG CYS c 98 " pdb="FE2 SF4 c 202 " - pdb=" SG CYS c 50 " pdb=" SF4 d 701 " pdb="FE4 SF4 d 701 " - pdb=" SG CYS d 18 " pdb="FE3 SF4 d 701 " - pdb=" SG CYS d 50 " pdb="FE2 SF4 d 701 " - pdb=" SG CYS d 22 " pdb="FE1 SF4 d 701 " - pdb=" SG CYS d 15 " pdb=" SF4 e 501 " pdb="FE4 SF4 e 501 " - pdb=" SG CYS e 311 " pdb="FE3 SF4 e 501 " - pdb=" ND1 HIS e 337 " pdb="FE1 SF4 e 501 " - pdb=" SG CYS e 308 " pdb="FE2 SF4 e 501 " - pdb=" SG CYS e 306 " pdb=" SF4 e 502 " pdb="FE1 SF4 e 502 " - pdb=" SG CYS e 296 " pdb="FE2 SF4 e 502 " - pdb=" SG CYS e 352 " pdb="FE4 SF4 e 502 " - pdb=" SG CYS e 293 " pdb="FE3 SF4 e 502 " - pdb=" SG CYS e 299 " pdb=" SF4 e 503 " pdb="FE4 SF4 e 503 " - pdb=" SG CYS e 348 " pdb="FE3 SF4 e 503 " - pdb=" SG CYS e 342 " pdb="FE2 SF4 e 503 " - pdb=" SG CYS e 345 " pdb="FE1 SF4 e 503 " - pdb=" SG CYS e 303 " pdb=" SF4 e 504 " pdb="FE2 SF4 e 504 " - pdb=" SG CYS e 129 " pdb="FE4 SF4 e 504 " - pdb=" SG CYS e 190 " pdb="FE3 SF4 e 504 " - pdb=" SG CYS e 193 " pdb="FE1 SF4 e 504 " - pdb=" SG CYS e 103 " pdb=" SF4 h 504 " pdb="FE4 SF4 h 504 " - pdb=" SG CYS h 10 " pdb="FE3 SF4 h 504 " - pdb=" SG CYS h 38 " pdb="FE2 SF4 h 504 " - pdb=" SG CYS h 13 " pdb="FE1 SF4 h 504 " - pdb=" SG CYS h 17 " pdb=" SF4 k 401 " pdb="FE1 SF4 k 401 " - pdb=" SG CYS k 333 " pdb="FE4 SF4 k 401 " - pdb=" SG CYS k 281 " pdb="FE2 SF4 k 401 " - pdb=" SG CYS k 288 " pdb="FE3 SF4 k 401 " - pdb=" SG CYS k 285 " pdb=" SF4 k 402 " pdb="FE4 SF4 k 402 " - pdb=" SG CYS k 329 " pdb="FE1 SF4 k 402 " - pdb=" SG CYS k 323 " pdb="FE3 SF4 k 402 " - pdb=" SG CYS k 326 " pdb="FE2 SF4 k 402 " - pdb=" SG CYS k 292 " pdb=" SF4 k 403 " pdb="FE3 SF4 k 403 " - pdb=" SG CYS k 78 " pdb="FE2 SF4 k 403 " - pdb=" SG CYS k 81 " pdb="FE4 SF4 k 403 " - pdb=" SG CYS k 84 " pdb="FE1 SF4 k 403 " - pdb=" SG CYS k 47 " pdb=" SF4 k 404 " pdb="FE2 SF4 k 404 " - pdb=" SG CYS k 88 " pdb="FE1 SF4 k 404 " - pdb=" SG CYS k 40 " pdb="FE4 SF4 k 404 " - pdb=" SG CYS k 37 " pdb="FE3 SF4 k 404 " - pdb=" SG CYS k 43 " pdb=" SF4 k 405 " pdb="FE4 SF4 k 405 " - pdb=" SG CYS k 128 " pdb="FE3 SF4 k 405 " - pdb=" SG CYS k 131 " pdb="FE1 SF4 k 405 " - pdb=" SG CYS k 259 " pdb="FE2 SF4 k 405 " - pdb=" SG CYS k 125 " pdb=" SF4 k 406 " pdb="FE1 SF4 k 406 " - pdb=" SG CYS k 135 " pdb="FE4 SF4 k 406 " - pdb=" SG CYS k 252 " pdb="FE3 SF4 k 406 " - pdb=" SG CYS k 255 " pdb="FE2 SF4 k 406 " - pdb=" SG CYS k 249 " pdb="FE4 SF4 k 406 " - pdb=" SG CYS k 250 " pdb=" SF4 k 407 " pdb="FE2 SF4 k 407 " - pdb=" SG CYS k 215 " pdb="FE3 SF4 k 407 " - pdb=" SG CYS k 184 " pdb="FE4 SF4 k 407 " - pdb=" SG CYS k 212 " pdb="FE1 SF4 k 407 " - pdb=" SG CYS k 218 " pdb=" SF4 k 408 " pdb="FE2 SF4 k 408 " - pdb=" SG CYS k 222 " pdb="FE3 SF4 k 408 " - pdb=" SG CYS k 180 " pdb="FE1 SF4 k 408 " - pdb=" SG CYS k 177 " pdb="FE4 SF4 k 408 " - pdb=" SG CYS k 174 " pdb=" SF4 l 201 " pdb="FE2 SF4 l 201 " - pdb=" SG CYS l 122 " pdb="FE1 SF4 l 201 " - pdb=" SG CYS l 119 " pdb="FE4 SF4 l 201 " - pdb=" SG CYS l 83 " pdb="FE3 SF4 l 201 " - pdb=" SG CYS l 125 " pdb=" SF4 l 202 " pdb="FE4 SF4 l 202 " - pdb=" SG CYS l 76 " pdb="FE2 SF4 l 202 " - pdb=" SG CYS l 73 " pdb="FE1 SF4 l 202 " - pdb=" SG CYS l 129 " pdb="FE3 SF4 l 202 " - pdb=" SG CYS l 79 " Number of angles added : 585 Zn2+ tetrahedral coordination pdb=" ZN G 601 " pdb="ZN ZN G 601 " - pdb=" NE2 HIS G 60 " pdb="ZN ZN G 601 " - pdb=" NE2 HIS G 58 " pdb=" ZN G 602 " pdb="ZN ZN G 602 " - pdb=" NE2 HIS G 237 " pdb="ZN ZN G 602 " - pdb=" NE2 HIS G 276 " pdb=" ZN g 601 " pdb="ZN ZN g 601 " - pdb=" NE2 HIS g 60 " pdb="ZN ZN g 601 " - pdb=" NE2 HIS g 58 " pdb=" ZN g 602 " pdb="ZN ZN g 602 " - pdb=" NE2 HIS g 237 " pdb="ZN ZN g 602 " - pdb=" NE2 HIS g 276 " 16324 Ramachandran restraints generated. 8162 Oldfield, 0 Emsley, 8162 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 15000 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 310 helices and 95 sheets defined 33.3% alpha, 12.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 9.67 Creating SS restraints... Processing helix chain 'A' and resid 26 through 35 Processing helix chain 'A' and resid 51 through 64 Processing helix chain 'A' and resid 76 through 88 Proline residue: A 81 - end of helix Processing helix chain 'A' and resid 116 through 133 Processing helix chain 'A' and resid 157 through 169 Processing helix chain 'A' and resid 199 through 212 removed outlier: 3.610A pdb=" N LEU A 203 " --> pdb=" O SER A 199 " (cutoff:3.500A) Proline residue: A 205 - end of helix Processing helix chain 'A' and resid 248 through 254 Processing helix chain 'A' and resid 266 through 270 Processing helix chain 'A' and resid 313 through 321 removed outlier: 6.140A pdb=" N ASP A 320 " --> pdb=" O GLU A 316 " (cutoff:3.500A) removed outlier: 7.002A pdb=" N LYS A 321 " --> pdb=" O ALA A 317 " (cutoff:3.500A) Processing helix chain 'A' and resid 351 through 353 No H-bonds generated for 'chain 'A' and resid 351 through 353' Processing helix chain 'A' and resid 368 through 375 Processing helix chain 'A' and resid 420 through 434 Processing helix chain 'A' and resid 454 through 464 Processing helix chain 'A' and resid 517 through 524 Processing helix chain 'A' and resid 555 through 558 Processing helix chain 'A' and resid 563 through 583 Proline residue: A 580 - end of helix Processing helix chain 'A' and resid 605 through 609 removed outlier: 3.868A pdb=" N ASN A 608 " --> pdb=" O MET A 605 " (cutoff:3.500A) Processing helix chain 'A' and resid 638 through 642 Processing helix chain 'A' and resid 655 through 666 Processing helix chain 'F' and resid 18 through 28 Processing helix chain 'F' and resid 44 through 46 No H-bonds generated for 'chain 'F' and resid 44 through 46' Processing helix chain 'F' and resid 49 through 58 Processing helix chain 'F' and resid 78 through 95 removed outlier: 3.621A pdb=" N ALA F 82 " --> pdb=" O GLY F 78 " (cutoff:3.500A) Processing helix chain 'F' and resid 100 through 102 No H-bonds generated for 'chain 'F' and resid 100 through 102' Processing helix chain 'F' and resid 113 through 130 Processing helix chain 'F' and resid 135 through 139 Processing helix chain 'E' and resid 15 through 20 Processing helix chain 'E' and resid 26 through 37 Processing helix chain 'E' and resid 63 through 65 No H-bonds generated for 'chain 'E' and resid 63 through 65' Processing helix chain 'E' and resid 81 through 87 Processing helix chain 'E' and resid 89 through 91 No H-bonds generated for 'chain 'E' and resid 89 through 91' Processing helix chain 'E' and resid 102 through 113 Processing helix chain 'E' and resid 135 through 144 Processing helix chain 'E' and resid 150 through 152 No H-bonds generated for 'chain 'E' and resid 150 through 152' Processing helix chain 'E' and resid 176 through 182 Processing helix chain 'E' and resid 188 through 192 Processing helix chain 'E' and resid 226 through 238 Processing helix chain 'E' and resid 248 through 275 Processing helix chain 'E' and resid 279 through 292 removed outlier: 3.594A pdb=" N MET E 287 " --> pdb=" O LYS E 284 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N SER E 291 " --> pdb=" O SER E 288 " (cutoff:3.500A) Processing helix chain 'E' and resid 298 through 302 Processing helix chain 'E' and resid 312 through 314 No H-bonds generated for 'chain 'E' and resid 312 through 314' Processing helix chain 'E' and resid 329 through 341 removed outlier: 3.664A pdb=" N ARG E 334 " --> pdb=" O PHE E 330 " (cutoff:3.500A) removed outlier: 5.237A pdb=" N ASP E 340 " --> pdb=" O ALA E 336 " (cutoff:3.500A) removed outlier: 5.587A pdb=" N SER E 341 " --> pdb=" O HIS E 337 " (cutoff:3.500A) Processing helix chain 'E' and resid 347 through 350 No H-bonds generated for 'chain 'E' and resid 347 through 350' Processing helix chain 'E' and resid 358 through 373 removed outlier: 4.339A pdb=" N GLU E 368 " --> pdb=" O SER E 364 " (cutoff:3.500A) Processing helix chain 'E' and resid 391 through 400 Processing helix chain 'C' and resid 9 through 14 Processing helix chain 'C' and resid 22 through 24 No H-bonds generated for 'chain 'C' and resid 22 through 24' Processing helix chain 'C' and resid 27 through 37 Processing helix chain 'C' and resid 41 through 43 No H-bonds generated for 'chain 'C' and resid 41 through 43' Processing helix chain 'C' and resid 49 through 53 Processing helix chain 'C' and resid 57 through 59 No H-bonds generated for 'chain 'C' and resid 57 through 59' Processing helix chain 'C' and resid 64 through 73 Processing helix chain 'C' and resid 83 through 85 No H-bonds generated for 'chain 'C' and resid 83 through 85' Processing helix chain 'C' and resid 93 through 97 Processing helix chain 'C' and resid 104 through 117 Processing helix chain 'C' and resid 123 through 135 Processing helix chain 'C' and resid 143 through 152 Processing helix chain 'C' and resid 166 through 178 removed outlier: 4.185A pdb=" N GLY C 170 " --> pdb=" O GLU C 166 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N TYR C 178 " --> pdb=" O ILE C 174 " (cutoff:3.500A) Processing helix chain 'C' and resid 180 through 188 removed outlier: 3.848A pdb=" N ARG C 186 " --> pdb=" O GLU C 182 " (cutoff:3.500A) Processing helix chain 'B' and resid 11 through 14 No H-bonds generated for 'chain 'B' and resid 11 through 14' Processing helix chain 'B' and resid 17 through 29 Processing helix chain 'B' and resid 54 through 71 removed outlier: 3.734A pdb=" N ALA B 68 " --> pdb=" O ASN B 64 " (cutoff:3.500A) Processing helix chain 'B' and resid 80 through 93 Processing helix chain 'B' and resid 97 through 110 removed outlier: 4.518A pdb=" N GLU B 109 " --> pdb=" O GLU B 105 " (cutoff:3.500A) removed outlier: 4.642A pdb=" N ILE B 110 " --> pdb=" O VAL B 106 " (cutoff:3.500A) Processing helix chain 'B' and resid 123 through 128 Processing helix chain 'B' and resid 135 through 141 Processing helix chain 'B' and resid 176 through 183 Processing helix chain 'B' and resid 201 through 207 removed outlier: 6.159A pdb=" N ARG B 205 " --> pdb=" O GLY B 202 " (cutoff:3.500A) Processing helix chain 'B' and resid 209 through 226 removed outlier: 3.603A pdb=" N LYS B 219 " --> pdb=" O ILE B 215 " (cutoff:3.500A) Processing helix chain 'B' and resid 236 through 252 removed outlier: 3.923A pdb=" N GLN B 246 " --> pdb=" O PHE B 242 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N ILE B 247 " --> pdb=" O ASP B 243 " (cutoff:3.500A) Processing helix chain 'B' and resid 264 through 272 Processing helix chain 'B' and resid 276 through 279 No H-bonds generated for 'chain 'B' and resid 276 through 279' Processing helix chain 'B' and resid 281 through 283 No H-bonds generated for 'chain 'B' and resid 281 through 283' Processing helix chain 'B' and resid 289 through 295 Processing helix chain 'D' and resid 51 through 54 No H-bonds generated for 'chain 'D' and resid 51 through 54' Processing helix chain 'D' and resid 82 through 100 Processing helix chain 'D' and resid 115 through 127 Processing helix chain 'D' and resid 145 through 152 Processing helix chain 'D' and resid 163 through 167 Processing helix chain 'D' and resid 183 through 195 removed outlier: 4.563A pdb=" N ARG D 188 " --> pdb=" O LEU D 184 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N ILE D 189 " --> pdb=" O ALA D 185 " (cutoff:3.500A) Processing helix chain 'D' and resid 224 through 238 Processing helix chain 'D' and resid 243 through 249 Processing helix chain 'D' and resid 253 through 262 removed outlier: 4.477A pdb=" N ASN D 262 " --> pdb=" O LYS D 258 " (cutoff:3.500A) Processing helix chain 'D' and resid 274 through 286 Processing helix chain 'D' and resid 306 through 317 removed outlier: 3.571A pdb=" N MET D 311 " --> pdb=" O ASN D 307 " (cutoff:3.500A) Processing helix chain 'D' and resid 337 through 343 Processing helix chain 'D' and resid 359 through 369 Processing helix chain 'D' and resid 382 through 387 Processing helix chain 'D' and resid 403 through 406 No H-bonds generated for 'chain 'D' and resid 403 through 406' Processing helix chain 'D' and resid 410 through 418 Processing helix chain 'D' and resid 433 through 436 Processing helix chain 'D' and resid 476 through 487 Processing helix chain 'D' and resid 497 through 507 Processing helix chain 'D' and resid 516 through 519 No H-bonds generated for 'chain 'D' and resid 516 through 519' Processing helix chain 'I' and resid 23 through 26 No H-bonds generated for 'chain 'I' and resid 23 through 26' Processing helix chain 'I' and resid 31 through 36 Processing helix chain 'L' and resid 86 through 88 No H-bonds generated for 'chain 'L' and resid 86 through 88' Processing helix chain 'L' and resid 124 through 128 Processing helix chain 'G' and resid 64 through 72 Processing helix chain 'G' and resid 103 through 113 Processing helix chain 'G' and resid 125 through 137 removed outlier: 3.662A pdb=" N ALA G 128 " --> pdb=" O PRO G 125 " (cutoff:3.500A) Proline residue: G 129 - end of helix removed outlier: 3.517A pdb=" N GLU G 134 " --> pdb=" O VAL G 131 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N PHE G 135 " --> pdb=" O HIS G 132 " (cutoff:3.500A) Processing helix chain 'G' and resid 154 through 161 removed outlier: 4.099A pdb=" N ILE G 159 " --> pdb=" O CYS G 155 " (cutoff:3.500A) Processing helix chain 'G' and resid 164 through 178 Processing helix chain 'G' and resid 190 through 196 removed outlier: 3.549A pdb=" N ALA G 195 " --> pdb=" O THR G 191 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N TRP G 196 " --> pdb=" O GLU G 192 " (cutoff:3.500A) Processing helix chain 'G' and resid 214 through 228 Processing helix chain 'G' and resid 247 through 257 removed outlier: 4.179A pdb=" N LEU G 256 " --> pdb=" O ASP G 252 " (cutoff:3.500A) removed outlier: 5.201A pdb=" N ALA G 257 " --> pdb=" O THR G 253 " (cutoff:3.500A) Processing helix chain 'G' and resid 277 through 280 No H-bonds generated for 'chain 'G' and resid 277 through 280' Processing helix chain 'G' and resid 294 through 303 Processing helix chain 'G' and resid 326 through 336 Processing helix chain 'G' and resid 363 through 378 removed outlier: 3.923A pdb=" N GLY G 372 " --> pdb=" O GLN G 368 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N LEU G 373 " --> pdb=" O TRP G 369 " (cutoff:3.500A) Processing helix chain 'G' and resid 397 through 408 Proline residue: G 401 - end of helix Processing helix chain 'G' and resid 410 through 419 Processing helix chain 'G' and resid 423 through 428 Processing helix chain 'G' and resid 441 through 456 removed outlier: 5.318A pdb=" N GLY G 451 " --> pdb=" O MET G 447 " (cutoff:3.500A) Proline residue: G 452 - end of helix Processing helix chain 'G' and resid 487 through 495 Processing helix chain 'G' and resid 532 through 544 Processing helix chain 'J' and resid 15 through 23 Processing helix chain 'J' and resid 28 through 34 Processing helix chain 'J' and resid 41 through 47 Processing helix chain 'J' and resid 86 through 89 No H-bonds generated for 'chain 'J' and resid 86 through 89' Processing helix chain 'J' and resid 122 through 130 Processing helix chain 'K' and resid 57 through 62 Processing helix chain 'K' and resid 83 through 86 No H-bonds generated for 'chain 'K' and resid 83 through 86' Processing helix chain 'K' and resid 104 through 107 No H-bonds generated for 'chain 'K' and resid 104 through 107' Processing helix chain 'K' and resid 130 through 134 Processing helix chain 'K' and resid 157 through 159 No H-bonds generated for 'chain 'K' and resid 157 through 159' Processing helix chain 'K' and resid 171 through 173 No H-bonds generated for 'chain 'K' and resid 171 through 173' Processing helix chain 'K' and resid 178 through 181 Processing helix chain 'K' and resid 209 through 211 No H-bonds generated for 'chain 'K' and resid 209 through 211' Processing helix chain 'K' and resid 217 through 221 Processing helix chain 'K' and resid 254 through 258 Processing helix chain 'K' and resid 278 through 280 No H-bonds generated for 'chain 'K' and resid 278 through 280' Processing helix chain 'K' and resid 287 through 291 Processing helix chain 'K' and resid 328 through 332 Processing helix chain 'K' and resid 354 through 363 Processing helix chain 'H' and resid 39 through 48 Processing helix chain 'H' and resid 71 through 84 Processing helix chain 'H' and resid 98 through 111 removed outlier: 3.578A pdb=" N ALA H 105 " --> pdb=" O GLN H 101 " (cutoff:3.500A) Processing helix chain 'H' and resid 124 through 133 removed outlier: 3.510A pdb=" N ASP H 132 " --> pdb=" O LEU H 128 " (cutoff:3.500A) Processing helix chain 'H' and resid 140 through 146 Processing helix chain 'H' and resid 162 through 164 No H-bonds generated for 'chain 'H' and resid 162 through 164' Processing helix chain 'H' and resid 180 through 183 removed outlier: 3.570A pdb=" N LYS H 183 " --> pdb=" O GLY H 180 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 180 through 183' Processing helix chain 'H' and resid 195 through 199 Processing helix chain 'H' and resid 211 through 223 Processing helix chain 'H' and resid 226 through 228 No H-bonds generated for 'chain 'H' and resid 226 through 228' Processing helix chain 'H' and resid 238 through 250 Processing helix chain 'H' and resid 260 through 263 No H-bonds generated for 'chain 'H' and resid 260 through 263' Processing helix chain 'H' and resid 268 through 284 removed outlier: 4.060A pdb=" N ILE H 272 " --> pdb=" O ARG H 268 " (cutoff:3.500A) removed outlier: 4.131A pdb=" N LYS H 284 " --> pdb=" O ARG H 280 " (cutoff:3.500A) Processing helix chain 'H' and resid 297 through 309 removed outlier: 4.457A pdb=" N ALA H 300 " --> pdb=" O TYR H 297 " (cutoff:3.500A) Proline residue: H 302 - end of helix removed outlier: 3.512A pdb=" N VAL H 305 " --> pdb=" O PRO H 302 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N TRP H 306 " --> pdb=" O GLY H 303 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N THR H 309 " --> pdb=" O TRP H 306 " (cutoff:3.500A) Processing helix chain 'H' and resid 328 through 331 No H-bonds generated for 'chain 'H' and resid 328 through 331' Processing helix chain 'H' and resid 333 through 338 Processing helix chain 'H' and resid 352 through 355 No H-bonds generated for 'chain 'H' and resid 352 through 355' Processing helix chain 'H' and resid 358 through 366 removed outlier: 4.047A pdb=" N LYS H 366 " --> pdb=" O LYS H 362 " (cutoff:3.500A) Processing helix chain 'H' and resid 378 through 381 No H-bonds generated for 'chain 'H' and resid 378 through 381' Processing helix chain 'H' and resid 423 through 436 Processing helix chain 'a' and resid 26 through 35 Processing helix chain 'a' and resid 51 through 64 Processing helix chain 'a' and resid 76 through 88 Proline residue: a 81 - end of helix Processing helix chain 'a' and resid 116 through 133 Processing helix chain 'a' and resid 157 through 169 Processing helix chain 'a' and resid 199 through 212 Proline residue: a 205 - end of helix Processing helix chain 'a' and resid 248 through 254 Processing helix chain 'a' and resid 266 through 270 Processing helix chain 'a' and resid 313 through 321 removed outlier: 6.140A pdb=" N ASP a 320 " --> pdb=" O GLU a 316 " (cutoff:3.500A) removed outlier: 7.003A pdb=" N LYS a 321 " --> pdb=" O ALA a 317 " (cutoff:3.500A) Processing helix chain 'a' and resid 351 through 353 No H-bonds generated for 'chain 'a' and resid 351 through 353' Processing helix chain 'a' and resid 368 through 375 Processing helix chain 'a' and resid 420 through 434 Processing helix chain 'a' and resid 454 through 464 Processing helix chain 'a' and resid 517 through 524 Processing helix chain 'a' and resid 555 through 558 Processing helix chain 'a' and resid 563 through 583 Proline residue: a 580 - end of helix Processing helix chain 'a' and resid 605 through 609 removed outlier: 3.869A pdb=" N ASN a 608 " --> pdb=" O MET a 605 " (cutoff:3.500A) Processing helix chain 'a' and resid 638 through 642 Processing helix chain 'a' and resid 655 through 666 Processing helix chain 'f' and resid 18 through 28 Processing helix chain 'f' and resid 44 through 46 No H-bonds generated for 'chain 'f' and resid 44 through 46' Processing helix chain 'f' and resid 49 through 58 Processing helix chain 'f' and resid 78 through 95 removed outlier: 3.621A pdb=" N ALA f 82 " --> pdb=" O GLY f 78 " (cutoff:3.500A) Processing helix chain 'f' and resid 100 through 102 No H-bonds generated for 'chain 'f' and resid 100 through 102' Processing helix chain 'f' and resid 113 through 130 Processing helix chain 'f' and resid 135 through 139 Processing helix chain 'e' and resid 15 through 20 Processing helix chain 'e' and resid 26 through 37 Processing helix chain 'e' and resid 63 through 65 No H-bonds generated for 'chain 'e' and resid 63 through 65' Processing helix chain 'e' and resid 81 through 87 Processing helix chain 'e' and resid 89 through 91 No H-bonds generated for 'chain 'e' and resid 89 through 91' Processing helix chain 'e' and resid 102 through 113 Processing helix chain 'e' and resid 135 through 144 Processing helix chain 'e' and resid 150 through 152 No H-bonds generated for 'chain 'e' and resid 150 through 152' Processing helix chain 'e' and resid 176 through 182 Processing helix chain 'e' and resid 188 through 192 Processing helix chain 'e' and resid 226 through 238 Processing helix chain 'e' and resid 248 through 275 Processing helix chain 'e' and resid 279 through 292 removed outlier: 3.595A pdb=" N MET e 287 " --> pdb=" O LYS e 284 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N SER e 291 " --> pdb=" O SER e 288 " (cutoff:3.500A) Processing helix chain 'e' and resid 298 through 302 Processing helix chain 'e' and resid 312 through 314 No H-bonds generated for 'chain 'e' and resid 312 through 314' Processing helix chain 'e' and resid 329 through 341 removed outlier: 3.665A pdb=" N ARG e 334 " --> pdb=" O PHE e 330 " (cutoff:3.500A) removed outlier: 5.236A pdb=" N ASP e 340 " --> pdb=" O ALA e 336 " (cutoff:3.500A) removed outlier: 5.587A pdb=" N SER e 341 " --> pdb=" O HIS e 337 " (cutoff:3.500A) Processing helix chain 'e' and resid 347 through 350 No H-bonds generated for 'chain 'e' and resid 347 through 350' Processing helix chain 'e' and resid 358 through 373 removed outlier: 4.339A pdb=" N GLU e 368 " --> pdb=" O SER e 364 " (cutoff:3.500A) Processing helix chain 'e' and resid 391 through 400 Processing helix chain 'c' and resid 9 through 14 Processing helix chain 'c' and resid 22 through 24 No H-bonds generated for 'chain 'c' and resid 22 through 24' Processing helix chain 'c' and resid 27 through 37 Processing helix chain 'c' and resid 41 through 43 No H-bonds generated for 'chain 'c' and resid 41 through 43' Processing helix chain 'c' and resid 49 through 53 Processing helix chain 'c' and resid 57 through 59 No H-bonds generated for 'chain 'c' and resid 57 through 59' Processing helix chain 'c' and resid 64 through 73 Processing helix chain 'c' and resid 83 through 85 No H-bonds generated for 'chain 'c' and resid 83 through 85' Processing helix chain 'c' and resid 93 through 97 Processing helix chain 'c' and resid 104 through 117 Processing helix chain 'c' and resid 123 through 135 Processing helix chain 'c' and resid 143 through 152 Processing helix chain 'c' and resid 166 through 178 removed outlier: 4.185A pdb=" N GLY c 170 " --> pdb=" O GLU c 166 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N TYR c 178 " --> pdb=" O ILE c 174 " (cutoff:3.500A) Processing helix chain 'c' and resid 180 through 188 removed outlier: 3.848A pdb=" N ARG c 186 " --> pdb=" O GLU c 182 " (cutoff:3.500A) Processing helix chain 'b' and resid 11 through 14 No H-bonds generated for 'chain 'b' and resid 11 through 14' Processing helix chain 'b' and resid 17 through 29 Processing helix chain 'b' and resid 54 through 71 removed outlier: 3.735A pdb=" N ALA b 68 " --> pdb=" O ASN b 64 " (cutoff:3.500A) Processing helix chain 'b' and resid 80 through 93 Processing helix chain 'b' and resid 97 through 110 removed outlier: 4.517A pdb=" N GLU b 109 " --> pdb=" O GLU b 105 " (cutoff:3.500A) removed outlier: 4.641A pdb=" N ILE b 110 " --> pdb=" O VAL b 106 " (cutoff:3.500A) Processing helix chain 'b' and resid 123 through 128 Processing helix chain 'b' and resid 135 through 141 Processing helix chain 'b' and resid 176 through 183 Processing helix chain 'b' and resid 201 through 207 removed outlier: 6.159A pdb=" N ARG b 205 " --> pdb=" O GLY b 202 " (cutoff:3.500A) Processing helix chain 'b' and resid 209 through 226 removed outlier: 3.603A pdb=" N LYS b 219 " --> pdb=" O ILE b 215 " (cutoff:3.500A) Processing helix chain 'b' and resid 236 through 252 removed outlier: 3.922A pdb=" N GLN b 246 " --> pdb=" O PHE b 242 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N ILE b 247 " --> pdb=" O ASP b 243 " (cutoff:3.500A) Processing helix chain 'b' and resid 264 through 272 Processing helix chain 'b' and resid 276 through 279 No H-bonds generated for 'chain 'b' and resid 276 through 279' Processing helix chain 'b' and resid 281 through 283 No H-bonds generated for 'chain 'b' and resid 281 through 283' Processing helix chain 'b' and resid 289 through 295 Processing helix chain 'd' and resid 51 through 54 No H-bonds generated for 'chain 'd' and resid 51 through 54' Processing helix chain 'd' and resid 82 through 100 Processing helix chain 'd' and resid 115 through 127 Processing helix chain 'd' and resid 145 through 152 Processing helix chain 'd' and resid 163 through 167 Processing helix chain 'd' and resid 183 through 195 removed outlier: 4.564A pdb=" N ARG d 188 " --> pdb=" O LEU d 184 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N ILE d 189 " --> pdb=" O ALA d 185 " (cutoff:3.500A) Processing helix chain 'd' and resid 224 through 238 Processing helix chain 'd' and resid 243 through 249 Processing helix chain 'd' and resid 253 through 262 removed outlier: 4.476A pdb=" N ASN d 262 " --> pdb=" O LYS d 258 " (cutoff:3.500A) Processing helix chain 'd' and resid 274 through 286 Processing helix chain 'd' and resid 306 through 317 removed outlier: 3.571A pdb=" N MET d 311 " --> pdb=" O ASN d 307 " (cutoff:3.500A) Processing helix chain 'd' and resid 337 through 343 Processing helix chain 'd' and resid 359 through 369 Processing helix chain 'd' and resid 382 through 387 Processing helix chain 'd' and resid 403 through 406 No H-bonds generated for 'chain 'd' and resid 403 through 406' Processing helix chain 'd' and resid 410 through 418 Processing helix chain 'd' and resid 433 through 436 Processing helix chain 'd' and resid 476 through 487 Processing helix chain 'd' and resid 497 through 507 Processing helix chain 'd' and resid 516 through 519 No H-bonds generated for 'chain 'd' and resid 516 through 519' Processing helix chain 'i' and resid 23 through 26 No H-bonds generated for 'chain 'i' and resid 23 through 26' Processing helix chain 'i' and resid 31 through 36 Processing helix chain 'l' and resid 86 through 88 No H-bonds generated for 'chain 'l' and resid 86 through 88' Processing helix chain 'l' and resid 124 through 128 Processing helix chain 'g' and resid 64 through 72 Processing helix chain 'g' and resid 103 through 113 Processing helix chain 'g' and resid 125 through 137 removed outlier: 3.663A pdb=" N ALA g 128 " --> pdb=" O PRO g 125 " (cutoff:3.500A) Proline residue: g 129 - end of helix removed outlier: 3.516A pdb=" N GLU g 134 " --> pdb=" O VAL g 131 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N PHE g 135 " --> pdb=" O HIS g 132 " (cutoff:3.500A) Processing helix chain 'g' and resid 154 through 161 removed outlier: 4.098A pdb=" N ILE g 159 " --> pdb=" O CYS g 155 " (cutoff:3.500A) Processing helix chain 'g' and resid 164 through 178 Processing helix chain 'g' and resid 190 through 196 removed outlier: 3.549A pdb=" N ALA g 195 " --> pdb=" O THR g 191 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N TRP g 196 " --> pdb=" O GLU g 192 " (cutoff:3.500A) Processing helix chain 'g' and resid 214 through 228 Processing helix chain 'g' and resid 247 through 257 removed outlier: 4.179A pdb=" N LEU g 256 " --> pdb=" O ASP g 252 " (cutoff:3.500A) removed outlier: 5.200A pdb=" N ALA g 257 " --> pdb=" O THR g 253 " (cutoff:3.500A) Processing helix chain 'g' and resid 277 through 280 No H-bonds generated for 'chain 'g' and resid 277 through 280' Processing helix chain 'g' and resid 294 through 303 Processing helix chain 'g' and resid 326 through 336 Processing helix chain 'g' and resid 363 through 378 removed outlier: 3.923A pdb=" N GLY g 372 " --> pdb=" O GLN g 368 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N LEU g 373 " --> pdb=" O TRP g 369 " (cutoff:3.500A) Processing helix chain 'g' and resid 397 through 408 Proline residue: g 401 - end of helix Processing helix chain 'g' and resid 410 through 419 Processing helix chain 'g' and resid 423 through 428 Processing helix chain 'g' and resid 441 through 456 removed outlier: 5.319A pdb=" N GLY g 451 " --> pdb=" O MET g 447 " (cutoff:3.500A) Proline residue: g 452 - end of helix Processing helix chain 'g' and resid 487 through 495 Processing helix chain 'g' and resid 532 through 544 Processing helix chain 'j' and resid 15 through 23 Processing helix chain 'j' and resid 28 through 34 Processing helix chain 'j' and resid 41 through 47 Processing helix chain 'j' and resid 86 through 89 No H-bonds generated for 'chain 'j' and resid 86 through 89' Processing helix chain 'j' and resid 122 through 130 Processing helix chain 'k' and resid 57 through 62 Processing helix chain 'k' and resid 83 through 86 No H-bonds generated for 'chain 'k' and resid 83 through 86' Processing helix chain 'k' and resid 104 through 107 No H-bonds generated for 'chain 'k' and resid 104 through 107' Processing helix chain 'k' and resid 130 through 134 Processing helix chain 'k' and resid 157 through 160 Processing helix chain 'k' and resid 171 through 173 No H-bonds generated for 'chain 'k' and resid 171 through 173' Processing helix chain 'k' and resid 179 through 183 removed outlier: 3.578A pdb=" N LEU k 183 " --> pdb=" O ILE k 179 " (cutoff:3.500A) No H-bonds generated for 'chain 'k' and resid 179 through 183' Processing helix chain 'k' and resid 209 through 211 No H-bonds generated for 'chain 'k' and resid 209 through 211' Processing helix chain 'k' and resid 217 through 221 Processing helix chain 'k' and resid 254 through 257 No H-bonds generated for 'chain 'k' and resid 254 through 257' Processing helix chain 'k' and resid 278 through 280 No H-bonds generated for 'chain 'k' and resid 278 through 280' Processing helix chain 'k' and resid 287 through 291 Processing helix chain 'k' and resid 328 through 332 Processing helix chain 'k' and resid 354 through 363 Processing helix chain 'h' and resid 39 through 48 Processing helix chain 'h' and resid 71 through 84 Processing helix chain 'h' and resid 98 through 111 removed outlier: 3.579A pdb=" N ALA h 105 " --> pdb=" O GLN h 101 " (cutoff:3.500A) Processing helix chain 'h' and resid 124 through 133 removed outlier: 3.510A pdb=" N ASP h 132 " --> pdb=" O LEU h 128 " (cutoff:3.500A) Processing helix chain 'h' and resid 140 through 146 Processing helix chain 'h' and resid 162 through 167 removed outlier: 4.246A pdb=" N MET h 165 " --> pdb=" O PRO h 162 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N SER h 166 " --> pdb=" O ARG h 163 " (cutoff:3.500A) Processing helix chain 'h' and resid 180 through 183 removed outlier: 3.571A pdb=" N LYS h 183 " --> pdb=" O GLY h 180 " (cutoff:3.500A) No H-bonds generated for 'chain 'h' and resid 180 through 183' Processing helix chain 'h' and resid 195 through 199 Processing helix chain 'h' and resid 211 through 223 Processing helix chain 'h' and resid 226 through 228 No H-bonds generated for 'chain 'h' and resid 226 through 228' Processing helix chain 'h' and resid 238 through 250 Processing helix chain 'h' and resid 260 through 263 No H-bonds generated for 'chain 'h' and resid 260 through 263' Processing helix chain 'h' and resid 268 through 284 removed outlier: 4.058A pdb=" N ILE h 272 " --> pdb=" O ARG h 268 " (cutoff:3.500A) removed outlier: 4.131A pdb=" N LYS h 284 " --> pdb=" O ARG h 280 " (cutoff:3.500A) Processing helix chain 'h' and resid 297 through 309 removed outlier: 4.456A pdb=" N ALA h 300 " --> pdb=" O TYR h 297 " (cutoff:3.500A) Proline residue: h 302 - end of helix removed outlier: 3.511A pdb=" N VAL h 305 " --> pdb=" O PRO h 302 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N TRP h 306 " --> pdb=" O GLY h 303 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N THR h 309 " --> pdb=" O TRP h 306 " (cutoff:3.500A) Processing helix chain 'h' and resid 328 through 331 No H-bonds generated for 'chain 'h' and resid 328 through 331' Processing helix chain 'h' and resid 333 through 338 Processing helix chain 'h' and resid 352 through 355 No H-bonds generated for 'chain 'h' and resid 352 through 355' Processing helix chain 'h' and resid 358 through 366 removed outlier: 4.047A pdb=" N LYS h 366 " --> pdb=" O LYS h 362 " (cutoff:3.500A) Processing helix chain 'h' and resid 378 through 381 No H-bonds generated for 'chain 'h' and resid 378 through 381' Processing helix chain 'h' and resid 423 through 436 Processing sheet with id= A, first strand: chain 'A' and resid 97 through 101 removed outlier: 6.349A pdb=" N VAL A 69 " --> pdb=" O GLU A 98 " (cutoff:3.500A) removed outlier: 7.711A pdb=" N ALA A 100 " --> pdb=" O VAL A 69 " (cutoff:3.500A) removed outlier: 6.562A pdb=" N VAL A 71 " --> pdb=" O ALA A 100 " (cutoff:3.500A) removed outlier: 7.482A pdb=" N VAL A 11 " --> pdb=" O ALA A 40 " (cutoff:3.500A) removed outlier: 4.206A pdb=" N ALA A 42 " --> pdb=" O VAL A 11 " (cutoff:3.500A) removed outlier: 7.329A pdb=" N VAL A 13 " --> pdb=" O ALA A 42 " (cutoff:3.500A) removed outlier: 4.450A pdb=" N GLN A 44 " --> pdb=" O VAL A 13 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 142 through 145 Processing sheet with id= C, first strand: chain 'A' and resid 551 through 553 removed outlier: 6.600A pdb=" N ALA A 340 " --> pdb=" O PHE A 552 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N THR A 339 " --> pdb=" O THR A 149 " (cutoff:3.500A) removed outlier: 6.577A pdb=" N LYS A 172 " --> pdb=" O ALA A 150 " (cutoff:3.500A) removed outlier: 7.820A pdb=" N VAL A 152 " --> pdb=" O LYS A 172 " (cutoff:3.500A) removed outlier: 6.180A pdb=" N TYR A 174 " --> pdb=" O VAL A 152 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 331 through 337 removed outlier: 3.508A pdb=" N LYS A 226 " --> pdb=" O THR A 237 " (cutoff:3.500A) removed outlier: 6.342A pdb=" N ARG A 239 " --> pdb=" O VAL A 224 " (cutoff:3.500A) removed outlier: 5.746A pdb=" N VAL A 224 " --> pdb=" O ARG A 239 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'A' and resid 274 through 276 Processing sheet with id= F, first strand: chain 'A' and resid 346 through 348 Processing sheet with id= G, first strand: chain 'A' and resid 365 through 367 removed outlier: 6.313A pdb=" N LEU A 505 " --> pdb=" O ILE A 366 " (cutoff:3.500A) removed outlier: 6.455A pdb=" N VAL A 439 " --> pdb=" O VAL A 397 " (cutoff:3.500A) removed outlier: 7.874A pdb=" N PHE A 399 " --> pdb=" O VAL A 439 " (cutoff:3.500A) removed outlier: 6.757A pdb=" N TYR A 441 " --> pdb=" O PHE A 399 " (cutoff:3.500A) removed outlier: 6.579A pdb=" N LYS A 467 " --> pdb=" O LEU A 442 " (cutoff:3.500A) removed outlier: 7.116A pdb=" N TYR A 444 " --> pdb=" O LYS A 467 " (cutoff:3.500A) removed outlier: 6.319A pdb=" N ILE A 469 " --> pdb=" O TYR A 444 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'A' and resid 475 through 478 removed outlier: 3.575A pdb=" N THR A 489 " --> pdb=" O VAL A 498 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'A' and resid 593 through 595 Processing sheet with id= J, first strand: chain 'A' and resid 615 through 620 Processing sheet with id= K, first strand: chain 'F' and resid 36 through 38 removed outlier: 6.784A pdb=" N ILE F 9 " --> pdb=" O ARG F 37 " (cutoff:3.500A) removed outlier: 6.725A pdb=" N GLY F 62 " --> pdb=" O LEU F 10 " (cutoff:3.500A) removed outlier: 8.456A pdb=" N ILE F 12 " --> pdb=" O GLY F 62 " (cutoff:3.500A) removed outlier: 6.970A pdb=" N LEU F 64 " --> pdb=" O ILE F 12 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'E' and resid 241 through 245 removed outlier: 6.624A pdb=" N LEU E 96 " --> pdb=" O ILE E 123 " (cutoff:3.500A) removed outlier: 7.799A pdb=" N ILE E 125 " --> pdb=" O LEU E 96 " (cutoff:3.500A) removed outlier: 6.380A pdb=" N VAL E 98 " --> pdb=" O ILE E 125 " (cutoff:3.500A) removed outlier: 7.442A pdb=" N VAL E 127 " --> pdb=" O VAL E 98 " (cutoff:3.500A) removed outlier: 6.664A pdb=" N CYS E 100 " --> pdb=" O VAL E 127 " (cutoff:3.500A) removed outlier: 6.815A pdb=" N ALA E 42 " --> pdb=" O ALA E 97 " (cutoff:3.500A) removed outlier: 8.491A pdb=" N THR E 99 " --> pdb=" O ALA E 42 " (cutoff:3.500A) removed outlier: 7.080A pdb=" N VAL E 44 " --> pdb=" O THR E 99 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'E' and resid 155 through 159 Processing sheet with id= N, first strand: chain 'B' and resid 32 through 36 removed outlier: 6.451A pdb=" N HIS B 2 " --> pdb=" O LYS B 33 " (cutoff:3.500A) removed outlier: 7.338A pdb=" N LEU B 35 " --> pdb=" O HIS B 2 " (cutoff:3.500A) removed outlier: 6.445A pdb=" N TYR B 4 " --> pdb=" O LEU B 35 " (cutoff:3.500A) removed outlier: 6.172A pdb=" N ASP B 74 " --> pdb=" O ALA B 5 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'B' and resid 187 through 189 removed outlier: 4.810A pdb=" N ALA B 153 " --> pdb=" O ILE B 189 " (cutoff:3.500A) removed outlier: 6.458A pdb=" N ALA B 230 " --> pdb=" O ALA B 152 " (cutoff:3.500A) removed outlier: 7.606A pdb=" N HIS B 154 " --> pdb=" O ALA B 230 " (cutoff:3.500A) removed outlier: 6.584A pdb=" N THR B 232 " --> pdb=" O HIS B 154 " (cutoff:3.500A) removed outlier: 8.023A pdb=" N GLU B 233 " --> pdb=" O PRO B 260 " (cutoff:3.500A) removed outlier: 6.647A pdb=" N LEU B 262 " --> pdb=" O GLU B 233 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'D' and resid 9 through 14 removed outlier: 3.683A pdb=" N GLY D 35 " --> pdb=" O VAL D 27 " (cutoff:3.500A) removed outlier: 6.533A pdb=" N SER D 29 " --> pdb=" O VAL D 33 " (cutoff:3.500A) removed outlier: 5.394A pdb=" N VAL D 33 " --> pdb=" O SER D 29 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'D' and resid 70 through 72 Processing sheet with id= R, first strand: chain 'D' and resid 106 through 108 removed outlier: 6.384A pdb=" N VAL D 439 " --> pdb=" O VAL D 425 " (cutoff:3.500A) removed outlier: 7.622A pdb=" N ASP D 427 " --> pdb=" O VAL D 439 " (cutoff:3.500A) removed outlier: 6.113A pdb=" N LEU D 441 " --> pdb=" O ASP D 427 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'D' and resid 198 through 201 removed outlier: 3.676A pdb=" N VAL D 291 " --> pdb=" O LEU D 170 " (cutoff:3.500A) removed outlier: 6.176A pdb=" N GLY D 327 " --> pdb=" O ILE D 292 " (cutoff:3.500A) removed outlier: 7.716A pdb=" N TYR D 294 " --> pdb=" O GLY D 327 " (cutoff:3.500A) removed outlier: 6.324A pdb=" N ASN D 329 " --> pdb=" O TYR D 294 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'D' and resid 452 through 454 Processing sheet with id= U, first strand: chain 'I' and resid 52 through 54 Processing sheet with id= V, first strand: chain 'I' and resid 39 through 41 Processing sheet with id= W, first strand: chain 'I' and resid 151 through 154 removed outlier: 6.943A pdb=" N THR I 170 " --> pdb=" O ILE I 152 " (cutoff:3.500A) removed outlier: 8.182A pdb=" N VAL I 154 " --> pdb=" O THR I 170 " (cutoff:3.500A) removed outlier: 6.732A pdb=" N ILE I 172 " --> pdb=" O VAL I 154 " (cutoff:3.500A) removed outlier: 6.677A pdb=" N THR I 189 " --> pdb=" O ILE I 171 " (cutoff:3.500A) removed outlier: 8.134A pdb=" N ILE I 173 " --> pdb=" O THR I 189 " (cutoff:3.500A) removed outlier: 6.439A pdb=" N ILE I 191 " --> pdb=" O ILE I 173 " (cutoff:3.500A) No H-bonds generated for sheet with id= W Processing sheet with id= X, first strand: chain 'I' and resid 223 through 228 removed outlier: 3.831A pdb=" N LYS I 223 " --> pdb=" O ILE I 243 " (cutoff:3.500A) removed outlier: 7.140A pdb=" N GLN I 241 " --> pdb=" O VAL I 225 " (cutoff:3.500A) removed outlier: 4.475A pdb=" N THR I 227 " --> pdb=" O PHE I 239 " (cutoff:3.500A) removed outlier: 6.254A pdb=" N PHE I 239 " --> pdb=" O THR I 227 " (cutoff:3.500A) Processing sheet with id= Y, first strand: chain 'L' and resid 65 through 68 removed outlier: 3.824A pdb=" N ALA L 65 " --> pdb=" O SER L 137 " (cutoff:3.500A) Processing sheet with id= Z, first strand: chain 'L' and resid 102 through 105 removed outlier: 3.579A pdb=" N ASP L 108 " --> pdb=" O ILE L 105 " (cutoff:3.500A) Processing sheet with id= AA, first strand: chain 'G' and resid 4 through 7 removed outlier: 6.475A pdb=" N GLN G 41 " --> pdb=" O LEU G 5 " (cutoff:3.500A) removed outlier: 7.411A pdb=" N LYS G 7 " --> pdb=" O GLN G 41 " (cutoff:3.500A) removed outlier: 6.078A pdb=" N ILE G 43 " --> pdb=" O LYS G 7 " (cutoff:3.500A) No H-bonds generated for sheet with id= AA Processing sheet with id= AB, first strand: chain 'G' and resid 26 through 28 removed outlier: 3.766A pdb=" N ALA G 26 " --> pdb=" O VAL G 33 " (cutoff:3.500A) Processing sheet with id= AC, first strand: chain 'G' and resid 49 through 52 removed outlier: 3.618A pdb=" N ALA G 474 " --> pdb=" O MET G 51 " (cutoff:3.500A) removed outlier: 6.200A pdb=" N LYS G 502 " --> pdb=" O VAL G 506 " (cutoff:3.500A) removed outlier: 5.481A pdb=" N VAL G 506 " --> pdb=" O LYS G 502 " (cutoff:3.500A) Processing sheet with id= AD, first strand: chain 'G' and resid 234 through 236 removed outlier: 3.681A pdb=" N THR G 308 " --> pdb=" O LEU G 272 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N THR G 388 " --> pdb=" O ILE G 311 " (cutoff:3.500A) Processing sheet with id= AE, first strand: chain 'G' and resid 282 through 284 Processing sheet with id= AF, first strand: chain 'G' and resid 318 through 323 Processing sheet with id= AG, first strand: chain 'G' and resid 523 through 525 Processing sheet with id= AH, first strand: chain 'G' and resid 11 through 13 removed outlier: 3.723A pdb=" N ASP G 21 " --> pdb=" O ILE G 11 " (cutoff:3.500A) removed outlier: 7.993A pdb=" N ASP G 13 " --> pdb=" O LYS G 19 " (cutoff:3.500A) removed outlier: 5.976A pdb=" N LYS G 19 " --> pdb=" O ASP G 13 " (cutoff:3.500A) Processing sheet with id= AI, first strand: chain 'G' and resid 54 through 56 removed outlier: 7.158A pdb=" N ASP G 56 " --> pdb=" O THR G 116 " (cutoff:3.500A) removed outlier: 4.278A pdb=" N THR G 118 " --> pdb=" O ASP G 56 " (cutoff:3.500A) removed outlier: 6.417A pdb=" N ASP G 142 " --> pdb=" O THR G 118 " (cutoff:3.500A) removed outlier: 7.395A pdb=" N GLU G 120 " --> pdb=" O ASP G 142 " (cutoff:3.500A) removed outlier: 6.476A pdb=" N ALA G 144 " --> pdb=" O GLU G 120 " (cutoff:3.500A) removed outlier: 7.579A pdb=" N ALA G 122 " --> pdb=" O ALA G 144 " (cutoff:3.500A) removed outlier: 6.159A pdb=" N MET G 146 " --> pdb=" O ALA G 122 " (cutoff:3.500A) Processing sheet with id= AJ, first strand: chain 'J' and resid 9 through 12 removed outlier: 6.020A pdb=" N CYS J 80 " --> pdb=" O ILE J 10 " (cutoff:3.500A) removed outlier: 7.444A pdb=" N GLN J 12 " --> pdb=" O CYS J 80 " (cutoff:3.500A) removed outlier: 6.301A pdb=" N ILE J 82 " --> pdb=" O GLN J 12 " (cutoff:3.500A) No H-bonds generated for sheet with id= AJ Processing sheet with id= AK, first strand: chain 'J' and resid 37 through 39 removed outlier: 3.619A pdb=" N THR J 53 " --> pdb=" O ALA J 68 " (cutoff:3.500A) Processing sheet with id= AL, first strand: chain 'K' and resid 7 through 13 Processing sheet with id= AM, first strand: chain 'K' and resid 52 through 54 Processing sheet with id= AN, first strand: chain 'K' and resid 140 through 143 Processing sheet with id= AO, first strand: chain 'K' and resid 187 through 191 Processing sheet with id= AP, first strand: chain 'K' and resid 270 through 276 removed outlier: 6.888A pdb=" N GLU K 273 " --> pdb=" O ARG K 343 " (cutoff:3.500A) removed outlier: 5.501A pdb=" N ARG K 343 " --> pdb=" O GLU K 273 " (cutoff:3.500A) removed outlier: 7.650A pdb=" N THR K 275 " --> pdb=" O LEU K 341 " (cutoff:3.500A) removed outlier: 5.759A pdb=" N LEU K 341 " --> pdb=" O THR K 275 " (cutoff:3.500A) Processing sheet with id= AQ, first strand: chain 'H' and resid 3 through 5 removed outlier: 3.605A pdb=" N VAL H 24 " --> pdb=" O LYS H 3 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N GLU H 33 " --> pdb=" O THR H 23 " (cutoff:3.500A) Processing sheet with id= AR, first strand: chain 'H' and resid 57 through 60 Processing sheet with id= AS, first strand: chain 'H' and resid 114 through 117 removed outlier: 5.882A pdb=" N MET H 344 " --> pdb=" O LEU H 89 " (cutoff:3.500A) removed outlier: 7.155A pdb=" N TYR H 91 " --> pdb=" O MET H 344 " (cutoff:3.500A) removed outlier: 5.941A pdb=" N ILE H 346 " --> pdb=" O TYR H 91 " (cutoff:3.500A) removed outlier: 7.853A pdb=" N ASN H 347 " --> pdb=" O PRO H 368 " (cutoff:3.500A) removed outlier: 6.576A pdb=" N VAL H 370 " --> pdb=" O ASN H 347 " (cutoff:3.500A) removed outlier: 6.403A pdb=" N LEU H 385 " --> pdb=" O THR H 371 " (cutoff:3.500A) Processing sheet with id= AT, first strand: chain 'H' and resid 185 through 189 Processing sheet with id= AU, first strand: chain 'H' and resid 398 through 401 Processing sheet with id= AV, first strand: chain 'a' and resid 97 through 101 removed outlier: 6.349A pdb=" N VAL a 69 " --> pdb=" O GLU a 98 " (cutoff:3.500A) removed outlier: 7.712A pdb=" N ALA a 100 " --> pdb=" O VAL a 69 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N VAL a 71 " --> pdb=" O ALA a 100 " (cutoff:3.500A) removed outlier: 7.481A pdb=" N VAL a 11 " --> pdb=" O ALA a 40 " (cutoff:3.500A) removed outlier: 4.205A pdb=" N ALA a 42 " --> pdb=" O VAL a 11 " (cutoff:3.500A) removed outlier: 7.330A pdb=" N VAL a 13 " --> pdb=" O ALA a 42 " (cutoff:3.500A) removed outlier: 4.451A pdb=" N GLN a 44 " --> pdb=" O VAL a 13 " (cutoff:3.500A) Processing sheet with id= AW, first strand: chain 'a' and resid 142 through 145 Processing sheet with id= AX, first strand: chain 'a' and resid 551 through 553 removed outlier: 6.601A pdb=" N ALA a 340 " --> pdb=" O PHE a 552 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N THR a 339 " --> pdb=" O THR a 149 " (cutoff:3.500A) removed outlier: 6.578A pdb=" N LYS a 172 " --> pdb=" O ALA a 150 " (cutoff:3.500A) removed outlier: 7.819A pdb=" N VAL a 152 " --> pdb=" O LYS a 172 " (cutoff:3.500A) removed outlier: 6.179A pdb=" N TYR a 174 " --> pdb=" O VAL a 152 " (cutoff:3.500A) Processing sheet with id= AY, first strand: chain 'a' and resid 331 through 337 removed outlier: 3.508A pdb=" N LYS a 226 " --> pdb=" O THR a 237 " (cutoff:3.500A) removed outlier: 6.343A pdb=" N ARG a 239 " --> pdb=" O VAL a 224 " (cutoff:3.500A) removed outlier: 5.745A pdb=" N VAL a 224 " --> pdb=" O ARG a 239 " (cutoff:3.500A) Processing sheet with id= AZ, first strand: chain 'a' and resid 274 through 276 Processing sheet with id= BA, first strand: chain 'a' and resid 346 through 348 Processing sheet with id= BB, first strand: chain 'a' and resid 365 through 367 removed outlier: 6.314A pdb=" N LEU a 505 " --> pdb=" O ILE a 366 " (cutoff:3.500A) removed outlier: 6.454A pdb=" N VAL a 439 " --> pdb=" O VAL a 397 " (cutoff:3.500A) removed outlier: 7.874A pdb=" N PHE a 399 " --> pdb=" O VAL a 439 " (cutoff:3.500A) removed outlier: 6.757A pdb=" N TYR a 441 " --> pdb=" O PHE a 399 " (cutoff:3.500A) removed outlier: 6.578A pdb=" N LYS a 467 " --> pdb=" O LEU a 442 " (cutoff:3.500A) removed outlier: 7.114A pdb=" N TYR a 444 " --> pdb=" O LYS a 467 " (cutoff:3.500A) removed outlier: 6.319A pdb=" N ILE a 469 " --> pdb=" O TYR a 444 " (cutoff:3.500A) Processing sheet with id= BC, first strand: chain 'a' and resid 475 through 478 removed outlier: 3.575A pdb=" N THR a 489 " --> pdb=" O VAL a 498 " (cutoff:3.500A) Processing sheet with id= BD, first strand: chain 'a' and resid 593 through 595 Processing sheet with id= BE, first strand: chain 'a' and resid 615 through 620 Processing sheet with id= BF, first strand: chain 'f' and resid 36 through 38 removed outlier: 6.785A pdb=" N ILE f 9 " --> pdb=" O ARG f 37 " (cutoff:3.500A) removed outlier: 6.725A pdb=" N GLY f 62 " --> pdb=" O LEU f 10 " (cutoff:3.500A) removed outlier: 8.455A pdb=" N ILE f 12 " --> pdb=" O GLY f 62 " (cutoff:3.500A) removed outlier: 6.970A pdb=" N LEU f 64 " --> pdb=" O ILE f 12 " (cutoff:3.500A) Processing sheet with id= BG, first strand: chain 'e' and resid 241 through 245 removed outlier: 6.623A pdb=" N LEU e 96 " --> pdb=" O ILE e 123 " (cutoff:3.500A) removed outlier: 7.797A pdb=" N ILE e 125 " --> pdb=" O LEU e 96 " (cutoff:3.500A) removed outlier: 6.380A pdb=" N VAL e 98 " --> pdb=" O ILE e 125 " (cutoff:3.500A) removed outlier: 7.442A pdb=" N VAL e 127 " --> pdb=" O VAL e 98 " (cutoff:3.500A) removed outlier: 6.664A pdb=" N CYS e 100 " --> pdb=" O VAL e 127 " (cutoff:3.500A) removed outlier: 6.815A pdb=" N ALA e 42 " --> pdb=" O ALA e 97 " (cutoff:3.500A) removed outlier: 8.492A pdb=" N THR e 99 " --> pdb=" O ALA e 42 " (cutoff:3.500A) removed outlier: 7.080A pdb=" N VAL e 44 " --> pdb=" O THR e 99 " (cutoff:3.500A) Processing sheet with id= BH, first strand: chain 'e' and resid 155 through 159 Processing sheet with id= BI, first strand: chain 'b' and resid 32 through 36 removed outlier: 6.452A pdb=" N HIS b 2 " --> pdb=" O LYS b 33 " (cutoff:3.500A) removed outlier: 7.336A pdb=" N LEU b 35 " --> pdb=" O HIS b 2 " (cutoff:3.500A) removed outlier: 6.445A pdb=" N TYR b 4 " --> pdb=" O LEU b 35 " (cutoff:3.500A) removed outlier: 6.172A pdb=" N ASP b 74 " --> pdb=" O ALA b 5 " (cutoff:3.500A) Processing sheet with id= BJ, first strand: chain 'b' and resid 187 through 189 removed outlier: 4.810A pdb=" N ALA b 153 " --> pdb=" O ILE b 189 " (cutoff:3.500A) removed outlier: 6.459A pdb=" N ALA b 230 " --> pdb=" O ALA b 152 " (cutoff:3.500A) removed outlier: 7.607A pdb=" N HIS b 154 " --> pdb=" O ALA b 230 " (cutoff:3.500A) removed outlier: 6.582A pdb=" N THR b 232 " --> pdb=" O HIS b 154 " (cutoff:3.500A) removed outlier: 8.023A pdb=" N GLU b 233 " --> pdb=" O PRO b 260 " (cutoff:3.500A) removed outlier: 6.646A pdb=" N LEU b 262 " --> pdb=" O GLU b 233 " (cutoff:3.500A) Processing sheet with id= BK, first strand: chain 'd' and resid 9 through 14 removed outlier: 3.682A pdb=" N GLY d 35 " --> pdb=" O VAL d 27 " (cutoff:3.500A) removed outlier: 6.534A pdb=" N SER d 29 " --> pdb=" O VAL d 33 " (cutoff:3.500A) removed outlier: 5.395A pdb=" N VAL d 33 " --> pdb=" O SER d 29 " (cutoff:3.500A) Processing sheet with id= BL, first strand: chain 'd' and resid 70 through 72 Processing sheet with id= BM, first strand: chain 'd' and resid 106 through 108 removed outlier: 6.384A pdb=" N VAL d 439 " --> pdb=" O VAL d 425 " (cutoff:3.500A) removed outlier: 7.621A pdb=" N ASP d 427 " --> pdb=" O VAL d 439 " (cutoff:3.500A) removed outlier: 6.114A pdb=" N LEU d 441 " --> pdb=" O ASP d 427 " (cutoff:3.500A) Processing sheet with id= BN, first strand: chain 'd' and resid 198 through 201 removed outlier: 3.678A pdb=" N VAL d 291 " --> pdb=" O LEU d 170 " (cutoff:3.500A) removed outlier: 6.176A pdb=" N GLY d 327 " --> pdb=" O ILE d 292 " (cutoff:3.500A) removed outlier: 7.717A pdb=" N TYR d 294 " --> pdb=" O GLY d 327 " (cutoff:3.500A) removed outlier: 6.323A pdb=" N ASN d 329 " --> pdb=" O TYR d 294 " (cutoff:3.500A) Processing sheet with id= BO, first strand: chain 'd' and resid 452 through 454 Processing sheet with id= BP, first strand: chain 'i' and resid 52 through 54 Processing sheet with id= BQ, first strand: chain 'i' and resid 39 through 41 Processing sheet with id= BR, first strand: chain 'i' and resid 151 through 154 removed outlier: 6.941A pdb=" N THR i 170 " --> pdb=" O ILE i 152 " (cutoff:3.500A) removed outlier: 8.183A pdb=" N VAL i 154 " --> pdb=" O THR i 170 " (cutoff:3.500A) removed outlier: 6.730A pdb=" N ILE i 172 " --> pdb=" O VAL i 154 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N THR i 189 " --> pdb=" O ILE i 171 " (cutoff:3.500A) removed outlier: 8.133A pdb=" N ILE i 173 " --> pdb=" O THR i 189 " (cutoff:3.500A) removed outlier: 6.438A pdb=" N ILE i 191 " --> pdb=" O ILE i 173 " (cutoff:3.500A) No H-bonds generated for sheet with id= BR Processing sheet with id= BS, first strand: chain 'i' and resid 223 through 228 removed outlier: 3.832A pdb=" N LYS i 223 " --> pdb=" O ILE i 243 " (cutoff:3.500A) removed outlier: 7.139A pdb=" N GLN i 241 " --> pdb=" O VAL i 225 " (cutoff:3.500A) removed outlier: 4.475A pdb=" N THR i 227 " --> pdb=" O PHE i 239 " (cutoff:3.500A) removed outlier: 6.253A pdb=" N PHE i 239 " --> pdb=" O THR i 227 " (cutoff:3.500A) Processing sheet with id= BT, first strand: chain 'l' and resid 65 through 68 removed outlier: 3.825A pdb=" N ALA l 65 " --> pdb=" O SER l 137 " (cutoff:3.500A) Processing sheet with id= BU, first strand: chain 'l' and resid 102 through 105 removed outlier: 3.579A pdb=" N ASP l 108 " --> pdb=" O ILE l 105 " (cutoff:3.500A) Processing sheet with id= BV, first strand: chain 'g' and resid 4 through 7 removed outlier: 6.476A pdb=" N GLN g 41 " --> pdb=" O LEU g 5 " (cutoff:3.500A) removed outlier: 7.411A pdb=" N LYS g 7 " --> pdb=" O GLN g 41 " (cutoff:3.500A) removed outlier: 6.077A pdb=" N ILE g 43 " --> pdb=" O LYS g 7 " (cutoff:3.500A) No H-bonds generated for sheet with id= BV Processing sheet with id= BW, first strand: chain 'g' and resid 26 through 28 removed outlier: 3.767A pdb=" N ALA g 26 " --> pdb=" O VAL g 33 " (cutoff:3.500A) Processing sheet with id= BX, first strand: chain 'g' and resid 49 through 52 removed outlier: 3.618A pdb=" N ALA g 474 " --> pdb=" O MET g 51 " (cutoff:3.500A) removed outlier: 6.201A pdb=" N LYS g 502 " --> pdb=" O VAL g 506 " (cutoff:3.500A) removed outlier: 5.480A pdb=" N VAL g 506 " --> pdb=" O LYS g 502 " (cutoff:3.500A) Processing sheet with id= BY, first strand: chain 'g' and resid 234 through 236 removed outlier: 3.682A pdb=" N THR g 308 " --> pdb=" O LEU g 272 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N THR g 388 " --> pdb=" O ILE g 311 " (cutoff:3.500A) Processing sheet with id= BZ, first strand: chain 'g' and resid 282 through 284 Processing sheet with id= CA, first strand: chain 'g' and resid 318 through 323 Processing sheet with id= CB, first strand: chain 'g' and resid 523 through 525 Processing sheet with id= CC, first strand: chain 'g' and resid 11 through 13 removed outlier: 3.721A pdb=" N ASP g 21 " --> pdb=" O ILE g 11 " (cutoff:3.500A) removed outlier: 7.994A pdb=" N ASP g 13 " --> pdb=" O LYS g 19 " (cutoff:3.500A) removed outlier: 5.976A pdb=" N LYS g 19 " --> pdb=" O ASP g 13 " (cutoff:3.500A) Processing sheet with id= CD, first strand: chain 'g' and resid 54 through 56 removed outlier: 7.158A pdb=" N ASP g 56 " --> pdb=" O THR g 116 " (cutoff:3.500A) removed outlier: 4.278A pdb=" N THR g 118 " --> pdb=" O ASP g 56 " (cutoff:3.500A) removed outlier: 6.416A pdb=" N ASP g 142 " --> pdb=" O THR g 118 " (cutoff:3.500A) removed outlier: 7.395A pdb=" N GLU g 120 " --> pdb=" O ASP g 142 " (cutoff:3.500A) removed outlier: 6.478A pdb=" N ALA g 144 " --> pdb=" O GLU g 120 " (cutoff:3.500A) removed outlier: 7.580A pdb=" N ALA g 122 " --> pdb=" O ALA g 144 " (cutoff:3.500A) removed outlier: 6.158A pdb=" N MET g 146 " --> pdb=" O ALA g 122 " (cutoff:3.500A) Processing sheet with id= CE, first strand: chain 'j' and resid 9 through 12 removed outlier: 6.020A pdb=" N CYS j 80 " --> pdb=" O ILE j 10 " (cutoff:3.500A) removed outlier: 7.444A pdb=" N GLN j 12 " --> pdb=" O CYS j 80 " (cutoff:3.500A) removed outlier: 6.301A pdb=" N ILE j 82 " --> pdb=" O GLN j 12 " (cutoff:3.500A) No H-bonds generated for sheet with id= CE Processing sheet with id= CF, first strand: chain 'j' and resid 37 through 39 removed outlier: 3.618A pdb=" N THR j 53 " --> pdb=" O ALA j 68 " (cutoff:3.500A) Processing sheet with id= CG, first strand: chain 'k' and resid 7 through 13 Processing sheet with id= CH, first strand: chain 'k' and resid 52 through 54 Processing sheet with id= CI, first strand: chain 'k' and resid 140 through 143 Processing sheet with id= CJ, first strand: chain 'k' and resid 163 through 168 Processing sheet with id= CK, first strand: chain 'k' and resid 187 through 191 Processing sheet with id= CL, first strand: chain 'k' and resid 270 through 276 removed outlier: 6.888A pdb=" N GLU k 273 " --> pdb=" O ARG k 343 " (cutoff:3.500A) removed outlier: 5.501A pdb=" N ARG k 343 " --> pdb=" O GLU k 273 " (cutoff:3.500A) removed outlier: 7.650A pdb=" N THR k 275 " --> pdb=" O LEU k 341 " (cutoff:3.500A) removed outlier: 5.760A pdb=" N LEU k 341 " --> pdb=" O THR k 275 " (cutoff:3.500A) Processing sheet with id= CM, first strand: chain 'h' and resid 3 through 5 removed outlier: 3.604A pdb=" N VAL h 24 " --> pdb=" O LYS h 3 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N GLU h 33 " --> pdb=" O THR h 23 " (cutoff:3.500A) Processing sheet with id= CN, first strand: chain 'h' and resid 57 through 60 Processing sheet with id= CO, first strand: chain 'h' and resid 114 through 117 removed outlier: 5.882A pdb=" N MET h 344 " --> pdb=" O LEU h 89 " (cutoff:3.500A) removed outlier: 7.155A pdb=" N TYR h 91 " --> pdb=" O MET h 344 " (cutoff:3.500A) removed outlier: 5.941A pdb=" N ILE h 346 " --> pdb=" O TYR h 91 " (cutoff:3.500A) removed outlier: 7.853A pdb=" N ASN h 347 " --> pdb=" O PRO h 368 " (cutoff:3.500A) removed outlier: 6.576A pdb=" N VAL h 370 " --> pdb=" O ASN h 347 " (cutoff:3.500A) removed outlier: 6.402A pdb=" N LEU h 385 " --> pdb=" O THR h 371 " (cutoff:3.500A) Processing sheet with id= CP, first strand: chain 'h' and resid 185 through 189 Processing sheet with id= CQ, first strand: chain 'h' and resid 398 through 401 1897 hydrogen bonds defined for protein. 5301 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: 24.44 Time building geometry restraints manager: 22.26 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.40: 25979 1.40 - 1.62: 38200 1.62 - 1.85: 853 1.85 - 2.07: 0 2.07 - 2.30: 624 Bond restraints: 65656 Sorted by residual: bond pdb=" C1' MGD h 502 " pdb=" C2' MGD h 502 " ideal model delta sigma weight residual 1.528 1.245 0.283 2.00e-02 2.50e+03 2.01e+02 bond pdb=" C1' MGD H 502 " pdb=" C2' MGD H 502 " ideal model delta sigma weight residual 1.528 1.245 0.283 2.00e-02 2.50e+03 2.00e+02 bond pdb=" C1' MGD H 503 " pdb=" C2' MGD H 503 " ideal model delta sigma weight residual 1.528 1.261 0.267 2.00e-02 2.50e+03 1.79e+02 bond pdb=" C1' MGD h 503 " pdb=" C2' MGD h 503 " ideal model delta sigma weight residual 1.528 1.263 0.265 2.00e-02 2.50e+03 1.75e+02 bond pdb=" C3' MGD h 503 " pdb=" C4' MGD h 503 " ideal model delta sigma weight residual 1.522 1.262 0.260 2.00e-02 2.50e+03 1.68e+02 ... (remaining 65651 not shown) Histogram of bond angle deviations from ideal: 70.60 - 88.58: 608 88.58 - 106.57: 2930 106.57 - 124.55: 84337 124.55 - 142.54: 1379 142.54 - 160.52: 4 Bond angle restraints: 89258 Sorted by residual: angle pdb=" S1 9S8 B 302 " pdb="FE4 9S8 B 302 " pdb=" S5 9S8 B 302 " ideal model delta sigma weight residual 156.31 73.44 82.87 3.00e+00 1.11e-01 7.63e+02 angle pdb=" S1 9S8 b 302 " pdb="FE4 9S8 b 302 " pdb=" S5 9S8 b 302 " ideal model delta sigma weight residual 156.31 73.48 82.83 3.00e+00 1.11e-01 7.62e+02 angle pdb=" S1 9S8 B 301 " pdb="FE4 9S8 B 301 " pdb=" S5 9S8 B 301 " ideal model delta sigma weight residual 156.31 73.87 82.44 3.00e+00 1.11e-01 7.55e+02 angle pdb=" S1 9S8 b 301 " pdb="FE4 9S8 b 301 " pdb=" S5 9S8 b 301 " ideal model delta sigma weight residual 156.31 73.90 82.41 3.00e+00 1.11e-01 7.55e+02 angle pdb="FE6 9S8 B 301 " pdb=" S7 9S8 B 301 " pdb="FE9 9S8 B 301 " ideal model delta sigma weight residual 157.67 103.62 54.05 3.00e+00 1.11e-01 3.25e+02 ... (remaining 89253 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.28: 38358 35.28 - 70.56: 1000 70.56 - 105.83: 94 105.83 - 141.11: 24 141.11 - 176.39: 22 Dihedral angle restraints: 39498 sinusoidal: 16046 harmonic: 23452 Sorted by residual: dihedral pdb=" C TRP D 527 " pdb=" N TRP D 527 " pdb=" CA TRP D 527 " pdb=" CB TRP D 527 " ideal model delta harmonic sigma weight residual -122.60 -152.92 30.32 0 2.50e+00 1.60e-01 1.47e+02 dihedral pdb=" C TRP d 527 " pdb=" N TRP d 527 " pdb=" CA TRP d 527 " pdb=" CB TRP d 527 " ideal model delta harmonic sigma weight residual -122.60 -152.80 30.20 0 2.50e+00 1.60e-01 1.46e+02 dihedral pdb=" N TRP D 527 " pdb=" C TRP D 527 " pdb=" CA TRP D 527 " pdb=" CB TRP D 527 " ideal model delta harmonic sigma weight residual 122.80 152.96 -30.16 0 2.50e+00 1.60e-01 1.46e+02 ... (remaining 39495 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.258: 9731 0.258 - 0.516: 161 0.516 - 0.775: 6 0.775 - 1.033: 6 1.033 - 1.291: 12 Chirality restraints: 9916 Sorted by residual: chirality pdb=" CA TRP D 527 " pdb=" N TRP D 527 " pdb=" C TRP D 527 " pdb=" CB TRP D 527 " both_signs ideal model delta sigma weight residual False 2.51 1.22 1.29 2.00e-01 2.50e+01 4.17e+01 chirality pdb=" CA TRP d 527 " pdb=" N TRP d 527 " pdb=" C TRP d 527 " pdb=" CB TRP d 527 " both_signs ideal model delta sigma weight residual False 2.51 1.22 1.29 2.00e-01 2.50e+01 4.14e+01 chirality pdb="FE2 SF4 H 504 " pdb=" S1 SF4 H 504 " pdb=" S3 SF4 H 504 " pdb=" S4 SF4 H 504 " both_signs ideal model delta sigma weight residual False 10.55 9.35 1.20 2.00e-01 2.50e+01 3.62e+01 ... (remaining 9913 not shown) Planarity restraints: 11364 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLN k 159 " -0.043 2.00e-02 2.50e+03 8.81e-02 7.76e+01 pdb=" C GLN k 159 " 0.152 2.00e-02 2.50e+03 pdb=" O GLN k 159 " -0.058 2.00e-02 2.50e+03 pdb=" N ALA k 160 " -0.051 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB HIS g 237 " -0.009 2.00e-02 2.50e+03 4.73e-02 3.35e+01 pdb=" CG HIS g 237 " -0.005 2.00e-02 2.50e+03 pdb=" ND1 HIS g 237 " -0.024 2.00e-02 2.50e+03 pdb=" CD2 HIS g 237 " 0.057 2.00e-02 2.50e+03 pdb=" CE1 HIS g 237 " 0.059 2.00e-02 2.50e+03 pdb=" NE2 HIS g 237 " -0.078 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB HIS G 237 " 0.009 2.00e-02 2.50e+03 4.70e-02 3.31e+01 pdb=" CG HIS G 237 " 0.005 2.00e-02 2.50e+03 pdb=" ND1 HIS G 237 " 0.024 2.00e-02 2.50e+03 pdb=" CD2 HIS G 237 " -0.056 2.00e-02 2.50e+03 pdb=" CE1 HIS G 237 " -0.059 2.00e-02 2.50e+03 pdb=" NE2 HIS G 237 " 0.077 2.00e-02 2.50e+03 ... (remaining 11361 not shown) Histogram of nonbonded interaction distances: 1.95 - 2.54: 428 2.54 - 3.13: 51698 3.13 - 3.72: 99402 3.72 - 4.31: 151240 4.31 - 4.90: 249634 Nonbonded interactions: 552402 Sorted by model distance: nonbonded pdb=" OQ2 KCX G 184 " pdb="ZN ZN G 601 " model vdw 1.954 2.230 nonbonded pdb=" OQ1 KCX g 184 " pdb="ZN ZN g 601 " model vdw 1.955 2.230 nonbonded pdb=" OD1 ASP g 390 " pdb="ZN ZN g 601 " model vdw 2.012 2.230 nonbonded pdb=" OD1 ASP G 390 " pdb="ZN ZN G 601 " model vdw 2.013 2.230 nonbonded pdb=" OQ2 KCX g 184 " pdb="ZN ZN g 602 " model vdw 2.077 2.230 ... (remaining 552397 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 'a' } ncs_group { reference = chain 'B' selection = chain 'b' } ncs_group { reference = chain 'C' selection = chain 'c' } ncs_group { reference = chain 'D' selection = chain 'd' } ncs_group { reference = chain 'E' selection = chain 'e' } ncs_group { reference = chain 'F' selection = chain 'f' } ncs_group { reference = chain 'G' selection = chain 'g' } ncs_group { reference = chain 'H' selection = chain 'h' } ncs_group { reference = chain 'I' selection = chain 'i' } ncs_group { reference = chain 'J' selection = chain 'j' } ncs_group { reference = chain 'K' selection = chain 'k' } ncs_group { reference = chain 'L' selection = chain 'l' } 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=1.00 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: 1.490 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.310 Construct map_model_manager: 0.070 Extract box with map and model: 10.220 Check model and map are aligned: 0.740 Set scattering table: 0.480 Process input model: 153.250 Find NCS groups from input model: 3.490 Set up NCS constraints: 0.740 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.020 Load rotamer database and sin/cos tables:2.160 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 172.970 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6378 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 : 0.012 0.283 65656 Z= 0.765 Angle : 1.382 82.874 89258 Z= 0.755 Chirality : 0.095 1.291 9916 Planarity : 0.006 0.088 11364 Dihedral : 16.765 176.388 24492 Min Nonbonded Distance : 1.954 Molprobity Statistics. All-atom Clashscore : 10.82 Ramachandran Plot: Outliers : 0.17 % Allowed : 7.71 % Favored : 92.12 % Rotamer: Outliers : 3.80 % Allowed : 2.89 % Favored : 93.30 % Cbeta Deviations : 0.64 % Peptide Plane: Cis-proline : 1.54 % 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 (0.09), residues: 8162 helix: -0.22 (0.09), residues: 2956 sheet: -1.65 (0.14), residues: 1194 loop : -1.57 (0.09), residues: 4012 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.003 TRP h 308 HIS 0.072 0.002 HIS g 237 PHE 0.031 0.003 PHE g 154 TYR 0.068 0.003 TYR d 516 ARG 0.011 0.001 ARG A 212 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16324 Ramachandran restraints generated. 8162 Oldfield, 0 Emsley, 8162 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16324 Ramachandran restraints generated. 8162 Oldfield, 0 Emsley, 8162 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1948 residues out of total 6810 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 259 poor density : 1689 time to evaluate : 5.750 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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 203 LEU cc_start: 0.8300 (tp) cc_final: 0.6905 (tp) REVERT: B 1 MET cc_start: 0.3945 (ttm) cc_final: 0.3521 (ttm) REVERT: B 176 TRP cc_start: 0.7266 (p-90) cc_final: 0.6909 (p-90) REVERT: D 159 THR cc_start: 0.5535 (p) cc_final: 0.5145 (p) REVERT: D 259 THR cc_start: 0.7801 (OUTLIER) cc_final: 0.7591 (t) REVERT: I 91 ASN cc_start: 0.8490 (m-40) cc_final: 0.7766 (m-40) REVERT: I 170 THR cc_start: 0.6012 (OUTLIER) cc_final: 0.5645 (p) REVERT: G 134 GLU cc_start: 0.7824 (OUTLIER) cc_final: 0.7550 (mt-10) REVERT: G 152 ASN cc_start: 0.8037 (t0) cc_final: 0.7799 (m-40) REVERT: G 156 PHE cc_start: 0.7250 (OUTLIER) cc_final: 0.6005 (m-10) REVERT: G 337 HIS cc_start: 0.7906 (m-70) cc_final: 0.7636 (m90) REVERT: G 470 ASP cc_start: 0.7434 (t0) cc_final: 0.7149 (t70) REVERT: G 525 LYS cc_start: 0.7712 (tptm) cc_final: 0.7250 (tptp) REVERT: J 17 GLU cc_start: 0.6805 (tm-30) cc_final: 0.6536 (tt0) REVERT: K 90 PHE cc_start: 0.6687 (OUTLIER) cc_final: 0.6397 (m-80) REVERT: K 157 LYS cc_start: 0.5709 (OUTLIER) cc_final: 0.5088 (tptp) REVERT: K 176 LYS cc_start: 0.7770 (OUTLIER) cc_final: 0.7109 (mptt) REVERT: K 265 THR cc_start: 0.6783 (m) cc_final: 0.6458 (t) REVERT: H 101 GLN cc_start: 0.8209 (mt0) cc_final: 0.7409 (mt0) REVERT: H 291 MET cc_start: 0.7485 (ttt) cc_final: 0.7269 (ttm) REVERT: H 331 THR cc_start: 0.8878 (p) cc_final: 0.8094 (p) REVERT: H 394 VAL cc_start: 0.7702 (t) cc_final: 0.7497 (p) REVERT: H 401 TYR cc_start: 0.8190 (m-80) cc_final: 0.7753 (m-10) REVERT: a 454 TYR cc_start: 0.4995 (m-10) cc_final: 0.4343 (m-10) REVERT: f 57 VAL cc_start: 0.8281 (p) cc_final: 0.7170 (p) REVERT: f 99 ASP cc_start: 0.3685 (t0) cc_final: 0.3449 (t0) REVERT: b 219 LYS cc_start: 0.6010 (OUTLIER) cc_final: 0.5480 (mmtt) REVERT: d 159 THR cc_start: 0.6551 (p) cc_final: 0.6340 (p) REVERT: i 36 ASP cc_start: 0.7805 (p0) cc_final: 0.7513 (p0) REVERT: i 166 MET cc_start: 0.7108 (ttt) cc_final: 0.6843 (ttt) REVERT: i 214 ASN cc_start: 0.8265 (m-40) cc_final: 0.8047 (m-40) REVERT: i 243 ILE cc_start: 0.8317 (tt) cc_final: 0.8079 (tp) REVERT: i 245 ASP cc_start: 0.6517 (t0) cc_final: 0.6118 (t0) REVERT: g 156 PHE cc_start: 0.8375 (OUTLIER) cc_final: 0.7937 (m-10) REVERT: g 439 LEU cc_start: 0.7610 (mm) cc_final: 0.7163 (mt) REVERT: g 472 ASN cc_start: 0.7551 (m-40) cc_final: 0.6946 (m-40) REVERT: g 524 THR cc_start: 0.8320 (m) cc_final: 0.7801 (p) REVERT: g 527 ASN cc_start: 0.7541 (m-40) cc_final: 0.7333 (m-40) REVERT: j 50 MET cc_start: 0.7398 (ttm) cc_final: 0.6964 (ttp) REVERT: k 81 CYS cc_start: 0.7637 (OUTLIER) cc_final: 0.7151 (p) REVERT: k 87 MET cc_start: 0.5948 (mmp) cc_final: 0.5242 (mmm) REVERT: k 157 LYS cc_start: 0.6483 (OUTLIER) cc_final: 0.5278 (tptp) REVERT: k 205 VAL cc_start: 0.8243 (OUTLIER) cc_final: 0.7902 (m) REVERT: k 238 LYS cc_start: 0.6891 (OUTLIER) cc_final: 0.6604 (ttmt) REVERT: h 212 TYR cc_start: 0.7289 (t80) cc_final: 0.7028 (t80) REVERT: h 263 THR cc_start: 0.8690 (p) cc_final: 0.8447 (t) REVERT: h 308 TRP cc_start: 0.8468 (OUTLIER) cc_final: 0.5823 (p90) REVERT: h 323 HIS cc_start: 0.7590 (p-80) cc_final: 0.7378 (p-80) REVERT: h 422 ASP cc_start: 0.7758 (p0) cc_final: 0.6751 (p0) REVERT: h 424 GLU cc_start: 0.7625 (OUTLIER) cc_final: 0.7225 (pm20) outliers start: 259 outliers final: 41 residues processed: 1876 average time/residue: 0.6443 time to fit residues: 1997.7629 Evaluate side-chains 939 residues out of total 6810 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 883 time to evaluate : 5.662 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 204 THR Chi-restraints excluded: chain A residue 420 CYS Chi-restraints excluded: chain E residue 53 TYR Chi-restraints excluded: chain B residue 219 LYS Chi-restraints excluded: chain D residue 259 THR Chi-restraints excluded: chain D residue 527 TRP Chi-restraints excluded: chain D residue 531 THR Chi-restraints excluded: chain I residue 73 VAL Chi-restraints excluded: chain I residue 170 THR Chi-restraints excluded: chain L residue 66 VAL Chi-restraints excluded: chain L residue 131 TYR Chi-restraints excluded: chain G residue 134 GLU Chi-restraints excluded: chain G residue 156 PHE Chi-restraints excluded: chain K residue 90 PHE Chi-restraints excluded: chain K residue 128 CYS Chi-restraints excluded: chain K residue 140 ILE Chi-restraints excluded: chain K residue 141 ASP Chi-restraints excluded: chain K residue 157 LYS Chi-restraints excluded: chain K residue 166 GLU Chi-restraints excluded: chain K residue 176 LYS Chi-restraints excluded: chain K residue 257 ILE Chi-restraints excluded: chain K residue 264 ILE Chi-restraints excluded: chain H residue 96 THR Chi-restraints excluded: chain H residue 408 ILE Chi-restraints excluded: chain a residue 420 CYS Chi-restraints excluded: chain e residue 53 TYR Chi-restraints excluded: chain b residue 179 GLU Chi-restraints excluded: chain b residue 218 GLU Chi-restraints excluded: chain b residue 219 LYS Chi-restraints excluded: chain d residue 259 THR Chi-restraints excluded: chain d residue 527 TRP Chi-restraints excluded: chain d residue 531 THR Chi-restraints excluded: chain i residue 16 LEU Chi-restraints excluded: chain i residue 90 ILE Chi-restraints excluded: chain i residue 92 SER Chi-restraints excluded: chain i residue 115 SER Chi-restraints excluded: chain l residue 131 TYR Chi-restraints excluded: chain l residue 132 ASP Chi-restraints excluded: chain g residue 156 PHE Chi-restraints excluded: chain g residue 346 GLU Chi-restraints excluded: chain k residue 42 ILE Chi-restraints excluded: chain k residue 81 CYS Chi-restraints excluded: chain k residue 90 PHE Chi-restraints excluded: chain k residue 157 LYS Chi-restraints excluded: chain k residue 175 THR Chi-restraints excluded: chain k residue 179 ILE Chi-restraints excluded: chain k residue 205 VAL Chi-restraints excluded: chain k residue 229 VAL Chi-restraints excluded: chain k residue 230 THR Chi-restraints excluded: chain k residue 237 LYS Chi-restraints excluded: chain k residue 238 LYS Chi-restraints excluded: chain k residue 252 CYS Chi-restraints excluded: chain k residue 261 THR Chi-restraints excluded: chain h residue 96 THR Chi-restraints excluded: chain h residue 308 TRP Chi-restraints excluded: chain h residue 424 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 808 random chunks: chunk 682 optimal weight: 4.9990 chunk 612 optimal weight: 0.9980 chunk 339 optimal weight: 6.9990 chunk 209 optimal weight: 20.0000 chunk 413 optimal weight: 0.9980 chunk 327 optimal weight: 0.9990 chunk 633 optimal weight: 0.9990 chunk 245 optimal weight: 1.9990 chunk 385 optimal weight: 2.9990 chunk 471 optimal weight: 1.9990 chunk 733 optimal weight: 3.9990 overall best weight: 1.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 15 ASN F 95 ASN ** E 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 363 HIS ** B 211 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 239 GLN D 59 HIS ** D 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 132 ASN D 133 ASN I 40 HIS G 152 ASN G 161 ASN ** G 264 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 270 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 12 GLN J 73 GLN ** J 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 374 GLN H 61 GLN H 161 HIS H 325 HIS H 327 ASN H 367 HIS ** H 377 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** f 15 ASN ** f 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 122 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** b 190 GLN ** b 246 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 59 HIS d 289 ASN d 335 ASN ** g 270 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 274 ASN ** g 531 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** j 12 GLN j 127 GLN k 21 GLN k 28 ASN h 47 HIS h 161 HIS h 216 ASN h 325 HIS h 327 ASN h 367 HIS ** h 386 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** h 409 GLN Total number of N/Q/H flips: 35 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6609 moved from start: 0.2757 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.075 65656 Z= 0.231 Angle : 0.686 13.792 89258 Z= 0.352 Chirality : 0.047 0.240 9916 Planarity : 0.005 0.072 11364 Dihedral : 10.755 179.681 9400 Min Nonbonded Distance : 1.909 Molprobity Statistics. All-atom Clashscore : 13.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.29 % Favored : 94.71 % Rotamer: Outliers : 3.17 % Allowed : 12.56 % Favored : 84.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.54 % 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: -1.09 (0.09), residues: 8162 helix: 0.19 (0.09), residues: 3000 sheet: -1.10 (0.15), residues: 1196 loop : -1.28 (0.10), residues: 3966 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP d 234 HIS 0.009 0.001 HIS G 276 PHE 0.030 0.002 PHE a 419 TYR 0.043 0.002 TYR h 297 ARG 0.010 0.001 ARG c 100 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16324 Ramachandran restraints generated. 8162 Oldfield, 0 Emsley, 8162 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16324 Ramachandran restraints generated. 8162 Oldfield, 0 Emsley, 8162 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1179 residues out of total 6810 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 216 poor density : 963 time to evaluate : 5.694 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 203 LEU cc_start: 0.8144 (tp) cc_final: 0.7887 (tp) REVERT: C 43 MET cc_start: 0.6409 (mmm) cc_final: 0.6030 (mmp) REVERT: B 175 MET cc_start: 0.6371 (mmm) cc_final: 0.5699 (mmm) REVERT: D 159 THR cc_start: 0.5960 (p) cc_final: 0.5632 (p) REVERT: I 91 ASN cc_start: 0.7967 (m-40) cc_final: 0.7111 (m110) REVERT: I 117 LEU cc_start: 0.8555 (tp) cc_final: 0.8263 (tp) REVERT: I 215 LEU cc_start: 0.8412 (OUTLIER) cc_final: 0.8163 (tp) REVERT: I 243 ILE cc_start: 0.7426 (tp) cc_final: 0.7206 (tp) REVERT: G 153 TRP cc_start: 0.7807 (m-10) cc_final: 0.7509 (m-10) REVERT: G 337 HIS cc_start: 0.7868 (m-70) cc_final: 0.7480 (m90) REVERT: G 408 MET cc_start: 0.6361 (tmm) cc_final: 0.5713 (tmm) REVERT: G 446 MET cc_start: 0.8010 (ttm) cc_final: 0.7510 (ttm) REVERT: G 525 LYS cc_start: 0.7844 (tptm) cc_final: 0.7639 (tptp) REVERT: G 533 GLN cc_start: 0.8198 (tp40) cc_final: 0.7875 (mp10) REVERT: J 111 VAL cc_start: 0.7107 (p) cc_final: 0.6887 (t) REVERT: K 227 ILE cc_start: 0.8287 (OUTLIER) cc_final: 0.8052 (mt) REVERT: H 33 GLU cc_start: 0.6338 (mp0) cc_final: 0.6109 (mp0) REVERT: H 101 GLN cc_start: 0.8089 (mt0) cc_final: 0.7515 (mt0) REVERT: H 114 MET cc_start: 0.5018 (mmt) cc_final: 0.4774 (mmt) REVERT: H 208 GLN cc_start: 0.7729 (tm-30) cc_final: 0.6918 (tm-30) REVERT: H 260 MET cc_start: 0.7640 (mmm) cc_final: 0.7312 (mmm) REVERT: H 293 MET cc_start: 0.8109 (mmt) cc_final: 0.7881 (tpp) REVERT: H 327 ASN cc_start: 0.8147 (OUTLIER) cc_final: 0.7922 (t0) REVERT: H 344 MET cc_start: 0.6800 (OUTLIER) cc_final: 0.6279 (tmm) REVERT: H 401 TYR cc_start: 0.8104 (m-80) cc_final: 0.7787 (m-10) REVERT: a 108 TRP cc_start: 0.6984 (m-10) cc_final: 0.6704 (m-10) REVERT: a 114 MET cc_start: 0.3878 (OUTLIER) cc_final: 0.3628 (ppp) REVERT: f 92 LEU cc_start: 0.7843 (OUTLIER) cc_final: 0.7462 (mp) REVERT: f 99 ASP cc_start: 0.5003 (t0) cc_final: 0.4750 (t0) REVERT: e 141 MET cc_start: 0.6279 (ttm) cc_final: 0.5732 (ttp) REVERT: e 163 PHE cc_start: 0.6557 (t80) cc_final: 0.6127 (t80) REVERT: b 128 TYR cc_start: 0.5641 (t80) cc_final: 0.4270 (t80) REVERT: d 159 THR cc_start: 0.6335 (p) cc_final: 0.6091 (p) REVERT: d 504 MET cc_start: 0.4715 (tmm) cc_final: 0.4466 (tmm) REVERT: i 75 ARG cc_start: 0.7168 (mmm160) cc_final: 0.6897 (mmm160) REVERT: i 93 ASP cc_start: 0.5631 (OUTLIER) cc_final: 0.5231 (m-30) REVERT: i 236 THR cc_start: 0.6633 (m) cc_final: 0.5819 (t) REVERT: i 243 ILE cc_start: 0.8359 (tt) cc_final: 0.8132 (tp) REVERT: i 245 ASP cc_start: 0.6346 (t0) cc_final: 0.6112 (t0) REVERT: g 115 TYR cc_start: 0.8263 (m-80) cc_final: 0.8052 (m-80) REVERT: g 298 MET cc_start: 0.6680 (OUTLIER) cc_final: 0.6117 (tpp) REVERT: g 439 LEU cc_start: 0.7459 (mm) cc_final: 0.7236 (mt) REVERT: g 446 MET cc_start: 0.7685 (OUTLIER) cc_final: 0.7464 (ttm) REVERT: j 26 THR cc_start: 0.7621 (p) cc_final: 0.7402 (p) REVERT: j 50 MET cc_start: 0.7398 (ttm) cc_final: 0.6947 (ttp) REVERT: k 157 LYS cc_start: 0.6357 (OUTLIER) cc_final: 0.5095 (tptt) REVERT: h 16 SER cc_start: 0.7589 (m) cc_final: 0.7375 (t) REVERT: h 212 TYR cc_start: 0.7351 (t80) cc_final: 0.7103 (t80) REVERT: h 263 THR cc_start: 0.8729 (p) cc_final: 0.8437 (t) REVERT: h 323 HIS cc_start: 0.7773 (p-80) cc_final: 0.7275 (p90) REVERT: h 409 GLN cc_start: 0.7295 (OUTLIER) cc_final: 0.6537 (mt0) outliers start: 216 outliers final: 121 residues processed: 1106 average time/residue: 0.6123 time to fit residues: 1144.0602 Evaluate side-chains 903 residues out of total 6810 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 132 poor density : 771 time to evaluate : 5.646 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 TYR Chi-restraints excluded: chain A residue 69 VAL Chi-restraints excluded: chain A residue 144 VAL Chi-restraints excluded: chain A residue 157 VAL Chi-restraints excluded: chain A residue 197 ASP Chi-restraints excluded: chain A residue 420 CYS Chi-restraints excluded: chain F residue 15 ASN Chi-restraints excluded: chain F residue 125 ASN Chi-restraints excluded: chain E residue 53 TYR Chi-restraints excluded: chain E residue 69 THR Chi-restraints excluded: chain E residue 79 LEU Chi-restraints excluded: chain E residue 120 ASP Chi-restraints excluded: chain E residue 141 MET Chi-restraints excluded: chain C residue 77 ASN Chi-restraints excluded: chain C residue 144 VAL Chi-restraints excluded: chain B residue 263 HIS Chi-restraints excluded: chain B residue 279 LEU Chi-restraints excluded: chain B residue 288 CYS Chi-restraints excluded: chain D residue 44 ILE Chi-restraints excluded: chain D residue 59 HIS Chi-restraints excluded: chain D residue 118 CYS Chi-restraints excluded: chain D residue 255 ASP Chi-restraints excluded: chain D residue 307 ASN Chi-restraints excluded: chain D residue 310 SER Chi-restraints excluded: chain D residue 399 LEU Chi-restraints excluded: chain D residue 441 LEU Chi-restraints excluded: chain D residue 531 THR Chi-restraints excluded: chain D residue 537 THR Chi-restraints excluded: chain I residue 20 SER Chi-restraints excluded: chain I residue 40 HIS Chi-restraints excluded: chain I residue 88 ILE Chi-restraints excluded: chain I residue 115 SER Chi-restraints excluded: chain I residue 136 VAL Chi-restraints excluded: chain I residue 173 ILE Chi-restraints excluded: chain I residue 200 VAL Chi-restraints excluded: chain I residue 215 LEU Chi-restraints excluded: chain I residue 228 VAL Chi-restraints excluded: chain L residue 66 VAL Chi-restraints excluded: chain L residue 97 SER Chi-restraints excluded: chain L residue 131 TYR Chi-restraints excluded: chain L residue 134 ILE Chi-restraints excluded: chain G residue 61 VAL Chi-restraints excluded: chain G residue 152 ASN Chi-restraints excluded: chain G residue 223 GLU Chi-restraints excluded: chain G residue 224 THR Chi-restraints excluded: chain G residue 304 ASN Chi-restraints excluded: chain G residue 307 ILE Chi-restraints excluded: chain G residue 314 VAL Chi-restraints excluded: chain G residue 560 VAL Chi-restraints excluded: chain J residue 44 MET Chi-restraints excluded: chain J residue 96 THR Chi-restraints excluded: chain K residue 44 SER Chi-restraints excluded: chain K residue 90 PHE Chi-restraints excluded: chain K residue 126 VAL Chi-restraints excluded: chain K residue 140 ILE Chi-restraints excluded: chain K residue 169 VAL Chi-restraints excluded: chain K residue 175 THR Chi-restraints excluded: chain K residue 189 VAL Chi-restraints excluded: chain K residue 222 CYS Chi-restraints excluded: chain K residue 227 ILE Chi-restraints excluded: chain K residue 243 ASN Chi-restraints excluded: chain H residue 7 ASN Chi-restraints excluded: chain H residue 34 VAL Chi-restraints excluded: chain H residue 299 ILE Chi-restraints excluded: chain H residue 327 ASN Chi-restraints excluded: chain H residue 344 MET Chi-restraints excluded: chain H residue 365 LYS Chi-restraints excluded: chain a residue 69 VAL Chi-restraints excluded: chain a residue 114 MET Chi-restraints excluded: chain a residue 116 ASP Chi-restraints excluded: chain a residue 144 VAL Chi-restraints excluded: chain a residue 192 THR Chi-restraints excluded: chain a residue 247 THR Chi-restraints excluded: chain a residue 420 CYS Chi-restraints excluded: chain a residue 571 GLU Chi-restraints excluded: chain f residue 15 ASN Chi-restraints excluded: chain f residue 39 ILE Chi-restraints excluded: chain f residue 64 LEU Chi-restraints excluded: chain f residue 92 LEU Chi-restraints excluded: chain f residue 98 LEU Chi-restraints excluded: chain e residue 53 TYR Chi-restraints excluded: chain e residue 120 ASP Chi-restraints excluded: chain e residue 403 THR Chi-restraints excluded: chain c residue 127 GLN Chi-restraints excluded: chain b residue 27 SER Chi-restraints excluded: chain b residue 160 MET Chi-restraints excluded: chain d residue 83 ASP Chi-restraints excluded: chain d residue 118 CYS Chi-restraints excluded: chain d residue 150 SER Chi-restraints excluded: chain d residue 234 TRP Chi-restraints excluded: chain d residue 243 LYS Chi-restraints excluded: chain d residue 259 THR Chi-restraints excluded: chain d residue 276 VAL Chi-restraints excluded: chain d residue 289 ASN Chi-restraints excluded: chain d residue 307 ASN Chi-restraints excluded: chain d residue 399 LEU Chi-restraints excluded: chain d residue 424 VAL Chi-restraints excluded: chain d residue 531 THR Chi-restraints excluded: chain d residue 537 THR Chi-restraints excluded: chain i residue 16 LEU Chi-restraints excluded: chain i residue 93 ASP Chi-restraints excluded: chain i residue 114 ASP Chi-restraints excluded: chain i residue 115 SER Chi-restraints excluded: chain i residue 117 LEU Chi-restraints excluded: chain l residue 105 ILE Chi-restraints excluded: chain l residue 131 TYR Chi-restraints excluded: chain l residue 132 ASP Chi-restraints excluded: chain g residue 25 ILE Chi-restraints excluded: chain g residue 249 ASP Chi-restraints excluded: chain g residue 298 MET Chi-restraints excluded: chain g residue 305 LYS Chi-restraints excluded: chain g residue 322 MET Chi-restraints excluded: chain g residue 346 GLU Chi-restraints excluded: chain g residue 424 ASP Chi-restraints excluded: chain g residue 446 MET Chi-restraints excluded: chain g residue 546 TYR Chi-restraints excluded: chain j residue 23 ILE Chi-restraints excluded: chain j residue 96 THR Chi-restraints excluded: chain k residue 90 PHE Chi-restraints excluded: chain k residue 105 ILE Chi-restraints excluded: chain k residue 157 LYS Chi-restraints excluded: chain k residue 175 THR Chi-restraints excluded: chain k residue 230 THR Chi-restraints excluded: chain k residue 234 VAL Chi-restraints excluded: chain k residue 261 THR Chi-restraints excluded: chain k residue 264 ILE Chi-restraints excluded: chain k residue 337 ASP Chi-restraints excluded: chain h residue 95 SER Chi-restraints excluded: chain h residue 96 THR Chi-restraints excluded: chain h residue 237 LYS Chi-restraints excluded: chain h residue 299 ILE Chi-restraints excluded: chain h residue 409 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 808 random chunks: chunk 407 optimal weight: 0.7980 chunk 227 optimal weight: 0.6980 chunk 610 optimal weight: 9.9990 chunk 499 optimal weight: 8.9990 chunk 202 optimal weight: 3.9990 chunk 735 optimal weight: 6.9990 chunk 794 optimal weight: 3.9990 chunk 654 optimal weight: 6.9990 chunk 728 optimal weight: 5.9990 chunk 250 optimal weight: 8.9990 chunk 589 optimal weight: 0.5980 overall best weight: 2.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 15 ASN ** E 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 74 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 358 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 211 HIS D 59 HIS ** D 100 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 161 ASN ** G 270 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 518 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 156 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 327 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 377 ASN ** H 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 79 HIS a 293 HIS f 15 ASN ** e 337 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** e 366 GLN c 130 GLN ** b 122 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** d 338 GLN g 167 ASN ** g 270 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 527 ASN ** g 531 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** k 21 GLN k 28 ASN ** h 164 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** h 325 HIS h 327 ASN h 367 HIS h 377 ASN h 386 HIS h 409 GLN Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6757 moved from start: 0.3550 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.098 65656 Z= 0.242 Angle : 0.632 15.031 89258 Z= 0.328 Chirality : 0.047 0.198 9916 Planarity : 0.005 0.067 11364 Dihedral : 10.260 176.067 9326 Min Nonbonded Distance : 1.898 Molprobity Statistics. All-atom Clashscore : 13.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.48 % Favored : 94.52 % Rotamer: Outliers : 3.38 % Allowed : 14.63 % Favored : 82.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.54 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.85 (0.09), residues: 8162 helix: 0.41 (0.09), residues: 2966 sheet: -0.94 (0.15), residues: 1182 loop : -1.15 (0.10), residues: 4014 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.002 TRP d 527 HIS 0.020 0.001 HIS I 40 PHE 0.031 0.002 PHE b 291 TYR 0.028 0.002 TYR h 297 ARG 0.010 0.001 ARG J 56 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16324 Ramachandran restraints generated. 8162 Oldfield, 0 Emsley, 8162 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16324 Ramachandran restraints generated. 8162 Oldfield, 0 Emsley, 8162 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1073 residues out of total 6810 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 230 poor density : 843 time to evaluate : 5.710 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 192 THR cc_start: 0.7831 (p) cc_final: 0.7316 (p) REVERT: A 219 MET cc_start: 0.5241 (mmm) cc_final: 0.4124 (mmm) REVERT: F 120 MET cc_start: 0.7560 (tpp) cc_final: 0.6986 (mmm) REVERT: E 52 LEU cc_start: 0.7871 (pt) cc_final: 0.7316 (pp) REVERT: E 286 MET cc_start: 0.7032 (mmp) cc_final: 0.6696 (mmp) REVERT: B 87 TRP cc_start: 0.6337 (t-100) cc_final: 0.5753 (t60) REVERT: D 129 PHE cc_start: 0.6007 (OUTLIER) cc_final: 0.4630 (p90) REVERT: I 40 HIS cc_start: 0.8510 (OUTLIER) cc_final: 0.8093 (t-90) REVERT: I 53 LYS cc_start: 0.8564 (ttpp) cc_final: 0.8356 (pttp) REVERT: I 91 ASN cc_start: 0.8353 (m-40) cc_final: 0.7490 (m-40) REVERT: I 243 ILE cc_start: 0.7397 (tp) cc_final: 0.7133 (tp) REVERT: G 113 MET cc_start: 0.7095 (mmp) cc_final: 0.6847 (mtt) REVERT: G 142 ASP cc_start: 0.7437 (OUTLIER) cc_final: 0.7208 (m-30) REVERT: G 335 LEU cc_start: 0.8141 (mm) cc_final: 0.7700 (mt) REVERT: G 337 HIS cc_start: 0.7774 (m-70) cc_final: 0.7510 (m90) REVERT: G 447 MET cc_start: 0.7506 (ppp) cc_final: 0.6958 (ppp) REVERT: K 227 ILE cc_start: 0.7996 (OUTLIER) cc_final: 0.7748 (mt) REVERT: K 239 LEU cc_start: 0.6180 (mp) cc_final: 0.5946 (mt) REVERT: H 16 SER cc_start: 0.9093 (OUTLIER) cc_final: 0.8834 (t) REVERT: H 114 MET cc_start: 0.5399 (mmt) cc_final: 0.5049 (mmt) REVERT: H 291 MET cc_start: 0.6554 (ttt) cc_final: 0.6346 (ttm) REVERT: H 293 MET cc_start: 0.8300 (mmt) cc_final: 0.8081 (mmt) REVERT: H 356 PHE cc_start: 0.8491 (m-80) cc_final: 0.8129 (m-80) REVERT: H 401 TYR cc_start: 0.8337 (m-80) cc_final: 0.7984 (m-10) REVERT: a 78 LEU cc_start: 0.6343 (tp) cc_final: 0.6140 (tt) REVERT: a 114 MET cc_start: 0.4651 (OUTLIER) cc_final: 0.4126 (ppp) REVERT: a 207 MET cc_start: 0.7916 (mtp) cc_final: 0.7651 (mtt) REVERT: f 49 MET cc_start: 0.7752 (mpp) cc_final: 0.7442 (mtm) REVERT: f 99 ASP cc_start: 0.5154 (t0) cc_final: 0.4890 (t70) REVERT: e 141 MET cc_start: 0.6101 (ttm) cc_final: 0.5703 (ttp) REVERT: e 365 GLN cc_start: 0.7212 (mm110) cc_final: 0.6961 (mm-40) REVERT: b 175 MET cc_start: 0.7606 (mmm) cc_final: 0.6710 (mmm) REVERT: i 93 ASP cc_start: 0.5739 (m-30) cc_final: 0.5391 (m-30) REVERT: i 166 MET cc_start: 0.7890 (tmm) cc_final: 0.7627 (tmm) REVERT: i 245 ASP cc_start: 0.6289 (t0) cc_final: 0.6050 (t0) REVERT: l 139 GLN cc_start: 0.7857 (tt0) cc_final: 0.7472 (mt0) REVERT: g 39 LYS cc_start: 0.8647 (ptpp) cc_final: 0.8077 (pptt) REVERT: g 298 MET cc_start: 0.6833 (OUTLIER) cc_final: 0.6422 (tpp) REVERT: j 26 THR cc_start: 0.7905 (p) cc_final: 0.7681 (p) REVERT: j 50 MET cc_start: 0.7443 (ttm) cc_final: 0.7083 (ttp) REVERT: k 157 LYS cc_start: 0.7180 (OUTLIER) cc_final: 0.5840 (tptt) REVERT: h 33 GLU cc_start: 0.7543 (mp0) cc_final: 0.7341 (mp0) REVERT: h 212 TYR cc_start: 0.7626 (t80) cc_final: 0.7346 (t80) outliers start: 230 outliers final: 135 residues processed: 1001 average time/residue: 0.5867 time to fit residues: 1016.3474 Evaluate side-chains 878 residues out of total 6810 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 143 poor density : 735 time to evaluate : 5.651 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 VAL Chi-restraints excluded: chain A residue 144 VAL Chi-restraints excluded: chain A residue 157 VAL Chi-restraints excluded: chain A residue 204 THR Chi-restraints excluded: chain A residue 627 VAL Chi-restraints excluded: chain F residue 125 ASN Chi-restraints excluded: chain E residue 69 THR Chi-restraints excluded: chain E residue 79 LEU Chi-restraints excluded: chain E residue 100 CYS Chi-restraints excluded: chain E residue 120 ASP Chi-restraints excluded: chain C residue 77 ASN Chi-restraints excluded: chain C residue 127 GLN Chi-restraints excluded: chain C residue 144 VAL Chi-restraints excluded: chain C residue 154 LEU Chi-restraints excluded: chain B residue 27 SER Chi-restraints excluded: chain B residue 279 LEU Chi-restraints excluded: chain D residue 13 THR Chi-restraints excluded: chain D residue 59 HIS Chi-restraints excluded: chain D residue 113 THR Chi-restraints excluded: chain D residue 118 CYS Chi-restraints excluded: chain D residue 129 PHE Chi-restraints excluded: chain D residue 151 LEU Chi-restraints excluded: chain D residue 255 ASP Chi-restraints excluded: chain D residue 307 ASN Chi-restraints excluded: chain D residue 346 TYR Chi-restraints excluded: chain D residue 399 LEU Chi-restraints excluded: chain D residue 431 THR Chi-restraints excluded: chain D residue 441 LEU Chi-restraints excluded: chain D residue 531 THR Chi-restraints excluded: chain D residue 537 THR Chi-restraints excluded: chain I residue 40 HIS Chi-restraints excluded: chain I residue 76 MET Chi-restraints excluded: chain I residue 88 ILE Chi-restraints excluded: chain I residue 92 SER Chi-restraints excluded: chain I residue 115 SER Chi-restraints excluded: chain I residue 136 VAL Chi-restraints excluded: chain I residue 170 THR Chi-restraints excluded: chain I residue 173 ILE Chi-restraints excluded: chain I residue 228 VAL Chi-restraints excluded: chain L residue 66 VAL Chi-restraints excluded: chain L residue 97 SER Chi-restraints excluded: chain L residue 131 TYR Chi-restraints excluded: chain L residue 134 ILE Chi-restraints excluded: chain G residue 41 GLN Chi-restraints excluded: chain G residue 61 VAL Chi-restraints excluded: chain G residue 88 ILE Chi-restraints excluded: chain G residue 142 ASP Chi-restraints excluded: chain G residue 223 GLU Chi-restraints excluded: chain G residue 224 THR Chi-restraints excluded: chain G residue 304 ASN Chi-restraints excluded: chain G residue 307 ILE Chi-restraints excluded: chain G residue 314 VAL Chi-restraints excluded: chain G residue 407 LEU Chi-restraints excluded: chain G residue 411 LYS Chi-restraints excluded: chain G residue 506 VAL Chi-restraints excluded: chain G residue 560 VAL Chi-restraints excluded: chain J residue 37 ILE Chi-restraints excluded: chain J residue 44 MET Chi-restraints excluded: chain J residue 109 VAL Chi-restraints excluded: chain K residue 31 ILE Chi-restraints excluded: chain K residue 90 PHE Chi-restraints excluded: chain K residue 169 VAL Chi-restraints excluded: chain K residue 175 THR Chi-restraints excluded: chain K residue 222 CYS Chi-restraints excluded: chain K residue 227 ILE Chi-restraints excluded: chain K residue 265 THR Chi-restraints excluded: chain K residue 269 ILE Chi-restraints excluded: chain H residue 7 ASN Chi-restraints excluded: chain H residue 16 SER Chi-restraints excluded: chain H residue 34 VAL Chi-restraints excluded: chain H residue 299 ILE Chi-restraints excluded: chain H residue 365 LYS Chi-restraints excluded: chain H residue 377 ASN Chi-restraints excluded: chain a residue 69 VAL Chi-restraints excluded: chain a residue 112 HIS Chi-restraints excluded: chain a residue 114 MET Chi-restraints excluded: chain a residue 116 ASP Chi-restraints excluded: chain a residue 144 VAL Chi-restraints excluded: chain a residue 153 VAL Chi-restraints excluded: chain a residue 192 THR Chi-restraints excluded: chain a residue 247 THR Chi-restraints excluded: chain a residue 487 VAL Chi-restraints excluded: chain a residue 571 GLU Chi-restraints excluded: chain f residue 39 ILE Chi-restraints excluded: chain f residue 98 LEU Chi-restraints excluded: chain e residue 53 TYR Chi-restraints excluded: chain e residue 58 THR Chi-restraints excluded: chain e residue 72 SER Chi-restraints excluded: chain e residue 120 ASP Chi-restraints excluded: chain e residue 149 ASP Chi-restraints excluded: chain e residue 338 VAL Chi-restraints excluded: chain e residue 403 THR Chi-restraints excluded: chain b residue 27 SER Chi-restraints excluded: chain d residue 134 VAL Chi-restraints excluded: chain d residue 151 LEU Chi-restraints excluded: chain d residue 234 TRP Chi-restraints excluded: chain d residue 243 LYS Chi-restraints excluded: chain d residue 259 THR Chi-restraints excluded: chain d residue 289 ASN Chi-restraints excluded: chain d residue 307 ASN Chi-restraints excluded: chain d residue 399 LEU Chi-restraints excluded: chain d residue 441 LEU Chi-restraints excluded: chain d residue 531 THR Chi-restraints excluded: chain d residue 537 THR Chi-restraints excluded: chain i residue 16 LEU Chi-restraints excluded: chain i residue 114 ASP Chi-restraints excluded: chain i residue 115 SER Chi-restraints excluded: chain i residue 117 LEU Chi-restraints excluded: chain i residue 170 THR Chi-restraints excluded: chain i residue 215 LEU Chi-restraints excluded: chain i residue 228 VAL Chi-restraints excluded: chain l residue 105 ILE Chi-restraints excluded: chain l residue 131 TYR Chi-restraints excluded: chain g residue 61 VAL Chi-restraints excluded: chain g residue 249 ASP Chi-restraints excluded: chain g residue 298 MET Chi-restraints excluded: chain g residue 305 LYS Chi-restraints excluded: chain g residue 320 THR Chi-restraints excluded: chain g residue 322 MET Chi-restraints excluded: chain g residue 346 GLU Chi-restraints excluded: chain g residue 402 CYS Chi-restraints excluded: chain g residue 424 ASP Chi-restraints excluded: chain g residue 546 TYR Chi-restraints excluded: chain j residue 12 GLN Chi-restraints excluded: chain j residue 63 GLU Chi-restraints excluded: chain j residue 96 THR Chi-restraints excluded: chain k residue 90 PHE Chi-restraints excluded: chain k residue 105 ILE Chi-restraints excluded: chain k residue 157 LYS Chi-restraints excluded: chain k residue 175 THR Chi-restraints excluded: chain k residue 205 VAL Chi-restraints excluded: chain k residue 230 THR Chi-restraints excluded: chain k residue 232 THR Chi-restraints excluded: chain k residue 233 VAL Chi-restraints excluded: chain k residue 234 VAL Chi-restraints excluded: chain k residue 261 THR Chi-restraints excluded: chain k residue 264 ILE Chi-restraints excluded: chain k residue 337 ASP Chi-restraints excluded: chain h residue 40 ILE Chi-restraints excluded: chain h residue 237 LYS Chi-restraints excluded: chain h residue 299 ILE Chi-restraints excluded: chain h residue 322 ASN Chi-restraints excluded: chain h residue 385 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 808 random chunks: chunk 726 optimal weight: 4.9990 chunk 552 optimal weight: 0.6980 chunk 381 optimal weight: 6.9990 chunk 81 optimal weight: 9.9990 chunk 350 optimal weight: 0.0050 chunk 493 optimal weight: 0.9990 chunk 737 optimal weight: 0.0870 chunk 781 optimal weight: 3.9990 chunk 385 optimal weight: 0.9980 chunk 699 optimal weight: 9.9990 chunk 210 optimal weight: 10.0000 overall best weight: 0.5574 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 79 HIS A 429 HIS ** F 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 230 ASN C 130 GLN B 211 HIS ** D 59 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 100 HIS L 106 ASN G 152 ASN ** G 264 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 270 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 561 HIS ** J 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 374 GLN H 367 HIS H 377 ASN H 386 HIS ** H 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 337 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** c 130 GLN ** b 122 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 100 HIS d 338 GLN ** d 534 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 264 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 270 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 531 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** h 327 ASN h 367 HIS Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6731 moved from start: 0.3895 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.071 65656 Z= 0.169 Angle : 0.584 12.235 89258 Z= 0.300 Chirality : 0.045 0.215 9916 Planarity : 0.004 0.070 11364 Dihedral : 10.038 178.431 9317 Min Nonbonded Distance : 1.968 Molprobity Statistics. All-atom Clashscore : 12.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.91 % Favored : 95.09 % Rotamer: Outliers : 3.08 % Allowed : 16.23 % Favored : 80.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.54 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.70 (0.09), residues: 8162 helix: 0.51 (0.10), residues: 2956 sheet: -0.85 (0.15), residues: 1168 loop : -1.04 (0.10), residues: 4038 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.001 TRP d 527 HIS 0.010 0.001 HIS A 429 PHE 0.029 0.002 PHE c 29 TYR 0.025 0.001 TYR d 350 ARG 0.005 0.000 ARG K 367 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16324 Ramachandran restraints generated. 8162 Oldfield, 0 Emsley, 8162 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16324 Ramachandran restraints generated. 8162 Oldfield, 0 Emsley, 8162 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1016 residues out of total 6810 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 210 poor density : 806 time to evaluate : 5.739 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 9 ILE cc_start: 0.6949 (OUTLIER) cc_final: 0.6629 (tp) REVERT: F 48 ASP cc_start: 0.4503 (t0) cc_final: 0.4260 (t0) REVERT: F 120 MET cc_start: 0.7399 (tpp) cc_final: 0.7077 (mmm) REVERT: E 52 LEU cc_start: 0.8030 (pt) cc_final: 0.7505 (pp) REVERT: E 286 MET cc_start: 0.7070 (mmp) cc_final: 0.6842 (mmp) REVERT: E 365 GLN cc_start: 0.6973 (mm110) cc_final: 0.6502 (mm-40) REVERT: D 129 PHE cc_start: 0.5882 (OUTLIER) cc_final: 0.4592 (p90) REVERT: I 6 MET cc_start: 0.7473 (ttp) cc_final: 0.7106 (mtp) REVERT: I 40 HIS cc_start: 0.8667 (OUTLIER) cc_final: 0.7380 (t-90) REVERT: I 243 ILE cc_start: 0.7353 (tp) cc_final: 0.7105 (tp) REVERT: L 139 GLN cc_start: 0.8447 (tt0) cc_final: 0.8112 (mm-40) REVERT: G 113 MET cc_start: 0.7354 (mmp) cc_final: 0.7084 (mtt) REVERT: G 141 LEU cc_start: 0.8482 (OUTLIER) cc_final: 0.8158 (mt) REVERT: G 335 LEU cc_start: 0.8154 (OUTLIER) cc_final: 0.7822 (mt) REVERT: G 408 MET cc_start: 0.6431 (tmm) cc_final: 0.6101 (tpt) REVERT: G 447 MET cc_start: 0.7346 (ppp) cc_final: 0.7041 (ppp) REVERT: J 22 GLU cc_start: 0.7846 (mm-30) cc_final: 0.7220 (tp30) REVERT: J 47 LEU cc_start: 0.8995 (mt) cc_final: 0.8679 (mp) REVERT: J 50 MET cc_start: 0.7244 (tpp) cc_final: 0.6532 (ttm) REVERT: K 227 ILE cc_start: 0.7847 (OUTLIER) cc_final: 0.7453 (mt) REVERT: H 16 SER cc_start: 0.9054 (m) cc_final: 0.8780 (t) REVERT: H 90 MET cc_start: 0.7151 (tpp) cc_final: 0.6838 (ttp) REVERT: H 208 GLN cc_start: 0.7841 (tm-30) cc_final: 0.7015 (pp30) REVERT: H 260 MET cc_start: 0.8373 (mmp) cc_final: 0.7883 (mmm) REVERT: H 293 MET cc_start: 0.8404 (mmt) cc_final: 0.8182 (mmt) REVERT: H 378 MET cc_start: 0.8432 (mmm) cc_final: 0.8159 (mmp) REVERT: H 401 TYR cc_start: 0.8182 (m-80) cc_final: 0.7901 (m-10) REVERT: H 421 MET cc_start: 0.7412 (ptp) cc_final: 0.7147 (ptp) REVERT: H 437 LEU cc_start: 0.8156 (mp) cc_final: 0.7838 (mt) REVERT: a 114 MET cc_start: 0.4587 (OUTLIER) cc_final: 0.4149 (ppp) REVERT: a 207 MET cc_start: 0.7825 (mtp) cc_final: 0.7529 (mtt) REVERT: a 594 MET cc_start: 0.6643 (ptp) cc_final: 0.5491 (ptp) REVERT: f 49 MET cc_start: 0.7711 (mpp) cc_final: 0.7390 (mtm) REVERT: e 243 ILE cc_start: 0.7064 (mt) cc_final: 0.6844 (tp) REVERT: i 166 MET cc_start: 0.7843 (tmm) cc_final: 0.7546 (tmm) REVERT: l 100 LYS cc_start: 0.6530 (OUTLIER) cc_final: 0.6329 (mtpp) REVERT: g 39 LYS cc_start: 0.8629 (ptpp) cc_final: 0.8035 (pptt) REVERT: g 298 MET cc_start: 0.6674 (OUTLIER) cc_final: 0.6447 (tpp) REVERT: g 439 LEU cc_start: 0.7432 (mm) cc_final: 0.6994 (mt) REVERT: j 50 MET cc_start: 0.7269 (ttm) cc_final: 0.6996 (ttm) REVERT: j 60 GLU cc_start: 0.8200 (pm20) cc_final: 0.7691 (pt0) REVERT: k 157 LYS cc_start: 0.6960 (OUTLIER) cc_final: 0.5671 (tptt) REVERT: h 35 GLU cc_start: 0.6607 (mp0) cc_final: 0.6309 (mp0) REVERT: h 212 TYR cc_start: 0.7504 (t80) cc_final: 0.7249 (t80) REVERT: h 323 HIS cc_start: 0.7579 (p90) cc_final: 0.6670 (p90) outliers start: 210 outliers final: 124 residues processed: 955 average time/residue: 0.6594 time to fit residues: 1080.5699 Evaluate side-chains 855 residues out of total 6810 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 134 poor density : 721 time to evaluate : 5.711 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 ILE Chi-restraints excluded: chain A residue 69 VAL Chi-restraints excluded: chain A residue 140 VAL Chi-restraints excluded: chain A residue 144 VAL Chi-restraints excluded: chain A residue 157 VAL Chi-restraints excluded: chain A residue 203 LEU Chi-restraints excluded: chain F residue 57 VAL Chi-restraints excluded: chain F residue 125 ASN Chi-restraints excluded: chain E residue 58 THR Chi-restraints excluded: chain E residue 100 CYS Chi-restraints excluded: chain E residue 120 ASP Chi-restraints excluded: chain C residue 77 ASN Chi-restraints excluded: chain C residue 130 GLN Chi-restraints excluded: chain C residue 144 VAL Chi-restraints excluded: chain B residue 29 LYS Chi-restraints excluded: chain B residue 248 GLU Chi-restraints excluded: chain B residue 279 LEU Chi-restraints excluded: chain D residue 118 CYS Chi-restraints excluded: chain D residue 129 PHE Chi-restraints excluded: chain D residue 151 LEU Chi-restraints excluded: chain D residue 220 ASN Chi-restraints excluded: chain D residue 255 ASP Chi-restraints excluded: chain D residue 307 ASN Chi-restraints excluded: chain D residue 531 THR Chi-restraints excluded: chain D residue 537 THR Chi-restraints excluded: chain I residue 40 HIS Chi-restraints excluded: chain I residue 76 MET Chi-restraints excluded: chain I residue 88 ILE Chi-restraints excluded: chain I residue 115 SER Chi-restraints excluded: chain I residue 136 VAL Chi-restraints excluded: chain I residue 170 THR Chi-restraints excluded: chain I residue 173 ILE Chi-restraints excluded: chain I residue 200 VAL Chi-restraints excluded: chain L residue 66 VAL Chi-restraints excluded: chain L residue 131 TYR Chi-restraints excluded: chain G residue 41 GLN Chi-restraints excluded: chain G residue 61 VAL Chi-restraints excluded: chain G residue 88 ILE Chi-restraints excluded: chain G residue 99 SER Chi-restraints excluded: chain G residue 141 LEU Chi-restraints excluded: chain G residue 152 ASN Chi-restraints excluded: chain G residue 304 ASN Chi-restraints excluded: chain G residue 307 ILE Chi-restraints excluded: chain G residue 314 VAL Chi-restraints excluded: chain G residue 335 LEU Chi-restraints excluded: chain G residue 407 LEU Chi-restraints excluded: chain G residue 411 LYS Chi-restraints excluded: chain J residue 37 ILE Chi-restraints excluded: chain J residue 44 MET Chi-restraints excluded: chain J residue 96 THR Chi-restraints excluded: chain K residue 90 PHE Chi-restraints excluded: chain K residue 169 VAL Chi-restraints excluded: chain K residue 222 CYS Chi-restraints excluded: chain K residue 227 ILE Chi-restraints excluded: chain K residue 229 VAL Chi-restraints excluded: chain K residue 243 ASN Chi-restraints excluded: chain K residue 265 THR Chi-restraints excluded: chain K residue 269 ILE Chi-restraints excluded: chain K residue 312 ILE Chi-restraints excluded: chain H residue 34 VAL Chi-restraints excluded: chain H residue 148 ASP Chi-restraints excluded: chain H residue 299 ILE Chi-restraints excluded: chain H residue 365 LYS Chi-restraints excluded: chain H residue 376 ILE Chi-restraints excluded: chain H residue 422 ASP Chi-restraints excluded: chain a residue 38 TYR Chi-restraints excluded: chain a residue 69 VAL Chi-restraints excluded: chain a residue 112 HIS Chi-restraints excluded: chain a residue 114 MET Chi-restraints excluded: chain a residue 116 ASP Chi-restraints excluded: chain a residue 140 VAL Chi-restraints excluded: chain a residue 144 VAL Chi-restraints excluded: chain a residue 153 VAL Chi-restraints excluded: chain a residue 192 THR Chi-restraints excluded: chain a residue 203 LEU Chi-restraints excluded: chain a residue 247 THR Chi-restraints excluded: chain a residue 487 VAL Chi-restraints excluded: chain a residue 571 GLU Chi-restraints excluded: chain f residue 64 LEU Chi-restraints excluded: chain f residue 98 LEU Chi-restraints excluded: chain e residue 53 TYR Chi-restraints excluded: chain e residue 58 THR Chi-restraints excluded: chain e residue 120 ASP Chi-restraints excluded: chain e residue 149 ASP Chi-restraints excluded: chain e residue 286 MET Chi-restraints excluded: chain e residue 403 THR Chi-restraints excluded: chain c residue 129 VAL Chi-restraints excluded: chain b residue 27 SER Chi-restraints excluded: chain b residue 211 HIS Chi-restraints excluded: chain b residue 289 THR Chi-restraints excluded: chain d residue 222 SER Chi-restraints excluded: chain d residue 243 LYS Chi-restraints excluded: chain d residue 259 THR Chi-restraints excluded: chain d residue 276 VAL Chi-restraints excluded: chain d residue 307 ASN Chi-restraints excluded: chain d residue 399 LEU Chi-restraints excluded: chain d residue 441 LEU Chi-restraints excluded: chain d residue 531 THR Chi-restraints excluded: chain d residue 537 THR Chi-restraints excluded: chain i residue 16 LEU Chi-restraints excluded: chain i residue 114 ASP Chi-restraints excluded: chain i residue 117 LEU Chi-restraints excluded: chain l residue 100 LYS Chi-restraints excluded: chain l residue 105 ILE Chi-restraints excluded: chain l residue 111 ILE Chi-restraints excluded: chain l residue 131 TYR Chi-restraints excluded: chain g residue 61 VAL Chi-restraints excluded: chain g residue 298 MET Chi-restraints excluded: chain g residue 305 LYS Chi-restraints excluded: chain g residue 346 GLU Chi-restraints excluded: chain g residue 424 ASP Chi-restraints excluded: chain g residue 431 ASN Chi-restraints excluded: chain g residue 458 LEU Chi-restraints excluded: chain g residue 482 ASP Chi-restraints excluded: chain g residue 546 TYR Chi-restraints excluded: chain j residue 12 GLN Chi-restraints excluded: chain j residue 63 GLU Chi-restraints excluded: chain j residue 96 THR Chi-restraints excluded: chain k residue 90 PHE Chi-restraints excluded: chain k residue 105 ILE Chi-restraints excluded: chain k residue 140 ILE Chi-restraints excluded: chain k residue 157 LYS Chi-restraints excluded: chain k residue 175 THR Chi-restraints excluded: chain k residue 230 THR Chi-restraints excluded: chain k residue 233 VAL Chi-restraints excluded: chain k residue 234 VAL Chi-restraints excluded: chain k residue 265 THR Chi-restraints excluded: chain h residue 44 ILE Chi-restraints excluded: chain h residue 96 THR Chi-restraints excluded: chain h residue 237 LYS Chi-restraints excluded: chain h residue 299 ILE Chi-restraints excluded: chain h residue 322 ASN Chi-restraints excluded: chain h residue 338 MET Chi-restraints excluded: chain h residue 385 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 808 random chunks: chunk 650 optimal weight: 3.9990 chunk 443 optimal weight: 30.0000 chunk 11 optimal weight: 8.9990 chunk 581 optimal weight: 9.9990 chunk 322 optimal weight: 0.9990 chunk 666 optimal weight: 9.9990 chunk 539 optimal weight: 6.9990 chunk 0 optimal weight: 20.0000 chunk 398 optimal weight: 0.7980 chunk 701 optimal weight: 0.3980 chunk 197 optimal weight: 20.0000 overall best weight: 2.6386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 93 ASN A 106 ASN ** A 293 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 74 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 358 ASN C 130 GLN D 59 HIS ** G 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 161 ASN ** G 270 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 518 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 127 GLN ** H 156 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 164 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 327 ASN H 377 ASN ** H 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 337 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** e 409 ASN c 130 GLN ** b 122 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 338 GLN l 139 GLN g 132 HIS ** g 264 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 270 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 531 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** h 327 ASN h 377 ASN h 409 GLN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6888 moved from start: 0.4488 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.090 65656 Z= 0.272 Angle : 0.626 13.568 89258 Z= 0.323 Chirality : 0.047 0.209 9916 Planarity : 0.005 0.069 11364 Dihedral : 10.142 179.364 9315 Min Nonbonded Distance : 1.890 Molprobity Statistics. All-atom Clashscore : 13.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.64 % Favored : 94.36 % Rotamer: Outliers : 3.69 % Allowed : 16.75 % Favored : 79.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.54 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.72 (0.09), residues: 8162 helix: 0.49 (0.10), residues: 2950 sheet: -0.88 (0.15), residues: 1208 loop : -1.04 (0.10), residues: 4004 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.002 TRP d 527 HIS 0.008 0.001 HIS e 337 PHE 0.021 0.002 PHE h 258 TYR 0.021 0.002 TYR A 423 ARG 0.029 0.001 ARG b 15 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16324 Ramachandran restraints generated. 8162 Oldfield, 0 Emsley, 8162 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16324 Ramachandran restraints generated. 8162 Oldfield, 0 Emsley, 8162 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1008 residues out of total 6810 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 251 poor density : 757 time to evaluate : 5.729 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 9 ILE cc_start: 0.7132 (OUTLIER) cc_final: 0.6715 (tp) REVERT: F 120 MET cc_start: 0.7633 (tpp) cc_final: 0.7303 (mmm) REVERT: E 156 GLU cc_start: 0.6277 (pm20) cc_final: 0.5989 (pm20) REVERT: E 286 MET cc_start: 0.7215 (mmp) cc_final: 0.6898 (mmp) REVERT: E 297 TYR cc_start: 0.7933 (m-10) cc_final: 0.7704 (m-10) REVERT: E 365 GLN cc_start: 0.7090 (mm110) cc_final: 0.6149 (mm-40) REVERT: B 291 PHE cc_start: 0.7065 (t80) cc_final: 0.6783 (t80) REVERT: D 129 PHE cc_start: 0.5998 (OUTLIER) cc_final: 0.4582 (p90) REVERT: D 208 MET cc_start: 0.8080 (tmm) cc_final: 0.7746 (tmm) REVERT: I 6 MET cc_start: 0.7839 (ttp) cc_final: 0.7373 (mtp) REVERT: I 30 SER cc_start: 0.7438 (p) cc_final: 0.6099 (t) REVERT: I 40 HIS cc_start: 0.8708 (OUTLIER) cc_final: 0.7423 (t-90) REVERT: I 74 ARG cc_start: 0.7767 (tpp80) cc_final: 0.7476 (tpp80) REVERT: L 139 GLN cc_start: 0.8696 (tt0) cc_final: 0.8400 (mm-40) REVERT: G 29 ASP cc_start: 0.6926 (OUTLIER) cc_final: 0.6723 (m-30) REVERT: G 161 ASN cc_start: 0.8368 (OUTLIER) cc_final: 0.7995 (t0) REVERT: G 335 LEU cc_start: 0.8309 (OUTLIER) cc_final: 0.7958 (mt) REVERT: G 408 MET cc_start: 0.6260 (tmm) cc_final: 0.6054 (tmm) REVERT: G 447 MET cc_start: 0.7463 (ppp) cc_final: 0.7169 (ppp) REVERT: G 458 LEU cc_start: 0.8113 (OUTLIER) cc_final: 0.7627 (pp) REVERT: G 533 GLN cc_start: 0.8823 (tp40) cc_final: 0.8577 (tp40) REVERT: G 551 GLU cc_start: 0.7954 (mp0) cc_final: 0.7678 (mm-30) REVERT: J 17 GLU cc_start: 0.7807 (OUTLIER) cc_final: 0.7556 (tp30) REVERT: J 50 MET cc_start: 0.7751 (tpp) cc_final: 0.6805 (ttp) REVERT: J 123 LEU cc_start: 0.7576 (mp) cc_final: 0.7300 (pt) REVERT: K 227 ILE cc_start: 0.7912 (OUTLIER) cc_final: 0.7488 (mt) REVERT: K 384 LYS cc_start: 0.8155 (OUTLIER) cc_final: 0.7921 (tttp) REVERT: H 13 CYS cc_start: 0.8520 (OUTLIER) cc_final: 0.8306 (p) REVERT: H 260 MET cc_start: 0.8872 (mmp) cc_final: 0.8510 (mmt) REVERT: H 293 MET cc_start: 0.8477 (mmt) cc_final: 0.8080 (mmt) REVERT: H 344 MET cc_start: 0.6959 (OUTLIER) cc_final: 0.6383 (tmt) REVERT: H 378 MET cc_start: 0.7815 (mmm) cc_final: 0.7220 (mmp) REVERT: H 421 MET cc_start: 0.7246 (ptp) cc_final: 0.7044 (ptp) REVERT: a 114 MET cc_start: 0.4752 (OUTLIER) cc_final: 0.4332 (ppp) REVERT: a 186 MET cc_start: 0.7115 (tmm) cc_final: 0.6903 (tmm) REVERT: a 594 MET cc_start: 0.6726 (ptp) cc_final: 0.5591 (ptp) REVERT: b 175 MET cc_start: 0.6715 (mmm) cc_final: 0.6430 (mmm) REVERT: d 245 PHE cc_start: 0.6734 (OUTLIER) cc_final: 0.6513 (m-80) REVERT: i 96 MET cc_start: 0.8178 (mtt) cc_final: 0.7895 (mtp) REVERT: i 166 MET cc_start: 0.7799 (tmm) cc_final: 0.7412 (tmm) REVERT: i 245 ASP cc_start: 0.6172 (t0) cc_final: 0.5948 (t0) REVERT: l 100 LYS cc_start: 0.7226 (OUTLIER) cc_final: 0.6920 (mtpp) REVERT: g 39 LYS cc_start: 0.8682 (ptpp) cc_final: 0.8123 (pptt) REVERT: g 298 MET cc_start: 0.6916 (OUTLIER) cc_final: 0.6515 (tpp) REVERT: j 50 MET cc_start: 0.7394 (ttm) cc_final: 0.7151 (ttm) REVERT: j 119 LEU cc_start: 0.7008 (mt) cc_final: 0.6770 (mt) REVERT: k 157 LYS cc_start: 0.7365 (OUTLIER) cc_final: 0.6469 (tptt) REVERT: h 19 ASP cc_start: 0.6281 (m-30) cc_final: 0.5925 (t0) REVERT: h 35 GLU cc_start: 0.6879 (mp0) cc_final: 0.6616 (mp0) REVERT: h 212 TYR cc_start: 0.7571 (t80) cc_final: 0.7239 (t80) REVERT: h 260 MET cc_start: 0.8787 (mmm) cc_final: 0.8051 (mmm) REVERT: h 336 MET cc_start: 0.7755 (ptm) cc_final: 0.7541 (ptm) REVERT: h 348 ILE cc_start: 0.9148 (OUTLIER) cc_final: 0.8916 (tt) REVERT: h 434 MET cc_start: 0.7043 (mtp) cc_final: 0.6507 (mtm) outliers start: 251 outliers final: 171 residues processed: 950 average time/residue: 0.5887 time to fit residues: 962.9800 Evaluate side-chains 870 residues out of total 6810 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 189 poor density : 681 time to evaluate : 5.742 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 ILE Chi-restraints excluded: chain A residue 69 VAL Chi-restraints excluded: chain A residue 140 VAL Chi-restraints excluded: chain A residue 144 VAL Chi-restraints excluded: chain A residue 157 VAL Chi-restraints excluded: chain A residue 192 THR Chi-restraints excluded: chain F residue 15 ASN Chi-restraints excluded: chain F residue 39 ILE Chi-restraints excluded: chain F residue 125 ASN Chi-restraints excluded: chain E residue 58 THR Chi-restraints excluded: chain E residue 59 VAL Chi-restraints excluded: chain E residue 69 THR Chi-restraints excluded: chain E residue 79 LEU Chi-restraints excluded: chain E residue 100 CYS Chi-restraints excluded: chain E residue 120 ASP Chi-restraints excluded: chain E residue 372 MET Chi-restraints excluded: chain C residue 77 ASN Chi-restraints excluded: chain C residue 130 GLN Chi-restraints excluded: chain C residue 144 VAL Chi-restraints excluded: chain B residue 29 LYS Chi-restraints excluded: chain B residue 248 GLU Chi-restraints excluded: chain B residue 279 LEU Chi-restraints excluded: chain D residue 13 THR Chi-restraints excluded: chain D residue 44 ILE Chi-restraints excluded: chain D residue 59 HIS Chi-restraints excluded: chain D residue 113 THR Chi-restraints excluded: chain D residue 118 CYS Chi-restraints excluded: chain D residue 129 PHE Chi-restraints excluded: chain D residue 151 LEU Chi-restraints excluded: chain D residue 220 ASN Chi-restraints excluded: chain D residue 307 ASN Chi-restraints excluded: chain D residue 399 LEU Chi-restraints excluded: chain D residue 431 THR Chi-restraints excluded: chain D residue 441 LEU Chi-restraints excluded: chain D residue 531 THR Chi-restraints excluded: chain D residue 537 THR Chi-restraints excluded: chain I residue 20 SER Chi-restraints excluded: chain I residue 40 HIS Chi-restraints excluded: chain I residue 88 ILE Chi-restraints excluded: chain I residue 115 SER Chi-restraints excluded: chain I residue 136 VAL Chi-restraints excluded: chain I residue 170 THR Chi-restraints excluded: chain I residue 173 ILE Chi-restraints excluded: chain I residue 179 ILE Chi-restraints excluded: chain I residue 189 THR Chi-restraints excluded: chain I residue 200 VAL Chi-restraints excluded: chain I residue 228 VAL Chi-restraints excluded: chain L residue 66 VAL Chi-restraints excluded: chain L residue 97 SER Chi-restraints excluded: chain L residue 131 TYR Chi-restraints excluded: chain L residue 134 ILE Chi-restraints excluded: chain G residue 29 ASP Chi-restraints excluded: chain G residue 88 ILE Chi-restraints excluded: chain G residue 99 SER Chi-restraints excluded: chain G residue 100 ILE Chi-restraints excluded: chain G residue 161 ASN Chi-restraints excluded: chain G residue 224 THR Chi-restraints excluded: chain G residue 304 ASN Chi-restraints excluded: chain G residue 307 ILE Chi-restraints excluded: chain G residue 314 VAL Chi-restraints excluded: chain G residue 335 LEU Chi-restraints excluded: chain G residue 407 LEU Chi-restraints excluded: chain G residue 411 LYS Chi-restraints excluded: chain G residue 458 LEU Chi-restraints excluded: chain G residue 560 VAL Chi-restraints excluded: chain J residue 17 GLU Chi-restraints excluded: chain J residue 21 MET Chi-restraints excluded: chain J residue 37 ILE Chi-restraints excluded: chain J residue 44 MET Chi-restraints excluded: chain J residue 63 GLU Chi-restraints excluded: chain J residue 96 THR Chi-restraints excluded: chain J residue 99 THR Chi-restraints excluded: chain K residue 31 ILE Chi-restraints excluded: chain K residue 90 PHE Chi-restraints excluded: chain K residue 125 CYS Chi-restraints excluded: chain K residue 169 VAL Chi-restraints excluded: chain K residue 175 THR Chi-restraints excluded: chain K residue 222 CYS Chi-restraints excluded: chain K residue 227 ILE Chi-restraints excluded: chain K residue 229 VAL Chi-restraints excluded: chain K residue 243 ASN Chi-restraints excluded: chain K residue 265 THR Chi-restraints excluded: chain K residue 269 ILE Chi-restraints excluded: chain K residue 312 ILE Chi-restraints excluded: chain K residue 371 VAL Chi-restraints excluded: chain K residue 384 LYS Chi-restraints excluded: chain H residue 7 ASN Chi-restraints excluded: chain H residue 13 CYS Chi-restraints excluded: chain H residue 34 VAL Chi-restraints excluded: chain H residue 52 ASP Chi-restraints excluded: chain H residue 148 ASP Chi-restraints excluded: chain H residue 299 ILE Chi-restraints excluded: chain H residue 331 THR Chi-restraints excluded: chain H residue 344 MET Chi-restraints excluded: chain H residue 365 LYS Chi-restraints excluded: chain H residue 376 ILE Chi-restraints excluded: chain H residue 377 ASN Chi-restraints excluded: chain H residue 385 LEU Chi-restraints excluded: chain H residue 422 ASP Chi-restraints excluded: chain a residue 38 TYR Chi-restraints excluded: chain a residue 69 VAL Chi-restraints excluded: chain a residue 70 VAL Chi-restraints excluded: chain a residue 112 HIS Chi-restraints excluded: chain a residue 114 MET Chi-restraints excluded: chain a residue 140 VAL Chi-restraints excluded: chain a residue 144 VAL Chi-restraints excluded: chain a residue 153 VAL Chi-restraints excluded: chain a residue 192 THR Chi-restraints excluded: chain a residue 203 LEU Chi-restraints excluded: chain a residue 220 THR Chi-restraints excluded: chain a residue 247 THR Chi-restraints excluded: chain a residue 487 VAL Chi-restraints excluded: chain a residue 551 VAL Chi-restraints excluded: chain f residue 39 ILE Chi-restraints excluded: chain f residue 98 LEU Chi-restraints excluded: chain f residue 99 ASP Chi-restraints excluded: chain e residue 58 THR Chi-restraints excluded: chain e residue 72 SER Chi-restraints excluded: chain e residue 120 ASP Chi-restraints excluded: chain e residue 149 ASP Chi-restraints excluded: chain e residue 287 MET Chi-restraints excluded: chain e residue 338 VAL Chi-restraints excluded: chain e residue 389 VAL Chi-restraints excluded: chain e residue 403 THR Chi-restraints excluded: chain c residue 129 VAL Chi-restraints excluded: chain b residue 27 SER Chi-restraints excluded: chain b residue 132 VAL Chi-restraints excluded: chain b residue 211 HIS Chi-restraints excluded: chain b residue 289 THR Chi-restraints excluded: chain d residue 71 ILE Chi-restraints excluded: chain d residue 134 VAL Chi-restraints excluded: chain d residue 222 SER Chi-restraints excluded: chain d residue 243 LYS Chi-restraints excluded: chain d residue 245 PHE Chi-restraints excluded: chain d residue 276 VAL Chi-restraints excluded: chain d residue 289 ASN Chi-restraints excluded: chain d residue 307 ASN Chi-restraints excluded: chain d residue 326 VAL Chi-restraints excluded: chain d residue 350 TYR Chi-restraints excluded: chain d residue 399 LEU Chi-restraints excluded: chain d residue 441 LEU Chi-restraints excluded: chain d residue 531 THR Chi-restraints excluded: chain d residue 537 THR Chi-restraints excluded: chain i residue 16 LEU Chi-restraints excluded: chain i residue 76 MET Chi-restraints excluded: chain i residue 114 ASP Chi-restraints excluded: chain i residue 115 SER Chi-restraints excluded: chain i residue 127 LEU Chi-restraints excluded: chain i residue 170 THR Chi-restraints excluded: chain i residue 228 VAL Chi-restraints excluded: chain l residue 66 VAL Chi-restraints excluded: chain l residue 100 LYS Chi-restraints excluded: chain l residue 105 ILE Chi-restraints excluded: chain g residue 61 VAL Chi-restraints excluded: chain g residue 249 ASP Chi-restraints excluded: chain g residue 298 MET Chi-restraints excluded: chain g residue 305 LYS Chi-restraints excluded: chain g residue 320 THR Chi-restraints excluded: chain g residue 346 GLU Chi-restraints excluded: chain g residue 424 ASP Chi-restraints excluded: chain g residue 431 ASN Chi-restraints excluded: chain g residue 458 LEU Chi-restraints excluded: chain g residue 546 TYR Chi-restraints excluded: chain j residue 12 GLN Chi-restraints excluded: chain j residue 37 ILE Chi-restraints excluded: chain j residue 63 GLU Chi-restraints excluded: chain k residue 90 PHE Chi-restraints excluded: chain k residue 105 ILE Chi-restraints excluded: chain k residue 157 LYS Chi-restraints excluded: chain k residue 175 THR Chi-restraints excluded: chain k residue 183 LEU Chi-restraints excluded: chain k residue 201 VAL Chi-restraints excluded: chain k residue 230 THR Chi-restraints excluded: chain k residue 232 THR Chi-restraints excluded: chain k residue 233 VAL Chi-restraints excluded: chain k residue 234 VAL Chi-restraints excluded: chain k residue 264 ILE Chi-restraints excluded: chain k residue 265 THR Chi-restraints excluded: chain k residue 269 ILE Chi-restraints excluded: chain h residue 40 ILE Chi-restraints excluded: chain h residue 89 LEU Chi-restraints excluded: chain h residue 143 VAL Chi-restraints excluded: chain h residue 237 LYS Chi-restraints excluded: chain h residue 299 ILE Chi-restraints excluded: chain h residue 322 ASN Chi-restraints excluded: chain h residue 348 ILE Chi-restraints excluded: chain h residue 376 ILE Chi-restraints excluded: chain h residue 385 LEU Chi-restraints excluded: chain h residue 389 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 808 random chunks: chunk 262 optimal weight: 9.9990 chunk 703 optimal weight: 5.9990 chunk 154 optimal weight: 0.9990 chunk 458 optimal weight: 5.9990 chunk 192 optimal weight: 7.9990 chunk 781 optimal weight: 7.9990 chunk 648 optimal weight: 0.4980 chunk 361 optimal weight: 0.5980 chunk 65 optimal weight: 3.9990 chunk 258 optimal weight: 9.9990 chunk 410 optimal weight: 10.0000 overall best weight: 2.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 74 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 130 GLN ** B 211 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 59 HIS ** G 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 270 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 156 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 164 HIS H 377 ASN ** H 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 337 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 130 GLN c 172 GLN ** b 122 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** b 239 GLN d 338 GLN ** d 534 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 264 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 270 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 531 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** h 327 ASN h 409 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6924 moved from start: 0.4874 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.067 65656 Z= 0.249 Angle : 0.619 13.278 89258 Z= 0.315 Chirality : 0.046 0.189 9916 Planarity : 0.004 0.070 11364 Dihedral : 9.778 179.379 9310 Min Nonbonded Distance : 1.878 Molprobity Statistics. All-atom Clashscore : 13.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.43 % Favored : 94.57 % Rotamer: Outliers : 3.64 % Allowed : 17.68 % Favored : 78.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.54 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.74 (0.09), residues: 8162 helix: 0.48 (0.10), residues: 2932 sheet: -0.89 (0.15), residues: 1228 loop : -1.05 (0.10), residues: 4002 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.002 TRP d 527 HIS 0.038 0.001 HIS D 59 PHE 0.041 0.002 PHE b 237 TYR 0.035 0.001 TYR D 350 ARG 0.013 0.001 ARG h 80 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16324 Ramachandran restraints generated. 8162 Oldfield, 0 Emsley, 8162 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16324 Ramachandran restraints generated. 8162 Oldfield, 0 Emsley, 8162 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 972 residues out of total 6810 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 248 poor density : 724 time to evaluate : 5.794 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 9 ILE cc_start: 0.7009 (OUTLIER) cc_final: 0.6747 (tp) REVERT: A 594 MET cc_start: 0.5802 (ptp) cc_final: 0.5438 (ptp) REVERT: E 286 MET cc_start: 0.7268 (mmp) cc_final: 0.6988 (mmp) REVERT: E 297 TYR cc_start: 0.8033 (m-10) cc_final: 0.7766 (m-10) REVERT: D 129 PHE cc_start: 0.6006 (OUTLIER) cc_final: 0.4625 (p90) REVERT: D 208 MET cc_start: 0.8000 (tmm) cc_final: 0.7766 (tmm) REVERT: I 6 MET cc_start: 0.7842 (ttp) cc_final: 0.7433 (mtp) REVERT: I 40 HIS cc_start: 0.8919 (OUTLIER) cc_final: 0.7351 (t-90) REVERT: I 173 ILE cc_start: 0.7105 (OUTLIER) cc_final: 0.6891 (mm) REVERT: L 139 GLN cc_start: 0.8580 (tt0) cc_final: 0.8258 (mm-40) REVERT: G 335 LEU cc_start: 0.8274 (OUTLIER) cc_final: 0.7889 (mt) REVERT: G 408 MET cc_start: 0.6302 (tmm) cc_final: 0.6090 (tpt) REVERT: G 458 LEU cc_start: 0.8091 (OUTLIER) cc_final: 0.7480 (pp) REVERT: G 533 GLN cc_start: 0.8891 (tp40) cc_final: 0.8645 (tp40) REVERT: J 17 GLU cc_start: 0.7785 (OUTLIER) cc_final: 0.7438 (tp30) REVERT: J 50 MET cc_start: 0.7892 (tpp) cc_final: 0.7241 (ttp) REVERT: J 123 LEU cc_start: 0.7834 (mp) cc_final: 0.7390 (pt) REVERT: K 227 ILE cc_start: 0.7872 (OUTLIER) cc_final: 0.7511 (mt) REVERT: K 384 LYS cc_start: 0.8268 (OUTLIER) cc_final: 0.8009 (tttp) REVERT: H 13 CYS cc_start: 0.8565 (OUTLIER) cc_final: 0.8287 (p) REVERT: H 66 MET cc_start: 0.5725 (mtp) cc_final: 0.5444 (mtp) REVERT: H 90 MET cc_start: 0.7737 (ttp) cc_final: 0.7328 (mtp) REVERT: H 293 MET cc_start: 0.8566 (mmt) cc_final: 0.8122 (mmt) REVERT: H 364 LEU cc_start: 0.7940 (mt) cc_final: 0.7701 (mt) REVERT: H 378 MET cc_start: 0.7862 (mmm) cc_final: 0.7198 (mmp) REVERT: a 114 MET cc_start: 0.4754 (OUTLIER) cc_final: 0.4429 (ppp) REVERT: a 594 MET cc_start: 0.6769 (ptp) cc_final: 0.5696 (ptp) REVERT: f 72 ASP cc_start: 0.6549 (m-30) cc_final: 0.6340 (m-30) REVERT: d 129 PHE cc_start: 0.5232 (OUTLIER) cc_final: 0.4545 (p90) REVERT: d 245 PHE cc_start: 0.6793 (OUTLIER) cc_final: 0.6559 (m-80) REVERT: d 396 MET cc_start: 0.4974 (tpp) cc_final: 0.4523 (tpt) REVERT: d 399 LEU cc_start: 0.5405 (OUTLIER) cc_final: 0.5027 (tp) REVERT: i 67 ILE cc_start: 0.7903 (mt) cc_final: 0.7619 (mt) REVERT: i 96 MET cc_start: 0.8171 (mtt) cc_final: 0.7878 (mtp) REVERT: i 166 MET cc_start: 0.7745 (tmm) cc_final: 0.7363 (tmm) REVERT: i 245 ASP cc_start: 0.6159 (t0) cc_final: 0.5728 (t0) REVERT: g 298 MET cc_start: 0.6836 (OUTLIER) cc_final: 0.6499 (tpp) REVERT: j 50 MET cc_start: 0.7385 (ttm) cc_final: 0.7124 (ttm) REVERT: j 117 GLU cc_start: 0.7920 (mt-10) cc_final: 0.7531 (mt-10) REVERT: j 119 LEU cc_start: 0.7383 (mt) cc_final: 0.7046 (mt) REVERT: k 157 LYS cc_start: 0.7470 (OUTLIER) cc_final: 0.6667 (tptt) REVERT: h 19 ASP cc_start: 0.6106 (m-30) cc_final: 0.5860 (t0) REVERT: h 35 GLU cc_start: 0.6936 (mp0) cc_final: 0.6693 (mp0) REVERT: h 212 TYR cc_start: 0.7866 (t80) cc_final: 0.6983 (t80) REVERT: h 237 LYS cc_start: 0.8106 (OUTLIER) cc_final: 0.7748 (mtmm) outliers start: 248 outliers final: 171 residues processed: 916 average time/residue: 0.5901 time to fit residues: 932.5562 Evaluate side-chains 871 residues out of total 6810 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 188 poor density : 683 time to evaluate : 5.687 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 ILE Chi-restraints excluded: chain A residue 69 VAL Chi-restraints excluded: chain A residue 71 VAL Chi-restraints excluded: chain A residue 144 VAL Chi-restraints excluded: chain A residue 157 VAL Chi-restraints excluded: chain A residue 192 THR Chi-restraints excluded: chain A residue 218 MET Chi-restraints excluded: chain A residue 223 GLU Chi-restraints excluded: chain A residue 624 THR Chi-restraints excluded: chain F residue 15 ASN Chi-restraints excluded: chain F residue 39 ILE Chi-restraints excluded: chain F residue 125 ASN Chi-restraints excluded: chain E residue 58 THR Chi-restraints excluded: chain E residue 59 VAL Chi-restraints excluded: chain E residue 69 THR Chi-restraints excluded: chain E residue 79 LEU Chi-restraints excluded: chain E residue 100 CYS Chi-restraints excluded: chain E residue 120 ASP Chi-restraints excluded: chain E residue 141 MET Chi-restraints excluded: chain C residue 77 ASN Chi-restraints excluded: chain C residue 130 GLN Chi-restraints excluded: chain C residue 144 VAL Chi-restraints excluded: chain B residue 29 LYS Chi-restraints excluded: chain B residue 132 VAL Chi-restraints excluded: chain B residue 279 LEU Chi-restraints excluded: chain D residue 13 THR Chi-restraints excluded: chain D residue 113 THR Chi-restraints excluded: chain D residue 118 CYS Chi-restraints excluded: chain D residue 129 PHE Chi-restraints excluded: chain D residue 134 VAL Chi-restraints excluded: chain D residue 220 ASN Chi-restraints excluded: chain D residue 307 ASN Chi-restraints excluded: chain D residue 310 SER Chi-restraints excluded: chain D residue 343 MET Chi-restraints excluded: chain D residue 346 TYR Chi-restraints excluded: chain D residue 399 LEU Chi-restraints excluded: chain D residue 431 THR Chi-restraints excluded: chain D residue 531 THR Chi-restraints excluded: chain D residue 537 THR Chi-restraints excluded: chain I residue 19 TYR Chi-restraints excluded: chain I residue 34 ILE Chi-restraints excluded: chain I residue 40 HIS Chi-restraints excluded: chain I residue 76 MET Chi-restraints excluded: chain I residue 88 ILE Chi-restraints excluded: chain I residue 92 SER Chi-restraints excluded: chain I residue 107 ILE Chi-restraints excluded: chain I residue 115 SER Chi-restraints excluded: chain I residue 136 VAL Chi-restraints excluded: chain I residue 170 THR Chi-restraints excluded: chain I residue 173 ILE Chi-restraints excluded: chain I residue 179 ILE Chi-restraints excluded: chain I residue 200 VAL Chi-restraints excluded: chain I residue 216 LEU Chi-restraints excluded: chain I residue 228 VAL Chi-restraints excluded: chain I residue 236 THR Chi-restraints excluded: chain I residue 264 LEU Chi-restraints excluded: chain L residue 66 VAL Chi-restraints excluded: chain L residue 97 SER Chi-restraints excluded: chain L residue 131 TYR Chi-restraints excluded: chain G residue 88 ILE Chi-restraints excluded: chain G residue 99 SER Chi-restraints excluded: chain G residue 100 ILE Chi-restraints excluded: chain G residue 307 ILE Chi-restraints excluded: chain G residue 314 VAL Chi-restraints excluded: chain G residue 335 LEU Chi-restraints excluded: chain G residue 407 LEU Chi-restraints excluded: chain G residue 411 LYS Chi-restraints excluded: chain G residue 435 MET Chi-restraints excluded: chain G residue 458 LEU Chi-restraints excluded: chain G residue 510 ASP Chi-restraints excluded: chain G residue 560 VAL Chi-restraints excluded: chain G residue 562 ASN Chi-restraints excluded: chain J residue 17 GLU Chi-restraints excluded: chain J residue 21 MET Chi-restraints excluded: chain J residue 37 ILE Chi-restraints excluded: chain J residue 44 MET Chi-restraints excluded: chain J residue 54 ASN Chi-restraints excluded: chain J residue 96 THR Chi-restraints excluded: chain J residue 99 THR Chi-restraints excluded: chain J residue 121 THR Chi-restraints excluded: chain K residue 31 ILE Chi-restraints excluded: chain K residue 90 PHE Chi-restraints excluded: chain K residue 106 LEU Chi-restraints excluded: chain K residue 169 VAL Chi-restraints excluded: chain K residue 213 ASP Chi-restraints excluded: chain K residue 222 CYS Chi-restraints excluded: chain K residue 227 ILE Chi-restraints excluded: chain K residue 229 VAL Chi-restraints excluded: chain K residue 243 ASN Chi-restraints excluded: chain K residue 265 THR Chi-restraints excluded: chain K residue 269 ILE Chi-restraints excluded: chain K residue 312 ILE Chi-restraints excluded: chain K residue 384 LYS Chi-restraints excluded: chain H residue 13 CYS Chi-restraints excluded: chain H residue 34 VAL Chi-restraints excluded: chain H residue 44 ILE Chi-restraints excluded: chain H residue 52 ASP Chi-restraints excluded: chain H residue 96 THR Chi-restraints excluded: chain H residue 299 ILE Chi-restraints excluded: chain H residue 365 LYS Chi-restraints excluded: chain H residue 422 ASP Chi-restraints excluded: chain a residue 38 TYR Chi-restraints excluded: chain a residue 69 VAL Chi-restraints excluded: chain a residue 70 VAL Chi-restraints excluded: chain a residue 112 HIS Chi-restraints excluded: chain a residue 114 MET Chi-restraints excluded: chain a residue 116 ASP Chi-restraints excluded: chain a residue 140 VAL Chi-restraints excluded: chain a residue 144 VAL Chi-restraints excluded: chain a residue 153 VAL Chi-restraints excluded: chain a residue 192 THR Chi-restraints excluded: chain a residue 203 LEU Chi-restraints excluded: chain a residue 247 THR Chi-restraints excluded: chain a residue 487 VAL Chi-restraints excluded: chain a residue 551 VAL Chi-restraints excluded: chain a residue 571 GLU Chi-restraints excluded: chain f residue 39 ILE Chi-restraints excluded: chain f residue 64 LEU Chi-restraints excluded: chain f residue 98 LEU Chi-restraints excluded: chain e residue 58 THR Chi-restraints excluded: chain e residue 120 ASP Chi-restraints excluded: chain e residue 149 ASP Chi-restraints excluded: chain e residue 287 MET Chi-restraints excluded: chain e residue 338 VAL Chi-restraints excluded: chain e residue 358 ASN Chi-restraints excluded: chain b residue 27 SER Chi-restraints excluded: chain b residue 211 HIS Chi-restraints excluded: chain b residue 289 THR Chi-restraints excluded: chain d residue 24 LEU Chi-restraints excluded: chain d residue 71 ILE Chi-restraints excluded: chain d residue 129 PHE Chi-restraints excluded: chain d residue 134 VAL Chi-restraints excluded: chain d residue 222 SER Chi-restraints excluded: chain d residue 243 LYS Chi-restraints excluded: chain d residue 245 PHE Chi-restraints excluded: chain d residue 276 VAL Chi-restraints excluded: chain d residue 289 ASN Chi-restraints excluded: chain d residue 307 ASN Chi-restraints excluded: chain d residue 326 VAL Chi-restraints excluded: chain d residue 343 MET Chi-restraints excluded: chain d residue 350 TYR Chi-restraints excluded: chain d residue 399 LEU Chi-restraints excluded: chain d residue 441 LEU Chi-restraints excluded: chain d residue 531 THR Chi-restraints excluded: chain d residue 537 THR Chi-restraints excluded: chain i residue 16 LEU Chi-restraints excluded: chain i residue 114 ASP Chi-restraints excluded: chain i residue 115 SER Chi-restraints excluded: chain i residue 127 LEU Chi-restraints excluded: chain i residue 215 LEU Chi-restraints excluded: chain i residue 228 VAL Chi-restraints excluded: chain l residue 66 VAL Chi-restraints excluded: chain l residue 105 ILE Chi-restraints excluded: chain g residue 100 ILE Chi-restraints excluded: chain g residue 249 ASP Chi-restraints excluded: chain g residue 298 MET Chi-restraints excluded: chain g residue 320 THR Chi-restraints excluded: chain g residue 346 GLU Chi-restraints excluded: chain g residue 402 CYS Chi-restraints excluded: chain g residue 424 ASP Chi-restraints excluded: chain g residue 431 ASN Chi-restraints excluded: chain g residue 458 LEU Chi-restraints excluded: chain g residue 546 TYR Chi-restraints excluded: chain j residue 12 GLN Chi-restraints excluded: chain j residue 21 MET Chi-restraints excluded: chain j residue 37 ILE Chi-restraints excluded: chain j residue 63 GLU Chi-restraints excluded: chain k residue 90 PHE Chi-restraints excluded: chain k residue 105 ILE Chi-restraints excluded: chain k residue 157 LYS Chi-restraints excluded: chain k residue 175 THR Chi-restraints excluded: chain k residue 201 VAL Chi-restraints excluded: chain k residue 230 THR Chi-restraints excluded: chain k residue 232 THR Chi-restraints excluded: chain k residue 233 VAL Chi-restraints excluded: chain k residue 234 VAL Chi-restraints excluded: chain k residue 265 THR Chi-restraints excluded: chain k residue 269 ILE Chi-restraints excluded: chain h residue 40 ILE Chi-restraints excluded: chain h residue 89 LEU Chi-restraints excluded: chain h residue 148 ASP Chi-restraints excluded: chain h residue 196 THR Chi-restraints excluded: chain h residue 237 LYS Chi-restraints excluded: chain h residue 299 ILE Chi-restraints excluded: chain h residue 322 ASN Chi-restraints excluded: chain h residue 364 LEU Chi-restraints excluded: chain h residue 385 LEU Chi-restraints excluded: chain h residue 389 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 808 random chunks: chunk 753 optimal weight: 5.9990 chunk 88 optimal weight: 2.9990 chunk 445 optimal weight: 8.9990 chunk 570 optimal weight: 20.0000 chunk 442 optimal weight: 2.9990 chunk 658 optimal weight: 8.9990 chunk 436 optimal weight: 10.0000 chunk 778 optimal weight: 1.9990 chunk 487 optimal weight: 0.9990 chunk 474 optimal weight: 7.9990 chunk 359 optimal weight: 5.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 409 ASN C 130 GLN B 113 GLN ** B 211 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 198 GLN ** D 385 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 270 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 273 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 90 GLN ** H 156 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 327 ASN ** H 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 337 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 122 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** d 115 ASN ** d 313 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 426 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 534 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 264 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 270 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 472 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 531 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** h 325 HIS h 327 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6990 moved from start: 0.5317 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.110 65656 Z= 0.289 Angle : 0.646 14.548 89258 Z= 0.330 Chirality : 0.047 0.225 9916 Planarity : 0.005 0.072 11364 Dihedral : 10.162 179.664 9310 Min Nonbonded Distance : 1.749 Molprobity Statistics. All-atom Clashscore : 14.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.98 % Favored : 94.02 % Rotamer: Outliers : 3.92 % Allowed : 18.05 % Favored : 78.03 % Cbeta Deviations : 0.01 % Peptide Plane: Cis-proline : 1.54 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.82 (0.09), residues: 8162 helix: 0.39 (0.10), residues: 2934 sheet: -0.97 (0.15), residues: 1146 loop : -1.06 (0.10), residues: 4082 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.043 0.002 TRP d 527 HIS 0.014 0.001 HIS D 59 PHE 0.092 0.002 PHE b 237 TYR 0.029 0.002 TYR D 350 ARG 0.007 0.001 ARG B 244 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16324 Ramachandran restraints generated. 8162 Oldfield, 0 Emsley, 8162 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16324 Ramachandran restraints generated. 8162 Oldfield, 0 Emsley, 8162 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 991 residues out of total 6810 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 267 poor density : 724 time to evaluate : 5.740 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 594 MET cc_start: 0.5809 (ptp) cc_final: 0.5393 (ptp) REVERT: F 136 LYS cc_start: 0.5653 (mttp) cc_final: 0.5158 (mptt) REVERT: E 297 TYR cc_start: 0.8150 (m-10) cc_final: 0.7818 (m-80) REVERT: D 129 PHE cc_start: 0.6086 (OUTLIER) cc_final: 0.4707 (p90) REVERT: I 6 MET cc_start: 0.7882 (ttp) cc_final: 0.7455 (mtp) REVERT: I 215 LEU cc_start: 0.8442 (tt) cc_final: 0.8218 (tp) REVERT: L 139 GLN cc_start: 0.8523 (tt0) cc_final: 0.8195 (mm-40) REVERT: G 298 MET cc_start: 0.6595 (tpt) cc_final: 0.6369 (tpt) REVERT: G 335 LEU cc_start: 0.8240 (OUTLIER) cc_final: 0.7860 (mt) REVERT: G 458 LEU cc_start: 0.8172 (OUTLIER) cc_final: 0.7563 (pp) REVERT: G 533 GLN cc_start: 0.8921 (tp40) cc_final: 0.8480 (tp40) REVERT: J 17 GLU cc_start: 0.7913 (OUTLIER) cc_final: 0.7562 (tp30) REVERT: J 50 MET cc_start: 0.7898 (tpp) cc_final: 0.7555 (ttp) REVERT: J 114 VAL cc_start: 0.8723 (p) cc_final: 0.8505 (m) REVERT: K 227 ILE cc_start: 0.7674 (OUTLIER) cc_final: 0.7339 (mt) REVERT: K 384 LYS cc_start: 0.8373 (OUTLIER) cc_final: 0.8048 (tttp) REVERT: H 13 CYS cc_start: 0.8589 (OUTLIER) cc_final: 0.8319 (p) REVERT: H 90 MET cc_start: 0.7427 (OUTLIER) cc_final: 0.7109 (mtp) REVERT: H 114 MET cc_start: 0.6083 (mmt) cc_final: 0.5859 (mmt) REVERT: H 148 ASP cc_start: 0.7936 (OUTLIER) cc_final: 0.7323 (t70) REVERT: H 293 MET cc_start: 0.8750 (mmt) cc_final: 0.8236 (mmt) REVERT: H 298 ASN cc_start: 0.7844 (t0) cc_final: 0.6953 (t0) REVERT: H 326 MET cc_start: 0.8858 (ttp) cc_final: 0.8582 (ttp) REVERT: H 373 ASP cc_start: 0.8173 (m-30) cc_final: 0.7876 (m-30) REVERT: H 378 MET cc_start: 0.7674 (mmm) cc_final: 0.6291 (mtm) REVERT: a 114 MET cc_start: 0.4818 (OUTLIER) cc_final: 0.4452 (ppp) REVERT: a 594 MET cc_start: 0.7084 (ptp) cc_final: 0.5900 (ptp) REVERT: a 650 MET cc_start: 0.6308 (mmm) cc_final: 0.5543 (mmp) REVERT: e 354 MET cc_start: 0.8526 (mmm) cc_final: 0.8276 (mmm) REVERT: e 394 GLU cc_start: 0.7308 (mm-30) cc_final: 0.7001 (mm-30) REVERT: d 115 ASN cc_start: 0.5983 (OUTLIER) cc_final: 0.5083 (m-40) REVERT: d 129 PHE cc_start: 0.5635 (OUTLIER) cc_final: 0.4832 (p90) REVERT: d 245 PHE cc_start: 0.6540 (OUTLIER) cc_final: 0.6283 (m-80) REVERT: d 399 LEU cc_start: 0.5663 (OUTLIER) cc_final: 0.5268 (tp) REVERT: d 527 TRP cc_start: 0.7057 (p-90) cc_final: 0.6680 (p-90) REVERT: i 34 ILE cc_start: 0.8376 (mm) cc_final: 0.8082 (mm) REVERT: i 67 ILE cc_start: 0.8052 (mt) cc_final: 0.7852 (mt) REVERT: i 96 MET cc_start: 0.8229 (mtt) cc_final: 0.7892 (mtp) REVERT: i 166 MET cc_start: 0.7825 (tmm) cc_final: 0.7431 (tmm) REVERT: i 245 ASP cc_start: 0.6378 (t0) cc_final: 0.5861 (t0) REVERT: l 127 ASP cc_start: 0.6398 (t0) cc_final: 0.6045 (t0) REVERT: g 67 ASN cc_start: 0.8378 (OUTLIER) cc_final: 0.8033 (t0) REVERT: g 298 MET cc_start: 0.6884 (OUTLIER) cc_final: 0.6507 (tpp) REVERT: j 30 TYR cc_start: 0.7582 (t80) cc_final: 0.7262 (t80) REVERT: j 32 ASP cc_start: 0.5582 (m-30) cc_final: 0.5317 (m-30) REVERT: j 50 MET cc_start: 0.7423 (ttm) cc_final: 0.7195 (ttm) REVERT: j 117 GLU cc_start: 0.8348 (mt-10) cc_final: 0.7848 (mt-10) REVERT: j 119 LEU cc_start: 0.7635 (mt) cc_final: 0.7297 (mt) REVERT: k 157 LYS cc_start: 0.7781 (OUTLIER) cc_final: 0.6826 (tptt) REVERT: h 35 GLU cc_start: 0.6971 (mp0) cc_final: 0.6720 (mp0) REVERT: h 212 TYR cc_start: 0.7924 (t80) cc_final: 0.7488 (t80) REVERT: h 237 LYS cc_start: 0.8121 (OUTLIER) cc_final: 0.7826 (mtmm) REVERT: h 338 MET cc_start: 0.8021 (mmp) cc_final: 0.7558 (mmp) outliers start: 267 outliers final: 196 residues processed: 924 average time/residue: 0.5865 time to fit residues: 929.5969 Evaluate side-chains 886 residues out of total 6810 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 214 poor density : 672 time to evaluate : 5.683 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 ILE Chi-restraints excluded: chain A residue 38 TYR Chi-restraints excluded: chain A residue 69 VAL Chi-restraints excluded: chain A residue 71 VAL Chi-restraints excluded: chain A residue 144 VAL Chi-restraints excluded: chain A residue 157 VAL Chi-restraints excluded: chain A residue 192 THR Chi-restraints excluded: chain A residue 218 MET Chi-restraints excluded: chain A residue 223 GLU Chi-restraints excluded: chain A residue 624 THR Chi-restraints excluded: chain F residue 15 ASN Chi-restraints excluded: chain F residue 39 ILE Chi-restraints excluded: chain E residue 58 THR Chi-restraints excluded: chain E residue 59 VAL Chi-restraints excluded: chain E residue 79 LEU Chi-restraints excluded: chain E residue 100 CYS Chi-restraints excluded: chain E residue 120 ASP Chi-restraints excluded: chain E residue 141 MET Chi-restraints excluded: chain C residue 77 ASN Chi-restraints excluded: chain C residue 130 GLN Chi-restraints excluded: chain C residue 144 VAL Chi-restraints excluded: chain B residue 29 LYS Chi-restraints excluded: chain B residue 132 VAL Chi-restraints excluded: chain D residue 13 THR Chi-restraints excluded: chain D residue 113 THR Chi-restraints excluded: chain D residue 118 CYS Chi-restraints excluded: chain D residue 129 PHE Chi-restraints excluded: chain D residue 134 VAL Chi-restraints excluded: chain D residue 220 ASN Chi-restraints excluded: chain D residue 291 VAL Chi-restraints excluded: chain D residue 307 ASN Chi-restraints excluded: chain D residue 310 SER Chi-restraints excluded: chain D residue 343 MET Chi-restraints excluded: chain D residue 346 TYR Chi-restraints excluded: chain D residue 399 LEU Chi-restraints excluded: chain D residue 431 THR Chi-restraints excluded: chain D residue 531 THR Chi-restraints excluded: chain I residue 19 TYR Chi-restraints excluded: chain I residue 34 ILE Chi-restraints excluded: chain I residue 40 HIS Chi-restraints excluded: chain I residue 76 MET Chi-restraints excluded: chain I residue 88 ILE Chi-restraints excluded: chain I residue 92 SER Chi-restraints excluded: chain I residue 107 ILE Chi-restraints excluded: chain I residue 115 SER Chi-restraints excluded: chain I residue 136 VAL Chi-restraints excluded: chain I residue 138 SER Chi-restraints excluded: chain I residue 170 THR Chi-restraints excluded: chain I residue 179 ILE Chi-restraints excluded: chain I residue 189 THR Chi-restraints excluded: chain I residue 200 VAL Chi-restraints excluded: chain I residue 216 LEU Chi-restraints excluded: chain I residue 228 VAL Chi-restraints excluded: chain I residue 236 THR Chi-restraints excluded: chain I residue 264 LEU Chi-restraints excluded: chain L residue 66 VAL Chi-restraints excluded: chain L residue 97 SER Chi-restraints excluded: chain L residue 131 TYR Chi-restraints excluded: chain L residue 134 ILE Chi-restraints excluded: chain L residue 135 GLN Chi-restraints excluded: chain G residue 88 ILE Chi-restraints excluded: chain G residue 99 SER Chi-restraints excluded: chain G residue 100 ILE Chi-restraints excluded: chain G residue 307 ILE Chi-restraints excluded: chain G residue 314 VAL Chi-restraints excluded: chain G residue 335 LEU Chi-restraints excluded: chain G residue 407 LEU Chi-restraints excluded: chain G residue 411 LYS Chi-restraints excluded: chain G residue 435 MET Chi-restraints excluded: chain G residue 456 LEU Chi-restraints excluded: chain G residue 458 LEU Chi-restraints excluded: chain G residue 472 ASN Chi-restraints excluded: chain G residue 510 ASP Chi-restraints excluded: chain G residue 560 VAL Chi-restraints excluded: chain J residue 17 GLU Chi-restraints excluded: chain J residue 21 MET Chi-restraints excluded: chain J residue 37 ILE Chi-restraints excluded: chain J residue 44 MET Chi-restraints excluded: chain J residue 54 ASN Chi-restraints excluded: chain J residue 63 GLU Chi-restraints excluded: chain J residue 96 THR Chi-restraints excluded: chain J residue 99 THR Chi-restraints excluded: chain J residue 109 VAL Chi-restraints excluded: chain J residue 121 THR Chi-restraints excluded: chain K residue 31 ILE Chi-restraints excluded: chain K residue 90 PHE Chi-restraints excluded: chain K residue 106 LEU Chi-restraints excluded: chain K residue 169 VAL Chi-restraints excluded: chain K residue 175 THR Chi-restraints excluded: chain K residue 213 ASP Chi-restraints excluded: chain K residue 222 CYS Chi-restraints excluded: chain K residue 227 ILE Chi-restraints excluded: chain K residue 229 VAL Chi-restraints excluded: chain K residue 243 ASN Chi-restraints excluded: chain K residue 265 THR Chi-restraints excluded: chain K residue 269 ILE Chi-restraints excluded: chain K residue 312 ILE Chi-restraints excluded: chain K residue 371 VAL Chi-restraints excluded: chain K residue 384 LYS Chi-restraints excluded: chain H residue 7 ASN Chi-restraints excluded: chain H residue 13 CYS Chi-restraints excluded: chain H residue 16 SER Chi-restraints excluded: chain H residue 52 ASP Chi-restraints excluded: chain H residue 89 LEU Chi-restraints excluded: chain H residue 90 MET Chi-restraints excluded: chain H residue 148 ASP Chi-restraints excluded: chain H residue 299 ILE Chi-restraints excluded: chain H residue 331 THR Chi-restraints excluded: chain H residue 365 LYS Chi-restraints excluded: chain H residue 422 ASP Chi-restraints excluded: chain a residue 38 TYR Chi-restraints excluded: chain a residue 69 VAL Chi-restraints excluded: chain a residue 112 HIS Chi-restraints excluded: chain a residue 114 MET Chi-restraints excluded: chain a residue 116 ASP Chi-restraints excluded: chain a residue 140 VAL Chi-restraints excluded: chain a residue 144 VAL Chi-restraints excluded: chain a residue 153 VAL Chi-restraints excluded: chain a residue 160 MET Chi-restraints excluded: chain a residue 192 THR Chi-restraints excluded: chain a residue 203 LEU Chi-restraints excluded: chain a residue 247 THR Chi-restraints excluded: chain a residue 418 ARG Chi-restraints excluded: chain a residue 487 VAL Chi-restraints excluded: chain a residue 541 LEU Chi-restraints excluded: chain a residue 548 THR Chi-restraints excluded: chain a residue 551 VAL Chi-restraints excluded: chain a residue 571 GLU Chi-restraints excluded: chain f residue 39 ILE Chi-restraints excluded: chain f residue 86 MET Chi-restraints excluded: chain f residue 98 LEU Chi-restraints excluded: chain e residue 58 THR Chi-restraints excluded: chain e residue 120 ASP Chi-restraints excluded: chain e residue 141 MET Chi-restraints excluded: chain e residue 149 ASP Chi-restraints excluded: chain e residue 287 MET Chi-restraints excluded: chain e residue 338 VAL Chi-restraints excluded: chain c residue 29 PHE Chi-restraints excluded: chain c residue 129 VAL Chi-restraints excluded: chain b residue 27 SER Chi-restraints excluded: chain b residue 132 VAL Chi-restraints excluded: chain b residue 146 LEU Chi-restraints excluded: chain b residue 289 THR Chi-restraints excluded: chain d residue 24 LEU Chi-restraints excluded: chain d residue 71 ILE Chi-restraints excluded: chain d residue 115 ASN Chi-restraints excluded: chain d residue 129 PHE Chi-restraints excluded: chain d residue 222 SER Chi-restraints excluded: chain d residue 243 LYS Chi-restraints excluded: chain d residue 245 PHE Chi-restraints excluded: chain d residue 276 VAL Chi-restraints excluded: chain d residue 289 ASN Chi-restraints excluded: chain d residue 307 ASN Chi-restraints excluded: chain d residue 326 VAL Chi-restraints excluded: chain d residue 343 MET Chi-restraints excluded: chain d residue 350 TYR Chi-restraints excluded: chain d residue 399 LEU Chi-restraints excluded: chain d residue 441 LEU Chi-restraints excluded: chain d residue 531 THR Chi-restraints excluded: chain d residue 537 THR Chi-restraints excluded: chain d residue 544 LYS Chi-restraints excluded: chain i residue 16 LEU Chi-restraints excluded: chain i residue 40 HIS Chi-restraints excluded: chain i residue 114 ASP Chi-restraints excluded: chain i residue 115 SER Chi-restraints excluded: chain i residue 127 LEU Chi-restraints excluded: chain i residue 170 THR Chi-restraints excluded: chain i residue 189 THR Chi-restraints excluded: chain i residue 215 LEU Chi-restraints excluded: chain i residue 228 VAL Chi-restraints excluded: chain l residue 66 VAL Chi-restraints excluded: chain l residue 105 ILE Chi-restraints excluded: chain l residue 114 VAL Chi-restraints excluded: chain l residue 124 ILE Chi-restraints excluded: chain l residue 132 ASP Chi-restraints excluded: chain g residue 67 ASN Chi-restraints excluded: chain g residue 110 TYR Chi-restraints excluded: chain g residue 249 ASP Chi-restraints excluded: chain g residue 298 MET Chi-restraints excluded: chain g residue 320 THR Chi-restraints excluded: chain g residue 346 GLU Chi-restraints excluded: chain g residue 385 VAL Chi-restraints excluded: chain g residue 402 CYS Chi-restraints excluded: chain g residue 424 ASP Chi-restraints excluded: chain g residue 431 ASN Chi-restraints excluded: chain g residue 458 LEU Chi-restraints excluded: chain g residue 497 THR Chi-restraints excluded: chain g residue 546 TYR Chi-restraints excluded: chain j residue 21 MET Chi-restraints excluded: chain j residue 37 ILE Chi-restraints excluded: chain j residue 63 GLU Chi-restraints excluded: chain j residue 96 THR Chi-restraints excluded: chain k residue 90 PHE Chi-restraints excluded: chain k residue 105 ILE Chi-restraints excluded: chain k residue 157 LYS Chi-restraints excluded: chain k residue 175 THR Chi-restraints excluded: chain k residue 201 VAL Chi-restraints excluded: chain k residue 232 THR Chi-restraints excluded: chain k residue 233 VAL Chi-restraints excluded: chain k residue 234 VAL Chi-restraints excluded: chain k residue 261 THR Chi-restraints excluded: chain k residue 265 THR Chi-restraints excluded: chain k residue 269 ILE Chi-restraints excluded: chain k residue 347 LYS Chi-restraints excluded: chain h residue 40 ILE Chi-restraints excluded: chain h residue 143 VAL Chi-restraints excluded: chain h residue 148 ASP Chi-restraints excluded: chain h residue 196 THR Chi-restraints excluded: chain h residue 237 LYS Chi-restraints excluded: chain h residue 299 ILE Chi-restraints excluded: chain h residue 322 ASN Chi-restraints excluded: chain h residue 364 LEU Chi-restraints excluded: chain h residue 385 LEU Chi-restraints excluded: chain h residue 389 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 808 random chunks: chunk 481 optimal weight: 2.9990 chunk 311 optimal weight: 1.9990 chunk 465 optimal weight: 0.7980 chunk 234 optimal weight: 9.9990 chunk 153 optimal weight: 50.0000 chunk 150 optimal weight: 6.9990 chunk 495 optimal weight: 10.0000 chunk 530 optimal weight: 6.9990 chunk 385 optimal weight: 2.9990 chunk 72 optimal weight: 7.9990 chunk 612 optimal weight: 9.9990 overall best weight: 3.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 293 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 130 GLN B 113 GLN B 211 HIS G 132 HIS ** G 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 270 GLN G 273 HIS K 28 ASN ** H 156 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 79 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** e 116 GLN ** e 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 233 ASN ** e 337 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 122 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** d 115 ASN ** d 313 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 426 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 534 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 180 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 264 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 270 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 472 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 518 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7021 moved from start: 0.5650 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.065 65656 Z= 0.298 Angle : 0.653 15.836 89258 Z= 0.333 Chirality : 0.047 0.194 9916 Planarity : 0.005 0.086 11364 Dihedral : 9.890 179.185 9309 Min Nonbonded Distance : 1.720 Molprobity Statistics. All-atom Clashscore : 14.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.99 % Favored : 94.01 % Rotamer: Outliers : 3.79 % Allowed : 18.88 % Favored : 77.33 % Cbeta Deviations : 0.01 % Peptide Plane: Cis-proline : 1.54 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.84 (0.09), residues: 8162 helix: 0.35 (0.10), residues: 2934 sheet: -0.93 (0.15), residues: 1118 loop : -1.08 (0.10), residues: 4110 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.002 TRP d 234 HIS 0.009 0.001 HIS e 337 PHE 0.142 0.002 PHE b 237 TYR 0.026 0.002 TYR D 350 ARG 0.011 0.001 ARG k 231 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16324 Ramachandran restraints generated. 8162 Oldfield, 0 Emsley, 8162 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16324 Ramachandran restraints generated. 8162 Oldfield, 0 Emsley, 8162 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 952 residues out of total 6810 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 258 poor density : 694 time to evaluate : 5.754 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 594 MET cc_start: 0.5880 (ptp) cc_final: 0.5406 (ptp) REVERT: F 120 MET cc_start: 0.7677 (mmm) cc_final: 0.7467 (tpp) REVERT: F 136 LYS cc_start: 0.5924 (mttp) cc_final: 0.5692 (mptt) REVERT: E 286 MET cc_start: 0.7222 (mmp) cc_final: 0.6838 (mmm) REVERT: D 129 PHE cc_start: 0.5903 (OUTLIER) cc_final: 0.4964 (p90) REVERT: D 208 MET cc_start: 0.7893 (OUTLIER) cc_final: 0.7545 (tmm) REVERT: I 6 MET cc_start: 0.8061 (ttp) cc_final: 0.7641 (mtp) REVERT: I 72 ASN cc_start: 0.7600 (t0) cc_final: 0.7344 (t0) REVERT: L 139 GLN cc_start: 0.8518 (tt0) cc_final: 0.8221 (mm-40) REVERT: G 235 HIS cc_start: 0.8108 (OUTLIER) cc_final: 0.7799 (t70) REVERT: G 335 LEU cc_start: 0.8232 (OUTLIER) cc_final: 0.7868 (mt) REVERT: G 458 LEU cc_start: 0.8143 (OUTLIER) cc_final: 0.7562 (pp) REVERT: G 533 GLN cc_start: 0.8886 (tp40) cc_final: 0.8563 (tp40) REVERT: J 17 GLU cc_start: 0.7933 (OUTLIER) cc_final: 0.7587 (tp30) REVERT: J 42 GLN cc_start: 0.7741 (mm-40) cc_final: 0.7483 (mm-40) REVERT: J 50 MET cc_start: 0.7922 (tpp) cc_final: 0.7608 (ttp) REVERT: K 157 LYS cc_start: 0.8088 (OUTLIER) cc_final: 0.6241 (tptt) REVERT: K 227 ILE cc_start: 0.7704 (OUTLIER) cc_final: 0.7340 (mt) REVERT: K 384 LYS cc_start: 0.8431 (OUTLIER) cc_final: 0.8060 (tttp) REVERT: H 13 CYS cc_start: 0.8540 (OUTLIER) cc_final: 0.8232 (p) REVERT: H 293 MET cc_start: 0.8757 (mmt) cc_final: 0.8191 (mmt) REVERT: H 298 ASN cc_start: 0.7945 (t0) cc_final: 0.7122 (t0) REVERT: H 372 ILE cc_start: 0.8580 (mp) cc_final: 0.8342 (mt) REVERT: H 378 MET cc_start: 0.7684 (mmm) cc_final: 0.6183 (mtm) REVERT: H 390 CYS cc_start: 0.7573 (m) cc_final: 0.7348 (m) REVERT: a 114 MET cc_start: 0.5085 (OUTLIER) cc_final: 0.4844 (ppp) REVERT: a 594 MET cc_start: 0.7077 (ptp) cc_final: 0.5878 (ptp) REVERT: e 75 CYS cc_start: 0.5962 (m) cc_final: 0.5729 (m) REVERT: e 354 MET cc_start: 0.8536 (mmm) cc_final: 0.8287 (mmm) REVERT: e 394 GLU cc_start: 0.7146 (mm-30) cc_final: 0.6818 (mm-30) REVERT: d 115 ASN cc_start: 0.5599 (OUTLIER) cc_final: 0.5251 (m-40) REVERT: d 129 PHE cc_start: 0.5806 (OUTLIER) cc_final: 0.4898 (p90) REVERT: d 245 PHE cc_start: 0.6460 (OUTLIER) cc_final: 0.6182 (m-80) REVERT: d 399 LEU cc_start: 0.6363 (OUTLIER) cc_final: 0.5876 (tp) REVERT: d 527 TRP cc_start: 0.7284 (p-90) cc_final: 0.6883 (p-90) REVERT: i 34 ILE cc_start: 0.8155 (OUTLIER) cc_final: 0.7905 (mm) REVERT: i 67 ILE cc_start: 0.8139 (mt) cc_final: 0.7916 (mt) REVERT: i 96 MET cc_start: 0.8205 (mtt) cc_final: 0.7875 (mtp) REVERT: i 166 MET cc_start: 0.7904 (tmm) cc_final: 0.7511 (tmm) REVERT: i 245 ASP cc_start: 0.6540 (t0) cc_final: 0.6052 (t0) REVERT: l 131 TYR cc_start: 0.7718 (OUTLIER) cc_final: 0.6700 (p90) REVERT: g 67 ASN cc_start: 0.8399 (OUTLIER) cc_final: 0.8148 (t0) REVERT: g 298 MET cc_start: 0.6858 (OUTLIER) cc_final: 0.6515 (tpp) REVERT: g 418 ASP cc_start: 0.7690 (m-30) cc_final: 0.7110 (m-30) REVERT: j 30 TYR cc_start: 0.7711 (t80) cc_final: 0.7361 (t80) REVERT: j 32 ASP cc_start: 0.5627 (m-30) cc_final: 0.5221 (m-30) REVERT: j 119 LEU cc_start: 0.7509 (mt) cc_final: 0.7158 (mt) REVERT: j 125 LEU cc_start: 0.7547 (mt) cc_final: 0.6837 (mp) REVERT: k 22 ARG cc_start: 0.7428 (tpp80) cc_final: 0.7148 (tpp-160) REVERT: k 157 LYS cc_start: 0.7924 (OUTLIER) cc_final: 0.7215 (tptt) REVERT: h 35 GLU cc_start: 0.6961 (mp0) cc_final: 0.6720 (mp0) REVERT: h 212 TYR cc_start: 0.8086 (t80) cc_final: 0.7719 (t80) REVERT: h 237 LYS cc_start: 0.8141 (OUTLIER) cc_final: 0.7834 (mtmm) REVERT: h 308 TRP cc_start: 0.8727 (OUTLIER) cc_final: 0.5419 (p90) REVERT: h 338 MET cc_start: 0.8130 (mmp) cc_final: 0.7702 (mmp) REVERT: h 390 CYS cc_start: 0.6182 (m) cc_final: 0.5937 (m) outliers start: 258 outliers final: 197 residues processed: 898 average time/residue: 0.5945 time to fit residues: 919.4015 Evaluate side-chains 883 residues out of total 6810 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 219 poor density : 664 time to evaluate : 5.720 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 ILE Chi-restraints excluded: chain A residue 38 TYR Chi-restraints excluded: chain A residue 69 VAL Chi-restraints excluded: chain A residue 71 VAL Chi-restraints excluded: chain A residue 144 VAL Chi-restraints excluded: chain A residue 192 THR Chi-restraints excluded: chain A residue 223 GLU Chi-restraints excluded: chain A residue 624 THR Chi-restraints excluded: chain A residue 627 VAL Chi-restraints excluded: chain F residue 15 ASN Chi-restraints excluded: chain F residue 39 ILE Chi-restraints excluded: chain E residue 58 THR Chi-restraints excluded: chain E residue 59 VAL Chi-restraints excluded: chain E residue 69 THR Chi-restraints excluded: chain E residue 79 LEU Chi-restraints excluded: chain E residue 100 CYS Chi-restraints excluded: chain E residue 120 ASP Chi-restraints excluded: chain E residue 141 MET Chi-restraints excluded: chain C residue 77 ASN Chi-restraints excluded: chain C residue 78 GLU Chi-restraints excluded: chain C residue 130 GLN Chi-restraints excluded: chain C residue 144 VAL Chi-restraints excluded: chain B residue 29 LYS Chi-restraints excluded: chain D residue 13 THR Chi-restraints excluded: chain D residue 113 THR Chi-restraints excluded: chain D residue 118 CYS Chi-restraints excluded: chain D residue 129 PHE Chi-restraints excluded: chain D residue 134 VAL Chi-restraints excluded: chain D residue 182 HIS Chi-restraints excluded: chain D residue 208 MET Chi-restraints excluded: chain D residue 220 ASN Chi-restraints excluded: chain D residue 291 VAL Chi-restraints excluded: chain D residue 307 ASN Chi-restraints excluded: chain D residue 310 SER Chi-restraints excluded: chain D residue 343 MET Chi-restraints excluded: chain D residue 346 TYR Chi-restraints excluded: chain D residue 431 THR Chi-restraints excluded: chain D residue 531 THR Chi-restraints excluded: chain D residue 537 THR Chi-restraints excluded: chain I residue 19 TYR Chi-restraints excluded: chain I residue 34 ILE Chi-restraints excluded: chain I residue 40 HIS Chi-restraints excluded: chain I residue 76 MET Chi-restraints excluded: chain I residue 88 ILE Chi-restraints excluded: chain I residue 92 SER Chi-restraints excluded: chain I residue 115 SER Chi-restraints excluded: chain I residue 136 VAL Chi-restraints excluded: chain I residue 138 SER Chi-restraints excluded: chain I residue 170 THR Chi-restraints excluded: chain I residue 179 ILE Chi-restraints excluded: chain I residue 189 THR Chi-restraints excluded: chain I residue 200 VAL Chi-restraints excluded: chain I residue 208 ASP Chi-restraints excluded: chain I residue 216 LEU Chi-restraints excluded: chain I residue 228 VAL Chi-restraints excluded: chain I residue 236 THR Chi-restraints excluded: chain I residue 264 LEU Chi-restraints excluded: chain L residue 66 VAL Chi-restraints excluded: chain L residue 97 SER Chi-restraints excluded: chain L residue 131 TYR Chi-restraints excluded: chain L residue 134 ILE Chi-restraints excluded: chain L residue 135 GLN Chi-restraints excluded: chain G residue 88 ILE Chi-restraints excluded: chain G residue 99 SER Chi-restraints excluded: chain G residue 100 ILE Chi-restraints excluded: chain G residue 235 HIS Chi-restraints excluded: chain G residue 307 ILE Chi-restraints excluded: chain G residue 314 VAL Chi-restraints excluded: chain G residue 335 LEU Chi-restraints excluded: chain G residue 407 LEU Chi-restraints excluded: chain G residue 411 LYS Chi-restraints excluded: chain G residue 435 MET Chi-restraints excluded: chain G residue 458 LEU Chi-restraints excluded: chain G residue 472 ASN Chi-restraints excluded: chain G residue 510 ASP Chi-restraints excluded: chain G residue 546 TYR Chi-restraints excluded: chain G residue 560 VAL Chi-restraints excluded: chain G residue 562 ASN Chi-restraints excluded: chain J residue 17 GLU Chi-restraints excluded: chain J residue 21 MET Chi-restraints excluded: chain J residue 37 ILE Chi-restraints excluded: chain J residue 44 MET Chi-restraints excluded: chain J residue 54 ASN Chi-restraints excluded: chain J residue 63 GLU Chi-restraints excluded: chain J residue 96 THR Chi-restraints excluded: chain J residue 121 THR Chi-restraints excluded: chain K residue 31 ILE Chi-restraints excluded: chain K residue 90 PHE Chi-restraints excluded: chain K residue 106 LEU Chi-restraints excluded: chain K residue 157 LYS Chi-restraints excluded: chain K residue 169 VAL Chi-restraints excluded: chain K residue 175 THR Chi-restraints excluded: chain K residue 222 CYS Chi-restraints excluded: chain K residue 227 ILE Chi-restraints excluded: chain K residue 229 VAL Chi-restraints excluded: chain K residue 243 ASN Chi-restraints excluded: chain K residue 269 ILE Chi-restraints excluded: chain K residue 312 ILE Chi-restraints excluded: chain K residue 371 VAL Chi-restraints excluded: chain K residue 384 LYS Chi-restraints excluded: chain H residue 7 ASN Chi-restraints excluded: chain H residue 13 CYS Chi-restraints excluded: chain H residue 52 ASP Chi-restraints excluded: chain H residue 89 LEU Chi-restraints excluded: chain H residue 299 ILE Chi-restraints excluded: chain H residue 331 THR Chi-restraints excluded: chain H residue 365 LYS Chi-restraints excluded: chain H residue 422 ASP Chi-restraints excluded: chain a residue 38 TYR Chi-restraints excluded: chain a residue 69 VAL Chi-restraints excluded: chain a residue 70 VAL Chi-restraints excluded: chain a residue 112 HIS Chi-restraints excluded: chain a residue 114 MET Chi-restraints excluded: chain a residue 116 ASP Chi-restraints excluded: chain a residue 140 VAL Chi-restraints excluded: chain a residue 144 VAL Chi-restraints excluded: chain a residue 153 VAL Chi-restraints excluded: chain a residue 160 MET Chi-restraints excluded: chain a residue 192 THR Chi-restraints excluded: chain a residue 203 LEU Chi-restraints excluded: chain a residue 247 THR Chi-restraints excluded: chain a residue 418 ARG Chi-restraints excluded: chain a residue 487 VAL Chi-restraints excluded: chain a residue 548 THR Chi-restraints excluded: chain a residue 551 VAL Chi-restraints excluded: chain a residue 571 GLU Chi-restraints excluded: chain f residue 39 ILE Chi-restraints excluded: chain f residue 86 MET Chi-restraints excluded: chain f residue 98 LEU Chi-restraints excluded: chain e residue 58 THR Chi-restraints excluded: chain e residue 66 ILE Chi-restraints excluded: chain e residue 72 SER Chi-restraints excluded: chain e residue 120 ASP Chi-restraints excluded: chain e residue 141 MET Chi-restraints excluded: chain e residue 149 ASP Chi-restraints excluded: chain e residue 177 ASP Chi-restraints excluded: chain e residue 210 VAL Chi-restraints excluded: chain e residue 338 VAL Chi-restraints excluded: chain c residue 29 PHE Chi-restraints excluded: chain b residue 27 SER Chi-restraints excluded: chain b residue 111 ASP Chi-restraints excluded: chain b residue 132 VAL Chi-restraints excluded: chain b residue 289 THR Chi-restraints excluded: chain d residue 24 LEU Chi-restraints excluded: chain d residue 71 ILE Chi-restraints excluded: chain d residue 115 ASN Chi-restraints excluded: chain d residue 129 PHE Chi-restraints excluded: chain d residue 150 SER Chi-restraints excluded: chain d residue 222 SER Chi-restraints excluded: chain d residue 243 LYS Chi-restraints excluded: chain d residue 245 PHE Chi-restraints excluded: chain d residue 276 VAL Chi-restraints excluded: chain d residue 289 ASN Chi-restraints excluded: chain d residue 307 ASN Chi-restraints excluded: chain d residue 317 LEU Chi-restraints excluded: chain d residue 326 VAL Chi-restraints excluded: chain d residue 350 TYR Chi-restraints excluded: chain d residue 399 LEU Chi-restraints excluded: chain d residue 441 LEU Chi-restraints excluded: chain d residue 531 THR Chi-restraints excluded: chain d residue 537 THR Chi-restraints excluded: chain d residue 544 LYS Chi-restraints excluded: chain i residue 34 ILE Chi-restraints excluded: chain i residue 40 HIS Chi-restraints excluded: chain i residue 114 ASP Chi-restraints excluded: chain i residue 115 SER Chi-restraints excluded: chain i residue 127 LEU Chi-restraints excluded: chain i residue 170 THR Chi-restraints excluded: chain i residue 189 THR Chi-restraints excluded: chain i residue 215 LEU Chi-restraints excluded: chain i residue 228 VAL Chi-restraints excluded: chain l residue 66 VAL Chi-restraints excluded: chain l residue 99 ASP Chi-restraints excluded: chain l residue 105 ILE Chi-restraints excluded: chain l residue 124 ILE Chi-restraints excluded: chain l residue 131 TYR Chi-restraints excluded: chain g residue 67 ASN Chi-restraints excluded: chain g residue 110 TYR Chi-restraints excluded: chain g residue 249 ASP Chi-restraints excluded: chain g residue 298 MET Chi-restraints excluded: chain g residue 320 THR Chi-restraints excluded: chain g residue 346 GLU Chi-restraints excluded: chain g residue 385 VAL Chi-restraints excluded: chain g residue 402 CYS Chi-restraints excluded: chain g residue 424 ASP Chi-restraints excluded: chain g residue 431 ASN Chi-restraints excluded: chain g residue 458 LEU Chi-restraints excluded: chain g residue 472 ASN Chi-restraints excluded: chain g residue 497 THR Chi-restraints excluded: chain g residue 546 TYR Chi-restraints excluded: chain j residue 21 MET Chi-restraints excluded: chain j residue 37 ILE Chi-restraints excluded: chain j residue 63 GLU Chi-restraints excluded: chain k residue 4 LEU Chi-restraints excluded: chain k residue 90 PHE Chi-restraints excluded: chain k residue 105 ILE Chi-restraints excluded: chain k residue 157 LYS Chi-restraints excluded: chain k residue 175 THR Chi-restraints excluded: chain k residue 201 VAL Chi-restraints excluded: chain k residue 233 VAL Chi-restraints excluded: chain k residue 234 VAL Chi-restraints excluded: chain k residue 261 THR Chi-restraints excluded: chain k residue 265 THR Chi-restraints excluded: chain k residue 269 ILE Chi-restraints excluded: chain k residue 347 LYS Chi-restraints excluded: chain h residue 40 ILE Chi-restraints excluded: chain h residue 90 MET Chi-restraints excluded: chain h residue 96 THR Chi-restraints excluded: chain h residue 143 VAL Chi-restraints excluded: chain h residue 148 ASP Chi-restraints excluded: chain h residue 196 THR Chi-restraints excluded: chain h residue 237 LYS Chi-restraints excluded: chain h residue 299 ILE Chi-restraints excluded: chain h residue 308 TRP Chi-restraints excluded: chain h residue 322 ASN Chi-restraints excluded: chain h residue 364 LEU Chi-restraints excluded: chain h residue 385 LEU Chi-restraints excluded: chain h residue 389 VAL Chi-restraints excluded: chain h residue 391 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 808 random chunks: chunk 708 optimal weight: 4.9990 chunk 746 optimal weight: 2.9990 chunk 680 optimal weight: 6.9990 chunk 725 optimal weight: 0.5980 chunk 745 optimal weight: 8.9990 chunk 436 optimal weight: 1.9990 chunk 316 optimal weight: 0.9990 chunk 569 optimal weight: 20.0000 chunk 222 optimal weight: 4.9990 chunk 655 optimal weight: 0.6980 chunk 686 optimal weight: 4.9990 overall best weight: 1.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 130 GLN B 211 HIS ** G 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 347 ASN H 386 HIS ** H 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 79 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** a 93 ASN ** f 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 337 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** c 130 GLN ** b 122 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** d 115 ASN ** d 313 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 334 GLN ** d 426 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 534 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 180 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 264 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** h 327 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6982 moved from start: 0.5790 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 65656 Z= 0.199 Angle : 0.617 14.171 89258 Z= 0.312 Chirality : 0.045 0.213 9916 Planarity : 0.004 0.066 11364 Dihedral : 9.719 178.556 9307 Min Nonbonded Distance : 1.794 Molprobity Statistics. All-atom Clashscore : 13.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.31 % Favored : 94.69 % Rotamer: Outliers : 3.11 % Allowed : 19.77 % Favored : 77.12 % Cbeta Deviations : 0.01 % Peptide Plane: Cis-proline : 1.54 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.01 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.71 (0.09), residues: 8162 helix: 0.46 (0.10), residues: 2904 sheet: -0.86 (0.15), residues: 1148 loop : -1.00 (0.10), residues: 4110 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.045 0.002 TRP d 234 HIS 0.011 0.001 HIS a 79 PHE 0.089 0.002 PHE b 237 TYR 0.023 0.001 TYR D 350 ARG 0.008 0.000 ARG j 28 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16324 Ramachandran restraints generated. 8162 Oldfield, 0 Emsley, 8162 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16324 Ramachandran restraints generated. 8162 Oldfield, 0 Emsley, 8162 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 919 residues out of total 6810 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 212 poor density : 707 time to evaluate : 5.755 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 160 MET cc_start: 0.7323 (mpp) cc_final: 0.7116 (mpp) REVERT: A 594 MET cc_start: 0.5796 (ptp) cc_final: 0.5390 (ptp) REVERT: F 120 MET cc_start: 0.7659 (mmm) cc_final: 0.7387 (tpp) REVERT: E 286 MET cc_start: 0.7223 (mmp) cc_final: 0.6842 (mmm) REVERT: B 160 MET cc_start: 0.6383 (mpp) cc_final: 0.5981 (mpp) REVERT: D 129 PHE cc_start: 0.6045 (OUTLIER) cc_final: 0.5079 (p90) REVERT: D 208 MET cc_start: 0.7819 (tmm) cc_final: 0.7469 (tmm) REVERT: D 441 LEU cc_start: 0.5636 (mt) cc_final: 0.5273 (mt) REVERT: I 6 MET cc_start: 0.8000 (ttp) cc_final: 0.7613 (mtp) REVERT: I 72 ASN cc_start: 0.7627 (t0) cc_final: 0.7344 (t0) REVERT: L 139 GLN cc_start: 0.8556 (tt0) cc_final: 0.8271 (mm-40) REVERT: G 335 LEU cc_start: 0.8271 (OUTLIER) cc_final: 0.7942 (mt) REVERT: G 454 LYS cc_start: 0.8016 (OUTLIER) cc_final: 0.7665 (mtmm) REVERT: G 458 LEU cc_start: 0.8062 (OUTLIER) cc_final: 0.7497 (pp) REVERT: G 533 GLN cc_start: 0.8810 (tp40) cc_final: 0.8450 (tp40) REVERT: J 32 ASP cc_start: 0.6805 (m-30) cc_final: 0.6531 (m-30) REVERT: J 42 GLN cc_start: 0.7814 (mm-40) cc_final: 0.7548 (mm-40) REVERT: J 50 MET cc_start: 0.7841 (tpp) cc_final: 0.7577 (ttp) REVERT: K 157 LYS cc_start: 0.8061 (OUTLIER) cc_final: 0.6237 (tptt) REVERT: K 227 ILE cc_start: 0.7878 (OUTLIER) cc_final: 0.7622 (mt) REVERT: K 384 LYS cc_start: 0.8407 (OUTLIER) cc_final: 0.8054 (tttp) REVERT: H 13 CYS cc_start: 0.8500 (OUTLIER) cc_final: 0.8221 (p) REVERT: H 208 GLN cc_start: 0.8371 (tm-30) cc_final: 0.8109 (tm-30) REVERT: H 293 MET cc_start: 0.8835 (mmt) cc_final: 0.8309 (mmt) REVERT: H 298 ASN cc_start: 0.7899 (t0) cc_final: 0.7073 (t0) REVERT: H 378 MET cc_start: 0.7570 (mmm) cc_final: 0.6125 (mtm) REVERT: a 594 MET cc_start: 0.7097 (ptp) cc_final: 0.5907 (ptp) REVERT: a 650 MET cc_start: 0.6076 (mmm) cc_final: 0.5610 (mmp) REVERT: e 75 CYS cc_start: 0.5977 (m) cc_final: 0.5772 (m) REVERT: e 394 GLU cc_start: 0.7101 (mm-30) cc_final: 0.6755 (mm-30) REVERT: c 162 HIS cc_start: 0.5366 (OUTLIER) cc_final: 0.5071 (m170) REVERT: b 26 THR cc_start: 0.8471 (p) cc_final: 0.8164 (p) REVERT: b 71 MET cc_start: 0.5179 (mpp) cc_final: 0.4979 (pmm) REVERT: d 115 ASN cc_start: 0.5449 (OUTLIER) cc_final: 0.5142 (m-40) REVERT: d 129 PHE cc_start: 0.5572 (OUTLIER) cc_final: 0.4763 (p90) REVERT: d 245 PHE cc_start: 0.6454 (OUTLIER) cc_final: 0.6176 (m-80) REVERT: d 399 LEU cc_start: 0.6357 (OUTLIER) cc_final: 0.5944 (tp) REVERT: d 527 TRP cc_start: 0.7281 (p-90) cc_final: 0.6960 (p-90) REVERT: i 34 ILE cc_start: 0.8287 (OUTLIER) cc_final: 0.7963 (mm) REVERT: i 67 ILE cc_start: 0.7953 (mt) cc_final: 0.7716 (mt) REVERT: i 96 MET cc_start: 0.8102 (mtt) cc_final: 0.7834 (mtp) REVERT: i 166 MET cc_start: 0.7676 (tmm) cc_final: 0.7271 (tmm) REVERT: i 245 ASP cc_start: 0.6525 (t0) cc_final: 0.6012 (t0) REVERT: l 131 TYR cc_start: 0.7926 (OUTLIER) cc_final: 0.6911 (p90) REVERT: g 418 ASP cc_start: 0.7415 (m-30) cc_final: 0.6927 (m-30) REVERT: j 30 TYR cc_start: 0.7605 (t80) cc_final: 0.7279 (t80) REVERT: j 32 ASP cc_start: 0.5654 (m-30) cc_final: 0.5244 (m-30) REVERT: j 117 GLU cc_start: 0.8341 (mt-10) cc_final: 0.7858 (mt-10) REVERT: j 125 LEU cc_start: 0.7780 (mt) cc_final: 0.7150 (mp) REVERT: k 157 LYS cc_start: 0.7937 (OUTLIER) cc_final: 0.7237 (tptt) REVERT: h 35 GLU cc_start: 0.6823 (mp0) cc_final: 0.5579 (mt-10) REVERT: h 82 LEU cc_start: 0.7499 (mt) cc_final: 0.7107 (mt) REVERT: h 135 TYR cc_start: 0.9227 (t80) cc_final: 0.8668 (t80) REVERT: h 212 TYR cc_start: 0.8003 (t80) cc_final: 0.7019 (t80) REVERT: h 237 LYS cc_start: 0.8055 (OUTLIER) cc_final: 0.7754 (mtmm) REVERT: h 338 MET cc_start: 0.7945 (mmp) cc_final: 0.7514 (mmp) REVERT: h 390 CYS cc_start: 0.6294 (m) cc_final: 0.5648 (m) outliers start: 212 outliers final: 163 residues processed: 866 average time/residue: 0.6109 time to fit residues: 910.5524 Evaluate side-chains 852 residues out of total 6810 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 180 poor density : 672 time to evaluate : 5.694 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 ILE Chi-restraints excluded: chain A residue 38 TYR Chi-restraints excluded: chain A residue 69 VAL Chi-restraints excluded: chain A residue 71 VAL Chi-restraints excluded: chain A residue 144 VAL Chi-restraints excluded: chain A residue 192 THR Chi-restraints excluded: chain A residue 223 GLU Chi-restraints excluded: chain F residue 39 ILE Chi-restraints excluded: chain E residue 58 THR Chi-restraints excluded: chain E residue 59 VAL Chi-restraints excluded: chain E residue 69 THR Chi-restraints excluded: chain E residue 79 LEU Chi-restraints excluded: chain E residue 100 CYS Chi-restraints excluded: chain E residue 120 ASP Chi-restraints excluded: chain E residue 141 MET Chi-restraints excluded: chain C residue 77 ASN Chi-restraints excluded: chain C residue 78 GLU Chi-restraints excluded: chain C residue 130 GLN Chi-restraints excluded: chain C residue 144 VAL Chi-restraints excluded: chain B residue 29 LYS Chi-restraints excluded: chain D residue 13 THR Chi-restraints excluded: chain D residue 113 THR Chi-restraints excluded: chain D residue 118 CYS Chi-restraints excluded: chain D residue 129 PHE Chi-restraints excluded: chain D residue 134 VAL Chi-restraints excluded: chain D residue 220 ASN Chi-restraints excluded: chain D residue 291 VAL Chi-restraints excluded: chain D residue 307 ASN Chi-restraints excluded: chain D residue 343 MET Chi-restraints excluded: chain D residue 346 TYR Chi-restraints excluded: chain D residue 399 LEU Chi-restraints excluded: chain D residue 531 THR Chi-restraints excluded: chain D residue 537 THR Chi-restraints excluded: chain I residue 34 ILE Chi-restraints excluded: chain I residue 40 HIS Chi-restraints excluded: chain I residue 76 MET Chi-restraints excluded: chain I residue 88 ILE Chi-restraints excluded: chain I residue 107 ILE Chi-restraints excluded: chain I residue 136 VAL Chi-restraints excluded: chain I residue 170 THR Chi-restraints excluded: chain I residue 189 THR Chi-restraints excluded: chain I residue 200 VAL Chi-restraints excluded: chain I residue 208 ASP Chi-restraints excluded: chain I residue 216 LEU Chi-restraints excluded: chain I residue 264 LEU Chi-restraints excluded: chain L residue 66 VAL Chi-restraints excluded: chain L residue 97 SER Chi-restraints excluded: chain L residue 131 TYR Chi-restraints excluded: chain L residue 135 GLN Chi-restraints excluded: chain G residue 88 ILE Chi-restraints excluded: chain G residue 99 SER Chi-restraints excluded: chain G residue 100 ILE Chi-restraints excluded: chain G residue 307 ILE Chi-restraints excluded: chain G residue 314 VAL Chi-restraints excluded: chain G residue 335 LEU Chi-restraints excluded: chain G residue 402 CYS Chi-restraints excluded: chain G residue 407 LEU Chi-restraints excluded: chain G residue 454 LYS Chi-restraints excluded: chain G residue 456 LEU Chi-restraints excluded: chain G residue 458 LEU Chi-restraints excluded: chain G residue 472 ASN Chi-restraints excluded: chain G residue 510 ASP Chi-restraints excluded: chain G residue 546 TYR Chi-restraints excluded: chain G residue 560 VAL Chi-restraints excluded: chain J residue 37 ILE Chi-restraints excluded: chain J residue 44 MET Chi-restraints excluded: chain J residue 54 ASN Chi-restraints excluded: chain J residue 63 GLU Chi-restraints excluded: chain J residue 96 THR Chi-restraints excluded: chain J residue 99 THR Chi-restraints excluded: chain K residue 90 PHE Chi-restraints excluded: chain K residue 106 LEU Chi-restraints excluded: chain K residue 157 LYS Chi-restraints excluded: chain K residue 169 VAL Chi-restraints excluded: chain K residue 175 THR Chi-restraints excluded: chain K residue 222 CYS Chi-restraints excluded: chain K residue 227 ILE Chi-restraints excluded: chain K residue 243 ASN Chi-restraints excluded: chain K residue 269 ILE Chi-restraints excluded: chain K residue 312 ILE Chi-restraints excluded: chain K residue 384 LYS Chi-restraints excluded: chain H residue 13 CYS Chi-restraints excluded: chain H residue 52 ASP Chi-restraints excluded: chain H residue 66 MET Chi-restraints excluded: chain H residue 299 ILE Chi-restraints excluded: chain H residue 331 THR Chi-restraints excluded: chain H residue 365 LYS Chi-restraints excluded: chain H residue 422 ASP Chi-restraints excluded: chain a residue 38 TYR Chi-restraints excluded: chain a residue 69 VAL Chi-restraints excluded: chain a residue 70 VAL Chi-restraints excluded: chain a residue 112 HIS Chi-restraints excluded: chain a residue 116 ASP Chi-restraints excluded: chain a residue 140 VAL Chi-restraints excluded: chain a residue 144 VAL Chi-restraints excluded: chain a residue 153 VAL Chi-restraints excluded: chain a residue 160 MET Chi-restraints excluded: chain a residue 192 THR Chi-restraints excluded: chain a residue 203 LEU Chi-restraints excluded: chain a residue 247 THR Chi-restraints excluded: chain a residue 418 ARG Chi-restraints excluded: chain a residue 487 VAL Chi-restraints excluded: chain a residue 571 GLU Chi-restraints excluded: chain f residue 39 ILE Chi-restraints excluded: chain f residue 86 MET Chi-restraints excluded: chain e residue 58 THR Chi-restraints excluded: chain e residue 66 ILE Chi-restraints excluded: chain e residue 120 ASP Chi-restraints excluded: chain e residue 141 MET Chi-restraints excluded: chain e residue 177 ASP Chi-restraints excluded: chain e residue 210 VAL Chi-restraints excluded: chain e residue 338 VAL Chi-restraints excluded: chain c residue 29 PHE Chi-restraints excluded: chain c residue 129 VAL Chi-restraints excluded: chain c residue 162 HIS Chi-restraints excluded: chain b residue 27 SER Chi-restraints excluded: chain b residue 111 ASP Chi-restraints excluded: chain b residue 132 VAL Chi-restraints excluded: chain b residue 289 THR Chi-restraints excluded: chain d residue 24 LEU Chi-restraints excluded: chain d residue 71 ILE Chi-restraints excluded: chain d residue 115 ASN Chi-restraints excluded: chain d residue 129 PHE Chi-restraints excluded: chain d residue 150 SER Chi-restraints excluded: chain d residue 243 LYS Chi-restraints excluded: chain d residue 245 PHE Chi-restraints excluded: chain d residue 289 ASN Chi-restraints excluded: chain d residue 307 ASN Chi-restraints excluded: chain d residue 326 VAL Chi-restraints excluded: chain d residue 350 TYR Chi-restraints excluded: chain d residue 399 LEU Chi-restraints excluded: chain d residue 441 LEU Chi-restraints excluded: chain d residue 531 THR Chi-restraints excluded: chain d residue 537 THR Chi-restraints excluded: chain i residue 20 SER Chi-restraints excluded: chain i residue 34 ILE Chi-restraints excluded: chain i residue 40 HIS Chi-restraints excluded: chain i residue 114 ASP Chi-restraints excluded: chain i residue 115 SER Chi-restraints excluded: chain i residue 170 THR Chi-restraints excluded: chain i residue 215 LEU Chi-restraints excluded: chain i residue 228 VAL Chi-restraints excluded: chain l residue 66 VAL Chi-restraints excluded: chain l residue 99 ASP Chi-restraints excluded: chain l residue 105 ILE Chi-restraints excluded: chain l residue 124 ILE Chi-restraints excluded: chain l residue 131 TYR Chi-restraints excluded: chain g residue 249 ASP Chi-restraints excluded: chain g residue 320 THR Chi-restraints excluded: chain g residue 346 GLU Chi-restraints excluded: chain g residue 424 ASP Chi-restraints excluded: chain g residue 431 ASN Chi-restraints excluded: chain g residue 458 LEU Chi-restraints excluded: chain g residue 546 TYR Chi-restraints excluded: chain j residue 37 ILE Chi-restraints excluded: chain j residue 63 GLU Chi-restraints excluded: chain k residue 4 LEU Chi-restraints excluded: chain k residue 90 PHE Chi-restraints excluded: chain k residue 105 ILE Chi-restraints excluded: chain k residue 157 LYS Chi-restraints excluded: chain k residue 175 THR Chi-restraints excluded: chain k residue 183 LEU Chi-restraints excluded: chain k residue 201 VAL Chi-restraints excluded: chain k residue 233 VAL Chi-restraints excluded: chain k residue 234 VAL Chi-restraints excluded: chain k residue 261 THR Chi-restraints excluded: chain k residue 265 THR Chi-restraints excluded: chain k residue 347 LYS Chi-restraints excluded: chain h residue 90 MET Chi-restraints excluded: chain h residue 96 THR Chi-restraints excluded: chain h residue 143 VAL Chi-restraints excluded: chain h residue 148 ASP Chi-restraints excluded: chain h residue 196 THR Chi-restraints excluded: chain h residue 237 LYS Chi-restraints excluded: chain h residue 246 GLU Chi-restraints excluded: chain h residue 299 ILE Chi-restraints excluded: chain h residue 322 ASN Chi-restraints excluded: chain h residue 364 LEU Chi-restraints excluded: chain h residue 389 VAL Chi-restraints excluded: chain h residue 391 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 808 random chunks: chunk 723 optimal weight: 5.9990 chunk 476 optimal weight: 0.9980 chunk 767 optimal weight: 4.9990 chunk 468 optimal weight: 10.0000 chunk 364 optimal weight: 4.9990 chunk 533 optimal weight: 8.9990 chunk 804 optimal weight: 0.3980 chunk 740 optimal weight: 0.9980 chunk 641 optimal weight: 10.0000 chunk 66 optimal weight: 3.9990 chunk 495 optimal weight: 9.9990 overall best weight: 2.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 293 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 77 ASN C 130 GLN C 177 HIS B 211 HIS ** G 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 28 ASN ** H 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 79 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 337 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** c 130 GLN c 172 GLN ** b 122 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 313 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 426 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 534 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 180 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** l 139 GLN ** g 264 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** h 327 ASN h 347 ASN h 367 HIS Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7013 moved from start: 0.5975 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 65656 Z= 0.244 Angle : 0.640 15.696 89258 Z= 0.322 Chirality : 0.046 0.178 9916 Planarity : 0.004 0.062 11364 Dihedral : 9.625 177.858 9307 Min Nonbonded Distance : 1.742 Molprobity Statistics. All-atom Clashscore : 14.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.71 % Favored : 94.29 % Rotamer: Outliers : 2.80 % Allowed : 20.15 % Favored : 77.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.54 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.74 (0.09), residues: 8162 helix: 0.44 (0.10), residues: 2904 sheet: -0.89 (0.15), residues: 1184 loop : -1.00 (0.10), residues: 4074 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.002 TRP d 234 HIS 0.012 0.001 HIS a 79 PHE 0.050 0.002 PHE b 237 TYR 0.031 0.001 TYR D 350 ARG 0.012 0.001 ARG h 80 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16324 Ramachandran restraints generated. 8162 Oldfield, 0 Emsley, 8162 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16324 Ramachandran restraints generated. 8162 Oldfield, 0 Emsley, 8162 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 873 residues out of total 6810 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 191 poor density : 682 time to evaluate : 5.820 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 594 MET cc_start: 0.6325 (ptp) cc_final: 0.5801 (ptp) REVERT: E 286 MET cc_start: 0.7458 (mmp) cc_final: 0.7043 (mmp) REVERT: B 160 MET cc_start: 0.6240 (mpp) cc_final: 0.5962 (mpp) REVERT: D 129 PHE cc_start: 0.5947 (OUTLIER) cc_final: 0.4980 (p90) REVERT: I 6 MET cc_start: 0.8018 (ttp) cc_final: 0.7620 (mtp) REVERT: I 72 ASN cc_start: 0.7744 (t0) cc_final: 0.7473 (t0) REVERT: L 139 GLN cc_start: 0.8592 (tt0) cc_final: 0.8319 (mm-40) REVERT: G 298 MET cc_start: 0.6099 (tpt) cc_final: 0.5740 (tpt) REVERT: G 335 LEU cc_start: 0.8188 (OUTLIER) cc_final: 0.7809 (mt) REVERT: G 454 LYS cc_start: 0.8155 (OUTLIER) cc_final: 0.7770 (mtmm) REVERT: G 458 LEU cc_start: 0.8090 (OUTLIER) cc_final: 0.7533 (pp) REVERT: J 17 GLU cc_start: 0.7832 (OUTLIER) cc_final: 0.6849 (tp30) REVERT: J 30 TYR cc_start: 0.7698 (t80) cc_final: 0.7497 (t80) REVERT: J 32 ASP cc_start: 0.6873 (m-30) cc_final: 0.6609 (m-30) REVERT: J 42 GLN cc_start: 0.7850 (mm-40) cc_final: 0.7560 (mm-40) REVERT: J 50 MET cc_start: 0.7864 (tpp) cc_final: 0.7618 (ttp) REVERT: J 117 GLU cc_start: 0.8001 (mp0) cc_final: 0.7249 (mp0) REVERT: K 227 ILE cc_start: 0.7686 (OUTLIER) cc_final: 0.7318 (mt) REVERT: K 384 LYS cc_start: 0.8443 (OUTLIER) cc_final: 0.8077 (tttp) REVERT: H 13 CYS cc_start: 0.8500 (OUTLIER) cc_final: 0.8212 (p) REVERT: H 293 MET cc_start: 0.8917 (mmt) cc_final: 0.8426 (mmt) REVERT: H 298 ASN cc_start: 0.8001 (t0) cc_final: 0.7207 (t0) REVERT: H 378 MET cc_start: 0.7539 (mmm) cc_final: 0.6998 (mmp) REVERT: a 594 MET cc_start: 0.6621 (ptp) cc_final: 0.5309 (ptp) REVERT: a 650 MET cc_start: 0.5896 (mmm) cc_final: 0.4624 (mmp) REVERT: c 162 HIS cc_start: 0.5339 (OUTLIER) cc_final: 0.5064 (m170) REVERT: b 26 THR cc_start: 0.8572 (p) cc_final: 0.8249 (p) REVERT: b 71 MET cc_start: 0.5515 (mpp) cc_final: 0.4714 (ptp) REVERT: b 112 MET cc_start: 0.5503 (tmm) cc_final: 0.4973 (tmm) REVERT: d 129 PHE cc_start: 0.5764 (OUTLIER) cc_final: 0.4897 (p90) REVERT: d 399 LEU cc_start: 0.6495 (OUTLIER) cc_final: 0.6029 (tp) REVERT: d 527 TRP cc_start: 0.7544 (p-90) cc_final: 0.7144 (p-90) REVERT: i 34 ILE cc_start: 0.8331 (OUTLIER) cc_final: 0.7996 (mm) REVERT: i 67 ILE cc_start: 0.7973 (mt) cc_final: 0.7741 (mt) REVERT: i 96 MET cc_start: 0.8195 (mtt) cc_final: 0.7898 (mtp) REVERT: i 166 MET cc_start: 0.7653 (tmm) cc_final: 0.7233 (tmm) REVERT: i 245 ASP cc_start: 0.6579 (t0) cc_final: 0.6069 (t0) REVERT: l 127 ASP cc_start: 0.6576 (t0) cc_final: 0.6219 (t0) REVERT: l 131 TYR cc_start: 0.7915 (OUTLIER) cc_final: 0.6898 (p90) REVERT: g 298 MET cc_start: 0.7088 (tpp) cc_final: 0.6347 (tpp) REVERT: g 418 ASP cc_start: 0.7231 (m-30) cc_final: 0.6897 (m-30) REVERT: j 30 TYR cc_start: 0.7694 (t80) cc_final: 0.7343 (t80) REVERT: j 32 ASP cc_start: 0.5716 (m-30) cc_final: 0.5453 (m-30) REVERT: j 117 GLU cc_start: 0.8380 (mt-10) cc_final: 0.7979 (mt-10) REVERT: j 125 LEU cc_start: 0.7558 (mt) cc_final: 0.6875 (mp) REVERT: h 6 GLU cc_start: 0.8002 (mp0) cc_final: 0.7506 (mm-30) REVERT: h 35 GLU cc_start: 0.6515 (mp0) cc_final: 0.5203 (mt-10) REVERT: h 76 ASP cc_start: 0.7766 (m-30) cc_final: 0.7454 (m-30) REVERT: h 80 ARG cc_start: 0.6798 (ptt-90) cc_final: 0.6204 (mtm110) REVERT: h 135 TYR cc_start: 0.9239 (t80) cc_final: 0.8698 (t80) REVERT: h 212 TYR cc_start: 0.8024 (t80) cc_final: 0.6935 (t80) REVERT: h 237 LYS cc_start: 0.8094 (OUTLIER) cc_final: 0.7793 (mtmm) REVERT: h 338 MET cc_start: 0.8119 (OUTLIER) cc_final: 0.7688 (mmp) REVERT: h 385 LEU cc_start: 0.9046 (OUTLIER) cc_final: 0.8628 (pp) REVERT: h 424 GLU cc_start: 0.7687 (tp30) cc_final: 0.6825 (tp30) outliers start: 191 outliers final: 159 residues processed: 826 average time/residue: 0.5905 time to fit residues: 837.1136 Evaluate side-chains 833 residues out of total 6810 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 175 poor density : 658 time to evaluate : 5.748 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 ILE Chi-restraints excluded: chain A residue 38 TYR Chi-restraints excluded: chain A residue 69 VAL Chi-restraints excluded: chain A residue 71 VAL Chi-restraints excluded: chain A residue 144 VAL Chi-restraints excluded: chain A residue 192 THR Chi-restraints excluded: chain A residue 218 MET Chi-restraints excluded: chain A residue 223 GLU Chi-restraints excluded: chain F residue 39 ILE Chi-restraints excluded: chain E residue 58 THR Chi-restraints excluded: chain E residue 69 THR Chi-restraints excluded: chain E residue 79 LEU Chi-restraints excluded: chain E residue 100 CYS Chi-restraints excluded: chain E residue 120 ASP Chi-restraints excluded: chain E residue 141 MET Chi-restraints excluded: chain E residue 177 ASP Chi-restraints excluded: chain C residue 77 ASN Chi-restraints excluded: chain C residue 78 GLU Chi-restraints excluded: chain C residue 130 GLN Chi-restraints excluded: chain C residue 144 VAL Chi-restraints excluded: chain B residue 29 LYS Chi-restraints excluded: chain D residue 13 THR Chi-restraints excluded: chain D residue 113 THR Chi-restraints excluded: chain D residue 118 CYS Chi-restraints excluded: chain D residue 129 PHE Chi-restraints excluded: chain D residue 134 VAL Chi-restraints excluded: chain D residue 220 ASN Chi-restraints excluded: chain D residue 274 LEU Chi-restraints excluded: chain D residue 291 VAL Chi-restraints excluded: chain D residue 307 ASN Chi-restraints excluded: chain D residue 343 MET Chi-restraints excluded: chain D residue 346 TYR Chi-restraints excluded: chain D residue 399 LEU Chi-restraints excluded: chain D residue 531 THR Chi-restraints excluded: chain D residue 537 THR Chi-restraints excluded: chain I residue 34 ILE Chi-restraints excluded: chain I residue 40 HIS Chi-restraints excluded: chain I residue 76 MET Chi-restraints excluded: chain I residue 88 ILE Chi-restraints excluded: chain I residue 107 ILE Chi-restraints excluded: chain I residue 136 VAL Chi-restraints excluded: chain I residue 170 THR Chi-restraints excluded: chain I residue 189 THR Chi-restraints excluded: chain I residue 200 VAL Chi-restraints excluded: chain I residue 208 ASP Chi-restraints excluded: chain I residue 216 LEU Chi-restraints excluded: chain I residue 264 LEU Chi-restraints excluded: chain L residue 66 VAL Chi-restraints excluded: chain L residue 97 SER Chi-restraints excluded: chain L residue 131 TYR Chi-restraints excluded: chain L residue 135 GLN Chi-restraints excluded: chain G residue 88 ILE Chi-restraints excluded: chain G residue 99 SER Chi-restraints excluded: chain G residue 100 ILE Chi-restraints excluded: chain G residue 307 ILE Chi-restraints excluded: chain G residue 314 VAL Chi-restraints excluded: chain G residue 335 LEU Chi-restraints excluded: chain G residue 402 CYS Chi-restraints excluded: chain G residue 407 LEU Chi-restraints excluded: chain G residue 454 LYS Chi-restraints excluded: chain G residue 456 LEU Chi-restraints excluded: chain G residue 458 LEU Chi-restraints excluded: chain G residue 472 ASN Chi-restraints excluded: chain G residue 512 GLU Chi-restraints excluded: chain G residue 546 TYR Chi-restraints excluded: chain G residue 560 VAL Chi-restraints excluded: chain J residue 17 GLU Chi-restraints excluded: chain J residue 21 MET Chi-restraints excluded: chain J residue 37 ILE Chi-restraints excluded: chain J residue 44 MET Chi-restraints excluded: chain J residue 54 ASN Chi-restraints excluded: chain J residue 63 GLU Chi-restraints excluded: chain J residue 96 THR Chi-restraints excluded: chain J residue 99 THR Chi-restraints excluded: chain K residue 90 PHE Chi-restraints excluded: chain K residue 106 LEU Chi-restraints excluded: chain K residue 175 THR Chi-restraints excluded: chain K residue 222 CYS Chi-restraints excluded: chain K residue 227 ILE Chi-restraints excluded: chain K residue 269 ILE Chi-restraints excluded: chain K residue 312 ILE Chi-restraints excluded: chain K residue 384 LYS Chi-restraints excluded: chain H residue 13 CYS Chi-restraints excluded: chain H residue 52 ASP Chi-restraints excluded: chain H residue 66 MET Chi-restraints excluded: chain H residue 299 ILE Chi-restraints excluded: chain H residue 331 THR Chi-restraints excluded: chain H residue 365 LYS Chi-restraints excluded: chain H residue 422 ASP Chi-restraints excluded: chain a residue 38 TYR Chi-restraints excluded: chain a residue 69 VAL Chi-restraints excluded: chain a residue 70 VAL Chi-restraints excluded: chain a residue 140 VAL Chi-restraints excluded: chain a residue 144 VAL Chi-restraints excluded: chain a residue 153 VAL Chi-restraints excluded: chain a residue 160 MET Chi-restraints excluded: chain a residue 192 THR Chi-restraints excluded: chain a residue 203 LEU Chi-restraints excluded: chain a residue 247 THR Chi-restraints excluded: chain a residue 418 ARG Chi-restraints excluded: chain a residue 487 VAL Chi-restraints excluded: chain a residue 571 GLU Chi-restraints excluded: chain f residue 39 ILE Chi-restraints excluded: chain e residue 58 THR Chi-restraints excluded: chain e residue 66 ILE Chi-restraints excluded: chain e residue 120 ASP Chi-restraints excluded: chain e residue 141 MET Chi-restraints excluded: chain e residue 177 ASP Chi-restraints excluded: chain e residue 210 VAL Chi-restraints excluded: chain e residue 338 VAL Chi-restraints excluded: chain c residue 29 PHE Chi-restraints excluded: chain c residue 162 HIS Chi-restraints excluded: chain b residue 27 SER Chi-restraints excluded: chain b residue 132 VAL Chi-restraints excluded: chain b residue 289 THR Chi-restraints excluded: chain d residue 24 LEU Chi-restraints excluded: chain d residue 71 ILE Chi-restraints excluded: chain d residue 113 THR Chi-restraints excluded: chain d residue 129 PHE Chi-restraints excluded: chain d residue 243 LYS Chi-restraints excluded: chain d residue 276 VAL Chi-restraints excluded: chain d residue 307 ASN Chi-restraints excluded: chain d residue 326 VAL Chi-restraints excluded: chain d residue 350 TYR Chi-restraints excluded: chain d residue 399 LEU Chi-restraints excluded: chain d residue 441 LEU Chi-restraints excluded: chain d residue 531 THR Chi-restraints excluded: chain d residue 537 THR Chi-restraints excluded: chain i residue 20 SER Chi-restraints excluded: chain i residue 34 ILE Chi-restraints excluded: chain i residue 40 HIS Chi-restraints excluded: chain i residue 114 ASP Chi-restraints excluded: chain i residue 115 SER Chi-restraints excluded: chain i residue 170 THR Chi-restraints excluded: chain i residue 215 LEU Chi-restraints excluded: chain i residue 228 VAL Chi-restraints excluded: chain l residue 66 VAL Chi-restraints excluded: chain l residue 99 ASP Chi-restraints excluded: chain l residue 105 ILE Chi-restraints excluded: chain l residue 124 ILE Chi-restraints excluded: chain l residue 131 TYR Chi-restraints excluded: chain g residue 249 ASP Chi-restraints excluded: chain g residue 320 THR Chi-restraints excluded: chain g residue 346 GLU Chi-restraints excluded: chain g residue 385 VAL Chi-restraints excluded: chain g residue 424 ASP Chi-restraints excluded: chain g residue 431 ASN Chi-restraints excluded: chain g residue 458 LEU Chi-restraints excluded: chain g residue 497 THR Chi-restraints excluded: chain g residue 546 TYR Chi-restraints excluded: chain j residue 37 ILE Chi-restraints excluded: chain j residue 63 GLU Chi-restraints excluded: chain k residue 4 LEU Chi-restraints excluded: chain k residue 90 PHE Chi-restraints excluded: chain k residue 105 ILE Chi-restraints excluded: chain k residue 175 THR Chi-restraints excluded: chain k residue 183 LEU Chi-restraints excluded: chain k residue 201 VAL Chi-restraints excluded: chain k residue 233 VAL Chi-restraints excluded: chain k residue 234 VAL Chi-restraints excluded: chain k residue 261 THR Chi-restraints excluded: chain k residue 265 THR Chi-restraints excluded: chain h residue 90 MET Chi-restraints excluded: chain h residue 96 THR Chi-restraints excluded: chain h residue 143 VAL Chi-restraints excluded: chain h residue 148 ASP Chi-restraints excluded: chain h residue 196 THR Chi-restraints excluded: chain h residue 237 LYS Chi-restraints excluded: chain h residue 246 GLU Chi-restraints excluded: chain h residue 299 ILE Chi-restraints excluded: chain h residue 322 ASN Chi-restraints excluded: chain h residue 338 MET Chi-restraints excluded: chain h residue 364 LEU Chi-restraints excluded: chain h residue 385 LEU Chi-restraints excluded: chain h residue 389 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 808 random chunks: chunk 393 optimal weight: 3.9990 chunk 509 optimal weight: 0.7980 chunk 682 optimal weight: 0.9980 chunk 196 optimal weight: 9.9990 chunk 591 optimal weight: 9.9990 chunk 94 optimal weight: 0.5980 chunk 178 optimal weight: 0.8980 chunk 642 optimal weight: 2.9990 chunk 268 optimal weight: 1.9990 chunk 659 optimal weight: 0.6980 chunk 81 optimal weight: 9.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 386 HIS B 211 HIS G 152 ASN ** H 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 79 HIS ** a 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 161 GLN ** f 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 337 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** c 172 GLN ** b 122 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 313 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 334 GLN ** d 426 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 534 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 180 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** l 139 GLN g 143 GLN ** g 264 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** h 327 ASN h 367 HIS Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4155 r_free = 0.4155 target = 0.129615 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3720 r_free = 0.3720 target = 0.101928 restraints weight = 150646.314| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3709 r_free = 0.3709 target = 0.102101 restraints weight = 88323.734| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3715 r_free = 0.3715 target = 0.102647 restraints weight = 54461.602| |-----------------------------------------------------------------------------| r_work (final): 0.3710 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7765 moved from start: 0.6047 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 65656 Z= 0.171 Angle : 0.612 14.726 89258 Z= 0.307 Chirality : 0.045 0.180 9916 Planarity : 0.004 0.056 11364 Dihedral : 9.084 176.935 9303 Min Nonbonded Distance : 1.805 Molprobity Statistics. All-atom Clashscore : 13.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.05 % Favored : 94.95 % Rotamer: Outliers : 2.36 % Allowed : 20.84 % Favored : 76.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.54 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.67 (0.09), residues: 8162 helix: 0.47 (0.10), residues: 2910 sheet: -0.83 (0.15), residues: 1182 loop : -0.94 (0.10), residues: 4070 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.001 TRP B 176 HIS 0.011 0.001 HIS a 79 PHE 0.025 0.001 PHE B 291 TYR 0.025 0.001 TYR D 350 ARG 0.011 0.000 ARG h 80 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 15755.50 seconds wall clock time: 277 minutes 54.17 seconds (16674.17 seconds total)