Starting phenix.real_space_refine on Sat Mar 23 21:09:32 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7kj4_22893/03_2024/7kj4_22893.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7kj4_22893/03_2024/7kj4_22893.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7kj4_22893/03_2024/7kj4_22893.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7kj4_22893/03_2024/7kj4_22893.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7kj4_22893/03_2024/7kj4_22893.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7kj4_22893/03_2024/7kj4_22893.pdb" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 192 5.16 5 C 24697 2.51 5 N 6307 2.21 5 O 7580 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 28": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 43": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 55": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 59": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 88": "OD1" <-> "OD2" Residue "A PHE 92": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 133": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 135": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 140": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 168": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 186": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 191": "OE1" <-> "OE2" Residue "A PHE 194": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 200": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 238": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 313": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 329": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 338": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 342": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 347": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 351": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 400": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 420": "OD1" <-> "OD2" Residue "A TYR 451": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 466": "NH1" <-> "NH2" Residue "A TYR 489": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 508": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 562": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 592": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 660": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 759": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 782": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 789": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 797": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 802": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 817": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 823": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 855": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 867": "OD1" <-> "OD2" Residue "A TYR 873": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 888": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 917": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 970": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1047": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1052": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1062": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1067": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1075": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1111": "OE1" <-> "OE2" Residue "A TYR 1138": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 28": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 43": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 55": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 59": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 88": "OD1" <-> "OD2" Residue "B PHE 92": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 135": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 186": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 194": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 200": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 201": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 238": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 313": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 329": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 338": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 347": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 351": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 377": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 380": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 421": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 453": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 464": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 505": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 508": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 562": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 592": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 660": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 695": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 707": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 748": "OE1" <-> "OE2" Residue "B PHE 759": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 782": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 789": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 797": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 800": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 802": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 817": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 873": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 888": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 898": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 917": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 970": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 1047": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 1052": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 1067": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 1084": "OD1" <-> "OD2" Residue "B PHE 1089": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 1103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 1111": "OE1" <-> "OE2" Residue "B PHE 1121": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 28": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 55": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 59": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 88": "OD1" <-> "OD2" Residue "C PHE 92": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 133": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 135": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 140": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 168": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 170": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 186": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 191": "OE1" <-> "OE2" Residue "C PHE 194": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 200": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 201": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 220": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 238": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 265": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 313": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 329": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 338": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 342": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 347": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 351": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 396": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 423": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 464": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 465": "OE1" <-> "OE2" Residue "C TYR 505": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 508": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 592": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 619": "OE1" <-> "OE2" Residue "C GLU 654": "OE1" <-> "OE2" Residue "C TYR 660": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 695": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 759": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 782": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 789": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 797": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 802": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 817": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 855": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 873": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 888": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 917": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 970": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 1047": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 1052": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 1062": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 1067": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 1084": "OD1" <-> "OD2" Residue "C PHE 1089": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 1092": "OE1" <-> "OE2" Residue "C PHE 1103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 1111": "OE1" <-> "OE2" Residue "C PHE 1121": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 23": "OE1" <-> "OE2" Residue "D ASP 38": "OD1" <-> "OD2" Residue "D GLU 56": "OE1" <-> "OE2" Residue "D GLU 57": "OE1" <-> "OE2" Residue "D ASP 67": "OD1" <-> "OD2" Residue "D ARG 115": "NH1" <-> "NH2" Residue "D ARG 169": "NH1" <-> "NH2" Residue "D ARG 177": "NH1" <-> "NH2" Residue "D TYR 183": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 192": "NH1" <-> "NH2" Residue "D TYR 196": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 198": "OD1" <-> "OD2" Residue "D TYR 202": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 208": "OE1" <-> "OE2" Residue "D TYR 215": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 227": "OE1" <-> "OE2" Residue "D TYR 243": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 245": "NH1" <-> "NH2" Residue "D ARG 273": "NH1" <-> "NH2" Residue "D PHE 285": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 306": "NH1" <-> "NH2" Residue "D PHE 308": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 315": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 329": "OE1" <-> "OE2" Residue "D GLU 406": "OE1" <-> "OE2" Residue "D GLU 435": "OE1" <-> "OE2" Residue "D PHE 452": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 457": "OE1" <-> "OE2" Residue "D GLU 467": "OE1" <-> "OE2" Residue "D ARG 518": "NH1" <-> "NH2" Residue "D GLU 527": "OE1" <-> "OE2" Residue "D GLU 549": "OE1" <-> "OE2" Residue "D GLU 564": "OE1" <-> "OE2" Residue "D TYR 587": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 603": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 23": "OE1" <-> "OE2" Residue "E ASP 38": "OD1" <-> "OD2" Residue "E TYR 41": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 56": "OE1" <-> "OE2" Residue "E ASP 67": "OD1" <-> "OD2" Residue "E TYR 83": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 115": "NH1" <-> "NH2" Residue "E TYR 127": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 169": "NH1" <-> "NH2" Residue "E ARG 177": "NH1" <-> "NH2" Residue "E TYR 183": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 192": "NH1" <-> "NH2" Residue "E TYR 196": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 198": "OD1" <-> "OD2" Residue "E TYR 202": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 206": "OD1" <-> "OD2" Residue "E TYR 215": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 227": "OE1" <-> "OE2" Residue "E ARG 245": "NH1" <-> "NH2" Residue "E ARG 273": "NH1" <-> "NH2" Residue "E PHE 274": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 306": "NH1" <-> "NH2" Residue "E PHE 308": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 329": "OE1" <-> "OE2" Residue "E ARG 357": "NH1" <-> "NH2" Residue "E PHE 369": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 435": "OE1" <-> "OE2" Residue "E PHE 438": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 452": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 457": "OE1" <-> "OE2" Residue "E ARG 518": "NH1" <-> "NH2" Residue "E PHE 523": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 527": "OE1" <-> "OE2" Residue "E GLU 549": "OE1" <-> "OE2" Residue "E GLU 564": "OE1" <-> "OE2" Residue "E TYR 587": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 613": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 23": "OE1" <-> "OE2" Residue "F GLU 37": "OE1" <-> "OE2" Residue "F ASP 38": "OD1" <-> "OD2" Residue "F GLU 56": "OE1" <-> "OE2" Residue "F GLU 57": "OE1" <-> "OE2" Residue "F ASP 67": "OD1" <-> "OD2" Residue "F ARG 115": "NH1" <-> "NH2" Residue "F TYR 127": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 158": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 169": "NH1" <-> "NH2" Residue "F ARG 177": "NH1" <-> "NH2" Residue "F TYR 183": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 192": "NH1" <-> "NH2" Residue "F TYR 196": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 198": "OD1" <-> "OD2" Residue "F TYR 202": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 206": "OD1" <-> "OD2" Residue "F TYR 215": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 227": "OE1" <-> "OE2" Residue "F ARG 245": "NH1" <-> "NH2" Residue "F ARG 273": "NH1" <-> "NH2" Residue "F ARG 306": "NH1" <-> "NH2" Residue "F PHE 308": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 310": "OE1" <-> "OE2" Residue "F GLU 329": "OE1" <-> "OE2" Residue "F PHE 356": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 357": "NH1" <-> "NH2" Residue "F PHE 369": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 428": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 435": "OE1" <-> "OE2" Residue "F PHE 452": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 457": "OE1" <-> "OE2" Residue "F ASP 494": "OD1" <-> "OD2" Residue "F TYR 510": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 516": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 518": "NH1" <-> "NH2" Residue "F GLU 527": "OE1" <-> "OE2" Residue "F GLU 549": "OE1" <-> "OE2" Residue "F GLU 564": "OE1" <-> "OE2" Residue "F PHE 603": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.12s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 38776 Number of models: 1 Model: "" Number of chains: 36 Chain: "A" Number of atoms: 7658 Number of conformers: 1 Conformer: "" Number of residues, atoms: 981, 7658 Classifications: {'peptide': 981} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 48, 'TRANS': 932} Chain breaks: 10 Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'GLN:plan1': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 7 Chain: "B" Number of atoms: 7665 Number of conformers: 1 Conformer: "" Number of residues, atoms: 981, 7665 Classifications: {'peptide': 981} Link IDs: {'PTRANS': 48, 'TRANS': 932} Chain breaks: 10 Chain: "C" Number of atoms: 7661 Number of conformers: 1 Conformer: "" Number of residues, atoms: 981, 7661 Classifications: {'peptide': 981} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 48, 'TRANS': 932} Chain breaks: 10 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "D" Number of atoms: 4844 Number of conformers: 1 Conformer: "" Number of residues, atoms: 593, 4844 Classifications: {'peptide': 593} Link IDs: {'PTRANS': 27, 'TRANS': 565} Chain: "E" Number of atoms: 4844 Number of conformers: 1 Conformer: "" Number of residues, atoms: 593, 4844 Classifications: {'peptide': 593} Link IDs: {'PTRANS': 27, 'TRANS': 565} Chain: "F" Number of atoms: 4844 Number of conformers: 1 Conformer: "" Number of residues, atoms: 593, 4844 Classifications: {'peptide': 593} Link IDs: {'PTRANS': 27, 'TRANS': 565} Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "L" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "P" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "R" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "S" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "T" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "U" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "V" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "W" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "X" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Y" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Z" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "a" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "b" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "c" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "d" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 182 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 182 Unusual residues: {'NAG': 13} Classifications: {'undetermined': 13} Link IDs: {None: 12} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 39 Unresolved non-hydrogen chiralities: 13 Chain: "B" Number of atoms: 182 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 182 Unusual residues: {'NAG': 13} Classifications: {'undetermined': 13} Link IDs: {None: 12} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 39 Unresolved non-hydrogen chiralities: 13 Chain: "C" Number of atoms: 182 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 182 Unusual residues: {'NAG': 13} Classifications: {'undetermined': 13} Link IDs: {None: 12} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 39 Unresolved non-hydrogen chiralities: 13 Chain: "D" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "E" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "F" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 18.62, per 1000 atoms: 0.48 Number of scatterers: 38776 At special positions: 0 Unit cell: (164.175, 164.175, 232.65, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 192 16.00 O 7580 8.00 N 6307 7.00 C 24697 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=48, symmetry=0 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.03 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.00 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.04 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.02 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.03 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.03 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.03 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.06 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.04 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.05 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.04 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.02 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.02 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.02 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.00 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.51 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.04 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.04 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.02 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=2.03 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.03 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.03 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 760 " distance=2.04 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.03 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.02 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.02 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.05 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.01 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.73 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.03 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.05 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " distance=2.03 Simple disulfide: pdb=" SG CYS C 538 " - pdb=" SG CYS C 590 " distance=2.04 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.04 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.04 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=2.18 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.04 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.01 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.02 Simple disulfide: pdb=" SG CYS D 133 " - pdb=" SG CYS D 141 " distance=2.04 Simple disulfide: pdb=" SG CYS D 344 " - pdb=" SG CYS D 361 " distance=2.05 Simple disulfide: pdb=" SG CYS D 530 " - pdb=" SG CYS D 542 " distance=2.01 Simple disulfide: pdb=" SG CYS E 133 " - pdb=" SG CYS E 141 " distance=2.51 Simple disulfide: pdb=" SG CYS E 344 " - pdb=" SG CYS E 361 " distance=2.06 Simple disulfide: pdb=" SG CYS E 530 " - pdb=" SG CYS E 542 " distance=2.02 Simple disulfide: pdb=" SG CYS F 133 " - pdb=" SG CYS F 141 " distance=2.03 Simple disulfide: pdb=" SG CYS F 344 " - pdb=" SG CYS F 361 " distance=2.05 Simple disulfide: pdb=" SG CYS F 530 " - pdb=" SG CYS F 542 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Atom "HETATM38214 O5 NAG A1302 .*. O " rejected from bonding due to valence issues. Atom "HETATM38564 O5 NAG C1301 .*. O " rejected from bonding due to valence issues. Atom "HETATM38648 O5 NAG C1307 .*. O " rejected from bonding due to valence issues. Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG L 1 " - " NAG L 2 " " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " " NAG P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " " NAG R 1 " - " NAG R 2 " " NAG S 1 " - " NAG S 2 " " NAG T 1 " - " NAG T 2 " " NAG U 1 " - " NAG U 2 " " NAG V 1 " - " NAG V 2 " " NAG W 1 " - " NAG W 2 " " NAG X 1 " - " NAG X 2 " " NAG Y 1 " - " NAG Y 2 " " NAG Z 1 " - " NAG Z 2 " " NAG a 1 " - " NAG a 2 " " NAG b 1 " - " NAG b 2 " " NAG c 1 " - " NAG c 2 " " NAG d 1 " - " NAG d 2 " NAG-ASN " NAG A1301 " - " ASN A 61 " " NAG A1302 " - " ASN A 122 " " NAG A1303 " - " ASN A 234 " " NAG A1304 " - " ASN A 282 " " NAG A1305 " - " ASN A 331 " " NAG A1309 " - " ASN A 657 " " NAG A1310 " - " ASN A 709 " " NAG A1311 " - " ASN A 717 " " NAG A1313 " - " ASN A 165 " " NAG B1301 " - " ASN B 61 " " NAG B1302 " - " ASN B 122 " " NAG B1304 " - " ASN B 282 " " NAG B1305 " - " ASN B 331 " " NAG B1306 " - " ASN B 343 " " NAG B1308 " - " ASN B 616 " " NAG B1309 " - " ASN B 657 " " NAG B1310 " - " ASN B 709 " " NAG B1311 " - " ASN B 717 " " NAG B1312 " - " ASN B1074 " " NAG B1313 " - " ASN B 165 " " NAG C1301 " - " ASN C 61 " " NAG C1302 " - " ASN C 122 " " NAG C1304 " - " ASN C 282 " " NAG C1305 " - " ASN C 331 " " NAG C1306 " - " ASN C 343 " " NAG C1308 " - " ASN C 616 " " NAG C1309 " - " ASN C 657 " " NAG C1310 " - " ASN C 709 " " NAG C1311 " - " ASN C 717 " " NAG D 701 " - " ASN D 322 " " NAG E 701 " - " ASN E 322 " " NAG G 1 " - " ASN A 801 " " NAG I 1 " - " ASN A1134 " " NAG J 1 " - " ASN B 801 " " NAG K 1 " - " ASN B1098 " " NAG L 1 " - " ASN B1134 " " NAG M 1 " - " ASN C 801 " " NAG N 1 " - " ASN C1098 " " NAG O 1 " - " ASN C1134 " " NAG P 1 " - " ASN D 53 " " NAG Q 1 " - " ASN D 90 " " NAG R 1 " - " ASN D 103 " " NAG S 1 " - " ASN D 432 " " NAG T 1 " - " ASN D 546 " " NAG U 1 " - " ASN E 53 " " NAG V 1 " - " ASN E 90 " " NAG W 1 " - " ASN E 103 " " NAG X 1 " - " ASN E 432 " " NAG Y 1 " - " ASN E 546 " " NAG Z 1 " - " ASN F 53 " " NAG a 1 " - " ASN F 90 " " NAG b 1 " - " ASN F 103 " " NAG c 1 " - " ASN F 432 " " NAG d 1 " - " ASN F 546 " Time building additional restraints: 16.33 Conformation dependent library (CDL) restraints added in 7.5 seconds 9300 Ramachandran restraints generated. 4650 Oldfield, 0 Emsley, 4650 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8886 Finding SS restraints... Secondary structure from input PDB file: 166 helices and 51 sheets defined 43.0% alpha, 16.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 5.86 Creating SS restraints... Processing helix chain 'A' and resid 294 through 303 Processing helix chain 'A' and resid 337 through 341 Processing helix chain 'A' and resid 364 through 371 Processing helix chain 'A' and resid 383 through 387 Processing helix chain 'A' and resid 405 through 410 removed outlier: 4.056A pdb=" N ARG A 408 " --> pdb=" O ASP A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 737 through 743 Processing helix chain 'A' and resid 746 through 754 removed outlier: 3.695A pdb=" N LEU A 752 " --> pdb=" O GLU A 748 " (cutoff:3.500A) Processing helix chain 'A' and resid 755 through 757 No H-bonds generated for 'chain 'A' and resid 755 through 757' Processing helix chain 'A' and resid 758 through 783 removed outlier: 4.121A pdb=" N ASP A 775 " --> pdb=" O ALA A 771 " (cutoff:3.500A) Processing helix chain 'A' and resid 801 through 805 removed outlier: 4.554A pdb=" N GLN A 804 " --> pdb=" O ASN A 801 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 825 Processing helix chain 'A' and resid 866 through 885 Processing helix chain 'A' and resid 886 through 891 removed outlier: 3.667A pdb=" N ALA A 890 " --> pdb=" O TRP A 886 " (cutoff:3.500A) Processing helix chain 'A' and resid 897 through 909 removed outlier: 3.522A pdb=" N ALA A 903 " --> pdb=" O ALA A 899 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ILE A 909 " --> pdb=" O ARG A 905 " (cutoff:3.500A) Processing helix chain 'A' and resid 913 through 918 removed outlier: 3.655A pdb=" N TYR A 917 " --> pdb=" O GLN A 913 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 941 Processing helix chain 'A' and resid 942 through 944 No H-bonds generated for 'chain 'A' and resid 942 through 944' Processing helix chain 'A' and resid 945 through 965 removed outlier: 3.740A pdb=" N ASN A 955 " --> pdb=" O VAL A 951 " (cutoff:3.500A) Processing helix chain 'A' and resid 976 through 982 Processing helix chain 'A' and resid 985 through 1033 removed outlier: 4.384A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) removed outlier: 4.363A pdb=" N ARG A 995 " --> pdb=" O VAL A 991 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N LEU A 996 " --> pdb=" O GLN A 992 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N VAL A1033 " --> pdb=" O MET A1029 " (cutoff:3.500A) Processing helix chain 'A' and resid 1127 through 1129 No H-bonds generated for 'chain 'A' and resid 1127 through 1129' Processing helix chain 'A' and resid 1140 through 1147 removed outlier: 4.131A pdb=" N GLU A1144 " --> pdb=" O PRO A1140 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 303 Processing helix chain 'B' and resid 337 through 341 Processing helix chain 'B' and resid 364 through 371 Processing helix chain 'B' and resid 383 through 389 removed outlier: 3.711A pdb=" N LEU B 387 " --> pdb=" O PRO B 384 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ASN B 388 " --> pdb=" O THR B 385 " (cutoff:3.500A) Processing helix chain 'B' and resid 404 through 408 removed outlier: 4.362A pdb=" N ARG B 408 " --> pdb=" O GLY B 404 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 404 through 408' Processing helix chain 'B' and resid 416 through 422 Processing helix chain 'B' and resid 502 through 505 Processing helix chain 'B' and resid 616 through 620 Processing helix chain 'B' and resid 737 through 744 Processing helix chain 'B' and resid 746 through 754 removed outlier: 3.924A pdb=" N LEU B 752 " --> pdb=" O GLU B 748 " (cutoff:3.500A) Processing helix chain 'B' and resid 755 through 757 No H-bonds generated for 'chain 'B' and resid 755 through 757' Processing helix chain 'B' and resid 758 through 783 removed outlier: 3.841A pdb=" N ASP B 775 " --> pdb=" O ALA B 771 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N LYS B 776 " --> pdb=" O VAL B 772 " (cutoff:3.500A) Processing helix chain 'B' and resid 801 through 805 removed outlier: 4.419A pdb=" N GLN B 804 " --> pdb=" O ASN B 801 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 825 Processing helix chain 'B' and resid 866 through 885 Processing helix chain 'B' and resid 886 through 891 removed outlier: 3.664A pdb=" N ALA B 890 " --> pdb=" O TRP B 886 " (cutoff:3.500A) Processing helix chain 'B' and resid 897 through 909 removed outlier: 3.593A pdb=" N ALA B 903 " --> pdb=" O ALA B 899 " (cutoff:3.500A) Processing helix chain 'B' and resid 913 through 918 Processing helix chain 'B' and resid 919 through 941 removed outlier: 3.526A pdb=" N GLN B 935 " --> pdb=" O ILE B 931 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N THR B 941 " --> pdb=" O SER B 937 " (cutoff:3.500A) Processing helix chain 'B' and resid 942 through 944 No H-bonds generated for 'chain 'B' and resid 942 through 944' Processing helix chain 'B' and resid 945 through 965 removed outlier: 3.616A pdb=" N VAL B 951 " --> pdb=" O LYS B 947 " (cutoff:3.500A) Processing helix chain 'B' and resid 976 through 984 removed outlier: 3.751A pdb=" N LEU B 984 " --> pdb=" O ILE B 980 " (cutoff:3.500A) Processing helix chain 'B' and resid 985 through 1032 removed outlier: 4.603A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N SER B1021 " --> pdb=" O GLU B1017 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N LEU B1024 " --> pdb=" O ALA B1020 " (cutoff:3.500A) Processing helix chain 'B' and resid 1140 through 1147 removed outlier: 4.003A pdb=" N GLU B1144 " --> pdb=" O PRO B1140 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 304 Processing helix chain 'C' and resid 338 through 343 Processing helix chain 'C' and resid 364 through 371 removed outlier: 3.976A pdb=" N LEU C 368 " --> pdb=" O ASP C 364 " (cutoff:3.500A) Processing helix chain 'C' and resid 383 through 389 removed outlier: 3.864A pdb=" N ASN C 388 " --> pdb=" O THR C 385 " (cutoff:3.500A) Processing helix chain 'C' and resid 405 through 410 Processing helix chain 'C' and resid 416 through 422 removed outlier: 3.506A pdb=" N ASP C 420 " --> pdb=" O GLY C 416 " (cutoff:3.500A) Processing helix chain 'C' and resid 438 through 443 Processing helix chain 'C' and resid 502 through 505 Processing helix chain 'C' and resid 616 through 620 Processing helix chain 'C' and resid 737 through 743 Processing helix chain 'C' and resid 746 through 754 removed outlier: 4.329A pdb=" N LEU C 752 " --> pdb=" O GLU C 748 " (cutoff:3.500A) Processing helix chain 'C' and resid 755 through 757 No H-bonds generated for 'chain 'C' and resid 755 through 757' Processing helix chain 'C' and resid 758 through 782 removed outlier: 4.058A pdb=" N ASP C 775 " --> pdb=" O ALA C 771 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N LYS C 776 " --> pdb=" O VAL C 772 " (cutoff:3.500A) Processing helix chain 'C' and resid 801 through 805 removed outlier: 4.227A pdb=" N GLN C 804 " --> pdb=" O ASN C 801 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 825 Processing helix chain 'C' and resid 866 through 885 Processing helix chain 'C' and resid 886 through 891 Processing helix chain 'C' and resid 897 through 909 Processing helix chain 'C' and resid 913 through 941 removed outlier: 3.628A pdb=" N TYR C 917 " --> pdb=" O GLN C 913 " (cutoff:3.500A) removed outlier: 5.724A pdb=" N LYS C 921 " --> pdb=" O TYR C 917 " (cutoff:3.500A) removed outlier: 6.484A pdb=" N LEU C 922 " --> pdb=" O GLU C 918 " (cutoff:3.500A) Processing helix chain 'C' and resid 942 through 944 No H-bonds generated for 'chain 'C' and resid 942 through 944' Processing helix chain 'C' and resid 945 through 965 Processing helix chain 'C' and resid 977 through 982 removed outlier: 3.577A pdb=" N LEU C 981 " --> pdb=" O LEU C 977 " (cutoff:3.500A) Processing helix chain 'C' and resid 985 through 1033 removed outlier: 4.816A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N ARG C 995 " --> pdb=" O VAL C 991 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N THR C 998 " --> pdb=" O ASP C 994 " (cutoff:3.500A) Processing helix chain 'C' and resid 1140 through 1147 removed outlier: 4.011A pdb=" N GLU C1144 " --> pdb=" O PRO C1140 " (cutoff:3.500A) Processing helix chain 'D' and resid 22 through 53 removed outlier: 5.449A pdb=" N ASP D 38 " --> pdb=" O HIS D 34 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N LEU D 39 " --> pdb=" O GLU D 35 " (cutoff:3.500A) Processing helix chain 'D' and resid 55 through 82 removed outlier: 4.199A pdb=" N ALA D 65 " --> pdb=" O ASN D 61 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N GLU D 75 " --> pdb=" O ALA D 71 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N THR D 78 " --> pdb=" O LYS D 74 " (cutoff:3.500A) Processing helix chain 'D' and resid 90 through 102 removed outlier: 4.103A pdb=" N GLN D 96 " --> pdb=" O THR D 92 " (cutoff:3.500A) Processing helix chain 'D' and resid 109 through 130 Processing helix chain 'D' and resid 147 through 155 removed outlier: 3.942A pdb=" N ILE D 151 " --> pdb=" O GLY D 147 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N MET D 152 " --> pdb=" O LEU D 148 " (cutoff:3.500A) Processing helix chain 'D' and resid 157 through 172 removed outlier: 3.699A pdb=" N ARG D 169 " --> pdb=" O TRP D 165 " (cutoff:3.500A) Processing helix chain 'D' and resid 172 through 194 removed outlier: 4.044A pdb=" N LEU D 176 " --> pdb=" O VAL D 172 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N ARG D 177 " --> pdb=" O GLY D 173 " (cutoff:3.500A) Proline residue: D 178 - end of helix removed outlier: 3.665A pdb=" N GLU D 182 " --> pdb=" O PRO D 178 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N VAL D 185 " --> pdb=" O GLU D 181 " (cutoff:3.500A) Processing helix chain 'D' and resid 198 through 205 removed outlier: 3.621A pdb=" N TYR D 202 " --> pdb=" O ASP D 198 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N TRP D 203 " --> pdb=" O TYR D 199 " (cutoff:3.500A) Processing helix chain 'D' and resid 206 through 208 No H-bonds generated for 'chain 'D' and resid 206 through 208' Processing helix chain 'D' and resid 220 through 252 removed outlier: 3.744A pdb=" N GLU D 231 " --> pdb=" O GLU D 227 " (cutoff:3.500A) removed outlier: 4.685A pdb=" N GLU D 232 " --> pdb=" O HIS D 228 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N ILE D 233 " --> pdb=" O THR D 229 " (cutoff:3.500A) Proline residue: D 235 - end of helix removed outlier: 3.953A pdb=" N HIS D 239 " --> pdb=" O PRO D 235 " (cutoff:3.500A) removed outlier: 4.111A pdb=" N ASN D 250 " --> pdb=" O ALA D 246 " (cutoff:3.500A) Processing helix chain 'D' and resid 265 through 267 No H-bonds generated for 'chain 'D' and resid 265 through 267' Processing helix chain 'D' and resid 274 through 277 removed outlier: 4.551A pdb=" N ASN D 277 " --> pdb=" O PHE D 274 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 274 through 277' Processing helix chain 'D' and resid 278 through 283 Processing helix chain 'D' and resid 293 through 300 removed outlier: 3.767A pdb=" N GLN D 300 " --> pdb=" O ALA D 296 " (cutoff:3.500A) Processing helix chain 'D' and resid 303 through 319 removed outlier: 4.108A pdb=" N PHE D 314 " --> pdb=" O GLU D 310 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N PHE D 315 " --> pdb=" O ALA D 311 " (cutoff:3.500A) Processing helix chain 'D' and resid 326 through 331 Processing helix chain 'D' and resid 365 through 383 Processing helix chain 'D' and resid 384 through 388 removed outlier: 4.476A pdb=" N ALA D 387 " --> pdb=" O ALA D 384 " (cutoff:3.500A) Processing helix chain 'D' and resid 389 through 393 Processing helix chain 'D' and resid 399 through 413 removed outlier: 4.021A pdb=" N GLY D 405 " --> pdb=" O HIS D 401 " (cutoff:3.500A) removed outlier: 4.442A pdb=" N MET D 408 " --> pdb=" O VAL D 404 " (cutoff:3.500A) removed outlier: 4.226A pdb=" N SER D 409 " --> pdb=" O GLY D 405 " (cutoff:3.500A) Processing helix chain 'D' and resid 414 through 421 Processing helix chain 'D' and resid 431 through 447 removed outlier: 3.845A pdb=" N LYS D 441 " --> pdb=" O ASN D 437 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N THR D 445 " --> pdb=" O LYS D 441 " (cutoff:3.500A) Processing helix chain 'D' and resid 448 through 466 removed outlier: 4.653A pdb=" N PHE D 452 " --> pdb=" O GLY D 448 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N LYS D 465 " --> pdb=" O TRP D 461 " (cutoff:3.500A) Processing helix chain 'D' and resid 472 through 484 removed outlier: 3.654A pdb=" N TRP D 478 " --> pdb=" O MET D 474 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N GLU D 479 " --> pdb=" O LYS D 475 " (cutoff:3.500A) Processing helix chain 'D' and resid 499 through 502 Processing helix chain 'D' and resid 503 through 508 Processing helix chain 'D' and resid 512 through 533 removed outlier: 4.047A pdb=" N TYR D 516 " --> pdb=" O PHE D 512 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N PHE D 523 " --> pdb=" O THR D 519 " (cutoff:3.500A) Processing helix chain 'D' and resid 538 through 542 Processing helix chain 'D' and resid 547 through 559 removed outlier: 3.769A pdb=" N GLY D 551 " --> pdb=" O SER D 547 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N LEU D 554 " --> pdb=" O ALA D 550 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N MET D 557 " --> pdb=" O LYS D 553 " (cutoff:3.500A) Processing helix chain 'D' and resid 565 through 574 removed outlier: 3.746A pdb=" N GLU D 571 " --> pdb=" O THR D 567 " (cutoff:3.500A) Processing helix chain 'D' and resid 581 through 599 removed outlier: 3.621A pdb=" N PHE D 588 " --> pdb=" O LEU D 584 " (cutoff:3.500A) Proline residue: D 590 - end of helix removed outlier: 3.954A pdb=" N TRP D 594 " --> pdb=" O PRO D 590 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N ASP D 597 " --> pdb=" O THR D 593 " (cutoff:3.500A) Processing helix chain 'E' and resid 22 through 53 removed outlier: 4.045A pdb=" N GLU E 37 " --> pdb=" O ASN E 33 " (cutoff:3.500A) removed outlier: 4.686A pdb=" N ASP E 38 " --> pdb=" O HIS E 34 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N LEU E 39 " --> pdb=" O GLU E 35 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N ALA E 46 " --> pdb=" O GLN E 42 " (cutoff:3.500A) Processing helix chain 'E' and resid 55 through 81 removed outlier: 3.655A pdb=" N LYS E 68 " --> pdb=" O ASN E 64 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N GLU E 75 " --> pdb=" O ALA E 71 " (cutoff:3.500A) Processing helix chain 'E' and resid 82 through 83 No H-bonds generated for 'chain 'E' and resid 82 through 83' Processing helix chain 'E' and resid 84 through 88 Processing helix chain 'E' and resid 90 through 102 removed outlier: 3.567A pdb=" N GLN E 102 " --> pdb=" O GLN E 98 " (cutoff:3.500A) Processing helix chain 'E' and resid 109 through 130 Processing helix chain 'E' and resid 147 through 155 removed outlier: 3.523A pdb=" N MET E 152 " --> pdb=" O LEU E 148 " (cutoff:3.500A) Processing helix chain 'E' and resid 157 through 172 removed outlier: 3.630A pdb=" N ARG E 169 " --> pdb=" O TRP E 165 " (cutoff:3.500A) Processing helix chain 'E' and resid 172 through 194 removed outlier: 3.920A pdb=" N LEU E 176 " --> pdb=" O VAL E 172 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N ARG E 177 " --> pdb=" O GLY E 173 " (cutoff:3.500A) Proline residue: E 178 - end of helix removed outlier: 4.003A pdb=" N GLU E 182 " --> pdb=" O PRO E 178 " (cutoff:3.500A) removed outlier: 4.497A pdb=" N VAL E 185 " --> pdb=" O GLU E 181 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N ASN E 188 " --> pdb=" O VAL E 184 " (cutoff:3.500A) Processing helix chain 'E' and resid 198 through 205 Processing helix chain 'E' and resid 206 through 208 No H-bonds generated for 'chain 'E' and resid 206 through 208' Processing helix chain 'E' and resid 218 through 252 removed outlier: 3.997A pdb=" N ILE E 223 " --> pdb=" O ARG E 219 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N GLU E 231 " --> pdb=" O GLU E 227 " (cutoff:3.500A) removed outlier: 4.802A pdb=" N GLU E 232 " --> pdb=" O HIS E 228 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N ILE E 233 " --> pdb=" O THR E 229 " (cutoff:3.500A) Proline residue: E 235 - end of helix removed outlier: 3.741A pdb=" N HIS E 239 " --> pdb=" O PRO E 235 " (cutoff:3.500A) removed outlier: 4.156A pdb=" N ASN E 250 " --> pdb=" O ALA E 246 " (cutoff:3.500A) Processing helix chain 'E' and resid 265 through 267 No H-bonds generated for 'chain 'E' and resid 265 through 267' Processing helix chain 'E' and resid 275 through 277 No H-bonds generated for 'chain 'E' and resid 275 through 277' Processing helix chain 'E' and resid 278 through 283 Processing helix chain 'E' and resid 293 through 300 Processing helix chain 'E' and resid 303 through 319 Processing helix chain 'E' and resid 326 through 331 Processing helix chain 'E' and resid 365 through 385 removed outlier: 3.634A pdb=" N TYR E 385 " --> pdb=" O TYR E 381 " (cutoff:3.500A) Processing helix chain 'E' and resid 386 through 388 No H-bonds generated for 'chain 'E' and resid 386 through 388' Processing helix chain 'E' and resid 389 through 393 Processing helix chain 'E' and resid 399 through 414 removed outlier: 4.543A pdb=" N GLY E 405 " --> pdb=" O HIS E 401 " (cutoff:3.500A) removed outlier: 4.552A pdb=" N MET E 408 " --> pdb=" O VAL E 404 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N THR E 414 " --> pdb=" O LEU E 410 " (cutoff:3.500A) Processing helix chain 'E' and resid 414 through 421 Processing helix chain 'E' and resid 431 through 447 removed outlier: 3.863A pdb=" N LYS E 441 " --> pdb=" O ASN E 437 " (cutoff:3.500A) Processing helix chain 'E' and resid 448 through 465 removed outlier: 4.535A pdb=" N PHE E 452 " --> pdb=" O GLY E 448 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N GLU E 457 " --> pdb=" O THR E 453 " (cutoff:3.500A) Processing helix chain 'E' and resid 472 through 484 Processing helix chain 'E' and resid 503 through 508 Processing helix chain 'E' and resid 512 through 533 removed outlier: 4.149A pdb=" N TYR E 516 " --> pdb=" O PHE E 512 " (cutoff:3.500A) removed outlier: 4.592A pdb=" N PHE E 523 " --> pdb=" O THR E 519 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N LEU E 529 " --> pdb=" O PHE E 525 " (cutoff:3.500A) Processing helix chain 'E' and resid 538 through 542 Processing helix chain 'E' and resid 548 through 559 removed outlier: 3.920A pdb=" N LEU E 554 " --> pdb=" O ALA E 550 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N MET E 557 " --> pdb=" O LYS E 553 " (cutoff:3.500A) Processing helix chain 'E' and resid 565 through 574 removed outlier: 4.136A pdb=" N GLU E 571 " --> pdb=" O THR E 567 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ASN E 572 " --> pdb=" O LEU E 568 " (cutoff:3.500A) Processing helix chain 'E' and resid 581 through 587 Processing helix chain 'E' and resid 588 through 599 removed outlier: 3.962A pdb=" N ASP E 597 " --> pdb=" O THR E 593 " (cutoff:3.500A) Processing helix chain 'F' and resid 22 through 51 removed outlier: 3.805A pdb=" N PHE F 28 " --> pdb=" O GLN F 24 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N LEU F 29 " --> pdb=" O ALA F 25 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N ASP F 30 " --> pdb=" O LYS F 26 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N LYS F 31 " --> pdb=" O THR F 27 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N HIS F 34 " --> pdb=" O ASP F 30 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N ASP F 38 " --> pdb=" O HIS F 34 " (cutoff:3.500A) Processing helix chain 'F' and resid 55 through 82 removed outlier: 3.600A pdb=" N THR F 78 " --> pdb=" O LYS F 74 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N LEU F 79 " --> pdb=" O GLU F 75 " (cutoff:3.500A) Processing helix chain 'F' and resid 83 through 88 removed outlier: 6.094A pdb=" N GLN F 86 " --> pdb=" O TYR F 83 " (cutoff:3.500A) Processing helix chain 'F' and resid 90 through 102 Processing helix chain 'F' and resid 109 through 129 Processing helix chain 'F' and resid 147 through 155 removed outlier: 3.557A pdb=" N ILE F 151 " --> pdb=" O GLY F 147 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N MET F 152 " --> pdb=" O LEU F 148 " (cutoff:3.500A) Processing helix chain 'F' and resid 157 through 172 removed outlier: 3.553A pdb=" N ARG F 169 " --> pdb=" O TRP F 165 " (cutoff:3.500A) Processing helix chain 'F' and resid 172 through 194 Proline residue: F 178 - end of helix removed outlier: 3.690A pdb=" N GLU F 182 " --> pdb=" O PRO F 178 " (cutoff:3.500A) removed outlier: 4.109A pdb=" N VAL F 185 " --> pdb=" O GLU F 181 " (cutoff:3.500A) Processing helix chain 'F' and resid 198 through 204 removed outlier: 3.782A pdb=" N TYR F 202 " --> pdb=" O ASP F 198 " (cutoff:3.500A) Processing helix chain 'F' and resid 205 through 208 Processing helix chain 'F' and resid 220 through 252 removed outlier: 4.093A pdb=" N GLU F 224 " --> pdb=" O GLY F 220 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N THR F 229 " --> pdb=" O ASP F 225 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N GLU F 231 " --> pdb=" O GLU F 227 " (cutoff:3.500A) removed outlier: 4.883A pdb=" N GLU F 232 " --> pdb=" O HIS F 228 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N ILE F 233 " --> pdb=" O THR F 229 " (cutoff:3.500A) Proline residue: F 235 - end of helix removed outlier: 4.030A pdb=" N ASN F 250 " --> pdb=" O ALA F 246 " (cutoff:3.500A) Processing helix chain 'F' and resid 265 through 267 No H-bonds generated for 'chain 'F' and resid 265 through 267' Processing helix chain 'F' and resid 274 through 277 removed outlier: 4.524A pdb=" N ASN F 277 " --> pdb=" O PHE F 274 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 274 through 277' Processing helix chain 'F' and resid 278 through 283 Processing helix chain 'F' and resid 293 through 300 removed outlier: 3.604A pdb=" N MET F 297 " --> pdb=" O VAL F 293 " (cutoff:3.500A) Processing helix chain 'F' and resid 303 through 319 removed outlier: 3.682A pdb=" N ALA F 311 " --> pdb=" O ILE F 307 " (cutoff:3.500A) Processing helix chain 'F' and resid 365 through 386 removed outlier: 3.582A pdb=" N HIS F 373 " --> pdb=" O PHE F 369 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N TYR F 381 " --> pdb=" O GLY F 377 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N ALA F 384 " --> pdb=" O GLN F 380 " (cutoff:3.500A) Processing helix chain 'F' and resid 387 through 388 No H-bonds generated for 'chain 'F' and resid 387 through 388' Processing helix chain 'F' and resid 389 through 393 Processing helix chain 'F' and resid 397 through 413 removed outlier: 3.722A pdb=" N HIS F 401 " --> pdb=" O ASN F 397 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N GLU F 402 " --> pdb=" O GLU F 398 " (cutoff:3.500A) removed outlier: 4.154A pdb=" N GLY F 405 " --> pdb=" O HIS F 401 " (cutoff:3.500A) removed outlier: 4.460A pdb=" N MET F 408 " --> pdb=" O VAL F 404 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N SER F 409 " --> pdb=" O GLY F 405 " (cutoff:3.500A) Processing helix chain 'F' and resid 414 through 421 removed outlier: 3.941A pdb=" N SER F 420 " --> pdb=" O LYS F 416 " (cutoff:3.500A) Processing helix chain 'F' and resid 431 through 447 removed outlier: 3.571A pdb=" N GLU F 435 " --> pdb=" O ASP F 431 " (cutoff:3.500A) Processing helix chain 'F' and resid 448 through 465 removed outlier: 4.314A pdb=" N PHE F 452 " --> pdb=" O GLY F 448 " (cutoff:3.500A) Processing helix chain 'F' and resid 469 through 471 No H-bonds generated for 'chain 'F' and resid 469 through 471' Processing helix chain 'F' and resid 472 through 484 removed outlier: 3.848A pdb=" N TRP F 478 " --> pdb=" O MET F 474 " (cutoff:3.500A) Processing helix chain 'F' and resid 499 through 502 Processing helix chain 'F' and resid 503 through 508 Processing helix chain 'F' and resid 512 through 534 removed outlier: 4.043A pdb=" N TYR F 516 " --> pdb=" O PHE F 512 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N THR F 519 " --> pdb=" O TYR F 515 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N LEU F 520 " --> pdb=" O TYR F 516 " (cutoff:3.500A) Processing helix chain 'F' and resid 538 through 542 Processing helix chain 'F' and resid 548 through 559 removed outlier: 3.915A pdb=" N MET F 557 " --> pdb=" O LYS F 553 " (cutoff:3.500A) Processing helix chain 'F' and resid 565 through 572 removed outlier: 4.213A pdb=" N GLU F 571 " --> pdb=" O THR F 567 " (cutoff:3.500A) Processing helix chain 'F' and resid 581 through 598 removed outlier: 3.681A pdb=" N PHE F 588 " --> pdb=" O LEU F 584 " (cutoff:3.500A) Proline residue: F 590 - end of helix removed outlier: 3.837A pdb=" N TRP F 594 " --> pdb=" O PRO F 590 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N ASP F 597 " --> pdb=" O THR F 593 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 28 through 30 removed outlier: 8.179A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 5.462A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 6.089A pdb=" N SER A 205 " --> pdb=" O PRO A 225 " (cutoff:3.500A) removed outlier: 9.349A pdb=" N HIS A 207 " --> pdb=" O LEU A 223 " (cutoff:3.500A) removed outlier: 9.594A pdb=" N LEU A 223 " --> pdb=" O HIS A 207 " (cutoff:3.500A) removed outlier: 6.963A pdb=" N VAL A 36 " --> pdb=" O LEU A 223 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 42 through 43 removed outlier: 5.542A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) removed outlier: 7.153A pdb=" N GLU B 324 " --> pdb=" O ASN B 540 " (cutoff:3.500A) removed outlier: 7.987A pdb=" N ASN B 542 " --> pdb=" O GLU B 324 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 47 through 55 removed outlier: 3.750A pdb=" N ASP A 53 " --> pdb=" O ARG A 273 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 84 through 85 Processing sheet with id=AA5, first strand: chain 'A' and resid 311 through 319 removed outlier: 6.755A pdb=" N VAL A 595 " --> pdb=" O THR A 315 " (cutoff:3.500A) removed outlier: 4.533A pdb=" N ASN A 317 " --> pdb=" O GLY A 593 " (cutoff:3.500A) removed outlier: 5.998A pdb=" N GLY A 593 " --> pdb=" O ASN A 317 " (cutoff:3.500A) removed outlier: 4.717A pdb=" N GLY A 594 " --> pdb=" O GLN A 613 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 325 through 328 removed outlier: 5.949A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 5.469A pdb=" N THR A 573 " --> pdb=" O ASP A 568 " (cutoff:3.500A) removed outlier: 6.412A pdb=" N ASP A 568 " --> pdb=" O THR A 573 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N ALA A 575 " --> pdb=" O GLY A 566 " (cutoff:3.500A) removed outlier: 6.671A pdb=" N PHE A 565 " --> pdb=" O PHE C 43 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 354 through 358 removed outlier: 3.648A pdb=" N ASN A 354 " --> pdb=" O SER A 399 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 361 through 362 removed outlier: 6.584A pdb=" N CYS A 361 " --> pdb=" O CYS A 525 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AB1, first strand: chain 'A' and resid 654 through 655 removed outlier: 5.844A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.239A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 6.581A pdb=" N ILE A 670 " --> pdb=" O ILE A 666 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 702 through 704 removed outlier: 6.500A pdb=" N ASN A 703 " --> pdb=" O LYS C 790 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'A' and resid 711 through 715 removed outlier: 3.915A pdb=" N ALA A1078 " --> pdb=" O PHE A1095 " (cutoff:3.500A) removed outlier: 4.512A pdb=" N PHE A1095 " --> pdb=" O ALA A1078 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 718 through 728 removed outlier: 6.077A pdb=" N TYR A1067 " --> pdb=" O HIS A1048 " (cutoff:3.500A) removed outlier: 5.524A pdb=" N HIS A1048 " --> pdb=" O TYR A1067 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 733 through 736 removed outlier: 4.389A pdb=" N LYS A 733 " --> pdb=" O LEU A 861 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 788 through 790 Processing sheet with id=AB7, first strand: chain 'A' and resid 1120 through 1125 removed outlier: 4.136A pdb=" N ALA A1087 " --> pdb=" O SER A1123 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 28 through 30 removed outlier: 8.784A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 6.371A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 4.128A pdb=" N ALA B 264 " --> pdb=" O THR B 95 " (cutoff:3.500A) removed outlier: 6.057A pdb=" N SER B 205 " --> pdb=" O PRO B 225 " (cutoff:3.500A) removed outlier: 9.438A pdb=" N HIS B 207 " --> pdb=" O LEU B 223 " (cutoff:3.500A) removed outlier: 9.385A pdb=" N LEU B 223 " --> pdb=" O HIS B 207 " (cutoff:3.500A) removed outlier: 7.252A pdb=" N VAL B 36 " --> pdb=" O LEU B 223 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 42 through 43 removed outlier: 5.431A pdb=" N ASP C 574 " --> pdb=" O ILE C 587 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 47 through 55 removed outlier: 7.408A pdb=" N THR B 274 " --> pdb=" O ASP B 290 " (cutoff:3.500A) removed outlier: 5.037A pdb=" N ASP B 290 " --> pdb=" O THR B 274 " (cutoff:3.500A) removed outlier: 6.556A pdb=" N LEU B 276 " --> pdb=" O ALA B 288 " (cutoff:3.500A) removed outlier: 4.334A pdb=" N ALA B 288 " --> pdb=" O LEU B 276 " (cutoff:3.500A) removed outlier: 6.662A pdb=" N LYS B 278 " --> pdb=" O THR B 286 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 83 through 85 Processing sheet with id=AC3, first strand: chain 'B' and resid 311 through 319 removed outlier: 6.920A pdb=" N VAL B 595 " --> pdb=" O THR B 315 " (cutoff:3.500A) removed outlier: 4.671A pdb=" N ASN B 317 " --> pdb=" O GLY B 593 " (cutoff:3.500A) removed outlier: 6.252A pdb=" N GLY B 593 " --> pdb=" O ASN B 317 " (cutoff:3.500A) removed outlier: 4.295A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 354 through 358 Processing sheet with id=AC5, first strand: chain 'B' and resid 361 through 362 removed outlier: 6.566A pdb=" N CYS B 361 " --> pdb=" O CYS B 525 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AC7, first strand: chain 'B' and resid 654 through 655 removed outlier: 6.202A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.350A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 6.801A pdb=" N ILE B 670 " --> pdb=" O ILE B 666 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 711 through 715 removed outlier: 4.026A pdb=" N ALA B1078 " --> pdb=" O PHE B1095 " (cutoff:3.500A) removed outlier: 4.587A pdb=" N PHE B1095 " --> pdb=" O ALA B1078 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 718 through 728 removed outlier: 5.870A pdb=" N TYR B1067 " --> pdb=" O HIS B1048 " (cutoff:3.500A) removed outlier: 5.464A pdb=" N HIS B1048 " --> pdb=" O TYR B1067 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 734 through 736 Processing sheet with id=AD2, first strand: chain 'B' and resid 789 through 790 Processing sheet with id=AD3, first strand: chain 'B' and resid 1120 through 1123 Processing sheet with id=AD4, first strand: chain 'C' and resid 28 through 30 removed outlier: 8.972A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 6.200A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 7.215A pdb=" N PHE C 201 " --> pdb=" O ASP C 228 " (cutoff:3.500A) removed outlier: 4.787A pdb=" N ASP C 228 " --> pdb=" O PHE C 201 " (cutoff:3.500A) removed outlier: 6.748A pdb=" N ILE C 203 " --> pdb=" O LEU C 226 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'C' and resid 48 through 55 removed outlier: 3.516A pdb=" N ASP C 53 " --> pdb=" O ARG C 273 " (cutoff:3.500A) removed outlier: 7.567A pdb=" N THR C 274 " --> pdb=" O ASP C 290 " (cutoff:3.500A) removed outlier: 5.204A pdb=" N ASP C 290 " --> pdb=" O THR C 274 " (cutoff:3.500A) removed outlier: 6.510A pdb=" N LEU C 276 " --> pdb=" O ALA C 288 " (cutoff:3.500A) removed outlier: 4.398A pdb=" N ALA C 288 " --> pdb=" O LEU C 276 " (cutoff:3.500A) removed outlier: 7.030A pdb=" N LYS C 278 " --> pdb=" O THR C 286 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 83 through 85 removed outlier: 3.528A pdb=" N GLY C 103 " --> pdb=" O LEU C 241 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N ASN C 125 " --> pdb=" O ASN C 122 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 311 through 319 removed outlier: 5.392A pdb=" N ILE C 312 " --> pdb=" O THR C 599 " (cutoff:3.500A) removed outlier: 7.383A pdb=" N THR C 599 " --> pdb=" O ILE C 312 " (cutoff:3.500A) removed outlier: 5.676A pdb=" N GLN C 314 " --> pdb=" O VAL C 597 " (cutoff:3.500A) removed outlier: 6.797A pdb=" N VAL C 597 " --> pdb=" O GLN C 314 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N SER C 316 " --> pdb=" O VAL C 595 " (cutoff:3.500A) removed outlier: 4.466A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 354 through 358 Processing sheet with id=AD9, first strand: chain 'C' and resid 391 through 392 Processing sheet with id=AE1, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AE2, first strand: chain 'C' and resid 654 through 655 removed outlier: 5.987A pdb=" N GLU C 654 " --> pdb=" O ALA C 694 " (cutoff:3.500A) removed outlier: 8.631A pdb=" N THR C 696 " --> pdb=" O GLU C 654 " (cutoff:3.500A) removed outlier: 6.437A pdb=" N ILE C 670 " --> pdb=" O ILE C 666 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 711 through 728 removed outlier: 6.627A pdb=" N GLN C1071 " --> pdb=" O THR C 716 " (cutoff:3.500A) removed outlier: 6.328A pdb=" N PHE C 718 " --> pdb=" O PRO C1069 " (cutoff:3.500A) removed outlier: 6.825A pdb=" N ILE C 720 " --> pdb=" O TYR C1067 " (cutoff:3.500A) removed outlier: 6.906A pdb=" N TYR C1067 " --> pdb=" O ILE C 720 " (cutoff:3.500A) removed outlier: 6.729A pdb=" N VAL C 722 " --> pdb=" O VAL C1065 " (cutoff:3.500A) removed outlier: 6.697A pdb=" N VAL C1065 " --> pdb=" O VAL C 722 " (cutoff:3.500A) removed outlier: 6.712A pdb=" N THR C 724 " --> pdb=" O LEU C1063 " (cutoff:3.500A) removed outlier: 6.915A pdb=" N LEU C1063 " --> pdb=" O THR C 724 " (cutoff:3.500A) removed outlier: 6.711A pdb=" N ILE C 726 " --> pdb=" O VAL C1061 " (cutoff:3.500A) removed outlier: 6.757A pdb=" N VAL C1061 " --> pdb=" O ILE C 726 " (cutoff:3.500A) removed outlier: 6.214A pdb=" N GLY C1059 " --> pdb=" O PRO C 728 " (cutoff:3.500A) removed outlier: 6.053A pdb=" N TYR C1067 " --> pdb=" O HIS C1048 " (cutoff:3.500A) removed outlier: 5.652A pdb=" N HIS C1048 " --> pdb=" O TYR C1067 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 733 through 736 removed outlier: 4.462A pdb=" N LYS C 733 " --> pdb=" O LEU C 861 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 1120 through 1125 removed outlier: 3.633A pdb=" N ALA C1087 " --> pdb=" O SER C1123 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 1094 through 1097 Processing sheet with id=AE7, first strand: chain 'D' and resid 132 through 133 Processing sheet with id=AE8, first strand: chain 'D' and resid 262 through 263 removed outlier: 6.130A pdb=" N LEU D 262 " --> pdb=" O VAL D 488 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE8 Processing sheet with id=AE9, first strand: chain 'D' and resid 347 through 350 Processing sheet with id=AF1, first strand: chain 'E' and resid 132 through 133 Processing sheet with id=AF2, first strand: chain 'E' and resid 262 through 263 removed outlier: 6.180A pdb=" N LEU E 262 " --> pdb=" O VAL E 488 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF2 Processing sheet with id=AF3, first strand: chain 'E' and resid 347 through 350 Processing sheet with id=AF4, first strand: chain 'F' and resid 131 through 133 Processing sheet with id=AF5, first strand: chain 'F' and resid 262 through 263 removed outlier: 6.101A pdb=" N LEU F 262 " --> pdb=" O VAL F 488 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF5 Processing sheet with id=AF6, first strand: chain 'F' and resid 347 through 350 1738 hydrogen bonds defined for protein. 4878 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: 15.98 Time building geometry restraints manager: 17.62 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.30: 6459 1.30 - 1.44: 10822 1.44 - 1.57: 22095 1.57 - 1.71: 39 1.71 - 1.84: 279 Bond restraints: 39694 Sorted by residual: bond pdb=" CG ASN C 717 " pdb=" ND2 ASN C 717 " ideal model delta sigma weight residual 1.328 1.203 0.125 2.10e-02 2.27e+03 3.53e+01 bond pdb=" CG ASN A 122 " pdb=" ND2 ASN A 122 " ideal model delta sigma weight residual 1.328 1.447 -0.119 2.10e-02 2.27e+03 3.23e+01 bond pdb=" CA CYS A 480 " pdb=" C CYS A 480 " ideal model delta sigma weight residual 1.519 1.581 -0.062 1.14e-02 7.69e+03 2.94e+01 bond pdb=" N CYS C 488 " pdb=" CA CYS C 488 " ideal model delta sigma weight residual 1.457 1.521 -0.064 1.24e-02 6.50e+03 2.68e+01 bond pdb=" N ASN C 343 " pdb=" CA ASN C 343 " ideal model delta sigma weight residual 1.458 1.513 -0.056 1.22e-02 6.72e+03 2.07e+01 ... (remaining 39689 not shown) Histogram of bond angle deviations from ideal: 96.64 - 104.43: 554 104.43 - 112.21: 16653 112.21 - 120.00: 18985 120.00 - 127.79: 17476 127.79 - 135.57: 291 Bond angle restraints: 53959 Sorted by residual: angle pdb=" N ARG B1107 " pdb=" CA ARG B1107 " pdb=" C ARG B1107 " ideal model delta sigma weight residual 111.71 122.03 -10.32 1.15e+00 7.56e-01 8.05e+01 angle pdb=" N SER F 547 " pdb=" CA SER F 547 " pdb=" C SER F 547 " ideal model delta sigma weight residual 112.89 123.32 -10.43 1.24e+00 6.50e-01 7.08e+01 angle pdb=" N ARG A1107 " pdb=" CA ARG A1107 " pdb=" C ARG A1107 " ideal model delta sigma weight residual 112.54 121.68 -9.14 1.22e+00 6.72e-01 5.61e+01 angle pdb=" N SER A 60 " pdb=" CA SER A 60 " pdb=" C SER A 60 " ideal model delta sigma weight residual 109.95 120.68 -10.73 1.44e+00 4.82e-01 5.56e+01 angle pdb=" N ARG C1107 " pdb=" CA ARG C1107 " pdb=" C ARG C1107 " ideal model delta sigma weight residual 111.75 121.22 -9.47 1.28e+00 6.10e-01 5.48e+01 ... (remaining 53954 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.00: 22487 18.00 - 35.99: 1698 35.99 - 53.99: 376 53.99 - 71.98: 105 71.98 - 89.98: 67 Dihedral angle restraints: 24733 sinusoidal: 10948 harmonic: 13785 Sorted by residual: dihedral pdb=" CB CYS B1032 " pdb=" SG CYS B1032 " pdb=" SG CYS B1043 " pdb=" CB CYS B1043 " ideal model delta sinusoidal sigma weight residual -86.00 -172.94 86.94 1 1.00e+01 1.00e-02 9.09e+01 dihedral pdb=" CB CYS A1032 " pdb=" SG CYS A1032 " pdb=" SG CYS A1043 " pdb=" CB CYS A1043 " ideal model delta sinusoidal sigma weight residual -86.00 -170.78 84.78 1 1.00e+01 1.00e-02 8.73e+01 dihedral pdb=" CB CYS E 133 " pdb=" SG CYS E 133 " pdb=" SG CYS E 141 " pdb=" CB CYS E 141 " ideal model delta sinusoidal sigma weight residual 93.00 9.52 83.48 1 1.00e+01 1.00e-02 8.51e+01 ... (remaining 24730 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.958: 6192 0.958 - 1.917: 3 1.917 - 2.875: 1 2.875 - 3.833: 0 3.833 - 4.792: 2 Chirality restraints: 6198 Sorted by residual: chirality pdb=" C1 NAG C1311 " pdb=" ND2 ASN C 717 " pdb=" C2 NAG C1311 " pdb=" O5 NAG C1311 " both_signs ideal model delta sigma weight residual False -2.40 2.39 -4.79 2.00e-01 2.50e+01 5.74e+02 chirality pdb=" C1 NAG C1309 " pdb=" ND2 ASN C 657 " pdb=" C2 NAG C1309 " pdb=" O5 NAG C1309 " both_signs ideal model delta sigma weight residual False -2.40 1.51 -3.91 2.00e-01 2.50e+01 3.82e+02 chirality pdb=" C1 NAG O 1 " pdb=" ND2 ASN C1134 " pdb=" C2 NAG O 1 " pdb=" O5 NAG O 1 " both_signs ideal model delta sigma weight residual False -2.40 0.05 -2.45 2.00e-01 2.50e+01 1.51e+02 ... (remaining 6195 not shown) Planarity restraints: 6912 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN D 546 " 0.261 2.00e-02 2.50e+03 3.07e-01 1.18e+03 pdb=" CG ASN D 546 " -0.093 2.00e-02 2.50e+03 pdb=" OD1 ASN D 546 " -0.004 2.00e-02 2.50e+03 pdb=" ND2 ASN D 546 " -0.519 2.00e-02 2.50e+03 pdb=" C1 NAG T 1 " 0.354 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG R 2 " -0.353 2.00e-02 2.50e+03 3.05e-01 1.16e+03 pdb=" C7 NAG R 2 " 0.084 2.00e-02 2.50e+03 pdb=" C8 NAG R 2 " -0.107 2.00e-02 2.50e+03 pdb=" N2 NAG R 2 " 0.543 2.00e-02 2.50e+03 pdb=" O7 NAG R 2 " -0.167 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN B 616 " 0.076 2.00e-02 2.50e+03 2.79e-01 9.72e+02 pdb=" CG ASN B 616 " -0.082 2.00e-02 2.50e+03 pdb=" OD1 ASN B 616 " 0.158 2.00e-02 2.50e+03 pdb=" ND2 ASN B 616 " -0.488 2.00e-02 2.50e+03 pdb=" C1 NAG B1308 " 0.336 2.00e-02 2.50e+03 ... (remaining 6909 not shown) Histogram of nonbonded interaction distances: 1.90 - 2.50: 53 2.50 - 3.10: 25699 3.10 - 3.70: 57619 3.70 - 4.30: 88235 4.30 - 4.90: 142912 Nonbonded interactions: 314518 Sorted by model distance: nonbonded pdb=" OD1 ASN B1134 " pdb=" C1 NAG L 1 " model vdw 1.904 2.776 nonbonded pdb=" NE2 GLN C 115 " pdb=" O ASN C 165 " model vdw 1.957 2.520 nonbonded pdb=" ND2 ASN C 603 " pdb=" O5 NAG C1307 " model vdw 1.970 2.520 nonbonded pdb=" ND2 ASN C 165 " pdb=" C1 NAG C1313 " model vdw 1.991 3.550 nonbonded pdb=" ND2 ASN B 603 " pdb=" C1 NAG B1307 " model vdw 1.992 3.550 ... (remaining 314513 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 27 through 223 or (resid 224 and (name N or name CA or nam \ e C or name O or name CB )) or resid 225 through 1147 or resid 1301 through 1313 \ )) selection = (chain 'B' and (resid 27 through 124 or (resid 125 and (name N or name CA or nam \ e C or name O or name CB )) or resid 126 through 223 or (resid 224 and (name N o \ r name CA or name C or name O or name CB )) or resid 225 through 505 or (resid 5 \ 06 and (name N or name CA or name C or name O or name CB )) or resid 507 through \ 1147 or resid 1301 through 1313)) selection = (chain 'C' and (resid 27 through 124 or (resid 125 and (name N or name CA or nam \ e C or name O or name CB )) or resid 126 through 505 or (resid 506 and (name N o \ r name CA or name C or name O or name CB )) or resid 507 through 1147 or resid 1 \ 301 through 1313)) } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'F' } ncs_group { reference = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' selection = chain 'U' selection = chain 'V' selection = chain 'W' selection = chain 'X' selection = chain 'Y' selection = chain 'Z' selection = chain 'a' selection = chain 'b' selection = chain 'c' selection = chain 'd' } 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 7.890 Set stop_for_unknowns flag: 0.010 Assert model is a single copy model: 0.010 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.040 Extract box with map and model: 25.200 Check model and map are aligned: 0.580 Set scattering table: 0.330 Process input model: 103.640 Find NCS groups from input model: 2.410 Set up NCS constraints: 0.590 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.960 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 143.670 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6996 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 : 0.014 0.125 39694 Z= 0.876 Angle : 1.836 12.635 53959 Z= 1.231 Chirality : 0.141 4.792 6198 Planarity : 0.014 0.305 6858 Dihedral : 14.391 89.981 15703 Min Nonbonded Distance : 1.904 Molprobity Statistics. All-atom Clashscore : 4.94 Ramachandran Plot: Outliers : 0.52 % Allowed : 6.09 % Favored : 93.40 % Rotamer: Outliers : 2.36 % Allowed : 4.43 % Favored : 93.20 % Cbeta Deviations : 0.32 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.39 (0.11), residues: 4650 helix: -2.20 (0.09), residues: 1697 sheet: 0.38 (0.22), residues: 492 loop : -1.50 (0.12), residues: 2461 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.184 0.029 TRP D 349 HIS 0.014 0.004 HIS A1088 PHE 0.100 0.016 PHE A 592 TYR 0.119 0.021 TYR B 380 ARG 0.015 0.001 ARG D 460 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9300 Ramachandran restraints generated. 4650 Oldfield, 0 Emsley, 4650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9300 Ramachandran restraints generated. 4650 Oldfield, 0 Emsley, 4650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 850 residues out of total 4152 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 98 poor density : 752 time to evaluate : 4.408 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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 460 ASN cc_start: 0.2970 (OUTLIER) cc_final: 0.2590 (m-40) REVERT: A 1000 ARG cc_start: 0.9040 (OUTLIER) cc_final: 0.8830 (mmt90) REVERT: B 140 PHE cc_start: 0.5461 (p90) cc_final: 0.5108 (p90) REVERT: B 1092 GLU cc_start: 0.6572 (OUTLIER) cc_final: 0.5535 (mt-10) REVERT: C 1101 HIS cc_start: 0.5033 (m90) cc_final: 0.4766 (m170) REVERT: E 140 GLU cc_start: 0.1894 (pt0) cc_final: 0.1398 (tp30) REVERT: E 309 LYS cc_start: 0.6881 (mmtt) cc_final: 0.6538 (tptm) REVERT: E 376 MET cc_start: 0.4190 (ttm) cc_final: 0.3978 (mtp) REVERT: E 446 ILE cc_start: 0.5342 (mm) cc_final: 0.4696 (mm) REVERT: E 557 MET cc_start: 0.5635 (tmm) cc_final: 0.5163 (tmm) REVERT: F 148 LEU cc_start: -0.0449 (tp) cc_final: -0.1553 (tp) REVERT: F 180 TYR cc_start: 0.1822 (t80) cc_final: 0.1504 (t80) REVERT: F 270 MET cc_start: -0.3363 (tpp) cc_final: -0.3787 (tpp) REVERT: F 273 ARG cc_start: 0.0706 (ttt180) cc_final: 0.0185 (mmm-85) REVERT: F 278 LEU cc_start: 0.3771 (mt) cc_final: 0.2856 (tp) REVERT: F 358 ILE cc_start: 0.3482 (mt) cc_final: 0.3240 (mt) REVERT: F 367 ASP cc_start: 0.2153 (t0) cc_final: 0.1923 (m-30) REVERT: F 371 THR cc_start: -0.0491 (m) cc_final: -0.0695 (p) REVERT: F 449 THR cc_start: 0.0249 (OUTLIER) cc_final: 0.0029 (t) REVERT: F 455 MET cc_start: 0.4020 (tmm) cc_final: 0.3545 (tmm) REVERT: F 462 MET cc_start: 0.3010 (mtp) cc_final: 0.2595 (mmt) REVERT: F 539 LEU cc_start: 0.1242 (tp) cc_final: 0.0741 (tp) REVERT: F 560 LEU cc_start: 0.2426 (mt) cc_final: 0.2088 (tt) REVERT: F 582 ARG cc_start: -0.1721 (OUTLIER) cc_final: -0.2146 (mmt90) outliers start: 98 outliers final: 21 residues processed: 836 average time/residue: 0.5286 time to fit residues: 694.0104 Evaluate side-chains 372 residues out of total 4152 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 346 time to evaluate : 4.070 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 403 ARG Chi-restraints excluded: chain A residue 414 GLN Chi-restraints excluded: chain A residue 460 ASN Chi-restraints excluded: chain A residue 466 ARG Chi-restraints excluded: chain A residue 711 SER Chi-restraints excluded: chain A residue 1000 ARG Chi-restraints excluded: chain A residue 1076 THR Chi-restraints excluded: chain B residue 391 CYS Chi-restraints excluded: chain B residue 523 THR Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 1029 MET Chi-restraints excluded: chain B residue 1092 GLU Chi-restraints excluded: chain C residue 88 ASP Chi-restraints excluded: chain C residue 488 CYS Chi-restraints excluded: chain C residue 546 LEU Chi-restraints excluded: chain C residue 1084 ASP Chi-restraints excluded: chain D residue 201 ASP Chi-restraints excluded: chain D residue 318 VAL Chi-restraints excluded: chain D residue 401 HIS Chi-restraints excluded: chain E residue 133 CYS Chi-restraints excluded: chain E residue 361 CYS Chi-restraints excluded: chain E residue 571 GLU Chi-restraints excluded: chain F residue 88 ILE Chi-restraints excluded: chain F residue 449 THR Chi-restraints excluded: chain F residue 485 VAL Chi-restraints excluded: chain F residue 582 ARG Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 471 random chunks: chunk 397 optimal weight: 9.9990 chunk 356 optimal weight: 7.9990 chunk 198 optimal weight: 2.9990 chunk 121 optimal weight: 0.5980 chunk 240 optimal weight: 5.9990 chunk 190 optimal weight: 0.6980 chunk 369 optimal weight: 6.9990 chunk 142 optimal weight: 3.9990 chunk 224 optimal weight: 0.0980 chunk 274 optimal weight: 0.6980 chunk 427 optimal weight: 6.9990 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 437 ASN A 607 GLN A 957 GLN A1048 HIS B 121 ASN B 125 ASN B 207 HIS B 394 ASN ** B 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 460 ASN B 474 GLN ** B 675 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 755 GLN B 779 GLN C 115 GLN C 271 GLN C 501 ASN C 762 GLN C 907 ASN C1005 GLN C1048 HIS C1071 GLN D 42 GLN D 63 ASN D 117 ASN D 154 ASN D 330 ASN D 505 HIS E 58 ASN E 63 ASN E 101 GLN E 121 ASN E 330 ASN E 345 HIS E 373 HIS E 378 HIS E 388 GLN E 417 HIS ** E 472 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 505 HIS E 508 ASN F 63 ASN F 89 GLN F 134 ASN F 149 ASN F 241 HIS ** F 417 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 572 ASN Total number of N/Q/H flips: 44 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7049 moved from start: 0.2888 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 39694 Z= 0.232 Angle : 0.734 12.489 53959 Z= 0.378 Chirality : 0.051 0.964 6198 Planarity : 0.004 0.071 6858 Dihedral : 7.953 59.577 6989 Min Nonbonded Distance : 2.075 Molprobity Statistics. All-atom Clashscore : 7.20 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.23 % Favored : 96.69 % Rotamer: Outliers : 2.34 % Allowed : 9.13 % Favored : 88.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.87 (0.12), residues: 4650 helix: -0.21 (0.12), residues: 1747 sheet: 0.24 (0.20), residues: 616 loop : -1.04 (0.13), residues: 2287 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP F 271 HIS 0.011 0.001 HIS E 505 PHE 0.032 0.002 PHE A 559 TYR 0.033 0.002 TYR F 199 ARG 0.006 0.001 ARG E 192 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9300 Ramachandran restraints generated. 4650 Oldfield, 0 Emsley, 4650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9300 Ramachandran restraints generated. 4650 Oldfield, 0 Emsley, 4650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 499 residues out of total 4152 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 97 poor density : 402 time to evaluate : 4.083 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 200 TYR cc_start: 0.6569 (p90) cc_final: 0.6350 (p90) REVERT: A 313 TYR cc_start: 0.8639 (m-80) cc_final: 0.8287 (m-80) REVERT: A 437 ASN cc_start: -0.0282 (OUTLIER) cc_final: -0.0933 (p0) REVERT: A 460 ASN cc_start: 0.3092 (OUTLIER) cc_final: 0.2633 (m-40) REVERT: A 900 MET cc_start: 0.7328 (mtp) cc_final: 0.7108 (mtp) REVERT: B 140 PHE cc_start: 0.5325 (p90) cc_final: 0.4902 (p90) REVERT: B 170 TYR cc_start: 0.6848 (t80) cc_final: 0.6552 (t80) REVERT: B 786 LYS cc_start: 0.7615 (ptpt) cc_final: 0.7073 (mtmt) REVERT: B 1005 GLN cc_start: 0.8165 (tp40) cc_final: 0.7835 (mm-40) REVERT: D 360 MET cc_start: 0.6169 (tmm) cc_final: 0.5951 (tmm) REVERT: E 82 MET cc_start: 0.3687 (mtt) cc_final: 0.3467 (ttt) REVERT: E 140 GLU cc_start: 0.1761 (pt0) cc_final: 0.1198 (tp30) REVERT: E 221 GLN cc_start: 0.5372 (mm-40) cc_final: 0.5157 (mm-40) REVERT: E 309 LYS cc_start: 0.6862 (mmtt) cc_final: 0.6488 (tptm) REVERT: F 116 LEU cc_start: 0.3205 (mt) cc_final: 0.2760 (mt) REVERT: F 152 MET cc_start: 0.3235 (mmt) cc_final: 0.2918 (mmt) REVERT: F 169 ARG cc_start: 0.1627 (mtt90) cc_final: 0.1337 (mmm160) REVERT: F 270 MET cc_start: -0.3229 (tpp) cc_final: -0.3706 (mtm) REVERT: F 362 THR cc_start: -0.1432 (OUTLIER) cc_final: -0.1664 (m) REVERT: F 366 MET cc_start: 0.1741 (tpt) cc_final: 0.1163 (tpp) REVERT: F 367 ASP cc_start: 0.2104 (t0) cc_final: 0.1883 (m-30) REVERT: F 462 MET cc_start: 0.2643 (mtp) cc_final: 0.2273 (mmt) REVERT: F 474 MET cc_start: 0.1143 (mmm) cc_final: 0.0806 (mmt) outliers start: 97 outliers final: 54 residues processed: 478 average time/residue: 0.5370 time to fit residues: 423.8185 Evaluate side-chains 348 residues out of total 4152 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 291 time to evaluate : 4.412 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 307 THR Chi-restraints excluded: chain A residue 414 GLN Chi-restraints excluded: chain A residue 437 ASN Chi-restraints excluded: chain A residue 460 ASN Chi-restraints excluded: chain A residue 489 TYR Chi-restraints excluded: chain A residue 572 THR Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 747 THR Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 912 THR Chi-restraints excluded: chain A residue 982 SER Chi-restraints excluded: chain A residue 994 ASP Chi-restraints excluded: chain A residue 1076 THR Chi-restraints excluded: chain B residue 326 ILE Chi-restraints excluded: chain B residue 402 ILE Chi-restraints excluded: chain B residue 427 ASP Chi-restraints excluded: chain B residue 565 PHE Chi-restraints excluded: chain B residue 572 THR Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 747 THR Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain B residue 1125 ASN Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 88 ASP Chi-restraints excluded: chain C residue 129 LYS Chi-restraints excluded: chain C residue 131 CYS Chi-restraints excluded: chain C residue 208 THR Chi-restraints excluded: chain C residue 316 SER Chi-restraints excluded: chain C residue 364 ASP Chi-restraints excluded: chain C residue 401 VAL Chi-restraints excluded: chain C residue 867 ASP Chi-restraints excluded: chain C residue 868 GLU Chi-restraints excluded: chain C residue 921 LYS Chi-restraints excluded: chain C residue 939 SER Chi-restraints excluded: chain D residue 28 PHE Chi-restraints excluded: chain D residue 70 SER Chi-restraints excluded: chain D residue 201 ASP Chi-restraints excluded: chain D residue 278 LEU Chi-restraints excluded: chain D residue 401 HIS Chi-restraints excluded: chain D residue 408 MET Chi-restraints excluded: chain D residue 411 SER Chi-restraints excluded: chain D residue 471 ASP Chi-restraints excluded: chain E residue 61 ASN Chi-restraints excluded: chain E residue 91 LEU Chi-restraints excluded: chain E residue 195 HIS Chi-restraints excluded: chain E residue 362 THR Chi-restraints excluded: chain E residue 571 GLU Chi-restraints excluded: chain E residue 589 GLU Chi-restraints excluded: chain F residue 28 PHE Chi-restraints excluded: chain F residue 55 THR Chi-restraints excluded: chain F residue 79 LEU Chi-restraints excluded: chain F residue 344 CYS Chi-restraints excluded: chain F residue 362 THR Chi-restraints excluded: chain F residue 431 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 471 random chunks: chunk 237 optimal weight: 0.0870 chunk 132 optimal weight: 3.9990 chunk 355 optimal weight: 30.0000 chunk 291 optimal weight: 2.9990 chunk 117 optimal weight: 3.9990 chunk 428 optimal weight: 50.0000 chunk 462 optimal weight: 9.9990 chunk 381 optimal weight: 0.7980 chunk 424 optimal weight: 10.0000 chunk 146 optimal weight: 3.9990 chunk 343 optimal weight: 9.9990 overall best weight: 2.3764 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 81 ASN A 207 HIS A 913 GLN ** A1005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1074 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 675 GLN ** B1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1048 HIS C 87 ASN ** C 762 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 895 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 907 ASN C1005 GLN D 49 ASN D 51 ASN ** E 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 76 GLN ** E 340 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 277 ASN ** F 380 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 417 HIS Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7133 moved from start: 0.3432 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.059 39694 Z= 0.312 Angle : 0.672 11.257 53959 Z= 0.344 Chirality : 0.048 0.870 6198 Planarity : 0.004 0.047 6858 Dihedral : 7.246 59.916 6951 Min Nonbonded Distance : 2.169 Molprobity Statistics. All-atom Clashscore : 8.91 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.94 % Favored : 95.98 % Rotamer: Outliers : 2.55 % Allowed : 11.45 % Favored : 86.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.61 (0.12), residues: 4650 helix: 0.23 (0.12), residues: 1739 sheet: 0.14 (0.19), residues: 644 loop : -1.02 (0.13), residues: 2267 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.002 TRP F 271 HIS 0.008 0.001 HIS C1101 PHE 0.021 0.002 PHE C 898 TYR 0.024 0.002 TYR B1067 ARG 0.007 0.001 ARG D 115 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9300 Ramachandran restraints generated. 4650 Oldfield, 0 Emsley, 4650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9300 Ramachandran restraints generated. 4650 Oldfield, 0 Emsley, 4650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 406 residues out of total 4152 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 106 poor density : 300 time to evaluate : 4.674 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: A 269 TYR cc_start: 0.7782 (m-80) cc_final: 0.7390 (m-80) REVERT: A 313 TYR cc_start: 0.8694 (m-80) cc_final: 0.8311 (m-80) REVERT: A 460 ASN cc_start: 0.3383 (OUTLIER) cc_final: 0.2893 (m-40) REVERT: B 170 TYR cc_start: 0.6884 (t80) cc_final: 0.6626 (t80) REVERT: B 1005 GLN cc_start: 0.8217 (tp40) cc_final: 0.7937 (tp40) REVERT: C 61 ASN cc_start: 0.5139 (OUTLIER) cc_final: 0.4339 (p0) REVERT: D 471 ASP cc_start: 0.7484 (OUTLIER) cc_final: 0.7183 (t0) REVERT: E 82 MET cc_start: 0.3900 (mtt) cc_final: 0.3551 (ttt) REVERT: E 140 GLU cc_start: 0.1915 (pt0) cc_final: 0.1276 (tp30) REVERT: E 152 MET cc_start: -0.2686 (mmt) cc_final: -0.3018 (mmt) REVERT: E 221 GLN cc_start: 0.5644 (mm-40) cc_final: 0.5403 (mm-40) REVERT: E 309 LYS cc_start: 0.6900 (mmtt) cc_final: 0.6511 (tptm) REVERT: F 152 MET cc_start: 0.3134 (mmt) cc_final: 0.2825 (mmt) REVERT: F 270 MET cc_start: -0.3011 (tpp) cc_final: -0.3441 (mtm) REVERT: F 455 MET cc_start: 0.3019 (ppp) cc_final: 0.1208 (ttp) REVERT: F 462 MET cc_start: 0.2704 (mtp) cc_final: 0.2411 (mmt) REVERT: F 474 MET cc_start: 0.0871 (mmm) cc_final: 0.0645 (mmt) outliers start: 106 outliers final: 72 residues processed: 380 average time/residue: 0.4980 time to fit residues: 312.9506 Evaluate side-chains 333 residues out of total 4152 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 258 time to evaluate : 4.094 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 81 ASN Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 307 THR Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 414 GLN Chi-restraints excluded: chain A residue 460 ASN Chi-restraints excluded: chain A residue 489 TYR Chi-restraints excluded: chain A residue 533 LEU Chi-restraints excluded: chain A residue 572 THR Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 747 THR Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 855 PHE Chi-restraints excluded: chain A residue 912 THR Chi-restraints excluded: chain A residue 982 SER Chi-restraints excluded: chain A residue 994 ASP Chi-restraints excluded: chain A residue 1076 THR Chi-restraints excluded: chain A residue 1116 THR Chi-restraints excluded: chain A residue 1118 ASP Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain B residue 48 LEU Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 308 VAL Chi-restraints excluded: chain B residue 326 ILE Chi-restraints excluded: chain B residue 367 VAL Chi-restraints excluded: chain B residue 402 ILE Chi-restraints excluded: chain B residue 489 TYR Chi-restraints excluded: chain B residue 523 THR Chi-restraints excluded: chain B residue 565 PHE Chi-restraints excluded: chain B residue 572 THR Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 675 GLN Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 747 THR Chi-restraints excluded: chain B residue 761 THR Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 913 GLN Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain B residue 1125 ASN Chi-restraints excluded: chain C residue 61 ASN Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 88 ASP Chi-restraints excluded: chain C residue 129 LYS Chi-restraints excluded: chain C residue 208 THR Chi-restraints excluded: chain C residue 267 VAL Chi-restraints excluded: chain C residue 316 SER Chi-restraints excluded: chain C residue 401 VAL Chi-restraints excluded: chain C residue 762 GLN Chi-restraints excluded: chain C residue 867 ASP Chi-restraints excluded: chain C residue 868 GLU Chi-restraints excluded: chain C residue 921 LYS Chi-restraints excluded: chain C residue 933 LYS Chi-restraints excluded: chain C residue 939 SER Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain D residue 28 PHE Chi-restraints excluded: chain D residue 70 SER Chi-restraints excluded: chain D residue 201 ASP Chi-restraints excluded: chain D residue 233 ILE Chi-restraints excluded: chain D residue 318 VAL Chi-restraints excluded: chain D residue 401 HIS Chi-restraints excluded: chain D residue 408 MET Chi-restraints excluded: chain D residue 411 SER Chi-restraints excluded: chain D residue 471 ASP Chi-restraints excluded: chain D residue 597 ASP Chi-restraints excluded: chain E residue 61 ASN Chi-restraints excluded: chain E residue 111 ASP Chi-restraints excluded: chain E residue 195 HIS Chi-restraints excluded: chain E residue 240 LEU Chi-restraints excluded: chain E residue 571 GLU Chi-restraints excluded: chain F residue 28 PHE Chi-restraints excluded: chain F residue 79 LEU Chi-restraints excluded: chain F residue 339 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 471 random chunks: chunk 423 optimal weight: 4.9990 chunk 322 optimal weight: 3.9990 chunk 222 optimal weight: 3.9990 chunk 47 optimal weight: 9.9990 chunk 204 optimal weight: 0.9980 chunk 287 optimal weight: 0.5980 chunk 430 optimal weight: 30.0000 chunk 455 optimal weight: 40.0000 chunk 224 optimal weight: 0.2980 chunk 407 optimal weight: 0.1980 chunk 122 optimal weight: 2.9990 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 81 ASN ** A 762 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 675 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1010 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 762 GLN C 907 ASN C1005 GLN ** E 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 340 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 380 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7089 moved from start: 0.3770 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.096 39694 Z= 0.193 Angle : 0.595 10.633 53959 Z= 0.304 Chirality : 0.045 0.686 6198 Planarity : 0.004 0.041 6858 Dihedral : 6.637 59.987 6951 Min Nonbonded Distance : 2.138 Molprobity Statistics. All-atom Clashscore : 8.50 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.53 % Favored : 96.39 % Rotamer: Outliers : 2.39 % Allowed : 12.46 % Favored : 85.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.32 (0.12), residues: 4650 helix: 0.53 (0.12), residues: 1765 sheet: 0.20 (0.19), residues: 645 loop : -0.90 (0.13), residues: 2240 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP C 436 HIS 0.004 0.001 HIS D 34 PHE 0.022 0.002 PHE B 429 TYR 0.027 0.001 TYR B 495 ARG 0.013 0.000 ARG F 169 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9300 Ramachandran restraints generated. 4650 Oldfield, 0 Emsley, 4650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9300 Ramachandran restraints generated. 4650 Oldfield, 0 Emsley, 4650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 401 residues out of total 4152 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 99 poor density : 302 time to evaluate : 4.310 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 269 TYR cc_start: 0.7743 (m-80) cc_final: 0.7220 (m-80) REVERT: A 313 TYR cc_start: 0.8657 (m-80) cc_final: 0.8245 (m-80) REVERT: A 460 ASN cc_start: 0.3358 (OUTLIER) cc_final: 0.2925 (m-40) REVERT: B 170 TYR cc_start: 0.6889 (t80) cc_final: 0.6674 (t80) REVERT: B 1005 GLN cc_start: 0.8127 (tp40) cc_final: 0.7893 (tp40) REVERT: C 61 ASN cc_start: 0.5230 (OUTLIER) cc_final: 0.4358 (p0) REVERT: D 62 MET cc_start: 0.5988 (ppp) cc_final: 0.5749 (ppp) REVERT: D 79 LEU cc_start: 0.7633 (mt) cc_final: 0.7207 (tp) REVERT: D 345 HIS cc_start: 0.6893 (t70) cc_final: 0.6235 (t70) REVERT: E 42 GLN cc_start: 0.5980 (OUTLIER) cc_final: 0.5726 (tm-30) REVERT: E 100 LEU cc_start: 0.5246 (tp) cc_final: 0.4558 (mt) REVERT: E 221 GLN cc_start: 0.5688 (mm-40) cc_final: 0.5399 (mm-40) REVERT: E 224 GLU cc_start: 0.3715 (OUTLIER) cc_final: 0.3286 (tm-30) REVERT: E 309 LYS cc_start: 0.6893 (mmtt) cc_final: 0.6529 (tptp) REVERT: F 152 MET cc_start: 0.3085 (mmt) cc_final: 0.2716 (mmt) REVERT: F 366 MET cc_start: 0.1758 (tpt) cc_final: 0.1426 (tpt) REVERT: F 455 MET cc_start: 0.2857 (ppp) cc_final: 0.1995 (ttp) REVERT: F 462 MET cc_start: 0.2750 (mtp) cc_final: 0.2430 (mmt) outliers start: 99 outliers final: 61 residues processed: 380 average time/residue: 0.5032 time to fit residues: 317.0804 Evaluate side-chains 335 residues out of total 4152 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 270 time to evaluate : 4.169 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 ASP Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 307 THR Chi-restraints excluded: chain A residue 414 GLN Chi-restraints excluded: chain A residue 460 ASN Chi-restraints excluded: chain A residue 489 TYR Chi-restraints excluded: chain A residue 533 LEU Chi-restraints excluded: chain A residue 539 VAL Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 747 THR Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 855 PHE Chi-restraints excluded: chain A residue 912 THR Chi-restraints excluded: chain A residue 982 SER Chi-restraints excluded: chain A residue 1076 THR Chi-restraints excluded: chain A residue 1118 ASP Chi-restraints excluded: chain B residue 48 LEU Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 326 ILE Chi-restraints excluded: chain B residue 406 GLU Chi-restraints excluded: chain B residue 489 TYR Chi-restraints excluded: chain B residue 523 THR Chi-restraints excluded: chain B residue 565 PHE Chi-restraints excluded: chain B residue 572 THR Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 738 CYS Chi-restraints excluded: chain B residue 761 THR Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 913 GLN Chi-restraints excluded: chain B residue 1125 ASN Chi-restraints excluded: chain C residue 61 ASN Chi-restraints excluded: chain C residue 88 ASP Chi-restraints excluded: chain C residue 208 THR Chi-restraints excluded: chain C residue 316 SER Chi-restraints excluded: chain C residue 401 VAL Chi-restraints excluded: chain C residue 762 GLN Chi-restraints excluded: chain C residue 867 ASP Chi-restraints excluded: chain C residue 868 GLU Chi-restraints excluded: chain C residue 921 LYS Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain D residue 28 PHE Chi-restraints excluded: chain D residue 70 SER Chi-restraints excluded: chain D residue 202 TYR Chi-restraints excluded: chain D residue 233 ILE Chi-restraints excluded: chain D residue 318 VAL Chi-restraints excluded: chain D residue 401 HIS Chi-restraints excluded: chain D residue 408 MET Chi-restraints excluded: chain D residue 411 SER Chi-restraints excluded: chain D residue 597 ASP Chi-restraints excluded: chain E residue 42 GLN Chi-restraints excluded: chain E residue 111 ASP Chi-restraints excluded: chain E residue 195 HIS Chi-restraints excluded: chain E residue 224 GLU Chi-restraints excluded: chain E residue 240 LEU Chi-restraints excluded: chain E residue 357 ARG Chi-restraints excluded: chain E residue 548 THR Chi-restraints excluded: chain E residue 571 GLU Chi-restraints excluded: chain E residue 589 GLU Chi-restraints excluded: chain F residue 28 PHE Chi-restraints excluded: chain F residue 79 LEU Chi-restraints excluded: chain F residue 90 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 471 random chunks: chunk 379 optimal weight: 30.0000 chunk 258 optimal weight: 0.8980 chunk 6 optimal weight: 4.9990 chunk 338 optimal weight: 8.9990 chunk 187 optimal weight: 2.9990 chunk 388 optimal weight: 50.0000 chunk 314 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 chunk 232 optimal weight: 9.9990 chunk 408 optimal weight: 0.0010 chunk 114 optimal weight: 1.9990 overall best weight: 2.1792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 81 ASN A 317 ASN ** A 762 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1074 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 239 GLN ** B 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 675 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 779 GLN ** B1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1010 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 762 GLN ** C 895 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 907 ASN C1005 GLN ** C1101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 373 HIS ** E 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 340 GLN ** E 522 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 380 GLN F 556 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7157 moved from start: 0.4072 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.090 39694 Z= 0.287 Angle : 0.633 11.718 53959 Z= 0.319 Chirality : 0.046 0.742 6198 Planarity : 0.004 0.040 6858 Dihedral : 6.446 59.438 6949 Min Nonbonded Distance : 2.121 Molprobity Statistics. All-atom Clashscore : 9.51 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.06 % Favored : 95.85 % Rotamer: Outliers : 2.84 % Allowed : 12.65 % Favored : 84.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.31 (0.12), residues: 4650 helix: 0.63 (0.12), residues: 1750 sheet: 0.10 (0.19), residues: 648 loop : -0.94 (0.13), residues: 2252 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP F 271 HIS 0.015 0.001 HIS F 345 PHE 0.021 0.002 PHE B 429 TYR 0.027 0.002 TYR B 495 ARG 0.008 0.000 ARG F 169 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9300 Ramachandran restraints generated. 4650 Oldfield, 0 Emsley, 4650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9300 Ramachandran restraints generated. 4650 Oldfield, 0 Emsley, 4650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 411 residues out of total 4152 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 118 poor density : 293 time to evaluate : 4.315 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 313 TYR cc_start: 0.8684 (m-80) cc_final: 0.8268 (m-80) REVERT: A 460 ASN cc_start: 0.3266 (OUTLIER) cc_final: 0.2993 (m-40) REVERT: B 170 TYR cc_start: 0.6994 (t80) cc_final: 0.6783 (t80) REVERT: B 1005 GLN cc_start: 0.8224 (tp40) cc_final: 0.7989 (tp40) REVERT: C 61 ASN cc_start: 0.5423 (OUTLIER) cc_final: 0.4539 (p0) REVERT: C 1005 GLN cc_start: 0.8216 (tp40) cc_final: 0.7907 (mm-40) REVERT: D 345 HIS cc_start: 0.6940 (t70) cc_final: 0.6344 (t70) REVERT: D 579 MET cc_start: 0.2690 (tpp) cc_final: 0.1521 (mpp) REVERT: E 42 GLN cc_start: 0.6043 (OUTLIER) cc_final: 0.5741 (tm-30) REVERT: E 217 TYR cc_start: 0.2868 (OUTLIER) cc_final: 0.1036 (m-80) REVERT: E 221 GLN cc_start: 0.5918 (mm-40) cc_final: 0.5518 (pt0) REVERT: E 224 GLU cc_start: 0.3712 (OUTLIER) cc_final: 0.3323 (tm-30) REVERT: E 309 LYS cc_start: 0.6914 (mmtt) cc_final: 0.6508 (tptp) REVERT: F 123 MET cc_start: -0.2302 (mmt) cc_final: -0.2661 (mmm) REVERT: F 366 MET cc_start: 0.1765 (tpt) cc_final: 0.1391 (tpt) REVERT: F 417 HIS cc_start: -0.0373 (OUTLIER) cc_final: -0.0648 (t-90) REVERT: F 455 MET cc_start: 0.3744 (ppp) cc_final: 0.2238 (ttp) REVERT: F 462 MET cc_start: 0.2649 (mtp) cc_final: 0.2367 (mmt) REVERT: F 485 VAL cc_start: 0.2200 (OUTLIER) cc_final: 0.1963 (t) outliers start: 118 outliers final: 73 residues processed: 385 average time/residue: 0.4921 time to fit residues: 315.2336 Evaluate side-chains 347 residues out of total 4152 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 80 poor density : 267 time to evaluate : 4.186 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 ASP Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 307 THR Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 460 ASN Chi-restraints excluded: chain A residue 489 TYR Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 533 LEU Chi-restraints excluded: chain A residue 538 CYS Chi-restraints excluded: chain A residue 572 THR Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 747 THR Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 855 PHE Chi-restraints excluded: chain A residue 912 THR Chi-restraints excluded: chain A residue 982 SER Chi-restraints excluded: chain A residue 1076 THR Chi-restraints excluded: chain A residue 1118 ASP Chi-restraints excluded: chain A residue 1127 ASP Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 326 ILE Chi-restraints excluded: chain B residue 367 VAL Chi-restraints excluded: chain B residue 406 GLU Chi-restraints excluded: chain B residue 427 ASP Chi-restraints excluded: chain B residue 455 LEU Chi-restraints excluded: chain B residue 489 TYR Chi-restraints excluded: chain B residue 523 THR Chi-restraints excluded: chain B residue 565 PHE Chi-restraints excluded: chain B residue 572 THR Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 738 CYS Chi-restraints excluded: chain B residue 747 THR Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 912 THR Chi-restraints excluded: chain B residue 913 GLN Chi-restraints excluded: chain B residue 1125 ASN Chi-restraints excluded: chain C residue 61 ASN Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 88 ASP Chi-restraints excluded: chain C residue 200 TYR Chi-restraints excluded: chain C residue 208 THR Chi-restraints excluded: chain C residue 316 SER Chi-restraints excluded: chain C residue 401 VAL Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 867 ASP Chi-restraints excluded: chain C residue 868 GLU Chi-restraints excluded: chain C residue 921 LYS Chi-restraints excluded: chain C residue 939 SER Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain D residue 28 PHE Chi-restraints excluded: chain D residue 70 SER Chi-restraints excluded: chain D residue 233 ILE Chi-restraints excluded: chain D residue 278 LEU Chi-restraints excluded: chain D residue 285 PHE Chi-restraints excluded: chain D residue 350 ASP Chi-restraints excluded: chain D residue 401 HIS Chi-restraints excluded: chain D residue 408 MET Chi-restraints excluded: chain D residue 411 SER Chi-restraints excluded: chain D residue 597 ASP Chi-restraints excluded: chain E residue 42 GLN Chi-restraints excluded: chain E residue 195 HIS Chi-restraints excluded: chain E residue 217 TYR Chi-restraints excluded: chain E residue 224 GLU Chi-restraints excluded: chain E residue 240 LEU Chi-restraints excluded: chain E residue 548 THR Chi-restraints excluded: chain E residue 571 GLU Chi-restraints excluded: chain F residue 28 PHE Chi-restraints excluded: chain F residue 53 ASN Chi-restraints excluded: chain F residue 78 THR Chi-restraints excluded: chain F residue 90 ASN Chi-restraints excluded: chain F residue 339 VAL Chi-restraints excluded: chain F residue 417 HIS Chi-restraints excluded: chain F residue 485 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 471 random chunks: chunk 153 optimal weight: 3.9990 chunk 409 optimal weight: 20.0000 chunk 89 optimal weight: 1.9990 chunk 267 optimal weight: 0.9980 chunk 112 optimal weight: 2.9990 chunk 455 optimal weight: 30.0000 chunk 378 optimal weight: 30.0000 chunk 210 optimal weight: 0.6980 chunk 37 optimal weight: 0.8980 chunk 150 optimal weight: 0.6980 chunk 239 optimal weight: 6.9990 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 81 ASN ** A 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 762 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 239 GLN B 354 ASN ** B 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 675 GLN ** B1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1010 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 907 ASN E 51 ASN ** E 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 522 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7111 moved from start: 0.4295 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.076 39694 Z= 0.193 Angle : 0.582 11.262 53959 Z= 0.294 Chirality : 0.045 0.699 6198 Planarity : 0.004 0.042 6858 Dihedral : 5.985 58.325 6946 Min Nonbonded Distance : 2.129 Molprobity Statistics. All-atom Clashscore : 9.18 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.46 % Favored : 96.47 % Rotamer: Outliers : 2.55 % Allowed : 13.45 % Favored : 84.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.17 (0.12), residues: 4650 helix: 0.76 (0.12), residues: 1780 sheet: 0.16 (0.19), residues: 673 loop : -0.89 (0.13), residues: 2197 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP C 436 HIS 0.006 0.001 HIS E 505 PHE 0.030 0.001 PHE C 135 TYR 0.025 0.001 TYR F 199 ARG 0.010 0.000 ARG B 237 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9300 Ramachandran restraints generated. 4650 Oldfield, 0 Emsley, 4650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9300 Ramachandran restraints generated. 4650 Oldfield, 0 Emsley, 4650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 398 residues out of total 4152 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 106 poor density : 292 time to evaluate : 4.035 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 460 ASN cc_start: 0.3336 (OUTLIER) cc_final: 0.3126 (m-40) REVERT: B 170 TYR cc_start: 0.7000 (t80) cc_final: 0.6800 (t80) REVERT: B 902 MET cc_start: 0.8751 (tpp) cc_final: 0.8509 (mmt) REVERT: B 1005 GLN cc_start: 0.8159 (tp40) cc_final: 0.7943 (tp40) REVERT: C 61 ASN cc_start: 0.5172 (OUTLIER) cc_final: 0.4342 (p0) REVERT: C 296 LEU cc_start: 0.8572 (tt) cc_final: 0.8348 (tp) REVERT: C 1005 GLN cc_start: 0.8196 (tp40) cc_final: 0.7867 (mm-40) REVERT: D 477 TRP cc_start: 0.4757 (OUTLIER) cc_final: 0.4235 (t-100) REVERT: D 579 MET cc_start: 0.2653 (tpp) cc_final: 0.1249 (mpp) REVERT: E 42 GLN cc_start: 0.5852 (OUTLIER) cc_final: 0.5600 (tm-30) REVERT: E 217 TYR cc_start: 0.2794 (OUTLIER) cc_final: 0.1023 (m-80) REVERT: E 221 GLN cc_start: 0.5976 (mm-40) cc_final: 0.5547 (pt0) REVERT: E 224 GLU cc_start: 0.3703 (OUTLIER) cc_final: 0.3305 (tm-30) REVERT: E 309 LYS cc_start: 0.6932 (mmtt) cc_final: 0.6601 (tptp) REVERT: F 123 MET cc_start: -0.1876 (mmt) cc_final: -0.2132 (mmt) REVERT: F 345 HIS cc_start: 0.0578 (OUTLIER) cc_final: 0.0175 (t-170) REVERT: F 366 MET cc_start: 0.1750 (tpt) cc_final: 0.1196 (tpp) REVERT: F 417 HIS cc_start: -0.0305 (OUTLIER) cc_final: -0.0668 (t-90) REVERT: F 455 MET cc_start: 0.3602 (ppp) cc_final: 0.2164 (ttp) REVERT: F 462 MET cc_start: 0.2707 (mtp) cc_final: 0.2378 (mmt) REVERT: F 474 MET cc_start: 0.1254 (mmm) cc_final: 0.1054 (mmp) REVERT: F 485 VAL cc_start: 0.2241 (OUTLIER) cc_final: 0.1893 (t) outliers start: 106 outliers final: 80 residues processed: 374 average time/residue: 0.4957 time to fit residues: 305.7597 Evaluate side-chains 358 residues out of total 4152 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 89 poor density : 269 time to evaluate : 3.902 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 ASN Chi-restraints excluded: chain A residue 88 ASP Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 307 THR Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 460 ASN Chi-restraints excluded: chain A residue 489 TYR Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 533 LEU Chi-restraints excluded: chain A residue 538 CYS Chi-restraints excluded: chain A residue 572 THR Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 738 CYS Chi-restraints excluded: chain A residue 747 THR Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 855 PHE Chi-restraints excluded: chain A residue 912 THR Chi-restraints excluded: chain A residue 982 SER Chi-restraints excluded: chain A residue 1076 THR Chi-restraints excluded: chain A residue 1116 THR Chi-restraints excluded: chain A residue 1118 ASP Chi-restraints excluded: chain A residue 1127 ASP Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 398 ASP Chi-restraints excluded: chain B residue 406 GLU Chi-restraints excluded: chain B residue 455 LEU Chi-restraints excluded: chain B residue 489 TYR Chi-restraints excluded: chain B residue 523 THR Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 565 PHE Chi-restraints excluded: chain B residue 572 THR Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 658 ASN Chi-restraints excluded: chain B residue 675 GLN Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 738 CYS Chi-restraints excluded: chain B residue 740 MET Chi-restraints excluded: chain B residue 754 LEU Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 912 THR Chi-restraints excluded: chain B residue 913 GLN Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain B residue 1125 ASN Chi-restraints excluded: chain C residue 61 ASN Chi-restraints excluded: chain C residue 88 ASP Chi-restraints excluded: chain C residue 200 TYR Chi-restraints excluded: chain C residue 208 THR Chi-restraints excluded: chain C residue 401 VAL Chi-restraints excluded: chain C residue 536 ASN Chi-restraints excluded: chain C residue 867 ASP Chi-restraints excluded: chain C residue 868 GLU Chi-restraints excluded: chain C residue 916 LEU Chi-restraints excluded: chain C residue 937 SER Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain D residue 28 PHE Chi-restraints excluded: chain D residue 70 SER Chi-restraints excluded: chain D residue 202 TYR Chi-restraints excluded: chain D residue 401 HIS Chi-restraints excluded: chain D residue 408 MET Chi-restraints excluded: chain D residue 411 SER Chi-restraints excluded: chain D residue 456 LEU Chi-restraints excluded: chain D residue 477 TRP Chi-restraints excluded: chain D residue 597 ASP Chi-restraints excluded: chain E residue 42 GLN Chi-restraints excluded: chain E residue 195 HIS Chi-restraints excluded: chain E residue 217 TYR Chi-restraints excluded: chain E residue 224 GLU Chi-restraints excluded: chain E residue 240 LEU Chi-restraints excluded: chain E residue 357 ARG Chi-restraints excluded: chain E residue 548 THR Chi-restraints excluded: chain E residue 574 VAL Chi-restraints excluded: chain E residue 589 GLU Chi-restraints excluded: chain F residue 28 PHE Chi-restraints excluded: chain F residue 53 ASN Chi-restraints excluded: chain F residue 78 THR Chi-restraints excluded: chain F residue 79 LEU Chi-restraints excluded: chain F residue 90 ASN Chi-restraints excluded: chain F residue 339 VAL Chi-restraints excluded: chain F residue 344 CYS Chi-restraints excluded: chain F residue 345 HIS Chi-restraints excluded: chain F residue 417 HIS Chi-restraints excluded: chain F residue 485 VAL Chi-restraints excluded: chain F residue 506 VAL Chi-restraints excluded: chain F residue 567 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 471 random chunks: chunk 439 optimal weight: 7.9990 chunk 51 optimal weight: 3.9990 chunk 259 optimal weight: 1.9990 chunk 332 optimal weight: 6.9990 chunk 257 optimal weight: 0.9990 chunk 383 optimal weight: 5.9990 chunk 254 optimal weight: 1.9990 chunk 453 optimal weight: 8.9990 chunk 284 optimal weight: 1.9990 chunk 276 optimal weight: 0.0170 chunk 209 optimal weight: 0.5980 overall best weight: 1.1224 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 81 ASN ** A 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 762 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1058 HIS B 81 ASN B 409 GLN ** B1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1010 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 907 ASN ** E 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 522 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7113 moved from start: 0.4459 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.076 39694 Z= 0.191 Angle : 0.573 12.949 53959 Z= 0.288 Chirality : 0.044 0.643 6198 Planarity : 0.004 0.042 6858 Dihedral : 5.689 58.547 6943 Min Nonbonded Distance : 2.138 Molprobity Statistics. All-atom Clashscore : 9.15 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.83 % Favored : 96.11 % Rotamer: Outliers : 2.63 % Allowed : 13.86 % Favored : 83.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.06 (0.12), residues: 4650 helix: 0.88 (0.12), residues: 1765 sheet: 0.21 (0.19), residues: 668 loop : -0.84 (0.13), residues: 2217 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.001 TRP C 436 HIS 0.004 0.001 HIS F 378 PHE 0.022 0.001 PHE C 92 TYR 0.022 0.001 TYR E 454 ARG 0.006 0.000 ARG A 567 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9300 Ramachandran restraints generated. 4650 Oldfield, 0 Emsley, 4650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9300 Ramachandran restraints generated. 4650 Oldfield, 0 Emsley, 4650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 381 residues out of total 4152 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 109 poor density : 272 time to evaluate : 4.376 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 133 PHE cc_start: 0.6000 (m-80) cc_final: 0.5409 (t80) REVERT: A 313 TYR cc_start: 0.8683 (m-80) cc_final: 0.8267 (m-80) REVERT: B 558 LYS cc_start: 0.8410 (mmmt) cc_final: 0.8182 (mmmm) REVERT: B 786 LYS cc_start: 0.7458 (ptpt) cc_final: 0.7139 (mtmt) REVERT: B 1005 GLN cc_start: 0.8148 (tp40) cc_final: 0.7921 (tp40) REVERT: C 296 LEU cc_start: 0.8585 (tt) cc_final: 0.8341 (tp) REVERT: C 1005 GLN cc_start: 0.8197 (tp40) cc_final: 0.7868 (mm-40) REVERT: D 149 ASN cc_start: 0.6129 (OUTLIER) cc_final: 0.5889 (m110) REVERT: D 579 MET cc_start: 0.2423 (tpp) cc_final: 0.1162 (mpp) REVERT: D 597 ASP cc_start: 0.6290 (OUTLIER) cc_final: 0.5438 (p0) REVERT: E 217 TYR cc_start: 0.2717 (OUTLIER) cc_final: 0.1001 (m-80) REVERT: E 221 GLN cc_start: 0.6018 (mm-40) cc_final: 0.5579 (pt0) REVERT: E 224 GLU cc_start: 0.3733 (OUTLIER) cc_final: 0.3304 (tm-30) REVERT: E 309 LYS cc_start: 0.6934 (mmtt) cc_final: 0.6602 (tptp) REVERT: E 323 MET cc_start: 0.3038 (mmm) cc_final: 0.2462 (tmm) REVERT: E 606 TRP cc_start: -0.0461 (p90) cc_final: -0.0920 (p90) REVERT: F 37 GLU cc_start: 0.3420 (mm-30) cc_final: 0.3007 (mt-10) REVERT: F 123 MET cc_start: -0.1829 (mmt) cc_final: -0.2129 (mmt) REVERT: F 366 MET cc_start: 0.1835 (tpt) cc_final: 0.1318 (tpp) REVERT: F 417 HIS cc_start: -0.0394 (OUTLIER) cc_final: -0.0845 (t-90) REVERT: F 455 MET cc_start: 0.3527 (ppp) cc_final: 0.2357 (ttp) REVERT: F 462 MET cc_start: 0.2620 (mtp) cc_final: 0.2343 (mmt) REVERT: F 485 VAL cc_start: 0.2291 (OUTLIER) cc_final: 0.1807 (t) outliers start: 109 outliers final: 78 residues processed: 351 average time/residue: 0.4896 time to fit residues: 287.6606 Evaluate side-chains 337 residues out of total 4152 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 84 poor density : 253 time to evaluate : 4.303 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 ASP Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 105 ILE Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 489 TYR Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 533 LEU Chi-restraints excluded: chain A residue 538 CYS Chi-restraints excluded: chain A residue 572 THR Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 738 CYS Chi-restraints excluded: chain A residue 747 THR Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 855 PHE Chi-restraints excluded: chain A residue 869 MET Chi-restraints excluded: chain A residue 982 SER Chi-restraints excluded: chain A residue 1076 THR Chi-restraints excluded: chain A residue 1116 THR Chi-restraints excluded: chain A residue 1118 ASP Chi-restraints excluded: chain A residue 1127 ASP Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 326 ILE Chi-restraints excluded: chain B residue 364 ASP Chi-restraints excluded: chain B residue 398 ASP Chi-restraints excluded: chain B residue 406 GLU Chi-restraints excluded: chain B residue 455 LEU Chi-restraints excluded: chain B residue 489 TYR Chi-restraints excluded: chain B residue 523 THR Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 565 PHE Chi-restraints excluded: chain B residue 572 THR Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 658 ASN Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 738 CYS Chi-restraints excluded: chain B residue 740 MET Chi-restraints excluded: chain B residue 761 THR Chi-restraints excluded: chain B residue 778 THR Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 912 THR Chi-restraints excluded: chain B residue 913 GLN Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain B residue 1125 ASN Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 88 ASP Chi-restraints excluded: chain C residue 200 TYR Chi-restraints excluded: chain C residue 208 THR Chi-restraints excluded: chain C residue 401 VAL Chi-restraints excluded: chain C residue 536 ASN Chi-restraints excluded: chain C residue 867 ASP Chi-restraints excluded: chain C residue 868 GLU Chi-restraints excluded: chain C residue 937 SER Chi-restraints excluded: chain C residue 939 SER Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain D residue 28 PHE Chi-restraints excluded: chain D residue 70 SER Chi-restraints excluded: chain D residue 149 ASN Chi-restraints excluded: chain D residue 350 ASP Chi-restraints excluded: chain D residue 401 HIS Chi-restraints excluded: chain D residue 408 MET Chi-restraints excluded: chain D residue 411 SER Chi-restraints excluded: chain D residue 456 LEU Chi-restraints excluded: chain D residue 597 ASP Chi-restraints excluded: chain E residue 62 MET Chi-restraints excluded: chain E residue 195 HIS Chi-restraints excluded: chain E residue 217 TYR Chi-restraints excluded: chain E residue 224 GLU Chi-restraints excluded: chain E residue 240 LEU Chi-restraints excluded: chain E residue 548 THR Chi-restraints excluded: chain E residue 589 GLU Chi-restraints excluded: chain F residue 28 PHE Chi-restraints excluded: chain F residue 53 ASN Chi-restraints excluded: chain F residue 90 ASN Chi-restraints excluded: chain F residue 339 VAL Chi-restraints excluded: chain F residue 344 CYS Chi-restraints excluded: chain F residue 417 HIS Chi-restraints excluded: chain F residue 485 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 471 random chunks: chunk 280 optimal weight: 1.9990 chunk 181 optimal weight: 0.7980 chunk 271 optimal weight: 3.9990 chunk 136 optimal weight: 0.0870 chunk 89 optimal weight: 2.9990 chunk 87 optimal weight: 0.9990 chunk 288 optimal weight: 4.9990 chunk 309 optimal weight: 10.0000 chunk 224 optimal weight: 0.0030 chunk 42 optimal weight: 0.7980 chunk 356 optimal weight: 5.9990 overall best weight: 0.5370 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 762 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 354 ASN ** B1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1010 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 907 ASN C1083 HIS ** E 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 101 GLN ** E 522 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7075 moved from start: 0.4621 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.062 39694 Z= 0.153 Angle : 0.549 9.816 53959 Z= 0.276 Chirality : 0.043 0.560 6198 Planarity : 0.004 0.043 6858 Dihedral : 5.356 58.151 6941 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 8.98 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.42 % Favored : 96.52 % Rotamer: Outliers : 1.83 % Allowed : 14.94 % Favored : 83.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.07 (0.12), residues: 4650 helix: 1.02 (0.12), residues: 1766 sheet: 0.33 (0.20), residues: 643 loop : -0.80 (0.13), residues: 2241 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.047 0.001 TRP D 478 HIS 0.013 0.001 HIS D 34 PHE 0.022 0.001 PHE E 438 TYR 0.017 0.001 TYR B1067 ARG 0.007 0.000 ARG B 995 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9300 Ramachandran restraints generated. 4650 Oldfield, 0 Emsley, 4650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9300 Ramachandran restraints generated. 4650 Oldfield, 0 Emsley, 4650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 355 residues out of total 4152 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 279 time to evaluate : 4.249 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: A 133 PHE cc_start: 0.5953 (m-80) cc_final: 0.5402 (t80) REVERT: B 558 LYS cc_start: 0.8379 (mmmt) cc_final: 0.8171 (mmmm) REVERT: B 786 LYS cc_start: 0.7465 (ptpt) cc_final: 0.7182 (mtmt) REVERT: C 296 LEU cc_start: 0.8496 (tt) cc_final: 0.8292 (tp) REVERT: C 1005 GLN cc_start: 0.8170 (tp40) cc_final: 0.7847 (mm-40) REVERT: D 477 TRP cc_start: 0.4815 (OUTLIER) cc_final: 0.4602 (t-100) REVERT: D 579 MET cc_start: 0.2381 (tpp) cc_final: 0.1341 (mpp) REVERT: D 597 ASP cc_start: 0.6262 (OUTLIER) cc_final: 0.5461 (p0) REVERT: E 217 TYR cc_start: 0.2515 (OUTLIER) cc_final: 0.2147 (m-80) REVERT: E 224 GLU cc_start: 0.3702 (OUTLIER) cc_final: 0.3181 (tm-30) REVERT: E 309 LYS cc_start: 0.6938 (mmtt) cc_final: 0.6633 (tptp) REVERT: E 323 MET cc_start: 0.3104 (mmm) cc_final: 0.2380 (tmm) REVERT: E 383 MET cc_start: 0.5333 (ppp) cc_final: 0.5011 (ppp) REVERT: E 606 TRP cc_start: -0.0320 (p90) cc_final: -0.0782 (p90) REVERT: F 37 GLU cc_start: 0.3392 (mm-30) cc_final: 0.3009 (mt-10) REVERT: F 120 LEU cc_start: 0.0629 (mt) cc_final: 0.0238 (tt) REVERT: F 366 MET cc_start: 0.1724 (tpt) cc_final: 0.1198 (tpp) REVERT: F 417 HIS cc_start: -0.0265 (OUTLIER) cc_final: -0.0708 (t-90) REVERT: F 455 MET cc_start: 0.3525 (ppp) cc_final: 0.2317 (ttp) REVERT: F 462 MET cc_start: 0.2593 (mtp) cc_final: 0.2304 (mmt) REVERT: F 485 VAL cc_start: 0.2241 (OUTLIER) cc_final: 0.1789 (t) outliers start: 76 outliers final: 55 residues processed: 339 average time/residue: 0.4776 time to fit residues: 272.7019 Evaluate side-chains 310 residues out of total 4152 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 249 time to evaluate : 4.205 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 105 ILE Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 489 TYR Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 538 CYS Chi-restraints excluded: chain A residue 572 THR Chi-restraints excluded: chain A residue 738 CYS Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 855 PHE Chi-restraints excluded: chain A residue 869 MET Chi-restraints excluded: chain A residue 912 THR Chi-restraints excluded: chain A residue 1118 ASP Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 364 ASP Chi-restraints excluded: chain B residue 398 ASP Chi-restraints excluded: chain B residue 406 GLU Chi-restraints excluded: chain B residue 455 LEU Chi-restraints excluded: chain B residue 489 TYR Chi-restraints excluded: chain B residue 523 THR Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 565 PHE Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 738 CYS Chi-restraints excluded: chain B residue 740 MET Chi-restraints excluded: chain B residue 778 THR Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 912 THR Chi-restraints excluded: chain B residue 1125 ASN Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 200 TYR Chi-restraints excluded: chain C residue 208 THR Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 867 ASP Chi-restraints excluded: chain C residue 868 GLU Chi-restraints excluded: chain C residue 939 SER Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain D residue 28 PHE Chi-restraints excluded: chain D residue 70 SER Chi-restraints excluded: chain D residue 401 HIS Chi-restraints excluded: chain D residue 411 SER Chi-restraints excluded: chain D residue 477 TRP Chi-restraints excluded: chain D residue 597 ASP Chi-restraints excluded: chain E residue 62 MET Chi-restraints excluded: chain E residue 217 TYR Chi-restraints excluded: chain E residue 224 GLU Chi-restraints excluded: chain E residue 240 LEU Chi-restraints excluded: chain E residue 548 THR Chi-restraints excluded: chain F residue 28 PHE Chi-restraints excluded: chain F residue 53 ASN Chi-restraints excluded: chain F residue 78 THR Chi-restraints excluded: chain F residue 79 LEU Chi-restraints excluded: chain F residue 90 ASN Chi-restraints excluded: chain F residue 339 VAL Chi-restraints excluded: chain F residue 344 CYS Chi-restraints excluded: chain F residue 417 HIS Chi-restraints excluded: chain F residue 485 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 471 random chunks: chunk 412 optimal weight: 6.9990 chunk 434 optimal weight: 40.0000 chunk 396 optimal weight: 20.0000 chunk 423 optimal weight: 0.0000 chunk 254 optimal weight: 0.6980 chunk 184 optimal weight: 0.9990 chunk 332 optimal weight: 20.0000 chunk 129 optimal weight: 8.9990 chunk 382 optimal weight: 9.9990 chunk 400 optimal weight: 6.9990 chunk 421 optimal weight: 4.9990 overall best weight: 2.7390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 762 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 239 GLN B 675 GLN ** B1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1005 GLN ** B1010 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1113 GLN C 655 HIS C 907 ASN C1135 ASN ** D 540 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 42 GLN ** E 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 401 HIS ** E 522 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 572 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7183 moved from start: 0.4751 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.084 39694 Z= 0.337 Angle : 0.643 10.155 53959 Z= 0.322 Chirality : 0.046 0.812 6198 Planarity : 0.004 0.041 6858 Dihedral : 5.785 59.375 6938 Min Nonbonded Distance : 2.110 Molprobity Statistics. All-atom Clashscore : 11.03 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.67 % Favored : 95.27 % Rotamer: Outliers : 2.36 % Allowed : 15.11 % Favored : 82.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.20 (0.12), residues: 4650 helix: 0.84 (0.12), residues: 1749 sheet: 0.10 (0.19), residues: 665 loop : -0.96 (0.13), residues: 2236 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP D 477 HIS 0.007 0.001 HIS B1064 PHE 0.023 0.002 PHE C 135 TYR 0.022 0.002 TYR A1138 ARG 0.005 0.001 ARG A 567 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9300 Ramachandran restraints generated. 4650 Oldfield, 0 Emsley, 4650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9300 Ramachandran restraints generated. 4650 Oldfield, 0 Emsley, 4650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 355 residues out of total 4152 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 98 poor density : 257 time to evaluate : 3.928 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: A 313 TYR cc_start: 0.8679 (m-80) cc_final: 0.8294 (m-80) REVERT: B 387 LEU cc_start: 0.5241 (mp) cc_final: 0.4908 (mp) REVERT: C 61 ASN cc_start: 0.5507 (OUTLIER) cc_final: 0.4613 (p0) REVERT: C 740 MET cc_start: 0.6399 (tpt) cc_final: 0.6178 (tpt) REVERT: C 1005 GLN cc_start: 0.8232 (tp40) cc_final: 0.7923 (mm-40) REVERT: D 323 MET cc_start: 0.5774 (mmm) cc_final: 0.5519 (mmm) REVERT: D 579 MET cc_start: 0.2468 (tpp) cc_final: 0.1451 (mpp) REVERT: E 217 TYR cc_start: 0.2637 (OUTLIER) cc_final: 0.1941 (m-80) REVERT: E 224 GLU cc_start: 0.3684 (OUTLIER) cc_final: 0.3184 (tm-30) REVERT: E 309 LYS cc_start: 0.6902 (mmtt) cc_final: 0.6585 (tptp) REVERT: E 323 MET cc_start: 0.3102 (mmm) cc_final: 0.2567 (mmm) REVERT: E 383 MET cc_start: 0.5332 (ppp) cc_final: 0.5108 (ppp) REVERT: E 606 TRP cc_start: -0.0208 (p90) cc_final: -0.0642 (p90) REVERT: F 37 GLU cc_start: 0.3343 (mm-30) cc_final: 0.3086 (mt-10) REVERT: F 120 LEU cc_start: 0.0615 (mt) cc_final: 0.0292 (tt) REVERT: F 366 MET cc_start: 0.1955 (tpt) cc_final: 0.1500 (tpp) REVERT: F 417 HIS cc_start: -0.0525 (OUTLIER) cc_final: -0.0883 (t-90) REVERT: F 455 MET cc_start: 0.3472 (ppp) cc_final: 0.2252 (ttp) REVERT: F 462 MET cc_start: 0.2725 (mtp) cc_final: 0.2455 (mmt) REVERT: F 485 VAL cc_start: 0.2269 (OUTLIER) cc_final: 0.1807 (t) outliers start: 98 outliers final: 79 residues processed: 332 average time/residue: 0.4669 time to fit residues: 263.5171 Evaluate side-chains 320 residues out of total 4152 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 84 poor density : 236 time to evaluate : 4.467 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 ASP Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 105 ILE Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 489 TYR Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 533 LEU Chi-restraints excluded: chain A residue 538 CYS Chi-restraints excluded: chain A residue 572 THR Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 738 CYS Chi-restraints excluded: chain A residue 747 THR Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 855 PHE Chi-restraints excluded: chain A residue 869 MET Chi-restraints excluded: chain A residue 912 THR Chi-restraints excluded: chain A residue 982 SER Chi-restraints excluded: chain A residue 1076 THR Chi-restraints excluded: chain A residue 1118 ASP Chi-restraints excluded: chain A residue 1127 ASP Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 326 ILE Chi-restraints excluded: chain B residue 364 ASP Chi-restraints excluded: chain B residue 398 ASP Chi-restraints excluded: chain B residue 402 ILE Chi-restraints excluded: chain B residue 406 GLU Chi-restraints excluded: chain B residue 455 LEU Chi-restraints excluded: chain B residue 489 TYR Chi-restraints excluded: chain B residue 523 THR Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 565 PHE Chi-restraints excluded: chain B residue 572 THR Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 658 ASN Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 738 CYS Chi-restraints excluded: chain B residue 747 THR Chi-restraints excluded: chain B residue 778 THR Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 912 THR Chi-restraints excluded: chain B residue 913 GLN Chi-restraints excluded: chain B residue 1125 ASN Chi-restraints excluded: chain C residue 61 ASN Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 208 THR Chi-restraints excluded: chain C residue 316 SER Chi-restraints excluded: chain C residue 382 VAL Chi-restraints excluded: chain C residue 536 ASN Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 867 ASP Chi-restraints excluded: chain C residue 868 GLU Chi-restraints excluded: chain C residue 937 SER Chi-restraints excluded: chain C residue 939 SER Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain D residue 28 PHE Chi-restraints excluded: chain D residue 70 SER Chi-restraints excluded: chain D residue 154 ASN Chi-restraints excluded: chain D residue 401 HIS Chi-restraints excluded: chain D residue 408 MET Chi-restraints excluded: chain D residue 411 SER Chi-restraints excluded: chain D residue 597 ASP Chi-restraints excluded: chain E residue 62 MET Chi-restraints excluded: chain E residue 102 GLN Chi-restraints excluded: chain E residue 217 TYR Chi-restraints excluded: chain E residue 224 GLU Chi-restraints excluded: chain E residue 240 LEU Chi-restraints excluded: chain E residue 548 THR Chi-restraints excluded: chain E residue 574 VAL Chi-restraints excluded: chain F residue 28 PHE Chi-restraints excluded: chain F residue 53 ASN Chi-restraints excluded: chain F residue 78 THR Chi-restraints excluded: chain F residue 90 ASN Chi-restraints excluded: chain F residue 339 VAL Chi-restraints excluded: chain F residue 417 HIS Chi-restraints excluded: chain F residue 485 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 471 random chunks: chunk 277 optimal weight: 3.9990 chunk 447 optimal weight: 8.9990 chunk 273 optimal weight: 0.9990 chunk 212 optimal weight: 7.9990 chunk 310 optimal weight: 8.9990 chunk 469 optimal weight: 30.0000 chunk 431 optimal weight: 6.9990 chunk 373 optimal weight: 10.0000 chunk 38 optimal weight: 5.9990 chunk 288 optimal weight: 0.8980 chunk 229 optimal weight: 5.9990 overall best weight: 3.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 762 GLN A 907 ASN ** A1005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1074 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1010 GLN ** C 354 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 895 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 907 ASN D 239 HIS D 540 HIS ** E 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 522 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 586 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7227 moved from start: 0.4939 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.093 39694 Z= 0.415 Angle : 0.692 11.835 53959 Z= 0.347 Chirality : 0.048 0.874 6198 Planarity : 0.004 0.073 6858 Dihedral : 6.350 59.985 6938 Min Nonbonded Distance : 2.050 Molprobity Statistics. All-atom Clashscore : 12.79 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.01 % Favored : 94.95 % Rotamer: Outliers : 2.31 % Allowed : 15.57 % Favored : 82.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.53 (0.12), residues: 4650 helix: 0.61 (0.12), residues: 1753 sheet: -0.14 (0.19), residues: 664 loop : -1.18 (0.13), residues: 2233 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP D 477 HIS 0.008 0.001 HIS B1064 PHE 0.023 0.002 PHE E 438 TYR 0.021 0.002 TYR B1067 ARG 0.009 0.001 ARG A 466 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9300 Ramachandran restraints generated. 4650 Oldfield, 0 Emsley, 4650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9300 Ramachandran restraints generated. 4650 Oldfield, 0 Emsley, 4650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 352 residues out of total 4152 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 96 poor density : 256 time to evaluate : 4.403 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: C 1005 GLN cc_start: 0.8247 (tp40) cc_final: 0.7941 (mm-40) REVERT: D 323 MET cc_start: 0.5909 (mmm) cc_final: 0.5650 (mmm) REVERT: D 465 LYS cc_start: 0.6495 (ptpt) cc_final: 0.6278 (tppt) REVERT: D 579 MET cc_start: 0.2347 (tpp) cc_final: 0.1125 (mpp) REVERT: E 217 TYR cc_start: 0.2669 (OUTLIER) cc_final: 0.1904 (m-80) REVERT: E 224 GLU cc_start: 0.3697 (OUTLIER) cc_final: 0.3240 (tm-30) REVERT: E 309 LYS cc_start: 0.6949 (mmtt) cc_final: 0.6600 (tptp) REVERT: E 323 MET cc_start: 0.3183 (mmm) cc_final: 0.2540 (mmm) REVERT: E 360 MET cc_start: 0.4501 (mtp) cc_final: 0.4091 (mtp) REVERT: E 383 MET cc_start: 0.5362 (ppp) cc_final: 0.5098 (ppp) REVERT: E 408 MET cc_start: 0.5047 (ptt) cc_final: 0.4317 (mmt) REVERT: E 606 TRP cc_start: -0.0078 (p90) cc_final: -0.0481 (p90) REVERT: F 37 GLU cc_start: 0.2819 (mm-30) cc_final: 0.2543 (mt-10) REVERT: F 120 LEU cc_start: 0.0667 (mt) cc_final: 0.0317 (tt) REVERT: F 190 MET cc_start: 0.2778 (ptm) cc_final: 0.2482 (mtt) REVERT: F 270 MET cc_start: -0.2760 (pmm) cc_final: -0.3345 (ptt) REVERT: F 366 MET cc_start: 0.1945 (tpt) cc_final: 0.1465 (tpp) REVERT: F 417 HIS cc_start: -0.0412 (OUTLIER) cc_final: -0.0766 (t-90) REVERT: F 455 MET cc_start: 0.3195 (ppp) cc_final: 0.1711 (ttp) REVERT: F 485 VAL cc_start: 0.2342 (OUTLIER) cc_final: 0.1794 (t) outliers start: 96 outliers final: 80 residues processed: 328 average time/residue: 0.4713 time to fit residues: 265.3023 Evaluate side-chains 324 residues out of total 4152 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 84 poor density : 240 time to evaluate : 4.248 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 ASP Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 105 ILE Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 489 TYR Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 533 LEU Chi-restraints excluded: chain A residue 538 CYS Chi-restraints excluded: chain A residue 572 THR Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 738 CYS Chi-restraints excluded: chain A residue 747 THR Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 855 PHE Chi-restraints excluded: chain A residue 869 MET Chi-restraints excluded: chain A residue 912 THR Chi-restraints excluded: chain A residue 982 SER Chi-restraints excluded: chain A residue 994 ASP Chi-restraints excluded: chain A residue 1076 THR Chi-restraints excluded: chain A residue 1118 ASP Chi-restraints excluded: chain A residue 1127 ASP Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 211 ASN Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 326 ILE Chi-restraints excluded: chain B residue 364 ASP Chi-restraints excluded: chain B residue 398 ASP Chi-restraints excluded: chain B residue 402 ILE Chi-restraints excluded: chain B residue 406 GLU Chi-restraints excluded: chain B residue 455 LEU Chi-restraints excluded: chain B residue 489 TYR Chi-restraints excluded: chain B residue 523 THR Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 565 PHE Chi-restraints excluded: chain B residue 572 THR Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 747 THR Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 912 THR Chi-restraints excluded: chain B residue 913 GLN Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain B residue 1125 ASN Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 208 THR Chi-restraints excluded: chain C residue 316 SER Chi-restraints excluded: chain C residue 536 ASN Chi-restraints excluded: chain C residue 867 ASP Chi-restraints excluded: chain C residue 868 GLU Chi-restraints excluded: chain C residue 921 LYS Chi-restraints excluded: chain C residue 937 SER Chi-restraints excluded: chain C residue 939 SER Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain D residue 28 PHE Chi-restraints excluded: chain D residue 55 THR Chi-restraints excluded: chain D residue 70 SER Chi-restraints excluded: chain D residue 154 ASN Chi-restraints excluded: chain D residue 401 HIS Chi-restraints excluded: chain D residue 408 MET Chi-restraints excluded: chain D residue 411 SER Chi-restraints excluded: chain D residue 597 ASP Chi-restraints excluded: chain E residue 62 MET Chi-restraints excluded: chain E residue 195 HIS Chi-restraints excluded: chain E residue 217 TYR Chi-restraints excluded: chain E residue 224 GLU Chi-restraints excluded: chain E residue 240 LEU Chi-restraints excluded: chain E residue 548 THR Chi-restraints excluded: chain E residue 574 VAL Chi-restraints excluded: chain F residue 28 PHE Chi-restraints excluded: chain F residue 53 ASN Chi-restraints excluded: chain F residue 78 THR Chi-restraints excluded: chain F residue 90 ASN Chi-restraints excluded: chain F residue 339 VAL Chi-restraints excluded: chain F residue 417 HIS Chi-restraints excluded: chain F residue 485 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 471 random chunks: chunk 296 optimal weight: 0.9980 chunk 398 optimal weight: 20.0000 chunk 114 optimal weight: 2.9990 chunk 344 optimal weight: 20.0000 chunk 55 optimal weight: 0.9980 chunk 103 optimal weight: 5.9990 chunk 374 optimal weight: 8.9990 chunk 156 optimal weight: 0.6980 chunk 384 optimal weight: 5.9990 chunk 47 optimal weight: 5.9990 chunk 68 optimal weight: 1.9990 overall best weight: 1.5384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1074 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 690 GLN ** B1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1010 GLN ** C 895 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 907 ASN ** E 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 522 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 42 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4619 r_free = 0.4619 target = 0.199711 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.4469 r_free = 0.4469 target = 0.187826 restraints weight = 87068.128| |-----------------------------------------------------------------------------| r_work (start): 0.4427 rms_B_bonded: 1.07 r_work: 0.4179 rms_B_bonded: 1.23 restraints_weight: 0.5000 r_work: 0.4089 rms_B_bonded: 2.74 restraints_weight: 0.2500 r_work: 0.3983 rms_B_bonded: 4.92 restraints_weight: 0.1250 r_work (final): 0.3983 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6887 moved from start: 0.5029 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.075 39694 Z= 0.228 Angle : 0.611 12.286 53959 Z= 0.306 Chirality : 0.045 0.741 6198 Planarity : 0.004 0.044 6858 Dihedral : 5.991 59.931 6938 Min Nonbonded Distance : 2.085 Molprobity Statistics. All-atom Clashscore : 10.60 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.34 % Favored : 95.61 % Rotamer: Outliers : 2.00 % Allowed : 15.96 % Favored : 82.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.27 (0.12), residues: 4650 helix: 0.85 (0.12), residues: 1754 sheet: -0.05 (0.19), residues: 662 loop : -1.03 (0.13), residues: 2234 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.001 TRP D 477 HIS 0.005 0.001 HIS F 378 PHE 0.032 0.002 PHE E 28 TYR 0.019 0.001 TYR B1067 ARG 0.006 0.000 ARG A 466 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9527.89 seconds wall clock time: 172 minutes 42.06 seconds (10362.06 seconds total)