Starting phenix.real_space_refine on Wed Feb 14 22:11:49 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7x3u_32993/02_2024/7x3u_32993_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7x3u_32993/02_2024/7x3u_32993.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7x3u_32993/02_2024/7x3u_32993.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7x3u_32993/02_2024/7x3u_32993.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7x3u_32993/02_2024/7x3u_32993_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7x3u_32993/02_2024/7x3u_32993_updated.pdb" } resolution = 3.3 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= 0.023 sd= 0.166 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: 5 Type Number sf(0) Gaussians P 32 5.49 5 S 385 5.16 5 C 39100 2.51 5 N 10894 2.21 5 O 12084 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "a PHE 8": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a GLU 15": "OE1" <-> "OE2" Residue "a GLU 68": "OE1" <-> "OE2" Residue "a PHE 168": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a TYR 190": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a ASP 261": "OD1" <-> "OD2" Residue "a ASP 294": "OD1" <-> "OD2" Residue "a TYR 299": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a GLU 302": "OE1" <-> "OE2" Residue "a ASP 358": "OD1" <-> "OD2" Residue "a PHE 441": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a PHE 504": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a PHE 516": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a ASP 528": "OD1" <-> "OD2" Residue "a ASP 529": "OD1" <-> "OD2" Residue "A PHE 8": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 15": "OE1" <-> "OE2" Residue "A GLU 77": "OE1" <-> "OE2" Residue "A PHE 167": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 168": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 174": "OD1" <-> "OD2" Residue "A ASP 183": "OD1" <-> "OD2" Residue "A GLU 207": "OE1" <-> "OE2" Residue "A ASP 293": "OD1" <-> "OD2" Residue "A PHE 300": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 354": "OE1" <-> "OE2" Residue "A ASP 358": "OD1" <-> "OD2" Residue "A ASP 359": "OD1" <-> "OD2" Residue "A PHE 383": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 386": "OD1" <-> "OD2" Residue "A GLU 387": "OE1" <-> "OE2" Residue "A PHE 441": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 479": "OE1" <-> "OE2" Residue "A PHE 504": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 516": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 528": "OD1" <-> "OD2" Residue "b PHE 12": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b GLU 18": "OE1" <-> "OE2" Residue "b GLU 19": "OE1" <-> "OE2" Residue "b PHE 29": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b ASP 66": "OD1" <-> "OD2" Residue "b ASP 86": "OD1" <-> "OD2" Residue "b PHE 179": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b TYR 213": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b PHE 252": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b ASP 259": "OD1" <-> "OD2" Residue "b PHE 304": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b GLU 339": "OE1" <-> "OE2" Residue "b TYR 408": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b TYR 439": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b TYR 456": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b ASP 460": "OD1" <-> "OD2" Residue "B PHE 12": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 19": "OE1" <-> "OE2" Residue "B PHE 29": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 49": "OD1" <-> "OD2" Residue "B ASP 86": "OD1" <-> "OD2" Residue "B TYR 213": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 221": "OD1" <-> "OD2" Residue "B GLU 233": "OE1" <-> "OE2" Residue "B ASP 245": "OD1" <-> "OD2" Residue "B ASP 247": "OD1" <-> "OD2" Residue "B PHE 252": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 273": "OE1" <-> "OE2" Residue "B GLU 280": "OE1" <-> "OE2" Residue "B PHE 304": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 313": "OE1" <-> "OE2" Residue "B GLU 321": "OE1" <-> "OE2" Residue "B GLU 339": "OE1" <-> "OE2" Residue "B GLU 356": "OE1" <-> "OE2" Residue "B TYR 408": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 439": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 456": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 24": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 26": "OD1" <-> "OD2" Residue "D ASP 28": "OD1" <-> "OD2" Residue "D PHE 35": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 46": "OD1" <-> "OD2" Residue "D ASP 67": "OD1" <-> "OD2" Residue "D GLU 156": "OE1" <-> "OE2" Residue "D TYR 179": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 316": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 360": "OE1" <-> "OE2" Residue "D GLU 400": "OE1" <-> "OE2" Residue "D TYR 439": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 454": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d TYR 24": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d PHE 35": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d ASP 46": "OD1" <-> "OD2" Residue "d ASP 63": "OD1" <-> "OD2" Residue "d ASP 73": "OD1" <-> "OD2" Residue "d TYR 179": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d ASP 219": "OD1" <-> "OD2" Residue "d ASP 268": "OD1" <-> "OD2" Residue "d TYR 269": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d GLU 279": "OE1" <-> "OE2" Residue "d GLU 329": "OE1" <-> "OE2" Residue "d ASP 332": "OD1" <-> "OD2" Residue "d GLU 334": "OE1" <-> "OE2" Residue "d ASP 354": "OD1" <-> "OD2" Residue "d PHE 454": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d ASP 533": "OD1" <-> "OD2" Residue "E ASP 56": "OD1" <-> "OD2" Residue "E ASP 80": "OD1" <-> "OD2" Residue "E ASP 82": "OD1" <-> "OD2" Residue "E GLU 99": "OE1" <-> "OE2" Residue "E PHE 204": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 210": "OE1" <-> "OE2" Residue "E ASP 231": "OD1" <-> "OD2" Residue "E PHE 232": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 242": "OE1" <-> "OE2" Residue "E PHE 253": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 265": "OD1" <-> "OD2" Residue "E GLU 270": "OE1" <-> "OE2" Residue "E ASP 271": "OD1" <-> "OD2" Residue "E TYR 278": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 281": "OE1" <-> "OE2" Residue "E PHE 283": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 285": "OE1" <-> "OE2" Residue "E GLU 292": "OE1" <-> "OE2" Residue "E PHE 304": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 305": "OD1" <-> "OD2" Residue "E GLU 329": "OE1" <-> "OE2" Residue "E PHE 343": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 349": "OE1" <-> "OE2" Residue "E GLU 395": "OE1" <-> "OE2" Residue "E TYR 418": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 474": "OE1" <-> "OE2" Residue "E ASP 530": "OD1" <-> "OD2" Residue "e ASP 123": "OD1" <-> "OD2" Residue "e ASP 156": "OD1" <-> "OD2" Residue "e PHE 204": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "e PHE 232": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "e ASP 243": "OD1" <-> "OD2" Residue "e TYR 278": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "e GLU 281": "OE1" <-> "OE2" Residue "e PHE 283": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "e PHE 304": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "e ASP 305": "OD1" <-> "OD2" Residue "e PHE 343": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "e GLU 349": "OE1" <-> "OE2" Residue "e PHE 353": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "e PHE 362": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "e GLU 394": "OE1" <-> "OE2" Residue "e GLU 395": "OE1" <-> "OE2" Residue "e TYR 418": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "e PHE 449": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "e GLU 506": "OE1" <-> "OE2" Residue "g ASP 150": "OD1" <-> "OD2" Residue "g GLU 187": "OE1" <-> "OE2" Residue "g ASP 255": "OD1" <-> "OD2" Residue "g ASP 263": "OD1" <-> "OD2" Residue "g PHE 264": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "g GLU 280": "OE1" <-> "OE2" Residue "g TYR 303": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "g ASP 357": "OD1" <-> "OD2" Residue "g TYR 359": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "g PHE 360": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "g ASP 393": "OD1" <-> "OD2" Residue "g GLU 473": "OE1" <-> "OE2" Residue "g GLU 476": "OE1" <-> "OE2" Residue "G PHE 185": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 187": "OE1" <-> "OE2" Residue "G TYR 198": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 263": "OD1" <-> "OD2" Residue "G GLU 272": "OE1" <-> "OE2" Residue "G ASP 298": "OD1" <-> "OD2" Residue "G ASP 341": "OD1" <-> "OD2" Residue "G PHE 362": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 393": "OD1" <-> "OD2" Residue "G TYR 506": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 521": "OD1" <-> "OD2" Residue "h ASP 14": "OD1" <-> "OD2" Residue "h ASP 81": "OD1" <-> "OD2" Residue "h PHE 104": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "h TYR 111": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "h ASP 147": "OD1" <-> "OD2" Residue "h PHE 174": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "h ASP 188": "OD1" <-> "OD2" Residue "h PHE 216": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "h TYR 222": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "h PHE 225": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "h TYR 232": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "h ASP 251": "OD1" <-> "OD2" Residue "h TYR 263": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "h PHE 303": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "h PHE 360": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "h PHE 361": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "h TYR 438": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 11": "OE1" <-> "OE2" Residue "H ASP 70": "OD1" <-> "OD2" Residue "H TYR 111": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ASP 147": "OD1" <-> "OD2" Residue "H ASP 187": "OD1" <-> "OD2" Residue "H PHE 216": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 225": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 232": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 263": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ASP 268": "OD1" <-> "OD2" Residue "H PHE 303": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 360": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 361": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ASP 391": "OD1" <-> "OD2" Residue "H TYR 438": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 475": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 491": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q PHE 11": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q PHE 22": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q PHE 64": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q PHE 103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q PHE 178": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q PHE 197": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q TYR 242": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q GLU 264": "OE1" <-> "OE2" Residue "Q PHE 268": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q GLU 272": "OE1" <-> "OE2" Residue "Q GLU 273": "OE1" <-> "OE2" Residue "Q TYR 304": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q TYR 351": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q GLU 366": "OE1" <-> "OE2" Residue "Q ASP 369": "OD1" <-> "OD2" Residue "Q TYR 436": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q PHE 441": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q PHE 445": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q TYR 468": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q GLU 485": "OE1" <-> "OE2" Residue "q PHE 22": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "q GLU 26": "OE1" <-> "OE2" Residue "q PHE 64": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "q PHE 103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "q ASP 158": "OD1" <-> "OD2" Residue "q PHE 178": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "q TYR 242": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "q GLU 264": "OE1" <-> "OE2" Residue "q PHE 268": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "q TYR 304": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "q TYR 308": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "q TYR 351": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "q ASP 357": "OD1" <-> "OD2" Residue "q GLU 366": "OE1" <-> "OE2" Residue "q TYR 436": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "q PHE 445": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "q TYR 468": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "q GLU 485": "OE1" <-> "OE2" Residue "Z ASP 32": "OD1" <-> "OD2" Residue "Z ASP 85": "OD1" <-> "OD2" Residue "Z ASP 107": "OD1" <-> "OD2" Residue "Z TYR 109": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z PHE 189": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z ASP 213": "OD1" <-> "OD2" Residue "Z PHE 248": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z PHE 249": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z TYR 250": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z ASP 269": "OD1" <-> "OD2" Residue "Z ASP 284": "OD1" <-> "OD2" Residue "Z PHE 336": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z TYR 351": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z TYR 353": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z PHE 440": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z ASP 442": "OD1" <-> "OD2" Residue "Z PHE 457": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z GLU 472": "OE1" <-> "OE2" Residue "z ASP 32": "OD1" <-> "OD2" Residue "z ASP 107": "OD1" <-> "OD2" Residue "z TYR 109": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "z ASP 166": "OD1" <-> "OD2" Residue "z PHE 189": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "z PHE 248": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "z TYR 250": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "z GLU 254": "OE1" <-> "OE2" Residue "z ASP 286": "OD1" <-> "OD2" Residue "z PHE 336": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "z ASP 337": "OD1" <-> "OD2" Residue "z ASP 342": "OD1" <-> "OD2" Residue "z TYR 351": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "z GLU 357": "OE1" <-> "OE2" Residue "z PHE 360": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "z ASP 389": "OD1" <-> "OD2" Residue "z ASP 393": "OD1" <-> "OD2" Residue "z ASP 404": "OD1" <-> "OD2" Residue "z PHE 440": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "z PHE 457": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.16s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 62495 Number of models: 1 Model: "" Number of chains: 32 Chain: "a" Number of atoms: 4017 Number of conformers: 1 Conformer: "" Number of residues, atoms: 529, 4017 Classifications: {'peptide': 529} Link IDs: {'PTRANS': 12, 'TRANS': 516} Chain: "A" Number of atoms: 3285 Number of conformers: 1 Conformer: "" Number of residues, atoms: 433, 3285 Classifications: {'peptide': 433} Link IDs: {'PTRANS': 10, 'TRANS': 422} Chain breaks: 6 Chain: "b" Number of atoms: 3891 Number of conformers: 1 Conformer: "" Number of residues, atoms: 517, 3891 Classifications: {'peptide': 517} Link IDs: {'PTRANS': 9, 'TRANS': 507} Chain: "B" Number of atoms: 3891 Number of conformers: 1 Conformer: "" Number of residues, atoms: 517, 3891 Classifications: {'peptide': 517} Link IDs: {'PTRANS': 9, 'TRANS': 507} Chain: "D" Number of atoms: 3341 Number of conformers: 1 Conformer: "" Number of residues, atoms: 439, 3341 Classifications: {'peptide': 439} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 12, 'TRANS': 426} Chain breaks: 8 Chain: "d" Number of atoms: 3902 Number of conformers: 1 Conformer: "" Number of residues, atoms: 516, 3902 Classifications: {'peptide': 516} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 14, 'TRANS': 500} Chain: "E" Number of atoms: 4000 Number of conformers: 1 Conformer: "" Number of residues, atoms: 520, 4000 Classifications: {'peptide': 520} Link IDs: {'PTRANS': 17, 'TRANS': 502} Chain: "e" Number of atoms: 4000 Number of conformers: 1 Conformer: "" Number of residues, atoms: 520, 4000 Classifications: {'peptide': 520} Link IDs: {'PTRANS': 17, 'TRANS': 502} Chain: "g" Number of atoms: 3979 Number of conformers: 1 Conformer: "" Number of residues, atoms: 512, 3979 Classifications: {'peptide': 512} Link IDs: {'PTRANS': 16, 'TRANS': 495} Chain: "G" Number of atoms: 3817 Number of conformers: 1 Conformer: "" Number of residues, atoms: 492, 3817 Classifications: {'peptide': 492} Link IDs: {'PTRANS': 16, 'TRANS': 475} Chain breaks: 1 Chain: "h" Number of atoms: 3987 Number of conformers: 1 Conformer: "" Number of residues, atoms: 519, 3987 Classifications: {'peptide': 519} Link IDs: {'PTRANS': 14, 'TRANS': 504} Chain: "H" Number of atoms: 3987 Number of conformers: 1 Conformer: "" Number of residues, atoms: 519, 3987 Classifications: {'peptide': 519} Link IDs: {'PTRANS': 14, 'TRANS': 504} Chain: "Q" Number of atoms: 3987 Number of conformers: 1 Conformer: "" Number of residues, atoms: 523, 3987 Classifications: {'peptide': 523} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 508} Chain: "q" Number of atoms: 3987 Number of conformers: 1 Conformer: "" Number of residues, atoms: 523, 3987 Classifications: {'peptide': 523} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 508} Chain: "Z" Number of atoms: 3996 Number of conformers: 1 Conformer: "" Number of residues, atoms: 521, 3996 Classifications: {'peptide': 521} Link IDs: {'PTRANS': 14, 'TRANS': 506} Chain: "z" Number of atoms: 3996 Number of conformers: 1 Conformer: "" Number of residues, atoms: 521, 3996 Classifications: {'peptide': 521} Link IDs: {'PTRANS': 14, 'TRANS': 506} Chain: "a" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "A" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "b" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "d" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "e" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "g" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "G" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "h" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "H" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "Q" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "q" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "Z" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "z" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 24.72, per 1000 atoms: 0.40 Number of scatterers: 62495 At special positions: 0 Unit cell: (221.424, 193.746, 209.562, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 385 16.00 P 32 15.00 O 12084 8.00 N 10894 7.00 C 39100 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=4, symmetry=0 Number of additional bonds: simple=4, symmetry=0 Coordination: Other bonds: Time building additional restraints: 19.40 Conformation dependent library (CDL) restraints added in 9.1 seconds 16118 Ramachandran restraints generated. 8059 Oldfield, 0 Emsley, 8059 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 15150 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 292 helices and 85 sheets defined 50.8% alpha, 7.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 10.15 Creating SS restraints... Processing helix chain 'a' and resid 15 through 32 removed outlier: 3.757A pdb=" N VAL a 32 " --> pdb=" O ILE a 28 " (cutoff:3.500A) Processing helix chain 'a' and resid 58 through 64 Processing helix chain 'a' and resid 70 through 85 removed outlier: 3.506A pdb=" N LEU a 75 " --> pdb=" O ALA a 71 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N LEU a 81 " --> pdb=" O GLU a 77 " (cutoff:3.500A) Processing helix chain 'a' and resid 90 through 110 removed outlier: 3.562A pdb=" N GLU a 106 " --> pdb=" O LYS a 102 " (cutoff:3.500A) Processing helix chain 'a' and resid 114 through 135 Processing helix chain 'a' and resid 149 through 156 Processing helix chain 'a' and resid 160 through 178 removed outlier: 3.604A pdb=" N ILE a 163 " --> pdb=" O ILE a 160 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N ASN a 164 " --> pdb=" O ILE a 161 " (cutoff:3.500A) removed outlier: 4.237A pdb=" N GLY a 165 " --> pdb=" O GLY a 162 " (cutoff:3.500A) removed outlier: 6.494A pdb=" N ASP a 166 " --> pdb=" O ILE a 163 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N PHE a 167 " --> pdb=" O ASN a 164 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N ASN a 170 " --> pdb=" O PHE a 167 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N VAL a 173 " --> pdb=" O ASN a 170 " (cutoff:3.500A) removed outlier: 4.232A pdb=" N ASP a 174 " --> pdb=" O MET a 171 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N LEU a 177 " --> pdb=" O ASP a 174 " (cutoff:3.500A) Processing helix chain 'a' and resid 205 through 207 No H-bonds generated for 'chain 'a' and resid 205 through 207' Processing helix chain 'a' and resid 257 through 280 removed outlier: 3.562A pdb=" N ASP a 261 " --> pdb=" O PRO a 257 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N GLN a 262 " --> pdb=" O GLU a 258 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N THR a 271 " --> pdb=" O GLU a 267 " (cutoff:3.500A) removed outlier: 4.351A pdb=" N LYS a 272 " --> pdb=" O SER a 268 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N GLU a 273 " --> pdb=" O ASP a 269 " (cutoff:3.500A) Processing helix chain 'a' and resid 294 through 303 Processing helix chain 'a' and resid 313 through 323 removed outlier: 3.525A pdb=" N ILE a 319 " --> pdb=" O ASP a 315 " (cutoff:3.500A) Processing helix chain 'a' and resid 382 through 404 removed outlier: 3.670A pdb=" N ARG a 390 " --> pdb=" O ASP a 386 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N CYS a 397 " --> pdb=" O HIS a 393 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N VAL a 402 " --> pdb=" O VAL a 398 " (cutoff:3.500A) Processing helix chain 'a' and resid 414 through 430 removed outlier: 3.811A pdb=" N ILE a 421 " --> pdb=" O ALA a 417 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N GLU a 424 " --> pdb=" O SER a 420 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N THR a 428 " --> pdb=" O GLU a 424 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N SER a 429 " --> pdb=" O ASN a 425 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N MET a 430 " --> pdb=" O TYR a 426 " (cutoff:3.500A) Processing helix chain 'a' and resid 435 through 455 removed outlier: 3.554A pdb=" N LEU a 445 " --> pdb=" O PHE a 441 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N LEU a 446 " --> pdb=" O ALA a 442 " (cutoff:3.500A) removed outlier: 4.415A pdb=" N VAL a 447 " --> pdb=" O ARG a 443 " (cutoff:3.500A) removed outlier: 4.883A pdb=" N ILE a 448 " --> pdb=" O SER a 444 " (cutoff:3.500A) Proline residue: a 449 - end of helix Processing helix chain 'a' and resid 460 through 476 removed outlier: 3.517A pdb=" N GLN a 475 " --> pdb=" O HIS a 471 " (cutoff:3.500A) Processing helix chain 'a' and resid 498 through 501 No H-bonds generated for 'chain 'a' and resid 498 through 501' Processing helix chain 'a' and resid 507 through 525 Processing helix chain 'A' and resid 15 through 32 removed outlier: 3.514A pdb=" N VAL A 32 " --> pdb=" O ILE A 28 " (cutoff:3.500A) Processing helix chain 'A' and resid 58 through 64 Processing helix chain 'A' and resid 70 through 85 removed outlier: 3.616A pdb=" N LEU A 75 " --> pdb=" O ALA A 71 " (cutoff:3.500A) Processing helix chain 'A' and resid 90 through 110 Processing helix chain 'A' and resid 114 through 135 Processing helix chain 'A' and resid 148 through 155 removed outlier: 4.110A pdb=" N ALA A 152 " --> pdb=" O LEU A 148 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N LYS A 153 " --> pdb=" O ILE A 149 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N THR A 154 " --> pdb=" O ASN A 150 " (cutoff:3.500A) removed outlier: 4.101A pdb=" N SER A 155 " --> pdb=" O ALA A 151 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 148 through 155' Processing helix chain 'A' and resid 161 through 163 No H-bonds generated for 'chain 'A' and resid 161 through 163' Processing helix chain 'A' and resid 165 through 178 removed outlier: 3.839A pdb=" N MET A 171 " --> pdb=" O PHE A 167 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N VAL A 172 " --> pdb=" O PHE A 168 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ASP A 174 " --> pdb=" O ASN A 170 " (cutoff:3.500A) Processing helix chain 'A' and resid 294 through 303 removed outlier: 3.992A pdb=" N LYS A 298 " --> pdb=" O ASP A 294 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N TYR A 299 " --> pdb=" O MET A 295 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N PHE A 300 " --> pdb=" O CYS A 296 " (cutoff:3.500A) Processing helix chain 'A' and resid 313 through 322 Processing helix chain 'A' and resid 382 through 404 removed outlier: 3.820A pdb=" N GLU A 387 " --> pdb=" O PHE A 383 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N ARG A 390 " --> pdb=" O ASP A 386 " (cutoff:3.500A) Processing helix chain 'A' and resid 414 through 430 removed outlier: 3.679A pdb=" N ILE A 421 " --> pdb=" O ALA A 417 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N GLU A 424 " --> pdb=" O SER A 420 " (cutoff:3.500A) removed outlier: 4.076A pdb=" N THR A 428 " --> pdb=" O GLU A 424 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N SER A 429 " --> pdb=" O ASN A 425 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N MET A 430 " --> pdb=" O TYR A 426 " (cutoff:3.500A) Processing helix chain 'A' and resid 435 through 455 removed outlier: 3.565A pdb=" N LEU A 445 " --> pdb=" O PHE A 441 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N LEU A 446 " --> pdb=" O ALA A 442 " (cutoff:3.500A) removed outlier: 4.111A pdb=" N VAL A 447 " --> pdb=" O ARG A 443 " (cutoff:3.500A) removed outlier: 4.875A pdb=" N ILE A 448 " --> pdb=" O SER A 444 " (cutoff:3.500A) Proline residue: A 449 - end of helix Processing helix chain 'A' and resid 460 through 476 Processing helix chain 'A' and resid 498 through 501 No H-bonds generated for 'chain 'A' and resid 498 through 501' Processing helix chain 'A' and resid 507 through 525 removed outlier: 3.678A pdb=" N LEU A 514 " --> pdb=" O LYS A 510 " (cutoff:3.500A) Processing helix chain 'b' and resid 21 through 39 removed outlier: 3.755A pdb=" N LEU b 26 " --> pdb=" O GLU b 22 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N PHE b 29 " --> pdb=" O ARG b 25 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N ILE b 35 " --> pdb=" O GLY b 31 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N VAL b 39 " --> pdb=" O ILE b 35 " (cutoff:3.500A) Processing helix chain 'b' and resid 67 through 73 removed outlier: 3.571A pdb=" N ASN b 73 " --> pdb=" O THR b 69 " (cutoff:3.500A) Processing helix chain 'b' and resid 79 through 94 removed outlier: 3.765A pdb=" N GLN b 91 " --> pdb=" O MET b 87 " (cutoff:3.500A) Processing helix chain 'b' and resid 99 through 119 removed outlier: 3.503A pdb=" N THR b 103 " --> pdb=" O THR b 99 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N SER b 115 " --> pdb=" O ARG b 111 " (cutoff:3.500A) Processing helix chain 'b' and resid 123 through 144 removed outlier: 3.580A pdb=" N GLY b 129 " --> pdb=" O THR b 125 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N LEU b 141 " --> pdb=" O ALA b 137 " (cutoff:3.500A) Processing helix chain 'b' and resid 152 through 167 Processing helix chain 'b' and resid 171 through 173 No H-bonds generated for 'chain 'b' and resid 171 through 173' Processing helix chain 'b' and resid 176 through 190 removed outlier: 3.949A pdb=" N LYS b 181 " --> pdb=" O ASP b 177 " (cutoff:3.500A) Processing helix chain 'b' and resid 196 through 198 No H-bonds generated for 'chain 'b' and resid 196 through 198' Processing helix chain 'b' and resid 209 through 211 No H-bonds generated for 'chain 'b' and resid 209 through 211' Processing helix chain 'b' and resid 261 through 285 removed outlier: 3.904A pdb=" N HIS b 285 " --> pdb=" O ARG b 281 " (cutoff:3.500A) Processing helix chain 'b' and resid 298 through 306 removed outlier: 3.556A pdb=" N LEU b 303 " --> pdb=" O TYR b 299 " (cutoff:3.500A) Processing helix chain 'b' and resid 317 through 326 removed outlier: 3.643A pdb=" N ALA b 324 " --> pdb=" O VAL b 320 " (cutoff:3.500A) removed outlier: 4.593A pdb=" N LEU b 325 " --> pdb=" O GLU b 321 " (cutoff:3.500A) Processing helix chain 'b' and resid 380 through 402 Processing helix chain 'b' and resid 412 through 426 removed outlier: 3.754A pdb=" N ASN b 426 " --> pdb=" O THR b 422 " (cutoff:3.500A) Processing helix chain 'b' and resid 430 through 454 removed outlier: 3.859A pdb=" N VAL b 434 " --> pdb=" O GLY b 430 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N SER b 438 " --> pdb=" O VAL b 434 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N LEU b 446 " --> pdb=" O ALA b 442 " (cutoff:3.500A) Proline residue: b 447 - end of helix Processing helix chain 'b' and resid 458 through 470 Processing helix chain 'b' and resid 488 through 491 No H-bonds generated for 'chain 'b' and resid 488 through 491' Processing helix chain 'b' and resid 497 through 516 removed outlier: 3.511A pdb=" N ILE b 514 " --> pdb=" O ALA b 510 " (cutoff:3.500A) Processing helix chain 'B' and resid 21 through 40 removed outlier: 3.647A pdb=" N ILE B 35 " --> pdb=" O GLY B 31 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N VAL B 39 " --> pdb=" O ILE B 35 " (cutoff:3.500A) Processing helix chain 'B' and resid 58 through 60 No H-bonds generated for 'chain 'B' and resid 58 through 60' Processing helix chain 'B' and resid 67 through 73 removed outlier: 3.789A pdb=" N ASN B 73 " --> pdb=" O THR B 69 " (cutoff:3.500A) Processing helix chain 'B' and resid 79 through 93 Processing helix chain 'B' and resid 99 through 119 removed outlier: 3.711A pdb=" N SER B 115 " --> pdb=" O ARG B 111 " (cutoff:3.500A) Processing helix chain 'B' and resid 123 through 144 Processing helix chain 'B' and resid 152 through 166 Processing helix chain 'B' and resid 171 through 173 No H-bonds generated for 'chain 'B' and resid 171 through 173' Processing helix chain 'B' and resid 176 through 190 removed outlier: 4.007A pdb=" N LYS B 181 " --> pdb=" O ASP B 177 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N VAL B 184 " --> pdb=" O THR B 180 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N LEU B 190 " --> pdb=" O ALA B 186 " (cutoff:3.500A) Processing helix chain 'B' and resid 209 through 211 No H-bonds generated for 'chain 'B' and resid 209 through 211' Processing helix chain 'B' and resid 261 through 285 removed outlier: 3.511A pdb=" N GLU B 268 " --> pdb=" O VAL B 264 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N LYS B 272 " --> pdb=" O GLU B 268 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N MET B 275 " --> pdb=" O GLU B 271 " (cutoff:3.500A) removed outlier: 4.318A pdb=" N HIS B 285 " --> pdb=" O ARG B 281 " (cutoff:3.500A) Processing helix chain 'B' and resid 298 through 306 removed outlier: 3.585A pdb=" N LEU B 303 " --> pdb=" O TYR B 299 " (cutoff:3.500A) Processing helix chain 'B' and resid 317 through 327 removed outlier: 3.858A pdb=" N LEU B 325 " --> pdb=" O GLU B 321 " (cutoff:3.500A) Processing helix chain 'B' and resid 380 through 402 removed outlier: 3.761A pdb=" N ARG B 388 " --> pdb=" O ASP B 384 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N GLN B 399 " --> pdb=" O CYS B 395 " (cutoff:3.500A) Processing helix chain 'B' and resid 412 through 426 removed outlier: 3.730A pdb=" N ASN B 426 " --> pdb=" O THR B 422 " (cutoff:3.500A) Processing helix chain 'B' and resid 430 through 454 removed outlier: 3.960A pdb=" N VAL B 434 " --> pdb=" O GLY B 430 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N ALA B 435 " --> pdb=" O LYS B 431 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N LEU B 446 " --> pdb=" O ALA B 442 " (cutoff:3.500A) Proline residue: B 447 - end of helix Processing helix chain 'B' and resid 458 through 469 Processing helix chain 'B' and resid 488 through 491 No H-bonds generated for 'chain 'B' and resid 488 through 491' Processing helix chain 'B' and resid 497 through 516 Processing helix chain 'D' and resid 30 through 51 removed outlier: 4.089A pdb=" N PHE D 35 " --> pdb=" O GLN D 32 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N ILE D 38 " --> pdb=" O PHE D 35 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N SER D 39 " --> pdb=" O SER D 36 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N ALA D 40 " --> pdb=" O ASN D 37 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N LYS D 42 " --> pdb=" O SER D 39 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N ALA D 43 " --> pdb=" O ALA D 40 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N ALA D 47 " --> pdb=" O VAL D 44 " (cutoff:3.500A) removed outlier: 4.337A pdb=" N ARG D 49 " --> pdb=" O ASP D 46 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N THR D 50 " --> pdb=" O ALA D 47 " (cutoff:3.500A) Processing helix chain 'D' and resid 74 through 79 Processing helix chain 'D' and resid 86 through 101 Processing helix chain 'D' and resid 106 through 125 removed outlier: 3.767A pdb=" N VAL D 110 " --> pdb=" O THR D 106 " (cutoff:3.500A) removed outlier: 4.109A pdb=" N LYS D 122 " --> pdb=" O ASP D 118 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N LEU D 123 " --> pdb=" O SER D 119 " (cutoff:3.500A) Processing helix chain 'D' and resid 130 through 151 Processing helix chain 'D' and resid 160 through 172 Processing helix chain 'D' and resid 180 through 194 Proline residue: D 185 - end of helix removed outlier: 3.650A pdb=" N VAL D 191 " --> pdb=" O SER D 187 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N VAL D 194 " --> pdb=" O ALA D 190 " (cutoff:3.500A) Processing helix chain 'D' and resid 205 through 207 No H-bonds generated for 'chain 'D' and resid 205 through 207' Processing helix chain 'D' and resid 275 through 292 Processing helix chain 'D' and resid 312 through 319 Processing helix chain 'D' and resid 331 through 339 Processing helix chain 'D' and resid 348 through 350 No H-bonds generated for 'chain 'D' and resid 348 through 350' Processing helix chain 'D' and resid 353 through 355 No H-bonds generated for 'chain 'D' and resid 353 through 355' Processing helix chain 'D' and resid 395 through 417 Processing helix chain 'D' and resid 427 through 442 removed outlier: 3.726A pdb=" N THR D 437 " --> pdb=" O ALA D 433 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N GLU D 438 " --> pdb=" O LEU D 434 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N ARG D 441 " --> pdb=" O THR D 437 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N THR D 442 " --> pdb=" O GLU D 438 " (cutoff:3.500A) Processing helix chain 'D' and resid 445 through 468 removed outlier: 3.882A pdb=" N SER D 448 " --> pdb=" O GLY D 445 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N TYR D 449 " --> pdb=" O MET D 446 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N VAL D 451 " --> pdb=" O SER D 448 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N ARG D 452 " --> pdb=" O TYR D 449 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N ALA D 457 " --> pdb=" O PHE D 454 " (cutoff:3.500A) Proline residue: D 462 - end of helix removed outlier: 3.852A pdb=" N ALA D 466 " --> pdb=" O SER D 463 " (cutoff:3.500A) Processing helix chain 'D' and resid 473 through 486 Processing helix chain 'D' and resid 512 through 530 Processing helix chain 'd' and resid 30 through 49 removed outlier: 3.618A pdb=" N PHE d 35 " --> pdb=" O GLN d 32 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N ILE d 38 " --> pdb=" O PHE d 35 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N SER d 39 " --> pdb=" O SER d 36 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N ALA d 40 " --> pdb=" O ASN d 37 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ALA d 43 " --> pdb=" O ALA d 40 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N ALA d 47 " --> pdb=" O VAL d 44 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N ARG d 49 " --> pdb=" O ASP d 46 " (cutoff:3.500A) Processing helix chain 'd' and resid 74 through 81 Processing helix chain 'd' and resid 86 through 101 removed outlier: 3.692A pdb=" N LEU d 91 " --> pdb=" O ALA d 87 " (cutoff:3.500A) Processing helix chain 'd' and resid 106 through 125 removed outlier: 3.959A pdb=" N VAL d 110 " --> pdb=" O THR d 106 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N LYS d 122 " --> pdb=" O ASP d 118 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N GLN d 125 " --> pdb=" O THR d 121 " (cutoff:3.500A) Processing helix chain 'd' and resid 130 through 150 removed outlier: 3.605A pdb=" N GLU d 146 " --> pdb=" O GLU d 142 " (cutoff:3.500A) Processing helix chain 'd' and resid 160 through 173 removed outlier: 3.597A pdb=" N SER d 173 " --> pdb=" O THR d 169 " (cutoff:3.500A) Processing helix chain 'd' and resid 180 through 194 Proline residue: d 185 - end of helix Processing helix chain 'd' and resid 205 through 207 No H-bonds generated for 'chain 'd' and resid 205 through 207' Processing helix chain 'd' and resid 269 through 293 removed outlier: 3.674A pdb=" N LEU d 276 " --> pdb=" O MET d 272 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N LEU d 286 " --> pdb=" O TYR d 282 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N THR d 293 " --> pdb=" O GLN d 289 " (cutoff:3.500A) Processing helix chain 'd' and resid 312 through 319 removed outlier: 3.754A pdb=" N PHE d 316 " --> pdb=" O LEU d 312 " (cutoff:3.500A) Processing helix chain 'd' and resid 330 through 340 removed outlier: 3.527A pdb=" N LYS d 338 " --> pdb=" O GLU d 334 " (cutoff:3.500A) Processing helix chain 'd' and resid 348 through 350 No H-bonds generated for 'chain 'd' and resid 348 through 350' Processing helix chain 'd' and resid 395 through 417 removed outlier: 3.662A pdb=" N ALA d 401 " --> pdb=" O VAL d 397 " (cutoff:3.500A) Processing helix chain 'd' and resid 427 through 442 removed outlier: 3.564A pdb=" N ARG d 441 " --> pdb=" O THR d 437 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N THR d 442 " --> pdb=" O GLU d 438 " (cutoff:3.500A) Processing helix chain 'd' and resid 445 through 468 removed outlier: 3.512A pdb=" N ARG d 452 " --> pdb=" O TYR d 449 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N ALA d 453 " --> pdb=" O CYS d 450 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N ASP d 456 " --> pdb=" O ALA d 453 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N ALA d 457 " --> pdb=" O PHE d 454 " (cutoff:3.500A) Proline residue: d 462 - end of helix removed outlier: 3.606A pdb=" N ALA d 466 " --> pdb=" O SER d 463 " (cutoff:3.500A) Processing helix chain 'd' and resid 473 through 486 removed outlier: 3.739A pdb=" N VAL d 477 " --> pdb=" O PRO d 473 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N ASN d 482 " --> pdb=" O THR d 478 " (cutoff:3.500A) Processing helix chain 'd' and resid 503 through 506 No H-bonds generated for 'chain 'd' and resid 503 through 506' Processing helix chain 'd' and resid 512 through 530 Processing helix chain 'E' and resid 29 through 47 removed outlier: 3.521A pdb=" N MET E 46 " --> pdb=" O VAL E 42 " (cutoff:3.500A) Processing helix chain 'E' and resid 72 through 78 Processing helix chain 'E' and resid 84 through 99 removed outlier: 3.523A pdb=" N MET E 89 " --> pdb=" O ILE E 85 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N SER E 95 " --> pdb=" O GLU E 91 " (cutoff:3.500A) removed outlier: 4.458A pdb=" N ASP E 98 " --> pdb=" O LYS E 94 " (cutoff:3.500A) Processing helix chain 'E' and resid 104 through 124 removed outlier: 3.635A pdb=" N VAL E 108 " --> pdb=" O THR E 104 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N GLN E 120 " --> pdb=" O GLU E 116 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N LEU E 121 " --> pdb=" O GLU E 117 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N ASP E 123 " --> pdb=" O GLU E 119 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N ARG E 124 " --> pdb=" O GLN E 120 " (cutoff:3.500A) Processing helix chain 'E' and resid 128 through 148 removed outlier: 3.826A pdb=" N ASP E 147 " --> pdb=" O ILE E 143 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N LYS E 148 " --> pdb=" O GLU E 144 " (cutoff:3.500A) Processing helix chain 'E' and resid 161 through 173 removed outlier: 3.847A pdb=" N ALA E 167 " --> pdb=" O LEU E 163 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N THR E 170 " --> pdb=" O THR E 166 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N LEU E 171 " --> pdb=" O ALA E 167 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N GLY E 172 " --> pdb=" O LYS E 168 " (cutoff:3.500A) removed outlier: 4.513A pdb=" N SER E 173 " --> pdb=" O THR E 169 " (cutoff:3.500A) Processing helix chain 'E' and resid 175 through 194 removed outlier: 4.146A pdb=" N SER E 178 " --> pdb=" O VAL E 175 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N HIS E 180 " --> pdb=" O ASN E 177 " (cutoff:3.500A) removed outlier: 6.168A pdb=" N ARG E 181 " --> pdb=" O SER E 178 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N GLU E 185 " --> pdb=" O GLN E 182 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ASN E 189 " --> pdb=" O ILE E 186 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N ALA E 190 " --> pdb=" O ALA E 187 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N VAL E 191 " --> pdb=" O VAL E 188 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N LEU E 192 " --> pdb=" O ASN E 189 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N VAL E 194 " --> pdb=" O VAL E 191 " (cutoff:3.500A) Processing helix chain 'E' and resid 217 through 219 No H-bonds generated for 'chain 'E' and resid 217 through 219' Processing helix chain 'E' and resid 269 through 293 removed outlier: 3.781A pdb=" N ALA E 274 " --> pdb=" O GLU E 270 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N LYS E 280 " --> pdb=" O GLN E 276 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N GLU E 284 " --> pdb=" O LYS E 280 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N GLU E 285 " --> pdb=" O GLU E 281 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N LYS E 291 " --> pdb=" O ILE E 287 " (cutoff:3.500A) Processing helix chain 'E' and resid 306 through 314 removed outlier: 3.583A pdb=" N LEU E 311 " --> pdb=" O GLU E 307 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N GLN E 314 " --> pdb=" O HIS E 310 " (cutoff:3.500A) Processing helix chain 'E' and resid 325 through 335 removed outlier: 4.169A pdb=" N GLU E 329 " --> pdb=" O GLY E 325 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N ILE E 331 " --> pdb=" O GLU E 327 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ALA E 334 " --> pdb=" O LEU E 330 " (cutoff:3.500A) Processing helix chain 'E' and resid 343 through 345 No H-bonds generated for 'chain 'E' and resid 343 through 345' Processing helix chain 'E' and resid 390 through 412 removed outlier: 3.581A pdb=" N ALA E 403 " --> pdb=" O SER E 399 " (cutoff:3.500A) Processing helix chain 'E' and resid 422 through 437 removed outlier: 3.938A pdb=" N ASP E 436 " --> pdb=" O SER E 432 " (cutoff:3.500A) removed outlier: 4.221A pdb=" N LYS E 437 " --> pdb=" O GLN E 433 " (cutoff:3.500A) Processing helix chain 'E' and resid 441 through 463 removed outlier: 3.565A pdb=" N TYR E 444 " --> pdb=" O LEU E 441 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N ARG E 447 " --> pdb=" O TYR E 444 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N ILE E 456 " --> pdb=" O LEU E 453 " (cutoff:3.500A) Proline residue: E 457 - end of helix removed outlier: 3.724A pdb=" N SER E 461 " --> pdb=" O MET E 458 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N ASN E 463 " --> pdb=" O LEU E 460 " (cutoff:3.500A) Processing helix chain 'E' and resid 468 through 478 Processing helix chain 'E' and resid 499 through 502 No H-bonds generated for 'chain 'E' and resid 499 through 502' Processing helix chain 'E' and resid 508 through 526 Processing helix chain 'e' and resid 29 through 49 removed outlier: 3.583A pdb=" N VAL e 42 " --> pdb=" O ALA e 38 " (cutoff:3.500A) removed outlier: 4.291A pdb=" N THR e 48 " --> pdb=" O ASN e 44 " (cutoff:3.500A) removed outlier: 4.784A pdb=" N SER e 49 " --> pdb=" O THR e 45 " (cutoff:3.500A) Processing helix chain 'e' and resid 72 through 78 Processing helix chain 'e' and resid 84 through 96 removed outlier: 4.131A pdb=" N SER e 93 " --> pdb=" O MET e 89 " (cutoff:3.500A) removed outlier: 4.165A pdb=" N LYS e 94 " --> pdb=" O VAL e 90 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N SER e 95 " --> pdb=" O GLU e 91 " (cutoff:3.500A) Processing helix chain 'e' and resid 105 through 123 removed outlier: 3.861A pdb=" N GLN e 120 " --> pdb=" O GLU e 116 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N LEU e 121 " --> pdb=" O GLU e 117 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N ASP e 123 " --> pdb=" O GLU e 119 " (cutoff:3.500A) Processing helix chain 'e' and resid 128 through 149 removed outlier: 3.568A pdb=" N ASP e 147 " --> pdb=" O ILE e 143 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N LYS e 148 " --> pdb=" O GLU e 144 " (cutoff:3.500A) Processing helix chain 'e' and resid 161 through 173 removed outlier: 3.824A pdb=" N GLN e 165 " --> pdb=" O GLU e 161 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N ALA e 167 " --> pdb=" O LEU e 163 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N THR e 169 " --> pdb=" O GLN e 165 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N GLY e 172 " --> pdb=" O LYS e 168 " (cutoff:3.500A) removed outlier: 4.124A pdb=" N SER e 173 " --> pdb=" O THR e 169 " (cutoff:3.500A) Processing helix chain 'e' and resid 175 through 194 removed outlier: 4.371A pdb=" N SER e 178 " --> pdb=" O VAL e 175 " (cutoff:3.500A) removed outlier: 5.842A pdb=" N ARG e 181 " --> pdb=" O SER e 178 " (cutoff:3.500A) removed outlier: 4.197A pdb=" N GLN e 182 " --> pdb=" O CYS e 179 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N MET e 183 " --> pdb=" O HIS e 180 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N ALA e 184 " --> pdb=" O ARG e 181 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N ILE e 186 " --> pdb=" O MET e 183 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ASN e 189 " --> pdb=" O ILE e 186 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N ALA e 190 " --> pdb=" O ALA e 187 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N VAL e 191 " --> pdb=" O VAL e 188 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N LEU e 192 " --> pdb=" O ASN e 189 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N VAL e 194 " --> pdb=" O VAL e 191 " (cutoff:3.500A) Processing helix chain 'e' and resid 217 through 219 No H-bonds generated for 'chain 'e' and resid 217 through 219' Processing helix chain 'e' and resid 269 through 293 removed outlier: 3.830A pdb=" N ALA e 274 " --> pdb=" O GLU e 270 " (cutoff:3.500A) removed outlier: 4.558A pdb=" N LYS e 291 " --> pdb=" O ILE e 287 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N GLU e 292 " --> pdb=" O GLN e 288 " (cutoff:3.500A) Processing helix chain 'e' and resid 306 through 315 removed outlier: 3.651A pdb=" N GLN e 314 " --> pdb=" O HIS e 310 " (cutoff:3.500A) Processing helix chain 'e' and resid 325 through 335 removed outlier: 3.561A pdb=" N GLU e 329 " --> pdb=" O GLY e 325 " (cutoff:3.500A) Processing helix chain 'e' and resid 343 through 345 No H-bonds generated for 'chain 'e' and resid 343 through 345' Processing helix chain 'e' and resid 390 through 412 removed outlier: 3.548A pdb=" N LEU e 400 " --> pdb=" O ALA e 396 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N ALA e 403 " --> pdb=" O SER e 399 " (cutoff:3.500A) Processing helix chain 'e' and resid 422 through 437 removed outlier: 3.559A pdb=" N LEU e 429 " --> pdb=" O ILE e 425 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N ASP e 436 " --> pdb=" O SER e 432 " (cutoff:3.500A) removed outlier: 4.260A pdb=" N LYS e 437 " --> pdb=" O GLN e 433 " (cutoff:3.500A) Processing helix chain 'e' and resid 441 through 464 removed outlier: 3.717A pdb=" N TYR e 444 " --> pdb=" O LEU e 441 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N ARG e 447 " --> pdb=" O TYR e 444 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ASP e 451 " --> pdb=" O ALA e 448 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N ILE e 456 " --> pdb=" O LEU e 453 " (cutoff:3.500A) Proline residue: e 457 - end of helix removed outlier: 4.026A pdb=" N SER e 461 " --> pdb=" O MET e 458 " (cutoff:3.500A) Processing helix chain 'e' and resid 468 through 480 Processing helix chain 'e' and resid 499 through 502 No H-bonds generated for 'chain 'e' and resid 499 through 502' Processing helix chain 'e' and resid 508 through 527 Processing helix chain 'g' and resid 19 through 36 removed outlier: 3.549A pdb=" N GLN g 23 " --> pdb=" O ARG g 20 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N SER g 24 " --> pdb=" O LYS g 21 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N ILE g 27 " --> pdb=" O SER g 24 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N LYS g 31 " --> pdb=" O ASN g 28 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N ILE g 36 " --> pdb=" O ILE g 33 " (cutoff:3.500A) Processing helix chain 'g' and resid 63 through 69 Processing helix chain 'g' and resid 75 through 90 Processing helix chain 'g' and resid 95 through 106 removed outlier: 3.660A pdb=" N ILE g 99 " --> pdb=" O THR g 95 " (cutoff:3.500A) Processing helix chain 'g' and resid 119 through 139 removed outlier: 3.579A pdb=" N ASP g 131 " --> pdb=" O ARG g 127 " (cutoff:3.500A) Processing helix chain 'g' and resid 149 through 160 removed outlier: 4.371A pdb=" N SER g 158 " --> pdb=" O ASN g 154 " (cutoff:3.500A) removed outlier: 5.201A pdb=" N SER g 159 " --> pdb=" O ILE g 155 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N ILE g 160 " --> pdb=" O ILE g 156 " (cutoff:3.500A) Processing helix chain 'g' and resid 164 through 183 removed outlier: 3.773A pdb=" N ARG g 167 " --> pdb=" O ALA g 164 " (cutoff:3.500A) removed outlier: 6.044A pdb=" N SER g 170 " --> pdb=" O ARG g 167 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ILE g 175 " --> pdb=" O ALA g 172 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N LEU g 177 " --> pdb=" O ASN g 174 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N ASP g 178 " --> pdb=" O ILE g 175 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N ALA g 179 " --> pdb=" O ALA g 176 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N VAL g 180 " --> pdb=" O LEU g 177 " (cutoff:3.500A) Processing helix chain 'g' and resid 186 through 188 No H-bonds generated for 'chain 'g' and resid 186 through 188' Processing helix chain 'g' and resid 195 through 198 No H-bonds generated for 'chain 'g' and resid 195 through 198' Processing helix chain 'g' and resid 209 through 211 No H-bonds generated for 'chain 'g' and resid 209 through 211' Processing helix chain 'g' and resid 261 through 285 removed outlier: 3.728A pdb=" N THR g 265 " --> pdb=" O GLU g 261 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N ARG g 266 " --> pdb=" O GLU g 262 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N TYR g 274 " --> pdb=" O MET g 270 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N ILE g 275 " --> pdb=" O GLU g 271 " (cutoff:3.500A) removed outlier: 4.416A pdb=" N LEU g 285 " --> pdb=" O ASP g 281 " (cutoff:3.500A) Processing helix chain 'g' and resid 298 through 306 removed outlier: 3.776A pdb=" N TYR g 303 " --> pdb=" O LEU g 299 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N LEU g 304 " --> pdb=" O ALA g 300 " (cutoff:3.500A) Processing helix chain 'g' and resid 317 through 326 removed outlier: 3.660A pdb=" N ILE g 323 " --> pdb=" O ASP g 319 " (cutoff:3.500A) Processing helix chain 'g' and resid 381 through 403 removed outlier: 3.928A pdb=" N ASP g 393 " --> pdb=" O ARG g 389 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N ALA g 394 " --> pdb=" O ASN g 390 " (cutoff:3.500A) Processing helix chain 'g' and resid 413 through 428 removed outlier: 3.547A pdb=" N ALA g 421 " --> pdb=" O ALA g 417 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N LYS g 427 " --> pdb=" O THR g 423 " (cutoff:3.500A) removed outlier: 4.712A pdb=" N ALA g 428 " --> pdb=" O GLU g 424 " (cutoff:3.500A) Processing helix chain 'g' and resid 432 through 455 removed outlier: 3.509A pdb=" N TRP g 435 " --> pdb=" O VAL g 432 " (cutoff:3.500A) Proline residue: g 436 - end of helix removed outlier: 3.672A pdb=" N VAL g 440 " --> pdb=" O TYR g 437 " (cutoff:3.500A) Proline residue: g 448 - end of helix removed outlier: 3.808A pdb=" N ILE g 452 " --> pdb=" O ARG g 449 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N ASN g 454 " --> pdb=" O LEU g 451 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N CYS g 455 " --> pdb=" O ILE g 452 " (cutoff:3.500A) Processing helix chain 'g' and resid 459 through 472 Processing helix chain 'g' and resid 499 through 518 Processing helix chain 'G' and resid 19 through 36 removed outlier: 3.513A pdb=" N GLN G 23 " --> pdb=" O ARG G 20 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N SER G 24 " --> pdb=" O LYS G 21 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N ASN G 26 " --> pdb=" O GLN G 23 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N ILE G 27 " --> pdb=" O SER G 24 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N LYS G 31 " --> pdb=" O ASN G 28 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ILE G 33 " --> pdb=" O ALA G 30 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N ILE G 36 " --> pdb=" O ILE G 33 " (cutoff:3.500A) Processing helix chain 'G' and resid 63 through 69 Processing helix chain 'G' and resid 75 through 90 removed outlier: 3.638A pdb=" N SER G 84 " --> pdb=" O MET G 80 " (cutoff:3.500A) Processing helix chain 'G' and resid 95 through 106 removed outlier: 3.626A pdb=" N ILE G 99 " --> pdb=" O THR G 95 " (cutoff:3.500A) Processing helix chain 'G' and resid 119 through 139 removed outlier: 3.761A pdb=" N LYS G 139 " --> pdb=" O SER G 135 " (cutoff:3.500A) Processing helix chain 'G' and resid 149 through 160 removed outlier: 3.557A pdb=" N ILE G 155 " --> pdb=" O MET G 151 " (cutoff:3.500A) removed outlier: 4.477A pdb=" N SER G 158 " --> pdb=" O ASN G 154 " (cutoff:3.500A) removed outlier: 4.717A pdb=" N SER G 159 " --> pdb=" O ILE G 155 " (cutoff:3.500A) Processing helix chain 'G' and resid 164 through 183 removed outlier: 3.674A pdb=" N ARG G 167 " --> pdb=" O ALA G 164 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N SER G 169 " --> pdb=" O SER G 166 " (cutoff:3.500A) removed outlier: 6.014A pdb=" N SER G 170 " --> pdb=" O ARG G 167 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N CYS G 173 " --> pdb=" O SER G 170 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N ILE G 175 " --> pdb=" O ALA G 172 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N LEU G 177 " --> pdb=" O ASN G 174 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N ASP G 178 " --> pdb=" O ILE G 175 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N VAL G 180 " --> pdb=" O LEU G 177 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N MET G 182 " --> pdb=" O ALA G 179 " (cutoff:3.500A) Processing helix chain 'G' and resid 186 through 188 No H-bonds generated for 'chain 'G' and resid 186 through 188' Processing helix chain 'G' and resid 195 through 198 No H-bonds generated for 'chain 'G' and resid 195 through 198' Processing helix chain 'G' and resid 209 through 211 No H-bonds generated for 'chain 'G' and resid 209 through 211' Processing helix chain 'G' and resid 263 through 285 removed outlier: 3.569A pdb=" N ILE G 267 " --> pdb=" O ASP G 263 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N MET G 270 " --> pdb=" O ARG G 266 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N LEU G 278 " --> pdb=" O TYR G 274 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N ASP G 281 " --> pdb=" O GLN G 277 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N ILE G 282 " --> pdb=" O LEU G 278 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N LEU G 285 " --> pdb=" O ASP G 281 " (cutoff:3.500A) Processing helix chain 'G' and resid 298 through 307 removed outlier: 3.548A pdb=" N ALA G 307 " --> pdb=" O TYR G 303 " (cutoff:3.500A) Processing helix chain 'G' and resid 317 through 327 removed outlier: 3.520A pdb=" N CYS G 327 " --> pdb=" O ILE G 323 " (cutoff:3.500A) Processing helix chain 'G' and resid 335 through 337 No H-bonds generated for 'chain 'G' and resid 335 through 337' Processing helix chain 'G' and resid 381 through 403 removed outlier: 3.848A pdb=" N GLU G 386 " --> pdb=" O GLU G 382 " (cutoff:3.500A) Processing helix chain 'G' and resid 413 through 428 removed outlier: 3.858A pdb=" N LYS G 427 " --> pdb=" O THR G 423 " (cutoff:3.500A) removed outlier: 4.310A pdb=" N ALA G 428 " --> pdb=" O GLU G 424 " (cutoff:3.500A) Processing helix chain 'G' and resid 432 through 455 removed outlier: 3.558A pdb=" N TRP G 435 " --> pdb=" O VAL G 432 " (cutoff:3.500A) Proline residue: G 436 - end of helix removed outlier: 3.608A pdb=" N VAL G 440 " --> pdb=" O TYR G 437 " (cutoff:3.500A) Proline residue: G 448 - end of helix removed outlier: 3.558A pdb=" N LEU G 451 " --> pdb=" O PRO G 448 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N ASN G 454 " --> pdb=" O LEU G 451 " (cutoff:3.500A) Processing helix chain 'G' and resid 459 through 472 Processing helix chain 'G' and resid 499 through 518 Processing helix chain 'h' and resid 19 through 34 Processing helix chain 'h' and resid 62 through 69 Processing helix chain 'h' and resid 74 through 89 removed outlier: 3.573A pdb=" N LEU h 79 " --> pdb=" O ALA h 75 " (cutoff:3.500A) Processing helix chain 'h' and resid 94 through 107 Processing helix chain 'h' and resid 109 through 113 Processing helix chain 'h' and resid 118 through 139 removed outlier: 3.598A pdb=" N ALA h 124 " --> pdb=" O ILE h 120 " (cutoff:3.500A) Processing helix chain 'h' and resid 146 through 148 No H-bonds generated for 'chain 'h' and resid 146 through 148' Processing helix chain 'h' and resid 151 through 163 Processing helix chain 'h' and resid 170 through 184 removed outlier: 4.568A pdb=" N ALA h 173 " --> pdb=" O GLN h 170 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N MET h 178 " --> pdb=" O PHE h 175 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N VAL h 179 " --> pdb=" O ALA h 176 " (cutoff:3.500A) Processing helix chain 'h' and resid 260 through 284 removed outlier: 3.535A pdb=" N GLN h 264 " --> pdb=" O VAL h 260 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N ALA h 265 " --> pdb=" O GLU h 261 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N LEU h 274 " --> pdb=" O GLU h 270 " (cutoff:3.500A) Processing helix chain 'h' and resid 297 through 305 removed outlier: 3.532A pdb=" N PHE h 303 " --> pdb=" O ALA h 299 " (cutoff:3.500A) Processing helix chain 'h' and resid 316 through 326 Processing helix chain 'h' and resid 353 through 355 No H-bonds generated for 'chain 'h' and resid 353 through 355' Processing helix chain 'h' and resid 379 through 401 removed outlier: 3.564A pdb=" N ARG h 387 " --> pdb=" O GLU h 383 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N ALA h 392 " --> pdb=" O SER h 388 " (cutoff:3.500A) Processing helix chain 'h' and resid 411 through 426 removed outlier: 3.993A pdb=" N THR h 426 " --> pdb=" O ASP h 422 " (cutoff:3.500A) Processing helix chain 'h' and resid 431 through 452 removed outlier: 3.548A pdb=" N LEU h 442 " --> pdb=" O TYR h 438 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N GLU h 443 " --> pdb=" O ALA h 439 " (cutoff:3.500A) removed outlier: 4.527A pdb=" N ILE h 444 " --> pdb=" O LYS h 440 " (cutoff:3.500A) removed outlier: 5.003A pdb=" N ILE h 445 " --> pdb=" O ALA h 441 " (cutoff:3.500A) Proline residue: h 446 - end of helix Processing helix chain 'h' and resid 457 through 470 Processing helix chain 'h' and resid 496 through 514 Processing helix chain 'H' and resid 19 through 36 removed outlier: 3.794A pdb=" N ILE H 32 " --> pdb=" O ALA H 28 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N VAL H 36 " --> pdb=" O ILE H 32 " (cutoff:3.500A) Processing helix chain 'H' and resid 62 through 69 removed outlier: 3.577A pdb=" N LEU H 68 " --> pdb=" O THR H 64 " (cutoff:3.500A) Processing helix chain 'H' and resid 74 through 89 removed outlier: 3.632A pdb=" N THR H 78 " --> pdb=" O PRO H 74 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N LEU H 79 " --> pdb=" O ALA H 75 " (cutoff:3.500A) Processing helix chain 'H' and resid 94 through 107 Processing helix chain 'H' and resid 109 through 113 Processing helix chain 'H' and resid 118 through 139 removed outlier: 3.663A pdb=" N GLN H 130 " --> pdb=" O ARG H 126 " (cutoff:3.500A) Processing helix chain 'H' and resid 146 through 148 No H-bonds generated for 'chain 'H' and resid 146 through 148' Processing helix chain 'H' and resid 151 through 162 removed outlier: 3.781A pdb=" N ALA H 162 " --> pdb=" O CYS H 158 " (cutoff:3.500A) Processing helix chain 'H' and resid 172 through 184 removed outlier: 3.502A pdb=" N VAL H 180 " --> pdb=" O ALA H 176 " (cutoff:3.500A) Processing helix chain 'H' and resid 205 through 207 No H-bonds generated for 'chain 'H' and resid 205 through 207' Processing helix chain 'H' and resid 260 through 284 removed outlier: 3.938A pdb=" N ALA H 265 " --> pdb=" O GLU H 261 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N ASP H 268 " --> pdb=" O GLN H 264 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N TRP H 271 " --> pdb=" O VAL H 267 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N LEU H 274 " --> pdb=" O GLU H 270 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ILE H 281 " --> pdb=" O LYS H 277 " (cutoff:3.500A) Processing helix chain 'H' and resid 297 through 305 Processing helix chain 'H' and resid 316 through 326 Processing helix chain 'H' and resid 334 through 336 No H-bonds generated for 'chain 'H' and resid 334 through 336' Processing helix chain 'H' and resid 353 through 355 No H-bonds generated for 'chain 'H' and resid 353 through 355' Processing helix chain 'H' and resid 379 through 401 removed outlier: 3.675A pdb=" N ASP H 391 " --> pdb=" O ARG H 387 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N LYS H 401 " --> pdb=" O ARG H 397 " (cutoff:3.500A) Processing helix chain 'H' and resid 411 through 425 removed outlier: 3.551A pdb=" N ARG H 425 " --> pdb=" O ARG H 421 " (cutoff:3.500A) Processing helix chain 'H' and resid 431 through 452 removed outlier: 3.629A pdb=" N LEU H 442 " --> pdb=" O TYR H 438 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N GLU H 443 " --> pdb=" O ALA H 439 " (cutoff:3.500A) removed outlier: 4.420A pdb=" N ILE H 444 " --> pdb=" O LYS H 440 " (cutoff:3.500A) removed outlier: 5.011A pdb=" N ILE H 445 " --> pdb=" O ALA H 441 " (cutoff:3.500A) Proline residue: H 446 - end of helix removed outlier: 3.538A pdb=" N LEU H 449 " --> pdb=" O ILE H 445 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N CYS H 450 " --> pdb=" O PRO H 446 " (cutoff:3.500A) Processing helix chain 'H' and resid 457 through 470 removed outlier: 3.501A pdb=" N ALA H 469 " --> pdb=" O ARG H 465 " (cutoff:3.500A) Processing helix chain 'H' and resid 496 through 514 Processing helix chain 'Q' and resid 28 through 44 removed outlier: 3.517A pdb=" N ASN Q 32 " --> pdb=" O ALA Q 28 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N CYS Q 36 " --> pdb=" O ASN Q 32 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N LEU Q 39 " --> pdb=" O ALA Q 35 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N THR Q 43 " --> pdb=" O LEU Q 39 " (cutoff:3.500A) Processing helix chain 'Q' and resid 69 through 75 Processing helix chain 'Q' and resid 81 through 94 removed outlier: 4.116A pdb=" N ILE Q 86 " --> pdb=" O ALA Q 82 " (cutoff:3.500A) Processing helix chain 'Q' and resid 101 through 121 removed outlier: 4.039A pdb=" N GLU Q 117 " --> pdb=" O GLU Q 113 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N LEU Q 118 " --> pdb=" O LEU Q 114 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N ILE Q 121 " --> pdb=" O GLU Q 117 " (cutoff:3.500A) Processing helix chain 'Q' and resid 125 through 146 removed outlier: 3.528A pdb=" N GLU Q 141 " --> pdb=" O ARG Q 137 " (cutoff:3.500A) Proline residue: Q 144 - end of helix Processing helix chain 'Q' and resid 157 through 168 removed outlier: 3.503A pdb=" N SER Q 162 " --> pdb=" O ASP Q 158 " (cutoff:3.500A) removed outlier: 4.899A pdb=" N THR Q 166 " --> pdb=" O SER Q 162 " (cutoff:3.500A) removed outlier: 4.711A pdb=" N SER Q 167 " --> pdb=" O LEU Q 163 " (cutoff:3.500A) Processing helix chain 'Q' and resid 176 through 191 removed outlier: 3.810A pdb=" N SER Q 189 " --> pdb=" O GLN Q 185 " (cutoff:3.500A) removed outlier: 4.284A pdb=" N ILE Q 190 " --> pdb=" O ALA Q 186 " (cutoff:3.500A) Processing helix chain 'Q' and resid 212 through 214 No H-bonds generated for 'chain 'Q' and resid 212 through 214' Processing helix chain 'Q' and resid 262 through 285 removed outlier: 3.505A pdb=" N ALA Q 284 " --> pdb=" O VAL Q 280 " (cutoff:3.500A) Processing helix chain 'Q' and resid 299 through 307 Processing helix chain 'Q' and resid 318 through 325 Processing helix chain 'Q' and resid 382 through 402 removed outlier: 3.531A pdb=" N ALA Q 391 " --> pdb=" O ASP Q 387 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N THR Q 398 " --> pdb=" O ASP Q 394 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N PHE Q 399 " --> pdb=" O GLY Q 395 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N LEU Q 402 " --> pdb=" O THR Q 398 " (cutoff:3.500A) Processing helix chain 'Q' and resid 414 through 429 Processing helix chain 'Q' and resid 434 through 455 removed outlier: 3.681A pdb=" N PHE Q 445 " --> pdb=" O PHE Q 441 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N GLU Q 446 " --> pdb=" O ALA Q 442 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N ALA Q 447 " --> pdb=" O GLU Q 443 " (cutoff:3.500A) removed outlier: 4.413A pdb=" N ILE Q 448 " --> pdb=" O ALA Q 444 " (cutoff:3.500A) Proline residue: Q 449 - end of helix Processing helix chain 'Q' and resid 460 through 472 Processing helix chain 'Q' and resid 492 through 495 No H-bonds generated for 'chain 'Q' and resid 492 through 495' Processing helix chain 'Q' and resid 501 through 520 Processing helix chain 'q' and resid 28 through 44 removed outlier: 3.757A pdb=" N ASN q 32 " --> pdb=" O ALA q 28 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N THR q 42 " --> pdb=" O GLU q 38 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N THR q 43 " --> pdb=" O LEU q 39 " (cutoff:3.500A) Processing helix chain 'q' and resid 69 through 75 Processing helix chain 'q' and resid 81 through 94 removed outlier: 4.128A pdb=" N ILE q 86 " --> pdb=" O ALA q 82 " (cutoff:3.500A) Processing helix chain 'q' and resid 101 through 121 removed outlier: 3.738A pdb=" N GLU q 117 " --> pdb=" O GLU q 113 " (cutoff:3.500A) Processing helix chain 'q' and resid 125 through 146 Proline residue: q 144 - end of helix Processing helix chain 'q' and resid 157 through 168 removed outlier: 3.554A pdb=" N ARG q 165 " --> pdb=" O SER q 161 " (cutoff:3.500A) removed outlier: 4.970A pdb=" N THR q 166 " --> pdb=" O SER q 162 " (cutoff:3.500A) removed outlier: 4.363A pdb=" N SER q 167 " --> pdb=" O LEU q 163 " (cutoff:3.500A) Processing helix chain 'q' and resid 176 through 191 removed outlier: 3.619A pdb=" N ALA q 186 " --> pdb=" O LEU q 182 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N SER q 189 " --> pdb=" O GLN q 185 " (cutoff:3.500A) removed outlier: 4.579A pdb=" N ILE q 190 " --> pdb=" O ALA q 186 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N PHE q 191 " --> pdb=" O CYS q 187 " (cutoff:3.500A) Processing helix chain 'q' and resid 199 through 201 No H-bonds generated for 'chain 'q' and resid 199 through 201' Processing helix chain 'q' and resid 212 through 214 No H-bonds generated for 'chain 'q' and resid 212 through 214' Processing helix chain 'q' and resid 262 through 285 removed outlier: 3.585A pdb=" N GLU q 273 " --> pdb=" O SER q 269 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ILE q 283 " --> pdb=" O GLN q 279 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ALA q 284 " --> pdb=" O VAL q 280 " (cutoff:3.500A) Processing helix chain 'q' and resid 299 through 307 removed outlier: 3.709A pdb=" N HIS q 303 " --> pdb=" O ASP q 299 " (cutoff:3.500A) Processing helix chain 'q' and resid 318 through 327 removed outlier: 3.773A pdb=" N LEU q 324 " --> pdb=" O ASP q 320 " (cutoff:3.500A) Processing helix chain 'q' and resid 382 through 402 removed outlier: 3.578A pdb=" N ARG q 390 " --> pdb=" O ASP q 386 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N PHE q 399 " --> pdb=" O GLY q 395 " (cutoff:3.500A) Processing helix chain 'q' and resid 414 through 429 Processing helix chain 'q' and resid 433 through 455 removed outlier: 3.521A pdb=" N TYR q 436 " --> pdb=" O LEU q 433 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N LYS q 440 " --> pdb=" O ALA q 437 " (cutoff:3.500A) Proline residue: q 449 - end of helix removed outlier: 3.536A pdb=" N ALA q 453 " --> pdb=" O ARG q 450 " (cutoff:3.500A) removed outlier: 4.076A pdb=" N ASN q 455 " --> pdb=" O LEU q 452 " (cutoff:3.500A) Processing helix chain 'q' and resid 460 through 472 removed outlier: 3.633A pdb=" N LYS q 466 " --> pdb=" O GLU q 462 " (cutoff:3.500A) Processing helix chain 'q' and resid 492 through 495 No H-bonds generated for 'chain 'q' and resid 492 through 495' Processing helix chain 'q' and resid 501 through 520 Processing helix chain 'Z' and resid 17 through 37 removed outlier: 3.520A pdb=" N VAL Z 22 " --> pdb=" O ALA Z 19 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N ILE Z 24 " --> pdb=" O ALA Z 21 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N LEU Z 34 " --> pdb=" O GLN Z 31 " (cutoff:3.500A) removed outlier: 4.218A pdb=" N ARG Z 35 " --> pdb=" O ASP Z 32 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N THR Z 36 " --> pdb=" O VAL Z 33 " (cutoff:3.500A) Processing helix chain 'Z' and resid 60 through 65 Processing helix chain 'Z' and resid 72 through 87 removed outlier: 3.713A pdb=" N LEU Z 76 " --> pdb=" O PRO Z 72 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N ILE Z 77 " --> pdb=" O THR Z 73 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N THR Z 82 " --> pdb=" O ALA Z 78 " (cutoff:3.500A) Processing helix chain 'Z' and resid 92 through 110 Processing helix chain 'Z' and resid 116 through 137 removed outlier: 3.592A pdb=" N GLU Z 135 " --> pdb=" O LEU Z 131 " (cutoff:3.500A) Processing helix chain 'Z' and resid 145 through 159 removed outlier: 4.410A pdb=" N THR Z 158 " --> pdb=" O THR Z 154 " (cutoff:3.500A) removed outlier: 4.142A pdb=" N LYS Z 159 " --> pdb=" O SER Z 155 " (cutoff:3.500A) Processing helix chain 'Z' and resid 164 through 179 removed outlier: 4.024A pdb=" N GLU Z 170 " --> pdb=" O ASP Z 166 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N ALA Z 171 " --> pdb=" O VAL Z 167 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N ILE Z 176 " --> pdb=" O VAL Z 172 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N ILE Z 179 " --> pdb=" O SER Z 175 " (cutoff:3.500A) Processing helix chain 'Z' and resid 188 through 190 No H-bonds generated for 'chain 'Z' and resid 188 through 190' Processing helix chain 'Z' and resid 253 through 280 removed outlier: 3.513A pdb=" N LYS Z 265 " --> pdb=" O LYS Z 261 " (cutoff:3.500A) removed outlier: 4.272A pdb=" N PHE Z 266 " --> pdb=" O ALA Z 262 " (cutoff:3.500A) removed outlier: 4.403A pdb=" N ILE Z 267 " --> pdb=" O GLU Z 263 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ASP Z 269 " --> pdb=" O LYS Z 265 " (cutoff:3.500A) removed outlier: 4.483A pdb=" N ARG Z 270 " --> pdb=" O PHE Z 266 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N LYS Z 273 " --> pdb=" O ASP Z 269 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ILE Z 275 " --> pdb=" O VAL Z 271 " (cutoff:3.500A) Processing helix chain 'Z' and resid 299 through 307 removed outlier: 3.682A pdb=" N LYS Z 307 " --> pdb=" O ASP Z 303 " (cutoff:3.500A) Processing helix chain 'Z' and resid 318 through 328 Processing helix chain 'Z' and resid 336 through 338 No H-bonds generated for 'chain 'Z' and resid 336 through 338' Processing helix chain 'Z' and resid 341 through 343 No H-bonds generated for 'chain 'Z' and resid 341 through 343' Processing helix chain 'Z' and resid 381 through 403 Processing helix chain 'Z' and resid 413 through 423 Processing helix chain 'Z' and resid 432 through 454 removed outlier: 3.515A pdb=" N VAL Z 437 " --> pdb=" O GLN Z 434 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N ASP Z 442 " --> pdb=" O ALA Z 439 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N LEU Z 445 " --> pdb=" O ASP Z 442 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ILE Z 447 " --> pdb=" O LEU Z 444 " (cutoff:3.500A) Proline residue: Z 448 - end of helix removed outlier: 3.914A pdb=" N LEU Z 451 " --> pdb=" O PRO Z 448 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N ASN Z 454 " --> pdb=" O LEU Z 451 " (cutoff:3.500A) Processing helix chain 'Z' and resid 459 through 468 removed outlier: 3.565A pdb=" N LEU Z 463 " --> pdb=" O LEU Z 459 " (cutoff:3.500A) Processing helix chain 'Z' and resid 489 through 491 No H-bonds generated for 'chain 'Z' and resid 489 through 491' Processing helix chain 'Z' and resid 498 through 516 Processing helix chain 'z' and resid 17 through 37 removed outlier: 3.537A pdb=" N SER z 25 " --> pdb=" O VAL z 22 " (cutoff:3.500A) removed outlier: 4.253A pdb=" N ARG z 35 " --> pdb=" O ASP z 32 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N THR z 36 " --> pdb=" O VAL z 33 " (cutoff:3.500A) Processing helix chain 'z' and resid 62 through 65 No H-bonds generated for 'chain 'z' and resid 62 through 65' Processing helix chain 'z' and resid 72 through 87 removed outlier: 3.892A pdb=" N LEU z 76 " --> pdb=" O PRO z 72 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N ILE z 77 " --> pdb=" O THR z 73 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ILE z 87 " --> pdb=" O ALA z 83 " (cutoff:3.500A) Processing helix chain 'z' and resid 92 through 110 removed outlier: 3.589A pdb=" N LEU z 108 " --> pdb=" O LYS z 104 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N TYR z 109 " --> pdb=" O GLN z 105 " (cutoff:3.500A) Processing helix chain 'z' and resid 116 through 137 removed outlier: 3.599A pdb=" N GLU z 135 " --> pdb=" O LEU z 131 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N GLU z 136 " --> pdb=" O GLN z 132 " (cutoff:3.500A) Processing helix chain 'z' and resid 145 through 156 removed outlier: 3.720A pdb=" N ASP z 150 " --> pdb=" O GLU z 146 " (cutoff:3.500A) Processing helix chain 'z' and resid 165 through 179 removed outlier: 3.849A pdb=" N GLU z 170 " --> pdb=" O ASP z 166 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N ALA z 171 " --> pdb=" O VAL z 167 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N ILE z 176 " --> pdb=" O VAL z 172 " (cutoff:3.500A) removed outlier: 4.113A pdb=" N ILE z 179 " --> pdb=" O SER z 175 " (cutoff:3.500A) Processing helix chain 'z' and resid 188 through 190 No H-bonds generated for 'chain 'z' and resid 188 through 190' Processing helix chain 'z' and resid 201 through 203 No H-bonds generated for 'chain 'z' and resid 201 through 203' Processing helix chain 'z' and resid 253 through 280 removed outlier: 4.175A pdb=" N PHE z 266 " --> pdb=" O ALA z 262 " (cutoff:3.500A) removed outlier: 4.304A pdb=" N ILE z 267 " --> pdb=" O GLU z 263 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N ARG z 270 " --> pdb=" O PHE z 266 " (cutoff:3.500A) Processing helix chain 'z' and resid 299 through 307 removed outlier: 3.516A pdb=" N ALA z 304 " --> pdb=" O PHE z 300 " (cutoff:3.500A) Processing helix chain 'z' and resid 318 through 328 Processing helix chain 'z' and resid 336 through 338 No H-bonds generated for 'chain 'z' and resid 336 through 338' Processing helix chain 'z' and resid 341 through 343 No H-bonds generated for 'chain 'z' and resid 341 through 343' Processing helix chain 'z' and resid 381 through 403 Processing helix chain 'z' and resid 413 through 423 Processing helix chain 'z' and resid 432 through 454 removed outlier: 3.552A pdb=" N GLN z 438 " --> pdb=" O LEU z 435 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ASP z 442 " --> pdb=" O ALA z 439 " (cutoff:3.500A) Proline residue: z 448 - end of helix removed outlier: 3.859A pdb=" N ASN z 454 " --> pdb=" O LEU z 451 " (cutoff:3.500A) Processing helix chain 'z' and resid 459 through 468 removed outlier: 3.716A pdb=" N LEU z 463 " --> pdb=" O LEU z 459 " (cutoff:3.500A) Processing helix chain 'z' and resid 489 through 492 No H-bonds generated for 'chain 'z' and resid 489 through 492' Processing helix chain 'z' and resid 498 through 516 removed outlier: 3.590A pdb=" N VAL z 510 " --> pdb=" O HIS z 506 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'a' and resid 10 through 13 Processing sheet with id= B, first strand: chain 'a' and resid 196 through 201 removed outlier: 3.810A pdb=" N SER a 374 " --> pdb=" O ILE a 211 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N ILE a 376 " --> pdb=" O MET a 209 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N MET a 209 " --> pdb=" O ILE a 376 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'a' and resid 234 through 237 removed outlier: 6.796A pdb=" N VAL a 285 " --> pdb=" O ALA a 235 " (cutoff:3.500A) removed outlier: 8.107A pdb=" N LEU a 237 " --> pdb=" O VAL a 285 " (cutoff:3.500A) removed outlier: 6.493A pdb=" N LEU a 287 " --> pdb=" O LEU a 237 " (cutoff:3.500A) removed outlier: 6.151A pdb=" N MET a 306 " --> pdb=" O ILE a 286 " (cutoff:3.500A) removed outlier: 7.656A pdb=" N THR a 288 " --> pdb=" O MET a 306 " (cutoff:3.500A) removed outlier: 6.451A pdb=" N VAL a 308 " --> pdb=" O THR a 288 " (cutoff:3.500A) No H-bonds generated for sheet with id= C Processing sheet with id= D, first strand: chain 'a' and resid 350 through 353 removed outlier: 3.600A pdb=" N GLU a 350 " --> pdb=" O LYS a 365 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'a' and resid 408 through 410 Processing sheet with id= F, first strand: chain 'a' and resid 486 through 489 removed outlier: 3.575A pdb=" N LYS a 494 " --> pdb=" O ASP a 489 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'A' and resid 11 through 13 Processing sheet with id= H, first strand: chain 'A' and resid 43 through 46 Processing sheet with id= I, first strand: chain 'A' and resid 196 through 200 removed outlier: 3.681A pdb=" N ILE A 375 " --> pdb=" O ASN A 196 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'A' and resid 234 through 237 removed outlier: 6.668A pdb=" N VAL A 285 " --> pdb=" O ALA A 235 " (cutoff:3.500A) removed outlier: 7.765A pdb=" N LEU A 237 " --> pdb=" O VAL A 285 " (cutoff:3.500A) removed outlier: 5.926A pdb=" N LEU A 287 " --> pdb=" O LEU A 237 " (cutoff:3.500A) No H-bonds generated for sheet with id= J Processing sheet with id= K, first strand: chain 'A' and resid 408 through 410 Processing sheet with id= L, first strand: chain 'A' and resid 486 through 489 Processing sheet with id= M, first strand: chain 'b' and resid 50 through 52 Processing sheet with id= N, first strand: chain 'b' and resid 199 through 205 removed outlier: 6.849A pdb=" N CYS b 371 " --> pdb=" O HIS b 200 " (cutoff:3.500A) removed outlier: 8.019A pdb=" N ILE b 202 " --> pdb=" O CYS b 371 " (cutoff:3.500A) removed outlier: 6.494A pdb=" N ILE b 373 " --> pdb=" O ILE b 202 " (cutoff:3.500A) removed outlier: 7.822A pdb=" N LYS b 204 " --> pdb=" O ILE b 373 " (cutoff:3.500A) removed outlier: 6.419A pdb=" N LEU b 375 " --> pdb=" O LYS b 204 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'b' and resid 237 through 240 removed outlier: 6.726A pdb=" N CYS b 289 " --> pdb=" O LEU b 238 " (cutoff:3.500A) removed outlier: 7.953A pdb=" N ALA b 240 " --> pdb=" O CYS b 289 " (cutoff:3.500A) removed outlier: 6.360A pdb=" N ILE b 291 " --> pdb=" O ALA b 240 " (cutoff:3.500A) removed outlier: 5.806A pdb=" N MET b 310 " --> pdb=" O PHE b 290 " (cutoff:3.500A) removed outlier: 7.437A pdb=" N ASN b 292 " --> pdb=" O MET b 310 " (cutoff:3.500A) removed outlier: 6.789A pdb=" N ILE b 312 " --> pdb=" O ASN b 292 " (cutoff:3.500A) No H-bonds generated for sheet with id= O Processing sheet with id= P, first strand: chain 'b' and resid 350 through 353 Processing sheet with id= Q, first strand: chain 'b' and resid 476 through 479 Processing sheet with id= R, first strand: chain 'B' and resid 17 through 19 removed outlier: 4.023A pdb=" N ILE B 520 " --> pdb=" O GLU B 19 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'B' and resid 50 through 52 Processing sheet with id= T, first strand: chain 'B' and resid 199 through 205 removed outlier: 6.807A pdb=" N CYS B 371 " --> pdb=" O HIS B 200 " (cutoff:3.500A) removed outlier: 8.191A pdb=" N ILE B 202 " --> pdb=" O CYS B 371 " (cutoff:3.500A) removed outlier: 6.707A pdb=" N ILE B 373 " --> pdb=" O ILE B 202 " (cutoff:3.500A) removed outlier: 7.828A pdb=" N LYS B 204 " --> pdb=" O ILE B 373 " (cutoff:3.500A) removed outlier: 5.995A pdb=" N LEU B 375 " --> pdb=" O LYS B 204 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'B' and resid 348 through 353 Processing sheet with id= V, first strand: chain 'B' and resid 476 through 479 Processing sheet with id= W, first strand: chain 'D' and resid 59 through 62 removed outlier: 3.697A pdb=" N THR D 71 " --> pdb=" O LYS D 59 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ILE D 61 " --> pdb=" O THR D 69 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain 'D' and resid 209 through 211 Processing sheet with id= Y, first strand: chain 'D' and resid 246 through 248 removed outlier: 6.693A pdb=" N VAL D 297 " --> pdb=" O GLY D 247 " (cutoff:3.500A) removed outlier: 7.021A pdb=" N MET D 323 " --> pdb=" O LEU D 298 " (cutoff:3.500A) No H-bonds generated for sheet with id= Y Processing sheet with id= Z, first strand: chain 'D' and resid 361 through 365 removed outlier: 3.633A pdb=" N LEU D 373 " --> pdb=" O VAL D 365 " (cutoff:3.500A) Processing sheet with id= AA, first strand: chain 'D' and resid 421 through 423 Processing sheet with id= AB, first strand: chain 'D' and resid 491 through 494 removed outlier: 3.819A pdb=" N GLY D 492 " --> pdb=" O SER D 501 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N SER D 501 " --> pdb=" O GLY D 492 " (cutoff:3.500A) Processing sheet with id= AC, first strand: chain 'd' and resid 59 through 62 Processing sheet with id= AD, first strand: chain 'd' and resid 208 through 214 removed outlier: 6.881A pdb=" N VAL d 386 " --> pdb=" O LYS d 209 " (cutoff:3.500A) removed outlier: 8.230A pdb=" N VAL d 211 " --> pdb=" O VAL d 386 " (cutoff:3.500A) removed outlier: 6.070A pdb=" N ILE d 388 " --> pdb=" O VAL d 211 " (cutoff:3.500A) removed outlier: 7.905A pdb=" N LYS d 213 " --> pdb=" O ILE d 388 " (cutoff:3.500A) removed outlier: 6.590A pdb=" N VAL d 390 " --> pdb=" O LYS d 213 " (cutoff:3.500A) Processing sheet with id= AE, first strand: chain 'd' and resid 227 through 229 removed outlier: 3.624A pdb=" N LEU d 374 " --> pdb=" O LEU d 229 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N GLY d 371 " --> pdb=" O LEU d 367 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N LEU d 367 " --> pdb=" O GLY d 371 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N THR d 377 " --> pdb=" O LEU d 361 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N LEU d 361 " --> pdb=" O THR d 377 " (cutoff:3.500A) Processing sheet with id= AF, first strand: chain 'd' and resid 246 through 249 removed outlier: 6.511A pdb=" N VAL d 297 " --> pdb=" O GLY d 247 " (cutoff:3.500A) removed outlier: 7.448A pdb=" N ILE d 249 " --> pdb=" O VAL d 297 " (cutoff:3.500A) removed outlier: 5.828A pdb=" N LEU d 299 " --> pdb=" O ILE d 249 " (cutoff:3.500A) removed outlier: 6.542A pdb=" N MET d 323 " --> pdb=" O LEU d 298 " (cutoff:3.500A) removed outlier: 7.337A pdb=" N ILE d 300 " --> pdb=" O MET d 323 " (cutoff:3.500A) removed outlier: 6.667A pdb=" N ILE d 325 " --> pdb=" O ILE d 300 " (cutoff:3.500A) No H-bonds generated for sheet with id= AF Processing sheet with id= AG, first strand: chain 'd' and resid 421 through 423 Processing sheet with id= AH, first strand: chain 'd' and resid 491 through 494 Processing sheet with id= AI, first strand: chain 'E' and resid 57 through 60 Processing sheet with id= AJ, first strand: chain 'E' and resid 207 through 213 removed outlier: 7.166A pdb=" N VAL E 381 " --> pdb=" O LYS E 208 " (cutoff:3.500A) removed outlier: 8.142A pdb=" N GLU E 210 " --> pdb=" O VAL E 381 " (cutoff:3.500A) removed outlier: 5.950A pdb=" N ILE E 383 " --> pdb=" O GLU E 210 " (cutoff:3.500A) removed outlier: 7.933A pdb=" N LYS E 212 " --> pdb=" O ILE E 383 " (cutoff:3.500A) removed outlier: 6.597A pdb=" N ILE E 385 " --> pdb=" O LYS E 212 " (cutoff:3.500A) Processing sheet with id= AK, first strand: chain 'E' and resid 225 through 228 removed outlier: 3.514A pdb=" N VAL E 226 " --> pdb=" O ILE E 372 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N ILE E 360 " --> pdb=" O MET E 369 " (cutoff:3.500A) Processing sheet with id= AL, first strand: chain 'E' and resid 246 through 248 removed outlier: 6.251A pdb=" N LEU E 297 " --> pdb=" O ALA E 247 " (cutoff:3.500A) No H-bonds generated for sheet with id= AL Processing sheet with id= AM, first strand: chain 'E' and resid 416 through 418 Processing sheet with id= AN, first strand: chain 'e' and resid 24 through 27 removed outlier: 3.529A pdb=" N LYS e 533 " --> pdb=" O SER e 24 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N LEU e 26 " --> pdb=" O ILE e 531 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N ILE e 531 " --> pdb=" O LEU e 26 " (cutoff:3.500A) Processing sheet with id= AO, first strand: chain 'e' and resid 57 through 60 Processing sheet with id= AP, first strand: chain 'e' and resid 207 through 213 removed outlier: 6.630A pdb=" N VAL e 381 " --> pdb=" O LYS e 208 " (cutoff:3.500A) removed outlier: 8.147A pdb=" N GLU e 210 " --> pdb=" O VAL e 381 " (cutoff:3.500A) removed outlier: 5.928A pdb=" N ILE e 383 " --> pdb=" O GLU e 210 " (cutoff:3.500A) removed outlier: 7.818A pdb=" N LYS e 212 " --> pdb=" O ILE e 383 " (cutoff:3.500A) removed outlier: 6.498A pdb=" N ILE e 385 " --> pdb=" O LYS e 212 " (cutoff:3.500A) Processing sheet with id= AQ, first strand: chain 'e' and resid 225 through 228 removed outlier: 3.877A pdb=" N VAL e 226 " --> pdb=" O ILE e 372 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N ILE e 360 " --> pdb=" O MET e 369 " (cutoff:3.500A) Processing sheet with id= AR, first strand: chain 'e' and resid 246 through 249 removed outlier: 6.417A pdb=" N LEU e 297 " --> pdb=" O ALA e 247 " (cutoff:3.500A) removed outlier: 7.516A pdb=" N LEU e 249 " --> pdb=" O LEU e 297 " (cutoff:3.500A) removed outlier: 6.235A pdb=" N ILE e 299 " --> pdb=" O LEU e 249 " (cutoff:3.500A) No H-bonds generated for sheet with id= AR Processing sheet with id= AS, first strand: chain 'e' and resid 416 through 418 Processing sheet with id= AT, first strand: chain 'g' and resid 199 through 204 removed outlier: 6.681A pdb=" N CYS g 372 " --> pdb=" O ARG g 200 " (cutoff:3.500A) removed outlier: 8.077A pdb=" N GLU g 202 " --> pdb=" O CYS g 372 " (cutoff:3.500A) removed outlier: 5.865A pdb=" N ILE g 374 " --> pdb=" O GLU g 202 " (cutoff:3.500A) removed outlier: 6.763A pdb=" N ILE g 204 " --> pdb=" O ILE g 374 " (cutoff:3.500A) removed outlier: 5.829A pdb=" N LEU g 376 " --> pdb=" O ILE g 204 " (cutoff:3.500A) Processing sheet with id= AU, first strand: chain 'g' and resid 238 through 241 removed outlier: 7.056A pdb=" N VAL g 289 " --> pdb=" O VAL g 239 " (cutoff:3.500A) removed outlier: 8.551A pdb=" N LEU g 241 " --> pdb=" O VAL g 289 " (cutoff:3.500A) removed outlier: 6.681A pdb=" N ILE g 291 " --> pdb=" O LEU g 241 " (cutoff:3.500A) removed outlier: 6.674A pdb=" N THR g 310 " --> pdb=" O VAL g 290 " (cutoff:3.500A) removed outlier: 7.888A pdb=" N THR g 292 " --> pdb=" O THR g 310 " (cutoff:3.500A) removed outlier: 6.879A pdb=" N ILE g 312 " --> pdb=" O THR g 292 " (cutoff:3.500A) No H-bonds generated for sheet with id= AU Processing sheet with id= AV, first strand: chain 'G' and resid 16 through 18 Processing sheet with id= AW, first strand: chain 'G' and resid 199 through 205 removed outlier: 6.678A pdb=" N CYS G 372 " --> pdb=" O ARG G 200 " (cutoff:3.500A) removed outlier: 8.283A pdb=" N GLU G 202 " --> pdb=" O CYS G 372 " (cutoff:3.500A) removed outlier: 6.129A pdb=" N ILE G 374 " --> pdb=" O GLU G 202 " (cutoff:3.500A) removed outlier: 6.756A pdb=" N ILE G 204 " --> pdb=" O ILE G 374 " (cutoff:3.500A) removed outlier: 6.090A pdb=" N LEU G 376 " --> pdb=" O ILE G 204 " (cutoff:3.500A) Processing sheet with id= AX, first strand: chain 'G' and resid 238 through 241 removed outlier: 6.844A pdb=" N VAL G 289 " --> pdb=" O VAL G 239 " (cutoff:3.500A) removed outlier: 8.409A pdb=" N LEU G 241 " --> pdb=" O VAL G 289 " (cutoff:3.500A) removed outlier: 6.783A pdb=" N ILE G 291 " --> pdb=" O LEU G 241 " (cutoff:3.500A) removed outlier: 6.555A pdb=" N THR G 310 " --> pdb=" O VAL G 290 " (cutoff:3.500A) removed outlier: 7.622A pdb=" N THR G 292 " --> pdb=" O THR G 310 " (cutoff:3.500A) removed outlier: 6.904A pdb=" N ILE G 312 " --> pdb=" O THR G 292 " (cutoff:3.500A) No H-bonds generated for sheet with id= AX Processing sheet with id= AY, first strand: chain 'G' and resid 407 through 409 Processing sheet with id= AZ, first strand: chain 'h' and resid 15 through 17 removed outlier: 4.101A pdb=" N SER h 16 " --> pdb=" O THR h 519 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N THR h 519 " --> pdb=" O SER h 16 " (cutoff:3.500A) No H-bonds generated for sheet with id= AZ Processing sheet with id= BA, first strand: chain 'h' and resid 47 through 50 Processing sheet with id= BB, first strand: chain 'h' and resid 195 through 201 removed outlier: 6.270A pdb=" N CYS h 370 " --> pdb=" O GLY h 196 " (cutoff:3.500A) removed outlier: 7.603A pdb=" N LYS h 198 " --> pdb=" O CYS h 370 " (cutoff:3.500A) removed outlier: 5.748A pdb=" N PHE h 372 " --> pdb=" O LYS h 198 " (cutoff:3.500A) removed outlier: 7.017A pdb=" N VAL h 200 " --> pdb=" O PHE h 372 " (cutoff:3.500A) removed outlier: 5.676A pdb=" N LEU h 374 " --> pdb=" O VAL h 200 " (cutoff:3.500A) No H-bonds generated for sheet with id= BB Processing sheet with id= BC, first strand: chain 'h' and resid 237 through 240 removed outlier: 6.701A pdb=" N VAL h 288 " --> pdb=" O ALA h 238 " (cutoff:3.500A) removed outlier: 7.512A pdb=" N LEU h 240 " --> pdb=" O VAL h 288 " (cutoff:3.500A) removed outlier: 6.318A pdb=" N SER h 290 " --> pdb=" O LEU h 240 " (cutoff:3.500A) removed outlier: 6.955A pdb=" N PHE h 309 " --> pdb=" O VAL h 289 " (cutoff:3.500A) removed outlier: 8.271A pdb=" N SER h 291 " --> pdb=" O PHE h 309 " (cutoff:3.500A) removed outlier: 6.820A pdb=" N ALA h 311 " --> pdb=" O SER h 291 " (cutoff:3.500A) No H-bonds generated for sheet with id= BC Processing sheet with id= BD, first strand: chain 'h' and resid 349 through 351 removed outlier: 3.602A pdb=" N GLU h 349 " --> pdb=" O PHE h 360 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N PHE h 360 " --> pdb=" O GLU h 349 " (cutoff:3.500A) Processing sheet with id= BE, first strand: chain 'h' and resid 405 through 407 Processing sheet with id= BF, first strand: chain 'h' and resid 475 through 477 Processing sheet with id= BG, first strand: chain 'H' and resid 47 through 50 Processing sheet with id= BH, first strand: chain 'H' and resid 195 through 201 removed outlier: 6.270A pdb=" N CYS H 370 " --> pdb=" O GLY H 196 " (cutoff:3.500A) removed outlier: 7.768A pdb=" N LYS H 198 " --> pdb=" O CYS H 370 " (cutoff:3.500A) removed outlier: 6.118A pdb=" N PHE H 372 " --> pdb=" O LYS H 198 " (cutoff:3.500A) removed outlier: 7.369A pdb=" N VAL H 200 " --> pdb=" O PHE H 372 " (cutoff:3.500A) removed outlier: 5.973A pdb=" N LEU H 374 " --> pdb=" O VAL H 200 " (cutoff:3.500A) Processing sheet with id= BI, first strand: chain 'H' and resid 238 through 240 removed outlier: 6.534A pdb=" N PHE H 309 " --> pdb=" O VAL H 289 " (cutoff:3.500A) removed outlier: 8.617A pdb=" N SER H 291 " --> pdb=" O PHE H 309 " (cutoff:3.500A) removed outlier: 7.090A pdb=" N ALA H 311 " --> pdb=" O SER H 291 " (cutoff:3.500A) Processing sheet with id= BJ, first strand: chain 'H' and resid 347 through 351 removed outlier: 3.556A pdb=" N GLU H 349 " --> pdb=" O PHE H 360 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N PHE H 360 " --> pdb=" O GLU H 349 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N THR H 351 " --> pdb=" O TYR H 358 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N TYR H 358 " --> pdb=" O THR H 351 " (cutoff:3.500A) Processing sheet with id= BK, first strand: chain 'H' and resid 405 through 407 Processing sheet with id= BL, first strand: chain 'H' and resid 475 through 477 Processing sheet with id= BM, first strand: chain 'Q' and resid 54 through 57 Processing sheet with id= BN, first strand: chain 'Q' and resid 202 through 208 removed outlier: 6.794A pdb=" N SER Q 373 " --> pdb=" O ARG Q 203 " (cutoff:3.500A) removed outlier: 7.799A pdb=" N CYS Q 205 " --> pdb=" O SER Q 373 " (cutoff:3.500A) removed outlier: 6.256A pdb=" N ILE Q 375 " --> pdb=" O CYS Q 205 " (cutoff:3.500A) removed outlier: 7.269A pdb=" N ILE Q 207 " --> pdb=" O ILE Q 375 " (cutoff:3.500A) removed outlier: 6.185A pdb=" N LEU Q 377 " --> pdb=" O ILE Q 207 " (cutoff:3.500A) Processing sheet with id= BO, first strand: chain 'Q' and resid 240 through 242 removed outlier: 6.170A pdb=" N MET Q 311 " --> pdb=" O VAL Q 291 " (cutoff:3.500A) removed outlier: 7.704A pdb=" N THR Q 293 " --> pdb=" O MET Q 311 " (cutoff:3.500A) removed outlier: 6.632A pdb=" N VAL Q 313 " --> pdb=" O THR Q 293 " (cutoff:3.500A) Processing sheet with id= BP, first strand: chain 'Q' and resid 349 through 354 Processing sheet with id= BQ, first strand: chain 'Q' and resid 408 through 410 Processing sheet with id= BR, first strand: chain 'Q' and resid 478 through 480 Processing sheet with id= BS, first strand: chain 'q' and resid 54 through 57 Processing sheet with id= BT, first strand: chain 'q' and resid 202 through 208 removed outlier: 6.473A pdb=" N SER q 373 " --> pdb=" O ARG q 203 " (cutoff:3.500A) removed outlier: 7.424A pdb=" N CYS q 205 " --> pdb=" O SER q 373 " (cutoff:3.500A) removed outlier: 5.734A pdb=" N ILE q 375 " --> pdb=" O CYS q 205 " (cutoff:3.500A) removed outlier: 7.198A pdb=" N ILE q 207 " --> pdb=" O ILE q 375 " (cutoff:3.500A) removed outlier: 6.203A pdb=" N LEU q 377 " --> pdb=" O ILE q 207 " (cutoff:3.500A) Processing sheet with id= BU, first strand: chain 'q' and resid 221 through 223 Processing sheet with id= BV, first strand: chain 'q' and resid 239 through 242 removed outlier: 6.859A pdb=" N VAL q 290 " --> pdb=" O ALA q 240 " (cutoff:3.500A) removed outlier: 8.022A pdb=" N TYR q 242 " --> pdb=" O VAL q 290 " (cutoff:3.500A) removed outlier: 6.279A pdb=" N VAL q 292 " --> pdb=" O TYR q 242 " (cutoff:3.500A) removed outlier: 6.369A pdb=" N MET q 311 " --> pdb=" O VAL q 291 " (cutoff:3.500A) removed outlier: 7.581A pdb=" N THR q 293 " --> pdb=" O MET q 311 " (cutoff:3.500A) removed outlier: 6.693A pdb=" N VAL q 313 " --> pdb=" O THR q 293 " (cutoff:3.500A) No H-bonds generated for sheet with id= BV Processing sheet with id= BW, first strand: chain 'q' and resid 408 through 410 Processing sheet with id= BX, first strand: chain 'q' and resid 478 through 480 removed outlier: 3.531A pdb=" N LYS q 490 " --> pdb=" O GLY q 479 " (cutoff:3.500A) Processing sheet with id= BY, first strand: chain 'Z' and resid 191 through 196 removed outlier: 6.872A pdb=" N VAL Z 372 " --> pdb=" O GLU Z 192 " (cutoff:3.500A) removed outlier: 7.998A pdb=" N MET Z 194 " --> pdb=" O VAL Z 372 " (cutoff:3.500A) removed outlier: 6.190A pdb=" N LEU Z 374 " --> pdb=" O MET Z 194 " (cutoff:3.500A) removed outlier: 7.732A pdb=" N MET Z 196 " --> pdb=" O LEU Z 374 " (cutoff:3.500A) removed outlier: 6.589A pdb=" N ILE Z 376 " --> pdb=" O MET Z 196 " (cutoff:3.500A) Processing sheet with id= BZ, first strand: chain 'Z' and resid 229 through 231 removed outlier: 3.709A pdb=" N VAL Z 290 " --> pdb=" O TYR Z 229 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N VAL Z 311 " --> pdb=" O PHE Z 289 " (cutoff:3.500A) Processing sheet with id= CA, first strand: chain 'Z' and resid 351 through 354 Processing sheet with id= CB, first strand: chain 'Z' and resid 407 through 409 Processing sheet with id= CC, first strand: chain 'z' and resid 191 through 196 removed outlier: 6.891A pdb=" N VAL z 372 " --> pdb=" O GLU z 192 " (cutoff:3.500A) removed outlier: 7.957A pdb=" N MET z 194 " --> pdb=" O VAL z 372 " (cutoff:3.500A) removed outlier: 6.528A pdb=" N LEU z 374 " --> pdb=" O MET z 194 " (cutoff:3.500A) removed outlier: 7.920A pdb=" N MET z 196 " --> pdb=" O LEU z 374 " (cutoff:3.500A) removed outlier: 6.588A pdb=" N ILE z 376 " --> pdb=" O MET z 196 " (cutoff:3.500A) Processing sheet with id= CD, first strand: chain 'z' and resid 229 through 231 removed outlier: 3.555A pdb=" N VAL z 311 " --> pdb=" O PHE z 289 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N VAL z 291 " --> pdb=" O VAL z 311 " (cutoff:3.500A) Processing sheet with id= CE, first strand: chain 'z' and resid 351 through 354 removed outlier: 3.523A pdb=" N PHE z 360 " --> pdb=" O TYR z 353 " (cutoff:3.500A) Processing sheet with id= CF, first strand: chain 'z' and resid 407 through 409 Processing sheet with id= CG, first strand: chain 'z' and resid 477 through 479 2768 hydrogen bonds defined for protein. 7476 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: 20.90 Time building geometry restraints manager: 21.32 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.35: 21065 1.35 - 1.47: 12093 1.47 - 1.59: 29381 1.59 - 1.71: 49 1.71 - 1.83: 636 Bond restraints: 63224 Sorted by residual: bond pdb=" C6 ADP z 601 " pdb=" N6 ADP z 601 " ideal model delta sigma weight residual 1.355 1.502 -0.147 2.00e-02 2.50e+03 5.38e+01 bond pdb=" C5 ADP z 601 " pdb=" C6 ADP z 601 " ideal model delta sigma weight residual 1.490 1.634 -0.144 2.00e-02 2.50e+03 5.21e+01 bond pdb=" CZ ARG z 157 " pdb=" NH2 ARG z 157 " ideal model delta sigma weight residual 1.330 1.394 -0.064 1.30e-02 5.92e+03 2.44e+01 bond pdb=" CZ ARG z 157 " pdb=" NH1 ARG z 157 " ideal model delta sigma weight residual 1.323 1.389 -0.066 1.40e-02 5.10e+03 2.25e+01 bond pdb=" C ASN A 477 " pdb=" N PRO A 478 " ideal model delta sigma weight residual 1.331 1.346 -0.015 7.90e-03 1.60e+04 3.51e+00 ... (remaining 63219 not shown) Histogram of bond angle deviations from ideal: 96.05 - 108.52: 2675 108.52 - 120.99: 65395 120.99 - 133.46: 17243 133.46 - 145.93: 59 145.93 - 158.40: 1 Bond angle restraints: 85373 Sorted by residual: angle pdb=" C5 ADP z 601 " pdb=" C6 ADP z 601 " pdb=" N6 ADP z 601 " ideal model delta sigma weight residual 120.00 158.40 -38.40 3.00e+00 1.11e-01 1.64e+02 angle pdb=" NH1 ARG z 157 " pdb=" CZ ARG z 157 " pdb=" NH2 ARG z 157 " ideal model delta sigma weight residual 119.30 130.83 -11.53 1.30e+00 5.92e-01 7.87e+01 angle pdb=" N1 ADP z 601 " pdb=" C6 ADP z 601 " pdb=" N6 ADP z 601 " ideal model delta sigma weight residual 120.00 96.05 23.95 3.00e+00 1.11e-01 6.38e+01 angle pdb=" NE ARG z 157 " pdb=" CZ ARG z 157 " pdb=" NH2 ARG z 157 " ideal model delta sigma weight residual 119.20 112.72 6.48 9.00e-01 1.23e+00 5.18e+01 angle pdb=" NE ARG z 157 " pdb=" CZ ARG z 157 " pdb=" NH1 ARG z 157 " ideal model delta sigma weight residual 121.50 116.45 5.05 1.00e+00 1.00e+00 2.55e+01 ... (remaining 85368 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 28.80: 38381 28.80 - 57.60: 636 57.60 - 86.41: 76 86.41 - 115.21: 15 115.21 - 144.01: 13 Dihedral angle restraints: 39121 sinusoidal: 15753 harmonic: 23368 Sorted by residual: dihedral pdb=" CA GLN A 187 " pdb=" C GLN A 187 " pdb=" N PRO A 188 " pdb=" CA PRO A 188 " ideal model delta harmonic sigma weight residual -180.00 -125.95 -54.05 0 5.00e+00 4.00e-02 1.17e+02 dihedral pdb=" CA GLN a 187 " pdb=" C GLN a 187 " pdb=" N PRO a 188 " pdb=" CA PRO a 188 " ideal model delta harmonic sigma weight residual -180.00 -127.10 -52.90 0 5.00e+00 4.00e-02 1.12e+02 dihedral pdb=" CA ASP a 146 " pdb=" C ASP a 146 " pdb=" N CYS a 147 " pdb=" CA CYS a 147 " ideal model delta harmonic sigma weight residual 180.00 141.58 38.42 0 5.00e+00 4.00e-02 5.90e+01 ... (remaining 39118 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.032: 7204 0.032 - 0.064: 1889 0.064 - 0.097: 576 0.097 - 0.129: 505 0.129 - 0.161: 39 Chirality restraints: 10213 Sorted by residual: chirality pdb=" CA PRO A 188 " pdb=" N PRO A 188 " pdb=" C PRO A 188 " pdb=" CB PRO A 188 " both_signs ideal model delta sigma weight residual False 2.72 2.56 0.16 2.00e-01 2.50e+01 6.49e-01 chirality pdb=" CA PRO a 188 " pdb=" N PRO a 188 " pdb=" C PRO a 188 " pdb=" CB PRO a 188 " both_signs ideal model delta sigma weight residual False 2.72 2.56 0.16 2.00e-01 2.50e+01 6.43e-01 chirality pdb=" CA ILE A 184 " pdb=" N ILE A 184 " pdb=" C ILE A 184 " pdb=" CB ILE A 184 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.15 2.00e-01 2.50e+01 5.82e-01 ... (remaining 10210 not shown) Planarity restraints: 10879 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLN a 187 " -0.057 5.00e-02 4.00e+02 8.64e-02 1.19e+01 pdb=" N PRO a 188 " 0.150 5.00e-02 4.00e+02 pdb=" CA PRO a 188 " -0.046 5.00e-02 4.00e+02 pdb=" CD PRO a 188 " -0.047 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLN A 187 " 0.055 5.00e-02 4.00e+02 8.33e-02 1.11e+01 pdb=" N PRO A 188 " -0.144 5.00e-02 4.00e+02 pdb=" CA PRO A 188 " 0.044 5.00e-02 4.00e+02 pdb=" CD PRO A 188 " 0.045 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE Q 191 " 0.036 5.00e-02 4.00e+02 5.40e-02 4.66e+00 pdb=" N PRO Q 192 " -0.093 5.00e-02 4.00e+02 pdb=" CA PRO Q 192 " 0.027 5.00e-02 4.00e+02 pdb=" CD PRO Q 192 " 0.030 5.00e-02 4.00e+02 ... (remaining 10876 not shown) Histogram of nonbonded interaction distances: 1.65 - 2.30: 33 2.30 - 2.95: 25471 2.95 - 3.60: 91457 3.60 - 4.25: 143561 4.25 - 4.90: 237210 Nonbonded interactions: 497732 Sorted by model distance: nonbonded pdb=" NH2 ARG z 157 " pdb=" C6 ADP z 601 " model vdw 1.650 2.672 nonbonded pdb=" CZ ARG z 157 " pdb=" N6 ADP z 601 " model vdw 1.904 2.680 nonbonded pdb=" CZ ARG z 157 " pdb=" C5 ADP z 601 " model vdw 2.041 2.792 nonbonded pdb=" OG SER d 358 " pdb=" O CYS d 379 " model vdw 2.079 2.440 nonbonded pdb=" NH2 ARG z 157 " pdb=" N6 ADP z 601 " model vdw 2.085 3.200 ... (remaining 497727 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 'B' selection = chain 'b' } ncs_group { reference = chain 'D' selection = (chain 'd' and (resid 24 through 212 or resid 221 through 224 or resid 240 throu \ gh 249 or resid 274 through 300 or resid 311 through 325 or resid 330 through 36 \ 6 or resid 372 through 377 or resid 386 through 390 or resid 394 through 539 or \ resid 601)) } ncs_group { reference = chain 'E' selection = chain 'e' } ncs_group { reference = chain 'G' selection = (chain 'g' and (resid 15 through 241 or resid 262 through 526 or resid 601)) } ncs_group { reference = chain 'H' selection = chain 'h' } ncs_group { reference = chain 'Q' selection = chain 'q' } ncs_group { reference = chain 'Z' selection = chain 'z' } 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: 1.080 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.060 Extract box with map and model: 6.150 Check model and map are aligned: 0.690 Set scattering table: 0.450 Process input model: 128.860 Find NCS groups from input model: 5.040 Set up NCS constraints: 0.540 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:2.360 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 145.240 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6138 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 : 0.003 0.147 63224 Z= 0.194 Angle : 0.582 38.399 85373 Z= 0.288 Chirality : 0.040 0.161 10213 Planarity : 0.003 0.086 10879 Dihedral : 12.380 144.009 23971 Min Nonbonded Distance : 1.650 Molprobity Statistics. All-atom Clashscore : 1.66 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.34 % Favored : 96.62 % Rotamer: Outliers : 0.03 % Allowed : 1.08 % Favored : 98.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.93 % Cis-general : 0.01 % Twisted Proline : 0.93 % Twisted General : 0.01 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.72 (0.07), residues: 8059 helix: -2.47 (0.05), residues: 4138 sheet: -2.64 (0.16), residues: 715 loop : -2.16 (0.10), residues: 3206 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP g 478 HIS 0.002 0.001 HIS q 59 PHE 0.015 0.001 PHE G 112 TYR 0.007 0.001 TYR H 263 ARG 0.004 0.000 ARG Z 157 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16118 Ramachandran restraints generated. 8059 Oldfield, 0 Emsley, 8059 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16118 Ramachandran restraints generated. 8059 Oldfield, 0 Emsley, 8059 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1343 residues out of total 6773 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 1341 time to evaluate : 5.477 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 244 MET cc_start: 0.1191 (mmm) cc_final: 0.0806 (mmm) REVERT: B 350 GLU cc_start: 0.3982 (mt-10) cc_final: 0.3496 (tt0) REVERT: B 384 ASP cc_start: 0.6013 (t0) cc_final: 0.5806 (t0) REVERT: d 260 MET cc_start: -0.0688 (mtt) cc_final: -0.2186 (ttt) REVERT: d 372 LYS cc_start: 0.2163 (mttt) cc_final: 0.1864 (mmtm) REVERT: d 460 VAL cc_start: 0.8238 (p) cc_final: 0.7999 (m) REVERT: e 227 ILE cc_start: 0.0568 (pt) cc_final: 0.0347 (pt) REVERT: H 361 PHE cc_start: 0.4035 (m-80) cc_final: 0.3815 (m-80) REVERT: Q 16 LYS cc_start: 0.2892 (mttt) cc_final: 0.2502 (mttm) REVERT: Q 249 MET cc_start: 0.2610 (mtp) cc_final: 0.2213 (mtt) REVERT: Q 464 ILE cc_start: 0.8061 (mm) cc_final: 0.7860 (mm) REVERT: q 39 LEU cc_start: 0.8209 (tp) cc_final: 0.7985 (tp) REVERT: q 249 MET cc_start: -0.0201 (tpt) cc_final: -0.0625 (tpt) REVERT: z 80 VAL cc_start: 0.6181 (t) cc_final: 0.5885 (t) outliers start: 2 outliers final: 0 residues processed: 1343 average time/residue: 0.6495 time to fit residues: 1424.9692 Evaluate side-chains 701 residues out of total 6773 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 701 time to evaluate : 5.453 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 805 random chunks: chunk 679 optimal weight: 6.9990 chunk 610 optimal weight: 4.9990 chunk 338 optimal weight: 8.9990 chunk 208 optimal weight: 4.9990 chunk 411 optimal weight: 7.9990 chunk 325 optimal weight: 6.9990 chunk 630 optimal weight: 20.0000 chunk 244 optimal weight: 10.0000 chunk 383 optimal weight: 3.9990 chunk 469 optimal weight: 1.9990 chunk 731 optimal weight: 0.9980 overall best weight: 3.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: a 435 GLN a 475 GLN A 201 HIS ** A 482 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 519 ASN ** B 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 294 GLN ** B 381 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 165 ASN D 189 ASN D 318 ASN D 406 HIS d 165 ASN ** e 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** e 182 GLN ** e 401 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** e 409 ASN g 277 GLN G 277 GLN G 308 ASN ** G 390 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 481 ASN G 526 HIS H 17 GLN ** H 301 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 50 ASN ** Q 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 523 GLN q 477 ASN Z 61 ASN Z 68 GLN Z 84 GLN ** Z 294 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** z 23 ASN z 382 HIS z 386 GLN z 453 GLN z 497 ASN Total number of N/Q/H flips: 29 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6504 moved from start: 0.2954 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.113 63224 Z= 0.309 Angle : 0.665 14.063 85373 Z= 0.329 Chirality : 0.045 0.568 10213 Planarity : 0.005 0.232 10879 Dihedral : 7.022 141.193 8787 Min Nonbonded Distance : 2.066 Molprobity Statistics. All-atom Clashscore : 9.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.77 % Favored : 96.23 % Rotamer: Outliers : 1.73 % Allowed : 8.65 % Favored : 89.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.93 % Cis-general : 0.01 % Twisted Proline : 0.93 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.72 (0.08), residues: 8059 helix: -0.45 (0.07), residues: 4221 sheet: -2.09 (0.17), residues: 720 loop : -1.73 (0.10), residues: 3118 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP E 302 HIS 0.014 0.001 HIS E 310 PHE 0.028 0.002 PHE A 8 TYR 0.020 0.002 TYR Z 353 ARG 0.013 0.001 ARG Z 157 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16118 Ramachandran restraints generated. 8059 Oldfield, 0 Emsley, 8059 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16118 Ramachandran restraints generated. 8059 Oldfield, 0 Emsley, 8059 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 860 residues out of total 6773 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 117 poor density : 743 time to evaluate : 5.475 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: a 80 ASP cc_start: 0.5040 (m-30) cc_final: 0.4703 (m-30) REVERT: b 310 MET cc_start: 0.3373 (mmm) cc_final: 0.3025 (mmt) REVERT: b 426 ASN cc_start: 0.5103 (m-40) cc_final: 0.4748 (m-40) REVERT: B 244 MET cc_start: 0.1247 (mmm) cc_final: 0.0974 (mmt) REVERT: B 350 GLU cc_start: 0.4380 (mt-10) cc_final: 0.3835 (tt0) REVERT: B 360 ILE cc_start: 0.4528 (OUTLIER) cc_final: 0.4198 (mt) REVERT: B 415 MET cc_start: 0.7903 (mmm) cc_final: 0.7545 (mmm) REVERT: D 206 ARG cc_start: 0.5948 (ptt90) cc_final: 0.4900 (tpm170) REVERT: d 260 MET cc_start: -0.0824 (mtt) cc_final: -0.2637 (ttt) REVERT: E 27 MET cc_start: 0.5715 (mpp) cc_final: 0.5455 (mtm) REVERT: E 472 MET cc_start: 0.6685 (tpp) cc_final: 0.5944 (tpp) REVERT: e 27 MET cc_start: 0.3404 (pmm) cc_final: 0.3090 (pmm) REVERT: e 79 MET cc_start: 0.7390 (ttm) cc_final: 0.7008 (ttm) REVERT: H 382 MET cc_start: 0.0362 (OUTLIER) cc_final: -0.0967 (ptm) REVERT: Q 249 MET cc_start: 0.2439 (mtp) cc_final: 0.2004 (mtt) outliers start: 117 outliers final: 78 residues processed: 820 average time/residue: 0.6041 time to fit residues: 833.7468 Evaluate side-chains 662 residues out of total 6773 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 80 poor density : 582 time to evaluate : 5.443 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 47 ASP Chi-restraints excluded: chain a residue 388 MET Chi-restraints excluded: chain a residue 405 SER Chi-restraints excluded: chain A residue 67 VAL Chi-restraints excluded: chain A residue 90 THR Chi-restraints excluded: chain A residue 166 ASP Chi-restraints excluded: chain A residue 377 LEU Chi-restraints excluded: chain A residue 384 MET Chi-restraints excluded: chain A residue 397 CYS Chi-restraints excluded: chain b residue 147 ASP Chi-restraints excluded: chain b residue 153 VAL Chi-restraints excluded: chain b residue 211 ASP Chi-restraints excluded: chain b residue 519 ASN Chi-restraints excluded: chain B residue 360 ILE Chi-restraints excluded: chain B residue 391 HIS Chi-restraints excluded: chain D residue 60 MET Chi-restraints excluded: chain D residue 151 MET Chi-restraints excluded: chain D residue 377 THR Chi-restraints excluded: chain D residue 409 LEU Chi-restraints excluded: chain D residue 477 VAL Chi-restraints excluded: chain D residue 524 GLU Chi-restraints excluded: chain D residue 536 VAL Chi-restraints excluded: chain d residue 165 ASN Chi-restraints excluded: chain E residue 66 VAL Chi-restraints excluded: chain E residue 168 LYS Chi-restraints excluded: chain E residue 183 MET Chi-restraints excluded: chain E residue 266 VAL Chi-restraints excluded: chain E residue 304 PHE Chi-restraints excluded: chain E residue 441 LEU Chi-restraints excluded: chain E residue 491 CYS Chi-restraints excluded: chain E residue 505 ILE Chi-restraints excluded: chain e residue 61 ASP Chi-restraints excluded: chain e residue 92 LEU Chi-restraints excluded: chain e residue 170 THR Chi-restraints excluded: chain e residue 304 PHE Chi-restraints excluded: chain e residue 441 LEU Chi-restraints excluded: chain e residue 458 MET Chi-restraints excluded: chain e residue 505 ILE Chi-restraints excluded: chain g residue 83 ILE Chi-restraints excluded: chain g residue 521 ASP Chi-restraints excluded: chain G residue 150 ASP Chi-restraints excluded: chain G residue 215 LEU Chi-restraints excluded: chain G residue 364 THR Chi-restraints excluded: chain G residue 497 GLU Chi-restraints excluded: chain h residue 17 GLN Chi-restraints excluded: chain h residue 46 ASP Chi-restraints excluded: chain h residue 58 ILE Chi-restraints excluded: chain h residue 94 THR Chi-restraints excluded: chain h residue 361 PHE Chi-restraints excluded: chain h residue 379 GLU Chi-restraints excluded: chain H residue 58 ILE Chi-restraints excluded: chain H residue 96 SER Chi-restraints excluded: chain H residue 116 LEU Chi-restraints excluded: chain H residue 187 ASP Chi-restraints excluded: chain H residue 382 MET Chi-restraints excluded: chain H residue 386 GLU Chi-restraints excluded: chain H residue 492 VAL Chi-restraints excluded: chain Q residue 104 VAL Chi-restraints excluded: chain Q residue 217 VAL Chi-restraints excluded: chain Q residue 302 LEU Chi-restraints excluded: chain Q residue 382 ASP Chi-restraints excluded: chain Q residue 384 LEU Chi-restraints excluded: chain Q residue 386 ASP Chi-restraints excluded: chain q residue 59 HIS Chi-restraints excluded: chain q residue 149 CYS Chi-restraints excluded: chain q residue 176 GLU Chi-restraints excluded: chain q residue 384 LEU Chi-restraints excluded: chain Z residue 15 ARG Chi-restraints excluded: chain Z residue 154 THR Chi-restraints excluded: chain Z residue 233 CYS Chi-restraints excluded: chain Z residue 242 THR Chi-restraints excluded: chain Z residue 282 CYS Chi-restraints excluded: chain Z residue 343 CYS Chi-restraints excluded: chain Z residue 354 THR Chi-restraints excluded: chain Z residue 380 ASN Chi-restraints excluded: chain Z residue 526 MET Chi-restraints excluded: chain z residue 188 LEU Chi-restraints excluded: chain z residue 239 TYR Chi-restraints excluded: chain z residue 406 CYS Chi-restraints excluded: chain z residue 487 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 805 random chunks: chunk 406 optimal weight: 3.9990 chunk 226 optimal weight: 3.9990 chunk 608 optimal weight: 0.8980 chunk 497 optimal weight: 0.7980 chunk 201 optimal weight: 0.0970 chunk 732 optimal weight: 0.8980 chunk 791 optimal weight: 10.0000 chunk 652 optimal weight: 0.0980 chunk 726 optimal weight: 9.9990 chunk 249 optimal weight: 7.9990 chunk 587 optimal weight: 5.9990 overall best weight: 0.5578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 482 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 464 GLN ** B 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 195 ASN D 406 HIS ** d 165 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 310 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** e 120 GLN e 401 HIS e 409 ASN G 308 ASN ** G 390 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 504 GLN H 301 GLN Q 140 HIS Q 435 GLN q 383 ASN Z 161 HIS ** Z 294 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 497 ASN z 198 HIS Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6434 moved from start: 0.3495 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.048 63224 Z= 0.148 Angle : 0.568 17.385 85373 Z= 0.273 Chirality : 0.041 0.227 10213 Planarity : 0.004 0.112 10879 Dihedral : 6.513 129.862 8787 Min Nonbonded Distance : 2.184 Molprobity Statistics. All-atom Clashscore : 7.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 1.55 % Allowed : 9.85 % Favored : 88.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.93 % Cis-general : 0.01 % Twisted Proline : 0.93 % 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: -0.73 (0.09), residues: 8059 helix: 0.48 (0.08), residues: 4200 sheet: -1.79 (0.17), residues: 764 loop : -1.40 (0.11), residues: 3095 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP E 302 HIS 0.013 0.001 HIS E 310 PHE 0.022 0.001 PHE E 343 TYR 0.028 0.001 TYR a 299 ARG 0.031 0.000 ARG Z 157 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16118 Ramachandran restraints generated. 8059 Oldfield, 0 Emsley, 8059 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16118 Ramachandran restraints generated. 8059 Oldfield, 0 Emsley, 8059 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 788 residues out of total 6773 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 105 poor density : 683 time to evaluate : 5.567 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 VAL cc_start: 0.8620 (p) cc_final: 0.8026 (m) REVERT: b 310 MET cc_start: 0.3282 (mmm) cc_final: 0.2971 (mmt) REVERT: b 353 MET cc_start: 0.4708 (mmp) cc_final: 0.4451 (mmm) REVERT: B 350 GLU cc_start: 0.4065 (mt-10) cc_final: 0.3757 (tt0) REVERT: B 353 MET cc_start: 0.3519 (mmm) cc_final: 0.2431 (tpt) REVERT: B 360 ILE cc_start: 0.4383 (OUTLIER) cc_final: 0.4018 (mm) REVERT: B 415 MET cc_start: 0.7808 (mmm) cc_final: 0.7525 (mmm) REVERT: D 206 ARG cc_start: 0.6033 (ptt90) cc_final: 0.4942 (tpm170) REVERT: d 60 MET cc_start: 0.6027 (mtm) cc_final: 0.5729 (mtm) REVERT: d 260 MET cc_start: -0.0532 (mtt) cc_final: -0.2464 (ttt) REVERT: d 338 LYS cc_start: 0.3541 (tptt) cc_final: 0.3024 (tppt) REVERT: E 27 MET cc_start: 0.5702 (mpp) cc_final: 0.5225 (mtm) REVERT: E 40 LYS cc_start: 0.8306 (mtmt) cc_final: 0.8001 (mtmt) REVERT: E 472 MET cc_start: 0.6874 (tpp) cc_final: 0.6068 (tpp) REVERT: e 79 MET cc_start: 0.7335 (ttm) cc_final: 0.7113 (ttm) REVERT: e 120 GLN cc_start: 0.7134 (OUTLIER) cc_final: 0.6899 (tm-30) REVERT: g 150 ASP cc_start: 0.5281 (p0) cc_final: 0.5079 (p0) REVERT: g 362 PHE cc_start: 0.5067 (m-80) cc_final: 0.4827 (m-80) REVERT: G 52 ASP cc_start: 0.6445 (OUTLIER) cc_final: 0.5762 (t0) REVERT: G 229 MET cc_start: 0.2238 (mmm) cc_final: 0.2001 (mmt) REVERT: H 275 TYR cc_start: 0.1863 (t80) cc_final: 0.1437 (t80) REVERT: Q 113 GLU cc_start: 0.6738 (tt0) cc_final: 0.6516 (tt0) REVERT: Q 249 MET cc_start: 0.2549 (mtp) cc_final: 0.2118 (mtt) REVERT: Z 188 LEU cc_start: 0.7722 (OUTLIER) cc_final: 0.7505 (mp) REVERT: Z 522 MET cc_start: 0.6893 (ptp) cc_final: 0.6514 (ptp) REVERT: z 300 PHE cc_start: 0.2482 (t80) cc_final: 0.2190 (t80) outliers start: 105 outliers final: 61 residues processed: 757 average time/residue: 0.5636 time to fit residues: 736.0810 Evaluate side-chains 632 residues out of total 6773 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 567 time to evaluate : 5.640 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 78 LEU Chi-restraints excluded: chain a residue 388 MET Chi-restraints excluded: chain a residue 405 SER Chi-restraints excluded: chain A residue 148 LEU Chi-restraints excluded: chain A residue 150 ASN Chi-restraints excluded: chain A residue 166 ASP Chi-restraints excluded: chain A residue 377 LEU Chi-restraints excluded: chain A residue 384 MET Chi-restraints excluded: chain A residue 397 CYS Chi-restraints excluded: chain B residue 360 ILE Chi-restraints excluded: chain B residue 379 THR Chi-restraints excluded: chain B residue 390 LEU Chi-restraints excluded: chain D residue 32 GLN Chi-restraints excluded: chain D residue 60 MET Chi-restraints excluded: chain D residue 151 MET Chi-restraints excluded: chain D residue 409 LEU Chi-restraints excluded: chain D residue 477 VAL Chi-restraints excluded: chain D residue 524 GLU Chi-restraints excluded: chain d residue 81 MET Chi-restraints excluded: chain d residue 220 ASP Chi-restraints excluded: chain E residue 183 MET Chi-restraints excluded: chain E residue 304 PHE Chi-restraints excluded: chain E residue 491 CYS Chi-restraints excluded: chain e residue 61 ASP Chi-restraints excluded: chain e residue 116 GLU Chi-restraints excluded: chain e residue 120 GLN Chi-restraints excluded: chain e residue 304 PHE Chi-restraints excluded: chain e residue 391 MET Chi-restraints excluded: chain e residue 466 MET Chi-restraints excluded: chain e residue 505 ILE Chi-restraints excluded: chain g residue 83 ILE Chi-restraints excluded: chain g residue 521 ASP Chi-restraints excluded: chain G residue 47 MET Chi-restraints excluded: chain G residue 52 ASP Chi-restraints excluded: chain G residue 215 LEU Chi-restraints excluded: chain G residue 364 THR Chi-restraints excluded: chain G residue 497 GLU Chi-restraints excluded: chain h residue 71 VAL Chi-restraints excluded: chain h residue 94 THR Chi-restraints excluded: chain h residue 484 ILE Chi-restraints excluded: chain h residue 519 THR Chi-restraints excluded: chain H residue 57 THR Chi-restraints excluded: chain H residue 58 ILE Chi-restraints excluded: chain H residue 96 SER Chi-restraints excluded: chain H residue 116 LEU Chi-restraints excluded: chain H residue 187 ASP Chi-restraints excluded: chain H residue 220 PHE Chi-restraints excluded: chain Q residue 104 VAL Chi-restraints excluded: chain Q residue 217 VAL Chi-restraints excluded: chain Q residue 382 ASP Chi-restraints excluded: chain Q residue 384 LEU Chi-restraints excluded: chain Q residue 386 ASP Chi-restraints excluded: chain q residue 149 CYS Chi-restraints excluded: chain q residue 176 GLU Chi-restraints excluded: chain q residue 309 ASN Chi-restraints excluded: chain q residue 384 LEU Chi-restraints excluded: chain Z residue 15 ARG Chi-restraints excluded: chain Z residue 47 LEU Chi-restraints excluded: chain Z residue 57 THR Chi-restraints excluded: chain Z residue 188 LEU Chi-restraints excluded: chain Z residue 233 CYS Chi-restraints excluded: chain Z residue 242 THR Chi-restraints excluded: chain z residue 188 LEU Chi-restraints excluded: chain z residue 239 TYR Chi-restraints excluded: chain z residue 487 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 805 random chunks: chunk 723 optimal weight: 9.9990 chunk 550 optimal weight: 9.9990 chunk 380 optimal weight: 6.9990 chunk 81 optimal weight: 6.9990 chunk 349 optimal weight: 0.0470 chunk 491 optimal weight: 7.9990 chunk 734 optimal weight: 0.0670 chunk 778 optimal weight: 10.0000 chunk 383 optimal weight: 8.9990 chunk 696 optimal weight: 7.9990 chunk 209 optimal weight: 4.9990 overall best weight: 3.8222 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: a 347 GLN a 450 ASN A 135 ASN ** A 231 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 284 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 482 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 148 HIS b 361 HIS b 464 GLN ** B 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 337 HIS B 381 GLN D 394 ASN D 406 HIS d 165 ASN d 366 ASN ** E 310 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** e 182 GLN ** e 234 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** e 262 HIS e 401 HIS e 409 ASN g 221 ASN g 392 GLN ** G 390 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** h 352 GLN h 462 ASN H 21 GLN H 352 GLN H 448 GLN Q 53 ASN ** Q 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** q 140 HIS Z 84 GLN Z 161 HIS z 198 HIS z 234 ASN z 386 GLN Total number of N/Q/H flips: 30 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6666 moved from start: 0.4334 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.142 63224 Z= 0.327 Angle : 0.676 12.189 85373 Z= 0.332 Chirality : 0.045 0.299 10213 Planarity : 0.004 0.093 10879 Dihedral : 6.461 128.888 8787 Min Nonbonded Distance : 2.064 Molprobity Statistics. All-atom Clashscore : 11.47 Ramachandran Plot: Outliers : 0.01 % Allowed : 4.68 % Favored : 95.31 % Rotamer: Outliers : 2.30 % Allowed : 11.83 % Favored : 85.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.93 % Cis-general : 0.01 % Twisted Proline : 0.93 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.67 (0.09), residues: 8059 helix: 0.53 (0.08), residues: 4211 sheet: -1.53 (0.19), residues: 702 loop : -1.46 (0.10), residues: 3146 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP E 302 HIS 0.010 0.001 HIS E 310 PHE 0.022 0.002 PHE Q 399 TYR 0.028 0.002 TYR a 299 ARG 0.011 0.001 ARG z 157 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16118 Ramachandran restraints generated. 8059 Oldfield, 0 Emsley, 8059 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16118 Ramachandran restraints generated. 8059 Oldfield, 0 Emsley, 8059 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 777 residues out of total 6773 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 156 poor density : 621 time to evaluate : 5.938 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 299 TYR cc_start: 0.2154 (m-80) cc_final: 0.1360 (m-80) REVERT: A 209 MET cc_start: 0.5548 (pmm) cc_final: 0.5341 (mmt) REVERT: b 310 MET cc_start: 0.3334 (mmm) cc_final: 0.2889 (mmt) REVERT: b 488 MET cc_start: 0.8337 (mmm) cc_final: 0.7171 (mmm) REVERT: B 350 GLU cc_start: 0.4900 (mt-10) cc_final: 0.4174 (tt0) REVERT: B 353 MET cc_start: 0.3963 (mmm) cc_final: 0.2731 (tpt) REVERT: B 415 MET cc_start: 0.8026 (mmm) cc_final: 0.7759 (mmm) REVERT: B 488 MET cc_start: 0.8733 (mmm) cc_final: 0.8429 (mmm) REVERT: D 206 ARG cc_start: 0.5878 (ptt90) cc_final: 0.4993 (tpm170) REVERT: D 398 ILE cc_start: 0.1444 (OUTLIER) cc_final: 0.1165 (tp) REVERT: d 260 MET cc_start: -0.0822 (mtt) cc_final: -0.2562 (ttt) REVERT: d 338 LYS cc_start: 0.3629 (tptt) cc_final: 0.3235 (tppt) REVERT: E 27 MET cc_start: 0.5970 (mpp) cc_final: 0.5591 (mtm) REVERT: E 40 LYS cc_start: 0.8311 (mtmt) cc_final: 0.8091 (mtmt) REVERT: E 472 MET cc_start: 0.7108 (OUTLIER) cc_final: 0.6425 (tpp) REVERT: e 59 MET cc_start: 0.6524 (mmm) cc_final: 0.6227 (mmm) REVERT: e 79 MET cc_start: 0.7403 (ttm) cc_final: 0.7148 (ttm) REVERT: g 215 LEU cc_start: 0.4694 (tp) cc_final: 0.4326 (tt) REVERT: Q 16 LYS cc_start: 0.4139 (mtpt) cc_final: 0.3861 (mttt) REVERT: Q 249 MET cc_start: 0.2660 (mtp) cc_final: 0.2371 (mtt) REVERT: Q 344 MET cc_start: 0.4984 (mtt) cc_final: 0.4644 (mtt) REVERT: q 526 MET cc_start: 0.6610 (mpt) cc_final: 0.6346 (mpp) REVERT: Z 15 ARG cc_start: 0.6212 (OUTLIER) cc_final: 0.5774 (ttt90) REVERT: Z 156 LEU cc_start: 0.8296 (OUTLIER) cc_final: 0.7845 (mm) REVERT: Z 522 MET cc_start: 0.6964 (ptp) cc_final: 0.6489 (ptp) outliers start: 156 outliers final: 107 residues processed: 726 average time/residue: 0.5567 time to fit residues: 698.6829 Evaluate side-chains 643 residues out of total 6773 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 111 poor density : 532 time to evaluate : 5.473 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 22 VAL Chi-restraints excluded: chain a residue 47 ASP Chi-restraints excluded: chain a residue 64 LEU Chi-restraints excluded: chain a residue 78 LEU Chi-restraints excluded: chain a residue 405 SER Chi-restraints excluded: chain a residue 486 ILE Chi-restraints excluded: chain A residue 78 LEU Chi-restraints excluded: chain A residue 90 THR Chi-restraints excluded: chain A residue 150 ASN Chi-restraints excluded: chain A residue 166 ASP Chi-restraints excluded: chain A residue 292 ILE Chi-restraints excluded: chain A residue 377 LEU Chi-restraints excluded: chain A residue 384 MET Chi-restraints excluded: chain A residue 397 CYS Chi-restraints excluded: chain b residue 88 SER Chi-restraints excluded: chain b residue 125 THR Chi-restraints excluded: chain b residue 147 ASP Chi-restraints excluded: chain b residue 153 VAL Chi-restraints excluded: chain b residue 211 ASP Chi-restraints excluded: chain b residue 352 VAL Chi-restraints excluded: chain B residue 360 ILE Chi-restraints excluded: chain B residue 391 HIS Chi-restraints excluded: chain D residue 60 MET Chi-restraints excluded: chain D residue 151 MET Chi-restraints excluded: chain D residue 377 THR Chi-restraints excluded: chain D residue 398 ILE Chi-restraints excluded: chain D residue 409 LEU Chi-restraints excluded: chain D residue 460 VAL Chi-restraints excluded: chain D residue 477 VAL Chi-restraints excluded: chain D residue 524 GLU Chi-restraints excluded: chain d residue 68 VAL Chi-restraints excluded: chain d residue 165 ASN Chi-restraints excluded: chain d residue 220 ASP Chi-restraints excluded: chain d residue 342 THR Chi-restraints excluded: chain E residue 66 VAL Chi-restraints excluded: chain E residue 129 ILE Chi-restraints excluded: chain E residue 183 MET Chi-restraints excluded: chain E residue 266 VAL Chi-restraints excluded: chain E residue 304 PHE Chi-restraints excluded: chain E residue 320 VAL Chi-restraints excluded: chain E residue 335 THR Chi-restraints excluded: chain E residue 472 MET Chi-restraints excluded: chain E residue 505 ILE Chi-restraints excluded: chain E residue 515 ILE Chi-restraints excluded: chain e residue 116 GLU Chi-restraints excluded: chain e residue 170 THR Chi-restraints excluded: chain e residue 304 PHE Chi-restraints excluded: chain e residue 364 THR Chi-restraints excluded: chain e residue 384 PHE Chi-restraints excluded: chain e residue 438 CYS Chi-restraints excluded: chain e residue 458 MET Chi-restraints excluded: chain e residue 505 ILE Chi-restraints excluded: chain g residue 59 MET Chi-restraints excluded: chain g residue 83 ILE Chi-restraints excluded: chain g residue 289 VAL Chi-restraints excluded: chain g residue 463 LEU Chi-restraints excluded: chain g residue 490 MET Chi-restraints excluded: chain g residue 521 ASP Chi-restraints excluded: chain G residue 52 ASP Chi-restraints excluded: chain G residue 83 ILE Chi-restraints excluded: chain G residue 219 MET Chi-restraints excluded: chain G residue 237 ARG Chi-restraints excluded: chain G residue 364 THR Chi-restraints excluded: chain G residue 497 GLU Chi-restraints excluded: chain h residue 94 THR Chi-restraints excluded: chain h residue 116 LEU Chi-restraints excluded: chain h residue 199 LYS Chi-restraints excluded: chain h residue 361 PHE Chi-restraints excluded: chain h residue 379 GLU Chi-restraints excluded: chain h residue 479 ILE Chi-restraints excluded: chain h residue 483 ASP Chi-restraints excluded: chain h residue 484 ILE Chi-restraints excluded: chain H residue 57 THR Chi-restraints excluded: chain H residue 58 ILE Chi-restraints excluded: chain H residue 96 SER Chi-restraints excluded: chain H residue 116 LEU Chi-restraints excluded: chain H residue 187 ASP Chi-restraints excluded: chain H residue 220 PHE Chi-restraints excluded: chain H residue 492 VAL Chi-restraints excluded: chain Q residue 104 VAL Chi-restraints excluded: chain Q residue 217 VAL Chi-restraints excluded: chain Q residue 302 LEU Chi-restraints excluded: chain Q residue 327 THR Chi-restraints excluded: chain Q residue 382 ASP Chi-restraints excluded: chain Q residue 384 LEU Chi-restraints excluded: chain Q residue 500 THR Chi-restraints excluded: chain q residue 141 GLU Chi-restraints excluded: chain q residue 149 CYS Chi-restraints excluded: chain q residue 176 GLU Chi-restraints excluded: chain q residue 212 ILE Chi-restraints excluded: chain q residue 309 ASN Chi-restraints excluded: chain q residue 384 LEU Chi-restraints excluded: chain Z residue 15 ARG Chi-restraints excluded: chain Z residue 47 LEU Chi-restraints excluded: chain Z residue 57 THR Chi-restraints excluded: chain Z residue 156 LEU Chi-restraints excluded: chain Z residue 233 CYS Chi-restraints excluded: chain Z residue 242 THR Chi-restraints excluded: chain Z residue 282 CYS Chi-restraints excluded: chain Z residue 354 THR Chi-restraints excluded: chain Z residue 380 ASN Chi-restraints excluded: chain Z residue 509 THR Chi-restraints excluded: chain Z residue 526 MET Chi-restraints excluded: chain z residue 22 VAL Chi-restraints excluded: chain z residue 57 THR Chi-restraints excluded: chain z residue 148 LEU Chi-restraints excluded: chain z residue 183 ASP Chi-restraints excluded: chain z residue 239 TYR Chi-restraints excluded: chain z residue 242 THR Chi-restraints excluded: chain z residue 406 CYS Chi-restraints excluded: chain z residue 487 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 805 random chunks: chunk 648 optimal weight: 8.9990 chunk 441 optimal weight: 0.7980 chunk 11 optimal weight: 0.9980 chunk 579 optimal weight: 0.8980 chunk 321 optimal weight: 10.0000 chunk 664 optimal weight: 4.9990 chunk 537 optimal weight: 5.9990 chunk 0 optimal weight: 30.0000 chunk 397 optimal weight: 0.7980 chunk 698 optimal weight: 8.9990 chunk 196 optimal weight: 6.9990 overall best weight: 1.6982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 231 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 284 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 482 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 124 GLN B 73 ASN ** B 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 406 HIS d 165 ASN E 310 HIS ** e 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 401 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** e 409 ASN e 497 ASN ** G 390 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** h 21 GLN H 170 GLN ** q 274 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 84 GLN z 198 HIS z 320 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6615 moved from start: 0.4559 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 63224 Z= 0.184 Angle : 0.574 14.341 85373 Z= 0.278 Chirality : 0.042 0.434 10213 Planarity : 0.004 0.084 10879 Dihedral : 6.098 124.378 8787 Min Nonbonded Distance : 2.083 Molprobity Statistics. All-atom Clashscore : 10.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.47 % Favored : 96.53 % Rotamer: Outliers : 2.14 % Allowed : 13.14 % Favored : 84.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.93 % Cis-general : 0.01 % Twisted Proline : 0.93 % Twisted General : 0.01 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.29 (0.09), residues: 8059 helix: 0.87 (0.08), residues: 4207 sheet: -1.34 (0.18), residues: 747 loop : -1.31 (0.11), residues: 3105 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP E 302 HIS 0.009 0.001 HIS E 310 PHE 0.022 0.001 PHE h 174 TYR 0.024 0.001 TYR a 299 ARG 0.016 0.000 ARG Z 157 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16118 Ramachandran restraints generated. 8059 Oldfield, 0 Emsley, 8059 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16118 Ramachandran restraints generated. 8059 Oldfield, 0 Emsley, 8059 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 754 residues out of total 6773 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 145 poor density : 609 time to evaluate : 5.586 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 299 TYR cc_start: 0.2316 (m-80) cc_final: 0.1847 (m-80) REVERT: A 388 MET cc_start: 0.4832 (mmm) cc_final: 0.3893 (mmm) REVERT: b 310 MET cc_start: 0.3274 (mmm) cc_final: 0.2773 (mmt) REVERT: b 353 MET cc_start: 0.4903 (OUTLIER) cc_final: 0.4416 (mmm) REVERT: b 488 MET cc_start: 0.8256 (mmm) cc_final: 0.7130 (mmm) REVERT: B 350 GLU cc_start: 0.4954 (mt-10) cc_final: 0.4340 (tt0) REVERT: B 353 MET cc_start: 0.3947 (mmm) cc_final: 0.2753 (tpt) REVERT: B 360 ILE cc_start: 0.4314 (OUTLIER) cc_final: 0.3938 (mt) REVERT: B 415 MET cc_start: 0.7921 (mmm) cc_final: 0.7607 (mmm) REVERT: D 206 ARG cc_start: 0.5803 (ptt90) cc_final: 0.4873 (tpm170) REVERT: d 260 MET cc_start: -0.0998 (mtt) cc_final: -0.2681 (ttt) REVERT: d 338 LYS cc_start: 0.3331 (tptt) cc_final: 0.2998 (tppt) REVERT: E 27 MET cc_start: 0.5924 (mpp) cc_final: 0.5400 (mtm) REVERT: E 40 LYS cc_start: 0.8213 (mtmt) cc_final: 0.7968 (mtmt) REVERT: E 379 ARG cc_start: 0.4573 (mmt180) cc_final: 0.3966 (ttt180) REVERT: E 472 MET cc_start: 0.7073 (tpp) cc_final: 0.6445 (tpp) REVERT: E 483 MET cc_start: 0.3949 (ppp) cc_final: 0.3735 (ppp) REVERT: e 79 MET cc_start: 0.7372 (ttm) cc_final: 0.7028 (ttm) REVERT: g 215 LEU cc_start: 0.4618 (tp) cc_final: 0.4296 (tt) REVERT: G 47 MET cc_start: 0.7042 (OUTLIER) cc_final: 0.6653 (mtp) REVERT: G 52 ASP cc_start: 0.6855 (OUTLIER) cc_final: 0.6218 (t0) REVERT: h 518 GLU cc_start: 0.6053 (tp30) cc_final: 0.5834 (tm-30) REVERT: Q 249 MET cc_start: 0.2560 (mtp) cc_final: 0.2226 (mtt) REVERT: Q 344 MET cc_start: 0.4756 (mtt) cc_final: 0.4547 (mtt) REVERT: q 526 MET cc_start: 0.6655 (mpt) cc_final: 0.6418 (mpp) REVERT: Z 7 LEU cc_start: 0.0970 (OUTLIER) cc_final: 0.0548 (pp) REVERT: Z 28 ARG cc_start: 0.8411 (mmm-85) cc_final: 0.8195 (mmm160) REVERT: Z 522 MET cc_start: 0.7043 (ptp) cc_final: 0.6602 (ptp) outliers start: 145 outliers final: 95 residues processed: 708 average time/residue: 0.6253 time to fit residues: 770.8160 Evaluate side-chains 650 residues out of total 6773 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 100 poor density : 550 time to evaluate : 5.518 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 64 LEU Chi-restraints excluded: chain a residue 78 LEU Chi-restraints excluded: chain a residue 405 SER Chi-restraints excluded: chain a residue 486 ILE Chi-restraints excluded: chain A residue 31 ILE Chi-restraints excluded: chain A residue 78 LEU Chi-restraints excluded: chain A residue 150 ASN Chi-restraints excluded: chain A residue 166 ASP Chi-restraints excluded: chain A residue 292 ILE Chi-restraints excluded: chain A residue 377 LEU Chi-restraints excluded: chain A residue 384 MET Chi-restraints excluded: chain A residue 394 ASP Chi-restraints excluded: chain A residue 397 CYS Chi-restraints excluded: chain b residue 28 SER Chi-restraints excluded: chain b residue 211 ASP Chi-restraints excluded: chain b residue 353 MET Chi-restraints excluded: chain B residue 360 ILE Chi-restraints excluded: chain B residue 390 LEU Chi-restraints excluded: chain B residue 391 HIS Chi-restraints excluded: chain D residue 60 MET Chi-restraints excluded: chain D residue 151 MET Chi-restraints excluded: chain D residue 377 THR Chi-restraints excluded: chain D residue 409 LEU Chi-restraints excluded: chain D residue 477 VAL Chi-restraints excluded: chain D residue 524 GLU Chi-restraints excluded: chain d residue 29 LYS Chi-restraints excluded: chain d residue 81 MET Chi-restraints excluded: chain d residue 165 ASN Chi-restraints excluded: chain E residue 66 VAL Chi-restraints excluded: chain E residue 129 ILE Chi-restraints excluded: chain E residue 176 VAL Chi-restraints excluded: chain E residue 183 MET Chi-restraints excluded: chain E residue 320 VAL Chi-restraints excluded: chain E residue 335 THR Chi-restraints excluded: chain E residue 505 ILE Chi-restraints excluded: chain e residue 60 VAL Chi-restraints excluded: chain e residue 116 GLU Chi-restraints excluded: chain e residue 304 PHE Chi-restraints excluded: chain e residue 364 THR Chi-restraints excluded: chain e residue 384 PHE Chi-restraints excluded: chain e residue 438 CYS Chi-restraints excluded: chain e residue 458 MET Chi-restraints excluded: chain e residue 491 CYS Chi-restraints excluded: chain e residue 505 ILE Chi-restraints excluded: chain g residue 59 MET Chi-restraints excluded: chain g residue 83 ILE Chi-restraints excluded: chain g residue 289 VAL Chi-restraints excluded: chain g residue 315 VAL Chi-restraints excluded: chain g residue 319 ASP Chi-restraints excluded: chain g residue 372 CYS Chi-restraints excluded: chain g residue 385 SER Chi-restraints excluded: chain g residue 490 MET Chi-restraints excluded: chain g residue 521 ASP Chi-restraints excluded: chain g residue 523 VAL Chi-restraints excluded: chain G residue 47 MET Chi-restraints excluded: chain G residue 52 ASP Chi-restraints excluded: chain G residue 83 ILE Chi-restraints excluded: chain G residue 150 ASP Chi-restraints excluded: chain G residue 219 MET Chi-restraints excluded: chain G residue 364 THR Chi-restraints excluded: chain G residue 497 GLU Chi-restraints excluded: chain h residue 32 ILE Chi-restraints excluded: chain h residue 94 THR Chi-restraints excluded: chain h residue 116 LEU Chi-restraints excluded: chain h residue 197 ILE Chi-restraints excluded: chain h residue 199 LYS Chi-restraints excluded: chain h residue 379 GLU Chi-restraints excluded: chain h residue 479 ILE Chi-restraints excluded: chain h residue 484 ILE Chi-restraints excluded: chain H residue 57 THR Chi-restraints excluded: chain H residue 96 SER Chi-restraints excluded: chain H residue 116 LEU Chi-restraints excluded: chain H residue 187 ASP Chi-restraints excluded: chain H residue 220 PHE Chi-restraints excluded: chain H residue 406 VAL Chi-restraints excluded: chain Q residue 104 VAL Chi-restraints excluded: chain Q residue 217 VAL Chi-restraints excluded: chain Q residue 231 VAL Chi-restraints excluded: chain Q residue 302 LEU Chi-restraints excluded: chain Q residue 376 VAL Chi-restraints excluded: chain Q residue 382 ASP Chi-restraints excluded: chain Q residue 384 LEU Chi-restraints excluded: chain Q residue 525 ILE Chi-restraints excluded: chain q residue 141 GLU Chi-restraints excluded: chain q residue 149 CYS Chi-restraints excluded: chain q residue 309 ASN Chi-restraints excluded: chain q residue 384 LEU Chi-restraints excluded: chain Z residue 7 LEU Chi-restraints excluded: chain Z residue 15 ARG Chi-restraints excluded: chain Z residue 47 LEU Chi-restraints excluded: chain Z residue 233 CYS Chi-restraints excluded: chain Z residue 242 THR Chi-restraints excluded: chain Z residue 526 MET Chi-restraints excluded: chain z residue 22 VAL Chi-restraints excluded: chain z residue 57 THR Chi-restraints excluded: chain z residue 148 LEU Chi-restraints excluded: chain z residue 239 TYR Chi-restraints excluded: chain z residue 242 THR Chi-restraints excluded: chain z residue 406 CYS Chi-restraints excluded: chain z residue 487 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 805 random chunks: chunk 261 optimal weight: 5.9990 chunk 700 optimal weight: 1.9990 chunk 153 optimal weight: 7.9990 chunk 456 optimal weight: 5.9990 chunk 192 optimal weight: 0.3980 chunk 778 optimal weight: 8.9990 chunk 646 optimal weight: 0.9980 chunk 360 optimal weight: 8.9990 chunk 64 optimal weight: 0.9980 chunk 257 optimal weight: 20.0000 chunk 408 optimal weight: 10.0000 overall best weight: 2.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 231 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 284 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 482 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 406 HIS d 165 ASN ** E 513 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** e 182 GLN ** e 401 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 443 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 184 GLN ** G 390 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 198 ASN ** q 274 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 84 GLN z 198 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6646 moved from start: 0.4804 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 63224 Z= 0.206 Angle : 0.582 15.113 85373 Z= 0.280 Chirality : 0.042 0.354 10213 Planarity : 0.004 0.289 10879 Dihedral : 6.000 117.965 8787 Min Nonbonded Distance : 2.131 Molprobity Statistics. All-atom Clashscore : 11.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.16 % Favored : 95.84 % Rotamer: Outliers : 2.35 % Allowed : 13.48 % Favored : 84.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.93 % Cis-general : 0.01 % Twisted Proline : 0.93 % 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: -0.15 (0.09), residues: 8059 helix: 0.99 (0.08), residues: 4205 sheet: -1.30 (0.19), residues: 722 loop : -1.26 (0.11), residues: 3132 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP E 302 HIS 0.007 0.001 HIS z 198 PHE 0.028 0.001 PHE D 35 TYR 0.024 0.001 TYR q 426 ARG 0.028 0.000 ARG Z 157 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16118 Ramachandran restraints generated. 8059 Oldfield, 0 Emsley, 8059 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16118 Ramachandran restraints generated. 8059 Oldfield, 0 Emsley, 8059 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 755 residues out of total 6773 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 159 poor density : 596 time to evaluate : 5.559 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 299 TYR cc_start: 0.2214 (m-80) cc_final: 0.1719 (m-80) REVERT: a 341 GLU cc_start: 0.3883 (mt-10) cc_final: 0.3453 (mt-10) REVERT: A 156 MET cc_start: 0.5086 (mmm) cc_final: 0.4666 (mmm) REVERT: b 353 MET cc_start: 0.4708 (OUTLIER) cc_final: 0.4284 (mmm) REVERT: b 488 MET cc_start: 0.8263 (mmm) cc_final: 0.7089 (mmm) REVERT: B 244 MET cc_start: 0.1889 (tpp) cc_final: 0.1452 (tpp) REVERT: B 350 GLU cc_start: 0.5094 (mt-10) cc_final: 0.4398 (tt0) REVERT: B 353 MET cc_start: 0.3972 (mmm) cc_final: 0.2737 (tpt) REVERT: B 415 MET cc_start: 0.7891 (mmm) cc_final: 0.7543 (mmm) REVERT: D 206 ARG cc_start: 0.5840 (ptt90) cc_final: 0.4978 (tpm170) REVERT: d 260 MET cc_start: -0.0996 (mtt) cc_final: -0.2712 (ttt) REVERT: d 338 LYS cc_start: 0.3317 (tptt) cc_final: 0.3034 (tppt) REVERT: E 27 MET cc_start: 0.5868 (mpp) cc_final: 0.5339 (mtm) REVERT: E 379 ARG cc_start: 0.4606 (mmt180) cc_final: 0.3980 (ttt180) REVERT: E 472 MET cc_start: 0.7103 (OUTLIER) cc_final: 0.6494 (tpp) REVERT: E 489 ILE cc_start: 0.8516 (OUTLIER) cc_final: 0.8254 (tt) REVERT: e 79 MET cc_start: 0.7403 (ttm) cc_final: 0.7127 (ttm) REVERT: e 183 MET cc_start: 0.5960 (mmm) cc_final: 0.5743 (mmm) REVERT: e 499 MET cc_start: 0.7210 (OUTLIER) cc_final: 0.6767 (mmm) REVERT: G 52 ASP cc_start: 0.6848 (OUTLIER) cc_final: 0.6276 (t0) REVERT: G 237 ARG cc_start: 0.4730 (OUTLIER) cc_final: 0.4527 (ttt90) REVERT: H 160 MET cc_start: 0.6078 (ptt) cc_final: 0.5740 (ptt) REVERT: Q 344 MET cc_start: 0.5099 (mtt) cc_final: 0.4846 (mtt) REVERT: Z 7 LEU cc_start: 0.0948 (OUTLIER) cc_final: 0.0547 (pp) REVERT: Z 522 MET cc_start: 0.6988 (ptp) cc_final: 0.6575 (ptp) outliers start: 159 outliers final: 120 residues processed: 709 average time/residue: 0.5813 time to fit residues: 716.8706 Evaluate side-chains 665 residues out of total 6773 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 127 poor density : 538 time to evaluate : 5.543 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 22 VAL Chi-restraints excluded: chain a residue 78 LEU Chi-restraints excluded: chain a residue 166 ASP Chi-restraints excluded: chain a residue 405 SER Chi-restraints excluded: chain a residue 486 ILE Chi-restraints excluded: chain A residue 78 LEU Chi-restraints excluded: chain A residue 150 ASN Chi-restraints excluded: chain A residue 166 ASP Chi-restraints excluded: chain A residue 292 ILE Chi-restraints excluded: chain A residue 377 LEU Chi-restraints excluded: chain A residue 384 MET Chi-restraints excluded: chain A residue 394 ASP Chi-restraints excluded: chain A residue 397 CYS Chi-restraints excluded: chain b residue 28 SER Chi-restraints excluded: chain b residue 125 THR Chi-restraints excluded: chain b residue 147 ASP Chi-restraints excluded: chain b residue 153 VAL Chi-restraints excluded: chain b residue 211 ASP Chi-restraints excluded: chain b residue 353 MET Chi-restraints excluded: chain B residue 224 ILE Chi-restraints excluded: chain B residue 360 ILE Chi-restraints excluded: chain B residue 379 THR Chi-restraints excluded: chain B residue 390 LEU Chi-restraints excluded: chain B residue 391 HIS Chi-restraints excluded: chain B residue 512 GLU Chi-restraints excluded: chain D residue 60 MET Chi-restraints excluded: chain D residue 151 MET Chi-restraints excluded: chain D residue 377 THR Chi-restraints excluded: chain D residue 388 ILE Chi-restraints excluded: chain D residue 409 LEU Chi-restraints excluded: chain D residue 460 VAL Chi-restraints excluded: chain D residue 477 VAL Chi-restraints excluded: chain D residue 524 GLU Chi-restraints excluded: chain d residue 29 LYS Chi-restraints excluded: chain d residue 81 MET Chi-restraints excluded: chain d residue 165 ASN Chi-restraints excluded: chain d residue 220 ASP Chi-restraints excluded: chain E residue 66 VAL Chi-restraints excluded: chain E residue 105 THR Chi-restraints excluded: chain E residue 129 ILE Chi-restraints excluded: chain E residue 176 VAL Chi-restraints excluded: chain E residue 183 MET Chi-restraints excluded: chain E residue 266 VAL Chi-restraints excluded: chain E residue 320 VAL Chi-restraints excluded: chain E residue 335 THR Chi-restraints excluded: chain E residue 472 MET Chi-restraints excluded: chain E residue 489 ILE Chi-restraints excluded: chain E residue 505 ILE Chi-restraints excluded: chain e residue 67 THR Chi-restraints excluded: chain e residue 81 VAL Chi-restraints excluded: chain e residue 116 GLU Chi-restraints excluded: chain e residue 170 THR Chi-restraints excluded: chain e residue 191 VAL Chi-restraints excluded: chain e residue 304 PHE Chi-restraints excluded: chain e residue 364 THR Chi-restraints excluded: chain e residue 438 CYS Chi-restraints excluded: chain e residue 440 THR Chi-restraints excluded: chain e residue 499 MET Chi-restraints excluded: chain e residue 505 ILE Chi-restraints excluded: chain g residue 59 MET Chi-restraints excluded: chain g residue 83 ILE Chi-restraints excluded: chain g residue 139 LYS Chi-restraints excluded: chain g residue 289 VAL Chi-restraints excluded: chain g residue 315 VAL Chi-restraints excluded: chain g residue 319 ASP Chi-restraints excluded: chain g residue 385 SER Chi-restraints excluded: chain g residue 490 MET Chi-restraints excluded: chain g residue 521 ASP Chi-restraints excluded: chain G residue 47 MET Chi-restraints excluded: chain G residue 52 ASP Chi-restraints excluded: chain G residue 83 ILE Chi-restraints excluded: chain G residue 150 ASP Chi-restraints excluded: chain G residue 219 MET Chi-restraints excluded: chain G residue 237 ARG Chi-restraints excluded: chain G residue 364 THR Chi-restraints excluded: chain G residue 497 GLU Chi-restraints excluded: chain h residue 32 ILE Chi-restraints excluded: chain h residue 94 THR Chi-restraints excluded: chain h residue 116 LEU Chi-restraints excluded: chain h residue 197 ILE Chi-restraints excluded: chain h residue 199 LYS Chi-restraints excluded: chain h residue 361 PHE Chi-restraints excluded: chain h residue 379 GLU Chi-restraints excluded: chain h residue 479 ILE Chi-restraints excluded: chain h residue 484 ILE Chi-restraints excluded: chain H residue 17 GLN Chi-restraints excluded: chain H residue 57 THR Chi-restraints excluded: chain H residue 58 ILE Chi-restraints excluded: chain H residue 96 SER Chi-restraints excluded: chain H residue 116 LEU Chi-restraints excluded: chain H residue 161 THR Chi-restraints excluded: chain H residue 187 ASP Chi-restraints excluded: chain H residue 220 PHE Chi-restraints excluded: chain H residue 406 VAL Chi-restraints excluded: chain Q residue 104 VAL Chi-restraints excluded: chain Q residue 198 ASN Chi-restraints excluded: chain Q residue 217 VAL Chi-restraints excluded: chain Q residue 231 VAL Chi-restraints excluded: chain Q residue 302 LEU Chi-restraints excluded: chain Q residue 376 VAL Chi-restraints excluded: chain Q residue 382 ASP Chi-restraints excluded: chain Q residue 384 LEU Chi-restraints excluded: chain Q residue 500 THR Chi-restraints excluded: chain q residue 141 GLU Chi-restraints excluded: chain q residue 149 CYS Chi-restraints excluded: chain q residue 176 GLU Chi-restraints excluded: chain q residue 309 ASN Chi-restraints excluded: chain q residue 384 LEU Chi-restraints excluded: chain Z residue 7 LEU Chi-restraints excluded: chain Z residue 15 ARG Chi-restraints excluded: chain Z residue 47 LEU Chi-restraints excluded: chain Z residue 137 VAL Chi-restraints excluded: chain Z residue 204 THR Chi-restraints excluded: chain Z residue 233 CYS Chi-restraints excluded: chain Z residue 242 THR Chi-restraints excluded: chain Z residue 290 VAL Chi-restraints excluded: chain Z residue 354 THR Chi-restraints excluded: chain Z residue 526 MET Chi-restraints excluded: chain z residue 22 VAL Chi-restraints excluded: chain z residue 57 THR Chi-restraints excluded: chain z residue 67 MET Chi-restraints excluded: chain z residue 148 LEU Chi-restraints excluded: chain z residue 183 ASP Chi-restraints excluded: chain z residue 239 TYR Chi-restraints excluded: chain z residue 242 THR Chi-restraints excluded: chain z residue 406 CYS Chi-restraints excluded: chain z residue 487 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 805 random chunks: chunk 750 optimal weight: 0.9990 chunk 87 optimal weight: 8.9990 chunk 443 optimal weight: 1.9990 chunk 568 optimal weight: 4.9990 chunk 440 optimal weight: 0.9990 chunk 655 optimal weight: 9.9990 chunk 434 optimal weight: 6.9990 chunk 775 optimal weight: 9.9990 chunk 485 optimal weight: 0.0670 chunk 473 optimal weight: 10.0000 chunk 358 optimal weight: 10.0000 overall best weight: 1.8126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: a 498 ASN ** A 231 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 284 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 482 ASN b 464 GLN ** B 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 406 HIS d 165 ASN ** d 366 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 513 GLN ** e 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** e 443 GLN G 184 GLN ** G 390 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 21 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** q 267 ASN z 198 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6645 moved from start: 0.4994 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 63224 Z= 0.191 Angle : 0.573 12.746 85373 Z= 0.277 Chirality : 0.042 0.336 10213 Planarity : 0.005 0.333 10879 Dihedral : 5.888 120.728 8787 Min Nonbonded Distance : 2.045 Molprobity Statistics. All-atom Clashscore : 10.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.00 % Favored : 96.00 % Rotamer: Outliers : 2.33 % Allowed : 14.09 % Favored : 83.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.93 % Cis-general : 0.01 % Twisted Proline : 0.93 % Twisted General : 0.01 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.02 (0.09), residues: 8059 helix: 1.11 (0.08), residues: 4186 sheet: -1.20 (0.19), residues: 745 loop : -1.23 (0.11), residues: 3128 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP E 302 HIS 0.008 0.001 HIS B 175 PHE 0.026 0.001 PHE Q 399 TYR 0.019 0.001 TYR a 299 ARG 0.010 0.000 ARG Z 157 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16118 Ramachandran restraints generated. 8059 Oldfield, 0 Emsley, 8059 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16118 Ramachandran restraints generated. 8059 Oldfield, 0 Emsley, 8059 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 735 residues out of total 6773 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 158 poor density : 577 time to evaluate : 6.501 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 299 TYR cc_start: 0.2112 (m-80) cc_final: 0.1693 (m-80) REVERT: a 341 GLU cc_start: 0.3987 (mt-10) cc_final: 0.3560 (mt-10) REVERT: a 430 MET cc_start: 0.7038 (mtp) cc_final: 0.6808 (ptp) REVERT: A 388 MET cc_start: 0.4482 (mmm) cc_final: 0.3562 (mmm) REVERT: b 353 MET cc_start: 0.4675 (OUTLIER) cc_final: 0.4097 (mmm) REVERT: b 488 MET cc_start: 0.8232 (mmm) cc_final: 0.7044 (mmm) REVERT: B 244 MET cc_start: 0.1624 (tpp) cc_final: 0.1181 (tpp) REVERT: B 350 GLU cc_start: 0.5168 (mt-10) cc_final: 0.4472 (tt0) REVERT: B 353 MET cc_start: 0.4075 (mmm) cc_final: 0.2675 (tpt) REVERT: B 415 MET cc_start: 0.7880 (mmm) cc_final: 0.7537 (mmm) REVERT: D 206 ARG cc_start: 0.5878 (ptt90) cc_final: 0.5057 (tpm170) REVERT: d 260 MET cc_start: -0.1021 (mtt) cc_final: -0.2724 (ttt) REVERT: d 338 LYS cc_start: 0.3415 (tptt) cc_final: 0.3119 (tppt) REVERT: E 27 MET cc_start: 0.5841 (mpp) cc_final: 0.5283 (mtm) REVERT: E 379 ARG cc_start: 0.4722 (mmt180) cc_final: 0.3989 (ttt180) REVERT: E 472 MET cc_start: 0.7103 (OUTLIER) cc_final: 0.6488 (tpp) REVERT: e 79 MET cc_start: 0.7358 (ttm) cc_final: 0.7058 (ttm) REVERT: e 499 MET cc_start: 0.7158 (OUTLIER) cc_final: 0.6785 (mmm) REVERT: G 237 ARG cc_start: 0.4854 (OUTLIER) cc_final: 0.4489 (ttt90) REVERT: h 99 LEU cc_start: 0.8253 (OUTLIER) cc_final: 0.7976 (tt) REVERT: H 160 MET cc_start: 0.6083 (ptt) cc_final: 0.5781 (ptt) REVERT: H 414 MET cc_start: 0.7603 (tpp) cc_final: 0.7237 (mmt) REVERT: Q 344 MET cc_start: 0.5112 (mtt) cc_final: 0.4877 (mtt) REVERT: Z 7 LEU cc_start: 0.1214 (OUTLIER) cc_final: 0.0841 (pp) REVERT: Z 522 MET cc_start: 0.6915 (ptp) cc_final: 0.6582 (ptp) outliers start: 158 outliers final: 125 residues processed: 690 average time/residue: 0.5635 time to fit residues: 677.0350 Evaluate side-chains 668 residues out of total 6773 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 131 poor density : 537 time to evaluate : 5.606 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 78 LEU Chi-restraints excluded: chain a residue 166 ASP Chi-restraints excluded: chain a residue 486 ILE Chi-restraints excluded: chain A residue 78 LEU Chi-restraints excluded: chain A residue 150 ASN Chi-restraints excluded: chain A residue 166 ASP Chi-restraints excluded: chain A residue 219 VAL Chi-restraints excluded: chain A residue 292 ILE Chi-restraints excluded: chain A residue 377 LEU Chi-restraints excluded: chain A residue 384 MET Chi-restraints excluded: chain A residue 394 ASP Chi-restraints excluded: chain A residue 397 CYS Chi-restraints excluded: chain b residue 28 SER Chi-restraints excluded: chain b residue 125 THR Chi-restraints excluded: chain b residue 153 VAL Chi-restraints excluded: chain b residue 211 ASP Chi-restraints excluded: chain b residue 353 MET Chi-restraints excluded: chain B residue 35 ILE Chi-restraints excluded: chain B residue 224 ILE Chi-restraints excluded: chain B residue 360 ILE Chi-restraints excluded: chain B residue 379 THR Chi-restraints excluded: chain B residue 391 HIS Chi-restraints excluded: chain B residue 512 GLU Chi-restraints excluded: chain D residue 60 MET Chi-restraints excluded: chain D residue 151 MET Chi-restraints excluded: chain D residue 377 THR Chi-restraints excluded: chain D residue 388 ILE Chi-restraints excluded: chain D residue 409 LEU Chi-restraints excluded: chain D residue 460 VAL Chi-restraints excluded: chain D residue 477 VAL Chi-restraints excluded: chain D residue 524 GLU Chi-restraints excluded: chain d residue 29 LYS Chi-restraints excluded: chain d residue 81 MET Chi-restraints excluded: chain d residue 220 ASP Chi-restraints excluded: chain d residue 300 ILE Chi-restraints excluded: chain d residue 474 ILE Chi-restraints excluded: chain E residue 66 VAL Chi-restraints excluded: chain E residue 105 THR Chi-restraints excluded: chain E residue 129 ILE Chi-restraints excluded: chain E residue 164 ILE Chi-restraints excluded: chain E residue 176 VAL Chi-restraints excluded: chain E residue 183 MET Chi-restraints excluded: chain E residue 266 VAL Chi-restraints excluded: chain E residue 320 VAL Chi-restraints excluded: chain E residue 335 THR Chi-restraints excluded: chain E residue 472 MET Chi-restraints excluded: chain E residue 505 ILE Chi-restraints excluded: chain e residue 60 VAL Chi-restraints excluded: chain e residue 67 THR Chi-restraints excluded: chain e residue 81 VAL Chi-restraints excluded: chain e residue 170 THR Chi-restraints excluded: chain e residue 191 VAL Chi-restraints excluded: chain e residue 304 PHE Chi-restraints excluded: chain e residue 364 THR Chi-restraints excluded: chain e residue 384 PHE Chi-restraints excluded: chain e residue 438 CYS Chi-restraints excluded: chain e residue 499 MET Chi-restraints excluded: chain e residue 505 ILE Chi-restraints excluded: chain g residue 59 MET Chi-restraints excluded: chain g residue 83 ILE Chi-restraints excluded: chain g residue 139 LYS Chi-restraints excluded: chain g residue 289 VAL Chi-restraints excluded: chain g residue 315 VAL Chi-restraints excluded: chain g residue 319 ASP Chi-restraints excluded: chain g residue 385 SER Chi-restraints excluded: chain g residue 490 MET Chi-restraints excluded: chain g residue 521 ASP Chi-restraints excluded: chain G residue 47 MET Chi-restraints excluded: chain G residue 52 ASP Chi-restraints excluded: chain G residue 83 ILE Chi-restraints excluded: chain G residue 150 ASP Chi-restraints excluded: chain G residue 219 MET Chi-restraints excluded: chain G residue 237 ARG Chi-restraints excluded: chain G residue 364 THR Chi-restraints excluded: chain G residue 497 GLU Chi-restraints excluded: chain h residue 17 GLN Chi-restraints excluded: chain h residue 32 ILE Chi-restraints excluded: chain h residue 94 THR Chi-restraints excluded: chain h residue 99 LEU Chi-restraints excluded: chain h residue 116 LEU Chi-restraints excluded: chain h residue 197 ILE Chi-restraints excluded: chain h residue 199 LYS Chi-restraints excluded: chain h residue 361 PHE Chi-restraints excluded: chain h residue 379 GLU Chi-restraints excluded: chain h residue 479 ILE Chi-restraints excluded: chain h residue 484 ILE Chi-restraints excluded: chain H residue 17 GLN Chi-restraints excluded: chain H residue 57 THR Chi-restraints excluded: chain H residue 58 ILE Chi-restraints excluded: chain H residue 96 SER Chi-restraints excluded: chain H residue 116 LEU Chi-restraints excluded: chain H residue 161 THR Chi-restraints excluded: chain H residue 183 VAL Chi-restraints excluded: chain H residue 187 ASP Chi-restraints excluded: chain H residue 220 PHE Chi-restraints excluded: chain H residue 374 LEU Chi-restraints excluded: chain H residue 406 VAL Chi-restraints excluded: chain H residue 492 VAL Chi-restraints excluded: chain Q residue 104 VAL Chi-restraints excluded: chain Q residue 217 VAL Chi-restraints excluded: chain Q residue 231 VAL Chi-restraints excluded: chain Q residue 302 LEU Chi-restraints excluded: chain Q residue 327 THR Chi-restraints excluded: chain Q residue 336 LEU Chi-restraints excluded: chain Q residue 376 VAL Chi-restraints excluded: chain Q residue 384 LEU Chi-restraints excluded: chain Q residue 499 ASP Chi-restraints excluded: chain q residue 141 GLU Chi-restraints excluded: chain q residue 149 CYS Chi-restraints excluded: chain q residue 176 GLU Chi-restraints excluded: chain q residue 274 ASN Chi-restraints excluded: chain q residue 309 ASN Chi-restraints excluded: chain q residue 384 LEU Chi-restraints excluded: chain Z residue 7 LEU Chi-restraints excluded: chain Z residue 15 ARG Chi-restraints excluded: chain Z residue 47 LEU Chi-restraints excluded: chain Z residue 204 THR Chi-restraints excluded: chain Z residue 233 CYS Chi-restraints excluded: chain Z residue 242 THR Chi-restraints excluded: chain Z residue 290 VAL Chi-restraints excluded: chain Z residue 291 VAL Chi-restraints excluded: chain Z residue 526 MET Chi-restraints excluded: chain z residue 22 VAL Chi-restraints excluded: chain z residue 57 THR Chi-restraints excluded: chain z residue 110 ILE Chi-restraints excluded: chain z residue 148 LEU Chi-restraints excluded: chain z residue 183 ASP Chi-restraints excluded: chain z residue 239 TYR Chi-restraints excluded: chain z residue 242 THR Chi-restraints excluded: chain z residue 406 CYS Chi-restraints excluded: chain z residue 487 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 805 random chunks: chunk 480 optimal weight: 6.9990 chunk 309 optimal weight: 2.9990 chunk 463 optimal weight: 0.8980 chunk 233 optimal weight: 2.9990 chunk 152 optimal weight: 5.9990 chunk 150 optimal weight: 7.9990 chunk 493 optimal weight: 7.9990 chunk 528 optimal weight: 20.0000 chunk 383 optimal weight: 0.7980 chunk 72 optimal weight: 0.0470 chunk 609 optimal weight: 5.9990 overall best weight: 1.5482 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** a 284 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 498 ASN ** A 231 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 284 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 175 HIS b 464 GLN ** B 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 406 HIS ** d 366 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 401 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 184 GLN ** G 390 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 21 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** z 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** z 198 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6639 moved from start: 0.5143 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 63224 Z= 0.177 Angle : 0.579 15.809 85373 Z= 0.277 Chirality : 0.041 0.330 10213 Planarity : 0.004 0.088 10879 Dihedral : 6.052 175.880 8787 Min Nonbonded Distance : 2.153 Molprobity Statistics. All-atom Clashscore : 10.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.07 % Favored : 95.93 % Rotamer: Outliers : 2.29 % Allowed : 14.19 % Favored : 83.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.93 % Cis-general : 0.01 % Twisted Proline : 0.93 % 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: 0.09 (0.09), residues: 8059 helix: 1.20 (0.08), residues: 4186 sheet: -1.03 (0.19), residues: 755 loop : -1.19 (0.11), residues: 3118 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP E 302 HIS 0.019 0.001 HIS e 401 PHE 0.027 0.001 PHE B 218 TYR 0.018 0.001 TYR a 299 ARG 0.022 0.000 ARG Z 157 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16118 Ramachandran restraints generated. 8059 Oldfield, 0 Emsley, 8059 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16118 Ramachandran restraints generated. 8059 Oldfield, 0 Emsley, 8059 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 729 residues out of total 6773 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 155 poor density : 574 time to evaluate : 5.645 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: a 299 TYR cc_start: 0.1853 (m-80) cc_final: 0.1525 (m-80) REVERT: a 341 GLU cc_start: 0.4054 (mt-10) cc_final: 0.3639 (mt-10) REVERT: A 23 MET cc_start: 0.6405 (mpp) cc_final: 0.5952 (mtt) REVERT: b 353 MET cc_start: 0.4366 (OUTLIER) cc_final: 0.4072 (mmm) REVERT: b 488 MET cc_start: 0.8205 (mmm) cc_final: 0.7003 (mmm) REVERT: B 244 MET cc_start: 0.1630 (tpp) cc_final: 0.1185 (tpp) REVERT: B 350 GLU cc_start: 0.5216 (mt-10) cc_final: 0.4544 (tt0) REVERT: B 353 MET cc_start: 0.4051 (mmm) cc_final: 0.2640 (tpt) REVERT: B 415 MET cc_start: 0.7870 (mmm) cc_final: 0.7528 (mmm) REVERT: D 206 ARG cc_start: 0.5899 (ptt90) cc_final: 0.5058 (tpm170) REVERT: D 323 MET cc_start: 0.2730 (mmm) cc_final: 0.2525 (mmm) REVERT: d 260 MET cc_start: -0.0893 (mtt) cc_final: -0.2740 (ttt) REVERT: d 338 LYS cc_start: 0.3389 (tptt) cc_final: 0.3126 (tppt) REVERT: E 27 MET cc_start: 0.5761 (mpp) cc_final: 0.5213 (mtm) REVERT: E 379 ARG cc_start: 0.4619 (mmt180) cc_final: 0.3940 (ttt180) REVERT: E 472 MET cc_start: 0.7115 (OUTLIER) cc_final: 0.6616 (tpp) REVERT: E 483 MET cc_start: 0.4011 (ppp) cc_final: 0.3750 (ppp) REVERT: e 79 MET cc_start: 0.7379 (ttm) cc_final: 0.7085 (ttm) REVERT: e 183 MET cc_start: 0.5633 (mmm) cc_final: 0.5416 (mmm) REVERT: e 499 MET cc_start: 0.7164 (OUTLIER) cc_final: 0.6780 (mmm) REVERT: g 229 MET cc_start: 0.4689 (mtp) cc_final: 0.4427 (mtm) REVERT: G 237 ARG cc_start: 0.4865 (OUTLIER) cc_final: 0.4530 (ttt90) REVERT: h 99 LEU cc_start: 0.8210 (OUTLIER) cc_final: 0.7932 (tt) REVERT: H 280 LYS cc_start: 0.6472 (OUTLIER) cc_final: 0.5556 (tptt) REVERT: H 414 MET cc_start: 0.7591 (tpp) cc_final: 0.7206 (mmt) REVERT: Q 344 MET cc_start: 0.5102 (mtt) cc_final: 0.4884 (mtt) REVERT: Z 7 LEU cc_start: 0.1442 (OUTLIER) cc_final: 0.1057 (pp) REVERT: Z 522 MET cc_start: 0.6914 (ptp) cc_final: 0.6560 (ptp) outliers start: 155 outliers final: 119 residues processed: 685 average time/residue: 0.5645 time to fit residues: 674.5853 Evaluate side-chains 673 residues out of total 6773 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 126 poor density : 547 time to evaluate : 5.493 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 78 LEU Chi-restraints excluded: chain a residue 166 ASP Chi-restraints excluded: chain a residue 486 ILE Chi-restraints excluded: chain A residue 31 ILE Chi-restraints excluded: chain A residue 78 LEU Chi-restraints excluded: chain A residue 90 THR Chi-restraints excluded: chain A residue 150 ASN Chi-restraints excluded: chain A residue 166 ASP Chi-restraints excluded: chain A residue 219 VAL Chi-restraints excluded: chain A residue 292 ILE Chi-restraints excluded: chain A residue 377 LEU Chi-restraints excluded: chain A residue 384 MET Chi-restraints excluded: chain A residue 394 ASP Chi-restraints excluded: chain A residue 397 CYS Chi-restraints excluded: chain b residue 28 SER Chi-restraints excluded: chain b residue 125 THR Chi-restraints excluded: chain b residue 153 VAL Chi-restraints excluded: chain b residue 211 ASP Chi-restraints excluded: chain b residue 353 MET Chi-restraints excluded: chain B residue 35 ILE Chi-restraints excluded: chain B residue 224 ILE Chi-restraints excluded: chain B residue 360 ILE Chi-restraints excluded: chain B residue 379 THR Chi-restraints excluded: chain B residue 391 HIS Chi-restraints excluded: chain B residue 512 GLU Chi-restraints excluded: chain D residue 60 MET Chi-restraints excluded: chain D residue 320 MET Chi-restraints excluded: chain D residue 377 THR Chi-restraints excluded: chain D residue 409 LEU Chi-restraints excluded: chain D residue 460 VAL Chi-restraints excluded: chain D residue 477 VAL Chi-restraints excluded: chain D residue 524 GLU Chi-restraints excluded: chain d residue 29 LYS Chi-restraints excluded: chain d residue 165 ASN Chi-restraints excluded: chain d residue 220 ASP Chi-restraints excluded: chain d residue 333 ILE Chi-restraints excluded: chain d residue 474 ILE Chi-restraints excluded: chain E residue 66 VAL Chi-restraints excluded: chain E residue 105 THR Chi-restraints excluded: chain E residue 164 ILE Chi-restraints excluded: chain E residue 183 MET Chi-restraints excluded: chain E residue 266 VAL Chi-restraints excluded: chain E residue 320 VAL Chi-restraints excluded: chain E residue 335 THR Chi-restraints excluded: chain E residue 391 MET Chi-restraints excluded: chain E residue 472 MET Chi-restraints excluded: chain E residue 505 ILE Chi-restraints excluded: chain e residue 67 THR Chi-restraints excluded: chain e residue 81 VAL Chi-restraints excluded: chain e residue 304 PHE Chi-restraints excluded: chain e residue 364 THR Chi-restraints excluded: chain e residue 384 PHE Chi-restraints excluded: chain e residue 438 CYS Chi-restraints excluded: chain e residue 499 MET Chi-restraints excluded: chain e residue 505 ILE Chi-restraints excluded: chain g residue 59 MET Chi-restraints excluded: chain g residue 83 ILE Chi-restraints excluded: chain g residue 139 LYS Chi-restraints excluded: chain g residue 289 VAL Chi-restraints excluded: chain g residue 315 VAL Chi-restraints excluded: chain g residue 319 ASP Chi-restraints excluded: chain g residue 490 MET Chi-restraints excluded: chain g residue 521 ASP Chi-restraints excluded: chain G residue 83 ILE Chi-restraints excluded: chain G residue 150 ASP Chi-restraints excluded: chain G residue 219 MET Chi-restraints excluded: chain G residue 237 ARG Chi-restraints excluded: chain G residue 364 THR Chi-restraints excluded: chain G residue 497 GLU Chi-restraints excluded: chain h residue 17 GLN Chi-restraints excluded: chain h residue 32 ILE Chi-restraints excluded: chain h residue 94 THR Chi-restraints excluded: chain h residue 99 LEU Chi-restraints excluded: chain h residue 116 LEU Chi-restraints excluded: chain h residue 197 ILE Chi-restraints excluded: chain h residue 199 LYS Chi-restraints excluded: chain h residue 379 GLU Chi-restraints excluded: chain h residue 479 ILE Chi-restraints excluded: chain h residue 484 ILE Chi-restraints excluded: chain H residue 57 THR Chi-restraints excluded: chain H residue 58 ILE Chi-restraints excluded: chain H residue 96 SER Chi-restraints excluded: chain H residue 116 LEU Chi-restraints excluded: chain H residue 161 THR Chi-restraints excluded: chain H residue 183 VAL Chi-restraints excluded: chain H residue 187 ASP Chi-restraints excluded: chain H residue 220 PHE Chi-restraints excluded: chain H residue 280 LYS Chi-restraints excluded: chain H residue 374 LEU Chi-restraints excluded: chain H residue 406 VAL Chi-restraints excluded: chain Q residue 104 VAL Chi-restraints excluded: chain Q residue 199 VAL Chi-restraints excluded: chain Q residue 217 VAL Chi-restraints excluded: chain Q residue 231 VAL Chi-restraints excluded: chain Q residue 300 MET Chi-restraints excluded: chain Q residue 302 LEU Chi-restraints excluded: chain Q residue 336 LEU Chi-restraints excluded: chain Q residue 376 VAL Chi-restraints excluded: chain Q residue 382 ASP Chi-restraints excluded: chain Q residue 384 LEU Chi-restraints excluded: chain Q residue 499 ASP Chi-restraints excluded: chain Q residue 500 THR Chi-restraints excluded: chain q residue 141 GLU Chi-restraints excluded: chain q residue 149 CYS Chi-restraints excluded: chain q residue 176 GLU Chi-restraints excluded: chain q residue 274 ASN Chi-restraints excluded: chain q residue 309 ASN Chi-restraints excluded: chain q residue 384 LEU Chi-restraints excluded: chain Z residue 7 LEU Chi-restraints excluded: chain Z residue 15 ARG Chi-restraints excluded: chain Z residue 47 LEU Chi-restraints excluded: chain Z residue 137 VAL Chi-restraints excluded: chain Z residue 204 THR Chi-restraints excluded: chain Z residue 233 CYS Chi-restraints excluded: chain Z residue 242 THR Chi-restraints excluded: chain Z residue 290 VAL Chi-restraints excluded: chain Z residue 331 VAL Chi-restraints excluded: chain Z residue 526 MET Chi-restraints excluded: chain z residue 22 VAL Chi-restraints excluded: chain z residue 110 ILE Chi-restraints excluded: chain z residue 148 LEU Chi-restraints excluded: chain z residue 239 TYR Chi-restraints excluded: chain z residue 242 THR Chi-restraints excluded: chain z residue 284 ASP Chi-restraints excluded: chain z residue 406 CYS Chi-restraints excluded: chain z residue 487 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 805 random chunks: chunk 705 optimal weight: 3.9990 chunk 743 optimal weight: 3.9990 chunk 678 optimal weight: 5.9990 chunk 723 optimal weight: 20.0000 chunk 435 optimal weight: 1.9990 chunk 314 optimal weight: 9.9990 chunk 567 optimal weight: 0.0870 chunk 221 optimal weight: 0.0370 chunk 653 optimal weight: 5.9990 chunk 683 optimal weight: 3.9990 chunk 720 optimal weight: 0.0670 overall best weight: 1.2378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** a 284 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 231 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 284 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 464 GLN ** B 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 406 HIS d 165 ASN ** e 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 401 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** g 434 GLN G 184 GLN ** G 390 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 21 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** q 523 GLN Z 65 HIS ** Z 453 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** z 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** z 198 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6625 moved from start: 0.5271 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.050 63224 Z= 0.166 Angle : 0.566 12.469 85373 Z= 0.272 Chirality : 0.041 0.323 10213 Planarity : 0.005 0.351 10879 Dihedral : 5.936 175.374 8787 Min Nonbonded Distance : 2.027 Molprobity Statistics. All-atom Clashscore : 10.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % Rotamer: Outliers : 2.13 % Allowed : 14.63 % Favored : 83.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.93 % Cis-general : 0.01 % Twisted Proline : 0.93 % Twisted General : 0.01 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.22 (0.09), residues: 8059 helix: 1.29 (0.08), residues: 4194 sheet: -0.94 (0.19), residues: 762 loop : -1.12 (0.11), residues: 3103 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP E 302 HIS 0.022 0.001 HIS e 401 PHE 0.023 0.001 PHE B 218 TYR 0.017 0.001 TYR a 299 ARG 0.061 0.000 ARG z 157 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16118 Ramachandran restraints generated. 8059 Oldfield, 0 Emsley, 8059 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16118 Ramachandran restraints generated. 8059 Oldfield, 0 Emsley, 8059 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 736 residues out of total 6773 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 144 poor density : 592 time to evaluate : 5.552 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: a 299 TYR cc_start: 0.1775 (m-80) cc_final: 0.1474 (m-80) REVERT: a 341 GLU cc_start: 0.4144 (mt-10) cc_final: 0.3735 (mt-10) REVERT: b 488 MET cc_start: 0.8178 (mmm) cc_final: 0.6988 (mmm) REVERT: B 244 MET cc_start: 0.1237 (tpp) cc_final: 0.0895 (tpp) REVERT: B 350 GLU cc_start: 0.5228 (mt-10) cc_final: 0.4580 (tt0) REVERT: B 353 MET cc_start: 0.3949 (mmm) cc_final: 0.2692 (tpt) REVERT: B 415 MET cc_start: 0.7887 (mmm) cc_final: 0.7493 (mmm) REVERT: D 323 MET cc_start: 0.2832 (mmm) cc_final: 0.2588 (mmm) REVERT: d 260 MET cc_start: -0.0948 (mtt) cc_final: -0.2745 (ttt) REVERT: d 338 LYS cc_start: 0.3471 (tptt) cc_final: 0.3161 (tppt) REVERT: E 379 ARG cc_start: 0.4730 (mmt180) cc_final: 0.3970 (ttt180) REVERT: E 472 MET cc_start: 0.7172 (OUTLIER) cc_final: 0.6700 (tpp) REVERT: e 79 MET cc_start: 0.7440 (ttm) cc_final: 0.7145 (ttm) REVERT: e 369 MET cc_start: -0.0447 (ptm) cc_final: -0.0657 (ptm) REVERT: e 499 MET cc_start: 0.7093 (OUTLIER) cc_final: 0.6767 (mmm) REVERT: G 237 ARG cc_start: 0.4862 (OUTLIER) cc_final: 0.4519 (ttt90) REVERT: h 99 LEU cc_start: 0.8176 (OUTLIER) cc_final: 0.7890 (tt) REVERT: h 394 MET cc_start: 0.6595 (mmp) cc_final: 0.6395 (mmp) REVERT: H 414 MET cc_start: 0.7512 (tpp) cc_final: 0.7214 (mmt) REVERT: Q 344 MET cc_start: 0.5063 (mtt) cc_final: 0.4845 (mtt) REVERT: q 85 MET cc_start: 0.7720 (mmm) cc_final: 0.7492 (mmm) REVERT: q 385 MET cc_start: 0.7539 (tpp) cc_final: 0.7160 (mmt) REVERT: q 526 MET cc_start: 0.6546 (mpp) cc_final: 0.6334 (mpp) REVERT: Z 7 LEU cc_start: 0.1301 (OUTLIER) cc_final: 0.0884 (pp) REVERT: Z 522 MET cc_start: 0.6898 (ptp) cc_final: 0.6560 (ptp) outliers start: 144 outliers final: 115 residues processed: 699 average time/residue: 0.6094 time to fit residues: 745.7019 Evaluate side-chains 657 residues out of total 6773 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 120 poor density : 537 time to evaluate : 5.571 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 78 LEU Chi-restraints excluded: chain a residue 166 ASP Chi-restraints excluded: chain a residue 486 ILE Chi-restraints excluded: chain A residue 78 LEU Chi-restraints excluded: chain A residue 90 THR Chi-restraints excluded: chain A residue 150 ASN Chi-restraints excluded: chain A residue 166 ASP Chi-restraints excluded: chain A residue 219 VAL Chi-restraints excluded: chain A residue 292 ILE Chi-restraints excluded: chain A residue 377 LEU Chi-restraints excluded: chain A residue 384 MET Chi-restraints excluded: chain A residue 394 ASP Chi-restraints excluded: chain A residue 397 CYS Chi-restraints excluded: chain A residue 529 ASP Chi-restraints excluded: chain b residue 28 SER Chi-restraints excluded: chain b residue 125 THR Chi-restraints excluded: chain b residue 211 ASP Chi-restraints excluded: chain B residue 35 ILE Chi-restraints excluded: chain B residue 224 ILE Chi-restraints excluded: chain B residue 360 ILE Chi-restraints excluded: chain B residue 379 THR Chi-restraints excluded: chain B residue 391 HIS Chi-restraints excluded: chain B residue 512 GLU Chi-restraints excluded: chain D residue 60 MET Chi-restraints excluded: chain D residue 320 MET Chi-restraints excluded: chain D residue 377 THR Chi-restraints excluded: chain D residue 409 LEU Chi-restraints excluded: chain D residue 460 VAL Chi-restraints excluded: chain D residue 477 VAL Chi-restraints excluded: chain D residue 524 GLU Chi-restraints excluded: chain d residue 165 ASN Chi-restraints excluded: chain d residue 220 ASP Chi-restraints excluded: chain d residue 333 ILE Chi-restraints excluded: chain d residue 474 ILE Chi-restraints excluded: chain E residue 66 VAL Chi-restraints excluded: chain E residue 105 THR Chi-restraints excluded: chain E residue 164 ILE Chi-restraints excluded: chain E residue 183 MET Chi-restraints excluded: chain E residue 266 VAL Chi-restraints excluded: chain E residue 335 THR Chi-restraints excluded: chain E residue 391 MET Chi-restraints excluded: chain E residue 472 MET Chi-restraints excluded: chain E residue 505 ILE Chi-restraints excluded: chain e residue 67 THR Chi-restraints excluded: chain e residue 81 VAL Chi-restraints excluded: chain e residue 116 GLU Chi-restraints excluded: chain e residue 191 VAL Chi-restraints excluded: chain e residue 304 PHE Chi-restraints excluded: chain e residue 364 THR Chi-restraints excluded: chain e residue 438 CYS Chi-restraints excluded: chain e residue 499 MET Chi-restraints excluded: chain e residue 505 ILE Chi-restraints excluded: chain g residue 59 MET Chi-restraints excluded: chain g residue 83 ILE Chi-restraints excluded: chain g residue 215 LEU Chi-restraints excluded: chain g residue 289 VAL Chi-restraints excluded: chain g residue 315 VAL Chi-restraints excluded: chain g residue 319 ASP Chi-restraints excluded: chain g residue 385 SER Chi-restraints excluded: chain g residue 463 LEU Chi-restraints excluded: chain g residue 490 MET Chi-restraints excluded: chain G residue 52 ASP Chi-restraints excluded: chain G residue 83 ILE Chi-restraints excluded: chain G residue 219 MET Chi-restraints excluded: chain G residue 237 ARG Chi-restraints excluded: chain G residue 364 THR Chi-restraints excluded: chain G residue 497 GLU Chi-restraints excluded: chain h residue 17 GLN Chi-restraints excluded: chain h residue 32 ILE Chi-restraints excluded: chain h residue 94 THR Chi-restraints excluded: chain h residue 99 LEU Chi-restraints excluded: chain h residue 116 LEU Chi-restraints excluded: chain h residue 197 ILE Chi-restraints excluded: chain h residue 199 LYS Chi-restraints excluded: chain h residue 379 GLU Chi-restraints excluded: chain h residue 484 ILE Chi-restraints excluded: chain H residue 57 THR Chi-restraints excluded: chain H residue 58 ILE Chi-restraints excluded: chain H residue 96 SER Chi-restraints excluded: chain H residue 116 LEU Chi-restraints excluded: chain H residue 161 THR Chi-restraints excluded: chain H residue 183 VAL Chi-restraints excluded: chain H residue 187 ASP Chi-restraints excluded: chain H residue 374 LEU Chi-restraints excluded: chain H residue 406 VAL Chi-restraints excluded: chain H residue 492 VAL Chi-restraints excluded: chain Q residue 104 VAL Chi-restraints excluded: chain Q residue 199 VAL Chi-restraints excluded: chain Q residue 217 VAL Chi-restraints excluded: chain Q residue 231 VAL Chi-restraints excluded: chain Q residue 302 LEU Chi-restraints excluded: chain Q residue 327 THR Chi-restraints excluded: chain Q residue 336 LEU Chi-restraints excluded: chain Q residue 376 VAL Chi-restraints excluded: chain Q residue 382 ASP Chi-restraints excluded: chain Q residue 384 LEU Chi-restraints excluded: chain Q residue 499 ASP Chi-restraints excluded: chain Q residue 500 THR Chi-restraints excluded: chain q residue 141 GLU Chi-restraints excluded: chain q residue 149 CYS Chi-restraints excluded: chain q residue 176 GLU Chi-restraints excluded: chain q residue 274 ASN Chi-restraints excluded: chain q residue 309 ASN Chi-restraints excluded: chain q residue 384 LEU Chi-restraints excluded: chain Z residue 7 LEU Chi-restraints excluded: chain Z residue 15 ARG Chi-restraints excluded: chain Z residue 47 LEU Chi-restraints excluded: chain Z residue 137 VAL Chi-restraints excluded: chain Z residue 233 CYS Chi-restraints excluded: chain Z residue 291 VAL Chi-restraints excluded: chain Z residue 526 MET Chi-restraints excluded: chain z residue 22 VAL Chi-restraints excluded: chain z residue 110 ILE Chi-restraints excluded: chain z residue 148 LEU Chi-restraints excluded: chain z residue 183 ASP Chi-restraints excluded: chain z residue 239 TYR Chi-restraints excluded: chain z residue 242 THR Chi-restraints excluded: chain z residue 284 ASP Chi-restraints excluded: chain z residue 406 CYS Chi-restraints excluded: chain z residue 487 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 805 random chunks: chunk 474 optimal weight: 0.9990 chunk 764 optimal weight: 2.9990 chunk 466 optimal weight: 20.0000 chunk 362 optimal weight: 9.9990 chunk 531 optimal weight: 0.2980 chunk 801 optimal weight: 0.0370 chunk 738 optimal weight: 0.0970 chunk 638 optimal weight: 3.9990 chunk 66 optimal weight: 8.9990 chunk 493 optimal weight: 0.9990 chunk 391 optimal weight: 0.1980 overall best weight: 0.3258 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** a 284 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 231 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 284 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 464 GLN ** B 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 406 HIS ** e 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 315 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 401 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 390 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 21 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 53 ASN ** Z 453 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** z 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** z 198 HIS z 234 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6569 moved from start: 0.5332 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 63224 Z= 0.137 Angle : 0.565 12.629 85373 Z= 0.270 Chirality : 0.041 0.238 10213 Planarity : 0.004 0.177 10879 Dihedral : 5.979 179.107 8787 Min Nonbonded Distance : 2.153 Molprobity Statistics. All-atom Clashscore : 10.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.34 % Favored : 96.66 % Rotamer: Outliers : 1.55 % Allowed : 15.44 % Favored : 83.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.93 % Cis-general : 0.01 % Twisted Proline : 0.93 % 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: 0.40 (0.09), residues: 8059 helix: 1.42 (0.08), residues: 4192 sheet: -0.86 (0.19), residues: 757 loop : -1.02 (0.11), residues: 3110 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP E 302 HIS 0.020 0.001 HIS e 401 PHE 0.024 0.001 PHE B 218 TYR 0.018 0.001 TYR a 299 ARG 0.020 0.000 ARG z 157 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16118 Ramachandran restraints generated. 8059 Oldfield, 0 Emsley, 8059 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16118 Ramachandran restraints generated. 8059 Oldfield, 0 Emsley, 8059 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 707 residues out of total 6773 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 105 poor density : 602 time to evaluate : 5.554 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 23 MET cc_start: 0.6461 (mpp) cc_final: 0.6199 (mtp) REVERT: b 353 MET cc_start: 0.4138 (mmm) cc_final: 0.3357 (mmp) REVERT: b 488 MET cc_start: 0.8111 (mmm) cc_final: 0.6869 (mmm) REVERT: B 350 GLU cc_start: 0.4991 (mt-10) cc_final: 0.4482 (tt0) REVERT: B 353 MET cc_start: 0.3820 (mmm) cc_final: 0.2591 (tpt) REVERT: B 360 ILE cc_start: 0.4271 (OUTLIER) cc_final: 0.3967 (mt) REVERT: B 415 MET cc_start: 0.7865 (mmm) cc_final: 0.7583 (mmm) REVERT: D 206 ARG cc_start: 0.6018 (ptt90) cc_final: 0.5063 (tpm170) REVERT: D 323 MET cc_start: 0.3079 (mmm) cc_final: 0.2827 (mmm) REVERT: d 260 MET cc_start: -0.1071 (mtt) cc_final: -0.2743 (ttt) REVERT: d 338 LYS cc_start: 0.3358 (tptt) cc_final: 0.3083 (tppt) REVERT: E 379 ARG cc_start: 0.4798 (mmt180) cc_final: 0.4017 (ttt180) REVERT: E 472 MET cc_start: 0.7041 (tpp) cc_final: 0.6794 (tpp) REVERT: E 483 MET cc_start: 0.3815 (ppp) cc_final: 0.3533 (ppp) REVERT: e 79 MET cc_start: 0.7360 (ttm) cc_final: 0.7119 (ttm) REVERT: e 253 PHE cc_start: 0.1500 (OUTLIER) cc_final: 0.0393 (t80) REVERT: g 229 MET cc_start: 0.4399 (mtm) cc_final: 0.4165 (mtm) REVERT: h 99 LEU cc_start: 0.8088 (OUTLIER) cc_final: 0.7793 (tt) REVERT: h 394 MET cc_start: 0.6528 (mmp) cc_final: 0.6321 (mmp) REVERT: H 414 MET cc_start: 0.7601 (tpp) cc_final: 0.7350 (mmt) REVERT: q 274 ASN cc_start: 0.2671 (OUTLIER) cc_final: 0.2447 (p0) REVERT: q 385 MET cc_start: 0.7442 (tpp) cc_final: 0.7021 (mmt) REVERT: Z 7 LEU cc_start: 0.1116 (OUTLIER) cc_final: 0.0727 (pp) REVERT: Z 289 PHE cc_start: 0.3233 (t80) cc_final: 0.2577 (t80) REVERT: Z 522 MET cc_start: 0.6871 (ptp) cc_final: 0.6489 (ptp) outliers start: 105 outliers final: 85 residues processed: 678 average time/residue: 0.5656 time to fit residues: 668.7198 Evaluate side-chains 636 residues out of total 6773 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 90 poor density : 546 time to evaluate : 5.515 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 78 LEU Chi-restraints excluded: chain a residue 166 ASP Chi-restraints excluded: chain a residue 486 ILE Chi-restraints excluded: chain A residue 31 ILE Chi-restraints excluded: chain A residue 78 LEU Chi-restraints excluded: chain A residue 166 ASP Chi-restraints excluded: chain A residue 219 VAL Chi-restraints excluded: chain A residue 292 ILE Chi-restraints excluded: chain A residue 377 LEU Chi-restraints excluded: chain A residue 384 MET Chi-restraints excluded: chain A residue 394 ASP Chi-restraints excluded: chain A residue 397 CYS Chi-restraints excluded: chain A residue 529 ASP Chi-restraints excluded: chain b residue 28 SER Chi-restraints excluded: chain B residue 35 ILE Chi-restraints excluded: chain B residue 224 ILE Chi-restraints excluded: chain B residue 360 ILE Chi-restraints excluded: chain B residue 379 THR Chi-restraints excluded: chain B residue 391 HIS Chi-restraints excluded: chain D residue 409 LEU Chi-restraints excluded: chain D residue 460 VAL Chi-restraints excluded: chain D residue 477 VAL Chi-restraints excluded: chain D residue 524 GLU Chi-restraints excluded: chain d residue 165 ASN Chi-restraints excluded: chain d residue 220 ASP Chi-restraints excluded: chain d residue 333 ILE Chi-restraints excluded: chain d residue 474 ILE Chi-restraints excluded: chain E residue 66 VAL Chi-restraints excluded: chain E residue 105 THR Chi-restraints excluded: chain E residue 164 ILE Chi-restraints excluded: chain E residue 183 MET Chi-restraints excluded: chain E residue 266 VAL Chi-restraints excluded: chain E residue 335 THR Chi-restraints excluded: chain E residue 391 MET Chi-restraints excluded: chain E residue 505 ILE Chi-restraints excluded: chain e residue 67 THR Chi-restraints excluded: chain e residue 81 VAL Chi-restraints excluded: chain e residue 116 GLU Chi-restraints excluded: chain e residue 253 PHE Chi-restraints excluded: chain e residue 304 PHE Chi-restraints excluded: chain e residue 438 CYS Chi-restraints excluded: chain e residue 505 ILE Chi-restraints excluded: chain g residue 54 MET Chi-restraints excluded: chain g residue 59 MET Chi-restraints excluded: chain g residue 83 ILE Chi-restraints excluded: chain g residue 215 LEU Chi-restraints excluded: chain g residue 289 VAL Chi-restraints excluded: chain g residue 319 ASP Chi-restraints excluded: chain g residue 490 MET Chi-restraints excluded: chain G residue 83 ILE Chi-restraints excluded: chain G residue 219 MET Chi-restraints excluded: chain G residue 237 ARG Chi-restraints excluded: chain G residue 497 GLU Chi-restraints excluded: chain h residue 17 GLN Chi-restraints excluded: chain h residue 99 LEU Chi-restraints excluded: chain h residue 116 LEU Chi-restraints excluded: chain h residue 197 ILE Chi-restraints excluded: chain h residue 199 LYS Chi-restraints excluded: chain h residue 379 GLU Chi-restraints excluded: chain h residue 484 ILE Chi-restraints excluded: chain H residue 57 THR Chi-restraints excluded: chain H residue 58 ILE Chi-restraints excluded: chain H residue 96 SER Chi-restraints excluded: chain H residue 116 LEU Chi-restraints excluded: chain H residue 183 VAL Chi-restraints excluded: chain H residue 187 ASP Chi-restraints excluded: chain Q residue 104 VAL Chi-restraints excluded: chain Q residue 217 VAL Chi-restraints excluded: chain Q residue 302 LEU Chi-restraints excluded: chain Q residue 327 THR Chi-restraints excluded: chain Q residue 336 LEU Chi-restraints excluded: chain Q residue 376 VAL Chi-restraints excluded: chain Q residue 382 ASP Chi-restraints excluded: chain Q residue 384 LEU Chi-restraints excluded: chain Q residue 499 ASP Chi-restraints excluded: chain q residue 141 GLU Chi-restraints excluded: chain q residue 149 CYS Chi-restraints excluded: chain q residue 274 ASN Chi-restraints excluded: chain q residue 309 ASN Chi-restraints excluded: chain q residue 384 LEU Chi-restraints excluded: chain Z residue 7 LEU Chi-restraints excluded: chain Z residue 15 ARG Chi-restraints excluded: chain Z residue 137 VAL Chi-restraints excluded: chain Z residue 233 CYS Chi-restraints excluded: chain z residue 22 VAL Chi-restraints excluded: chain z residue 110 ILE Chi-restraints excluded: chain z residue 148 LEU Chi-restraints excluded: chain z residue 239 TYR Chi-restraints excluded: chain z residue 284 ASP Chi-restraints excluded: chain z residue 487 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 805 random chunks: chunk 507 optimal weight: 4.9990 chunk 680 optimal weight: 1.9990 chunk 195 optimal weight: 3.9990 chunk 588 optimal weight: 0.0020 chunk 94 optimal weight: 10.0000 chunk 177 optimal weight: 2.9990 chunk 639 optimal weight: 0.9990 chunk 267 optimal weight: 9.9990 chunk 656 optimal weight: 0.0570 chunk 80 optimal weight: 7.9990 chunk 117 optimal weight: 10.0000 overall best weight: 1.2112 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** a 284 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 231 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 284 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 406 HIS ** E 234 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 401 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 184 GLN ** G 390 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 53 ASN ** q 316 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 453 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** z 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** z 198 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4400 r_free = 0.4400 target = 0.151531 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3990 r_free = 0.3990 target = 0.125852 restraints weight = 174294.597| |-----------------------------------------------------------------------------| r_work (start): 0.3945 rms_B_bonded: 2.75 r_work: 0.3847 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work (final): 0.3847 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7239 moved from start: 0.5458 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.050 63224 Z= 0.165 Angle : 0.571 12.900 85373 Z= 0.274 Chirality : 0.041 0.215 10213 Planarity : 0.004 0.195 10879 Dihedral : 5.963 178.291 8787 Min Nonbonded Distance : 2.162 Molprobity Statistics. All-atom Clashscore : 10.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.62 % Favored : 96.38 % Rotamer: Outliers : 1.40 % Allowed : 15.89 % Favored : 82.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.93 % Cis-general : 0.01 % Twisted Proline : 0.93 % 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: 0.43 (0.10), residues: 8059 helix: 1.43 (0.08), residues: 4192 sheet: -0.79 (0.19), residues: 785 loop : -0.98 (0.11), residues: 3082 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP E 302 HIS 0.021 0.001 HIS e 401 PHE 0.022 0.001 PHE Q 399 TYR 0.027 0.001 TYR a 299 ARG 0.015 0.000 ARG z 157 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 13995.20 seconds wall clock time: 247 minutes 29.46 seconds (14849.46 seconds total)