Starting phenix.real_space_refine on Tue Mar 12 13:54:27 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7x3j_32989/03_2024/7x3j_32989_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7x3j_32989/03_2024/7x3j_32989.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7x3j_32989/03_2024/7x3j_32989.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7x3j_32989/03_2024/7x3j_32989.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7x3j_32989/03_2024/7x3j_32989_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7x3j_32989/03_2024/7x3j_32989_updated.pdb" } resolution = 4.2 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= 0.020 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 48 5.49 5 S 389 5.16 5 C 39472 2.51 5 N 11001 2.21 5 O 12278 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ASP 42": "OD1" <-> "OD2" Residue "A ASP 48": "OD1" <-> "OD2" Residue "A ASP 80": "OD1" <-> "OD2" Residue "A ASP 83": "OD1" <-> "OD2" Residue "A ASP 88": "OD1" <-> "OD2" Residue "A ASP 166": "OD1" <-> "OD2" Residue "A ASP 183": "OD1" <-> "OD2" Residue "A TYR 190": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 238": "OD1" <-> "OD2" Residue "A PHE 239": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 256": "OD1" <-> "OD2" Residue "A GLU 258": "OE1" <-> "OE2" Residue "A GLU 302": "OE1" <-> "OE2" Residue "A GLU 335": "OE1" <-> "OE2" Residue "A GLU 338": "OE1" <-> "OE2" Residue "A GLU 350": "OE1" <-> "OE2" Residue "A GLU 354": "OE1" <-> "OE2" Residue "A ASP 358": "OD1" <-> "OD2" Residue "A ASP 386": "OD1" <-> "OD2" Residue "A GLU 387": "OE1" <-> "OE2" Residue "A GLU 389": "OE1" <-> "OE2" Residue "A PHE 441": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 473": "OE1" <-> "OE2" Residue "A ASP 489": "OD1" <-> "OD2" Residue "A ASP 497": "OD1" <-> "OD2" Residue "B ASP 77": "OD1" <-> "OD2" Residue "B ASP 86": "OD1" <-> "OD2" Residue "B ASP 97": "OD1" <-> "OD2" Residue "B GLU 114": "OE1" <-> "OE2" Residue "B ASP 177": "OD1" <-> "OD2" Residue "B PHE 179": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 213": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 216": "OE1" <-> "OE2" Residue "B PHE 218": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 221": "OD1" <-> "OD2" Residue "B ASP 247": "OD1" <-> "OD2" Residue "B GLU 266": "OE1" <-> "OE2" Residue "B TYR 299": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 330": "OE1" <-> "OE2" Residue "B PHE 335": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 336": "OD1" <-> "OD2" Residue "B ASP 384": "OD1" <-> "OD2" Residue "B GLU 437": "OE1" <-> "OE2" Residue "B TYR 439": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 512": "OE1" <-> "OE2" Residue "D GLU 93": "OE1" <-> "OE2" Residue "D ASP 104": "OD1" <-> "OD2" Residue "D GLU 135": "OE1" <-> "OE2" Residue "D GLU 142": "OE1" <-> "OE2" Residue "D ASP 150": "OD1" <-> "OD2" Residue "D GLU 156": "OE1" <-> "OE2" Residue "D ASP 204": "OD1" <-> "OD2" Residue "D ASP 207": "OD1" <-> "OD2" Residue "D ASP 219": "OD1" <-> "OD2" Residue "D GLU 331": "OE1" <-> "OE2" Residue "D ASP 349": "OD1" <-> "OD2" Residue "D ASP 354": "OD1" <-> "OD2" Residue "D GLU 399": "OE1" <-> "OE2" Residue "D GLU 431": "OE1" <-> "OE2" Residue "D TYR 449": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 454": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 534": "OD1" <-> "OD2" Residue "E ASP 63": "OD1" <-> "OD2" Residue "E GLU 99": "OE1" <-> "OE2" Residue "E ASP 102": "OD1" <-> "OD2" Residue "E GLU 116": "OE1" <-> "OE2" Residue "E GLU 117": "OE1" <-> "OE2" Residue "E ASP 123": "OD1" <-> "OD2" Residue "E GLU 161": "OE1" <-> "OE2" Residue "E GLU 185": "OE1" <-> "OE2" Residue "E ASP 203": "OD1" <-> "OD2" Residue "E GLU 218": "OE1" <-> "OE2" Residue "E ASP 219": "OD1" <-> "OD2" Residue "E ASP 243": "OD1" <-> "OD2" Residue "E ASP 265": "OD1" <-> "OD2" Residue "E ASP 271": "OD1" <-> "OD2" Residue "E GLU 284": "OE1" <-> "OE2" Residue "E GLU 292": "OE1" <-> "OE2" Residue "E GLU 349": "OE1" <-> "OE2" Residue "E PHE 362": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 402": "OD1" <-> "OD2" Residue "E TYR 444": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 530": "OD1" <-> "OD2" Residue "G GLU 82": "OE1" <-> "OE2" Residue "G GLU 192": "OE1" <-> "OE2" Residue "G ASP 194": "OD1" <-> "OD2" Residue "G ASP 211": "OD1" <-> "OD2" Residue "G TYR 232": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 242": "OD1" <-> "OD2" Residue "G GLU 246": "OE1" <-> "OE2" Residue "G TYR 247": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 251": "OE1" <-> "OE2" Residue "G GLU 271": "OE1" <-> "OE2" Residue "G GLU 272": "OE1" <-> "OE2" Residue "G GLU 273": "OE1" <-> "OE2" Residue "G GLU 280": "OE1" <-> "OE2" Residue "G ASP 298": "OD1" <-> "OD2" Residue "G TYR 303": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 359": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 368": "OD1" <-> "OD2" Residue "G GLU 415": "OE1" <-> "OE2" Residue "G GLU 433": "OE1" <-> "OE2" Residue "G ASP 521": "OD1" <-> "OD2" Residue "H ASP 46": "OD1" <-> "OD2" Residue "H ASP 70": "OD1" <-> "OD2" Residue "H ASP 81": "OD1" <-> "OD2" Residue "H ASP 87": "OD1" <-> "OD2" Residue "H ASP 147": "OD1" <-> "OD2" Residue "H GLU 156": "OE1" <-> "OE2" Residue "H GLU 254": "OE1" <-> "OE2" Residue "H GLU 261": "OE1" <-> "OE2" Residue "H ASP 268": "OD1" <-> "OD2" Residue "H PHE 303": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ASP 307": "OD1" <-> "OD2" Residue "H PHE 309": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 349": "OE1" <-> "OE2" Residue "H PHE 360": "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 GLU 508": "OE1" <-> "OE2" Residue "Q GLU 61": "OE1" <-> "OE2" Residue "Q PHE 64": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q ASP 68": "OD1" <-> "OD2" Residue "Q GLU 77": "OE1" <-> "OE2" Residue "Q GLU 96": "OE1" <-> "OE2" Residue "Q PHE 103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q ASP 158": "OD1" <-> "OD2" Residue "Q ASP 200": "OD1" <-> "OD2" Residue "Q PHE 223": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q ASP 230": "OD1" <-> "OD2" Residue "Q ASP 247": "OD1" <-> "OD2" Residue "Q GLU 252": "OE1" <-> "OE2" Residue "Q PHE 268": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q GLU 272": "OE1" <-> "OE2" Residue "Q ASP 357": "OD1" <-> "OD2" Residue "Q GLU 389": "OE1" <-> "OE2" Residue "Q PHE 399": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q GLU 418": "OE1" <-> "OE2" Residue "Q GLU 473": "OE1" <-> "OE2" Residue "Q ASP 481": "OD1" <-> "OD2" Residue "Q GLU 485": "OE1" <-> "OE2" Residue "Z GLU 66": "OE1" <-> "OE2" Residue "Z ASP 90": "OD1" <-> "OD2" Residue "Z GLU 142": "OE1" <-> "OE2" Residue "Z GLU 146": "OE1" <-> "OE2" Residue "Z ASP 187": "OD1" <-> "OD2" Residue "Z ASP 220": "OD1" <-> "OD2" Residue "Z TYR 229": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z GLU 243": "OE1" <-> "OE2" Residue "Z GLU 255": "OE1" <-> "OE2" Residue "Z GLU 257": "OE1" <-> "OE2" Residue "Z PHE 266": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z ASP 269": "OD1" <-> "OD2" Residue "Z GLU 308": "OE1" <-> "OE2" Residue "Z ASP 342": "OD1" <-> "OD2" Residue "Z ASP 393": "OD1" <-> "OD2" Residue "Z GLU 420": "OE1" <-> "OE2" Residue "Z ASP 480": "OD1" <-> "OD2" Residue "Z GLU 485": "OE1" <-> "OE2" Residue "Z GLU 520": "OE1" <-> "OE2" Residue "b GLU 19": "OE1" <-> "OE2" Residue "b GLU 22": "OE1" <-> "OE2" Residue "b ASP 49": "OD1" <-> "OD2" Residue "b ASP 58": "OD1" <-> "OD2" Residue "b ASP 66": "OD1" <-> "OD2" Residue "b ASP 77": "OD1" <-> "OD2" Residue "b ASP 86": "OD1" <-> "OD2" Residue "b GLU 94": "OE1" <-> "OE2" Residue "b GLU 108": "OE1" <-> "OE2" Residue "b GLU 112": "OE1" <-> "OE2" Residue "b GLU 114": "OE1" <-> "OE2" Residue "b GLU 197": "OE1" <-> "OE2" Residue "b GLU 266": "OE1" <-> "OE2" Residue "b GLU 301": "OE1" <-> "OE2" Residue "b ASP 336": "OD1" <-> "OD2" Residue "b GLU 339": "OE1" <-> "OE2" Residue "b GLU 351": "OE1" <-> "OE2" Residue "b GLU 369": "OE1" <-> "OE2" Residue "b ASP 384": "OD1" <-> "OD2" Residue "b ASP 452": "OD1" <-> "OD2" Residue "b ASP 457": "OD1" <-> "OD2" Residue "d ASP 63": "OD1" <-> "OD2" Residue "d GLU 101": "OE1" <-> "OE2" Residue "d GLU 156": "OE1" <-> "OE2" Residue "d ASP 159": "OD1" <-> "OD2" Residue "d ASP 196": "OD1" <-> "OD2" Residue "d ASP 220": "OD1" <-> "OD2" Residue "d ASP 259": "OD1" <-> "OD2" Residue "d TYR 269": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d GLU 278": "OE1" <-> "OE2" Residue "d ASP 311": "OD1" <-> "OD2" Residue "d ASP 327": "OD1" <-> "OD2" Residue "d GLU 334": "OE1" <-> "OE2" Residue "d GLU 360": "OE1" <-> "OE2" Residue "d GLU 400": "OE1" <-> "OE2" Residue "d PHE 454": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d GLU 505": "OE1" <-> "OE2" Residue "d GLU 524": "OE1" <-> "OE2" Residue "d ASP 534": "OD1" <-> "OD2" Residue "e ASP 56": "OD1" <-> "OD2" Residue "e ASP 65": "OD1" <-> "OD2" Residue "e GLU 91": "OE1" <-> "OE2" Residue "e ASP 97": "OD1" <-> "OD2" Residue "e GLU 116": "OE1" <-> "OE2" Residue "e GLU 119": "OE1" <-> "OE2" Residue "e ASP 123": "OD1" <-> "OD2" Residue "e ASP 133": "OD1" <-> "OD2" Residue "e ASP 156": "OD1" <-> "OD2" Residue "e ASP 196": "OD1" <-> "OD2" Residue "e ASP 243": "OD1" <-> "OD2" Residue "e ASP 265": "OD1" <-> "OD2" Residue "e GLU 281": "OE1" <-> "OE2" Residue "e GLU 285": "OE1" <-> "OE2" Residue "e GLU 307": "OE1" <-> "OE2" Residue "e PHE 353": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "e GLU 454": "OE1" <-> "OE2" Residue "e GLU 536": "OE1" <-> "OE2" Residue "g ASP 52": "OD1" <-> "OD2" Residue "g ASP 93": "OD1" <-> "OD2" Residue "g PHE 112": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "g ASP 148": "OD1" <-> "OD2" Residue "g GLU 187": "OE1" <-> "OE2" Residue "g TYR 232": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "g GLU 251": "OE1" <-> "OE2" Residue "g ASP 263": "OD1" <-> "OD2" Residue "g PHE 264": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "g GLU 273": "OE1" <-> "OE2" Residue "g ASP 298": "OD1" <-> "OD2" Residue "g GLU 340": "OE1" <-> "OE2" Residue "g ASP 341": "OD1" <-> "OD2" Residue "g PHE 362": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "g ASP 368": "OD1" <-> "OD2" Residue "g ASP 520": "OD1" <-> "OD2" Residue "g ASP 521": "OD1" <-> "OD2" Residue "h ASP 70": "OD1" <-> "OD2" Residue "h GLU 113": "OE1" <-> "OE2" Residue "h GLU 114": "OE1" <-> "OE2" Residue "h PHE 175": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "h ASP 188": "OD1" <-> "OD2" Residue "h PHE 216": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "h GLU 249": "OE1" <-> "OE2" Residue "h ASP 262": "OD1" <-> "OD2" Residue "h TYR 302": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "h PHE 309": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "h ASP 340": "OD1" <-> "OD2" Residue "h TYR 358": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "h PHE 360": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "h PHE 372": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "h GLU 415": "OE1" <-> "OE2" Residue "h TYR 438": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "q PHE 11": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "q PHE 22": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "q GLU 26": "OE1" <-> "OE2" Residue "q ASP 68": "OD1" <-> "OD2" Residue "q GLU 96": "OE1" <-> "OE2" Residue "q ASP 99": "OD1" <-> "OD2" Residue "q ASP 156": "OD1" <-> "OD2" Residue "q GLU 252": "OE1" <-> "OE2" Residue "q ASP 320": "OD1" <-> "OD2" Residue "q GLU 342": "OE1" <-> "OE2" Residue "q GLU 366": "OE1" <-> "OE2" Residue "q ASP 369": "OD1" <-> "OD2" Residue "q ASP 393": "OD1" <-> "OD2" Residue "q PHE 399": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "q GLU 462": "OE1" <-> "OE2" Residue "q GLU 494": "OE1" <-> "OE2" Residue "z GLU 12": "OE1" <-> "OE2" Residue "z ASP 32": "OD1" <-> "OD2" Residue "z GLU 66": "OE1" <-> "OE2" Residue "z ASP 85": "OD1" <-> "OD2" Residue "z ASP 86": "OD1" <-> "OD2" Residue "z ASP 90": "OD1" <-> "OD2" Residue "z GLU 121": "OE1" <-> "OE2" Residue "z ASP 166": "OD1" <-> "OD2" Residue "z GLU 184": "OE1" <-> "OE2" Residue "z ASP 187": "OD1" <-> "OD2" Residue "z PHE 248": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "z TYR 250": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "z GLU 254": "OE1" <-> "OE2" Residue "z PHE 266": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "z ASP 269": "OD1" <-> "OD2" Residue "z ASP 284": "OD1" <-> "OD2" Residue "z ASP 303": "OD1" <-> "OD2" Residue "z GLU 322": "OE1" <-> "OE2" Residue "z PHE 360": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "z PHE 362": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "z ASP 393": "OD1" <-> "OD2" Residue "z GLU 461": "OE1" <-> "OE2" Residue "z GLU 472": "OE1" <-> "OE2" Residue "a ASP 42": "OD1" <-> "OD2" Residue "a ASP 48": "OD1" <-> "OD2" Residue "a ASP 80": "OD1" <-> "OD2" Residue "a ASP 83": "OD1" <-> "OD2" Residue "a ASP 88": "OD1" <-> "OD2" Residue "a ASP 166": "OD1" <-> "OD2" Residue "a ASP 183": "OD1" <-> "OD2" Residue "a TYR 190": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a ASP 238": "OD1" <-> "OD2" Residue "a PHE 239": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a ASP 256": "OD1" <-> "OD2" Residue "a GLU 258": "OE1" <-> "OE2" Residue "a ARG 264": "NH1" <-> "NH2" Residue "a GLU 302": "OE1" <-> "OE2" Residue "a GLU 335": "OE1" <-> "OE2" Residue "a GLU 338": "OE1" <-> "OE2" Residue "a GLU 350": "OE1" <-> "OE2" Residue "a GLU 354": "OE1" <-> "OE2" Residue "a ASP 358": "OD1" <-> "OD2" Residue "a ASP 386": "OD1" <-> "OD2" Residue "a GLU 389": "OE1" <-> "OE2" Residue "a PHE 441": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a GLU 473": "OE1" <-> "OE2" Residue "a ASP 489": "OD1" <-> "OD2" Residue "a ASP 497": "OD1" <-> "OD2" Time to flip residues: 0.16s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 63188 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: "B" Number of atoms: 3796 Number of conformers: 1 Conformer: "" Number of residues, atoms: 504, 3796 Classifications: {'peptide': 504} Link IDs: {'PTRANS': 8, 'TRANS': 495} Chain: "D" Number of atoms: 3513 Number of conformers: 1 Conformer: "" Number of residues, atoms: 469, 3513 Classifications: {'peptide': 469} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 12, 'TRANS': 455} Chain breaks: 2 Chain: "E" Number of atoms: 3914 Number of conformers: 1 Conformer: "" Number of residues, atoms: 509, 3914 Classifications: {'peptide': 509} Link IDs: {'PTRANS': 16, 'TRANS': 492} 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: "H" Number of atoms: 3913 Number of conformers: 1 Conformer: "" Number of residues, atoms: 509, 3913 Classifications: {'peptide': 509} Link IDs: {'PTRANS': 14, 'TRANS': 494} Chain: "Q" Number of atoms: 3858 Number of conformers: 1 Conformer: "" Number of residues, atoms: 506, 3858 Classifications: {'peptide': 506} Link IDs: {'PTRANS': 13, 'TRANS': 492} Chain: "Z" Number of atoms: 3943 Number of conformers: 1 Conformer: "" Number of residues, atoms: 514, 3943 Classifications: {'peptide': 514} Link IDs: {'PTRANS': 13, 'TRANS': 500} 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: 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: "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: "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: "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: 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: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Chain: "G" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Chain: "H" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Chain: "Q" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Chain: "Z" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Chain: "b" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Chain: "d" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Chain: "e" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Chain: "g" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Chain: "h" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Chain: "q" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Chain: "z" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Chain: "a" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 24.66, per 1000 atoms: 0.39 Number of scatterers: 63188 At special positions: 0 Unit cell: (184.52, 217.47, 196.382, 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 389 16.00 P 48 15.00 O 12278 8.00 N 11001 7.00 C 39472 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 Atom "HETATM63058 O3B ATP g 601 .*. O " rejected from bonding due to valence issues. Number of custom bonds: simple=26, symmetry=0 Number of additional bonds: simple=26, symmetry=0 Coordination: Other bonds: Time building additional restraints: 18.73 Conformation dependent library (CDL) restraints added in 8.9 seconds 16346 Ramachandran restraints generated. 8173 Oldfield, 0 Emsley, 8173 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 15300 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 296 helices and 84 sheets defined 47.1% alpha, 7.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 9.49 Creating SS restraints... Processing helix chain 'A' and resid 16 through 31 removed outlier: 3.510A pdb=" N SER A 27 " --> pdb=" O MET A 23 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N ILE A 28 " --> pdb=" O ALA A 24 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ALA A 29 " --> pdb=" O ALA A 25 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ILE A 31 " --> pdb=" O SER A 27 " (cutoff:3.500A) Processing helix chain 'A' and resid 58 through 64 removed outlier: 3.578A pdb=" N LYS A 63 " --> pdb=" O ALA A 59 " (cutoff:3.500A) Processing helix chain 'A' and resid 70 through 83 removed outlier: 4.151A pdb=" N LEU A 75 " --> pdb=" O ALA A 71 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N CYS A 76 " --> pdb=" O ALA A 72 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N GLU A 77 " --> pdb=" O LYS A 73 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N LEU A 78 " --> pdb=" O VAL A 74 " (cutoff:3.500A) removed outlier: 4.307A pdb=" N ALA A 79 " --> pdb=" O LEU A 75 " (cutoff:3.500A) removed outlier: 4.185A pdb=" N ASP A 80 " --> pdb=" O CYS A 76 " (cutoff:3.500A) Processing helix chain 'A' and resid 90 through 109 removed outlier: 3.832A pdb=" N VAL A 94 " --> pdb=" O THR A 90 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N LYS A 109 " --> pdb=" O ASP A 105 " (cutoff:3.500A) Processing helix chain 'A' and resid 114 through 135 removed outlier: 3.619A pdb=" N LEU A 123 " --> pdb=" O SER A 119 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N ASN A 135 " --> pdb=" O TYR A 131 " (cutoff:3.500A) Processing helix chain 'A' and resid 149 through 158 removed outlier: 3.713A pdb=" N THR A 154 " --> pdb=" O ASN A 150 " (cutoff:3.500A) removed outlier: 4.186A pdb=" N SER A 155 " --> pdb=" O ALA A 151 " (cutoff:3.500A) removed outlier: 4.914A pdb=" N SER A 158 " --> pdb=" O THR A 154 " (cutoff:3.500A) Processing helix chain 'A' and resid 160 through 163 removed outlier: 3.795A pdb=" N ILE A 163 " --> pdb=" O ILE A 160 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 160 through 163' Processing helix chain 'A' and resid 165 through 176 removed outlier: 3.953A pdb=" N ASN A 170 " --> pdb=" O ASP A 166 " (cutoff:3.500A) removed outlier: 4.235A pdb=" N MET A 171 " --> pdb=" O PHE A 167 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N VAL A 172 " --> pdb=" O PHE A 168 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N ASP A 174 " --> pdb=" O ASN A 170 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N ALA A 175 " --> pdb=" O MET A 171 " (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 278 removed outlier: 3.631A pdb=" N ASP A 261 " --> pdb=" O PRO A 257 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N ILE A 263 " --> pdb=" O LYS A 259 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N ARG A 264 " --> pdb=" O LEU A 260 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N LYS A 272 " --> pdb=" O SER A 268 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N GLU A 273 " --> pdb=" O ASP A 269 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N ILE A 275 " --> pdb=" O THR A 271 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N GLN A 276 " --> pdb=" O LYS A 272 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N LYS A 277 " --> pdb=" O GLU A 273 " (cutoff:3.500A) Processing helix chain 'A' and resid 300 through 303 No H-bonds generated for 'chain 'A' and resid 300 through 303' Processing helix chain 'A' and resid 313 through 322 removed outlier: 3.764A pdb=" N ARG A 318 " --> pdb=" O ARG A 314 " (cutoff:3.500A) Processing helix chain 'A' and resid 382 through 404 removed outlier: 3.610A pdb=" N GLU A 387 " --> pdb=" O PHE A 383 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N ARG A 390 " --> pdb=" O ASP A 386 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N VAL A 398 " --> pdb=" O ASP A 394 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N VAL A 399 " --> pdb=" O ALA A 395 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N VAL A 402 " --> pdb=" O VAL A 398 " (cutoff:3.500A) Processing helix chain 'A' and resid 414 through 430 removed outlier: 3.567A pdb=" N ALA A 418 " --> pdb=" O ALA A 414 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N ILE A 421 " --> pdb=" O ALA A 417 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N TYR A 422 " --> pdb=" O ALA A 418 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N GLU A 424 " --> pdb=" O SER A 420 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N SER A 429 " --> pdb=" O ASN A 425 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N MET A 430 " --> pdb=" O TYR A 426 " (cutoff:3.500A) Processing helix chain 'A' and resid 435 through 455 removed outlier: 3.762A pdb=" N LEU A 446 " --> pdb=" O ALA A 442 " (cutoff:3.500A) removed outlier: 4.498A pdb=" N VAL A 447 " --> pdb=" O ARG A 443 " (cutoff:3.500A) removed outlier: 5.336A 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 471 removed outlier: 3.667A pdb=" N VAL A 464 " --> pdb=" O SER A 460 " (cutoff:3.500A) removed outlier: 4.162A pdb=" N ALA A 465 " --> pdb=" O THR A 461 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N LEU A 467 " --> pdb=" O LEU A 463 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N PHE A 470 " --> pdb=" O LYS A 466 " (cutoff:3.500A) Processing helix chain 'A' and resid 473 through 476 No H-bonds generated for 'chain 'A' and resid 473 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: 3.647A pdb=" N SER A 513 " --> pdb=" O VAL A 509 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N LEU A 514 " --> pdb=" O LYS A 510 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N THR A 518 " --> pdb=" O LEU A 514 " (cutoff:3.500A) Processing helix chain 'B' and resid 23 through 36 removed outlier: 3.621A pdb=" N THR B 27 " --> pdb=" O THR B 23 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N PHE B 29 " --> pdb=" O ARG B 25 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N ILE B 30 " --> pdb=" O LEU B 26 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N ILE B 35 " --> pdb=" O GLY B 31 " (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 71 removed outlier: 3.884A pdb=" N LEU B 71 " --> pdb=" O GLY B 67 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 67 through 71' Processing helix chain 'B' and resid 79 through 94 removed outlier: 3.799A pdb=" N VAL B 83 " --> pdb=" O PRO B 79 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N LEU B 84 " --> pdb=" O ALA B 80 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N GLN B 91 " --> pdb=" O MET B 87 " (cutoff:3.500A) Processing helix chain 'B' and resid 99 through 118 removed outlier: 3.826A pdb=" N THR B 103 " --> pdb=" O THR B 99 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N GLU B 108 " --> pdb=" O VAL B 104 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N SER B 115 " --> pdb=" O ARG B 111 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N LEU B 116 " --> pdb=" O GLU B 112 " (cutoff:3.500A) Processing helix chain 'B' and resid 123 through 143 removed outlier: 3.521A pdb=" N ILE B 127 " --> pdb=" O PRO B 123 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N LYS B 135 " --> pdb=" O ARG B 131 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N ALA B 136 " --> pdb=" O GLU B 132 " (cutoff:3.500A) Processing helix chain 'B' and resid 152 through 166 removed outlier: 3.725A pdb=" N MET B 160 " --> pdb=" O ARG B 156 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N ASN B 161 " --> pdb=" O GLN B 157 " (cutoff:3.500A) Processing helix chain 'B' and resid 176 through 188 removed outlier: 3.795A pdb=" N LYS B 181 " --> pdb=" O ASP B 177 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N VAL B 184 " --> pdb=" O THR B 180 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N GLU B 185 " --> pdb=" O LYS B 181 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N ALA B 186 " --> pdb=" O LEU B 182 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N VAL B 187 " --> pdb=" O ALA B 183 " (cutoff:3.500A) Processing helix chain 'B' and resid 261 through 285 removed outlier: 3.590A pdb=" N LYS B 272 " --> pdb=" O GLU B 268 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N LYS B 278 " --> pdb=" O LYS B 274 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N HIS B 285 " --> pdb=" O ARG B 281 " (cutoff:3.500A) Processing helix chain 'B' and resid 301 through 306 Processing helix chain 'B' and resid 319 through 327 removed outlier: 4.135A pdb=" N ALA B 324 " --> pdb=" O VAL B 320 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N LEU B 325 " --> pdb=" O GLU B 321 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N THR B 327 " --> pdb=" O LEU B 323 " (cutoff:3.500A) Processing helix chain 'B' and resid 380 through 402 removed outlier: 3.604A pdb=" N ARG B 388 " --> pdb=" O ASP B 384 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N CYS B 395 " --> pdb=" O HIS B 391 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N VAL B 396 " --> pdb=" O ASP B 392 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N VAL B 401 " --> pdb=" O LEU B 397 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N LYS B 402 " --> pdb=" O ALA B 398 " (cutoff:3.500A) Processing helix chain 'B' and resid 412 through 426 removed outlier: 3.537A pdb=" N ALA B 420 " --> pdb=" O LEU B 416 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N VAL B 421 " --> pdb=" O MET B 417 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N ASN B 426 " --> pdb=" O THR B 422 " (cutoff:3.500A) Processing helix chain 'B' and resid 430 through 444 removed outlier: 3.859A pdb=" N VAL B 434 " --> pdb=" O GLY B 430 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N ALA B 435 " --> pdb=" O LYS B 431 " (cutoff:3.500A) Processing helix chain 'B' and resid 446 through 453 removed outlier: 3.692A pdb=" N ILE B 450 " --> pdb=" O LEU B 446 " (cutoff:3.500A) Processing helix chain 'B' and resid 458 through 468 removed outlier: 3.697A pdb=" N VAL B 462 " --> pdb=" O SER B 458 " (cutoff:3.500A) removed outlier: 4.345A pdb=" N ALA B 463 " --> pdb=" O ALA B 459 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N ALA B 467 " --> pdb=" O ALA B 463 " (cutoff:3.500A) 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: 3.745A pdb=" N ILE B 514 " --> pdb=" O ALA B 510 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N LEU B 515 " --> pdb=" O ALA B 511 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N ARG B 516 " --> pdb=" O GLU B 512 " (cutoff:3.500A) Processing helix chain 'D' and resid 31 through 51 removed outlier: 3.612A pdb=" N SER D 36 " --> pdb=" O GLN D 32 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N VAL D 44 " --> pdb=" O ALA D 40 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N ALA D 47 " --> pdb=" O ALA D 43 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ARG D 49 " --> pdb=" O ALA D 45 " (cutoff:3.500A) removed outlier: 5.235A pdb=" N THR D 50 " --> pdb=" O ASP D 46 " (cutoff:3.500A) removed outlier: 4.870A pdb=" N SER D 51 " --> 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 removed outlier: 3.604A pdb=" N LEU D 91 " --> pdb=" O ALA D 87 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N GLN D 98 " --> pdb=" O LEU D 94 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N ASP D 99 " --> pdb=" O SER D 95 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N ILE D 100 " --> pdb=" O LYS D 96 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N GLU D 101 " --> pdb=" O ALA D 97 " (cutoff:3.500A) Processing helix chain 'D' and resid 107 through 125 removed outlier: 3.662A pdb=" N ILE D 111 " --> pdb=" O THR D 107 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N ILE D 112 " --> pdb=" O SER D 108 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N LEU D 117 " --> pdb=" O ALA D 113 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N LYS D 122 " --> pdb=" O ASP D 118 " (cutoff:3.500A) Processing helix chain 'D' and resid 130 through 150 removed outlier: 3.703A pdb=" N GLU D 135 " --> pdb=" O THR D 131 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N GLU D 146 " --> pdb=" O GLU D 142 " (cutoff:3.500A) Processing helix chain 'D' and resid 160 through 173 removed outlier: 3.775A pdb=" N SER D 170 " --> pdb=" O SER D 166 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N LEU D 171 " --> pdb=" O ALA D 167 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N ASN D 172 " --> pdb=" O THR D 168 " (cutoff:3.500A) removed outlier: 4.259A pdb=" N SER D 173 " --> pdb=" O THR D 169 " (cutoff:3.500A) Processing helix chain 'D' and resid 180 through 194 removed outlier: 3.525A pdb=" N SER D 184 " --> pdb=" O SER D 180 " (cutoff:3.500A) Proline residue: D 185 - end of helix removed outlier: 3.587A pdb=" N ALA D 190 " --> pdb=" O MET D 186 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N VAL D 191 " --> pdb=" O SER D 187 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N LYS D 193 " --> pdb=" O ASN D 189 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N VAL D 194 " --> pdb=" O ALA D 190 " (cutoff:3.500A) Processing helix chain 'D' and resid 287 through 292 Processing helix chain 'D' and resid 312 through 319 removed outlier: 4.364A pdb=" N PHE D 316 " --> pdb=" O LEU D 312 " (cutoff:3.500A) Processing helix chain 'D' and resid 330 through 339 removed outlier: 3.949A pdb=" N GLU D 334 " --> pdb=" O ARG D 330 " (cutoff:3.500A) removed outlier: 4.092A pdb=" N PHE D 335 " --> pdb=" O GLU D 331 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N LYS D 338 " --> pdb=" O GLU D 334 " (cutoff:3.500A) 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 removed outlier: 3.524A pdb=" N GLU D 399 " --> pdb=" O LYS D 395 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N GLU D 400 " --> pdb=" O LEU D 396 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ARG D 403 " --> pdb=" O GLU D 399 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N ILE D 412 " --> pdb=" O ALA D 408 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N LEU D 415 " --> pdb=" O VAL D 411 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N LYS D 417 " --> pdb=" O ARG D 413 " (cutoff:3.500A) Processing helix chain 'D' and resid 428 through 440 removed outlier: 3.716A pdb=" N LEU D 436 " --> pdb=" O LEU D 432 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N THR D 437 " --> pdb=" O ALA D 433 " (cutoff:3.500A) Processing helix chain 'D' and resid 445 through 448 removed outlier: 4.035A pdb=" N SER D 448 " --> pdb=" O GLY D 445 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 445 through 448' Processing helix chain 'D' and resid 450 through 469 removed outlier: 3.919A pdb=" N GLU D 459 " --> pdb=" O ALA D 455 " (cutoff:3.500A) removed outlier: 4.663A pdb=" N VAL D 460 " --> pdb=" O ASP D 456 " (cutoff:3.500A) removed outlier: 5.262A pdb=" N ILE D 461 " --> pdb=" O ALA D 457 " (cutoff:3.500A) Proline residue: D 462 - end of helix Processing helix chain 'D' and resid 475 through 486 removed outlier: 3.550A pdb=" N ASN D 482 " --> pdb=" O THR D 478 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N GLN D 486 " --> pdb=" O ASN D 482 " (cutoff:3.500A) Processing helix chain 'D' and resid 513 through 530 removed outlier: 4.131A pdb=" N ALA D 518 " --> pdb=" O VAL D 514 " (cutoff:3.500A) Processing helix chain 'E' and resid 29 through 45 removed outlier: 3.518A pdb=" N ALA E 41 " --> pdb=" O MET E 37 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N VAL E 42 " --> pdb=" O ALA E 38 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N THR E 45 " --> pdb=" O ALA E 41 " (cutoff:3.500A) Processing helix chain 'E' and resid 72 through 78 removed outlier: 3.602A pdb=" N LEU E 76 " --> pdb=" O GLY E 72 " (cutoff:3.500A) Processing helix chain 'E' and resid 84 through 94 removed outlier: 3.536A pdb=" N LEU E 88 " --> pdb=" O GLN E 84 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N MET E 89 " --> pdb=" O ILE E 85 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N LYS E 94 " --> pdb=" O VAL E 90 " (cutoff:3.500A) Processing helix chain 'E' and resid 96 through 99 No H-bonds generated for 'chain 'E' and resid 96 through 99' Processing helix chain 'E' and resid 105 through 122 removed outlier: 3.678A pdb=" N VAL E 109 " --> pdb=" O THR E 105 " (cutoff:3.500A) Processing helix chain 'E' and resid 128 through 146 removed outlier: 3.732A pdb=" N VAL E 141 " --> pdb=" O GLN E 137 " (cutoff:3.500A) Processing helix chain 'E' and resid 161 through 173 removed outlier: 3.744A pdb=" N GLN E 165 " --> pdb=" O GLU E 161 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N THR E 166 " --> pdb=" O PRO E 162 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N ALA E 167 " --> pdb=" O LEU E 163 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N THR E 169 " --> pdb=" O GLN E 165 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N THR E 170 " --> pdb=" O THR E 166 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N LEU E 171 " --> pdb=" O ALA E 167 " (cutoff:3.500A) removed outlier: 4.091A pdb=" N GLY E 172 " --> pdb=" O LYS E 168 " (cutoff:3.500A) removed outlier: 4.907A pdb=" N SER E 173 " --> pdb=" O THR E 169 " (cutoff:3.500A) Processing helix chain 'E' and resid 180 through 194 removed outlier: 3.569A pdb=" N ALA E 184 " --> pdb=" O HIS E 180 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ILE E 186 " --> pdb=" O GLN E 182 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N VAL E 188 " --> pdb=" O ALA E 184 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N ASN E 189 " --> pdb=" O GLU E 185 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N VAL E 194 " --> pdb=" O ALA E 190 " (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 285 removed outlier: 3.666A pdb=" N LYS E 280 " --> pdb=" O GLN E 276 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N GLU E 281 " --> pdb=" O LYS E 277 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N LYS E 282 " --> pdb=" O TYR E 278 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N GLU E 284 " --> pdb=" O LYS E 280 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N GLU E 285 " --> pdb=" O GLU E 281 " (cutoff:3.500A) Processing helix chain 'E' and resid 289 through 293 Processing helix chain 'E' and resid 309 through 314 removed outlier: 3.611A pdb=" N GLN E 314 " --> pdb=" O HIS E 310 " (cutoff:3.500A) Processing helix chain 'E' and resid 326 through 335 removed outlier: 3.723A pdb=" N LEU E 330 " --> pdb=" O PRO E 326 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N ILE E 331 " --> pdb=" O GLU E 327 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ILE E 333 " --> pdb=" O GLU E 329 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N ALA E 334 " --> pdb=" O LEU E 330 " (cutoff:3.500A) Processing helix chain 'E' and resid 390 through 412 removed outlier: 3.975A pdb=" N GLU E 394 " --> pdb=" O LYS E 390 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N GLU E 395 " --> pdb=" O MET E 391 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N ARG E 398 " --> pdb=" O GLU E 394 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N VAL E 406 " --> pdb=" O ASP E 402 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ILE E 407 " --> pdb=" O ALA E 403 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N ILE E 411 " --> pdb=" O ILE E 407 " (cutoff:3.500A) Processing helix chain 'E' and resid 422 through 434 removed outlier: 3.620A pdb=" N ALA E 430 " --> pdb=" O SER E 426 " (cutoff:3.500A) Processing helix chain 'E' and resid 441 through 463 removed outlier: 3.767A pdb=" N TYR E 444 " --> pdb=" O LEU E 441 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N ARG E 447 " --> pdb=" O TYR E 444 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N ALA E 448 " --> pdb=" O ALA E 445 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N ASP E 451 " --> pdb=" O ALA E 448 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N ALA E 452 " --> pdb=" O PHE E 449 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N LEU E 453 " --> pdb=" O ALA E 450 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N GLU E 454 " --> pdb=" O ASP E 451 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N VAL E 455 " --> pdb=" O ALA E 452 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N ILE E 456 " --> pdb=" O LEU E 453 " (cutoff:3.500A) Proline residue: E 457 - end of helix removed outlier: 3.658A pdb=" N GLU E 462 " --> pdb=" O ALA E 459 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N ASN E 463 " --> pdb=" O LEU E 460 " (cutoff:3.500A) Processing helix chain 'E' and resid 470 through 478 removed outlier: 3.682A pdb=" N ALA E 477 " --> pdb=" O THR E 473 " (cutoff:3.500A) Processing helix chain 'E' and resid 509 through 512 No H-bonds generated for 'chain 'E' and resid 509 through 512' Processing helix chain 'E' and resid 514 through 526 removed outlier: 3.549A pdb=" N ALA E 518 " --> pdb=" O GLN E 514 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N THR E 519 " --> pdb=" O ILE E 515 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N VAL E 522 " --> pdb=" O ALA E 518 " (cutoff:3.500A) Processing helix chain 'G' and resid 21 through 36 removed outlier: 3.861A pdb=" N ILE G 27 " --> pdb=" O GLN G 23 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N ILE G 33 " --> pdb=" O ALA G 29 " (cutoff:3.500A) Processing helix chain 'G' and resid 63 through 68 removed outlier: 3.534A pdb=" N LEU G 67 " --> pdb=" O GLY G 63 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ARG G 68 " --> pdb=" O ASN G 64 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 63 through 68' Processing helix chain 'G' and resid 75 through 90 removed outlier: 3.582A pdb=" N ILE G 81 " --> pdb=" O ALA G 77 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N GLU G 82 " --> pdb=" O LYS G 78 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ILE G 83 " --> pdb=" O SER G 79 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N SER G 84 " --> pdb=" O MET G 80 " (cutoff:3.500A) Processing helix chain 'G' and resid 95 through 105 removed outlier: 3.709A pdb=" N ILE G 99 " --> pdb=" O THR G 95 " (cutoff:3.500A) Processing helix chain 'G' and resid 119 through 137 removed outlier: 3.566A pdb=" N LYS G 128 " --> pdb=" O SER G 124 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N ASP G 131 " --> pdb=" O ARG G 127 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N ASP G 132 " --> pdb=" O LYS G 128 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N ILE G 134 " --> pdb=" O LEU G 130 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N SER G 135 " --> pdb=" O ASP G 131 " (cutoff:3.500A) Processing helix chain 'G' and resid 149 through 160 removed outlier: 3.600A pdb=" N ASN G 154 " --> pdb=" O ASP G 150 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N ILE G 155 " --> pdb=" O MET G 151 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N ILE G 156 " --> pdb=" O MET G 152 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N ASN G 157 " --> pdb=" O LEU G 153 " (cutoff:3.500A) removed outlier: 5.498A pdb=" N SER G 158 " --> pdb=" O ASN G 154 " (cutoff:3.500A) removed outlier: 5.356A pdb=" N SER G 159 " --> pdb=" O ILE G 155 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N ILE G 160 " --> pdb=" O ILE G 156 " (cutoff:3.500A) Processing helix chain 'G' and resid 164 through 183 removed outlier: 4.055A pdb=" N ARG G 167 " --> pdb=" O ALA G 164 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N SER G 169 " --> pdb=" O SER G 166 " (cutoff:3.500A) removed outlier: 5.630A pdb=" N SER G 170 " --> pdb=" O ARG G 167 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N ALA G 172 " --> pdb=" O SER G 169 " (cutoff:3.500A) removed outlier: 4.399A pdb=" N CYS G 173 " --> pdb=" O SER G 170 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N ALA G 176 " --> pdb=" O CYS G 173 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N LEU G 177 " --> pdb=" O ASN G 174 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N ASP G 178 " --> pdb=" O ILE G 175 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N VAL G 180 " --> pdb=" O LEU G 177 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N LYS G 181 " --> pdb=" O ASP G 178 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N MET G 182 " --> pdb=" O ALA G 179 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N VAL G 183 " --> pdb=" O VAL G 180 " (cutoff:3.500A) 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 261 through 279 removed outlier: 3.580A pdb=" N ARG G 266 " --> pdb=" O GLU G 262 " (cutoff:3.500A) Processing helix chain 'G' and resid 283 through 285 No H-bonds generated for 'chain 'G' and resid 283 through 285' Processing helix chain 'G' and resid 317 through 327 removed outlier: 3.664A pdb=" N ASN G 321 " --> pdb=" O LYS G 317 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N ARG G 322 " --> pdb=" O THR G 318 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ILE G 323 " --> pdb=" O ASP G 319 " (cutoff:3.500A) Processing helix chain 'G' and resid 381 through 403 removed outlier: 3.548A pdb=" N GLU G 388 " --> pdb=" O LEU G 384 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N ARG G 389 " --> pdb=" O SER G 385 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N ASP G 393 " --> pdb=" O ARG G 389 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N GLN G 396 " --> pdb=" O GLN G 392 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N VAL G 397 " --> pdb=" O ASP G 393 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N VAL G 401 " --> pdb=" O VAL G 397 " (cutoff:3.500A) Processing helix chain 'G' and resid 413 through 426 removed outlier: 3.674A pdb=" N THR G 423 " --> pdb=" O ALA G 419 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N GLU G 424 " --> pdb=" O HIS G 420 " (cutoff:3.500A) Processing helix chain 'G' and resid 432 through 455 removed outlier: 3.599A pdb=" N TRP G 435 " --> pdb=" O VAL G 432 " (cutoff:3.500A) Proline residue: G 436 - end of helix removed outlier: 3.760A pdb=" N VAL G 440 " --> pdb=" O TYR G 437 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N GLN G 442 " --> pdb=" O ALA G 439 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N LEU G 444 " --> pdb=" O ALA G 441 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N GLU G 445 " --> pdb=" O GLN G 442 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N VAL G 446 " --> pdb=" O ALA G 443 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N ILE G 447 " --> pdb=" O LEU G 444 " (cutoff:3.500A) Proline residue: G 448 - end of helix removed outlier: 3.682A pdb=" N LEU G 451 " --> pdb=" O PRO G 448 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N ILE G 452 " --> pdb=" O ARG G 449 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N GLN G 453 " --> pdb=" O THR G 450 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N ASN G 454 " --> pdb=" O LEU G 451 " (cutoff:3.500A) Processing helix chain 'G' and resid 459 through 472 removed outlier: 3.888A pdb=" N SER G 465 " --> pdb=" O ARG G 461 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N GLN G 472 " --> pdb=" O ALA G 468 " (cutoff:3.500A) Processing helix chain 'G' and resid 499 through 516 removed outlier: 3.509A pdb=" N TYR G 506 " --> pdb=" O LYS G 502 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N LEU G 515 " --> pdb=" O GLU G 511 " (cutoff:3.500A) Processing helix chain 'H' and resid 19 through 33 removed outlier: 3.691A pdb=" N ALA H 28 " --> pdb=" O SER H 24 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N GLN H 30 " --> pdb=" O ILE H 26 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N VAL H 31 " --> pdb=" O SER H 27 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N ILE H 32 " --> pdb=" O ALA H 28 " (cutoff:3.500A) Processing helix chain 'H' and resid 62 through 69 removed outlier: 3.567A pdb=" N LEU H 68 " --> pdb=" O THR H 64 " (cutoff:3.500A) Processing helix chain 'H' and resid 77 through 89 removed outlier: 3.566A pdb=" N ALA H 83 " --> pdb=" O LEU H 79 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N ALA H 88 " --> pdb=" O LYS H 84 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N GLU H 89 " --> pdb=" O SER H 85 " (cutoff:3.500A) Processing helix chain 'H' and resid 96 through 112 removed outlier: 3.516A pdb=" N ALA H 101 " --> pdb=" O VAL H 97 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N LEU H 105 " --> pdb=" O ALA H 101 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N GLN H 107 " --> pdb=" O GLU H 103 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N VAL H 108 " --> pdb=" O PHE H 104 " (cutoff:3.500A) Proline residue: H 110 - end of helix Processing helix chain 'H' and resid 118 through 139 removed outlier: 3.763A pdb=" N THR H 127 " --> pdb=" O ARG H 123 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N GLN H 130 " --> pdb=" O ARG H 126 " (cutoff:3.500A) Processing helix chain 'H' and resid 151 through 162 removed outlier: 3.577A pdb=" N MET H 160 " --> pdb=" O GLU H 156 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N THR H 161 " --> pdb=" O LYS H 157 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N ALA H 162 " --> pdb=" O CYS H 158 " (cutoff:3.500A) Processing helix chain 'H' and resid 172 through 185 removed outlier: 3.672A pdb=" N LYS H 177 " --> pdb=" O ALA H 173 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N MET H 178 " --> pdb=" O PHE H 174 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N VAL H 179 " --> pdb=" O PHE H 175 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N VAL H 180 " --> pdb=" O ALA H 176 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N MET H 184 " --> pdb=" O VAL H 180 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N MET H 185 " --> pdb=" O ASP H 181 " (cutoff:3.500A) Processing helix chain 'H' and resid 260 through 284 removed outlier: 3.804A pdb=" N GLN H 264 " --> pdb=" O VAL H 260 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N ALA H 265 " --> pdb=" O GLU H 261 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N VAL H 267 " --> pdb=" O TYR H 263 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N LEU H 274 " --> pdb=" O GLU H 270 " (cutoff:3.500A) removed outlier: 3.877A 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 removed outlier: 3.557A pdb=" N ARG H 321 " --> pdb=" O GLU H 317 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N MET H 324 " --> pdb=" O LYS H 320 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N ALA H 325 " --> pdb=" O ARG H 321 " (cutoff:3.500A) 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 380 through 401 removed outlier: 4.245A pdb=" N THR H 385 " --> pdb=" O PHE H 381 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N ASP H 391 " --> pdb=" O ARG H 387 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N ILE H 400 " --> pdb=" O VAL H 396 " (cutoff:3.500A) Processing helix chain 'H' and resid 411 through 422 removed outlier: 3.650A pdb=" N ARG H 421 " --> pdb=" O SER H 417 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N ASP H 422 " --> pdb=" O LYS H 418 " (cutoff:3.500A) Processing helix chain 'H' and resid 432 through 452 removed outlier: 3.713A pdb=" N ALA H 437 " --> pdb=" O LEU H 433 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N LYS H 440 " --> pdb=" O GLY H 436 " (cutoff:3.500A) removed outlier: 4.071A pdb=" N GLU H 443 " --> pdb=" O ALA H 439 " (cutoff:3.500A) removed outlier: 4.910A pdb=" N ILE H 444 " --> pdb=" O LYS H 440 " (cutoff:3.500A) removed outlier: 5.900A pdb=" N ILE H 445 " --> pdb=" O ALA H 441 " (cutoff:3.500A) Proline residue: H 446 - end of helix removed outlier: 3.728A pdb=" N CYS H 450 " --> pdb=" O PRO H 446 " (cutoff:3.500A) Processing helix chain 'H' and resid 457 through 470 removed outlier: 3.678A pdb=" N GLN H 470 " --> pdb=" O ALA H 466 " (cutoff:3.500A) Processing helix chain 'H' and resid 496 through 514 removed outlier: 3.658A pdb=" N ILE H 513 " --> pdb=" O ALA H 509 " (cutoff:3.500A) Processing helix chain 'Q' and resid 31 through 44 removed outlier: 3.585A pdb=" N ALA Q 35 " --> pdb=" O ARG Q 31 " (cutoff:3.500A) removed outlier: 4.135A pdb=" N CYS Q 36 " --> pdb=" O ASN Q 32 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N LEU Q 39 " --> pdb=" O ALA Q 35 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N THR Q 42 " --> pdb=" O GLU Q 38 " (cutoff:3.500A) removed outlier: 4.337A pdb=" N THR Q 43 " --> pdb=" O LEU Q 39 " (cutoff:3.500A) Processing helix chain 'Q' and resid 69 through 75 removed outlier: 3.614A pdb=" N LEU Q 73 " --> pdb=" O ALA Q 69 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N GLU Q 75 " --> pdb=" O THR Q 71 " (cutoff:3.500A) Processing helix chain 'Q' and resid 84 through 94 Processing helix chain 'Q' and resid 101 through 119 removed outlier: 3.635A pdb=" N LEU Q 105 " --> pdb=" O THR Q 101 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N GLY Q 109 " --> pdb=" O LEU Q 105 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N GLU Q 116 " --> pdb=" O LEU Q 112 " (cutoff:3.500A) removed outlier: 4.094A pdb=" N GLU Q 117 " --> pdb=" O GLU Q 113 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N LEU Q 118 " --> pdb=" O LEU Q 114 " (cutoff:3.500A) Processing helix chain 'Q' and resid 125 through 146 removed outlier: 3.603A pdb=" N GLU Q 130 " --> pdb=" O SER Q 126 " (cutoff:3.500A) removed outlier: 3.703A 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: 3.603A pdb=" N SER Q 162 " --> pdb=" O ASP Q 158 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N LEU Q 163 " --> pdb=" O GLU Q 159 " (cutoff:3.500A) removed outlier: 5.011A pdb=" N THR Q 166 " --> pdb=" O SER Q 162 " (cutoff:3.500A) removed outlier: 4.172A pdb=" N SER Q 167 " --> pdb=" O LEU Q 163 " (cutoff:3.500A) Processing helix chain 'Q' and resid 176 through 191 removed outlier: 4.398A pdb=" N LYS Q 181 " --> pdb=" O VAL Q 177 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N LEU Q 182 " --> pdb=" O PHE Q 178 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ILE Q 183 " --> pdb=" O LEU Q 179 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N ALA Q 184 " --> pdb=" O ALA Q 180 " (cutoff:3.500A) removed outlier: 4.235A pdb=" N SER Q 189 " --> pdb=" O GLN Q 185 " (cutoff:3.500A) removed outlier: 3.848A 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: 3.552A pdb=" N GLU Q 273 " --> pdb=" O SER Q 269 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N ILE Q 283 " --> pdb=" O GLN Q 279 " (cutoff:3.500A) Processing helix chain 'Q' and resid 299 through 307 Processing helix chain 'Q' and resid 318 through 325 removed outlier: 3.858A pdb=" N LEU Q 324 " --> pdb=" O ASP Q 320 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N CYS Q 325 " --> pdb=" O LEU Q 321 " (cutoff:3.500A) Processing helix chain 'Q' and resid 382 through 403 removed outlier: 4.020A pdb=" N ASP Q 387 " --> pdb=" O ASN Q 383 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N PHE Q 399 " --> pdb=" O GLY Q 395 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N LEU Q 402 " --> pdb=" O THR Q 398 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N THR Q 403 " --> pdb=" O PHE Q 399 " (cutoff:3.500A) Processing helix chain 'Q' and resid 414 through 429 removed outlier: 3.639A pdb=" N GLU Q 418 " --> pdb=" O ALA Q 414 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N ALA Q 420 " --> pdb=" O GLU Q 416 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N THR Q 424 " --> pdb=" O ALA Q 420 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N THR Q 429 " --> pdb=" O SER Q 425 " (cutoff:3.500A) Processing helix chain 'Q' and resid 433 through 443 removed outlier: 3.700A pdb=" N TYR Q 436 " --> pdb=" O LEU Q 433 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N ALA Q 437 " --> pdb=" O GLU Q 434 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N ILE Q 438 " --> pdb=" O GLN Q 435 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N LYS Q 439 " --> pdb=" O TYR Q 436 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N LYS Q 440 " --> pdb=" O ALA Q 437 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ALA Q 442 " --> pdb=" O LYS Q 439 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N GLU Q 443 " --> pdb=" O LYS Q 440 " (cutoff:3.500A) Processing helix chain 'Q' and resid 446 through 455 Processing helix chain 'Q' and resid 460 through 472 removed outlier: 3.712A pdb=" N SER Q 465 " --> pdb=" O ASN Q 461 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N VAL Q 470 " --> pdb=" O LYS Q 466 " (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 removed outlier: 3.692A pdb=" N ALA Q 507 " --> pdb=" O GLY Q 503 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ILE Q 508 " --> pdb=" O LYS Q 504 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N THR Q 517 " --> pdb=" O ASN Q 513 " (cutoff:3.500A) Processing helix chain 'Z' and resid 17 through 37 removed outlier: 4.113A pdb=" N VAL Z 22 " --> pdb=" O ALA Z 19 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N ILE Z 24 " --> pdb=" O ALA Z 21 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N SER Z 25 " --> pdb=" O VAL Z 22 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N ARG Z 28 " --> pdb=" O SER Z 25 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N GLY Z 29 " --> pdb=" O ALA Z 26 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N LEU Z 30 " --> pdb=" O ALA Z 27 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N ASP Z 32 " --> pdb=" O GLY Z 29 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N VAL Z 33 " --> pdb=" O LEU Z 30 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N LEU Z 34 " --> pdb=" O GLN Z 31 " (cutoff:3.500A) removed outlier: 4.322A pdb=" N ARG Z 35 " --> pdb=" O ASP Z 32 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N THR Z 36 " --> pdb=" O VAL Z 33 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N ASN Z 37 " --> pdb=" O LEU Z 34 " (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 84 removed outlier: 3.747A pdb=" N LEU Z 76 " --> pdb=" O PRO Z 72 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N ILE Z 77 " --> pdb=" O THR Z 73 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ALA Z 81 " --> pdb=" O ILE Z 77 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N THR Z 82 " --> pdb=" O ALA Z 78 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N ALA Z 83 " --> pdb=" O LYS Z 79 " (cutoff:3.500A) Processing helix chain 'Z' and resid 93 through 110 removed outlier: 3.543A pdb=" N LEU Z 97 " --> pdb=" O THR Z 93 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N ILE Z 98 " --> pdb=" O SER Z 94 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ILE Z 99 " --> pdb=" O ASN Z 95 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N GLU Z 101 " --> pdb=" O LEU Z 97 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N ASP Z 107 " --> pdb=" O LEU Z 103 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N LEU Z 108 " --> pdb=" O LYS Z 104 " (cutoff:3.500A) removed outlier: 4.332A pdb=" N TYR Z 109 " --> pdb=" O GLN Z 105 " (cutoff:3.500A) Processing helix chain 'Z' and resid 116 through 137 removed outlier: 3.741A pdb=" N ALA Z 125 " --> pdb=" O GLU Z 121 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N LYS Z 129 " --> pdb=" O ALA Z 125 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N GLU Z 135 " --> pdb=" O LEU Z 131 " (cutoff:3.500A) removed outlier: 4.150A pdb=" N GLU Z 136 " --> pdb=" O GLN Z 132 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N VAL Z 137 " --> pdb=" O PHE Z 133 " (cutoff:3.500A) Processing helix chain 'Z' and resid 145 through 158 removed outlier: 3.734A pdb=" N ASP Z 150 " --> pdb=" O GLU Z 146 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N SER Z 155 " --> pdb=" O VAL Z 151 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N ARG Z 157 " --> pdb=" O ARG Z 153 " (cutoff:3.500A) removed outlier: 4.852A pdb=" N THR Z 158 " --> pdb=" O THR Z 154 " (cutoff:3.500A) Processing helix chain 'Z' and resid 167 through 178 removed outlier: 3.881A pdb=" N ALA Z 171 " --> pdb=" O VAL Z 167 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N VAL Z 172 " --> pdb=" O LEU Z 168 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ASP Z 174 " --> pdb=" O GLU Z 170 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N SER Z 175 " --> pdb=" O ALA Z 171 " (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: 3.619A pdb=" N LYS Z 261 " --> pdb=" O GLU Z 257 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N LYS Z 265 " --> pdb=" O LYS Z 261 " (cutoff:3.500A) removed outlier: 4.883A pdb=" N PHE Z 266 " --> pdb=" O ALA Z 262 " (cutoff:3.500A) removed outlier: 4.653A pdb=" N ILE Z 267 " --> pdb=" O GLU Z 263 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N ASP Z 269 " --> pdb=" O LYS Z 265 " (cutoff:3.500A) removed outlier: 4.906A pdb=" N ARG Z 270 " --> pdb=" O PHE Z 266 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N ILE Z 275 " --> pdb=" O VAL Z 271 " (cutoff:3.500A) Processing helix chain 'Z' and resid 299 through 306 removed outlier: 3.822A pdb=" N ASP Z 303 " --> pdb=" O PRO Z 299 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N ALA Z 304 " --> pdb=" O PHE Z 300 " (cutoff:3.500A) Processing helix chain 'Z' and resid 318 through 327 removed outlier: 3.595A pdb=" N GLU Z 322 " --> pdb=" O ARG Z 318 " (cutoff:3.500A) 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 removed outlier: 3.501A pdb=" N ASP Z 393 " --> pdb=" O ASP Z 389 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ARG Z 396 " --> pdb=" O ARG Z 392 " (cutoff:3.500A) Processing helix chain 'Z' and resid 413 through 423 Processing helix chain 'Z' and resid 432 through 455 removed outlier: 3.945A pdb=" N LEU Z 435 " --> pdb=" O ARG Z 432 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N VAL Z 437 " --> pdb=" O GLN Z 434 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N ALA Z 439 " --> pdb=" O GLY Z 436 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N PHE Z 440 " --> pdb=" O VAL Z 437 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ASP Z 442 " --> pdb=" O ALA Z 439 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N ALA Z 443 " --> pdb=" O PHE Z 440 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N LEU Z 444 " --> pdb=" O ALA Z 441 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N ILE Z 446 " --> pdb=" O ALA Z 443 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N ILE Z 447 " --> pdb=" O LEU Z 444 " (cutoff:3.500A) Proline residue: Z 448 - end of helix removed outlier: 3.859A pdb=" N LEU Z 451 " --> pdb=" O PRO Z 448 " (cutoff:3.500A) removed outlier: 4.091A pdb=" N ASN Z 454 " --> pdb=" O LEU Z 451 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N SER Z 455 " --> pdb=" O ALA Z 452 " (cutoff:3.500A) Processing helix chain 'Z' and resid 459 through 468 removed outlier: 3.656A pdb=" N LEU Z 463 " --> pdb=" O LEU Z 459 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N LYS Z 465 " --> pdb=" O GLU Z 461 " (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: 3.611A pdb=" N THR Z 509 " --> pdb=" O LEU Z 505 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N VAL Z 510 " --> pdb=" O HIS Z 506 " (cutoff:3.500A) Processing helix chain 'b' and resid 23 through 36 removed outlier: 3.624A pdb=" N PHE b 29 " --> pdb=" O ARG b 25 " (cutoff:3.500A) Processing helix chain 'b' and resid 67 through 73 removed outlier: 3.730A pdb=" N ASN b 73 " --> pdb=" O THR b 69 " (cutoff:3.500A) Processing helix chain 'b' and resid 79 through 94 removed outlier: 3.682A pdb=" N VAL b 83 " --> pdb=" O PRO b 79 " (cutoff:3.500A) removed outlier: 4.340A pdb=" N LEU b 84 " --> pdb=" O ALA b 80 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N ASP b 86 " --> pdb=" O LYS b 82 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N MET b 87 " --> pdb=" O VAL b 83 " (cutoff:3.500A) removed outlier: 4.142A pdb=" N GLU b 94 " --> pdb=" O VAL b 90 " (cutoff:3.500A) Processing helix chain 'b' and resid 99 through 118 removed outlier: 3.749A pdb=" N THR b 103 " --> pdb=" O THR b 99 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N ALA b 106 " --> pdb=" O VAL b 102 " (cutoff:3.500A) removed outlier: 4.475A pdb=" N SER b 115 " --> pdb=" O ARG b 111 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N LEU b 116 " --> pdb=" O GLU b 112 " (cutoff:3.500A) Processing helix chain 'b' and resid 123 through 144 removed outlier: 3.670A pdb=" N GLU b 132 " --> pdb=" O ALA b 128 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N LYS b 135 " --> pdb=" O ARG b 131 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N LEU b 141 " --> pdb=" O ALA b 137 " (cutoff:3.500A) Processing helix chain 'b' and resid 152 through 166 removed outlier: 3.640A pdb=" N GLN b 157 " --> pdb=" O VAL b 153 " (cutoff:3.500A) 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 188 removed outlier: 4.095A pdb=" N LYS b 181 " --> pdb=" O ASP b 177 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N LEU b 182 " --> pdb=" O HIS b 178 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N VAL b 184 " --> pdb=" O THR b 180 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N GLU b 185 " --> pdb=" O LYS b 181 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N VAL b 187 " --> pdb=" O ALA b 183 " (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 261 through 285 removed outlier: 3.553A pdb=" N LYS b 284 " --> pdb=" O GLU b 280 " (cutoff:3.500A) removed outlier: 4.519A pdb=" N HIS b 285 " --> pdb=" O ARG b 281 " (cutoff:3.500A) Processing helix chain 'b' and resid 298 through 306 removed outlier: 3.515A pdb=" N LEU b 303 " --> pdb=" O TYR b 299 " (cutoff:3.500A) Processing helix chain 'b' and resid 317 through 326 removed outlier: 3.753A pdb=" N ARG b 322 " --> pdb=" O ALA b 318 " (cutoff:3.500A) removed outlier: 4.439A pdb=" N LEU b 325 " --> pdb=" O GLU b 321 " (cutoff:3.500A) Processing helix chain 'b' and resid 380 through 402 removed outlier: 4.024A pdb=" N ALA b 393 " --> pdb=" O SER b 389 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N VAL b 396 " --> pdb=" O ASP b 392 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N VAL b 401 " --> pdb=" O LEU b 397 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N LYS b 402 " --> pdb=" O ALA b 398 " (cutoff:3.500A) Processing helix chain 'b' and resid 412 through 426 removed outlier: 3.653A pdb=" N ASN b 426 " --> pdb=" O THR b 422 " (cutoff:3.500A) Processing helix chain 'b' and resid 431 through 444 removed outlier: 4.243A pdb=" N ALA b 435 " --> pdb=" O LYS b 431 " (cutoff:3.500A) Processing helix chain 'b' and resid 446 through 453 removed outlier: 3.768A pdb=" N ILE b 450 " --> pdb=" O LEU b 446 " (cutoff:3.500A) Processing helix chain 'b' and resid 458 through 470 removed outlier: 4.121A pdb=" N ALA b 463 " --> pdb=" O ALA b 459 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N GLN b 464 " --> pdb=" O ASP b 460 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N LEU b 465 " --> pdb=" O LEU b 461 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N ARG b 466 " --> pdb=" O VAL b 462 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N ALA b 467 " --> pdb=" O ALA b 463 " (cutoff:3.500A) 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: 3.635A pdb=" N LEU b 504 " --> pdb=" O LYS b 500 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N ALA b 507 " --> pdb=" O VAL b 503 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N ALA b 511 " --> pdb=" O ALA b 507 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N ILE b 514 " --> pdb=" O ALA b 510 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N LEU b 515 " --> pdb=" O ALA b 511 " (cutoff:3.500A) Processing helix chain 'd' and resid 31 through 47 removed outlier: 3.916A pdb=" N VAL d 44 " --> pdb=" O ALA d 40 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ALA d 45 " --> pdb=" O ALA d 41 " (cutoff:3.500A) Processing helix chain 'd' and resid 49 through 51 No H-bonds generated for 'chain 'd' and resid 49 through 51' Processing helix chain 'd' and resid 74 through 81 removed outlier: 3.645A pdb=" N LYS d 79 " --> pdb=" O ALA d 75 " (cutoff:3.500A) Processing helix chain 'd' and resid 88 through 101 removed outlier: 3.639A pdb=" N LEU d 91 " --> pdb=" O ALA d 88 " (cutoff:3.500A) removed outlier: 4.165A pdb=" N GLU d 93 " --> pdb=" O MET d 90 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N LEU d 94 " --> pdb=" O LEU d 91 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N ALA d 97 " --> pdb=" O LEU d 94 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ILE d 100 " --> pdb=" O ALA d 97 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N GLU d 101 " --> pdb=" O GLN d 98 " (cutoff:3.500A) Processing helix chain 'd' and resid 106 through 125 removed outlier: 4.121A pdb=" N VAL d 110 " --> pdb=" O THR d 106 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N LYS d 122 " --> pdb=" O ASP d 118 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N GLN d 125 " --> pdb=" O THR d 121 " (cutoff:3.500A) Processing helix chain 'd' and resid 130 through 150 removed outlier: 3.523A pdb=" N GLU d 135 " --> pdb=" O THR d 131 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N GLU d 146 " --> pdb=" O GLU d 142 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N LEU d 148 " --> pdb=" O GLY d 144 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N ASP d 150 " --> pdb=" O GLU d 146 " (cutoff:3.500A) Processing helix chain 'd' and resid 160 through 171 removed outlier: 3.649A pdb=" N ALA d 167 " --> pdb=" O LEU d 163 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N THR d 168 " --> pdb=" O LEU d 164 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N THR d 169 " --> pdb=" O ASN d 165 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N SER d 170 " --> pdb=" O SER d 166 " (cutoff:3.500A) Processing helix chain 'd' and resid 183 through 194 removed outlier: 3.657A pdb=" N VAL d 191 " --> pdb=" O SER d 187 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N LYS d 193 " --> pdb=" O ASN d 189 " (cutoff:3.500A) removed outlier: 3.756A 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 269 through 292 removed outlier: 3.569A pdb=" N ASP d 273 " --> pdb=" O TYR d 269 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N LEU d 276 " --> pdb=" O MET d 272 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N ILE d 283 " --> pdb=" O GLU d 279 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N LYS d 292 " --> pdb=" O LYS d 288 " (cutoff:3.500A) Processing helix chain 'd' and resid 311 through 319 removed outlier: 3.834A pdb=" N HIS d 315 " --> pdb=" O ASP d 311 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N LEU d 317 " --> pdb=" O ALA d 313 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N ASN d 318 " --> pdb=" O LEU d 314 " (cutoff:3.500A) Processing helix chain 'd' and resid 330 through 337 removed outlier: 3.689A pdb=" N GLU d 334 " --> pdb=" O ARG d 330 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N PHE d 335 " --> pdb=" O GLU d 331 " (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: 3.539A pdb=" N GLU d 399 " --> pdb=" O LYS d 395 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N GLU d 400 " --> pdb=" O LEU d 396 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N VAL d 411 " --> pdb=" O ASP d 407 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N ILE d 412 " --> pdb=" O ALA d 408 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N LEU d 415 " --> pdb=" O VAL d 411 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N LYS d 417 " --> pdb=" O ARG d 413 " (cutoff:3.500A) Processing helix chain 'd' and resid 427 through 440 removed outlier: 3.854A pdb=" N THR d 437 " --> pdb=" O ALA d 433 " (cutoff:3.500A) Processing helix chain 'd' and resid 445 through 456 removed outlier: 3.595A pdb=" N SER d 448 " --> pdb=" O GLY d 445 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N CYS d 450 " --> pdb=" O GLU d 447 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N VAL d 451 " --> pdb=" O SER d 448 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N PHE d 454 " --> pdb=" O VAL d 451 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N ASP d 456 " --> pdb=" O ALA d 453 " (cutoff:3.500A) Processing helix chain 'd' and resid 459 through 468 Processing helix chain 'd' and resid 473 through 486 removed outlier: 4.154A pdb=" N VAL d 477 " --> pdb=" O PRO d 473 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N GLU d 479 " --> pdb=" O SER d 475 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N ASN d 482 " --> pdb=" O THR d 478 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N GLN d 486 " --> pdb=" O ASN d 482 " (cutoff:3.500A) Processing helix chain 'd' and resid 512 through 531 removed outlier: 3.642A pdb=" N THR d 520 " --> pdb=" O VAL d 516 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ALA d 522 " --> pdb=" O ALA d 518 " (cutoff:3.500A) Processing helix chain 'e' and resid 30 through 46 removed outlier: 4.265A pdb=" N VAL e 42 " --> pdb=" O ALA e 38 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N THR e 45 " --> pdb=" O ALA e 41 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N MET e 46 " --> pdb=" O VAL e 42 " (cutoff:3.500A) Processing helix chain 'e' and resid 72 through 78 removed outlier: 3.594A pdb=" N SER e 77 " --> pdb=" O ALA e 73 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N MET e 78 " --> pdb=" O THR e 74 " (cutoff:3.500A) Processing helix chain 'e' and resid 84 through 96 removed outlier: 3.561A pdb=" N MET e 89 " --> pdb=" O ILE e 85 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N LEU e 92 " --> pdb=" O LEU e 88 " (cutoff:3.500A) removed outlier: 4.645A pdb=" N SER e 93 " --> pdb=" O MET e 89 " (cutoff:3.500A) removed outlier: 4.426A pdb=" N LYS e 94 " --> pdb=" O VAL e 90 " (cutoff:3.500A) removed outlier: 4.464A pdb=" N SER e 95 " --> pdb=" O GLU e 91 " (cutoff:3.500A) Processing helix chain 'e' and resid 104 through 124 removed outlier: 3.962A pdb=" N VAL e 108 " --> pdb=" O THR e 104 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N VAL e 109 " --> pdb=" O THR e 105 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N LEU e 115 " --> pdb=" O ALA e 111 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N ASP e 123 " --> pdb=" O GLU e 119 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N ARG e 124 " --> pdb=" O GLN e 120 " (cutoff:3.500A) Processing helix chain 'e' and resid 128 through 149 removed outlier: 3.534A pdb=" N ASP e 133 " --> pdb=" O ILE e 129 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N ARG e 140 " --> pdb=" O GLU e 136 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N VAL e 141 " --> pdb=" O GLN e 137 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N LYS e 148 " --> pdb=" O GLU e 144 " (cutoff:3.500A) Processing helix chain 'e' and resid 161 through 171 removed outlier: 3.816A pdb=" N GLN e 165 " --> pdb=" O GLU e 161 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N THR e 169 " --> pdb=" O GLN e 165 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N THR e 170 " --> pdb=" O THR e 166 " (cutoff:3.500A) Processing helix chain 'e' and resid 175 through 179 removed outlier: 4.356A pdb=" N SER e 178 " --> pdb=" O VAL e 175 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N CYS e 179 " --> pdb=" O VAL e 176 " (cutoff:3.500A) No H-bonds generated for 'chain 'e' and resid 175 through 179' Processing helix chain 'e' and resid 181 through 194 removed outlier: 3.778A pdb=" N GLU e 185 " --> pdb=" O ARG e 181 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N ILE e 186 " --> pdb=" O GLN e 182 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N ALA e 187 " --> pdb=" O MET e 183 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N VAL e 188 " --> pdb=" O ALA e 184 " (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 288 removed outlier: 3.615A pdb=" N ALA e 274 " --> pdb=" O GLU e 270 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N LYS e 277 " --> pdb=" O LYS e 273 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N LYS e 282 " --> pdb=" O TYR e 278 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N MET e 286 " --> pdb=" O LYS e 282 " (cutoff:3.500A) removed outlier: 4.326A pdb=" N ILE e 287 " --> pdb=" O PHE e 283 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N GLN e 288 " --> pdb=" O GLU e 284 " (cutoff:3.500A) Processing helix chain 'e' and resid 306 through 314 removed outlier: 3.651A pdb=" N LEU e 311 " --> pdb=" O GLU e 307 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N LEU e 313 " --> pdb=" O ASN e 309 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N GLN e 314 " --> pdb=" O HIS e 310 " (cutoff:3.500A) Processing helix chain 'e' and resid 325 through 334 removed outlier: 4.018A pdb=" N GLU e 329 " --> pdb=" O GLY e 325 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N ILE e 331 " --> pdb=" O GLU e 327 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ILE e 333 " --> pdb=" O GLU e 329 " (cutoff:3.500A) removed outlier: 3.867A 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: 3.570A pdb=" N ARG e 398 " --> pdb=" O GLU e 394 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N CYS e 405 " --> pdb=" O HIS e 401 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N VAL e 406 " --> pdb=" O ASP e 402 " (cutoff:3.500A) Processing helix chain 'e' and resid 422 through 434 removed outlier: 3.582A pdb=" N SER e 426 " --> pdb=" O ALA e 422 " (cutoff:3.500A) Processing helix chain 'e' and resid 441 through 463 removed outlier: 3.956A pdb=" N TYR e 444 " --> pdb=" O LEU e 441 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N ARG e 447 " --> pdb=" O TYR e 444 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N ALA e 452 " --> pdb=" O PHE e 449 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N LEU e 453 " --> pdb=" O ALA e 450 " (cutoff:3.500A) removed outlier: 4.118A pdb=" N ILE e 456 " --> pdb=" O LEU e 453 " (cutoff:3.500A) Proline residue: e 457 - end of helix removed outlier: 3.604A pdb=" N LEU e 460 " --> pdb=" O PRO e 457 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N SER e 461 " --> pdb=" O MET e 458 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N GLU e 462 " --> pdb=" O ALA e 459 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N ASN e 463 " --> pdb=" O LEU e 460 " (cutoff:3.500A) Processing helix chain 'e' and resid 468 through 478 removed outlier: 3.743A pdb=" N GLU e 474 " --> pdb=" O GLN e 470 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N VAL e 475 " --> pdb=" O THR e 471 " (cutoff:3.500A) Processing helix chain 'e' and resid 508 through 527 removed outlier: 3.555A pdb=" N ILE e 515 " --> pdb=" O LYS e 511 " (cutoff:3.500A) Processing helix chain 'g' and resid 19 through 34 removed outlier: 3.656A pdb=" N VAL g 22 " --> pdb=" O GLY g 19 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N SER g 24 " --> pdb=" O LYS g 21 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N ASN g 26 " --> pdb=" O GLN g 23 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N ILE g 27 " --> pdb=" O SER g 24 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N ASN g 28 " --> pdb=" O GLY g 25 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N ALA g 29 " --> pdb=" O ASN g 26 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N LYS g 31 " --> pdb=" O ASN g 28 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N THR g 32 " --> pdb=" O ALA g 29 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ALA g 34 " --> pdb=" O LYS g 31 " (cutoff:3.500A) Processing helix chain 'g' and resid 63 through 69 removed outlier: 3.626A pdb=" N LEU g 67 " --> pdb=" O GLY g 63 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N ARG g 68 " --> pdb=" O ASN g 64 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N GLU g 69 " --> pdb=" O ALA g 65 " (cutoff:3.500A) No H-bonds generated for 'chain 'g' and resid 63 through 69' Processing helix chain 'g' and resid 75 through 90 removed outlier: 3.809A pdb=" N MET g 80 " --> pdb=" O ALA g 76 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N ILE g 81 " --> pdb=" O ALA g 77 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N SER g 84 " --> pdb=" O MET g 80 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N GLU g 89 " --> pdb=" O ARG g 85 " (cutoff:3.500A) Processing helix chain 'g' and resid 95 through 104 removed outlier: 4.020A pdb=" N ILE g 99 " --> pdb=" O THR g 95 " (cutoff:3.500A) Processing helix chain 'g' and resid 119 through 139 removed outlier: 3.532A pdb=" N LYS g 128 " --> pdb=" O SER g 124 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N ASP g 131 " --> pdb=" O ARG g 127 " (cutoff:3.500A) removed outlier: 4.294A pdb=" N ASP g 132 " --> pdb=" O LYS g 128 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N LEU g 137 " --> pdb=" O MET g 133 " (cutoff:3.500A) Processing helix chain 'g' and resid 156 through 160 removed outlier: 3.999A pdb=" N ILE g 160 " --> pdb=" O ASN g 157 " (cutoff:3.500A) Processing helix chain 'g' and resid 165 through 183 removed outlier: 3.797A pdb=" N SER g 169 " --> pdb=" O SER g 166 " (cutoff:3.500A) removed outlier: 5.779A pdb=" N SER g 170 " --> pdb=" O ARG g 167 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N ALA g 172 " --> pdb=" O SER g 169 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N CYS g 173 " --> pdb=" O SER g 170 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N ALA g 176 " --> pdb=" O CYS g 173 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N LEU g 177 " --> pdb=" O ASN g 174 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N ASP g 178 " --> pdb=" O ILE g 175 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N ALA g 179 " --> pdb=" O ALA g 176 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N VAL g 180 " --> pdb=" O LEU g 177 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N LYS g 181 " --> pdb=" O ASP g 178 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N MET g 182 " --> pdb=" O ALA g 179 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N VAL g 183 " --> pdb=" O VAL g 180 " (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 280 removed outlier: 3.553A pdb=" N LEU g 268 " --> pdb=" O PHE g 264 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N MET g 270 " --> pdb=" O ARG g 266 " (cutoff:3.500A) Processing helix chain 'g' and resid 298 through 306 removed outlier: 3.607A pdb=" N TYR g 303 " --> pdb=" O LEU g 299 " (cutoff:3.500A) Processing helix chain 'g' and resid 317 through 327 removed outlier: 3.635A pdb=" N ARG g 322 " --> pdb=" O THR g 318 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ARG g 325 " --> pdb=" O ASN g 321 " (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: 3.654A pdb=" N ARG g 389 " --> pdb=" O SER g 385 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N ASP g 393 " --> pdb=" O ARG g 389 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N ASN g 400 " --> pdb=" O GLN g 396 " (cutoff:3.500A) Processing helix chain 'g' and resid 413 through 425 removed outlier: 3.573A pdb=" N ALA g 419 " --> pdb=" O GLU g 415 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N ALA g 421 " --> pdb=" O ALA g 417 " (cutoff:3.500A) Processing helix chain 'g' and resid 432 through 455 removed outlier: 3.804A pdb=" N TRP g 435 " --> pdb=" O VAL g 432 " (cutoff:3.500A) Proline residue: g 436 - end of helix removed outlier: 3.690A pdb=" N VAL g 440 " --> pdb=" O TYR g 437 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N GLN g 442 " --> pdb=" O ALA g 439 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N GLU g 445 " --> pdb=" O GLN g 442 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N VAL g 446 " --> pdb=" O ALA g 443 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N ILE g 447 " --> pdb=" O LEU g 444 " (cutoff:3.500A) Proline residue: g 448 - end of helix removed outlier: 3.724A pdb=" N LEU g 451 " --> pdb=" O PRO g 448 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N ASN g 454 " --> pdb=" O LEU g 451 " (cutoff:3.500A) Processing helix chain 'g' and resid 459 through 470 removed outlier: 3.581A pdb=" N THR g 464 " --> pdb=" O ILE g 460 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N SER g 465 " --> pdb=" O ARG g 461 " (cutoff:3.500A) Processing helix chain 'g' and resid 499 through 517 removed outlier: 3.552A pdb=" N LEU g 517 " --> pdb=" O ALA g 513 " (cutoff:3.500A) Processing helix chain 'h' and resid 19 through 35 removed outlier: 3.560A pdb=" N GLN h 30 " --> pdb=" O ILE h 26 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N VAL h 31 " --> pdb=" O SER h 27 " (cutoff:3.500A) removed outlier: 4.286A pdb=" N ILE h 32 " --> pdb=" O ALA h 28 " (cutoff:3.500A) Processing helix chain 'h' and resid 62 through 69 removed outlier: 3.542A pdb=" N LYS h 67 " --> pdb=" O ALA h 63 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N LEU h 68 " --> pdb=" O THR h 64 " (cutoff:3.500A) Processing helix chain 'h' and resid 74 through 89 removed outlier: 3.648A pdb=" N THR h 78 " --> pdb=" O PRO h 74 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N LEU h 79 " --> pdb=" O ALA h 75 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N VAL h 80 " --> pdb=" O ALA h 76 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N ASP h 81 " --> pdb=" O LYS h 77 " (cutoff:3.500A) removed outlier: 4.137A pdb=" N ILE h 82 " --> pdb=" O THR h 78 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N ALA h 83 " --> pdb=" O LEU h 79 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N ASP h 87 " --> pdb=" O ALA h 83 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N ALA h 88 " --> pdb=" O LYS h 84 " (cutoff:3.500A) Processing helix chain 'h' and resid 94 through 107 removed outlier: 3.675A pdb=" N LEU h 99 " --> pdb=" O THR h 95 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N ALA h 102 " --> pdb=" O THR h 98 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N PHE h 104 " --> pdb=" O LEU h 100 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N LEU h 105 " --> pdb=" O ALA h 101 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N GLN h 107 " --> pdb=" O GLU h 103 " (cutoff:3.500A) Processing helix chain 'h' and resid 109 through 113 removed outlier: 3.751A pdb=" N GLU h 113 " --> pdb=" O LYS h 109 " (cutoff:3.500A) No H-bonds generated for 'chain 'h' and resid 109 through 113' Processing helix chain 'h' and resid 118 through 139 removed outlier: 3.569A pdb=" N THR h 127 " --> pdb=" O ARG h 123 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N GLN h 130 " --> pdb=" O ARG h 126 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N ASN h 134 " --> pdb=" O GLN h 130 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N LYS h 137 " --> pdb=" O VAL h 133 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N GLU h 138 " --> pdb=" O ASN h 134 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N ILE h 139 " --> pdb=" O LYS h 135 " (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: 3.696A pdb=" N ALA h 159 " --> pdb=" O LEU h 155 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N THR h 161 " --> pdb=" O LYS h 157 " (cutoff:3.500A) Processing helix chain 'h' and resid 172 through 184 removed outlier: 3.873A pdb=" N LYS h 177 " --> pdb=" O ALA h 173 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N MET h 178 " --> pdb=" O PHE h 174 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N VAL h 179 " --> pdb=" O PHE h 175 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N VAL h 180 " --> pdb=" O ALA h 176 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N ASP h 181 " --> pdb=" O LYS h 177 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N VAL h 183 " --> pdb=" O VAL h 179 " (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: 4.257A pdb=" N GLN h 264 " --> pdb=" O VAL h 260 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N ALA h 265 " --> pdb=" O GLU h 261 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N VAL h 267 " --> pdb=" O TYR h 263 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N LEU h 274 " --> pdb=" O GLU h 270 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N LYS h 277 " --> pdb=" O ILE h 273 " (cutoff:3.500A) removed outlier: 4.181A pdb=" N ILE h 281 " --> pdb=" O LYS h 277 " (cutoff:3.500A) Processing helix chain 'h' and resid 297 through 305 removed outlier: 3.758A pdb=" N ASP h 305 " --> pdb=" O GLN h 301 " (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: 3.517A pdb=" N VAL h 396 " --> pdb=" O ALA h 392 " (cutoff:3.500A) Processing helix chain 'h' and resid 411 through 426 removed outlier: 3.529A pdb=" N ARG h 425 " --> pdb=" O ARG h 421 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N THR h 426 " --> pdb=" O ASP h 422 " (cutoff:3.500A) Processing helix chain 'h' and resid 432 through 452 removed outlier: 3.929A pdb=" N GLU h 443 " --> pdb=" O ALA h 439 " (cutoff:3.500A) removed outlier: 4.785A pdb=" N ILE h 444 " --> pdb=" O LYS h 440 " (cutoff:3.500A) removed outlier: 5.651A pdb=" N ILE h 445 " --> pdb=" O ALA h 441 " (cutoff:3.500A) Proline residue: h 446 - end of helix removed outlier: 3.624A pdb=" N CYS h 450 " --> pdb=" O PRO h 446 " (cutoff:3.500A) Processing helix chain 'h' and resid 457 through 470 removed outlier: 3.656A pdb=" N LEU h 461 " --> pdb=" O ALA h 457 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N LYS h 463 " --> pdb=" O ASN h 459 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ALA h 466 " --> pdb=" O ASN h 462 " (cutoff:3.500A) Processing helix chain 'h' and resid 496 through 514 removed outlier: 3.668A pdb=" N ILE h 513 " --> pdb=" O ALA h 509 " (cutoff:3.500A) Processing helix chain 'q' and resid 28 through 44 removed outlier: 4.132A pdb=" N ASN q 32 " --> pdb=" O ALA q 28 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N ILE q 33 " --> pdb=" O VAL q 29 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N LEU q 39 " --> pdb=" O ALA q 35 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N THR q 42 " --> pdb=" O GLU q 38 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N THR q 43 " --> pdb=" O LEU q 39 " (cutoff:3.500A) Processing helix chain 'q' and resid 69 through 75 removed outlier: 3.603A pdb=" N LEU q 73 " --> pdb=" O ALA q 69 " (cutoff:3.500A) Processing helix chain 'q' and resid 84 through 94 Processing helix chain 'q' and resid 101 through 119 removed outlier: 3.515A pdb=" N GLY q 109 " --> pdb=" O LEU q 105 " (cutoff:3.500A) removed outlier: 4.115A pdb=" N GLU q 117 " --> pdb=" O GLU q 113 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N LEU q 118 " --> pdb=" O LEU q 114 " (cutoff:3.500A) Processing helix chain 'q' and resid 125 through 145 removed outlier: 3.846A pdb=" N GLU q 130 " --> pdb=" O SER q 126 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N GLU q 133 " --> pdb=" O ILE q 129 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N GLU q 141 " --> pdb=" O ARG q 137 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N ILE q 142 " --> pdb=" O LYS q 138 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N LEU q 143 " --> pdb=" O ALA q 139 " (cutoff:3.500A) Proline residue: q 144 - end of helix Processing helix chain 'q' and resid 157 through 163 Processing helix chain 'q' and resid 165 through 168 No H-bonds generated for 'chain 'q' and resid 165 through 168' Processing helix chain 'q' and resid 179 through 182 No H-bonds generated for 'chain 'q' and resid 179 through 182' Processing helix chain 'q' and resid 184 through 189 removed outlier: 4.014A pdb=" N VAL q 188 " --> pdb=" O ALA q 184 " (cutoff:3.500A) removed outlier: 4.905A pdb=" N SER q 189 " --> pdb=" O GLN q 185 " (cutoff:3.500A) No H-bonds generated for 'chain 'q' and resid 184 through 189' 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 284 removed outlier: 3.683A pdb=" N ASN q 267 " --> pdb=" O GLU q 263 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N ILE q 283 " --> pdb=" O GLN q 279 " (cutoff:3.500A) Processing helix chain 'q' and resid 299 through 307 removed outlier: 3.591A pdb=" N HIS q 303 " --> pdb=" O ASP q 299 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ASN q 306 " --> pdb=" O LEU q 302 " (cutoff:3.500A) Processing helix chain 'q' and resid 318 through 325 removed outlier: 3.732A pdb=" N LEU q 324 " --> pdb=" O ASP q 320 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N CYS q 325 " --> pdb=" O LEU q 321 " (cutoff:3.500A) Processing helix chain 'q' and resid 382 through 403 removed outlier: 3.635A pdb=" N ASP q 387 " --> pdb=" O ASN q 383 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N ASP q 393 " --> pdb=" O GLU q 389 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N THR q 398 " --> pdb=" O ASP q 394 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N PHE q 399 " --> pdb=" O GLY q 395 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N VAL q 401 " --> pdb=" O ASN q 397 " (cutoff:3.500A) removed outlier: 4.399A pdb=" N LEU q 402 " --> pdb=" O THR q 398 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N THR q 403 " --> pdb=" O PHE q 399 " (cutoff:3.500A) Processing helix chain 'q' and resid 414 through 429 removed outlier: 3.648A pdb=" N GLU q 418 " --> pdb=" O ALA q 414 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N LEU q 419 " --> pdb=" O THR q 415 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N THR q 424 " --> pdb=" O ALA q 420 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N THR q 429 " --> pdb=" O SER q 425 " (cutoff:3.500A) Processing helix chain 'q' and resid 433 through 443 removed outlier: 3.549A pdb=" N TYR q 436 " --> pdb=" O LEU q 433 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N ALA q 437 " --> pdb=" O GLU q 434 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N ILE q 438 " --> pdb=" O GLN q 435 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N LYS q 439 " --> pdb=" O TYR q 436 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N LYS q 440 " --> pdb=" O ALA q 437 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ALA q 442 " --> pdb=" O LYS q 439 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N GLU q 443 " --> pdb=" O LYS q 440 " (cutoff:3.500A) Processing helix chain 'q' and resid 446 through 454 Processing helix chain 'q' and resid 460 through 472 removed outlier: 3.602A pdb=" N VAL q 470 " --> pdb=" O LYS q 466 " (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 removed outlier: 3.596A pdb=" N ALA q 507 " --> pdb=" O GLY q 503 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N ILE q 508 " --> pdb=" O LYS q 504 " (cutoff:3.500A) Processing helix chain 'z' and resid 17 through 36 removed outlier: 3.610A pdb=" N VAL z 22 " --> pdb=" O ALA z 19 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N ASN z 23 " --> pdb=" O LEU z 20 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N ILE z 24 " --> pdb=" O ALA z 21 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N ALA z 26 " --> pdb=" O ASN z 23 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N ARG z 28 " --> pdb=" O SER z 25 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N GLN z 31 " --> pdb=" O ARG z 28 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N ASP z 32 " --> pdb=" O GLY z 29 " (cutoff:3.500A) removed outlier: 4.201A pdb=" N ARG z 35 " --> pdb=" O ASP z 32 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N THR z 36 " --> pdb=" O VAL z 33 " (cutoff:3.500A) Processing helix chain 'z' and resid 73 through 87 removed outlier: 3.541A pdb=" N ILE z 77 " --> pdb=" O ALA z 74 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N ALA z 81 " --> pdb=" O ALA z 78 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N THR z 82 " --> pdb=" O LYS z 79 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N ASP z 85 " --> pdb=" O THR z 82 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N ASP z 86 " --> pdb=" O ALA z 83 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N ILE z 87 " --> pdb=" O GLN z 84 " (cutoff:3.500A) Processing helix chain 'z' and resid 93 through 110 removed outlier: 3.686A pdb=" N LEU z 97 " --> pdb=" O THR z 93 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ILE z 98 " --> pdb=" O SER z 94 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ILE z 99 " --> pdb=" O ASN z 95 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N LYS z 104 " --> pdb=" O GLY z 100 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N LEU z 108 " --> pdb=" O LYS z 104 " (cutoff:3.500A) removed outlier: 4.298A pdb=" N TYR z 109 " --> pdb=" O GLN z 105 " (cutoff:3.500A) Processing helix chain 'z' and resid 116 through 137 removed outlier: 3.684A pdb=" N GLU z 124 " --> pdb=" O THR z 120 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N GLU z 128 " --> pdb=" O GLU z 124 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N LYS z 129 " --> pdb=" O ALA z 125 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N GLU z 135 " --> pdb=" O LEU z 131 " (cutoff:3.500A) removed outlier: 4.463A pdb=" N GLU z 136 " --> pdb=" O GLN z 132 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N VAL z 137 " --> pdb=" O PHE z 133 " (cutoff:3.500A) Processing helix chain 'z' and resid 145 through 158 removed outlier: 3.536A pdb=" N ASP z 150 " --> pdb=" O GLU z 146 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N ARG z 157 " --> pdb=" O ARG z 153 " (cutoff:3.500A) removed outlier: 4.461A pdb=" N THR z 158 " --> pdb=" O THR z 154 " (cutoff:3.500A) Processing helix chain 'z' and resid 165 through 177 removed outlier: 3.972A pdb=" N GLU z 170 " --> pdb=" O ASP z 166 " (cutoff:3.500A) removed outlier: 4.109A pdb=" N ALA z 171 " --> pdb=" O VAL z 167 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N VAL z 172 " --> pdb=" O LEU z 168 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N ASP z 174 " --> pdb=" O GLU z 170 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N SER z 175 " --> pdb=" O ALA z 171 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N ILE z 176 " --> pdb=" O VAL z 172 " (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 256 through 263 Processing helix chain 'z' and resid 265 through 280 removed outlier: 4.363A pdb=" N ARG z 270 " --> pdb=" O PHE z 266 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N ILE z 274 " --> pdb=" O ARG z 270 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N ILE z 275 " --> pdb=" O VAL z 271 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N LYS z 280 " --> pdb=" O GLU z 276 " (cutoff:3.500A) Processing helix chain 'z' and resid 299 through 307 removed outlier: 3.955A pdb=" N ALA z 304 " --> pdb=" O PHE z 300 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N LEU z 305 " --> pdb=" O SER z 301 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N LYS z 307 " --> pdb=" O ASP z 303 " (cutoff:3.500A) Processing helix chain 'z' and resid 318 through 327 removed outlier: 3.740A pdb=" N ARG z 323 " --> pdb=" O ARG z 319 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N LEU z 326 " --> pdb=" O GLU z 322 " (cutoff:3.500A) 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 removed outlier: 3.632A pdb=" N ARG z 396 " --> pdb=" O ARG z 392 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N ALA z 397 " --> pdb=" O ASP z 393 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N VAL z 398 " --> pdb=" O GLY z 394 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ALA z 401 " --> pdb=" O ALA z 397 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N ILE z 402 " --> pdb=" O VAL z 398 " (cutoff:3.500A) Processing helix chain 'z' and resid 413 through 423 Processing helix chain 'z' and resid 432 through 455 removed outlier: 3.549A pdb=" N LEU z 435 " --> pdb=" O ARG z 432 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N GLN z 438 " --> pdb=" O LEU z 435 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N ALA z 439 " --> pdb=" O GLY z 436 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N ASP z 442 " --> pdb=" O ALA z 439 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N LEU z 444 " --> pdb=" O ALA z 441 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ILE z 446 " --> pdb=" O ALA z 443 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N ILE z 447 " --> pdb=" O LEU z 444 " (cutoff:3.500A) Proline residue: z 448 - end of helix removed outlier: 3.856A pdb=" N LEU z 451 " --> pdb=" O PRO z 448 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N ASN z 454 " --> pdb=" O LEU z 451 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N SER z 455 " --> pdb=" O ALA z 452 " (cutoff:3.500A) Processing helix chain 'z' and resid 459 through 467 removed outlier: 3.713A pdb=" N LYS z 465 " --> pdb=" O GLU z 461 " (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: 3.647A pdb=" N CYS z 508 " --> pdb=" O LEU z 504 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N THR z 509 " --> pdb=" O LEU z 505 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N THR z 513 " --> pdb=" O THR z 509 " (cutoff:3.500A) Processing helix chain 'a' and resid 16 through 31 removed outlier: 3.511A pdb=" N SER a 27 " --> pdb=" O MET a 23 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N ILE a 28 " --> pdb=" O ALA a 24 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ALA a 29 " --> pdb=" O ALA a 25 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N ILE a 31 " --> pdb=" O SER a 27 " (cutoff:3.500A) Processing helix chain 'a' and resid 58 through 64 removed outlier: 3.579A pdb=" N LYS a 63 " --> pdb=" O ALA a 59 " (cutoff:3.500A) Processing helix chain 'a' and resid 70 through 83 removed outlier: 4.153A pdb=" N LEU a 75 " --> pdb=" O ALA a 71 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N CYS a 76 " --> pdb=" O ALA a 72 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N GLU a 77 " --> pdb=" O LYS a 73 " (cutoff:3.500A) removed outlier: 4.040A pdb=" N LEU a 78 " --> pdb=" O VAL a 74 " (cutoff:3.500A) removed outlier: 4.309A pdb=" N ALA a 79 " --> pdb=" O LEU a 75 " (cutoff:3.500A) removed outlier: 4.186A pdb=" N ASP a 80 " --> pdb=" O CYS a 76 " (cutoff:3.500A) Processing helix chain 'a' and resid 90 through 109 removed outlier: 3.832A pdb=" N VAL a 94 " --> pdb=" O THR a 90 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N LYS a 109 " --> pdb=" O ASP a 105 " (cutoff:3.500A) Processing helix chain 'a' and resid 114 through 135 removed outlier: 3.619A pdb=" N LEU a 123 " --> pdb=" O SER a 119 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N ASN a 135 " --> pdb=" O TYR a 131 " (cutoff:3.500A) Processing helix chain 'a' and resid 149 through 158 removed outlier: 3.715A pdb=" N THR a 154 " --> pdb=" O ASN a 150 " (cutoff:3.500A) removed outlier: 4.188A pdb=" N SER a 155 " --> pdb=" O ALA a 151 " (cutoff:3.500A) removed outlier: 4.914A pdb=" N SER a 158 " --> pdb=" O THR a 154 " (cutoff:3.500A) Processing helix chain 'a' and resid 160 through 163 removed outlier: 3.795A pdb=" N ILE a 163 " --> pdb=" O ILE a 160 " (cutoff:3.500A) No H-bonds generated for 'chain 'a' and resid 160 through 163' Processing helix chain 'a' and resid 165 through 176 removed outlier: 3.954A pdb=" N ASN a 170 " --> pdb=" O ASP a 166 " (cutoff:3.500A) removed outlier: 4.237A pdb=" N MET a 171 " --> pdb=" O PHE a 167 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N VAL a 172 " --> pdb=" O PHE a 168 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N ASP a 174 " --> pdb=" O ASN a 170 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N ALA a 175 " --> pdb=" O MET a 171 " (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 278 removed outlier: 3.630A pdb=" N ASP a 261 " --> pdb=" O PRO a 257 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N ILE a 263 " --> pdb=" O LYS a 259 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N ARG a 264 " --> pdb=" O LEU a 260 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N LYS a 272 " --> pdb=" O SER a 268 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N GLU a 273 " --> pdb=" O ASP a 269 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N ILE a 275 " --> pdb=" O THR a 271 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N GLN a 276 " --> pdb=" O LYS a 272 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N LYS a 277 " --> pdb=" O GLU a 273 " (cutoff:3.500A) Processing helix chain 'a' and resid 300 through 303 No H-bonds generated for 'chain 'a' and resid 300 through 303' Processing helix chain 'a' and resid 313 through 322 removed outlier: 3.764A pdb=" N ARG a 318 " --> pdb=" O ARG a 314 " (cutoff:3.500A) Processing helix chain 'a' and resid 382 through 404 removed outlier: 3.612A pdb=" N GLU a 387 " --> pdb=" O PHE a 383 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N ARG a 390 " --> pdb=" O ASP a 386 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N VAL a 398 " --> pdb=" O ASP a 394 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N VAL a 399 " --> pdb=" O ALA a 395 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N VAL a 402 " --> pdb=" O VAL a 398 " (cutoff:3.500A) Processing helix chain 'a' and resid 414 through 430 removed outlier: 3.564A pdb=" N ALA a 418 " --> pdb=" O ALA a 414 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N ILE a 421 " --> pdb=" O ALA a 417 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N TYR a 422 " --> pdb=" O ALA a 418 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N GLU a 424 " --> pdb=" O SER a 420 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N SER a 429 " --> pdb=" O ASN a 425 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N MET a 430 " --> pdb=" O TYR a 426 " (cutoff:3.500A) Processing helix chain 'a' and resid 435 through 455 removed outlier: 3.761A pdb=" N LEU a 446 " --> pdb=" O ALA a 442 " (cutoff:3.500A) removed outlier: 4.496A pdb=" N VAL a 447 " --> pdb=" O ARG a 443 " (cutoff:3.500A) removed outlier: 5.336A 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 471 removed outlier: 3.667A pdb=" N VAL a 464 " --> pdb=" O SER a 460 " (cutoff:3.500A) removed outlier: 4.161A pdb=" N ALA a 465 " --> pdb=" O THR a 461 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N LEU a 467 " --> pdb=" O LEU a 463 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N PHE a 470 " --> pdb=" O LYS a 466 " (cutoff:3.500A) Processing helix chain 'a' and resid 473 through 476 No H-bonds generated for 'chain 'a' and resid 473 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: 3.647A pdb=" N SER a 513 " --> pdb=" O VAL a 509 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N LEU a 514 " --> pdb=" O LYS a 510 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N THR a 518 " --> pdb=" O LEU a 514 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 11 through 13 removed outlier: 3.563A pdb=" N SER A 12 " --> pdb=" O LEU A 530 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 43 through 46 removed outlier: 3.601A pdb=" N THR A 55 " --> pdb=" O LYS A 43 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 196 through 200 removed outlier: 3.829A pdb=" N ILE A 376 " --> pdb=" O MET A 209 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N MET A 209 " --> pdb=" O ILE A 376 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 234 through 237 removed outlier: 6.062A pdb=" N VAL A 285 " --> pdb=" O ALA A 235 " (cutoff:3.500A) removed outlier: 7.413A pdb=" N LEU A 237 " --> pdb=" O VAL A 285 " (cutoff:3.500A) removed outlier: 6.322A pdb=" N LEU A 287 " --> pdb=" O LEU A 237 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'A' and resid 350 through 354 removed outlier: 3.792A pdb=" N GLU A 350 " --> pdb=" O LYS A 365 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N VAL A 352 " --> pdb=" O LEU A 363 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N LEU A 363 " --> pdb=" O VAL A 352 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N GLU A 354 " --> pdb=" O LEU A 361 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N LEU A 361 " --> pdb=" O GLU A 354 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'A' and resid 486 through 489 removed outlier: 3.724A pdb=" N ASP A 489 " --> pdb=" O LYS A 494 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N LYS A 494 " --> pdb=" O ASP A 489 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 50 through 52 Processing sheet with id= H, first strand: chain 'B' and resid 200 through 205 removed outlier: 3.700A pdb=" N ILE B 202 " --> pdb=" O ILE B 373 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N LYS B 204 " --> pdb=" O LEU B 375 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N GLY B 377 " --> pdb=" O LYS B 204 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'B' and resid 289 through 291 removed outlier: 5.818A pdb=" N MET B 310 " --> pdb=" O PHE B 290 " (cutoff:3.500A) No H-bonds generated for sheet with id= I Processing sheet with id= J, first strand: chain 'B' and resid 348 through 353 removed outlier: 3.583A pdb=" N LEU B 348 " --> pdb=" O SER B 363 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'B' and resid 406 through 408 Processing sheet with id= L, first strand: chain 'B' and resid 476 through 479 removed outlier: 3.530A pdb=" N THR B 484 " --> pdb=" O ASP B 479 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'D' and resid 59 through 62 removed outlier: 3.677A pdb=" N LYS D 59 " --> pdb=" O THR D 71 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N THR D 71 " --> pdb=" O LYS D 59 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'D' and resid 209 through 212 removed outlier: 3.568A pdb=" N ILE D 388 " --> pdb=" O LYS D 209 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N VAL D 211 " --> pdb=" O ILE D 388 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N GLU D 222 " --> pdb=" O VAL D 389 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'D' and resid 227 through 229 removed outlier: 3.689A pdb=" N LEU D 229 " --> pdb=" O LEU D 374 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N LEU D 373 " --> pdb=" O VAL D 365 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N THR D 377 " --> pdb=" O LEU D 361 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N LEU D 361 " --> pdb=" O THR D 377 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'D' and resid 246 through 248 removed outlier: 6.937A pdb=" N VAL D 297 " --> pdb=" O GLY D 247 " (cutoff:3.500A) removed outlier: 6.574A pdb=" N MET D 323 " --> pdb=" O LEU D 298 " (cutoff:3.500A) No H-bonds generated for sheet with id= P Processing sheet with id= Q, first strand: chain 'D' and resid 421 through 423 Processing sheet with id= R, first strand: chain 'D' and resid 491 through 494 Processing sheet with id= S, first strand: chain 'E' and resid 57 through 60 Processing sheet with id= T, first strand: chain 'E' and resid 207 through 211 removed outlier: 6.792A pdb=" N VAL E 381 " --> pdb=" O LYS E 208 " (cutoff:3.500A) removed outlier: 8.239A pdb=" N GLU E 210 " --> pdb=" O VAL E 381 " (cutoff:3.500A) removed outlier: 6.797A pdb=" N ILE E 383 " --> pdb=" O GLU E 210 " (cutoff:3.500A) removed outlier: 4.164A pdb=" N THR E 382 " --> pdb=" O ILE E 223 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N ILE E 223 " --> pdb=" O THR E 382 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N PHE E 384 " --> pdb=" O LYS E 221 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N LYS E 221 " --> pdb=" O PHE E 384 " (cutoff:3.500A) No H-bonds generated for sheet with id= T Processing sheet with id= U, first strand: chain 'E' and resid 225 through 228 removed outlier: 3.652A pdb=" N VAL E 226 " --> pdb=" O ILE E 372 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N ILE E 372 " --> pdb=" O VAL E 226 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N MET E 369 " --> pdb=" O ILE E 360 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N ILE E 360 " --> pdb=" O MET E 369 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'E' and resid 246 through 248 removed outlier: 6.117A pdb=" N LEU E 297 " --> pdb=" O ALA E 247 " (cutoff:3.500A) No H-bonds generated for sheet with id= V Processing sheet with id= W, first strand: chain 'E' and resid 416 through 418 Processing sheet with id= X, first strand: chain 'G' and resid 199 through 203 removed outlier: 7.178A pdb=" N CYS G 372 " --> pdb=" O ARG G 200 " (cutoff:3.500A) removed outlier: 8.145A pdb=" N GLU G 202 " --> pdb=" O CYS G 372 " (cutoff:3.500A) removed outlier: 5.904A pdb=" N ILE G 374 " --> pdb=" O GLU G 202 " (cutoff:3.500A) No H-bonds generated for sheet with id= X Processing sheet with id= Y, first strand: chain 'G' and resid 238 through 241 removed outlier: 7.098A pdb=" N VAL G 289 " --> pdb=" O VAL G 239 " (cutoff:3.500A) removed outlier: 8.528A pdb=" N LEU G 241 " --> pdb=" O VAL G 289 " (cutoff:3.500A) removed outlier: 6.739A pdb=" N ILE G 291 " --> pdb=" O LEU G 241 " (cutoff:3.500A) removed outlier: 6.290A pdb=" N THR G 310 " --> pdb=" O VAL G 290 " (cutoff:3.500A) removed outlier: 7.742A pdb=" N THR G 292 " --> pdb=" O THR G 310 " (cutoff:3.500A) removed outlier: 7.012A pdb=" N ILE G 312 " --> pdb=" O THR G 292 " (cutoff:3.500A) No H-bonds generated for sheet with id= Y Processing sheet with id= Z, first strand: chain 'G' and resid 407 through 409 Processing sheet with id= AA, first strand: chain 'H' and resid 47 through 50 Processing sheet with id= AB, first strand: chain 'H' and resid 195 through 199 removed outlier: 6.782A pdb=" N CYS H 370 " --> pdb=" O GLY H 196 " (cutoff:3.500A) removed outlier: 8.100A pdb=" N LYS H 198 " --> pdb=" O CYS H 370 " (cutoff:3.500A) removed outlier: 6.795A pdb=" N PHE H 372 " --> pdb=" O LYS H 198 " (cutoff:3.500A) No H-bonds generated for sheet with id= AB Processing sheet with id= AC, first strand: chain 'H' and resid 237 through 240 removed outlier: 6.934A pdb=" N VAL H 288 " --> pdb=" O ALA H 238 " (cutoff:3.500A) removed outlier: 7.914A pdb=" N LEU H 240 " --> pdb=" O VAL H 288 " (cutoff:3.500A) removed outlier: 6.062A pdb=" N SER H 290 " --> pdb=" O LEU H 240 " (cutoff:3.500A) removed outlier: 7.477A pdb=" N PHE H 309 " --> pdb=" O VAL H 289 " (cutoff:3.500A) removed outlier: 9.190A pdb=" N SER H 291 " --> pdb=" O PHE H 309 " (cutoff:3.500A) removed outlier: 7.391A pdb=" N ALA H 311 " --> pdb=" O SER H 291 " (cutoff:3.500A) No H-bonds generated for sheet with id= AC Processing sheet with id= AD, first strand: chain 'H' and resid 347 through 351 removed outlier: 4.001A pdb=" N GLU H 349 " --> pdb=" O PHE H 360 " (cutoff:3.500A) removed outlier: 4.178A pdb=" N PHE H 360 " --> pdb=" O GLU H 349 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N THR H 351 " --> pdb=" O TYR H 358 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N TYR H 358 " --> pdb=" O THR H 351 " (cutoff:3.500A) Processing sheet with id= AE, first strand: chain 'H' and resid 405 through 407 Processing sheet with id= AF, first strand: chain 'H' and resid 475 through 477 removed outlier: 3.683A pdb=" N ALA H 485 " --> pdb=" O GLY H 476 " (cutoff:3.500A) Processing sheet with id= AG, first strand: chain 'Q' and resid 54 through 57 Processing sheet with id= AH, first strand: chain 'Q' and resid 202 through 208 removed outlier: 6.801A pdb=" N SER Q 373 " --> pdb=" O ARG Q 203 " (cutoff:3.500A) removed outlier: 7.924A pdb=" N CYS Q 205 " --> pdb=" O SER Q 373 " (cutoff:3.500A) removed outlier: 6.483A pdb=" N ILE Q 375 " --> pdb=" O CYS Q 205 " (cutoff:3.500A) removed outlier: 7.432A pdb=" N ILE Q 207 " --> pdb=" O ILE Q 375 " (cutoff:3.500A) removed outlier: 5.799A pdb=" N LEU Q 377 " --> pdb=" O ILE Q 207 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N SER Q 216 " --> pdb=" O VAL Q 376 " (cutoff:3.500A) Processing sheet with id= AI, first strand: chain 'Q' and resid 221 through 223 removed outlier: 3.559A pdb=" N MET Q 221 " --> pdb=" O PHE Q 363 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N VAL Q 361 " --> pdb=" O PHE Q 223 " (cutoff:3.500A) Processing sheet with id= AJ, first strand: chain 'Q' and resid 311 through 314 removed outlier: 8.043A pdb=" N LYS Q 238 " --> pdb=" O ASN Q 289 " (cutoff:3.500A) removed outlier: 5.929A pdb=" N VAL Q 291 " --> pdb=" O LYS Q 238 " (cutoff:3.500A) removed outlier: 6.828A pdb=" N ALA Q 240 " --> pdb=" O VAL Q 291 " (cutoff:3.500A) removed outlier: 5.929A pdb=" N THR Q 293 " --> pdb=" O ALA Q 240 " (cutoff:3.500A) removed outlier: 6.874A pdb=" N TYR Q 242 " --> pdb=" O THR Q 293 " (cutoff:3.500A) Processing sheet with id= AK, first strand: chain 'Q' and resid 478 through 480 Processing sheet with id= AL, first strand: chain 'Z' and resid 45 through 48 Processing sheet with id= AM, first strand: chain 'Z' and resid 191 through 196 removed outlier: 6.718A pdb=" N VAL Z 372 " --> pdb=" O GLU Z 192 " (cutoff:3.500A) removed outlier: 7.922A pdb=" N MET Z 194 " --> pdb=" O VAL Z 372 " (cutoff:3.500A) removed outlier: 6.496A pdb=" N LEU Z 374 " --> pdb=" O MET Z 194 " (cutoff:3.500A) removed outlier: 7.805A pdb=" N MET Z 196 " --> pdb=" O LEU Z 374 " (cutoff:3.500A) removed outlier: 6.776A pdb=" N ILE Z 376 " --> pdb=" O MET Z 196 " (cutoff:3.500A) Processing sheet with id= AN, first strand: chain 'Z' and resid 229 through 231 Processing sheet with id= AO, first strand: chain 'Z' and resid 351 through 354 Processing sheet with id= AP, first strand: chain 'Z' and resid 407 through 409 Processing sheet with id= AQ, first strand: chain 'b' and resid 17 through 19 removed outlier: 3.835A pdb=" N ASP b 17 " --> pdb=" O LYS b 522 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N LYS b 522 " --> pdb=" O ASP b 17 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N ILE b 520 " --> pdb=" O GLU b 19 " (cutoff:3.500A) Processing sheet with id= AR, first strand: chain 'b' and resid 199 through 205 removed outlier: 7.083A pdb=" N CYS b 371 " --> pdb=" O HIS b 200 " (cutoff:3.500A) removed outlier: 8.356A pdb=" N ILE b 202 " --> pdb=" O CYS b 371 " (cutoff:3.500A) removed outlier: 7.120A pdb=" N ILE b 373 " --> pdb=" O ILE b 202 " (cutoff:3.500A) removed outlier: 8.164A pdb=" N LYS b 204 " --> pdb=" O ILE b 373 " (cutoff:3.500A) removed outlier: 6.656A pdb=" N LEU b 375 " --> pdb=" O LYS b 204 " (cutoff:3.500A) Processing sheet with id= AS, first strand: chain 'b' and resid 231 through 233 removed outlier: 4.005A pdb=" N ILE b 232 " --> pdb=" O ILE b 349 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N ILE b 349 " --> pdb=" O ILE b 232 " (cutoff:3.500A) Processing sheet with id= AT, first strand: chain 'b' and resid 237 through 240 removed outlier: 6.411A pdb=" N CYS b 289 " --> pdb=" O LEU b 238 " (cutoff:3.500A) removed outlier: 7.773A pdb=" N ALA b 240 " --> pdb=" O CYS b 289 " (cutoff:3.500A) removed outlier: 6.232A pdb=" N ILE b 291 " --> pdb=" O ALA b 240 " (cutoff:3.500A) removed outlier: 6.064A pdb=" N MET b 310 " --> pdb=" O PHE b 290 " (cutoff:3.500A) removed outlier: 7.524A pdb=" N ASN b 292 " --> pdb=" O MET b 310 " (cutoff:3.500A) removed outlier: 6.408A pdb=" N ILE b 312 " --> pdb=" O ASN b 292 " (cutoff:3.500A) No H-bonds generated for sheet with id= AT Processing sheet with id= AU, first strand: chain 'b' and resid 476 through 479 removed outlier: 3.541A pdb=" N ASP b 479 " --> pdb=" O THR b 484 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N THR b 484 " --> pdb=" O ASP b 479 " (cutoff:3.500A) Processing sheet with id= AV, first strand: chain 'd' and resid 60 through 62 removed outlier: 3.778A pdb=" N ILE d 61 " --> pdb=" O THR d 69 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N THR d 69 " --> pdb=" O ILE d 61 " (cutoff:3.500A) No H-bonds generated for sheet with id= AV Processing sheet with id= AW, first strand: chain 'd' and resid 208 through 214 removed outlier: 6.821A pdb=" N VAL d 386 " --> pdb=" O LYS d 209 " (cutoff:3.500A) removed outlier: 7.919A pdb=" N VAL d 211 " --> pdb=" O VAL d 386 " (cutoff:3.500A) removed outlier: 6.259A pdb=" N ILE d 388 " --> pdb=" O VAL d 211 " (cutoff:3.500A) removed outlier: 7.989A pdb=" N LYS d 213 " --> pdb=" O ILE d 388 " (cutoff:3.500A) removed outlier: 6.934A pdb=" N VAL d 390 " --> pdb=" O LYS d 213 " (cutoff:3.500A) Processing sheet with id= AX, first strand: chain 'd' and resid 227 through 229 removed outlier: 3.830A pdb=" N GLY d 371 " --> pdb=" O LEU d 367 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N LEU d 367 " --> pdb=" O GLY d 371 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N LEU d 361 " --> pdb=" O THR d 377 " (cutoff:3.500A) Processing sheet with id= AY, first strand: chain 'd' and resid 246 through 249 removed outlier: 6.001A pdb=" N VAL d 297 " --> pdb=" O GLY d 247 " (cutoff:3.500A) removed outlier: 7.042A pdb=" N ILE d 249 " --> pdb=" O VAL d 297 " (cutoff:3.500A) removed outlier: 5.684A pdb=" N LEU d 299 " --> pdb=" O ILE d 249 " (cutoff:3.500A) removed outlier: 6.423A pdb=" N MET d 323 " --> pdb=" O LEU d 298 " (cutoff:3.500A) removed outlier: 7.725A pdb=" N ILE d 300 " --> pdb=" O MET d 323 " (cutoff:3.500A) removed outlier: 6.860A pdb=" N ILE d 325 " --> pdb=" O ILE d 300 " (cutoff:3.500A) No H-bonds generated for sheet with id= AY Processing sheet with id= AZ, first strand: chain 'd' and resid 421 through 423 Processing sheet with id= BA, first strand: chain 'd' and resid 491 through 494 removed outlier: 3.587A pdb=" N GLY d 492 " --> pdb=" O SER d 501 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N SER d 501 " --> pdb=" O GLY d 492 " (cutoff:3.500A) Processing sheet with id= BB, first strand: chain 'e' and resid 23 through 26 removed outlier: 3.630A pdb=" N ILE e 531 " --> pdb=" O LEU e 26 " (cutoff:3.500A) Processing sheet with id= BC, first strand: chain 'e' and resid 57 through 60 removed outlier: 3.626A pdb=" N THR e 67 " --> pdb=" O MET e 59 " (cutoff:3.500A) Processing sheet with id= BD, first strand: chain 'e' and resid 207 through 213 removed outlier: 6.734A pdb=" N VAL e 381 " --> pdb=" O LYS e 208 " (cutoff:3.500A) removed outlier: 8.156A pdb=" N GLU e 210 " --> pdb=" O VAL e 381 " (cutoff:3.500A) removed outlier: 6.062A pdb=" N ILE e 383 " --> pdb=" O GLU e 210 " (cutoff:3.500A) removed outlier: 7.959A pdb=" N LYS e 212 " --> pdb=" O ILE e 383 " (cutoff:3.500A) removed outlier: 6.790A pdb=" N ILE e 385 " --> pdb=" O LYS e 212 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N PHE e 384 " --> pdb=" O LYS e 221 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N LYS e 221 " --> pdb=" O PHE e 384 " (cutoff:3.500A) Processing sheet with id= BE, first strand: chain 'e' and resid 225 through 228 removed outlier: 3.622A pdb=" N MET e 369 " --> pdb=" O ILE e 360 " (cutoff:3.500A) Processing sheet with id= BF, first strand: chain 'e' and resid 246 through 248 removed outlier: 6.230A pdb=" N LEU e 297 " --> pdb=" O ALA e 247 " (cutoff:3.500A) No H-bonds generated for sheet with id= BF Processing sheet with id= BG, first strand: chain 'g' and resid 201 through 205 removed outlier: 5.802A pdb=" N ILE g 374 " --> pdb=" O GLU g 202 " (cutoff:3.500A) removed outlier: 6.690A pdb=" N ILE g 204 " --> pdb=" O ILE g 374 " (cutoff:3.500A) removed outlier: 5.802A pdb=" N LEU g 376 " --> pdb=" O ILE g 204 " (cutoff:3.500A) Processing sheet with id= BH, first strand: chain 'g' and resid 238 through 241 removed outlier: 7.280A pdb=" N VAL g 289 " --> pdb=" O VAL g 239 " (cutoff:3.500A) removed outlier: 8.445A pdb=" N LEU g 241 " --> pdb=" O VAL g 289 " (cutoff:3.500A) removed outlier: 7.065A pdb=" N ILE g 291 " --> pdb=" O LEU g 241 " (cutoff:3.500A) removed outlier: 6.579A pdb=" N THR g 310 " --> pdb=" O VAL g 290 " (cutoff:3.500A) removed outlier: 7.710A pdb=" N THR g 292 " --> pdb=" O THR g 310 " (cutoff:3.500A) removed outlier: 6.690A pdb=" N ILE g 312 " --> pdb=" O THR g 292 " (cutoff:3.500A) No H-bonds generated for sheet with id= BH Processing sheet with id= BI, first strand: chain 'g' and resid 407 through 409 Processing sheet with id= BJ, first strand: chain 'h' and resid 47 through 50 removed outlier: 3.673A pdb=" N SER h 59 " --> pdb=" O LYS h 47 " (cutoff:3.500A) Processing sheet with id= BK, first strand: chain 'h' and resid 195 through 201 removed outlier: 6.124A pdb=" N CYS h 370 " --> pdb=" O GLY h 196 " (cutoff:3.500A) removed outlier: 7.370A pdb=" N LYS h 198 " --> pdb=" O CYS h 370 " (cutoff:3.500A) removed outlier: 5.743A pdb=" N PHE h 372 " --> pdb=" O LYS h 198 " (cutoff:3.500A) removed outlier: 6.875A pdb=" N VAL h 200 " --> pdb=" O PHE h 372 " (cutoff:3.500A) removed outlier: 5.732A pdb=" N LEU h 374 " --> pdb=" O VAL h 200 " (cutoff:3.500A) Processing sheet with id= BL, first strand: chain 'h' and resid 237 through 240 removed outlier: 6.863A pdb=" N VAL h 288 " --> pdb=" O ALA h 238 " (cutoff:3.500A) removed outlier: 7.647A pdb=" N LEU h 240 " --> pdb=" O VAL h 288 " (cutoff:3.500A) removed outlier: 6.402A pdb=" N SER h 290 " --> pdb=" O LEU h 240 " (cutoff:3.500A) removed outlier: 7.118A pdb=" N PHE h 309 " --> pdb=" O VAL h 289 " (cutoff:3.500A) removed outlier: 8.557A pdb=" N SER h 291 " --> pdb=" O PHE h 309 " (cutoff:3.500A) removed outlier: 6.942A pdb=" N ALA h 311 " --> pdb=" O SER h 291 " (cutoff:3.500A) No H-bonds generated for sheet with id= BL Processing sheet with id= BM, first strand: chain 'h' and resid 347 through 351 removed outlier: 3.603A pdb=" N GLU h 349 " --> pdb=" O PHE h 360 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N PHE h 360 " --> pdb=" O GLU h 349 " (cutoff:3.500A) Processing sheet with id= BN, first strand: chain 'h' and resid 405 through 407 Processing sheet with id= BO, first strand: chain 'h' and resid 475 through 477 Processing sheet with id= BP, first strand: chain 'q' and resid 54 through 57 Processing sheet with id= BQ, first strand: chain 'q' and resid 202 through 208 removed outlier: 6.268A pdb=" N SER q 373 " --> pdb=" O ARG q 203 " (cutoff:3.500A) removed outlier: 7.353A pdb=" N CYS q 205 " --> pdb=" O SER q 373 " (cutoff:3.500A) removed outlier: 5.837A pdb=" N ILE q 375 " --> pdb=" O CYS q 205 " (cutoff:3.500A) removed outlier: 7.210A pdb=" N ILE q 207 " --> pdb=" O ILE q 375 " (cutoff:3.500A) removed outlier: 6.026A pdb=" N LEU q 377 " --> pdb=" O ILE q 207 " (cutoff:3.500A) Processing sheet with id= BR, first strand: chain 'q' and resid 221 through 223 Processing sheet with id= BS, first strand: chain 'q' and resid 239 through 242 removed outlier: 6.705A pdb=" N VAL q 290 " --> pdb=" O ALA q 240 " (cutoff:3.500A) removed outlier: 7.573A pdb=" N TYR q 242 " --> pdb=" O VAL q 290 " (cutoff:3.500A) removed outlier: 6.082A pdb=" N VAL q 292 " --> pdb=" O TYR q 242 " (cutoff:3.500A) removed outlier: 6.204A pdb=" N MET q 311 " --> pdb=" O VAL q 291 " (cutoff:3.500A) removed outlier: 7.264A pdb=" N THR q 293 " --> pdb=" O MET q 311 " (cutoff:3.500A) removed outlier: 6.526A pdb=" N VAL q 313 " --> pdb=" O THR q 293 " (cutoff:3.500A) No H-bonds generated for sheet with id= BS Processing sheet with id= BT, first strand: chain 'q' and resid 408 through 410 Processing sheet with id= BU, first strand: chain 'q' and resid 478 through 480 Processing sheet with id= BV, first strand: chain 'z' and resid 45 through 48 removed outlier: 3.728A pdb=" N LYS z 45 " --> pdb=" O THR z 57 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N THR z 57 " --> pdb=" O LYS z 45 " (cutoff:3.500A) Processing sheet with id= BW, first strand: chain 'z' and resid 191 through 196 removed outlier: 6.831A pdb=" N VAL z 372 " --> pdb=" O GLU z 192 " (cutoff:3.500A) removed outlier: 7.960A pdb=" N MET z 194 " --> pdb=" O VAL z 372 " (cutoff:3.500A) removed outlier: 6.509A pdb=" N LEU z 374 " --> pdb=" O MET z 194 " (cutoff:3.500A) removed outlier: 7.884A pdb=" N MET z 196 " --> pdb=" O LEU z 374 " (cutoff:3.500A) removed outlier: 6.618A pdb=" N ILE z 376 " --> pdb=" O MET z 196 " (cutoff:3.500A) Processing sheet with id= BX, first strand: chain 'z' and resid 344 through 347 removed outlier: 4.141A pdb=" N ALA z 228 " --> pdb=" O ALA z 347 " (cutoff:3.500A) Processing sheet with id= BY, first strand: chain 'z' and resid 350 through 354 Processing sheet with id= BZ, first strand: chain 'z' and resid 407 through 409 Processing sheet with id= CA, first strand: chain 'a' and resid 11 through 13 removed outlier: 3.564A pdb=" N SER a 12 " --> pdb=" O LEU a 530 " (cutoff:3.500A) Processing sheet with id= CB, first strand: chain 'a' and resid 43 through 46 removed outlier: 3.602A pdb=" N THR a 55 " --> pdb=" O LYS a 43 " (cutoff:3.500A) Processing sheet with id= CC, first strand: chain 'a' and resid 196 through 200 removed outlier: 3.828A pdb=" N ILE a 376 " --> pdb=" O MET a 209 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N MET a 209 " --> pdb=" O ILE a 376 " (cutoff:3.500A) Processing sheet with id= CD, first strand: chain 'a' and resid 234 through 237 removed outlier: 6.061A pdb=" N VAL a 285 " --> pdb=" O ALA a 235 " (cutoff:3.500A) removed outlier: 7.415A pdb=" N LEU a 237 " --> pdb=" O VAL a 285 " (cutoff:3.500A) removed outlier: 6.325A pdb=" N LEU a 287 " --> pdb=" O LEU a 237 " (cutoff:3.500A) removed outlier: 6.407A pdb=" N MET a 306 " --> pdb=" O ILE a 286 " (cutoff:3.500A) removed outlier: 7.746A pdb=" N THR a 288 " --> pdb=" O MET a 306 " (cutoff:3.500A) removed outlier: 6.714A pdb=" N VAL a 308 " --> pdb=" O THR a 288 " (cutoff:3.500A) No H-bonds generated for sheet with id= CD Processing sheet with id= CE, first strand: chain 'a' and resid 350 through 354 removed outlier: 3.793A pdb=" N GLU a 350 " --> pdb=" O LYS a 365 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N VAL a 352 " --> pdb=" O LEU a 363 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N GLU a 354 " --> pdb=" O LEU a 361 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N LEU a 361 " --> pdb=" O GLU a 354 " (cutoff:3.500A) Processing sheet with id= CF, first strand: chain 'a' and resid 486 through 489 removed outlier: 3.724A pdb=" N ASP a 489 " --> pdb=" O LYS a 494 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N LYS a 494 " --> pdb=" O ASP a 489 " (cutoff:3.500A) 2090 hydrogen bonds defined for protein. 5910 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: 20.60 Time building geometry restraints manager: 20.64 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 21308 1.35 - 1.47: 12084 1.47 - 1.59: 29812 1.59 - 1.71: 80 1.71 - 1.83: 642 Bond restraints: 63926 Sorted by residual: bond pdb=" C4 ATP q 601 " pdb=" C5 ATP q 601 " ideal model delta sigma weight residual 1.388 1.474 -0.086 1.00e-02 1.00e+04 7.32e+01 bond pdb=" C4 ATP Q 601 " pdb=" C5 ATP Q 601 " ideal model delta sigma weight residual 1.388 1.473 -0.085 1.00e-02 1.00e+04 7.24e+01 bond pdb=" C4 ATP D 601 " pdb=" C5 ATP D 601 " ideal model delta sigma weight residual 1.388 1.471 -0.083 1.00e-02 1.00e+04 6.97e+01 bond pdb=" C4 ATP a 601 " pdb=" C5 ATP a 601 " ideal model delta sigma weight residual 1.388 1.471 -0.083 1.00e-02 1.00e+04 6.94e+01 bond pdb=" C4 ATP B 601 " pdb=" C5 ATP B 601 " ideal model delta sigma weight residual 1.388 1.471 -0.083 1.00e-02 1.00e+04 6.93e+01 ... (remaining 63921 not shown) Histogram of bond angle deviations from ideal: 94.38 - 102.89: 365 102.89 - 111.39: 28122 111.39 - 119.90: 28953 119.90 - 128.40: 28621 128.40 - 136.91: 299 Bond angle restraints: 86360 Sorted by residual: angle pdb=" PB ATP A 601 " pdb=" O3B ATP A 601 " pdb=" PG ATP A 601 " ideal model delta sigma weight residual 139.87 117.54 22.33 1.00e+00 1.00e+00 4.98e+02 angle pdb=" PB ATP a 601 " pdb=" O3B ATP a 601 " pdb=" PG ATP a 601 " ideal model delta sigma weight residual 139.87 117.56 22.31 1.00e+00 1.00e+00 4.98e+02 angle pdb=" PA ATP Q 601 " pdb=" O3A ATP Q 601 " pdb=" PB ATP Q 601 " ideal model delta sigma weight residual 136.83 115.32 21.51 1.00e+00 1.00e+00 4.63e+02 angle pdb=" PA ATP q 601 " pdb=" O3A ATP q 601 " pdb=" PB ATP q 601 " ideal model delta sigma weight residual 136.83 115.33 21.50 1.00e+00 1.00e+00 4.62e+02 angle pdb=" PB ATP q 601 " pdb=" O3B ATP q 601 " pdb=" PG ATP q 601 " ideal model delta sigma weight residual 139.87 118.42 21.45 1.00e+00 1.00e+00 4.60e+02 ... (remaining 86355 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.99: 36023 17.99 - 35.99: 3063 35.99 - 53.98: 586 53.98 - 71.97: 147 71.97 - 89.96: 75 Dihedral angle restraints: 39894 sinusoidal: 16276 harmonic: 23618 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 -120.59 -59.41 0 5.00e+00 4.00e-02 1.41e+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 -120.76 -59.24 0 5.00e+00 4.00e-02 1.40e+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 180.00 129.18 50.82 0 5.00e+00 4.00e-02 1.03e+02 ... (remaining 39891 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.061: 8751 0.061 - 0.123: 1398 0.123 - 0.184: 158 0.184 - 0.245: 7 0.245 - 0.307: 8 Chirality restraints: 10322 Sorted by residual: chirality pdb=" CB ILE D 70 " pdb=" CA ILE D 70 " pdb=" CG1 ILE D 70 " pdb=" CG2 ILE D 70 " both_signs ideal model delta sigma weight residual False 2.64 2.34 0.31 2.00e-01 2.50e+01 2.35e+00 chirality pdb=" CB ILE b 331 " pdb=" CA ILE b 331 " pdb=" CG1 ILE b 331 " pdb=" CG2 ILE b 331 " both_signs ideal model delta sigma weight residual False 2.64 2.36 0.28 2.00e-01 2.50e+01 1.98e+00 chirality pdb=" CA THR a 90 " pdb=" N THR a 90 " pdb=" C THR a 90 " pdb=" CB THR a 90 " both_signs ideal model delta sigma weight residual False 2.53 2.25 0.28 2.00e-01 2.50e+01 1.90e+00 ... (remaining 10319 not shown) Planarity restraints: 10999 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLN a 187 " 0.066 5.00e-02 4.00e+02 1.02e-01 1.65e+01 pdb=" N PRO a 188 " -0.176 5.00e-02 4.00e+02 pdb=" CA PRO a 188 " 0.055 5.00e-02 4.00e+02 pdb=" CD PRO a 188 " 0.054 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLN A 187 " -0.066 5.00e-02 4.00e+02 1.01e-01 1.64e+01 pdb=" N PRO A 188 " 0.175 5.00e-02 4.00e+02 pdb=" CA PRO A 188 " -0.055 5.00e-02 4.00e+02 pdb=" CD PRO A 188 " -0.054 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE Q 191 " 0.047 5.00e-02 4.00e+02 7.00e-02 7.85e+00 pdb=" N PRO Q 192 " -0.121 5.00e-02 4.00e+02 pdb=" CA PRO Q 192 " 0.035 5.00e-02 4.00e+02 pdb=" CD PRO Q 192 " 0.039 5.00e-02 4.00e+02 ... (remaining 10996 not shown) Histogram of nonbonded interaction distances: 1.14 - 1.89: 11 1.89 - 2.64: 649 2.64 - 3.39: 81143 3.39 - 4.15: 145404 4.15 - 4.90: 261252 Nonbonded interactions: 488459 Sorted by model distance: nonbonded pdb=" CD2 LEU D 84 " pdb=" CB SER a 6 " model vdw 1.136 3.860 nonbonded pdb=" NH2 ARG G 330 " pdb=" NZ LYS a 243 " model vdw 1.240 3.200 nonbonded pdb=" NE ARG G 334 " pdb=" O GLY a 249 " model vdw 1.316 2.520 nonbonded pdb=" CD2 LEU D 84 " pdb=" CA SER a 6 " model vdw 1.317 3.890 nonbonded pdb=" CG ARG G 334 " pdb=" OE1 GLN a 251 " model vdw 1.436 3.440 ... (remaining 488454 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'a' } ncs_group { reference = chain 'B' selection = (chain 'b' and (resid 19 through 522 or resid 601)) } ncs_group { reference = chain 'D' selection = (chain 'd' and (resid 30 through 254 or resid 286 through 300 or resid 311 throu \ gh 539 or resid 601)) } ncs_group { reference = chain 'E' selection = (chain 'e' and (resid 25 through 533 or resid 601)) } ncs_group { reference = chain 'G' selection = chain 'g' } ncs_group { reference = chain 'H' selection = (chain 'h' and (resid 16 through 524 or resid 601)) } ncs_group { reference = chain 'Q' selection = (chain 'q' and (resid 24 through 529 or resid 601)) } ncs_group { reference = chain 'Z' selection = (chain 'z' and (resid 13 through 526 or resid 601)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.190 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: 0.050 Extract box with map and model: 6.270 Check model and map are aligned: 0.700 Set scattering table: 0.460 Process input model: 127.070 Find NCS groups from input model: 5.970 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: 0.020 Load rotamer database and sin/cos tables:2.220 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 144.490 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5278 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 : 0.004 0.086 63926 Z= 0.260 Angle : 0.860 22.325 86360 Z= 0.601 Chirality : 0.045 0.307 10322 Planarity : 0.005 0.102 10999 Dihedral : 14.405 89.963 24594 Min Nonbonded Distance : 1.136 Molprobity Statistics. All-atom Clashscore : 5.37 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.17 % Favored : 96.78 % Rotamer: Outliers : 0.10 % Allowed : 4.99 % Favored : 94.90 % Cbeta Deviations : 0.01 % Peptide Plane: Cis-proline : 0.47 % Cis-general : 0.03 % Twisted Proline : 0.93 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -5.53 (0.06), residues: 8173 helix: -4.97 (0.02), residues: 3922 sheet: -1.51 (0.18), residues: 684 loop : -2.30 (0.08), residues: 3567 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP h 493 HIS 0.006 0.001 HIS q 21 PHE 0.022 0.001 PHE E 204 TYR 0.018 0.001 TYR Q 47 ARG 0.008 0.000 ARG D 206 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16346 Ramachandran restraints generated. 8173 Oldfield, 0 Emsley, 8173 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16346 Ramachandran restraints generated. 8173 Oldfield, 0 Emsley, 8173 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1633 residues out of total 6848 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 1626 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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 163 ILE cc_start: 0.5753 (mm) cc_final: 0.5411 (mm) REVERT: A 295 MET cc_start: -0.1963 (ppp) cc_final: -0.3366 (mpp) REVERT: A 459 ASP cc_start: 0.5996 (t0) cc_final: 0.5414 (p0) REVERT: B 76 VAL cc_start: 0.6102 (t) cc_final: 0.5769 (t) REVERT: B 97 ASP cc_start: 0.8276 (t70) cc_final: 0.7999 (t0) REVERT: B 131 ARG cc_start: 0.7070 (mtt180) cc_final: 0.6262 (mtp85) REVERT: B 159 LEU cc_start: 0.5105 (mt) cc_final: 0.4607 (mt) REVERT: B 182 LEU cc_start: 0.7060 (mt) cc_final: 0.6791 (mt) REVERT: B 488 MET cc_start: 0.7621 (mmp) cc_final: 0.6872 (mmt) REVERT: B 512 GLU cc_start: 0.5897 (tt0) cc_final: 0.5328 (tt0) REVERT: B 518 ASP cc_start: 0.4973 (p0) cc_final: 0.4520 (p0) REVERT: D 139 LYS cc_start: 0.8001 (mttt) cc_final: 0.7597 (ttmm) REVERT: D 192 MET cc_start: 0.6270 (ptm) cc_final: 0.5939 (ptm) REVERT: D 208 ILE cc_start: 0.4517 (tp) cc_final: 0.4090 (mm) REVERT: D 349 ASP cc_start: 0.3326 (p0) cc_final: 0.2764 (t0) REVERT: E 78 MET cc_start: 0.6042 (mmt) cc_final: 0.5473 (mmt) REVERT: E 197 MET cc_start: 0.1224 (ttt) cc_final: 0.0948 (ttt) REVERT: E 321 ARG cc_start: 0.3071 (ptt180) cc_final: 0.1967 (mtp180) REVERT: E 436 ASP cc_start: 0.4825 (m-30) cc_final: 0.4502 (t0) REVERT: E 529 ASP cc_start: 0.5170 (p0) cc_final: 0.3996 (t0) REVERT: G 46 MET cc_start: 0.8435 (mmm) cc_final: 0.8195 (mtt) REVERT: G 83 ILE cc_start: 0.7321 (tp) cc_final: 0.7070 (tp) REVERT: G 229 MET cc_start: 0.0632 (mtt) cc_final: 0.0390 (mtt) REVERT: H 39 THR cc_start: 0.8125 (p) cc_final: 0.7805 (p) REVERT: H 95 THR cc_start: 0.7918 (t) cc_final: 0.7608 (m) REVERT: H 357 ARG cc_start: 0.3384 (mmt90) cc_final: 0.3089 (ptt-90) REVERT: Q 276 MET cc_start: 0.2169 (mtm) cc_final: 0.1714 (ttp) REVERT: Q 326 LYS cc_start: 0.4863 (mmtt) cc_final: 0.4658 (tttm) REVERT: Q 461 ASN cc_start: 0.7973 (m-40) cc_final: 0.7736 (m-40) REVERT: Z 95 ASN cc_start: 0.7912 (t0) cc_final: 0.7693 (t0) REVERT: Z 131 LEU cc_start: 0.8161 (mt) cc_final: 0.7804 (tt) REVERT: Z 221 MET cc_start: 0.3940 (mmt) cc_final: 0.1471 (ptm) REVERT: Z 321 MET cc_start: 0.3775 (ttp) cc_final: 0.3197 (ttm) REVERT: b 90 VAL cc_start: 0.8091 (m) cc_final: 0.7881 (p) REVERT: b 112 GLU cc_start: 0.4813 (tp30) cc_final: 0.4603 (mm-30) REVERT: b 272 LYS cc_start: 0.2684 (mmtt) cc_final: 0.2080 (tttt) REVERT: b 353 MET cc_start: 0.4121 (mmp) cc_final: 0.3643 (mmp) REVERT: b 488 MET cc_start: 0.6909 (mmp) cc_final: 0.6618 (mmm) REVERT: d 133 ILE cc_start: 0.8517 (mt) cc_final: 0.8283 (mm) REVERT: d 260 MET cc_start: -0.1376 (mtt) cc_final: -0.2090 (mtt) REVERT: d 302 LYS cc_start: 0.3207 (tttt) cc_final: 0.2693 (mttt) REVERT: e 104 THR cc_start: 0.7898 (m) cc_final: 0.7658 (m) REVERT: e 197 MET cc_start: 0.4007 (ttm) cc_final: 0.3601 (tpt) REVERT: e 288 GLN cc_start: 0.5421 (mm110) cc_final: 0.4390 (mt0) REVERT: e 411 ILE cc_start: 0.3510 (mt) cc_final: 0.3252 (mt) REVERT: e 472 MET cc_start: 0.7288 (mmm) cc_final: 0.6925 (tpp) REVERT: g 54 MET cc_start: 0.4933 (mpp) cc_final: 0.4322 (mmt) REVERT: g 145 ASP cc_start: 0.7648 (p0) cc_final: 0.7160 (p0) REVERT: g 330 ARG cc_start: 0.2456 (ttt180) cc_final: 0.1401 (tpt170) REVERT: g 362 PHE cc_start: 0.2921 (m-80) cc_final: 0.2474 (m-80) REVERT: g 516 LEU cc_start: 0.8752 (mp) cc_final: 0.8496 (mt) REVERT: h 319 LEU cc_start: 0.5586 (mt) cc_final: 0.4994 (tp) REVERT: h 500 ILE cc_start: 0.8616 (mt) cc_final: 0.8395 (pt) REVERT: q 129 ILE cc_start: 0.8661 (tt) cc_final: 0.8403 (tp) REVERT: q 164 LEU cc_start: 0.8422 (mt) cc_final: 0.8053 (mm) REVERT: q 401 VAL cc_start: 0.6587 (p) cc_final: 0.6218 (p) REVERT: q 404 ARG cc_start: 0.2440 (mtt180) cc_final: 0.2098 (mmp80) REVERT: z 68 GLN cc_start: 0.3924 (mm-40) cc_final: 0.3701 (mm110) REVERT: z 87 ILE cc_start: 0.3929 (tp) cc_final: 0.3563 (tp) REVERT: z 101 GLU cc_start: 0.6524 (tm-30) cc_final: 0.6255 (tm-30) REVERT: z 206 LEU cc_start: 0.7842 (mt) cc_final: 0.7344 (tt) REVERT: z 295 LYS cc_start: 0.5472 (mmtt) cc_final: 0.4466 (mtmt) REVERT: a 28 ILE cc_start: 0.8843 (mm) cc_final: 0.8585 (mm) REVERT: a 36 LEU cc_start: 0.7765 (tp) cc_final: 0.7522 (tp) REVERT: a 108 VAL cc_start: 0.6226 (t) cc_final: 0.5677 (p) REVERT: a 156 MET cc_start: 0.1490 (mmt) cc_final: 0.0803 (mmp) REVERT: a 306 MET cc_start: -0.0948 (ttt) cc_final: -0.1858 (mmm) outliers start: 7 outliers final: 4 residues processed: 1632 average time/residue: 0.6297 time to fit residues: 1669.8308 Evaluate side-chains 973 residues out of total 6848 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 969 time to evaluate : 5.366 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 812 random chunks: chunk 685 optimal weight: 0.8980 chunk 615 optimal weight: 1.9990 chunk 341 optimal weight: 0.9990 chunk 210 optimal weight: 3.9990 chunk 415 optimal weight: 4.9990 chunk 328 optimal weight: 7.9990 chunk 636 optimal weight: 6.9990 chunk 246 optimal weight: 1.9990 chunk 386 optimal weight: 8.9990 chunk 473 optimal weight: 10.0000 chunk 737 optimal weight: 0.6980 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 20 GLN A 103 ASN A 193 ASN A 223 GLN ** A 262 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 475 GLN ** B 175 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 228 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 234 ASN D 37 ASN D 80 GLN ** D 165 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 96 GLN E 189 ASN E 234 HIS E 310 HIS ** E 513 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 111 HIS G 226 HIS G 276 GLN H 17 GLN H 21 GLN H 25 ASN H 264 GLN ** H 380 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 402 ASN H 431 GLN H 459 ASN Q 34 GLN Q 41 GLN Q 50 ASN Q 53 ASN Q 153 ASN Q 175 ASN Z 161 HIS Z 182 GLN ** Z 198 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Z 382 HIS b 285 HIS b 288 ASN d 62 GLN d 129 HIS d 262 ASN ** d 289 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 406 HIS e 20 GLN ** e 262 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** e 288 GLN e 315 ASN ** e 520 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 226 HIS g 235 ASN h 151 GLN h 448 GLN ** h 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** q 93 GLN ** q 279 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** q 346 HIS z 245 ASN z 497 ASN a 20 GLN a 242 GLN ** a 262 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 482 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 50 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5503 moved from start: 0.2789 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 63926 Z= 0.174 Angle : 0.559 10.218 86360 Z= 0.291 Chirality : 0.042 0.209 10322 Planarity : 0.005 0.100 10999 Dihedral : 7.304 88.844 9257 Min Nonbonded Distance : 1.976 Molprobity Statistics. All-atom Clashscore : 9.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 0.15 % Allowed : 4.88 % Favored : 94.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.47 % Cis-general : 0.03 % 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: -3.63 (0.07), residues: 8173 helix: -3.01 (0.06), residues: 3929 sheet: -1.02 (0.19), residues: 715 loop : -1.77 (0.09), residues: 3529 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP Z 495 HIS 0.011 0.001 HIS E 35 PHE 0.013 0.001 PHE h 303 TYR 0.021 0.001 TYR Q 30 ARG 0.009 0.001 ARG z 157 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16346 Ramachandran restraints generated. 8173 Oldfield, 0 Emsley, 8173 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16346 Ramachandran restraints generated. 8173 Oldfield, 0 Emsley, 8173 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1263 residues out of total 6848 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 1253 time to evaluate : 5.389 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: A 30 ASN cc_start: 0.7894 (m-40) cc_final: 0.7625 (t0) REVERT: A 156 MET cc_start: 0.3604 (mmp) cc_final: 0.3350 (mmt) REVERT: A 163 ILE cc_start: 0.5751 (mm) cc_final: 0.5466 (mm) REVERT: A 171 MET cc_start: 0.3813 (mmt) cc_final: 0.3493 (mmt) REVERT: A 275 ILE cc_start: 0.4582 (pt) cc_final: 0.4330 (pt) REVERT: A 295 MET cc_start: -0.1599 (ppp) cc_final: -0.2966 (mpp) REVERT: A 459 ASP cc_start: 0.6226 (t0) cc_final: 0.5581 (p0) REVERT: A 485 TRP cc_start: 0.4262 (m-10) cc_final: 0.3700 (m-10) REVERT: B 131 ARG cc_start: 0.7235 (mtt180) cc_final: 0.6877 (ptp-110) REVERT: B 159 LEU cc_start: 0.5285 (mt) cc_final: 0.4718 (mt) REVERT: B 512 GLU cc_start: 0.5937 (tt0) cc_final: 0.5355 (tt0) REVERT: D 58 ASP cc_start: 0.5808 (t0) cc_final: 0.5566 (t0) REVERT: D 95 SER cc_start: 0.8105 (t) cc_final: 0.7894 (t) REVERT: D 161 GLU cc_start: 0.6228 (mm-30) cc_final: 0.4294 (tm-30) REVERT: E 35 HIS cc_start: 0.6949 (m-70) cc_final: 0.6746 (m-70) REVERT: E 78 MET cc_start: 0.6330 (mmt) cc_final: 0.5825 (mmt) REVERT: E 183 MET cc_start: 0.4707 (mtm) cc_final: 0.4352 (mtm) REVERT: E 197 MET cc_start: 0.2147 (ttt) cc_final: 0.1710 (ttt) REVERT: E 321 ARG cc_start: 0.3470 (ptt180) cc_final: 0.2073 (mtp180) REVERT: E 436 ASP cc_start: 0.6010 (m-30) cc_final: 0.4836 (t0) REVERT: E 529 ASP cc_start: 0.5002 (p0) cc_final: 0.3848 (t0) REVERT: G 35 ASP cc_start: 0.7589 (m-30) cc_final: 0.7109 (m-30) REVERT: G 432 VAL cc_start: 0.8218 (t) cc_final: 0.7921 (t) REVERT: H 46 ASP cc_start: 0.7277 (m-30) cc_final: 0.6865 (m-30) REVERT: H 218 LYS cc_start: 0.4950 (tttt) cc_final: 0.4424 (tppt) REVERT: H 357 ARG cc_start: 0.3800 (mmt90) cc_final: 0.3128 (ptp90) REVERT: H 382 MET cc_start: 0.3741 (ttm) cc_final: 0.3327 (ttm) REVERT: H 524 ARG cc_start: 0.5444 (mmt-90) cc_final: 0.5043 (tpt170) REVERT: Q 50 ASN cc_start: 0.7335 (m110) cc_final: 0.7076 (m-40) REVERT: Q 276 MET cc_start: 0.2307 (mtm) cc_final: 0.2042 (mtm) REVERT: Q 326 LYS cc_start: 0.5179 (mmtt) cc_final: 0.4815 (tttm) REVERT: Z 131 LEU cc_start: 0.8038 (mt) cc_final: 0.7787 (tt) REVERT: Z 221 MET cc_start: 0.4413 (mmt) cc_final: 0.1470 (ptm) REVERT: b 82 LYS cc_start: 0.7377 (tppt) cc_final: 0.7169 (ttpt) REVERT: b 112 GLU cc_start: 0.5283 (tp30) cc_final: 0.5068 (mm-30) REVERT: b 141 LEU cc_start: 0.7180 (mp) cc_final: 0.6954 (mp) REVERT: b 310 MET cc_start: 0.2090 (mtp) cc_final: 0.1815 (mtp) REVERT: b 353 MET cc_start: 0.4157 (mmp) cc_final: 0.3676 (mmp) REVERT: b 388 ARG cc_start: 0.3555 (tpt90) cc_final: 0.3245 (tpt-90) REVERT: b 488 MET cc_start: 0.6838 (mmp) cc_final: 0.6578 (mmm) REVERT: d 80 GLN cc_start: 0.7466 (mm-40) cc_final: 0.7075 (mt0) REVERT: d 260 MET cc_start: -0.1204 (mtt) cc_final: -0.1895 (mtt) REVERT: e 79 MET cc_start: 0.6388 (mtp) cc_final: 0.6040 (mtp) REVERT: e 197 MET cc_start: 0.4063 (ttm) cc_final: 0.3614 (tpt) REVERT: g 145 ASP cc_start: 0.7339 (p0) cc_final: 0.6719 (p0) REVERT: g 175 ILE cc_start: 0.4354 (tt) cc_final: 0.3907 (tt) REVERT: g 270 MET cc_start: 0.3146 (ppp) cc_final: 0.2796 (ppp) REVERT: g 322 ARG cc_start: 0.6531 (mtm180) cc_final: 0.6226 (mtm180) REVERT: g 330 ARG cc_start: 0.3161 (ttt180) cc_final: 0.1690 (tpt170) REVERT: g 362 PHE cc_start: 0.3762 (m-80) cc_final: 0.2859 (m-80) REVERT: g 429 MET cc_start: 0.5985 (ttp) cc_final: 0.5740 (ttp) REVERT: g 516 LEU cc_start: 0.8694 (mp) cc_final: 0.8483 (mt) REVERT: h 160 MET cc_start: 0.5398 (ptt) cc_final: 0.4980 (ptt) REVERT: h 167 LEU cc_start: 0.2738 (tp) cc_final: 0.2320 (tp) REVERT: h 319 LEU cc_start: 0.5556 (mt) cc_final: 0.5051 (tp) REVERT: h 413 GLU cc_start: 0.8391 (mm-30) cc_final: 0.8020 (mm-30) REVERT: h 494 GLU cc_start: 0.6389 (tt0) cc_final: 0.5452 (tt0) REVERT: q 16 LYS cc_start: 0.5915 (mttt) cc_final: 0.5576 (mttt) REVERT: q 92 MET cc_start: 0.6862 (mmm) cc_final: 0.6591 (mmm) REVERT: q 129 ILE cc_start: 0.8532 (tt) cc_final: 0.8097 (tp) REVERT: q 223 PHE cc_start: 0.3916 (m-80) cc_final: 0.3593 (m-10) REVERT: q 401 VAL cc_start: 0.6931 (p) cc_final: 0.6668 (p) REVERT: q 404 ARG cc_start: 0.3108 (mtt180) cc_final: 0.2345 (mmp80) REVERT: q 492 MET cc_start: 0.7218 (tpp) cc_final: 0.6996 (tpp) REVERT: z 63 LEU cc_start: 0.7348 (mt) cc_final: 0.7128 (mt) REVERT: z 143 MET cc_start: 0.3180 (ppp) cc_final: 0.2355 (ppp) REVERT: z 206 LEU cc_start: 0.7637 (mt) cc_final: 0.7273 (tt) REVERT: z 295 LYS cc_start: 0.5707 (mmtt) cc_final: 0.4579 (mtmt) REVERT: z 487 MET cc_start: 0.6358 (ptm) cc_final: 0.5463 (ppp) REVERT: a 28 ILE cc_start: 0.9020 (mm) cc_final: 0.8750 (mm) REVERT: a 68 GLU cc_start: 0.6223 (mm-30) cc_final: 0.5876 (mp0) REVERT: a 103 ASN cc_start: 0.6043 (m-40) cc_final: 0.4794 (m-40) REVERT: a 171 MET cc_start: 0.2478 (mmp) cc_final: 0.1174 (tpp) REVERT: a 306 MET cc_start: -0.1334 (ttt) cc_final: -0.2447 (mmm) REVERT: a 394 ASP cc_start: 0.5232 (t0) cc_final: 0.3638 (p0) REVERT: a 528 ASP cc_start: 0.6264 (m-30) cc_final: 0.5316 (m-30) REVERT: a 530 LEU cc_start: 0.7818 (tp) cc_final: 0.7506 (tt) outliers start: 10 outliers final: 1 residues processed: 1260 average time/residue: 0.5786 time to fit residues: 1234.2698 Evaluate side-chains 899 residues out of total 6848 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 898 time to evaluate : 5.381 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 812 random chunks: chunk 409 optimal weight: 0.8980 chunk 228 optimal weight: 0.7980 chunk 613 optimal weight: 0.9980 chunk 502 optimal weight: 8.9990 chunk 203 optimal weight: 6.9990 chunk 738 optimal weight: 9.9990 chunk 798 optimal weight: 2.9990 chunk 657 optimal weight: 20.0000 chunk 732 optimal weight: 3.9990 chunk 251 optimal weight: 8.9990 chunk 592 optimal weight: 0.9980 overall best weight: 1.3382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 458 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 482 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 175 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 165 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 127 HIS E 409 ASN E 443 GLN E 470 GLN ** E 513 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 64 ASN G 111 HIS G 116 GLN H 17 GLN ** H 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 209 GLN Q 53 ASN d 37 ASN d 129 HIS d 366 ASN d 406 HIS e 35 HIS ** e 262 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** e 497 ASN ** e 520 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 87 GLN h 151 GLN ** h 380 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 462 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** q 140 HIS ** q 279 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** q 346 HIS z 68 GLN z 105 GLN Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5576 moved from start: 0.3454 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.046 63926 Z= 0.163 Angle : 0.523 9.829 86360 Z= 0.269 Chirality : 0.042 0.266 10322 Planarity : 0.004 0.125 10999 Dihedral : 7.059 88.779 9257 Min Nonbonded Distance : 1.967 Molprobity Statistics. All-atom Clashscore : 10.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.07 % Favored : 96.93 % Rotamer: Outliers : 0.09 % Allowed : 3.43 % Favored : 96.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.47 % Cis-general : 0.03 % 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: -2.33 (0.08), residues: 8173 helix: -1.63 (0.07), residues: 3905 sheet: -0.93 (0.19), residues: 720 loop : -1.41 (0.09), residues: 3548 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP h 493 HIS 0.008 0.001 HIS E 35 PHE 0.017 0.001 PHE Z 362 TYR 0.019 0.001 TYR a 422 ARG 0.040 0.000 ARG Z 157 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16346 Ramachandran restraints generated. 8173 Oldfield, 0 Emsley, 8173 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16346 Ramachandran restraints generated. 8173 Oldfield, 0 Emsley, 8173 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1140 residues out of total 6848 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 1134 time to evaluate : 5.469 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 30 ASN cc_start: 0.7951 (m-40) cc_final: 0.7744 (t0) REVERT: A 161 ILE cc_start: 0.4023 (tt) cc_final: 0.3081 (tt) REVERT: A 163 ILE cc_start: 0.5793 (mm) cc_final: 0.5514 (mm) REVERT: A 171 MET cc_start: 0.3883 (mmt) cc_final: 0.3625 (mmt) REVERT: A 274 ARG cc_start: 0.3489 (mtm180) cc_final: 0.2765 (mmm160) REVERT: A 388 MET cc_start: 0.2019 (mmp) cc_final: 0.0781 (tpp) REVERT: A 390 ARG cc_start: 0.4601 (ptm-80) cc_final: 0.2976 (mmm-85) REVERT: A 421 ILE cc_start: 0.7295 (mm) cc_final: 0.7022 (mm) REVERT: A 485 TRP cc_start: 0.4445 (m-10) cc_final: 0.3950 (m-10) REVERT: B 131 ARG cc_start: 0.7378 (mtt180) cc_final: 0.7007 (ptp-110) REVERT: B 159 LEU cc_start: 0.6050 (mt) cc_final: 0.5539 (mt) REVERT: B 415 MET cc_start: 0.8538 (mmm) cc_final: 0.8334 (tpp) REVERT: B 488 MET cc_start: 0.6525 (mmm) cc_final: 0.6222 (mmt) REVERT: B 512 GLU cc_start: 0.6559 (tt0) cc_final: 0.5896 (tt0) REVERT: B 520 ILE cc_start: 0.7357 (mm) cc_final: 0.7013 (mm) REVERT: D 95 SER cc_start: 0.8362 (t) cc_final: 0.8141 (t) REVERT: D 161 GLU cc_start: 0.6217 (mm-30) cc_final: 0.4322 (tm-30) REVERT: E 78 MET cc_start: 0.6525 (mmt) cc_final: 0.5968 (mmt) REVERT: E 197 MET cc_start: 0.1773 (ttt) cc_final: -0.0092 (mmp) REVERT: E 286 MET cc_start: 0.2972 (mmm) cc_final: 0.2756 (mmp) REVERT: E 321 ARG cc_start: 0.3429 (ptt180) cc_final: 0.2267 (mtp180) REVERT: E 391 MET cc_start: 0.3996 (ptp) cc_final: 0.3743 (ptp) REVERT: E 436 ASP cc_start: 0.6367 (m-30) cc_final: 0.4868 (t0) REVERT: E 529 ASP cc_start: 0.5185 (p0) cc_final: 0.3857 (t0) REVERT: E 530 ASP cc_start: 0.5601 (t0) cc_final: 0.5248 (t0) REVERT: G 35 ASP cc_start: 0.7718 (m-30) cc_final: 0.7493 (m-30) REVERT: G 152 MET cc_start: 0.6631 (mmm) cc_final: 0.6240 (tpt) REVERT: G 229 MET cc_start: -0.0013 (mtt) cc_final: -0.0305 (mtp) REVERT: G 286 LYS cc_start: 0.3548 (mttt) cc_final: 0.2846 (ptpp) REVERT: H 178 MET cc_start: 0.2708 (tpp) cc_final: 0.0961 (tpp) REVERT: H 357 ARG cc_start: 0.3981 (mmt90) cc_final: 0.3160 (ptp90) REVERT: H 524 ARG cc_start: 0.5616 (mmt-90) cc_final: 0.5106 (tpt170) REVERT: Z 63 LEU cc_start: 0.7202 (mt) cc_final: 0.6933 (mt) REVERT: Z 131 LEU cc_start: 0.7969 (mt) cc_final: 0.7641 (tt) REVERT: Z 221 MET cc_start: 0.4561 (mmt) cc_final: 0.1286 (ptm) REVERT: b 310 MET cc_start: 0.2222 (mtp) cc_final: 0.1891 (mtp) REVERT: b 353 MET cc_start: 0.4160 (mmp) cc_final: 0.3786 (mmp) REVERT: d 355 MET cc_start: 0.3667 (tmm) cc_final: 0.3385 (ppp) REVERT: e 79 MET cc_start: 0.6122 (mtp) cc_final: 0.5803 (mtp) REVERT: e 197 MET cc_start: 0.4141 (ttm) cc_final: 0.3729 (tpt) REVERT: e 391 MET cc_start: 0.5090 (ptp) cc_final: 0.3992 (ptp) REVERT: e 517 LEU cc_start: 0.8690 (tp) cc_final: 0.8246 (tp) REVERT: g 54 MET cc_start: 0.5376 (mpp) cc_final: 0.4086 (mpp) REVERT: g 330 ARG cc_start: 0.2803 (ttt180) cc_final: 0.1371 (tpt170) REVERT: g 362 PHE cc_start: 0.3868 (m-80) cc_final: 0.3121 (m-80) REVERT: g 389 ARG cc_start: 0.7402 (mtm-85) cc_final: 0.6471 (mmm160) REVERT: h 405 VAL cc_start: 0.8515 (p) cc_final: 0.8242 (t) REVERT: h 479 ILE cc_start: 0.8331 (pt) cc_final: 0.8096 (pt) REVERT: h 482 GLU cc_start: 0.7421 (mp0) cc_final: 0.6605 (tm-30) REVERT: h 518 GLU cc_start: 0.6010 (tm-30) cc_final: 0.5259 (tm-30) REVERT: q 16 LYS cc_start: 0.5967 (mttt) cc_final: 0.5582 (mttt) REVERT: q 73 LEU cc_start: 0.8030 (mt) cc_final: 0.7827 (mt) REVERT: q 129 ILE cc_start: 0.8556 (tt) cc_final: 0.8229 (tp) REVERT: q 179 LEU cc_start: 0.7507 (mt) cc_final: 0.7293 (mt) REVERT: q 300 MET cc_start: 0.4441 (ttm) cc_final: 0.4222 (ttm) REVERT: q 401 VAL cc_start: 0.6959 (p) cc_final: 0.6755 (p) REVERT: q 404 ARG cc_start: 0.2797 (mtt180) cc_final: 0.2147 (mmp80) REVERT: z 63 LEU cc_start: 0.7289 (mt) cc_final: 0.7035 (mt) REVERT: z 206 LEU cc_start: 0.7784 (mt) cc_final: 0.7360 (tt) REVERT: z 295 LYS cc_start: 0.5595 (mmtt) cc_final: 0.4445 (mtmt) REVERT: z 459 LEU cc_start: 0.7275 (tt) cc_final: 0.6998 (tt) REVERT: z 495 TRP cc_start: 0.7052 (m100) cc_final: 0.6839 (m100) REVERT: a 103 ASN cc_start: 0.5737 (m-40) cc_final: 0.5103 (m-40) REVERT: a 156 MET cc_start: 0.0210 (mmm) cc_final: -0.0042 (mmp) REVERT: a 171 MET cc_start: 0.2460 (mmp) cc_final: 0.1176 (tpp) REVERT: a 306 MET cc_start: -0.1537 (ttt) cc_final: -0.2633 (mmm) REVERT: a 510 LYS cc_start: 0.7900 (tppt) cc_final: 0.7659 (mmmm) outliers start: 6 outliers final: 0 residues processed: 1138 average time/residue: 0.5920 time to fit residues: 1141.0628 Evaluate side-chains 846 residues out of total 6848 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 846 time to evaluate : 5.418 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 812 random chunks: chunk 729 optimal weight: 5.9990 chunk 555 optimal weight: 0.0000 chunk 383 optimal weight: 6.9990 chunk 81 optimal weight: 8.9990 chunk 352 optimal weight: 8.9990 chunk 496 optimal weight: 0.9990 chunk 741 optimal weight: 7.9990 chunk 784 optimal weight: 0.1980 chunk 387 optimal weight: 0.9990 chunk 702 optimal weight: 9.9990 chunk 211 optimal weight: 9.9990 overall best weight: 1.6390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 458 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 482 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 148 HIS ** B 175 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 165 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 406 HIS ** D 468 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 127 HIS E 236 GLN E 409 ASN ** E 513 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 308 ASN G 526 HIS H 17 GLN ** H 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 228 GLN ** H 380 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 359 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 460 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 80 GLN d 129 HIS ** d 482 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 262 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 520 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** h 462 ASN ** h 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 279 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** q 346 HIS z 497 ASN a 82 GLN a 103 ASN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5662 moved from start: 0.4004 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.076 63926 Z= 0.181 Angle : 0.536 10.204 86360 Z= 0.275 Chirality : 0.043 0.447 10322 Planarity : 0.004 0.098 10999 Dihedral : 7.187 89.351 9257 Min Nonbonded Distance : 1.955 Molprobity Statistics. All-atom Clashscore : 11.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % Rotamer: Outliers : 0.03 % Allowed : 3.50 % Favored : 96.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.47 % Cis-general : 0.03 % 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: -1.75 (0.09), residues: 8173 helix: -0.97 (0.08), residues: 3936 sheet: -0.90 (0.19), residues: 710 loop : -1.28 (0.10), residues: 3527 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP G 496 HIS 0.014 0.001 HIS E 35 PHE 0.017 0.001 PHE E 449 TYR 0.018 0.001 TYR a 422 ARG 0.036 0.001 ARG Z 157 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16346 Ramachandran restraints generated. 8173 Oldfield, 0 Emsley, 8173 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16346 Ramachandran restraints generated. 8173 Oldfield, 0 Emsley, 8173 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1089 residues out of total 6848 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 1087 time to evaluate : 5.407 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: A 275 ILE cc_start: 0.4808 (pt) cc_final: 0.4525 (pt) REVERT: A 388 MET cc_start: 0.2273 (mmp) cc_final: 0.1460 (tpp) REVERT: A 390 ARG cc_start: 0.4404 (ptm-80) cc_final: 0.3151 (mmm-85) REVERT: A 485 TRP cc_start: 0.4504 (m-10) cc_final: 0.4040 (m-10) REVERT: A 504 PHE cc_start: 0.7585 (m-80) cc_final: 0.7348 (m-10) REVERT: A 530 LEU cc_start: 0.7518 (tp) cc_final: 0.7028 (tp) REVERT: B 50 LYS cc_start: 0.6438 (mtmt) cc_final: 0.6124 (mtmt) REVERT: B 131 ARG cc_start: 0.7389 (mtt180) cc_final: 0.7013 (ptp-110) REVERT: B 159 LEU cc_start: 0.6359 (mt) cc_final: 0.5844 (mt) REVERT: B 436 MET cc_start: 0.6700 (mmm) cc_final: 0.6325 (mmt) REVERT: B 512 GLU cc_start: 0.6806 (tt0) cc_final: 0.6087 (tt0) REVERT: B 520 ILE cc_start: 0.7249 (mm) cc_final: 0.7007 (mm) REVERT: D 95 SER cc_start: 0.8274 (t) cc_final: 0.8035 (t) REVERT: D 161 GLU cc_start: 0.6473 (mm-30) cc_final: 0.4587 (tm-30) REVERT: D 384 LYS cc_start: 0.6361 (mttt) cc_final: 0.6107 (mttm) REVERT: E 78 MET cc_start: 0.6554 (mmt) cc_final: 0.6064 (mmt) REVERT: E 197 MET cc_start: 0.0758 (ttt) cc_final: -0.0414 (ptm) REVERT: E 321 ARG cc_start: 0.3686 (ptt180) cc_final: 0.2277 (mtp180) REVERT: E 436 ASP cc_start: 0.6342 (m-30) cc_final: 0.4808 (t0) REVERT: E 529 ASP cc_start: 0.5671 (p0) cc_final: 0.4106 (t0) REVERT: E 530 ASP cc_start: 0.5474 (t0) cc_final: 0.4297 (t0) REVERT: G 152 MET cc_start: 0.6737 (mmm) cc_final: 0.6137 (mmt) REVERT: G 286 LYS cc_start: 0.3456 (mttt) cc_final: 0.2649 (ptpp) REVERT: G 432 VAL cc_start: 0.8300 (t) cc_final: 0.7981 (t) REVERT: H 357 ARG cc_start: 0.4053 (mmt90) cc_final: 0.2932 (ptp90) REVERT: H 498 VAL cc_start: 0.8026 (t) cc_final: 0.7520 (t) REVERT: H 524 ARG cc_start: 0.5743 (mmt-90) cc_final: 0.5221 (tpt170) REVERT: Q 123 LEU cc_start: 0.8782 (tp) cc_final: 0.8380 (mt) REVERT: Z 63 LEU cc_start: 0.7408 (mt) cc_final: 0.7137 (mt) REVERT: Z 131 LEU cc_start: 0.7907 (mt) cc_final: 0.7634 (tt) REVERT: Z 143 MET cc_start: 0.5714 (mpp) cc_final: 0.5128 (mpp) REVERT: Z 221 MET cc_start: 0.4476 (mmt) cc_final: 0.1033 (ptm) REVERT: b 310 MET cc_start: 0.0510 (mtp) cc_final: 0.0121 (mtp) REVERT: b 353 MET cc_start: 0.4251 (mmp) cc_final: 0.3859 (mmp) REVERT: b 415 MET cc_start: 0.6014 (mmm) cc_final: 0.5788 (mmm) REVERT: b 480 MET cc_start: 0.6089 (ppp) cc_final: 0.5681 (ppp) REVERT: d 151 MET cc_start: 0.7263 (tmm) cc_final: 0.6999 (tmm) REVERT: d 355 MET cc_start: 0.3738 (tmm) cc_final: 0.3479 (ppp) REVERT: e 79 MET cc_start: 0.6201 (mtp) cc_final: 0.5951 (mtp) REVERT: e 197 MET cc_start: 0.4461 (ttm) cc_final: 0.3989 (tpt) REVERT: e 391 MET cc_start: 0.4998 (ptp) cc_final: 0.3698 (ptp) REVERT: e 517 LEU cc_start: 0.8836 (tp) cc_final: 0.8321 (tp) REVERT: g 54 MET cc_start: 0.5795 (mpp) cc_final: 0.5394 (mpp) REVERT: g 131 ASP cc_start: 0.7931 (p0) cc_final: 0.7399 (p0) REVERT: g 133 MET cc_start: 0.7215 (mtm) cc_final: 0.6981 (mtm) REVERT: g 145 ASP cc_start: 0.7700 (p0) cc_final: 0.7207 (p0) REVERT: g 182 MET cc_start: 0.3577 (ttm) cc_final: 0.3349 (ttp) REVERT: g 229 MET cc_start: 0.2356 (mtt) cc_final: 0.1956 (ptp) REVERT: g 330 ARG cc_start: 0.3015 (ttt180) cc_final: 0.1321 (tpt170) REVERT: g 362 PHE cc_start: 0.4099 (m-80) cc_final: 0.3394 (m-80) REVERT: g 389 ARG cc_start: 0.6999 (mpt-90) cc_final: 0.6767 (mmm160) REVERT: g 512 THR cc_start: 0.8360 (t) cc_final: 0.8159 (m) REVERT: h 405 VAL cc_start: 0.8603 (p) cc_final: 0.8270 (t) REVERT: h 479 ILE cc_start: 0.8327 (pt) cc_final: 0.8122 (pt) REVERT: q 16 LYS cc_start: 0.5810 (mttt) cc_final: 0.5490 (mttt) REVERT: q 129 ILE cc_start: 0.8593 (tt) cc_final: 0.8297 (tp) REVERT: q 300 MET cc_start: 0.4440 (ttm) cc_final: 0.4110 (ttm) REVERT: q 401 VAL cc_start: 0.7160 (p) cc_final: 0.6835 (p) REVERT: q 404 ARG cc_start: 0.3184 (mtt180) cc_final: 0.2317 (mmp80) REVERT: z 128 GLU cc_start: 0.6349 (pp20) cc_final: 0.6145 (pt0) REVERT: z 143 MET cc_start: 0.2843 (ppp) cc_final: 0.2044 (ppp) REVERT: z 167 VAL cc_start: 0.6521 (p) cc_final: 0.6308 (p) REVERT: z 206 LEU cc_start: 0.7771 (mt) cc_final: 0.7220 (tt) REVERT: z 295 LYS cc_start: 0.5682 (mmtt) cc_final: 0.4485 (mtmt) REVERT: z 449 LYS cc_start: 0.7862 (mttp) cc_final: 0.6650 (mttm) REVERT: z 495 TRP cc_start: 0.7168 (m100) cc_final: 0.6896 (m100) REVERT: a 103 ASN cc_start: 0.5964 (m110) cc_final: 0.5328 (m110) REVERT: a 127 GLU cc_start: 0.7106 (tp30) cc_final: 0.6747 (tp30) REVERT: a 171 MET cc_start: 0.2395 (mmp) cc_final: 0.0891 (tpp) REVERT: a 306 MET cc_start: -0.1103 (ttt) cc_final: -0.2382 (mmm) outliers start: 2 outliers final: 1 residues processed: 1088 average time/residue: 0.5745 time to fit residues: 1059.1041 Evaluate side-chains 832 residues out of total 6848 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 831 time to evaluate : 5.473 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 812 random chunks: chunk 653 optimal weight: 0.7980 chunk 445 optimal weight: 0.9990 chunk 11 optimal weight: 0.9990 chunk 584 optimal weight: 2.9990 chunk 323 optimal weight: 6.9990 chunk 669 optimal weight: 0.9980 chunk 542 optimal weight: 0.0970 chunk 0 optimal weight: 30.0000 chunk 400 optimal weight: 4.9990 chunk 704 optimal weight: 0.0670 chunk 198 optimal weight: 0.0010 overall best weight: 0.3922 ------------------------------------------------------------------------------- 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 175 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 337 HIS ** D 165 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 468 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 470 GLN E 513 GLN G 526 HIS H 17 GLN ** H 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 380 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 480 ASN Q 346 HIS ** Q 359 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 460 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 129 HIS ** e 262 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** e 497 ASN ** e 520 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 264 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** q 91 HIS q 140 HIS ** q 279 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** q 346 HIS ** z 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5580 moved from start: 0.4172 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 63926 Z= 0.131 Angle : 0.493 10.194 86360 Z= 0.251 Chirality : 0.042 0.227 10322 Planarity : 0.003 0.109 10999 Dihedral : 6.979 89.498 9257 Min Nonbonded Distance : 1.973 Molprobity Statistics. All-atom Clashscore : 9.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 0.03 % Allowed : 1.69 % Favored : 98.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.47 % Cis-general : 0.03 % 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: -1.28 (0.09), residues: 8173 helix: -0.50 (0.08), residues: 3921 sheet: -0.74 (0.19), residues: 769 loop : -1.14 (0.10), residues: 3483 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP Q 319 HIS 0.005 0.000 HIS E 35 PHE 0.023 0.001 PHE A 167 TYR 0.018 0.001 TYR A 426 ARG 0.037 0.000 ARG Z 157 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16346 Ramachandran restraints generated. 8173 Oldfield, 0 Emsley, 8173 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16346 Ramachandran restraints generated. 8173 Oldfield, 0 Emsley, 8173 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1084 residues out of total 6848 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 1082 time to evaluate : 5.506 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 275 ILE cc_start: 0.4569 (pt) cc_final: 0.4319 (pt) REVERT: A 388 MET cc_start: 0.2434 (mmp) cc_final: 0.1733 (tpp) REVERT: A 390 ARG cc_start: 0.4418 (ptm-80) cc_final: 0.3132 (mmm-85) REVERT: A 485 TRP cc_start: 0.4412 (m-10) cc_final: 0.4053 (m-10) REVERT: A 530 LEU cc_start: 0.7531 (tp) cc_final: 0.7007 (tp) REVERT: B 50 LYS cc_start: 0.6317 (mtmt) cc_final: 0.6035 (mtmt) REVERT: B 131 ARG cc_start: 0.7436 (mtt180) cc_final: 0.7086 (ptp-110) REVERT: B 159 LEU cc_start: 0.6375 (mt) cc_final: 0.6013 (mt) REVERT: B 473 ASN cc_start: 0.8527 (m-40) cc_final: 0.8311 (t0) REVERT: B 488 MET cc_start: 0.6767 (mmm) cc_final: 0.6298 (mmt) REVERT: B 512 GLU cc_start: 0.6708 (tt0) cc_final: 0.6045 (tt0) REVERT: B 520 ILE cc_start: 0.7186 (mm) cc_final: 0.6984 (mm) REVERT: D 161 GLU cc_start: 0.6582 (mm-30) cc_final: 0.4629 (tm-30) REVERT: D 384 LYS cc_start: 0.6513 (mttt) cc_final: 0.6242 (mttm) REVERT: E 78 MET cc_start: 0.6526 (mmt) cc_final: 0.5925 (mmt) REVERT: E 197 MET cc_start: 0.0691 (ttt) cc_final: -0.0436 (ptm) REVERT: E 286 MET cc_start: 0.3248 (mmm) cc_final: 0.2860 (mmp) REVERT: E 321 ARG cc_start: 0.3451 (ptt180) cc_final: 0.2363 (mtp180) REVERT: E 436 ASP cc_start: 0.6166 (m-30) cc_final: 0.4999 (t0) REVERT: E 529 ASP cc_start: 0.5272 (p0) cc_final: 0.3895 (t0) REVERT: G 49 MET cc_start: 0.6797 (mmm) cc_final: 0.6576 (mmm) REVERT: G 152 MET cc_start: 0.6787 (mmm) cc_final: 0.6212 (mmt) REVERT: G 229 MET cc_start: 0.0491 (mtt) cc_final: 0.0237 (mtp) REVERT: G 286 LYS cc_start: 0.3253 (mttt) cc_final: 0.2485 (ptpp) REVERT: H 227 MET cc_start: 0.2532 (tpt) cc_final: 0.0487 (mtt) REVERT: H 357 ARG cc_start: 0.4037 (mmt90) cc_final: 0.2917 (ptp90) REVERT: H 501 ASN cc_start: 0.8265 (m-40) cc_final: 0.7925 (m-40) REVERT: H 524 ARG cc_start: 0.5666 (mmt-90) cc_final: 0.5143 (tpt170) REVERT: Z 143 MET cc_start: 0.5458 (mpp) cc_final: 0.4934 (mpp) REVERT: Z 221 MET cc_start: 0.4690 (mmt) cc_final: 0.1345 (ptm) REVERT: b 62 MET cc_start: 0.4222 (ppp) cc_final: 0.3855 (ppp) REVERT: b 114 GLU cc_start: 0.6053 (pp20) cc_final: 0.5691 (pp20) REVERT: b 141 LEU cc_start: 0.7139 (mp) cc_final: 0.6736 (mp) REVERT: b 310 MET cc_start: 0.0492 (mtp) cc_final: 0.0117 (mtp) REVERT: b 353 MET cc_start: 0.4127 (mmp) cc_final: 0.3807 (mmm) REVERT: b 480 MET cc_start: 0.6453 (ppp) cc_final: 0.6153 (tmm) REVERT: d 131 THR cc_start: 0.7390 (t) cc_final: 0.7177 (t) REVERT: d 134 SER cc_start: 0.8019 (t) cc_final: 0.7724 (t) REVERT: d 151 MET cc_start: 0.7300 (tmm) cc_final: 0.7092 (tmm) REVERT: d 194 VAL cc_start: 0.3481 (t) cc_final: 0.3252 (t) REVERT: d 355 MET cc_start: 0.3751 (tmm) cc_final: 0.3467 (ppp) REVERT: e 79 MET cc_start: 0.6159 (mtp) cc_final: 0.5851 (mtp) REVERT: e 197 MET cc_start: 0.4441 (ttm) cc_final: 0.3976 (tpt) REVERT: e 283 PHE cc_start: -0.1199 (m-80) cc_final: -0.1810 (m-80) REVERT: e 446 MET cc_start: 0.8190 (mmm) cc_final: 0.7769 (tpp) REVERT: e 517 LEU cc_start: 0.8887 (tp) cc_final: 0.8395 (tp) REVERT: g 131 ASP cc_start: 0.7970 (p0) cc_final: 0.7385 (p0) REVERT: g 145 ASP cc_start: 0.7431 (p0) cc_final: 0.6921 (p0) REVERT: g 156 ILE cc_start: 0.6447 (mt) cc_final: 0.6235 (mt) REVERT: g 182 MET cc_start: 0.3459 (ttm) cc_final: 0.2838 (ttp) REVERT: g 362 PHE cc_start: 0.3718 (m-80) cc_final: 0.3024 (m-80) REVERT: g 490 MET cc_start: 0.7550 (tpp) cc_final: 0.7165 (tpp) REVERT: h 178 MET cc_start: 0.6138 (ptm) cc_final: 0.5751 (ptm) REVERT: h 405 VAL cc_start: 0.8642 (p) cc_final: 0.8241 (t) REVERT: h 445 ILE cc_start: 0.8323 (mm) cc_final: 0.8082 (mm) REVERT: h 487 ASN cc_start: 0.7776 (m-40) cc_final: 0.7491 (m110) REVERT: q 111 LEU cc_start: 0.7804 (mt) cc_final: 0.7576 (mt) REVERT: q 129 ILE cc_start: 0.8600 (tt) cc_final: 0.8209 (tp) REVERT: q 134 ILE cc_start: 0.7648 (mt) cc_final: 0.7423 (mt) REVERT: q 401 VAL cc_start: 0.6863 (p) cc_final: 0.6593 (p) REVERT: q 404 ARG cc_start: 0.2775 (mtt180) cc_final: 0.2001 (mmp80) REVERT: z 63 LEU cc_start: 0.7110 (mt) cc_final: 0.6881 (mt) REVERT: z 167 VAL cc_start: 0.6605 (p) cc_final: 0.6383 (p) REVERT: z 206 LEU cc_start: 0.7810 (mt) cc_final: 0.7273 (tt) REVERT: z 295 LYS cc_start: 0.5629 (mmtt) cc_final: 0.4278 (mtmt) REVERT: z 449 LYS cc_start: 0.7795 (mttp) cc_final: 0.6541 (mttm) REVERT: a 102 LYS cc_start: 0.7504 (tmtt) cc_final: 0.7290 (tttt) REVERT: a 122 ARG cc_start: 0.7046 (mmm160) cc_final: 0.6833 (mmt180) REVERT: a 171 MET cc_start: 0.2355 (mmp) cc_final: 0.0920 (tpp) REVERT: a 306 MET cc_start: -0.1474 (ttt) cc_final: -0.2544 (mmm) outliers start: 2 outliers final: 0 residues processed: 1082 average time/residue: 0.5686 time to fit residues: 1053.5516 Evaluate side-chains 839 residues out of total 6848 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 839 time to evaluate : 5.434 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 812 random chunks: chunk 264 optimal weight: 5.9990 chunk 706 optimal weight: 2.9990 chunk 155 optimal weight: 20.0000 chunk 460 optimal weight: 0.8980 chunk 193 optimal weight: 6.9990 chunk 785 optimal weight: 7.9990 chunk 652 optimal weight: 5.9990 chunk 363 optimal weight: 0.9980 chunk 65 optimal weight: 0.9990 chunk 259 optimal weight: 1.9990 chunk 412 optimal weight: 3.9990 overall best weight: 1.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 482 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 175 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 337 HIS ** D 165 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 250 GLN D 406 HIS ** D 468 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 479 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 513 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 111 HIS H 17 GLN ** H 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 380 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 102 ASN Q 346 HIS ** Q 359 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 460 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 391 HIS d 80 GLN d 129 HIS ** d 482 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 84 GLN ** e 262 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** e 497 ASN ** h 264 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 279 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** q 346 HIS ** q 523 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** z 132 GLN ** a 435 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5696 moved from start: 0.4563 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 63926 Z= 0.175 Angle : 0.533 10.707 86360 Z= 0.272 Chirality : 0.043 0.187 10322 Planarity : 0.003 0.098 10999 Dihedral : 7.093 88.021 9257 Min Nonbonded Distance : 1.956 Molprobity Statistics. All-atom Clashscore : 11.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.90 % Favored : 96.10 % Rotamer: Outliers : 0.04 % Allowed : 1.83 % Favored : 98.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.47 % Cis-general : 0.03 % 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: -1.12 (0.09), residues: 8173 helix: -0.31 (0.08), residues: 3923 sheet: -0.82 (0.18), residues: 785 loop : -1.10 (0.10), residues: 3465 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP g 496 HIS 0.006 0.001 HIS E 35 PHE 0.020 0.001 PHE h 174 TYR 0.018 0.001 TYR q 47 ARG 0.036 0.001 ARG Z 157 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16346 Ramachandran restraints generated. 8173 Oldfield, 0 Emsley, 8173 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16346 Ramachandran restraints generated. 8173 Oldfield, 0 Emsley, 8173 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1072 residues out of total 6848 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 1069 time to evaluate : 5.493 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 388 MET cc_start: 0.2586 (mmp) cc_final: 0.1646 (tpp) REVERT: A 390 ARG cc_start: 0.4468 (ptm-80) cc_final: 0.3147 (mmm-85) REVERT: A 485 TRP cc_start: 0.4696 (m-10) cc_final: 0.4252 (m-10) REVERT: A 530 LEU cc_start: 0.7147 (tp) cc_final: 0.6741 (tp) REVERT: B 50 LYS cc_start: 0.6656 (mtmt) cc_final: 0.6305 (mtmt) REVERT: B 131 ARG cc_start: 0.7470 (mtt180) cc_final: 0.7080 (ptp-110) REVERT: B 159 LEU cc_start: 0.5963 (mt) cc_final: 0.5638 (mt) REVERT: B 488 MET cc_start: 0.6653 (mmm) cc_final: 0.6225 (mmt) REVERT: B 512 GLU cc_start: 0.6740 (tt0) cc_final: 0.6155 (tt0) REVERT: D 134 SER cc_start: 0.8903 (m) cc_final: 0.8625 (p) REVERT: D 161 GLU cc_start: 0.6375 (mm-30) cc_final: 0.4540 (tm-30) REVERT: E 78 MET cc_start: 0.6636 (mmt) cc_final: 0.6074 (mmt) REVERT: E 197 MET cc_start: 0.0829 (ttt) cc_final: -0.0198 (ptm) REVERT: E 321 ARG cc_start: 0.3733 (ptt180) cc_final: 0.2489 (mtp180) REVERT: E 436 ASP cc_start: 0.6059 (m-30) cc_final: 0.4988 (t0) REVERT: E 529 ASP cc_start: 0.5812 (p0) cc_final: 0.4036 (t0) REVERT: G 152 MET cc_start: 0.6802 (mmm) cc_final: 0.6220 (mmt) REVERT: G 285 LEU cc_start: 0.4370 (mt) cc_final: 0.4065 (mp) REVERT: G 286 LYS cc_start: 0.3181 (mttt) cc_final: 0.2480 (ptpp) REVERT: H 227 MET cc_start: 0.2341 (tpt) cc_final: -0.0119 (mtp) REVERT: H 357 ARG cc_start: 0.4171 (mmt90) cc_final: 0.3052 (ptp90) REVERT: H 498 VAL cc_start: 0.7984 (t) cc_final: 0.7505 (t) REVERT: Q 54 LYS cc_start: 0.7865 (mmtp) cc_final: 0.7632 (mmmm) REVERT: Z 143 MET cc_start: 0.5481 (mpp) cc_final: 0.5069 (mpp) REVERT: Z 221 MET cc_start: 0.4586 (mmt) cc_final: 0.1047 (ptt) REVERT: b 114 GLU cc_start: 0.6327 (pp20) cc_final: 0.6102 (pp20) REVERT: b 141 LEU cc_start: 0.7100 (mp) cc_final: 0.6682 (mp) REVERT: b 213 TYR cc_start: 0.6815 (t80) cc_final: 0.6486 (t80) REVERT: b 310 MET cc_start: 0.0938 (mtp) cc_final: 0.0698 (mtp) REVERT: b 353 MET cc_start: 0.4275 (mmp) cc_final: 0.3902 (mmp) REVERT: b 480 MET cc_start: 0.6497 (ppp) cc_final: 0.6250 (tmm) REVERT: d 151 MET cc_start: 0.7521 (tmm) cc_final: 0.7239 (tmm) REVERT: d 355 MET cc_start: 0.3762 (tmm) cc_final: 0.3346 (ppp) REVERT: e 79 MET cc_start: 0.6168 (mtp) cc_final: 0.5789 (mtp) REVERT: e 197 MET cc_start: 0.4862 (ttm) cc_final: 0.4181 (tpt) REVERT: e 283 PHE cc_start: -0.0979 (m-80) cc_final: -0.1943 (m-10) REVERT: e 391 MET cc_start: 0.4936 (ptp) cc_final: 0.4208 (ptp) REVERT: e 446 MET cc_start: 0.8163 (mmm) cc_final: 0.7834 (tpp) REVERT: g 131 ASP cc_start: 0.7968 (p0) cc_final: 0.7394 (p0) REVERT: g 145 ASP cc_start: 0.7666 (p0) cc_final: 0.7147 (p0) REVERT: g 156 ILE cc_start: 0.6789 (mt) cc_final: 0.6555 (mt) REVERT: g 182 MET cc_start: 0.3641 (ttm) cc_final: 0.3123 (ttp) REVERT: g 270 MET cc_start: 0.4112 (ppp) cc_final: 0.3569 (ppp) REVERT: g 362 PHE cc_start: 0.3852 (m-80) cc_final: 0.3183 (m-80) REVERT: h 382 MET cc_start: 0.0818 (mtp) cc_final: 0.0582 (mtp) REVERT: h 405 VAL cc_start: 0.8703 (p) cc_final: 0.8323 (t) REVERT: h 445 ILE cc_start: 0.8391 (mm) cc_final: 0.8150 (mm) REVERT: q 111 LEU cc_start: 0.7813 (mt) cc_final: 0.7591 (mt) REVERT: q 129 ILE cc_start: 0.8734 (tt) cc_final: 0.8310 (tp) REVERT: q 223 PHE cc_start: 0.4200 (m-80) cc_final: 0.3997 (m-80) REVERT: q 401 VAL cc_start: 0.7053 (p) cc_final: 0.6712 (p) REVERT: q 404 ARG cc_start: 0.3563 (mtt180) cc_final: 0.2454 (mmp80) REVERT: z 63 LEU cc_start: 0.7427 (mt) cc_final: 0.6587 (mt) REVERT: z 206 LEU cc_start: 0.7630 (mt) cc_final: 0.7130 (tt) REVERT: z 295 LYS cc_start: 0.5618 (mmtt) cc_final: 0.4314 (mtmt) REVERT: a 122 ARG cc_start: 0.7093 (mmm160) cc_final: 0.6844 (mmt180) REVERT: a 244 THR cc_start: 0.5165 (t) cc_final: 0.4649 (m) REVERT: a 306 MET cc_start: -0.1104 (ttt) cc_final: -0.2374 (mmm) outliers start: 3 outliers final: 1 residues processed: 1070 average time/residue: 0.5701 time to fit residues: 1040.9962 Evaluate side-chains 815 residues out of total 6848 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 814 time to evaluate : 5.531 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 812 random chunks: chunk 757 optimal weight: 0.7980 chunk 88 optimal weight: 10.0000 chunk 447 optimal weight: 3.9990 chunk 573 optimal weight: 6.9990 chunk 444 optimal weight: 7.9990 chunk 661 optimal weight: 2.9990 chunk 438 optimal weight: 6.9990 chunk 782 optimal weight: 7.9990 chunk 489 optimal weight: 5.9990 chunk 477 optimal weight: 0.8980 chunk 361 optimal weight: 2.9990 overall best weight: 2.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 201 HIS ** A 251 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 482 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 175 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 337 HIS ** D 165 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 406 HIS E 443 GLN ** E 479 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 513 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 17 GLN ** H 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 380 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 432 GLN Q 53 ASN Q 346 HIS ** Q 359 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 460 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 129 HIS ** d 482 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 262 HIS g 115 GLN h 191 GLN ** h 264 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 380 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** h 390 HIS q 140 HIS ** q 279 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 383 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 523 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** z 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 435 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 498 ASN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5807 moved from start: 0.5081 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.077 63926 Z= 0.217 Angle : 0.605 12.985 86360 Z= 0.306 Chirality : 0.045 0.466 10322 Planarity : 0.004 0.161 10999 Dihedral : 7.772 164.178 9257 Min Nonbonded Distance : 1.932 Molprobity Statistics. All-atom Clashscore : 13.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.64 % Favored : 95.36 % Rotamer: Outliers : 0.03 % Allowed : 1.85 % Favored : 98.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.47 % Cis-general : 0.03 % 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: -1.18 (0.09), residues: 8173 helix: -0.29 (0.08), residues: 3887 sheet: -0.86 (0.18), residues: 778 loop : -1.21 (0.10), residues: 3508 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP g 496 HIS 0.010 0.001 HIS d 406 PHE 0.023 0.002 PHE A 167 TYR 0.036 0.002 TYR A 131 ARG 0.046 0.001 ARG Z 157 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16346 Ramachandran restraints generated. 8173 Oldfield, 0 Emsley, 8173 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16346 Ramachandran restraints generated. 8173 Oldfield, 0 Emsley, 8173 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1025 residues out of total 6848 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 1023 time to evaluate : 5.769 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 388 MET cc_start: 0.2514 (mmp) cc_final: 0.2243 (tpp) REVERT: A 390 ARG cc_start: 0.4205 (ptm-80) cc_final: 0.3110 (mmm-85) REVERT: A 485 TRP cc_start: 0.4950 (m-10) cc_final: 0.4519 (m-10) REVERT: A 530 LEU cc_start: 0.7101 (tp) cc_final: 0.6779 (tp) REVERT: B 50 LYS cc_start: 0.7069 (mtmt) cc_final: 0.6429 (mtmt) REVERT: B 131 ARG cc_start: 0.7409 (mtt180) cc_final: 0.7067 (ptp-110) REVERT: B 159 LEU cc_start: 0.5882 (mt) cc_final: 0.5541 (mt) REVERT: B 380 GLN cc_start: 0.6993 (mm-40) cc_final: 0.6759 (mm-40) REVERT: B 445 MET cc_start: 0.8066 (mmp) cc_final: 0.7731 (tpp) REVERT: B 488 MET cc_start: 0.6786 (mmm) cc_final: 0.6305 (mmt) REVERT: B 512 GLU cc_start: 0.6752 (tt0) cc_final: 0.6129 (tt0) REVERT: D 46 ASP cc_start: 0.7480 (m-30) cc_final: 0.7209 (m-30) REVERT: D 161 GLU cc_start: 0.6330 (mm-30) cc_final: 0.4503 (tm-30) REVERT: E 197 MET cc_start: 0.0909 (ttt) cc_final: -0.0196 (ptm) REVERT: E 321 ARG cc_start: 0.3403 (ptt180) cc_final: 0.2422 (mtp180) REVERT: E 391 MET cc_start: 0.2031 (ptp) cc_final: 0.1119 (pmm) REVERT: E 436 ASP cc_start: 0.6211 (m-30) cc_final: 0.4929 (t0) REVERT: E 529 ASP cc_start: 0.6231 (p0) cc_final: 0.3988 (t0) REVERT: G 59 MET cc_start: 0.7443 (mmm) cc_final: 0.7083 (tpt) REVERT: G 152 MET cc_start: 0.7327 (mmm) cc_final: 0.6666 (mmt) REVERT: G 219 MET cc_start: 0.3628 (ptp) cc_final: 0.3283 (mtt) REVERT: G 222 LYS cc_start: 0.1892 (tttm) cc_final: 0.1194 (tptp) REVERT: G 229 MET cc_start: 0.1136 (mtt) cc_final: 0.0580 (ttp) REVERT: G 286 LYS cc_start: 0.3531 (mttt) cc_final: 0.2678 (ptpp) REVERT: H 218 LYS cc_start: 0.5689 (tttt) cc_final: 0.4906 (tppt) REVERT: H 357 ARG cc_start: 0.4351 (mmt90) cc_final: 0.3119 (ptp90) REVERT: Q 54 LYS cc_start: 0.8090 (mmtp) cc_final: 0.7847 (mmmm) REVERT: Z 98 ILE cc_start: 0.8951 (mm) cc_final: 0.8459 (mt) REVERT: Z 143 MET cc_start: 0.5420 (mpp) cc_final: 0.5181 (mpp) REVERT: b 213 TYR cc_start: 0.6403 (t80) cc_final: 0.6134 (t80) REVERT: b 268 GLU cc_start: 0.1599 (mm-30) cc_final: 0.0945 (tp30) REVERT: b 353 MET cc_start: 0.4181 (mmp) cc_final: 0.3914 (mmp) REVERT: b 478 LEU cc_start: 0.6499 (mm) cc_final: 0.6181 (mp) REVERT: b 480 MET cc_start: 0.6560 (ppp) cc_final: 0.6275 (tmm) REVERT: d 131 THR cc_start: 0.7660 (t) cc_final: 0.7448 (t) REVERT: d 134 SER cc_start: 0.8329 (t) cc_final: 0.7754 (t) REVERT: d 355 MET cc_start: 0.3994 (tmm) cc_final: 0.3622 (tmm) REVERT: e 79 MET cc_start: 0.6119 (mtp) cc_final: 0.5849 (mtp) REVERT: e 197 MET cc_start: 0.4715 (ttm) cc_final: 0.4116 (tpt) REVERT: e 283 PHE cc_start: -0.0841 (m-80) cc_final: -0.1996 (m-10) REVERT: e 446 MET cc_start: 0.8173 (mmm) cc_final: 0.7877 (tpp) REVERT: g 133 MET cc_start: 0.7213 (mtm) cc_final: 0.6910 (mtm) REVERT: g 145 ASP cc_start: 0.7850 (p0) cc_final: 0.7344 (p0) REVERT: g 156 ILE cc_start: 0.6902 (mt) cc_final: 0.6660 (mt) REVERT: g 490 MET cc_start: 0.7317 (tpp) cc_final: 0.6971 (tpp) REVERT: g 512 THR cc_start: 0.8431 (t) cc_final: 0.8149 (m) REVERT: h 405 VAL cc_start: 0.8624 (p) cc_final: 0.8350 (t) REVERT: h 424 SER cc_start: 0.8601 (p) cc_final: 0.8367 (m) REVERT: h 445 ILE cc_start: 0.8476 (mm) cc_final: 0.8232 (mm) REVERT: q 129 ILE cc_start: 0.8790 (tt) cc_final: 0.8443 (tp) REVERT: q 223 PHE cc_start: 0.4676 (m-80) cc_final: 0.4388 (m-80) REVERT: q 401 VAL cc_start: 0.7213 (p) cc_final: 0.6988 (p) REVERT: q 404 ARG cc_start: 0.3728 (mtt180) cc_final: 0.2581 (mmp80) REVERT: z 44 MET cc_start: 0.6716 (mtt) cc_final: 0.6440 (mtt) REVERT: z 63 LEU cc_start: 0.7139 (mt) cc_final: 0.6155 (mt) REVERT: z 206 LEU cc_start: 0.7657 (mt) cc_final: 0.7118 (tt) REVERT: z 211 VAL cc_start: 0.5222 (t) cc_final: 0.4817 (t) REVERT: z 295 LYS cc_start: 0.5660 (mmtt) cc_final: 0.4312 (mtmt) REVERT: a 122 ARG cc_start: 0.7095 (mmm160) cc_final: 0.6862 (mmt180) REVERT: a 228 ARG cc_start: 0.5766 (tpt90) cc_final: 0.2126 (mpt180) REVERT: a 244 THR cc_start: 0.5279 (t) cc_final: 0.4802 (m) outliers start: 2 outliers final: 0 residues processed: 1023 average time/residue: 0.6152 time to fit residues: 1084.0233 Evaluate side-chains 796 residues out of total 6848 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 796 time to evaluate : 5.649 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 812 random chunks: chunk 484 optimal weight: 10.0000 chunk 312 optimal weight: 0.0980 chunk 467 optimal weight: 5.9990 chunk 235 optimal weight: 0.9980 chunk 153 optimal weight: 9.9990 chunk 151 optimal weight: 3.9990 chunk 497 optimal weight: 6.9990 chunk 533 optimal weight: 2.9990 chunk 386 optimal weight: 7.9990 chunk 72 optimal weight: 0.0010 chunk 615 optimal weight: 0.9990 overall best weight: 1.0190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 251 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 482 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 175 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 337 HIS ** D 165 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 406 HIS ** D 468 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 513 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 111 HIS ** H 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 380 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 359 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 460 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 129 HIS ** d 482 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** g 115 GLN ** h 264 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 380 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 279 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** q 346 HIS q 435 GLN ** q 523 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** z 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** z 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** z 503 GLN a 103 ASN ** a 435 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5733 moved from start: 0.5196 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.085 63926 Z= 0.155 Angle : 0.553 13.320 86360 Z= 0.278 Chirality : 0.043 0.192 10322 Planarity : 0.004 0.154 10999 Dihedral : 7.378 89.633 9257 Min Nonbonded Distance : 1.953 Molprobity Statistics. All-atom Clashscore : 12.08 Ramachandran Plot: Outliers : 0.01 % Allowed : 3.62 % Favored : 96.37 % Rotamer: Outliers : 0.01 % Allowed : 0.85 % Favored : 99.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.47 % Cis-general : 0.03 % 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: -0.90 (0.09), residues: 8173 helix: -0.06 (0.08), residues: 3874 sheet: -0.72 (0.19), residues: 742 loop : -1.06 (0.10), residues: 3557 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP g 496 HIS 0.009 0.001 HIS q 140 PHE 0.019 0.001 PHE A 167 TYR 0.027 0.001 TYR h 423 ARG 0.063 0.001 ARG z 157 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16346 Ramachandran restraints generated. 8173 Oldfield, 0 Emsley, 8173 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16346 Ramachandran restraints generated. 8173 Oldfield, 0 Emsley, 8173 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1041 residues out of total 6848 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 1040 time to evaluate : 5.722 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 109 LYS cc_start: 0.7626 (mmtt) cc_final: 0.7406 (mptt) REVERT: A 388 MET cc_start: 0.2637 (mmp) cc_final: 0.2322 (tpp) REVERT: A 390 ARG cc_start: 0.4488 (ptm-80) cc_final: 0.3338 (mmm-85) REVERT: A 485 TRP cc_start: 0.4670 (m-10) cc_final: 0.4291 (m-10) REVERT: A 530 LEU cc_start: 0.7073 (tp) cc_final: 0.6723 (tp) REVERT: B 50 LYS cc_start: 0.6940 (mtmt) cc_final: 0.6371 (mtmt) REVERT: B 131 ARG cc_start: 0.7383 (mtt180) cc_final: 0.7051 (ptp-110) REVERT: B 380 GLN cc_start: 0.7022 (mm-40) cc_final: 0.6786 (mm-40) REVERT: B 445 MET cc_start: 0.7952 (mmp) cc_final: 0.7713 (tpp) REVERT: B 488 MET cc_start: 0.6766 (mmm) cc_final: 0.6313 (mmt) REVERT: B 512 GLU cc_start: 0.6479 (tt0) cc_final: 0.5935 (tt0) REVERT: D 42 LYS cc_start: 0.7878 (mmmt) cc_final: 0.7483 (mmtp) REVERT: D 58 ASP cc_start: 0.7192 (t0) cc_final: 0.6912 (t0) REVERT: D 161 GLU cc_start: 0.6330 (mm-30) cc_final: 0.4479 (tm-30) REVERT: E 197 MET cc_start: 0.0348 (ttt) cc_final: -0.0873 (ptm) REVERT: E 321 ARG cc_start: 0.3136 (ptt180) cc_final: 0.2166 (mtp180) REVERT: E 436 ASP cc_start: 0.5886 (m-30) cc_final: 0.4447 (t0) REVERT: E 529 ASP cc_start: 0.5864 (p0) cc_final: 0.3937 (t0) REVERT: G 59 MET cc_start: 0.7463 (mmm) cc_final: 0.7108 (tpt) REVERT: G 152 MET cc_start: 0.7293 (mmm) cc_final: 0.6492 (mmt) REVERT: G 219 MET cc_start: 0.3724 (ptp) cc_final: 0.3191 (mtm) REVERT: G 222 LYS cc_start: 0.1852 (tttm) cc_final: 0.1191 (tptp) REVERT: G 229 MET cc_start: 0.1153 (mtt) cc_final: 0.0748 (ttp) REVERT: G 285 LEU cc_start: 0.4382 (mt) cc_final: 0.4138 (mp) REVERT: G 286 LYS cc_start: 0.3647 (mttt) cc_final: 0.2822 (ptpp) REVERT: G 330 ARG cc_start: 0.3241 (ttt180) cc_final: 0.2992 (tpt170) REVERT: G 432 VAL cc_start: 0.8187 (t) cc_final: 0.7869 (t) REVERT: H 218 LYS cc_start: 0.5482 (tttt) cc_final: 0.4777 (tppt) REVERT: H 357 ARG cc_start: 0.4312 (mmt90) cc_final: 0.3130 (ptp90) REVERT: H 498 VAL cc_start: 0.7881 (t) cc_final: 0.7610 (t) REVERT: Q 50 ASN cc_start: 0.7586 (m110) cc_final: 0.7217 (m-40) REVERT: Q 54 LYS cc_start: 0.8033 (mmtp) cc_final: 0.7797 (mmmm) REVERT: Z 98 ILE cc_start: 0.8888 (mm) cc_final: 0.8402 (mt) REVERT: Z 143 MET cc_start: 0.5373 (mpp) cc_final: 0.5078 (mpp) REVERT: Z 176 ILE cc_start: 0.8225 (tp) cc_final: 0.7812 (tp) REVERT: Z 526 MET cc_start: 0.5391 (tpt) cc_final: 0.4995 (tpp) REVERT: b 213 TYR cc_start: 0.6644 (t80) cc_final: 0.6348 (t80) REVERT: b 290 PHE cc_start: 0.4582 (t80) cc_final: 0.3711 (t80) REVERT: b 353 MET cc_start: 0.4413 (mmp) cc_final: 0.4154 (mmm) REVERT: b 480 MET cc_start: 0.6768 (ppp) cc_final: 0.6374 (tmm) REVERT: d 355 MET cc_start: 0.3896 (tmm) cc_final: 0.3385 (tmm) REVERT: e 79 MET cc_start: 0.6072 (mtp) cc_final: 0.5545 (mtp) REVERT: e 183 MET cc_start: 0.4683 (mtt) cc_final: 0.4456 (mtt) REVERT: e 197 MET cc_start: 0.4901 (ttm) cc_final: 0.4236 (tpt) REVERT: e 283 PHE cc_start: -0.0840 (m-80) cc_final: -0.1918 (m-10) REVERT: e 391 MET cc_start: 0.4878 (ptp) cc_final: 0.4225 (ptp) REVERT: e 446 MET cc_start: 0.8163 (mmm) cc_final: 0.7885 (tpp) REVERT: g 131 ASP cc_start: 0.7930 (p0) cc_final: 0.7465 (p0) REVERT: g 133 MET cc_start: 0.6851 (mtm) cc_final: 0.6590 (mtm) REVERT: g 145 ASP cc_start: 0.7878 (p0) cc_final: 0.7501 (p0) REVERT: g 395 MET cc_start: 0.6131 (ppp) cc_final: 0.5868 (tmm) REVERT: g 490 MET cc_start: 0.7216 (tpp) cc_final: 0.6988 (tpp) REVERT: h 308 MET cc_start: 0.2552 (ttm) cc_final: 0.1731 (ttp) REVERT: h 405 VAL cc_start: 0.8581 (p) cc_final: 0.8327 (t) REVERT: h 445 ILE cc_start: 0.8418 (mm) cc_final: 0.8195 (mm) REVERT: h 487 ASN cc_start: 0.7713 (m-40) cc_final: 0.7504 (m-40) REVERT: q 129 ILE cc_start: 0.8672 (tt) cc_final: 0.8377 (tp) REVERT: q 223 PHE cc_start: 0.4492 (m-80) cc_final: 0.4207 (m-80) REVERT: q 401 VAL cc_start: 0.6865 (p) cc_final: 0.6531 (p) REVERT: q 404 ARG cc_start: 0.3616 (mtt180) cc_final: 0.2404 (mmp80) REVERT: z 44 MET cc_start: 0.6675 (mtt) cc_final: 0.6410 (mtt) REVERT: z 63 LEU cc_start: 0.7230 (mt) cc_final: 0.6827 (mt) REVERT: z 68 GLN cc_start: 0.4113 (mm-40) cc_final: 0.3845 (mm110) REVERT: z 167 VAL cc_start: 0.6357 (p) cc_final: 0.6154 (p) REVERT: z 206 LEU cc_start: 0.7542 (mt) cc_final: 0.7123 (tt) REVERT: z 295 LYS cc_start: 0.5441 (mmtt) cc_final: 0.4164 (mtmt) REVERT: a 122 ARG cc_start: 0.7084 (mmm160) cc_final: 0.6871 (mmt180) REVERT: a 244 THR cc_start: 0.5251 (t) cc_final: 0.4873 (m) REVERT: a 306 MET cc_start: -0.0981 (ttm) cc_final: -0.1684 (mmm) outliers start: 1 outliers final: 0 residues processed: 1041 average time/residue: 0.5711 time to fit residues: 1019.1249 Evaluate side-chains 803 residues out of total 6848 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 803 time to evaluate : 5.468 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 812 random chunks: chunk 711 optimal weight: 0.9980 chunk 749 optimal weight: 1.9990 chunk 684 optimal weight: 0.8980 chunk 729 optimal weight: 7.9990 chunk 438 optimal weight: 0.8980 chunk 317 optimal weight: 6.9990 chunk 572 optimal weight: 0.5980 chunk 223 optimal weight: 10.0000 chunk 659 optimal weight: 10.0000 chunk 689 optimal weight: 0.9980 chunk 726 optimal weight: 5.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- 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 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 175 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 337 HIS ** D 165 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 406 HIS ** D 468 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 111 HIS G 390 ASN H 17 GLN ** H 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 380 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 448 GLN Q 175 ASN ** Q 359 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 460 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 129 HIS d 189 ASN ** d 482 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** g 115 GLN ** h 264 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 380 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 279 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** q 435 GLN q 461 ASN ** q 523 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** z 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** z 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** z 503 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 435 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5714 moved from start: 0.5330 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.069 63926 Z= 0.150 Angle : 0.538 10.956 86360 Z= 0.271 Chirality : 0.043 0.229 10322 Planarity : 0.004 0.137 10999 Dihedral : 7.168 89.877 9257 Min Nonbonded Distance : 1.963 Molprobity Statistics. All-atom Clashscore : 11.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.15 % Favored : 95.85 % Rotamer: Outliers : 0.03 % Allowed : 0.53 % Favored : 99.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.47 % Cis-general : 0.03 % 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: -0.72 (0.09), residues: 8173 helix: 0.10 (0.08), residues: 3869 sheet: -0.66 (0.19), residues: 720 loop : -0.98 (0.10), residues: 3584 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP G 496 HIS 0.013 0.001 HIS Q 140 PHE 0.021 0.001 PHE A 167 TYR 0.019 0.001 TYR A 131 ARG 0.032 0.000 ARG z 157 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16346 Ramachandran restraints generated. 8173 Oldfield, 0 Emsley, 8173 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16346 Ramachandran restraints generated. 8173 Oldfield, 0 Emsley, 8173 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1026 residues out of total 6848 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 1024 time to evaluate : 5.726 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 485 TRP cc_start: 0.4591 (m-10) cc_final: 0.4284 (m-10) REVERT: A 530 LEU cc_start: 0.7070 (tp) cc_final: 0.6787 (tp) REVERT: B 50 LYS cc_start: 0.7037 (mtmt) cc_final: 0.6442 (mtmt) REVERT: B 131 ARG cc_start: 0.7403 (mtt180) cc_final: 0.7006 (ptp-110) REVERT: B 445 MET cc_start: 0.7833 (mmp) cc_final: 0.7577 (tpp) REVERT: B 480 MET cc_start: 0.6668 (ppp) cc_final: 0.6301 (ppp) REVERT: B 488 MET cc_start: 0.6779 (mmm) cc_final: 0.6326 (mmt) REVERT: B 512 GLU cc_start: 0.6494 (tt0) cc_final: 0.6172 (tt0) REVERT: D 42 LYS cc_start: 0.7945 (mmmt) cc_final: 0.7696 (mmtp) REVERT: D 58 ASP cc_start: 0.7214 (t0) cc_final: 0.6849 (t0) REVERT: D 161 GLU cc_start: 0.6275 (mm-30) cc_final: 0.4379 (tm-30) REVERT: D 192 MET cc_start: 0.4818 (ptp) cc_final: 0.4393 (ptt) REVERT: E 197 MET cc_start: 0.0270 (ttt) cc_final: -0.0935 (ptm) REVERT: E 321 ARG cc_start: 0.3117 (ptt180) cc_final: 0.2085 (mtp180) REVERT: E 391 MET cc_start: 0.2139 (ptp) cc_final: 0.1044 (pmm) REVERT: E 436 ASP cc_start: 0.6003 (m-30) cc_final: 0.4640 (t0) REVERT: E 529 ASP cc_start: 0.5735 (p0) cc_final: 0.3893 (t0) REVERT: G 152 MET cc_start: 0.7394 (mmm) cc_final: 0.6646 (mmt) REVERT: G 219 MET cc_start: 0.3236 (ptp) cc_final: 0.2949 (mtm) REVERT: G 222 LYS cc_start: 0.1953 (tttm) cc_final: 0.1243 (tptp) REVERT: G 229 MET cc_start: 0.0886 (mtt) cc_final: 0.0490 (ttp) REVERT: G 285 LEU cc_start: 0.4364 (mt) cc_final: 0.4025 (mp) REVERT: G 286 LYS cc_start: 0.3534 (mttt) cc_final: 0.2691 (ptpp) REVERT: G 330 ARG cc_start: 0.3210 (ttt180) cc_final: 0.2917 (tpt170) REVERT: H 194 MET cc_start: 0.3442 (mmm) cc_final: 0.1858 (mmt) REVERT: H 216 PHE cc_start: 0.2029 (p90) cc_final: 0.1814 (p90) REVERT: H 218 LYS cc_start: 0.5267 (tttt) cc_final: 0.4547 (tppt) REVERT: H 324 MET cc_start: 0.4377 (tmm) cc_final: 0.3804 (tpp) REVERT: H 357 ARG cc_start: 0.4281 (mmt90) cc_final: 0.3089 (ptp90) REVERT: H 493 TRP cc_start: 0.5320 (m-10) cc_final: 0.4980 (m-10) REVERT: H 498 VAL cc_start: 0.7774 (t) cc_final: 0.7512 (t) REVERT: Q 50 ASN cc_start: 0.7380 (m110) cc_final: 0.7075 (m-40) REVERT: Z 98 ILE cc_start: 0.8876 (mm) cc_final: 0.8392 (mt) REVERT: Z 143 MET cc_start: 0.5607 (mpp) cc_final: 0.5266 (mpp) REVERT: Z 526 MET cc_start: 0.5478 (tpt) cc_final: 0.5078 (tpp) REVERT: b 62 MET cc_start: 0.4010 (ppp) cc_final: 0.3626 (ppp) REVERT: b 268 GLU cc_start: 0.1804 (mm-30) cc_final: 0.1005 (tp30) REVERT: b 290 PHE cc_start: 0.4571 (t80) cc_final: 0.3685 (t80) REVERT: b 431 LYS cc_start: 0.7870 (mmmt) cc_final: 0.6720 (mtmt) REVERT: b 480 MET cc_start: 0.6942 (ppp) cc_final: 0.6665 (tmm) REVERT: b 488 MET cc_start: 0.4378 (tpp) cc_final: 0.4104 (tpp) REVERT: d 355 MET cc_start: 0.3708 (tmm) cc_final: 0.3492 (tmm) REVERT: e 71 ASP cc_start: 0.7805 (t70) cc_final: 0.7491 (t0) REVERT: e 79 MET cc_start: 0.6347 (mtp) cc_final: 0.6071 (mtp) REVERT: e 197 MET cc_start: 0.4832 (ttm) cc_final: 0.4163 (tpt) REVERT: e 283 PHE cc_start: -0.0790 (m-80) cc_final: -0.1967 (m-10) REVERT: e 391 MET cc_start: 0.4875 (ptp) cc_final: 0.4262 (ptp) REVERT: e 446 MET cc_start: 0.8123 (mmm) cc_final: 0.7792 (tpp) REVERT: e 453 LEU cc_start: 0.7625 (mm) cc_final: 0.7348 (mm) REVERT: e 493 HIS cc_start: 0.5990 (t70) cc_final: 0.5755 (t70) REVERT: g 131 ASP cc_start: 0.8020 (p0) cc_final: 0.7512 (p0) REVERT: g 145 ASP cc_start: 0.7851 (p0) cc_final: 0.7468 (p0) REVERT: g 156 ILE cc_start: 0.7117 (mm) cc_final: 0.6843 (mm) REVERT: h 308 MET cc_start: 0.2422 (ttm) cc_final: 0.1576 (ttp) REVERT: h 405 VAL cc_start: 0.8665 (p) cc_final: 0.8424 (t) REVERT: q 129 ILE cc_start: 0.8650 (tt) cc_final: 0.8323 (tp) REVERT: q 223 PHE cc_start: 0.4497 (m-80) cc_final: 0.4139 (m-80) REVERT: q 401 VAL cc_start: 0.6805 (p) cc_final: 0.6412 (p) REVERT: q 404 ARG cc_start: 0.3539 (mtt180) cc_final: 0.2446 (mmp80) REVERT: z 44 MET cc_start: 0.6741 (mtt) cc_final: 0.6464 (mtt) REVERT: z 59 ASP cc_start: 0.4770 (t0) cc_final: 0.4497 (t0) REVERT: z 63 LEU cc_start: 0.7396 (mt) cc_final: 0.6124 (mt) REVERT: z 206 LEU cc_start: 0.7606 (mt) cc_final: 0.7096 (tt) REVERT: z 295 LYS cc_start: 0.5215 (mmtt) cc_final: 0.3946 (mtmt) REVERT: z 522 MET cc_start: 0.7696 (ppp) cc_final: 0.7430 (ppp) REVERT: a 78 LEU cc_start: 0.5099 (pp) cc_final: 0.4755 (pp) REVERT: a 84 LYS cc_start: 0.6822 (mppt) cc_final: 0.6584 (tmmt) REVERT: a 102 LYS cc_start: 0.7499 (tttt) cc_final: 0.6837 (tptp) REVERT: a 171 MET cc_start: 0.2299 (mmm) cc_final: -0.0095 (tpt) REVERT: a 244 THR cc_start: 0.5373 (t) cc_final: 0.4972 (m) REVERT: a 306 MET cc_start: -0.1063 (ttm) cc_final: -0.1873 (mmm) outliers start: 2 outliers final: 1 residues processed: 1025 average time/residue: 0.5800 time to fit residues: 1021.5385 Evaluate side-chains 796 residues out of total 6848 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 795 time to evaluate : 6.293 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 812 random chunks: chunk 478 optimal weight: 8.9990 chunk 771 optimal weight: 0.8980 chunk 470 optimal weight: 4.9990 chunk 365 optimal weight: 9.9990 chunk 536 optimal weight: 0.6980 chunk 808 optimal weight: 0.0170 chunk 744 optimal weight: 3.9990 chunk 644 optimal weight: 2.9990 chunk 66 optimal weight: 0.8980 chunk 497 optimal weight: 8.9990 chunk 394 optimal weight: 0.9990 overall best weight: 0.7020 ------------------------------------------------------------------------------- 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 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 175 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 337 HIS ** D 165 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 111 HIS G 154 ASN G 390 ASN H 17 GLN ** H 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 331 GLN ** H 380 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 175 ASN ** Q 359 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 460 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 129 HIS h 191 GLN ** h 264 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 380 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 279 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** q 435 GLN ** q 523 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** z 68 GLN ** z 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** z 503 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 435 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5690 moved from start: 0.5447 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.060 63926 Z= 0.144 Angle : 0.548 16.346 86360 Z= 0.275 Chirality : 0.043 0.206 10322 Planarity : 0.004 0.119 10999 Dihedral : 7.157 89.999 9257 Min Nonbonded Distance : 1.973 Molprobity Statistics. All-atom Clashscore : 11.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.62 % Favored : 96.38 % Rotamer: Outliers : 0.01 % Allowed : 0.19 % Favored : 99.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.47 % Cis-general : 0.03 % 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: -0.61 (0.09), residues: 8173 helix: 0.22 (0.08), residues: 3864 sheet: -0.66 (0.19), residues: 707 loop : -0.96 (0.10), residues: 3602 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP q 506 HIS 0.012 0.001 HIS Q 140 PHE 0.020 0.001 PHE A 167 TYR 0.036 0.001 TYR h 423 ARG 0.016 0.000 ARG z 157 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16346 Ramachandran restraints generated. 8173 Oldfield, 0 Emsley, 8173 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16346 Ramachandran restraints generated. 8173 Oldfield, 0 Emsley, 8173 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 998 residues out of total 6848 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 997 time to evaluate : 5.632 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 485 TRP cc_start: 0.4633 (m-10) cc_final: 0.4314 (m-10) REVERT: A 530 LEU cc_start: 0.7101 (tp) cc_final: 0.6833 (tp) REVERT: B 50 LYS cc_start: 0.6786 (mtmt) cc_final: 0.6269 (mtmt) REVERT: B 112 GLU cc_start: 0.5853 (pp20) cc_final: 0.5288 (pp20) REVERT: B 131 ARG cc_start: 0.7453 (mtt180) cc_final: 0.7039 (ptp-110) REVERT: B 415 MET cc_start: 0.8004 (tpp) cc_final: 0.7804 (tpp) REVERT: B 473 ASN cc_start: 0.8588 (m-40) cc_final: 0.8299 (t0) REVERT: B 488 MET cc_start: 0.6574 (mmm) cc_final: 0.6210 (mmt) REVERT: D 42 LYS cc_start: 0.8018 (mmmt) cc_final: 0.7680 (mmtp) REVERT: D 58 ASP cc_start: 0.7162 (t0) cc_final: 0.6719 (t0) REVERT: D 95 SER cc_start: 0.8476 (t) cc_final: 0.8265 (t) REVERT: D 161 GLU cc_start: 0.6263 (mm-30) cc_final: 0.4380 (tm-30) REVERT: D 192 MET cc_start: 0.4748 (ptp) cc_final: 0.4285 (ptt) REVERT: E 197 MET cc_start: 0.0230 (ttt) cc_final: -0.0938 (ptm) REVERT: E 321 ARG cc_start: 0.2975 (ptt180) cc_final: 0.1930 (mtt180) REVERT: E 391 MET cc_start: 0.2096 (ptp) cc_final: 0.1019 (pmm) REVERT: E 436 ASP cc_start: 0.5863 (m-30) cc_final: 0.4685 (t0) REVERT: E 529 ASP cc_start: 0.5634 (p0) cc_final: 0.3745 (t0) REVERT: G 219 MET cc_start: 0.3202 (ptp) cc_final: 0.2943 (mtm) REVERT: G 222 LYS cc_start: 0.1962 (tttm) cc_final: 0.1090 (tptp) REVERT: G 229 MET cc_start: 0.0916 (mtt) cc_final: 0.0532 (ttp) REVERT: G 285 LEU cc_start: 0.4422 (mt) cc_final: 0.4093 (mp) REVERT: G 286 LYS cc_start: 0.3525 (mttt) cc_final: 0.2677 (ptpp) REVERT: G 330 ARG cc_start: 0.3473 (ttt180) cc_final: 0.2912 (tpt170) REVERT: H 194 MET cc_start: 0.3751 (mmm) cc_final: 0.2356 (mmt) REVERT: H 216 PHE cc_start: 0.2325 (p90) cc_final: 0.2071 (p90) REVERT: H 218 LYS cc_start: 0.5086 (tttt) cc_final: 0.4591 (tppt) REVERT: H 324 MET cc_start: 0.4537 (tmm) cc_final: 0.4062 (tpp) REVERT: H 357 ARG cc_start: 0.4274 (mmt90) cc_final: 0.3075 (ptp90) REVERT: H 493 TRP cc_start: 0.5417 (m-10) cc_final: 0.4987 (m-10) REVERT: H 498 VAL cc_start: 0.7788 (t) cc_final: 0.7511 (t) REVERT: Q 50 ASN cc_start: 0.7369 (m110) cc_final: 0.6983 (m-40) REVERT: Z 143 MET cc_start: 0.5505 (mpp) cc_final: 0.5214 (mpp) REVERT: Z 176 ILE cc_start: 0.8211 (tp) cc_final: 0.7745 (tp) REVERT: Z 526 MET cc_start: 0.5461 (tpt) cc_final: 0.4886 (tpp) REVERT: b 268 GLU cc_start: 0.1743 (mm-30) cc_final: 0.1330 (tp30) REVERT: b 431 LYS cc_start: 0.7991 (mmmt) cc_final: 0.6893 (mtpt) REVERT: b 480 MET cc_start: 0.6720 (ppp) cc_final: 0.6443 (tmm) REVERT: d 29 LYS cc_start: 0.7514 (tttm) cc_final: 0.6851 (pptt) REVERT: d 58 ASP cc_start: 0.7352 (m-30) cc_final: 0.7129 (m-30) REVERT: d 355 MET cc_start: 0.3555 (tmm) cc_final: 0.3326 (ppp) REVERT: e 71 ASP cc_start: 0.7736 (t70) cc_final: 0.7371 (t0) REVERT: e 79 MET cc_start: 0.6153 (mtp) cc_final: 0.5748 (mtp) REVERT: e 117 GLU cc_start: 0.5867 (tt0) cc_final: 0.5636 (tt0) REVERT: e 168 LYS cc_start: 0.6203 (mmtm) cc_final: 0.4735 (mmtt) REVERT: e 197 MET cc_start: 0.4828 (ttm) cc_final: 0.4111 (tpt) REVERT: e 391 MET cc_start: 0.4757 (ptp) cc_final: 0.4132 (ptp) REVERT: e 446 MET cc_start: 0.8035 (mmm) cc_final: 0.7618 (tpp) REVERT: g 131 ASP cc_start: 0.8037 (p0) cc_final: 0.7381 (p0) REVERT: g 133 MET cc_start: 0.6591 (mtm) cc_final: 0.6012 (mtm) REVERT: g 145 ASP cc_start: 0.7848 (p0) cc_final: 0.7498 (p0) REVERT: g 156 ILE cc_start: 0.7099 (mm) cc_final: 0.6776 (mm) REVERT: h 220 PHE cc_start: 0.5449 (t80) cc_final: 0.4137 (t80) REVERT: h 227 MET cc_start: 0.3303 (ptt) cc_final: 0.2912 (ptm) REVERT: h 308 MET cc_start: 0.2328 (ttm) cc_final: 0.1533 (ttp) REVERT: h 405 VAL cc_start: 0.8618 (p) cc_final: 0.8315 (t) REVERT: q 129 ILE cc_start: 0.8745 (tt) cc_final: 0.8352 (tp) REVERT: q 223 PHE cc_start: 0.4433 (m-80) cc_final: 0.4114 (m-80) REVERT: q 401 VAL cc_start: 0.6756 (p) cc_final: 0.6285 (p) REVERT: q 404 ARG cc_start: 0.3482 (mtt180) cc_final: 0.2357 (mmp80) REVERT: z 44 MET cc_start: 0.6590 (mtt) cc_final: 0.6338 (mtt) REVERT: z 63 LEU cc_start: 0.7910 (mt) cc_final: 0.7522 (mt) REVERT: z 143 MET cc_start: 0.3110 (ppp) cc_final: 0.2644 (tmm) REVERT: z 206 LEU cc_start: 0.7573 (mt) cc_final: 0.7103 (tt) REVERT: z 295 LYS cc_start: 0.5102 (mmtt) cc_final: 0.3932 (mtmt) REVERT: z 522 MET cc_start: 0.7581 (ppp) cc_final: 0.7341 (ppp) REVERT: a 78 LEU cc_start: 0.5163 (pp) cc_final: 0.4749 (pp) REVERT: a 84 LYS cc_start: 0.6786 (mppt) cc_final: 0.6493 (tmmt) REVERT: a 99 GLU cc_start: 0.6005 (tm-30) cc_final: 0.5741 (tm-30) REVERT: a 102 LYS cc_start: 0.7415 (tttt) cc_final: 0.6696 (tptp) REVERT: a 171 MET cc_start: 0.1779 (mmm) cc_final: -0.0229 (tpt) REVERT: a 244 THR cc_start: 0.5384 (t) cc_final: 0.4993 (m) REVERT: a 306 MET cc_start: -0.0352 (ttm) cc_final: -0.1415 (mmm) REVERT: a 519 GLU cc_start: 0.7294 (tm-30) cc_final: 0.6809 (tt0) outliers start: 1 outliers final: 0 residues processed: 998 average time/residue: 0.5788 time to fit residues: 996.1171 Evaluate side-chains 784 residues out of total 6848 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 784 time to evaluate : 5.504 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 812 random chunks: chunk 511 optimal weight: 6.9990 chunk 686 optimal weight: 5.9990 chunk 197 optimal weight: 0.8980 chunk 593 optimal weight: 0.0050 chunk 95 optimal weight: 0.9980 chunk 179 optimal weight: 0.6980 chunk 645 optimal weight: 3.9990 chunk 270 optimal weight: 4.9990 chunk 662 optimal weight: 0.0570 chunk 81 optimal weight: 8.9990 chunk 118 optimal weight: 0.6980 overall best weight: 0.4712 ------------------------------------------------------------------------------- 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 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 175 HIS B 337 HIS ** D 165 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 406 HIS G 111 HIS H 17 GLN ** H 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 380 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 175 ASN ** Q 359 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 460 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 129 HIS d 189 ASN h 191 GLN ** h 264 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 380 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 279 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** q 346 HIS q 435 GLN ** q 523 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** z 68 GLN ** z 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** z 503 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 435 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4564 r_free = 0.4564 target = 0.198253 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4476 r_free = 0.4476 target = 0.190205 restraints weight = 133636.286| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 51)----------------| | r_work = 0.4450 r_free = 0.4450 target = 0.188122 restraints weight = 182735.212| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 57)----------------| | r_work = 0.4422 r_free = 0.4422 target = 0.185972 restraints weight = 195499.495| |-----------------------------------------------------------------------------| r_work (final): 0.4424 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5571 moved from start: 0.5524 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.066 63926 Z= 0.135 Angle : 0.531 15.459 86360 Z= 0.268 Chirality : 0.042 0.199 10322 Planarity : 0.004 0.213 10999 Dihedral : 7.040 89.760 9257 Min Nonbonded Distance : 1.974 Molprobity Statistics. All-atom Clashscore : 11.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.46 % Favored : 96.54 % Rotamer: Outliers : 0.03 % Allowed : 0.18 % Favored : 99.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.47 % Cis-general : 0.03 % 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: -0.47 (0.09), residues: 8173 helix: 0.37 (0.09), residues: 3872 sheet: -0.56 (0.19), residues: 730 loop : -0.92 (0.10), residues: 3571 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP q 506 HIS 0.012 0.001 HIS Q 140 PHE 0.019 0.001 PHE A 167 TYR 0.036 0.001 TYR h 423 ARG 0.055 0.000 ARG Z 157 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 16221.97 seconds wall clock time: 284 minutes 56.53 seconds (17096.53 seconds total)