Starting phenix.real_space_refine on Sun Feb 18 10:58:21 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jtk_22475/02_2024/7jtk_22475_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jtk_22475/02_2024/7jtk_22475.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jtk_22475/02_2024/7jtk_22475.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jtk_22475/02_2024/7jtk_22475.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jtk_22475/02_2024/7jtk_22475_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jtk_22475/02_2024/7jtk_22475_updated.pdb" } resolution = 3.2 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= 0.000 sd= 0.001 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 4 5.49 5 S 240 5.16 5 C 46302 2.51 5 N 12498 2.21 5 O 13763 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 21": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 26": "OE1" <-> "OE2" Residue "A GLU 65": "OE1" <-> "OE2" Residue "A ARG 91": "NH1" <-> "NH2" Residue "A GLU 227": "OE1" <-> "OE2" Residue "A ARG 232": "NH1" <-> "NH2" Residue "A ARG 291": "NH1" <-> "NH2" Residue "A ARG 297": "NH1" <-> "NH2" Residue "A GLU 302": "OE1" <-> "OE2" Residue "A GLU 348": "OE1" <-> "OE2" Residue "A ARG 352": "NH1" <-> "NH2" Residue "A GLU 427": "OE1" <-> "OE2" Residue "A TYR 433": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 439": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 441": "OD1" <-> "OD2" Residue "A TYR 454": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 465": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 515": "OE1" <-> "OE2" Residue "A PHE 527": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 540": "OE1" <-> "OE2" Residue "A ASP 555": "OD1" <-> "OD2" Residue "A ARG 562": "NH1" <-> "NH2" Residue "A TYR 592": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 603": "OE1" <-> "OE2" Residue "A ARG 612": "NH1" <-> "NH2" Residue "A PHE 617": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 626": "OE1" <-> "OE2" Residue "A ARG 639": "NH1" <-> "NH2" Residue "A TYR 646": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 690": "NH1" <-> "NH2" Residue "A ARG 712": "NH1" <-> "NH2" Residue "B PHE 21": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 64": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 71": "OE1" <-> "OE2" Residue "B ASP 79": "OD1" <-> "OD2" Residue "B ARG 91": "NH1" <-> "NH2" Residue "B TYR 124": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 232": "NH1" <-> "NH2" Residue "B ARG 291": "NH1" <-> "NH2" Residue "B ARG 297": "NH1" <-> "NH2" Residue "B ARG 300": "NH1" <-> "NH2" Residue "B GLU 348": "OE1" <-> "OE2" Residue "B ARG 352": "NH1" <-> "NH2" Residue "B GLU 417": "OE1" <-> "OE2" Residue "B TYR 433": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 514": "OE1" <-> "OE2" Residue "B PHE 527": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 552": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 562": "NH1" <-> "NH2" Residue "B TYR 577": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 584": "OD1" <-> "OD2" Residue "B GLU 603": "OE1" <-> "OE2" Residue "B TYR 604": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 612": "NH1" <-> "NH2" Residue "B PHE 627": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 630": "OD1" <-> "OD2" Residue "B TYR 638": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 639": "NH1" <-> "NH2" Residue "B GLU 685": "OE1" <-> "OE2" Residue "B ARG 690": "NH1" <-> "NH2" Residue "B ARG 712": "NH1" <-> "NH2" Residue "B GLU 772": "OE1" <-> "OE2" Residue "B GLU 794": "OE1" <-> "OE2" Residue "C GLU 19": "OE1" <-> "OE2" Residue "C GLU 91": "OE1" <-> "OE2" Residue "C ARG 260": "NH1" <-> "NH2" Residue "C GLU 285": "OE1" <-> "OE2" Residue "C GLU 324": "OE1" <-> "OE2" Residue "C GLU 445": "OE1" <-> "OE2" Residue "C ARG 484": "NH1" <-> "NH2" Residue "C ARG 506": "NH1" <-> "NH2" Residue "C ARG 516": "NH1" <-> "NH2" Residue "C PHE 521": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 524": "NH1" <-> "NH2" Residue "C GLU 537": "OE1" <-> "OE2" Residue "C ARG 538": "NH1" <-> "NH2" Residue "C ARG 545": "NH1" <-> "NH2" Residue "C TYR 550": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 562": "OE1" <-> "OE2" Residue "C ARG 580": "NH1" <-> "NH2" Residue "C ARG 581": "NH1" <-> "NH2" Residue "C ARG 584": "NH1" <-> "NH2" Residue "C ARG 590": "NH1" <-> "NH2" Residue "D TYR 39": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 102": "OE1" <-> "OE2" Residue "D GLU 105": "OE1" <-> "OE2" Residue "D TYR 124": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 234": "OE1" <-> "OE2" Residue "D GLU 258": "OE1" <-> "OE2" Residue "D ARG 260": "NH1" <-> "NH2" Residue "D ARG 265": "NH1" <-> "NH2" Residue "D PHE 296": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 321": "NH1" <-> "NH2" Residue "D GLU 461": "OE1" <-> "OE2" Residue "D ARG 484": "NH1" <-> "NH2" Residue "D ARG 506": "NH1" <-> "NH2" Residue "D ARG 516": "NH1" <-> "NH2" Residue "D ARG 524": "NH1" <-> "NH2" Residue "D PHE 526": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 538": "NH1" <-> "NH2" Residue "D ARG 545": "NH1" <-> "NH2" Residue "D ARG 547": "NH1" <-> "NH2" Residue "D GLU 562": "OE1" <-> "OE2" Residue "D ARG 580": "NH1" <-> "NH2" Residue "D ARG 581": "NH1" <-> "NH2" Residue "D ARG 584": "NH1" <-> "NH2" Residue "D ARG 590": "NH1" <-> "NH2" Residue "D GLU 591": "OE1" <-> "OE2" Residue "E GLU 200": "OE1" <-> "OE2" Residue "E GLU 211": "OE1" <-> "OE2" Residue "E ARG 221": "NH1" <-> "NH2" Residue "E ARG 246": "NH1" <-> "NH2" Residue "E ARG 297": "NH1" <-> "NH2" Residue "E GLU 342": "OE1" <-> "OE2" Residue "E GLU 384": "OE1" <-> "OE2" Residue "F PHE 156": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 159": "OE1" <-> "OE2" Residue "F GLU 191": "OE1" <-> "OE2" Residue "F ARG 197": "NH1" <-> "NH2" Residue "F ARG 206": "NH1" <-> "NH2" Residue "F GLU 216": "OE1" <-> "OE2" Residue "F ARG 221": "NH1" <-> "NH2" Residue "F ARG 228": "NH1" <-> "NH2" Residue "F ARG 236": "NH1" <-> "NH2" Residue "F PHE 278": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 349": "OE1" <-> "OE2" Residue "F ARG 354": "NH1" <-> "NH2" Residue "F ARG 360": "NH1" <-> "NH2" Residue "F TYR 504": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 60": "OD1" <-> "OD2" Residue "G GLU 99": "OE1" <-> "OE2" Residue "G GLU 145": "OE1" <-> "OE2" Residue "G GLU 171": "OE1" <-> "OE2" Residue "G GLU 203": "OE1" <-> "OE2" Residue "G GLU 208": "OE1" <-> "OE2" Residue "G GLU 267": "OE1" <-> "OE2" Residue "G ARG 272": "NH1" <-> "NH2" Residue "G ASP 288": "OD1" <-> "OD2" Residue "G GLU 303": "OE1" <-> "OE2" Residue "G GLU 306": "OE1" <-> "OE2" Residue "G ARG 323": "NH1" <-> "NH2" Residue "G ARG 331": "NH1" <-> "NH2" Residue "G GLU 345": "OE1" <-> "OE2" Residue "G GLU 356": "OE1" <-> "OE2" Residue "G ASP 359": "OD1" <-> "OD2" Residue "G GLU 365": "OE1" <-> "OE2" Residue "G GLU 442": "OE1" <-> "OE2" Residue "H GLU 108": "OE1" <-> "OE2" Residue "H GLU 110": "OE1" <-> "OE2" Residue "H GLU 131": "OE1" <-> "OE2" Residue "H ARG 272": "NH1" <-> "NH2" Residue "H GLU 303": "OE1" <-> "OE2" Residue "H GLU 306": "OE1" <-> "OE2" Residue "H GLU 312": "OE1" <-> "OE2" Residue "H ARG 323": "NH1" <-> "NH2" Residue "H ARG 331": "NH1" <-> "NH2" Residue "H GLU 373": "OE1" <-> "OE2" Residue "H GLU 411": "OE1" <-> "OE2" Residue "H GLU 442": "OE1" <-> "OE2" Residue "I TYR 25": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ARG 29": "NH1" <-> "NH2" Residue "I GLU 33": "OE1" <-> "OE2" Residue "I TYR 87": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ARG 92": "NH1" <-> "NH2" Residue "I GLU 126": "OE1" <-> "OE2" Residue "I GLU 131": "OE1" <-> "OE2" Residue "I ARG 191": "NH1" <-> "NH2" Residue "I ARG 220": "NH1" <-> "NH2" Residue "I GLU 222": "OE1" <-> "OE2" Residue "I ARG 225": "NH1" <-> "NH2" Residue "I GLU 258": "OE1" <-> "OE2" Residue "I ARG 263": "NH1" <-> "NH2" Residue "I ARG 265": "NH1" <-> "NH2" Residue "I ARG 308": "NH1" <-> "NH2" Residue "I ARG 343": "NH1" <-> "NH2" Residue "I GLU 360": "OE1" <-> "OE2" Residue "I ARG 407": "NH1" <-> "NH2" Residue "I ARG 473": "NH1" <-> "NH2" Residue "J TYR 25": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ARG 29": "NH1" <-> "NH2" Residue "J GLU 81": "OE1" <-> "OE2" Residue "J GLU 86": "OE1" <-> "OE2" Residue "J GLU 133": "OE1" <-> "OE2" Residue "J GLU 143": "OE1" <-> "OE2" Residue "J ARG 191": "NH1" <-> "NH2" Residue "J GLU 196": "OE1" <-> "OE2" Residue "J ARG 220": "NH1" <-> "NH2" Residue "J GLU 222": "OE1" <-> "OE2" Residue "J ARG 225": "NH1" <-> "NH2" Residue "J GLU 258": "OE1" <-> "OE2" Residue "J ARG 263": "NH1" <-> "NH2" Residue "J ARG 265": "NH1" <-> "NH2" Residue "J PHE 294": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ARG 308": "NH1" <-> "NH2" Residue "J ARG 343": "NH1" <-> "NH2" Residue "J ASP 373": "OD1" <-> "OD2" Residue "J ARG 407": "NH1" <-> "NH2" Residue "J ARG 473": "NH1" <-> "NH2" Residue "J GLU 481": "OE1" <-> "OE2" Residue "K TYR 24": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K GLU 104": "OE1" <-> "OE2" Residue "K GLU 108": "OE1" <-> "OE2" Residue "K ARG 126": "NH1" <-> "NH2" Residue "K GLU 128": "OE1" <-> "OE2" Residue "K ARG 138": "NH1" <-> "NH2" Residue "K ARG 151": "NH1" <-> "NH2" Residue "K ARG 232": "NH1" <-> "NH2" Residue "K ARG 252": "NH1" <-> "NH2" Residue "K PHE 269": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ARG 291": "NH1" <-> "NH2" Residue "K GLU 292": "OE1" <-> "OE2" Residue "K ARG 398": "NH1" <-> "NH2" Residue "K TYR 404": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 24": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L GLU 36": "OE1" <-> "OE2" Residue "L GLU 95": "OE1" <-> "OE2" Residue "L GLU 104": "OE1" <-> "OE2" Residue "L GLU 108": "OE1" <-> "OE2" Residue "L ASP 115": "OD1" <-> "OD2" Residue "L ARG 126": "NH1" <-> "NH2" Residue "L ARG 138": "NH1" <-> "NH2" Residue "L ARG 151": "NH1" <-> "NH2" Residue "L PHE 166": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 213": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ARG 232": "NH1" <-> "NH2" Residue "L ARG 252": "NH1" <-> "NH2" Residue "L GLU 278": "OE1" <-> "OE2" Residue "L ARG 291": "NH1" <-> "NH2" Residue "L GLU 335": "OE1" <-> "OE2" Residue "L ARG 398": "NH1" <-> "NH2" Residue "L GLU 414": "OE1" <-> "OE2" Residue "M TYR 5": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M GLU 36": "OE1" <-> "OE2" Residue "N GLU 25": "OE1" <-> "OE2" Residue "O GLU 5": "OE1" <-> "OE2" Residue "O GLU 79": "OE1" <-> "OE2" Residue "O PHE 83": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O ARG 90": "NH1" <-> "NH2" Residue "O GLU 100": "OE1" <-> "OE2" Residue "O ARG 107": "NH1" <-> "NH2" Residue "O GLU 123": "OE1" <-> "OE2" Residue "O ARG 154": "NH1" <-> "NH2" Residue "O GLU 196": "OE1" <-> "OE2" Residue "O TYR 198": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O PHE 202": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O ARG 216": "NH1" <-> "NH2" Residue "O PHE 242": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P PHE 83": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P ARG 90": "NH1" <-> "NH2" Residue "P ARG 107": "NH1" <-> "NH2" Residue "P ARG 154": "NH1" <-> "NH2" Residue "P ARG 201": "NH1" <-> "NH2" Residue "P PHE 202": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P ARG 216": "NH1" <-> "NH2" Residue "P TYR 244": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q TYR 66": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q ARG 90": "NH1" <-> "NH2" Residue "Q ARG 107": "NH1" <-> "NH2" Residue "Q ARG 154": "NH1" <-> "NH2" Residue "Q GLU 193": "OE1" <-> "OE2" Residue "Q ARG 216": "NH1" <-> "NH2" Residue "Q PHE 237": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q TYR 240": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q PHE 241": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R ARG 90": "NH1" <-> "NH2" Residue "R ARG 107": "NH1" <-> "NH2" Residue "R ARG 154": "NH1" <-> "NH2" Residue "R TYR 191": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R ARG 216": "NH1" <-> "NH2" Residue "R PHE 237": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R GLU 248": "OE1" <-> "OE2" Residue "S TYR 63": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S ARG 155": "NH1" <-> "NH2" Residue "S GLU 192": "OE1" <-> "OE2" Residue "S GLU 212": "OE1" <-> "OE2" Residue "T TYR 95": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T GLU 101": "OE1" <-> "OE2" Residue "T TYR 110": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T PHE 151": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T ARG 155": "NH1" <-> "NH2" Residue "U PHE 7": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U GLU 10": "OE1" <-> "OE2" Residue "U ASP 20": "OD1" <-> "OD2" Residue "V GLU 28": "OE1" <-> "OE2" Residue "V TYR 44": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W GLU 162": "OE1" <-> "OE2" Residue "W TYR 177": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X PHE 35": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X GLU 46": "OE1" <-> "OE2" Residue "X GLU 95": "OE1" <-> "OE2" Residue "X TYR 99": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X ASP 139": "OD1" <-> "OD2" Residue "X GLU 140": "OE1" <-> "OE2" Residue "X GLU 177": "OE1" <-> "OE2" Residue "X GLU 226": "OE1" <-> "OE2" Residue "X GLU 296": "OE1" <-> "OE2" Residue "X GLU 328": "OE1" <-> "OE2" Residue "X GLU 331": "OE1" <-> "OE2" Residue "X ARG 369": "NH1" <-> "NH2" Residue "X PHE 370": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y TYR 169": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y ASP 179": "OD1" <-> "OD2" Residue "Y ARG 251": "NH1" <-> "NH2" Residue "Y ARG 262": "NH1" <-> "NH2" Residue "Y GLU 272": "OE1" <-> "OE2" Residue "Y GLU 300": "OE1" <-> "OE2" Residue "Y GLU 320": "OE1" <-> "OE2" Residue "Y GLU 330": "OE1" <-> "OE2" Residue "Y ARG 346": "NH1" <-> "NH2" Residue "Z GLU 142": "OE1" <-> "OE2" Residue "Z GLU 146": "OE1" <-> "OE2" Residue "Z ARG 251": "NH1" <-> "NH2" Residue "Z ARG 262": "NH1" <-> "NH2" Residue "Z GLU 289": "OE1" <-> "OE2" Residue "Z GLU 321": "OE1" <-> "OE2" Residue "Z GLU 330": "OE1" <-> "OE2" Residue "Z ARG 346": "NH1" <-> "NH2" Residue "a ASP 22": "OD1" <-> "OD2" Residue "a ASP 49": "OD1" <-> "OD2" Residue "a GLU 71": "OE1" <-> "OE2" Residue "b GLU 47": "OE1" <-> "OE2" Residue "c ASP 14": "OD1" <-> "OD2" Residue "c GLU 17": "OE1" <-> "OE2" Residue "c GLU 37": "OE1" <-> "OE2" Residue "c ARG 62": "NH1" <-> "NH2" Residue "c TYR 67": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c TYR 77": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d ASP 25": "OD1" <-> "OD2" Residue "d ASP 49": "OD1" <-> "OD2" Residue "i GLU 23": "OE1" <-> "OE2" Residue "i PHE 33": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "i ARG 88": "NH1" <-> "NH2" Residue "i GLU 132": "OE1" <-> "OE2" Residue "i GLU 155": "OE1" <-> "OE2" Residue "i ARG 174": "NH1" <-> "NH2" Residue "j GLU 5": "OE1" <-> "OE2" Residue "j ASP 14": "OD1" <-> "OD2" Residue "j GLU 59": "OE1" <-> "OE2" Residue "j ARG 88": "NH1" <-> "NH2" Residue "j ASP 143": "OD1" <-> "OD2" Residue "j TYR 147": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "j GLU 149": "OE1" <-> "OE2" Residue "j ARG 160": "NH1" <-> "NH2" Residue "j ARG 174": "NH1" <-> "NH2" Residue "j GLU 175": "OE1" <-> "OE2" Residue "k ARG 10": "NH1" <-> "NH2" Residue "k TYR 35": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "k ASP 59": "OD1" <-> "OD2" Residue "k GLU 82": "OE1" <-> "OE2" Residue "k ARG 83": "NH1" <-> "NH2" Residue "k ARG 113": "NH1" <-> "NH2" Residue "k ARG 126": "NH1" <-> "NH2" Residue "k ARG 131": "NH1" <-> "NH2" Residue "k ARG 133": "NH1" <-> "NH2" Residue "k ARG 155": "NH1" <-> "NH2" Residue "k GLU 156": "OE1" <-> "OE2" Residue "k ARG 157": "NH1" <-> "NH2" Residue "k GLU 186": "OE1" <-> "OE2" Residue "k GLU 194": "OE1" <-> "OE2" Residue "s ARG 375": "NH1" <-> "NH2" Residue "s ARG 392": "NH1" <-> "NH2" Residue "u ARG 25": "NH1" <-> "NH2" Residue "u ASP 43": "OD1" <-> "OD2" Residue "u GLU 63": "OE1" <-> "OE2" Residue "v ARG 25": "NH1" <-> "NH2" Residue "v GLU 63": "OE1" <-> "OE2" Residue "y ARG 24": "NH1" <-> "NH2" Residue "y ARG 28": "NH1" <-> "NH2" Residue "y GLU 46": "OE1" <-> "OE2" Residue "y ARG 49": "NH1" <-> "NH2" Residue "y GLU 52": "OE1" <-> "OE2" Residue "y PHE 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "z GLU 9": "OE1" <-> "OE2" Residue "z ARG 28": "NH1" <-> "NH2" Residue "z ASP 40": "OD1" <-> "OD2" Residue "z ARG 49": "NH1" <-> "NH2" Residue "z GLU 52": "OE1" <-> "OE2" Residue "z GLU 55": "OE1" <-> "OE2" Time to flip residues: 0.19s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 72807 Number of models: 1 Model: "" Number of chains: 43 Chain: "A" Number of atoms: 5698 Number of conformers: 1 Conformer: "" Number of residues, atoms: 749, 5698 Classifications: {'peptide': 749} Link IDs: {'PTRANS': 59, 'TRANS': 689} Chain breaks: 3 Chain: "B" Number of atoms: 5698 Number of conformers: 1 Conformer: "" Number of residues, atoms: 749, 5698 Classifications: {'peptide': 749} Link IDs: {'PTRANS': 59, 'TRANS': 689} Chain breaks: 3 Chain: "C" Number of atoms: 3248 Number of conformers: 1 Conformer: "" Number of residues, atoms: 427, 3248 Classifications: {'peptide': 427} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 409} Chain breaks: 2 Chain: "D" Number of atoms: 3248 Number of conformers: 1 Conformer: "" Number of residues, atoms: 427, 3248 Classifications: {'peptide': 427} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 409} Chain breaks: 2 Chain: "E" Number of atoms: 2216 Number of conformers: 1 Conformer: "" Number of residues, atoms: 284, 2216 Classifications: {'peptide': 284} Link IDs: {'PTRANS': 6, 'TRANS': 277} Chain breaks: 2 Chain: "F" Number of atoms: 2232 Number of conformers: 1 Conformer: "" Number of residues, atoms: 287, 2232 Classifications: {'peptide': 287} Link IDs: {'PTRANS': 6, 'TRANS': 280} Chain breaks: 2 Chain: "G" Number of atoms: 3207 Number of conformers: 1 Conformer: "" Number of residues, atoms: 421, 3207 Classifications: {'peptide': 421} Link IDs: {'PTRANS': 39, 'TRANS': 381} Chain breaks: 1 Chain: "H" Number of atoms: 3207 Number of conformers: 1 Conformer: "" Number of residues, atoms: 421, 3207 Classifications: {'peptide': 421} Link IDs: {'PTRANS': 39, 'TRANS': 381} Chain breaks: 1 Chain: "I" Number of atoms: 3644 Number of conformers: 1 Conformer: "" Number of residues, atoms: 483, 3644 Classifications: {'peptide': 483} Link IDs: {'PCIS': 1, 'PTRANS': 38, 'TRANS': 443} Chain breaks: 2 Chain: "J" Number of atoms: 3644 Number of conformers: 1 Conformer: "" Number of residues, atoms: 483, 3644 Classifications: {'peptide': 483} Link IDs: {'PCIS': 1, 'PTRANS': 38, 'TRANS': 443} Chain breaks: 2 Chain: "K" Number of atoms: 3214 Number of conformers: 1 Conformer: "" Number of residues, atoms: 428, 3214 Classifications: {'peptide': 428} Link IDs: {'PCIS': 1, 'PTRANS': 45, 'TRANS': 381} Chain breaks: 2 Chain: "L" Number of atoms: 3214 Number of conformers: 1 Conformer: "" Number of residues, atoms: 428, 3214 Classifications: {'peptide': 428} Link IDs: {'PCIS': 1, 'PTRANS': 45, 'TRANS': 381} Chain breaks: 2 Chain: "M" Number of atoms: 373 Number of conformers: 1 Conformer: "" Number of residues, atoms: 47, 373 Classifications: {'peptide': 47} Link IDs: {'PTRANS': 4, 'TRANS': 42} Chain: "N" Number of atoms: 316 Number of conformers: 1 Conformer: "" Number of residues, atoms: 40, 316 Classifications: {'peptide': 40} Link IDs: {'PTRANS': 3, 'TRANS': 36} Chain: "O" Number of atoms: 1930 Number of conformers: 1 Conformer: "" Number of residues, atoms: 249, 1930 Classifications: {'peptide': 249} Link IDs: {'PTRANS': 10, 'TRANS': 238} Chain breaks: 1 Chain: "P" Number of atoms: 1930 Number of conformers: 1 Conformer: "" Number of residues, atoms: 249, 1930 Classifications: {'peptide': 249} Link IDs: {'PTRANS': 10, 'TRANS': 238} Chain breaks: 1 Chain: "Q" Number of atoms: 1930 Number of conformers: 1 Conformer: "" Number of residues, atoms: 249, 1930 Classifications: {'peptide': 249} Link IDs: {'PTRANS': 10, 'TRANS': 238} Chain breaks: 1 Chain: "R" Number of atoms: 1930 Number of conformers: 1 Conformer: "" Number of residues, atoms: 249, 1930 Classifications: {'peptide': 249} Link IDs: {'PTRANS': 10, 'TRANS': 238} Chain breaks: 1 Chain: "S" Number of atoms: 1530 Number of conformers: 1 Conformer: "" Number of residues, atoms: 199, 1530 Classifications: {'peptide': 199} Link IDs: {'PTRANS': 12, 'TRANS': 186} Chain breaks: 1 Chain: "T" Number of atoms: 1530 Number of conformers: 1 Conformer: "" Number of residues, atoms: 199, 1530 Classifications: {'peptide': 199} Link IDs: {'PTRANS': 12, 'TRANS': 186} Chain breaks: 1 Chain: "U" Number of atoms: 382 Number of conformers: 1 Conformer: "" Number of residues, atoms: 48, 382 Classifications: {'peptide': 48} Link IDs: {'PTRANS': 2, 'TRANS': 45} Chain: "V" Number of atoms: 1055 Number of conformers: 1 Conformer: "" Number of residues, atoms: 182, 1055 Classifications: {'peptide': 182} Incomplete info: {'truncation_to_alanine': 103} Link IDs: {'PTRANS': 11, 'TRANS': 170} Chain breaks: 4 Unresolved chain link angles: 8 Unresolved non-hydrogen bonds: 335 Unresolved non-hydrogen angles: 429 Unresolved non-hydrogen dihedrals: 271 Unresolved non-hydrogen chiralities: 37 Planarities with less than four sites: {'GLN:plan1': 5, 'HIS:plan': 1, 'TYR:plan': 2, 'ASN:plan1': 2, 'ASP:plan': 9, 'PHE:plan': 7, 'GLU:plan': 8, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 161 Chain: "W" Number of atoms: 1241 Number of conformers: 1 Conformer: "" Number of residues, atoms: 163, 1241 Classifications: {'peptide': 163} Link IDs: {'PTRANS': 13, 'TRANS': 149} Chain: "X" Number of atoms: 2787 Number of conformers: 1 Conformer: "" Number of residues, atoms: 379, 2787 Classifications: {'peptide': 379} Link IDs: {'PTRANS': 22, 'TRANS': 356} Chain: "Y" Number of atoms: 1693 Number of conformers: 1 Conformer: "" Number of residues, atoms: 213, 1693 Classifications: {'peptide': 213} Link IDs: {'PTRANS': 20, 'TRANS': 192} Chain: "Z" Number of atoms: 1693 Number of conformers: 1 Conformer: "" Number of residues, atoms: 213, 1693 Classifications: {'peptide': 213} Link IDs: {'PTRANS': 20, 'TRANS': 192} Chain: "a" Number of atoms: 686 Number of conformers: 1 Conformer: "" Number of residues, atoms: 84, 686 Classifications: {'peptide': 84} Link IDs: {'PTRANS': 1, 'TRANS': 82} Chain: "b" Number of atoms: 686 Number of conformers: 1 Conformer: "" Number of residues, atoms: 84, 686 Classifications: {'peptide': 84} Link IDs: {'PTRANS': 1, 'TRANS': 82} Chain: "c" Number of atoms: 686 Number of conformers: 1 Conformer: "" Number of residues, atoms: 84, 686 Classifications: {'peptide': 84} Link IDs: {'PTRANS': 1, 'TRANS': 82} Chain: "d" Number of atoms: 686 Number of conformers: 1 Conformer: "" Number of residues, atoms: 84, 686 Classifications: {'peptide': 84} Link IDs: {'PTRANS': 1, 'TRANS': 82} Chain: "e" Number of atoms: 170 Number of conformers: 1 Conformer: "" Number of residues, atoms: 34, 170 Classifications: {'peptide': 34} Incomplete info: {'truncation_to_alanine': 34} Link IDs: {'TRANS': 33} Unresolved non-hydrogen bonds: 68 Unresolved non-hydrogen angles: 102 Unresolved non-hydrogen dihedrals: 34 Planarities with less than four sites: {'UNK:plan-1': 34} Unresolved non-hydrogen planarities: 34 Chain: "i" Number of atoms: 1558 Number of conformers: 1 Conformer: "" Number of residues, atoms: 201, 1558 Classifications: {'peptide': 201} Link IDs: {'PTRANS': 14, 'TRANS': 186} Chain: "j" Number of atoms: 1558 Number of conformers: 1 Conformer: "" Number of residues, atoms: 201, 1558 Classifications: {'peptide': 201} Link IDs: {'PTRANS': 14, 'TRANS': 186} Chain: "k" Number of atoms: 1756 Number of conformers: 1 Conformer: "" Number of residues, atoms: 213, 1756 Classifications: {'peptide': 213} Link IDs: {'PTRANS': 17, 'TRANS': 195} Chain breaks: 1 Chain: "s" Number of atoms: 301 Number of conformers: 1 Conformer: "" Number of residues, atoms: 37, 301 Classifications: {'peptide': 37} Link IDs: {'PTRANS': 2, 'TRANS': 34} Chain: "u" Number of atoms: 427 Number of conformers: 1 Conformer: "" Number of residues, atoms: 50, 427 Classifications: {'peptide': 50} Link IDs: {'PTRANS': 3, 'TRANS': 46} Chain: "v" Number of atoms: 427 Number of conformers: 1 Conformer: "" Number of residues, atoms: 50, 427 Classifications: {'peptide': 50} Link IDs: {'PTRANS': 3, 'TRANS': 46} Chain: "y" Number of atoms: 528 Number of conformers: 1 Conformer: "" Number of residues, atoms: 64, 528 Classifications: {'peptide': 64} Link IDs: {'PTRANS': 2, 'TRANS': 61} Chain: "z" Number of atoms: 528 Number of conformers: 1 Conformer: "" Number of residues, atoms: 64, 528 Classifications: {'peptide': 64} Link IDs: {'PTRANS': 2, 'TRANS': 61} Chain: "G" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 5 Unusual residues: {'PO4': 1} Classifications: {'undetermined': 1} Chain: "H" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 5 Unusual residues: {'PO4': 1} Classifications: {'undetermined': 1} Chain: "K" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 5 Unusual residues: {'PO4': 1} Classifications: {'undetermined': 1} Chain: "L" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 5 Unusual residues: {'PO4': 1} Classifications: {'undetermined': 1} Time building chain proxies: 29.65, per 1000 atoms: 0.41 Number of scatterers: 72807 At special positions: 0 Unit cell: (289.94, 349.89, 332.45, 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 240 16.00 P 4 15.00 O 13763 8.00 N 12498 7.00 C 46302 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS O 105 " - pdb=" SG CYS O 155 " distance=2.03 Simple disulfide: pdb=" SG CYS P 105 " - pdb=" SG CYS P 155 " distance=2.04 Simple disulfide: pdb=" SG CYS Q 105 " - pdb=" SG CYS Q 155 " distance=2.03 Simple disulfide: pdb=" SG CYS R 105 " - pdb=" SG CYS R 155 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 30.66 Conformation dependent library (CDL) restraints added in 14.0 seconds 18672 Ramachandran restraints generated. 9336 Oldfield, 0 Emsley, 9336 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 17614 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 271 helices and 84 sheets defined 36.8% alpha, 14.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 11.96 Creating SS restraints... Processing helix chain 'A' and resid 86 through 88 No H-bonds generated for 'chain 'A' and resid 86 through 88' Processing helix chain 'A' and resid 139 through 143 Processing helix chain 'A' and resid 181 through 194 Processing helix chain 'A' and resid 200 through 204 removed outlier: 3.592A pdb=" N ALA A 204 " --> pdb=" O ASP A 200 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 200 through 204' Processing helix chain 'A' and resid 225 through 230 Processing helix chain 'A' and resid 359 through 361 No H-bonds generated for 'chain 'A' and resid 359 through 361' Processing helix chain 'A' and resid 406 through 414 Processing helix chain 'A' and resid 461 through 468 Processing helix chain 'A' and resid 473 through 478 Processing helix chain 'A' and resid 481 through 511 Processing helix chain 'A' and resid 540 through 550 removed outlier: 6.118A pdb=" N HIS A 544 " --> pdb=" O ALA A 541 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N LYS A 547 " --> pdb=" O HIS A 544 " (cutoff:3.500A) removed outlier: 4.838A pdb=" N ASN A 548 " --> pdb=" O ASP A 545 " (cutoff:3.500A) Processing helix chain 'A' and resid 711 through 713 No H-bonds generated for 'chain 'A' and resid 711 through 713' Processing helix chain 'A' and resid 721 through 723 No H-bonds generated for 'chain 'A' and resid 721 through 723' Processing helix chain 'B' and resid 139 through 144 removed outlier: 4.336A pdb=" N GLN B 144 " --> pdb=" O PRO B 140 " (cutoff:3.500A) Processing helix chain 'B' and resid 181 through 193 removed outlier: 3.565A pdb=" N ILE B 188 " --> pdb=" O LEU B 184 " (cutoff:3.500A) Processing helix chain 'B' and resid 200 through 204 Processing helix chain 'B' and resid 225 through 230 Processing helix chain 'B' and resid 406 through 414 Processing helix chain 'B' and resid 464 through 468 removed outlier: 3.680A pdb=" N ALA B 468 " --> pdb=" O VAL B 464 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 464 through 468' Processing helix chain 'B' and resid 473 through 476 No H-bonds generated for 'chain 'B' and resid 473 through 476' Processing helix chain 'B' and resid 481 through 511 Processing helix chain 'B' and resid 539 through 551 removed outlier: 3.835A pdb=" N ILE B 542 " --> pdb=" O LEU B 539 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N GLU B 543 " --> pdb=" O GLU B 540 " (cutoff:3.500A) removed outlier: 6.233A pdb=" N HIS B 544 " --> pdb=" O ALA B 541 " (cutoff:3.500A) Processing helix chain 'B' and resid 721 through 723 No H-bonds generated for 'chain 'B' and resid 721 through 723' Processing helix chain 'C' and resid 9 through 31 removed outlier: 7.119A pdb=" N GLU C 19 " --> pdb=" O GLU C 15 " (cutoff:3.500A) removed outlier: 6.222A pdb=" N ALA C 20 " --> pdb=" O THR C 16 " (cutoff:3.500A) Processing helix chain 'C' and resid 36 through 98 removed outlier: 3.613A pdb=" N LEU C 96 " --> pdb=" O ALA C 92 " (cutoff:3.500A) removed outlier: 4.401A pdb=" N ALA C 97 " --> pdb=" O ALA C 93 " (cutoff:3.500A) removed outlier: 4.150A pdb=" N LEU C 98 " --> pdb=" O ASP C 94 " (cutoff:3.500A) Processing helix chain 'C' and resid 103 through 117 Processing helix chain 'C' and resid 238 through 244 Processing helix chain 'C' and resid 306 through 336 Processing helix chain 'C' and resid 342 through 359 Processing helix chain 'C' and resid 435 through 484 removed outlier: 3.997A pdb=" N HIS C 475 " --> pdb=" O LEU C 471 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N SER C 476 " --> pdb=" O ALA C 472 " (cutoff:3.500A) removed outlier: 5.498A pdb=" N ASP C 477 " --> pdb=" O SER C 473 " (cutoff:3.500A) removed outlier: 6.285A pdb=" N ALA C 478 " --> pdb=" O SER C 474 " (cutoff:3.500A) Processing helix chain 'C' and resid 491 through 503 Processing helix chain 'C' and resid 514 through 520 removed outlier: 4.367A pdb=" N SER C 519 " --> pdb=" O LYS C 515 " (cutoff:3.500A) removed outlier: 4.170A pdb=" N HIS C 520 " --> pdb=" O ARG C 516 " (cutoff:3.500A) Processing helix chain 'C' and resid 523 through 531 removed outlier: 3.955A pdb=" N GLU C 527 " --> pdb=" O PRO C 523 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N ALA C 530 " --> pdb=" O PHE C 526 " (cutoff:3.500A) Processing helix chain 'C' and resid 540 through 551 removed outlier: 3.791A pdb=" N ARG C 545 " --> pdb=" O ALA C 541 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N VAL C 546 " --> pdb=" O VAL C 542 " (cutoff:3.500A) Processing helix chain 'C' and resid 556 through 562 Processing helix chain 'C' and resid 568 through 609 Processing helix chain 'D' and resid 9 through 31 removed outlier: 6.741A pdb=" N GLU D 19 " --> pdb=" O GLU D 15 " (cutoff:3.500A) removed outlier: 6.270A pdb=" N ALA D 20 " --> pdb=" O THR D 16 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N ARG D 23 " --> pdb=" O GLU D 19 " (cutoff:3.500A) Processing helix chain 'D' and resid 36 through 98 removed outlier: 4.026A pdb=" N LEU D 98 " --> pdb=" O ASP D 94 " (cutoff:3.500A) Processing helix chain 'D' and resid 103 through 117 Processing helix chain 'D' and resid 238 through 244 Processing helix chain 'D' and resid 306 through 334 Processing helix chain 'D' and resid 340 through 361 removed outlier: 3.917A pdb=" N GLU D 345 " --> pdb=" O GLU D 341 " (cutoff:3.500A) Processing helix chain 'D' and resid 435 through 484 removed outlier: 3.998A pdb=" N HIS D 475 " --> pdb=" O LEU D 471 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N SER D 476 " --> pdb=" O ALA D 472 " (cutoff:3.500A) removed outlier: 5.448A pdb=" N ASP D 477 " --> pdb=" O SER D 473 " (cutoff:3.500A) removed outlier: 6.177A pdb=" N ALA D 478 " --> pdb=" O SER D 474 " (cutoff:3.500A) Processing helix chain 'D' and resid 491 through 504 Processing helix chain 'D' and resid 514 through 519 removed outlier: 4.705A pdb=" N SER D 519 " --> pdb=" O LYS D 515 " (cutoff:3.500A) Processing helix chain 'D' and resid 523 through 531 removed outlier: 3.643A pdb=" N ALA D 530 " --> pdb=" O PHE D 526 " (cutoff:3.500A) Processing helix chain 'D' and resid 540 through 551 Processing helix chain 'D' and resid 556 through 560 Processing helix chain 'D' and resid 569 through 609 Processing helix chain 'E' and resid 154 through 260 Proline residue: E 160 - end of helix removed outlier: 3.778A pdb=" N ALA E 245 " --> pdb=" O ALA E 241 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N GLY E 251 " --> pdb=" O GLY E 247 " (cutoff:3.500A) Processing helix chain 'E' and resid 270 through 360 Proline residue: E 280 - end of helix Proline residue: E 355 - end of helix Processing helix chain 'E' and resid 369 through 384 Processing helix chain 'E' and resid 472 through 482 Processing helix chain 'E' and resid 487 through 498 Processing helix chain 'E' and resid 500 through 502 No H-bonds generated for 'chain 'E' and resid 500 through 502' Processing helix chain 'F' and resid 155 through 263 Proline residue: F 160 - end of helix removed outlier: 3.620A pdb=" N ARG F 226 " --> pdb=" O MET F 222 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N ALA F 240 " --> pdb=" O ARG F 236 " (cutoff:3.500A) Processing helix chain 'F' and resid 270 through 360 Proline residue: F 280 - end of helix Proline residue: F 355 - end of helix Processing helix chain 'F' and resid 369 through 385 Processing helix chain 'F' and resid 472 through 481 Processing helix chain 'F' and resid 487 through 498 Processing helix chain 'G' and resid 7 through 14 Processing helix chain 'G' and resid 25 through 38 Processing helix chain 'G' and resid 47 through 57 Processing helix chain 'G' and resid 77 through 85 removed outlier: 3.952A pdb=" N ILE G 85 " --> pdb=" O ALA G 81 " (cutoff:3.500A) Processing helix chain 'G' and resid 114 through 124 Processing helix chain 'G' and resid 131 through 145 Processing helix chain 'G' and resid 212 through 215 Processing helix chain 'G' and resid 236 through 244 removed outlier: 3.814A pdb=" N ARG G 244 " --> pdb=" O LYS G 240 " (cutoff:3.500A) Processing helix chain 'G' and resid 267 through 282 Processing helix chain 'G' and resid 287 through 289 No H-bonds generated for 'chain 'G' and resid 287 through 289' Processing helix chain 'G' and resid 316 through 318 No H-bonds generated for 'chain 'G' and resid 316 through 318' Processing helix chain 'G' and resid 364 through 366 No H-bonds generated for 'chain 'G' and resid 364 through 366' Processing helix chain 'H' and resid 7 through 14 Processing helix chain 'H' and resid 25 through 39 Processing helix chain 'H' and resid 47 through 57 Processing helix chain 'H' and resid 77 through 85 removed outlier: 3.999A pdb=" N ILE H 85 " --> pdb=" O ALA H 81 " (cutoff:3.500A) Processing helix chain 'H' and resid 114 through 124 Processing helix chain 'H' and resid 130 through 145 Processing helix chain 'H' and resid 212 through 214 No H-bonds generated for 'chain 'H' and resid 212 through 214' Processing helix chain 'H' and resid 236 through 244 removed outlier: 3.976A pdb=" N ARG H 244 " --> pdb=" O LYS H 240 " (cutoff:3.500A) Processing helix chain 'H' and resid 267 through 282 Processing helix chain 'H' and resid 316 through 318 No H-bonds generated for 'chain 'H' and resid 316 through 318' Processing helix chain 'H' and resid 364 through 366 No H-bonds generated for 'chain 'H' and resid 364 through 366' Processing helix chain 'I' and resid 19 through 25 Processing helix chain 'I' and resid 53 through 57 Processing helix chain 'I' and resid 85 through 95 removed outlier: 3.955A pdb=" N LEU I 90 " --> pdb=" O GLU I 86 " (cutoff:3.500A) removed outlier: 4.857A pdb=" N VAL I 91 " --> pdb=" O TYR I 87 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N ARG I 92 " --> pdb=" O ASN I 88 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N ALA I 95 " --> pdb=" O VAL I 91 " (cutoff:3.500A) Processing helix chain 'I' and resid 98 through 120 Processing helix chain 'I' and resid 123 through 154 removed outlier: 4.025A pdb=" N ALA I 127 " --> pdb=" O PRO I 123 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N SER I 154 " --> pdb=" O LYS I 150 " (cutoff:3.500A) Processing helix chain 'I' and resid 162 through 173 Processing helix chain 'I' and resid 209 through 224 Processing helix chain 'I' and resid 243 through 248 Processing helix chain 'I' and resid 250 through 268 Processing helix chain 'I' and resid 300 through 310 Processing helix chain 'I' and resid 341 through 350 Processing helix chain 'I' and resid 370 through 378 Processing helix chain 'I' and resid 415 through 425 Processing helix chain 'I' and resid 428 through 445 removed outlier: 3.616A pdb=" N HIS I 445 " --> pdb=" O ILE I 441 " (cutoff:3.500A) Processing helix chain 'I' and resid 451 through 459 Processing helix chain 'I' and resid 476 through 478 No H-bonds generated for 'chain 'I' and resid 476 through 478' Processing helix chain 'I' and resid 486 through 489 No H-bonds generated for 'chain 'I' and resid 486 through 489' Processing helix chain 'I' and resid 497 through 499 No H-bonds generated for 'chain 'I' and resid 497 through 499' Processing helix chain 'I' and resid 508 through 517 Processing helix chain 'J' and resid 19 through 24 Processing helix chain 'J' and resid 53 through 56 No H-bonds generated for 'chain 'J' and resid 53 through 56' Processing helix chain 'J' and resid 85 through 94 removed outlier: 4.335A pdb=" N LEU J 90 " --> pdb=" O GLU J 86 " (cutoff:3.500A) removed outlier: 4.741A pdb=" N VAL J 91 " --> pdb=" O TYR J 87 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N ARG J 92 " --> pdb=" O ASN J 88 " (cutoff:3.500A) Processing helix chain 'J' and resid 98 through 120 Processing helix chain 'J' and resid 123 through 155 removed outlier: 4.071A pdb=" N ALA J 127 " --> pdb=" O PRO J 123 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N SER J 154 " --> pdb=" O LYS J 150 " (cutoff:3.500A) Processing helix chain 'J' and resid 162 through 173 Processing helix chain 'J' and resid 191 through 194 No H-bonds generated for 'chain 'J' and resid 191 through 194' Processing helix chain 'J' and resid 209 through 224 Processing helix chain 'J' and resid 243 through 246 No H-bonds generated for 'chain 'J' and resid 243 through 246' Processing helix chain 'J' and resid 250 through 268 Processing helix chain 'J' and resid 300 through 310 Processing helix chain 'J' and resid 341 through 349 Processing helix chain 'J' and resid 369 through 378 Processing helix chain 'J' and resid 415 through 425 Processing helix chain 'J' and resid 428 through 445 removed outlier: 3.673A pdb=" N HIS J 445 " --> pdb=" O ILE J 441 " (cutoff:3.500A) Processing helix chain 'J' and resid 449 through 459 removed outlier: 3.814A pdb=" N ALA J 453 " --> pdb=" O PRO J 449 " (cutoff:3.500A) Processing helix chain 'J' and resid 471 through 473 No H-bonds generated for 'chain 'J' and resid 471 through 473' Processing helix chain 'J' and resid 476 through 478 No H-bonds generated for 'chain 'J' and resid 476 through 478' Processing helix chain 'J' and resid 486 through 489 No H-bonds generated for 'chain 'J' and resid 486 through 489' Processing helix chain 'J' and resid 497 through 499 No H-bonds generated for 'chain 'J' and resid 497 through 499' Processing helix chain 'J' and resid 508 through 516 Processing helix chain 'K' and resid 5 through 12 Processing helix chain 'K' and resid 23 through 37 Processing helix chain 'K' and resid 42 through 48 removed outlier: 4.022A pdb=" N GLU K 47 " --> pdb=" O VAL K 43 " (cutoff:3.500A) Processing helix chain 'K' and resid 69 through 81 removed outlier: 3.751A pdb=" N LEU K 81 " --> pdb=" O ALA K 77 " (cutoff:3.500A) Processing helix chain 'K' and resid 110 through 120 Processing helix chain 'K' and resid 126 through 141 removed outlier: 3.633A pdb=" N TYR K 130 " --> pdb=" O ARG K 126 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N ALA K 131 " --> pdb=" O GLN K 127 " (cutoff:3.500A) Processing helix chain 'K' and resid 216 through 224 removed outlier: 4.184A pdb=" N LEU K 224 " --> pdb=" O LYS K 220 " (cutoff:3.500A) Processing helix chain 'K' and resid 247 through 261 Processing helix chain 'K' and resid 290 through 294 removed outlier: 3.814A pdb=" N MET K 293 " --> pdb=" O GLY K 290 " (cutoff:3.500A) Processing helix chain 'K' and resid 296 through 298 No H-bonds generated for 'chain 'K' and resid 296 through 298' Processing helix chain 'L' and resid 5 through 12 Processing helix chain 'L' and resid 23 through 37 Processing helix chain 'L' and resid 42 through 48 removed outlier: 3.789A pdb=" N GLU L 47 " --> pdb=" O VAL L 43 " (cutoff:3.500A) Processing helix chain 'L' and resid 69 through 80 Processing helix chain 'L' and resid 110 through 120 Processing helix chain 'L' and resid 126 through 141 removed outlier: 3.621A pdb=" N TYR L 130 " --> pdb=" O ARG L 126 " (cutoff:3.500A) Processing helix chain 'L' and resid 216 through 224 removed outlier: 4.467A pdb=" N LEU L 224 " --> pdb=" O LYS L 220 " (cutoff:3.500A) Processing helix chain 'L' and resid 247 through 262 Processing helix chain 'L' and resid 291 through 294 Processing helix chain 'L' and resid 296 through 298 No H-bonds generated for 'chain 'L' and resid 296 through 298' Processing helix chain 'M' and resid 15 through 29 Processing helix chain 'M' and resid 34 through 46 Processing helix chain 'N' and resid 15 through 29 Processing helix chain 'N' and resid 34 through 46 Processing helix chain 'O' and resid 8 through 14 removed outlier: 3.537A pdb=" N LEU O 12 " --> pdb=" O ILE O 8 " (cutoff:3.500A) Processing helix chain 'O' and resid 24 through 40 Proline residue: O 35 - end of helix Processing helix chain 'O' and resid 99 through 104 Processing helix chain 'O' and resid 149 through 164 Processing helix chain 'O' and resid 195 through 197 No H-bonds generated for 'chain 'O' and resid 195 through 197' Processing helix chain 'O' and resid 265 through 268 No H-bonds generated for 'chain 'O' and resid 265 through 268' Processing helix chain 'P' and resid 8 through 14 Processing helix chain 'P' and resid 24 through 40 Proline residue: P 35 - end of helix Processing helix chain 'P' and resid 99 through 107 removed outlier: 4.019A pdb=" N ARG P 107 " --> pdb=" O THR P 103 " (cutoff:3.500A) Processing helix chain 'P' and resid 149 through 163 Processing helix chain 'P' and resid 195 through 197 No H-bonds generated for 'chain 'P' and resid 195 through 197' Processing helix chain 'Q' and resid 9 through 14 Processing helix chain 'Q' and resid 24 through 40 Proline residue: Q 35 - end of helix Processing helix chain 'Q' and resid 99 through 104 Processing helix chain 'Q' and resid 149 through 164 Processing helix chain 'Q' and resid 195 through 197 No H-bonds generated for 'chain 'Q' and resid 195 through 197' Processing helix chain 'Q' and resid 216 through 218 No H-bonds generated for 'chain 'Q' and resid 216 through 218' Processing helix chain 'Q' and resid 265 through 268 No H-bonds generated for 'chain 'Q' and resid 265 through 268' Processing helix chain 'R' and resid 8 through 14 Processing helix chain 'R' and resid 24 through 41 Proline residue: R 35 - end of helix Processing helix chain 'R' and resid 99 through 107 removed outlier: 3.744A pdb=" N ARG R 107 " --> pdb=" O THR R 103 " (cutoff:3.500A) Processing helix chain 'R' and resid 149 through 163 Processing helix chain 'R' and resid 195 through 197 No H-bonds generated for 'chain 'R' and resid 195 through 197' Processing helix chain 'R' and resid 265 through 268 No H-bonds generated for 'chain 'R' and resid 265 through 268' Processing helix chain 'S' and resid 18 through 20 No H-bonds generated for 'chain 'S' and resid 18 through 20' Processing helix chain 'T' and resid 18 through 20 No H-bonds generated for 'chain 'T' and resid 18 through 20' Processing helix chain 'U' and resid 9 through 11 No H-bonds generated for 'chain 'U' and resid 9 through 11' Processing helix chain 'U' and resid 18 through 32 Processing helix chain 'U' and resid 37 through 51 Processing helix chain 'V' and resid 18 through 32 Processing helix chain 'V' and resid 37 through 53 Processing helix chain 'V' and resid 61 through 72 Processing helix chain 'V' and resid 80 through 89 Processing helix chain 'V' and resid 96 through 106 Processing helix chain 'V' and resid 117 through 126 removed outlier: 3.543A pdb=" N SER V 126 " --> pdb=" O CYS V 122 " (cutoff:3.500A) Processing helix chain 'V' and resid 130 through 141 Processing helix chain 'V' and resid 149 through 159 removed outlier: 3.527A pdb=" N LEU V 153 " --> pdb=" O ALA V 149 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N LEU V 159 " --> pdb=" O LEU V 155 " (cutoff:3.500A) Processing helix chain 'V' and resid 169 through 178 Processing helix chain 'V' and resid 188 through 192 Processing helix chain 'W' and resid 45 through 56 Processing helix chain 'W' and resid 129 through 131 No H-bonds generated for 'chain 'W' and resid 129 through 131' Processing helix chain 'W' and resid 144 through 155 removed outlier: 4.361A pdb=" N THR W 155 " --> pdb=" O LEU W 151 " (cutoff:3.500A) Processing helix chain 'X' and resid 3 through 16 Processing helix chain 'X' and resid 36 through 48 removed outlier: 3.581A pdb=" N ALA X 39 " --> pdb=" O GLU X 36 " (cutoff:3.500A) Proline residue: X 41 - end of helix removed outlier: 3.974A pdb=" N LEU X 47 " --> pdb=" O VAL X 44 " (cutoff:3.500A) Processing helix chain 'X' and resid 52 through 65 Processing helix chain 'X' and resid 69 through 77 Processing helix chain 'X' and resid 81 through 89 Processing helix chain 'X' and resid 94 through 109 removed outlier: 3.923A pdb=" N ALA X 109 " --> pdb=" O LYS X 105 " (cutoff:3.500A) Processing helix chain 'X' and resid 111 through 119 Processing helix chain 'X' and resid 122 through 131 removed outlier: 4.272A pdb=" N GLU X 131 " --> pdb=" O ALA X 127 " (cutoff:3.500A) Processing helix chain 'X' and resid 136 through 150 removed outlier: 3.753A pdb=" N ARG X 150 " --> pdb=" O ILE X 146 " (cutoff:3.500A) Processing helix chain 'X' and resid 152 through 159 Processing helix chain 'X' and resid 166 through 178 Processing helix chain 'X' and resid 183 through 197 Processing helix chain 'X' and resid 203 through 213 Processing helix chain 'X' and resid 215 through 223 Processing helix chain 'X' and resid 229 through 244 removed outlier: 4.389A pdb=" N THR X 244 " --> pdb=" O GLY X 240 " (cutoff:3.500A) Processing helix chain 'X' and resid 246 through 255 Processing helix chain 'X' and resid 258 through 264 removed outlier: 3.556A pdb=" N ALA X 264 " --> pdb=" O LEU X 260 " (cutoff:3.500A) Processing helix chain 'X' and resid 271 through 286 removed outlier: 4.220A pdb=" N ILE X 286 " --> pdb=" O GLY X 282 " (cutoff:3.500A) Processing helix chain 'X' and resid 288 through 296 Processing helix chain 'X' and resid 300 through 307 Processing helix chain 'X' and resid 313 through 328 removed outlier: 3.912A pdb=" N GLU X 328 " --> pdb=" O SER X 324 " (cutoff:3.500A) Processing helix chain 'X' and resid 332 through 338 Processing helix chain 'X' and resid 341 through 351 Processing helix chain 'X' and resid 355 through 368 Processing helix chain 'Y' and resid 145 through 150 Processing helix chain 'Y' and resid 234 through 238 Processing helix chain 'Y' and resid 300 through 310 Processing helix chain 'Y' and resid 320 through 333 Processing helix chain 'Z' and resid 145 through 150 Processing helix chain 'Z' and resid 234 through 238 Processing helix chain 'Z' and resid 300 through 310 Processing helix chain 'Z' and resid 320 through 333 Processing helix chain 'a' and resid 17 through 32 removed outlier: 3.626A pdb=" N GLU a 32 " --> pdb=" O THR a 28 " (cutoff:3.500A) Processing helix chain 'a' and resid 37 through 51 Processing helix chain 'b' and resid 17 through 33 Processing helix chain 'b' and resid 37 through 51 removed outlier: 3.578A pdb=" N LYS b 51 " --> pdb=" O GLU b 47 " (cutoff:3.500A) Processing helix chain 'c' and resid 17 through 33 Processing helix chain 'c' and resid 37 through 50 Processing helix chain 'd' and resid 17 through 33 Processing helix chain 'd' and resid 37 through 51 Processing helix chain 'e' and resid 6 through 19 removed outlier: 4.505A pdb=" N UNK e 16 " --> pdb=" O UNK e 12 " (cutoff:3.500A) removed outlier: 5.968A pdb=" N UNK e 17 " --> pdb=" O UNK e 13 " (cutoff:3.500A) removed outlier: 4.223A pdb=" N UNK e 18 " --> pdb=" O UNK e 14 " (cutoff:3.500A) Processing helix chain 'e' and resid 23 through 37 Processing helix chain 'i' and resid 13 through 17 removed outlier: 4.109A pdb=" N ARG i 17 " --> pdb=" O ASP i 14 " (cutoff:3.500A) Processing helix chain 'i' and resid 21 through 31 Processing helix chain 'i' and resid 45 through 51 Processing helix chain 'i' and resid 61 through 68 Processing helix chain 'i' and resid 83 through 91 Processing helix chain 'i' and resid 96 through 102 Processing helix chain 'i' and resid 107 through 110 No H-bonds generated for 'chain 'i' and resid 107 through 110' Processing helix chain 'i' and resid 126 through 136 Processing helix chain 'i' and resid 150 through 175 removed outlier: 3.844A pdb=" N GLN i 162 " --> pdb=" O THR i 158 " (cutoff:3.500A) Proline residue: i 163 - end of helix removed outlier: 4.947A pdb=" N ALA i 166 " --> pdb=" O GLN i 162 " (cutoff:3.500A) removed outlier: 5.537A pdb=" N LYS i 167 " --> pdb=" O PRO i 163 " (cutoff:3.500A) Processing helix chain 'i' and resid 181 through 194 Processing helix chain 'j' and resid 13 through 17 Processing helix chain 'j' and resid 21 through 31 Processing helix chain 'j' and resid 45 through 51 Processing helix chain 'j' and resid 61 through 68 Processing helix chain 'j' and resid 83 through 91 Processing helix chain 'j' and resid 96 through 102 removed outlier: 3.703A pdb=" N ALA j 101 " --> pdb=" O PHE j 97 " (cutoff:3.500A) Processing helix chain 'j' and resid 107 through 111 Processing helix chain 'j' and resid 126 through 136 Processing helix chain 'j' and resid 150 through 159 Processing helix chain 'j' and resid 161 through 175 removed outlier: 3.910A pdb=" N LYS j 167 " --> pdb=" O PRO j 163 " (cutoff:3.500A) Processing helix chain 'j' and resid 181 through 194 Processing helix chain 'k' and resid 14 through 19 Processing helix chain 'k' and resid 38 through 43 Processing helix chain 'k' and resid 50 through 53 No H-bonds generated for 'chain 'k' and resid 50 through 53' Processing helix chain 'k' and resid 61 through 63 No H-bonds generated for 'chain 'k' and resid 61 through 63' Processing helix chain 'k' and resid 115 through 118 No H-bonds generated for 'chain 'k' and resid 115 through 118' Processing helix chain 'k' and resid 151 through 160 removed outlier: 4.386A pdb=" N GLU k 160 " --> pdb=" O GLU k 156 " (cutoff:3.500A) Processing helix chain 'k' and resid 202 through 207 Processing helix chain 'u' and resid 18 through 28 removed outlier: 3.507A pdb=" N MET u 24 " --> pdb=" O LEU u 20 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N TYR u 27 " --> pdb=" O LYS u 23 " (cutoff:3.500A) Processing helix chain 'u' and resid 31 through 47 removed outlier: 4.093A pdb=" N LYS u 39 " --> pdb=" O GLU u 35 " (cutoff:3.500A) Processing helix chain 'u' and resid 52 through 64 Processing helix chain 'v' and resid 19 through 28 Processing helix chain 'v' and resid 31 through 47 Processing helix chain 'v' and resid 52 through 64 Processing helix chain 'y' and resid 19 through 33 Processing helix chain 'y' and resid 41 through 58 Processing helix chain 'y' and resid 60 through 67 Processing helix chain 'z' and resid 19 through 32 Processing helix chain 'z' and resid 45 through 57 Processing helix chain 'z' and resid 60 through 68 Processing sheet with id= A, first strand: chain 'A' and resid 132 through 137 Processing sheet with id= B, first strand: chain 'A' and resid 31 through 38 removed outlier: 3.741A pdb=" N ALA A 153 " --> pdb=" O PHE A 98 " (cutoff:3.500A) removed outlier: 6.824A pdb=" N ALA A 100 " --> pdb=" O ILE A 151 " (cutoff:3.500A) removed outlier: 5.616A pdb=" N ILE A 151 " --> pdb=" O ALA A 100 " (cutoff:3.500A) removed outlier: 7.801A pdb=" N ALA A 102 " --> pdb=" O SER A 149 " (cutoff:3.500A) removed outlier: 5.941A pdb=" N SER A 149 " --> pdb=" O ALA A 102 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 222 through 224 Processing sheet with id= D, first strand: chain 'A' and resid 353 through 358 removed outlier: 4.140A pdb=" N ASP A 353 " --> pdb=" O LEU A 246 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N LEU A 246 " --> pdb=" O ASP A 353 " (cutoff:3.500A) removed outlier: 4.198A pdb=" N ALA A 431 " --> pdb=" O LEU A 392 " (cutoff:3.500A) removed outlier: 6.253A pdb=" N ASP A 394 " --> pdb=" O VAL A 429 " (cutoff:3.500A) removed outlier: 5.677A pdb=" N VAL A 429 " --> pdb=" O ASP A 394 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'A' and resid 285 through 287 removed outlier: 3.932A pdb=" N SER A 368 " --> pdb=" O TYR A 276 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N LEU A 371 " --> pdb=" O LEU A 450 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'A' and resid 567 through 570 removed outlier: 3.629A pdb=" N THR A 576 " --> pdb=" O ALA A 593 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N PHE A 578 " --> pdb=" O LEU A 591 " (cutoff:3.500A) removed outlier: 5.658A pdb=" N ARG A 612 " --> pdb=" O GLU A 603 " (cutoff:3.500A) removed outlier: 5.470A pdb=" N GLN A 635 " --> pdb=" O GLU A 626 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N GLY A 634 " --> pdb=" O TRP A 650 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N THR A 647 " --> pdb=" O VAL A 660 " (cutoff:3.500A) removed outlier: 4.684A pdb=" N GLU A 672 " --> pdb=" O LYS A 681 " (cutoff:3.500A) removed outlier: 6.595A pdb=" N LYS A 681 " --> pdb=" O GLU A 672 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'A' and resid 737 through 739 Processing sheet with id= H, first strand: chain 'B' and resid 132 through 137 removed outlier: 3.691A pdb=" N ILE B 19 " --> pdb=" O ASP B 80 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'B' and resid 170 through 172 removed outlier: 3.539A pdb=" N ASP B 170 " --> pdb=" O ILE B 151 " (cutoff:3.500A) removed outlier: 7.138A pdb=" N PHE B 98 " --> pdb=" O VAL B 152 " (cutoff:3.500A) removed outlier: 4.779A pdb=" N VAL B 154 " --> pdb=" O LEU B 96 " (cutoff:3.500A) removed outlier: 6.821A pdb=" N LEU B 96 " --> pdb=" O VAL B 154 " (cutoff:3.500A) removed outlier: 4.780A pdb=" N TYR B 156 " --> pdb=" O GLU B 94 " (cutoff:3.500A) removed outlier: 8.468A pdb=" N GLU B 94 " --> pdb=" O TYR B 156 " (cutoff:3.500A) removed outlier: 6.650A pdb=" N PHE B 38 " --> pdb=" O GLU B 94 " (cutoff:3.500A) removed outlier: 4.502A pdb=" N LEU B 96 " --> pdb=" O VAL B 36 " (cutoff:3.500A) removed outlier: 6.447A pdb=" N VAL B 36 " --> pdb=" O LEU B 96 " (cutoff:3.500A) removed outlier: 4.643A pdb=" N PHE B 98 " --> pdb=" O SER B 34 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N SER B 34 " --> pdb=" O PHE B 98 " (cutoff:3.500A) removed outlier: 4.722A pdb=" N ALA B 100 " --> pdb=" O ASP B 32 " (cutoff:3.500A) removed outlier: 7.013A pdb=" N ASP B 32 " --> pdb=" O ALA B 100 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N CYS B 35 " --> pdb=" O LEU B 48 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N ASP B 46 " --> pdb=" O ALA B 37 " (cutoff:3.500A) removed outlier: 6.387A pdb=" N ASP B 39 " --> pdb=" O LEU B 44 " (cutoff:3.500A) removed outlier: 7.356A pdb=" N LEU B 44 " --> pdb=" O ASP B 39 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'B' and resid 154 through 157 Processing sheet with id= K, first strand: chain 'B' and resid 221 through 224 removed outlier: 4.211A pdb=" N GLN B 221 " --> pdb=" O ALA B 529 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'B' and resid 353 through 358 removed outlier: 3.766A pdb=" N ALA B 431 " --> pdb=" O LEU B 392 " (cutoff:3.500A) removed outlier: 6.616A pdb=" N ASP B 394 " --> pdb=" O VAL B 429 " (cutoff:3.500A) removed outlier: 5.997A pdb=" N VAL B 429 " --> pdb=" O ASP B 394 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'B' and resid 532 through 534 removed outlier: 3.521A pdb=" N LEU B 372 " --> pdb=" O ASN B 272 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N GLN B 284 " --> pdb=" O MET B 275 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'B' and resid 567 through 569 removed outlier: 5.776A pdb=" N ARG B 612 " --> pdb=" O GLU B 603 " (cutoff:3.500A) removed outlier: 5.651A pdb=" N GLN B 635 " --> pdb=" O GLU B 626 " (cutoff:3.500A) removed outlier: 5.166A pdb=" N VAL B 628 " --> pdb=" O GLU B 633 " (cutoff:3.500A) removed outlier: 5.675A pdb=" N GLU B 633 " --> pdb=" O VAL B 628 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'B' and resid 657 through 662 removed outlier: 4.494A pdb=" N GLU B 672 " --> pdb=" O LYS B 681 " (cutoff:3.500A) removed outlier: 6.516A pdb=" N LYS B 681 " --> pdb=" O GLU B 672 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'B' and resid 737 through 739 Processing sheet with id= Q, first strand: chain 'C' and resid 122 through 126 removed outlier: 6.654A pdb=" N VAL C 278 " --> pdb=" O LYS C 287 " (cutoff:3.500A) removed outlier: 5.397A pdb=" N LEU C 289 " --> pdb=" O CYS C 276 " (cutoff:3.500A) removed outlier: 6.614A pdb=" N CYS C 276 " --> pdb=" O LEU C 289 " (cutoff:3.500A) removed outlier: 4.328A pdb=" N ALA C 291 " --> pdb=" O GLN C 274 " (cutoff:3.500A) removed outlier: 6.641A pdb=" N GLN C 274 " --> pdb=" O ALA C 291 " (cutoff:3.500A) removed outlier: 5.190A pdb=" N ASP C 293 " --> pdb=" O SER C 272 " (cutoff:3.500A) removed outlier: 6.784A pdb=" N SER C 272 " --> pdb=" O ASP C 293 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'D' and resid 122 through 126 removed outlier: 6.811A pdb=" N VAL D 278 " --> pdb=" O LYS D 287 " (cutoff:3.500A) removed outlier: 4.619A pdb=" N LEU D 289 " --> pdb=" O CYS D 276 " (cutoff:3.500A) removed outlier: 6.111A pdb=" N CYS D 276 " --> pdb=" O LEU D 289 " (cutoff:3.500A) removed outlier: 4.241A pdb=" N ALA D 291 " --> pdb=" O GLN D 274 " (cutoff:3.500A) removed outlier: 6.506A pdb=" N GLN D 274 " --> pdb=" O ALA D 291 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'G' and resid 158 through 160 removed outlier: 3.508A pdb=" N GLY G 158 " --> pdb=" O VAL G 169 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'G' and resid 284 through 286 Processing sheet with id= U, first strand: chain 'G' and resid 290 through 293 Processing sheet with id= V, first strand: chain 'G' and resid 377 through 381 removed outlier: 5.406A pdb=" N ALA G 403 " --> pdb=" O SER G 397 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'G' and resid 151 through 156 removed outlier: 6.583A pdb=" N ALA G 173 " --> pdb=" O ARG G 152 " (cutoff:3.500A) removed outlier: 4.440A pdb=" N VAL G 154 " --> pdb=" O GLU G 171 " (cutoff:3.500A) removed outlier: 6.792A pdb=" N GLU G 171 " --> pdb=" O VAL G 154 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain 'H' and resid 158 through 160 removed outlier: 3.773A pdb=" N GLY H 158 " --> pdb=" O VAL H 169 " (cutoff:3.500A) Processing sheet with id= Y, first strand: chain 'H' and resid 284 through 286 Processing sheet with id= Z, first strand: chain 'H' and resid 290 through 293 Processing sheet with id= AA, first strand: chain 'H' and resid 378 through 381 Processing sheet with id= AB, first strand: chain 'H' and resid 151 through 156 removed outlier: 6.489A pdb=" N ALA H 173 " --> pdb=" O ARG H 152 " (cutoff:3.500A) removed outlier: 4.387A pdb=" N VAL H 154 " --> pdb=" O GLU H 171 " (cutoff:3.500A) removed outlier: 6.755A pdb=" N GLU H 171 " --> pdb=" O VAL H 154 " (cutoff:3.500A) Processing sheet with id= AC, first strand: chain 'I' and resid 178 through 180 removed outlier: 8.502A pdb=" N GLU I 179 " --> pdb=" O ILE I 43 " (cutoff:3.500A) removed outlier: 6.616A pdb=" N ASN I 45 " --> pdb=" O GLU I 179 " (cutoff:3.500A) removed outlier: 6.982A pdb=" N SER I 46 " --> pdb=" O PRO I 464 " (cutoff:3.500A) removed outlier: 6.032A pdb=" N VAL I 466 " --> pdb=" O SER I 46 " (cutoff:3.500A) removed outlier: 7.519A pdb=" N ILE I 334 " --> pdb=" O THR I 355 " (cutoff:3.500A) removed outlier: 6.716A pdb=" N VAL I 357 " --> pdb=" O ILE I 334 " (cutoff:3.500A) removed outlier: 6.685A pdb=" N LEU I 336 " --> pdb=" O VAL I 357 " (cutoff:3.500A) removed outlier: 6.183A pdb=" N VAL I 359 " --> pdb=" O LEU I 336 " (cutoff:3.500A) removed outlier: 6.106A pdb=" N VAL I 287 " --> pdb=" O GLY I 335 " (cutoff:3.500A) removed outlier: 7.485A pdb=" N VAL I 337 " --> pdb=" O VAL I 287 " (cutoff:3.500A) removed outlier: 6.801A pdb=" N LEU I 289 " --> pdb=" O VAL I 337 " (cutoff:3.500A) Processing sheet with id= AD, first strand: chain 'J' and resid 43 through 46 removed outlier: 7.067A pdb=" N SER J 46 " --> pdb=" O PRO J 464 " (cutoff:3.500A) removed outlier: 6.400A pdb=" N VAL J 466 " --> pdb=" O SER J 46 " (cutoff:3.500A) removed outlier: 7.427A pdb=" N ILE J 334 " --> pdb=" O THR J 355 " (cutoff:3.500A) removed outlier: 6.594A pdb=" N VAL J 357 " --> pdb=" O ILE J 334 " (cutoff:3.500A) removed outlier: 6.640A pdb=" N LEU J 336 " --> pdb=" O VAL J 357 " (cutoff:3.500A) removed outlier: 5.932A pdb=" N VAL J 359 " --> pdb=" O LEU J 336 " (cutoff:3.500A) removed outlier: 6.201A pdb=" N VAL J 287 " --> pdb=" O GLY J 335 " (cutoff:3.500A) removed outlier: 7.531A pdb=" N VAL J 337 " --> pdb=" O VAL J 287 " (cutoff:3.500A) removed outlier: 6.706A pdb=" N LEU J 289 " --> pdb=" O VAL J 337 " (cutoff:3.500A) Processing sheet with id= AE, first strand: chain 'K' and resid 366 through 369 removed outlier: 3.913A pdb=" N ALA K 381 " --> pdb=" O CYS K 395 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N CYS K 395 " --> pdb=" O ALA K 381 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N GLY K 154 " --> pdb=" O VAL K 165 " (cutoff:3.500A) Processing sheet with id= AF, first strand: chain 'K' and resid 264 through 266 Processing sheet with id= AG, first strand: chain 'K' and resid 270 through 272 Processing sheet with id= AH, first strand: chain 'K' and resid 147 through 152 removed outlier: 6.829A pdb=" N THR K 169 " --> pdb=" O SER K 148 " (cutoff:3.500A) removed outlier: 4.614A pdb=" N VAL K 150 " --> pdb=" O GLU K 167 " (cutoff:3.500A) removed outlier: 6.730A pdb=" N GLU K 167 " --> pdb=" O VAL K 150 " (cutoff:3.500A) Processing sheet with id= AI, first strand: chain 'L' and resid 391 through 396 removed outlier: 3.530A pdb=" N GLY L 154 " --> pdb=" O VAL L 165 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N VAL L 165 " --> pdb=" O GLY L 154 " (cutoff:3.500A) Processing sheet with id= AJ, first strand: chain 'L' and resid 264 through 266 Processing sheet with id= AK, first strand: chain 'L' and resid 270 through 272 Processing sheet with id= AL, first strand: chain 'L' and resid 365 through 369 Processing sheet with id= AM, first strand: chain 'L' and resid 147 through 150 removed outlier: 6.726A pdb=" N THR L 169 " --> pdb=" O SER L 148 " (cutoff:3.500A) Processing sheet with id= AN, first strand: chain 'O' and resid 92 through 94 removed outlier: 4.780A pdb=" N TYR O 82 " --> pdb=" O LEU O 94 " (cutoff:3.500A) removed outlier: 5.856A pdb=" N GLU O 64 " --> pdb=" O LEU O 48 " (cutoff:3.500A) removed outlier: 5.361A pdb=" N LEU O 48 " --> pdb=" O GLU O 64 " (cutoff:3.500A) Processing sheet with id= AO, first strand: chain 'O' and resid 69 through 72 Processing sheet with id= AP, first strand: chain 'O' and resid 119 through 122 Processing sheet with id= AQ, first strand: chain 'O' and resid 166 through 168 Processing sheet with id= AR, first strand: chain 'O' and resid 172 through 174 Processing sheet with id= AS, first strand: chain 'O' and resid 219 through 224 removed outlier: 4.867A pdb=" N TYR O 240 " --> pdb=" O SER O 234 " (cutoff:3.500A) Processing sheet with id= AT, first strand: chain 'P' and resid 80 through 85 removed outlier: 5.670A pdb=" N GLU P 64 " --> pdb=" O LEU P 48 " (cutoff:3.500A) removed outlier: 5.335A pdb=" N LEU P 48 " --> pdb=" O GLU P 64 " (cutoff:3.500A) removed outlier: 7.564A pdb=" N TYR P 66 " --> pdb=" O LEU P 46 " (cutoff:3.500A) removed outlier: 5.384A pdb=" N LEU P 46 " --> pdb=" O TYR P 66 " (cutoff:3.500A) Processing sheet with id= AU, first strand: chain 'P' and resid 69 through 71 removed outlier: 3.709A pdb=" N SER P 70 " --> pdb=" O VAL P 77 " (cutoff:3.500A) Processing sheet with id= AV, first strand: chain 'P' and resid 119 through 122 Processing sheet with id= AW, first strand: chain 'P' and resid 166 through 168 Processing sheet with id= AX, first strand: chain 'P' and resid 219 through 224 removed outlier: 4.817A pdb=" N TYR P 240 " --> pdb=" O SER P 234 " (cutoff:3.500A) Processing sheet with id= AY, first strand: chain 'Q' and resid 92 through 94 removed outlier: 4.753A pdb=" N TYR Q 82 " --> pdb=" O LEU Q 94 " (cutoff:3.500A) removed outlier: 5.919A pdb=" N GLU Q 64 " --> pdb=" O LEU Q 48 " (cutoff:3.500A) removed outlier: 5.464A pdb=" N LEU Q 48 " --> pdb=" O GLU Q 64 " (cutoff:3.500A) removed outlier: 7.958A pdb=" N TYR Q 66 " --> pdb=" O LEU Q 46 " (cutoff:3.500A) removed outlier: 6.013A pdb=" N LEU Q 46 " --> pdb=" O TYR Q 66 " (cutoff:3.500A) Processing sheet with id= AZ, first strand: chain 'Q' and resid 69 through 72 Processing sheet with id= BA, first strand: chain 'Q' and resid 119 through 122 Processing sheet with id= BB, first strand: chain 'Q' and resid 166 through 168 Processing sheet with id= BC, first strand: chain 'Q' and resid 172 through 174 Processing sheet with id= BD, first strand: chain 'Q' and resid 219 through 224 removed outlier: 4.812A pdb=" N TYR Q 240 " --> pdb=" O SER Q 234 " (cutoff:3.500A) Processing sheet with id= BE, first strand: chain 'R' and resid 80 through 85 removed outlier: 5.943A pdb=" N GLU R 64 " --> pdb=" O LEU R 48 " (cutoff:3.500A) removed outlier: 5.484A pdb=" N LEU R 48 " --> pdb=" O GLU R 64 " (cutoff:3.500A) removed outlier: 7.670A pdb=" N TYR R 66 " --> pdb=" O LEU R 46 " (cutoff:3.500A) removed outlier: 5.482A pdb=" N LEU R 46 " --> pdb=" O TYR R 66 " (cutoff:3.500A) Processing sheet with id= BF, first strand: chain 'R' and resid 69 through 72 Processing sheet with id= BG, first strand: chain 'R' and resid 119 through 122 Processing sheet with id= BH, first strand: chain 'R' and resid 166 through 168 Processing sheet with id= BI, first strand: chain 'R' and resid 219 through 224 removed outlier: 4.856A pdb=" N TYR R 240 " --> pdb=" O SER R 234 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N THR R 250 " --> pdb=" O ALA R 245 " (cutoff:3.500A) Processing sheet with id= BJ, first strand: chain 'S' and resid 11 through 13 Processing sheet with id= BK, first strand: chain 'S' and resid 83 through 88 removed outlier: 5.780A pdb=" N GLN S 107 " --> pdb=" O ASP S 98 " (cutoff:3.500A) removed outlier: 4.091A pdb=" N ALA S 121 " --> pdb=" O LYS S 130 " (cutoff:3.500A) removed outlier: 5.602A pdb=" N LYS S 130 " --> pdb=" O ALA S 121 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N TYR S 153 " --> pdb=" O ASP S 145 " (cutoff:3.500A) removed outlier: 6.260A pdb=" N ALA S 147 " --> pdb=" O PHE S 151 " (cutoff:3.500A) removed outlier: 5.037A pdb=" N PHE S 151 " --> pdb=" O ALA S 147 " (cutoff:3.500A) removed outlier: 4.582A pdb=" N THR S 152 " --> pdb=" O PHE S 168 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ALA S 179 " --> pdb=" O LYS S 167 " (cutoff:3.500A) removed outlier: 6.665A pdb=" N THR S 178 " --> pdb=" O PHE S 195 " (cutoff:3.500A) Processing sheet with id= BL, first strand: chain 'T' and resid 11 through 13 removed outlier: 4.186A pdb=" N THR T 51 " --> pdb=" O LYS T 60 " (cutoff:3.500A) removed outlier: 5.822A pdb=" N LYS T 60 " --> pdb=" O THR T 51 " (cutoff:3.500A) removed outlier: 6.285A pdb=" N LYS T 84 " --> pdb=" O ASP T 75 " (cutoff:3.500A) removed outlier: 5.828A pdb=" N GLN T 107 " --> pdb=" O ASP T 98 " (cutoff:3.500A) removed outlier: 5.802A pdb=" N LYS T 130 " --> pdb=" O ALA T 121 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N TYR T 153 " --> pdb=" O ASP T 145 " (cutoff:3.500A) removed outlier: 5.818A pdb=" N ALA T 147 " --> pdb=" O PHE T 151 " (cutoff:3.500A) removed outlier: 5.175A pdb=" N PHE T 151 " --> pdb=" O ALA T 147 " (cutoff:3.500A) removed outlier: 4.914A pdb=" N THR T 152 " --> pdb=" O PHE T 168 " (cutoff:3.500A) removed outlier: 6.360A pdb=" N THR T 178 " --> pdb=" O PHE T 195 " (cutoff:3.500A) Processing sheet with id= BM, first strand: chain 'W' and resid 173 through 176 removed outlier: 3.584A pdb=" N TYR W 20 " --> pdb=" O ILE W 176 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N THR W 19 " --> pdb=" O LEU W 39 " (cutoff:3.500A) Processing sheet with id= BN, first strand: chain 'W' and resid 25 through 27 Processing sheet with id= BO, first strand: chain 'W' and resid 72 through 75 Processing sheet with id= BP, first strand: chain 'Y' and resid 137 through 143 Processing sheet with id= BQ, first strand: chain 'Y' and resid 153 through 162 Processing sheet with id= BR, first strand: chain 'Y' and resid 219 through 222 removed outlier: 6.506A pdb=" N VAL Y 287 " --> pdb=" O HIS Y 228 " (cutoff:3.500A) removed outlier: 7.455A pdb=" N VAL Y 230 " --> pdb=" O VAL Y 287 " (cutoff:3.500A) removed outlier: 6.408A pdb=" N GLU Y 289 " --> pdb=" O VAL Y 230 " (cutoff:3.500A) removed outlier: 7.116A pdb=" N LEU Y 232 " --> pdb=" O GLU Y 289 " (cutoff:3.500A) removed outlier: 6.075A pdb=" N ASP Y 291 " --> pdb=" O LEU Y 232 " (cutoff:3.500A) Processing sheet with id= BS, first strand: chain 'Y' and resid 242 through 246 Processing sheet with id= BT, first strand: chain 'Z' and resid 137 through 143 Processing sheet with id= BU, first strand: chain 'Z' and resid 154 through 162 removed outlier: 3.662A pdb=" N VAL Z 170 " --> pdb=" O VAL Z 162 " (cutoff:3.500A) Processing sheet with id= BV, first strand: chain 'Z' and resid 219 through 222 removed outlier: 3.683A pdb=" N ASP Z 225 " --> pdb=" O ARG Z 222 " (cutoff:3.500A) removed outlier: 6.375A pdb=" N ASN Z 285 " --> pdb=" O LEU Z 226 " (cutoff:3.500A) removed outlier: 7.978A pdb=" N HIS Z 228 " --> pdb=" O ASN Z 285 " (cutoff:3.500A) removed outlier: 6.366A pdb=" N VAL Z 287 " --> pdb=" O HIS Z 228 " (cutoff:3.500A) removed outlier: 7.239A pdb=" N VAL Z 230 " --> pdb=" O VAL Z 287 " (cutoff:3.500A) removed outlier: 6.184A pdb=" N GLU Z 289 " --> pdb=" O VAL Z 230 " (cutoff:3.500A) removed outlier: 7.092A pdb=" N LEU Z 232 " --> pdb=" O GLU Z 289 " (cutoff:3.500A) removed outlier: 6.261A pdb=" N ASP Z 291 " --> pdb=" O LEU Z 232 " (cutoff:3.500A) Processing sheet with id= BW, first strand: chain 'Z' and resid 242 through 246 Processing sheet with id= BX, first strand: chain 'a' and resid 57 through 61 removed outlier: 7.012A pdb=" N TYR a 79 " --> pdb=" O ILE a 10 " (cutoff:3.500A) removed outlier: 5.655A pdb=" N ILE a 10 " --> pdb=" O TYR a 79 " (cutoff:3.500A) Processing sheet with id= BY, first strand: chain 'b' and resid 57 through 61 removed outlier: 6.815A pdb=" N TYR b 79 " --> pdb=" O ILE b 10 " (cutoff:3.500A) removed outlier: 5.395A pdb=" N ILE b 10 " --> pdb=" O TYR b 79 " (cutoff:3.500A) Processing sheet with id= BZ, first strand: chain 'c' and resid 56 through 61 removed outlier: 6.659A pdb=" N TYR c 79 " --> pdb=" O ILE c 10 " (cutoff:3.500A) removed outlier: 6.429A pdb=" N ILE c 10 " --> pdb=" O TYR c 79 " (cutoff:3.500A) Processing sheet with id= CA, first strand: chain 'd' and resid 57 through 61 removed outlier: 4.201A pdb=" N VAL d 83 " --> pdb=" O LEU d 80 " (cutoff:3.500A) removed outlier: 6.831A pdb=" N TYR d 79 " --> pdb=" O ILE d 10 " (cutoff:3.500A) removed outlier: 5.469A pdb=" N ILE d 10 " --> pdb=" O TYR d 79 " (cutoff:3.500A) Processing sheet with id= CB, first strand: chain 'i' and resid 120 through 122 removed outlier: 3.813A pdb=" N ALA i 37 " --> pdb=" O VAL i 77 " (cutoff:3.500A) removed outlier: 7.097A pdb=" N ALA i 79 " --> pdb=" O ILE i 35 " (cutoff:3.500A) removed outlier: 5.920A pdb=" N ILE i 35 " --> pdb=" O ALA i 79 " (cutoff:3.500A) Processing sheet with id= CC, first strand: chain 'j' and resid 120 through 122 removed outlier: 3.898A pdb=" N ALA j 37 " --> pdb=" O VAL j 77 " (cutoff:3.500A) removed outlier: 6.856A pdb=" N ALA j 79 " --> pdb=" O ILE j 35 " (cutoff:3.500A) removed outlier: 6.042A pdb=" N ILE j 35 " --> pdb=" O ALA j 79 " (cutoff:3.500A) Processing sheet with id= CD, first strand: chain 'k' and resid 27 through 30 Processing sheet with id= CE, first strand: chain 'k' and resid 73 through 75 Processing sheet with id= CF, first strand: chain 'k' and resid 139 through 146 removed outlier: 3.734A pdb=" N GLN k 139 " --> pdb=" O ASN k 134 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N ASN k 134 " --> pdb=" O GLN k 139 " (cutoff:3.500A) removed outlier: 7.895A pdb=" N VAL k 218 " --> pdb=" O LEU k 173 " (cutoff:3.500A) removed outlier: 4.527A pdb=" N LEU k 173 " --> pdb=" O VAL k 218 " (cutoff:3.500A) 3230 hydrogen bonds defined for protein. 9213 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: 34.49 Time building geometry restraints manager: 33.12 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 15307 1.33 - 1.45: 16699 1.45 - 1.57: 42090 1.57 - 1.70: 1 1.70 - 1.82: 378 Bond restraints: 74475 Sorted by residual: bond pdb=" CA PRO H 432 " pdb=" C PRO H 432 " ideal model delta sigma weight residual 1.514 1.536 -0.022 5.50e-03 3.31e+04 1.54e+01 bond pdb=" C PRO H 432 " pdb=" O PRO H 432 " ideal model delta sigma weight residual 1.246 1.215 0.031 8.50e-03 1.38e+04 1.31e+01 bond pdb=" N TYR O 191 " pdb=" CA TYR O 191 " ideal model delta sigma weight residual 1.458 1.483 -0.025 7.40e-03 1.83e+04 1.18e+01 bond pdb=" N ILE W 176 " pdb=" CA ILE W 176 " ideal model delta sigma weight residual 1.456 1.495 -0.039 1.14e-02 7.69e+03 1.16e+01 bond pdb=" N GLN j 162 " pdb=" CA GLN j 162 " ideal model delta sigma weight residual 1.459 1.494 -0.035 1.04e-02 9.25e+03 1.14e+01 ... (remaining 74470 not shown) Histogram of bond angle deviations from ideal: 97.92 - 105.85: 2403 105.85 - 113.79: 41311 113.79 - 121.73: 41184 121.73 - 129.66: 15855 129.66 - 137.60: 471 Bond angle restraints: 101224 Sorted by residual: angle pdb=" CA GLY H 129 " pdb=" C GLY H 129 " pdb=" O GLY H 129 " ideal model delta sigma weight residual 122.23 117.91 4.32 6.90e-01 2.10e+00 3.93e+01 angle pdb=" CA GLY O 188 " pdb=" C GLY O 188 " pdb=" O GLY O 188 " ideal model delta sigma weight residual 122.45 118.27 4.18 7.20e-01 1.93e+00 3.37e+01 angle pdb=" N ALA K 239 " pdb=" CA ALA K 239 " pdb=" C ALA K 239 " ideal model delta sigma weight residual 113.12 106.34 6.78 1.25e+00 6.40e-01 2.94e+01 angle pdb=" N PRO H 432 " pdb=" CA PRO H 432 " pdb=" C PRO H 432 " ideal model delta sigma weight residual 110.47 115.58 -5.11 9.60e-01 1.09e+00 2.83e+01 angle pdb=" N VAL G 322 " pdb=" CA VAL G 322 " pdb=" C VAL G 322 " ideal model delta sigma weight residual 113.71 108.78 4.93 9.50e-01 1.11e+00 2.69e+01 ... (remaining 101219 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.99: 40936 17.99 - 35.98: 3214 35.98 - 53.97: 509 53.97 - 71.96: 94 71.96 - 89.95: 55 Dihedral angle restraints: 44808 sinusoidal: 17436 harmonic: 27372 Sorted by residual: dihedral pdb=" CB CYS R 105 " pdb=" SG CYS R 105 " pdb=" SG CYS R 155 " pdb=" CB CYS R 155 " ideal model delta sinusoidal sigma weight residual 93.00 31.41 61.59 1 1.00e+01 1.00e-02 5.03e+01 dihedral pdb=" CA HIS X 312 " pdb=" C HIS X 312 " pdb=" N GLU X 313 " pdb=" CA GLU X 313 " ideal model delta harmonic sigma weight residual -180.00 -152.02 -27.98 0 5.00e+00 4.00e-02 3.13e+01 dihedral pdb=" CA ASN b 53 " pdb=" C ASN b 53 " pdb=" N PRO b 54 " pdb=" CA PRO b 54 " ideal model delta harmonic sigma weight residual -180.00 -152.10 -27.90 0 5.00e+00 4.00e-02 3.11e+01 ... (remaining 44805 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.082: 10080 0.082 - 0.164: 991 0.164 - 0.247: 87 0.247 - 0.329: 13 0.329 - 0.411: 1 Chirality restraints: 11172 Sorted by residual: chirality pdb=" CA THR A 517 " pdb=" N THR A 517 " pdb=" C THR A 517 " pdb=" CB THR A 517 " both_signs ideal model delta sigma weight residual False 2.53 2.11 0.41 2.00e-01 2.50e+01 4.23e+00 chirality pdb=" CA TYR W 177 " pdb=" N TYR W 177 " pdb=" C TYR W 177 " pdb=" CB TYR W 177 " both_signs ideal model delta sigma weight residual False 2.51 2.18 0.33 2.00e-01 2.50e+01 2.68e+00 chirality pdb=" CA ASP A 471 " pdb=" N ASP A 471 " pdb=" C ASP A 471 " pdb=" CB ASP A 471 " both_signs ideal model delta sigma weight residual False 2.51 2.22 0.29 2.00e-01 2.50e+01 2.15e+00 ... (remaining 11169 not shown) Planarity restraints: 13313 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LEU A 199 " 0.029 2.00e-02 2.50e+03 5.76e-02 3.32e+01 pdb=" C LEU A 199 " -0.100 2.00e-02 2.50e+03 pdb=" O LEU A 199 " 0.037 2.00e-02 2.50e+03 pdb=" N ASP A 200 " 0.033 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU B 199 " 0.025 2.00e-02 2.50e+03 4.90e-02 2.40e+01 pdb=" C LEU B 199 " -0.085 2.00e-02 2.50e+03 pdb=" O LEU B 199 " 0.032 2.00e-02 2.50e+03 pdb=" N ASP B 200 " 0.028 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ARG X 200 " 0.021 2.00e-02 2.50e+03 4.28e-02 1.83e+01 pdb=" C ARG X 200 " -0.074 2.00e-02 2.50e+03 pdb=" O ARG X 200 " 0.027 2.00e-02 2.50e+03 pdb=" N HIS X 201 " 0.026 2.00e-02 2.50e+03 ... (remaining 13310 not shown) Histogram of nonbonded interaction distances: 1.95 - 2.54: 463 2.54 - 3.13: 56773 3.13 - 3.72: 111773 3.72 - 4.31: 149899 4.31 - 4.90: 254342 Nonbonded interactions: 573250 Sorted by model distance: nonbonded pdb=" NH2 ARG A 300 " pdb=" OE1 GLU A 351 " model vdw 1.951 2.520 nonbonded pdb=" OE2 GLU H 99 " pdb=" O HIS Z 297 " model vdw 1.971 3.040 nonbonded pdb=" NH1 ARG B 300 " pdb=" OE2 GLU B 351 " model vdw 2.048 2.520 nonbonded pdb=" NH2 ARG A 300 " pdb=" OE2 GLU A 351 " model vdw 2.054 2.520 nonbonded pdb=" OG SER C 300 " pdb=" OE2 GLU S 212 " model vdw 2.069 2.440 ... (remaining 573245 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } ncs_group { reference = chain 'C' selection = chain 'D' } ncs_group { reference = chain 'E' selection = (chain 'F' and (resid 139 through 261 or resid 268 through 509)) } ncs_group { reference = chain 'G' selection = chain 'H' } ncs_group { reference = chain 'I' selection = chain 'J' } ncs_group { reference = chain 'K' selection = chain 'L' } ncs_group { reference = (chain 'M' and resid 8 through 47) selection = chain 'N' } ncs_group { reference = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' } ncs_group { reference = chain 'S' selection = chain 'T' } ncs_group { reference = chain 'Y' selection = chain 'Z' } ncs_group { reference = chain 'a' selection = chain 'b' selection = chain 'c' selection = chain 'd' } ncs_group { reference = chain 'i' selection = chain 'j' } ncs_group { reference = chain 'u' selection = chain 'v' } ncs_group { reference = chain 'y' selection = chain 'z' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.53 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 21.570 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: 0.000 Extract box with map and model: 38.320 Check model and map are aligned: 1.110 Set scattering table: 0.680 Process input model: 177.580 Find NCS groups from input model: 3.810 Set up NCS constraints: 0.850 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:2.670 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 246.610 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7201 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 : 0.005 0.086 74475 Z= 0.313 Angle : 0.751 12.600 101224 Z= 0.476 Chirality : 0.049 0.411 11172 Planarity : 0.005 0.091 13313 Dihedral : 13.431 89.954 27182 Min Nonbonded Distance : 1.951 Molprobity Statistics. All-atom Clashscore : 9.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % Rotamer: Outliers : 0.51 % Allowed : 0.72 % Favored : 98.77 % Cbeta Deviations : 0.02 % Peptide Plane: Cis-proline : 0.96 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.30 (0.09), residues: 9336 helix: 1.44 (0.09), residues: 3529 sheet: -0.94 (0.13), residues: 1545 loop : -1.31 (0.09), residues: 4262 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP B 673 HIS 0.013 0.001 HIS C 502 PHE 0.033 0.002 PHE a 48 TYR 0.026 0.002 TYR c 67 ARG 0.019 0.001 ARG i 160 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 18672 Ramachandran restraints generated. 9336 Oldfield, 0 Emsley, 9336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 18672 Ramachandran restraints generated. 9336 Oldfield, 0 Emsley, 9336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 737 residues out of total 7562 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 699 time to evaluate : 6.433 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 348 PHE cc_start: 0.7532 (t80) cc_final: 0.7296 (t80) REVERT: Q 111 MET cc_start: 0.8617 (ttm) cc_final: 0.8409 (ttp) REVERT: b 73 LYS cc_start: 0.5842 (tptp) cc_final: 0.5608 (tptt) REVERT: i 14 ASP cc_start: 0.8031 (p0) cc_final: 0.7815 (p0) REVERT: j 161 ILE cc_start: 0.7945 (OUTLIER) cc_final: 0.7111 (pt) outliers start: 38 outliers final: 10 residues processed: 729 average time/residue: 0.7020 time to fit residues: 867.1573 Evaluate side-chains 536 residues out of total 7562 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 525 time to evaluate : 6.424 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 199 LEU Chi-restraints excluded: chain A residue 470 VAL Chi-restraints excluded: chain A residue 477 ILE Chi-restraints excluded: chain B residue 199 LEU Chi-restraints excluded: chain J residue 419 LEU Chi-restraints excluded: chain W residue 131 LEU Chi-restraints excluded: chain W residue 176 ILE Chi-restraints excluded: chain X residue 370 PHE Chi-restraints excluded: chain X residue 371 LYS Chi-restraints excluded: chain j residue 161 ILE Chi-restraints excluded: chain k residue 75 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 932 random chunks: chunk 787 optimal weight: 2.9990 chunk 706 optimal weight: 7.9990 chunk 391 optimal weight: 5.9990 chunk 241 optimal weight: 2.9990 chunk 476 optimal weight: 0.9990 chunk 377 optimal weight: 2.9990 chunk 730 optimal weight: 2.9990 chunk 282 optimal weight: 0.0010 chunk 444 optimal weight: 1.9990 chunk 543 optimal weight: 3.9990 chunk 846 optimal weight: 4.9990 overall best weight: 1.7994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 290 ASN A 472 ASN A 479 GLN B 290 ASN ** B 548 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 285 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 506 ASN I 45 ASN ** J 134 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 183 GLN J 313 GLN J 423 ASN ** S 23 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 65 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 367 GLN Y 158 HIS ** Y 236 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Z 216 HIS b 52 HIS ** b 57 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 57 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 369 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7265 moved from start: 0.0802 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.059 74475 Z= 0.345 Angle : 0.612 12.057 101224 Z= 0.313 Chirality : 0.043 0.191 11172 Planarity : 0.005 0.064 13313 Dihedral : 4.863 49.974 10246 Min Nonbonded Distance : 2.049 Molprobity Statistics. All-atom Clashscore : 9.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.88 % Favored : 96.12 % Rotamer: Outliers : 0.97 % Allowed : 7.41 % Favored : 91.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.96 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.22 (0.09), residues: 9336 helix: 1.47 (0.09), residues: 3558 sheet: -0.91 (0.13), residues: 1577 loop : -1.26 (0.09), residues: 4201 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 673 HIS 0.010 0.001 HIS d 52 PHE 0.026 0.002 PHE a 48 TYR 0.032 0.002 TYR W 177 ARG 0.006 0.000 ARG j 108 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 18672 Ramachandran restraints generated. 9336 Oldfield, 0 Emsley, 9336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 18672 Ramachandran restraints generated. 9336 Oldfield, 0 Emsley, 9336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 619 residues out of total 7562 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 547 time to evaluate : 6.758 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 275 MET cc_start: 0.7431 (mmm) cc_final: 0.6996 (mmm) REVERT: Q 111 MET cc_start: 0.8695 (ttm) cc_final: 0.8378 (ttp) REVERT: i 45 ARG cc_start: 0.8093 (tpp80) cc_final: 0.7863 (tpp80) outliers start: 72 outliers final: 55 residues processed: 587 average time/residue: 0.6775 time to fit residues: 683.2253 Evaluate side-chains 557 residues out of total 7562 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 502 time to evaluate : 6.373 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 LEU Chi-restraints excluded: chain A residue 113 ASP Chi-restraints excluded: chain A residue 176 SER Chi-restraints excluded: chain A residue 199 LEU Chi-restraints excluded: chain A residue 445 THR Chi-restraints excluded: chain A residue 470 VAL Chi-restraints excluded: chain A residue 477 ILE Chi-restraints excluded: chain B residue 35 CYS Chi-restraints excluded: chain B residue 113 ASP Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 540 GLU Chi-restraints excluded: chain C residue 448 THR Chi-restraints excluded: chain D residue 477 ASP Chi-restraints excluded: chain E residue 257 PHE Chi-restraints excluded: chain E residue 368 SER Chi-restraints excluded: chain F residue 177 VAL Chi-restraints excluded: chain F residue 182 GLU Chi-restraints excluded: chain F residue 343 LEU Chi-restraints excluded: chain F residue 368 SER Chi-restraints excluded: chain F residue 506 ASN Chi-restraints excluded: chain G residue 43 ASN Chi-restraints excluded: chain H residue 93 ILE Chi-restraints excluded: chain I residue 495 VAL Chi-restraints excluded: chain K residue 280 SER Chi-restraints excluded: chain K residue 418 CYS Chi-restraints excluded: chain L residue 418 CYS Chi-restraints excluded: chain P residue 111 MET Chi-restraints excluded: chain Q residue 2 VAL Chi-restraints excluded: chain Q residue 8 ILE Chi-restraints excluded: chain S residue 73 THR Chi-restraints excluded: chain S residue 114 ASN Chi-restraints excluded: chain S residue 152 THR Chi-restraints excluded: chain T residue 87 MET Chi-restraints excluded: chain T residue 114 ASN Chi-restraints excluded: chain V residue 4 GLU Chi-restraints excluded: chain V residue 46 THR Chi-restraints excluded: chain W residue 65 HIS Chi-restraints excluded: chain W residue 80 ASP Chi-restraints excluded: chain W residue 176 ILE Chi-restraints excluded: chain X residue 7 ILE Chi-restraints excluded: chain X residue 32 THR Chi-restraints excluded: chain X residue 370 PHE Chi-restraints excluded: chain X residue 371 LYS Chi-restraints excluded: chain Y residue 142 GLU Chi-restraints excluded: chain Y residue 169 TYR Chi-restraints excluded: chain b residue 36 ILE Chi-restraints excluded: chain d residue 31 LEU Chi-restraints excluded: chain i residue 65 VAL Chi-restraints excluded: chain j residue 65 VAL Chi-restraints excluded: chain j residue 174 ARG Chi-restraints excluded: chain k residue 75 ILE Chi-restraints excluded: chain k residue 92 ILE Chi-restraints excluded: chain k residue 225 ASP Chi-restraints excluded: chain y residue 13 LEU Chi-restraints excluded: chain z residue 18 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 932 random chunks: chunk 470 optimal weight: 0.8980 chunk 262 optimal weight: 0.8980 chunk 704 optimal weight: 9.9990 chunk 576 optimal weight: 2.9990 chunk 233 optimal weight: 5.9990 chunk 847 optimal weight: 2.9990 chunk 915 optimal weight: 1.9990 chunk 755 optimal weight: 4.9990 chunk 840 optimal weight: 0.7980 chunk 289 optimal weight: 2.9990 chunk 680 optimal weight: 3.9990 overall best weight: 1.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 463 ASN ** B 548 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 285 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 506 ASN ** J 134 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 26 GLN ** R 183 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 23 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 47 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 158 HIS ** Y 236 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** b 52 HIS ** b 57 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** c 20 GLN c 29 GLN ** d 57 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** j 162 GLN u 64 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7262 moved from start: 0.0987 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 74475 Z= 0.297 Angle : 0.571 11.764 101224 Z= 0.291 Chirality : 0.042 0.183 11172 Planarity : 0.004 0.063 13313 Dihedral : 4.694 52.253 10238 Min Nonbonded Distance : 2.063 Molprobity Statistics. All-atom Clashscore : 9.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.73 % Favored : 96.27 % Rotamer: Outliers : 1.49 % Allowed : 9.99 % Favored : 88.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.96 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.10 (0.09), residues: 9336 helix: 1.58 (0.09), residues: 3549 sheet: -0.83 (0.13), residues: 1573 loop : -1.19 (0.09), residues: 4214 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP S 99 HIS 0.007 0.001 HIS b 52 PHE 0.022 0.002 PHE B 21 TYR 0.026 0.002 TYR a 34 ARG 0.007 0.000 ARG i 160 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 18672 Ramachandran restraints generated. 9336 Oldfield, 0 Emsley, 9336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 18672 Ramachandran restraints generated. 9336 Oldfield, 0 Emsley, 9336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 639 residues out of total 7562 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 111 poor density : 528 time to evaluate : 6.671 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: C 527 GLU cc_start: 0.5927 (OUTLIER) cc_final: 0.5623 (mp0) REVERT: E 257 PHE cc_start: 0.5556 (OUTLIER) cc_final: 0.5211 (t80) REVERT: M 1 MET cc_start: 0.5195 (ptt) cc_final: 0.4892 (ptt) REVERT: S 28 MET cc_start: 0.6858 (ttm) cc_final: 0.6600 (mtp) REVERT: X 99 TYR cc_start: 0.7292 (m-80) cc_final: 0.7026 (m-80) REVERT: k 144 GLU cc_start: 0.3025 (mp0) cc_final: 0.2568 (mp0) REVERT: v 56 MET cc_start: 0.8296 (mtt) cc_final: 0.8085 (mtt) outliers start: 111 outliers final: 72 residues processed: 599 average time/residue: 0.7304 time to fit residues: 764.0085 Evaluate side-chains 570 residues out of total 7562 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 496 time to evaluate : 6.505 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 CYS Chi-restraints excluded: chain A residue 44 LEU Chi-restraints excluded: chain A residue 113 ASP Chi-restraints excluded: chain A residue 176 SER Chi-restraints excluded: chain A residue 199 LEU Chi-restraints excluded: chain A residue 445 THR Chi-restraints excluded: chain A residue 477 ILE Chi-restraints excluded: chain B residue 35 CYS Chi-restraints excluded: chain B residue 113 ASP Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 540 GLU Chi-restraints excluded: chain B residue 740 ILE Chi-restraints excluded: chain C residue 448 THR Chi-restraints excluded: chain C residue 502 HIS Chi-restraints excluded: chain C residue 527 GLU Chi-restraints excluded: chain D residue 249 MET Chi-restraints excluded: chain E residue 257 PHE Chi-restraints excluded: chain F residue 158 VAL Chi-restraints excluded: chain F residue 182 GLU Chi-restraints excluded: chain F residue 270 VAL Chi-restraints excluded: chain F residue 278 PHE Chi-restraints excluded: chain F residue 343 LEU Chi-restraints excluded: chain F residue 506 ASN Chi-restraints excluded: chain G residue 43 ASN Chi-restraints excluded: chain G residue 72 VAL Chi-restraints excluded: chain H residue 93 ILE Chi-restraints excluded: chain H residue 223 SER Chi-restraints excluded: chain I residue 216 THR Chi-restraints excluded: chain I residue 290 VAL Chi-restraints excluded: chain I residue 406 VAL Chi-restraints excluded: chain I residue 495 VAL Chi-restraints excluded: chain J residue 290 VAL Chi-restraints excluded: chain K residue 89 LEU Chi-restraints excluded: chain K residue 280 SER Chi-restraints excluded: chain K residue 405 VAL Chi-restraints excluded: chain L residue 50 VAL Chi-restraints excluded: chain M residue 10 THR Chi-restraints excluded: chain O residue 105 CYS Chi-restraints excluded: chain P residue 111 MET Chi-restraints excluded: chain Q residue 2 VAL Chi-restraints excluded: chain Q residue 8 ILE Chi-restraints excluded: chain S residue 73 THR Chi-restraints excluded: chain S residue 114 ASN Chi-restraints excluded: chain T residue 87 MET Chi-restraints excluded: chain T residue 114 ASN Chi-restraints excluded: chain V residue 3 VAL Chi-restraints excluded: chain V residue 4 GLU Chi-restraints excluded: chain V residue 6 ILE Chi-restraints excluded: chain V residue 46 THR Chi-restraints excluded: chain W residue 65 HIS Chi-restraints excluded: chain W residue 80 ASP Chi-restraints excluded: chain W residue 176 ILE Chi-restraints excluded: chain X residue 32 THR Chi-restraints excluded: chain X residue 154 THR Chi-restraints excluded: chain X residue 370 PHE Chi-restraints excluded: chain Y residue 142 GLU Chi-restraints excluded: chain Y residue 180 VAL Chi-restraints excluded: chain Y residue 281 SER Chi-restraints excluded: chain Z residue 162 VAL Chi-restraints excluded: chain Z residue 180 VAL Chi-restraints excluded: chain b residue 36 ILE Chi-restraints excluded: chain c residue 53 ASN Chi-restraints excluded: chain d residue 55 THR Chi-restraints excluded: chain d residue 72 THR Chi-restraints excluded: chain i residue 65 VAL Chi-restraints excluded: chain j residue 65 VAL Chi-restraints excluded: chain j residue 178 SER Chi-restraints excluded: chain k residue 75 ILE Chi-restraints excluded: chain k residue 92 ILE Chi-restraints excluded: chain k residue 225 ASP Chi-restraints excluded: chain v residue 18 THR Chi-restraints excluded: chain y residue 13 LEU Chi-restraints excluded: chain y residue 14 THR Chi-restraints excluded: chain z residue 18 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 932 random chunks: chunk 837 optimal weight: 5.9990 chunk 637 optimal weight: 0.9980 chunk 440 optimal weight: 0.8980 chunk 93 optimal weight: 2.9990 chunk 404 optimal weight: 0.6980 chunk 569 optimal weight: 0.0670 chunk 850 optimal weight: 3.9990 chunk 900 optimal weight: 0.9990 chunk 444 optimal weight: 5.9990 chunk 806 optimal weight: 0.8980 chunk 242 optimal weight: 0.6980 overall best weight: 0.6518 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 144 GLN B 30 ASN ** B 548 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 285 GLN F 285 GLN F 506 ASN ** I 288 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 358 GLN ** J 134 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 309 GLN Q 67 ASN ** R 183 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 54 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 33 GLN ** V 47 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 154 GLN Y 158 HIS ** Y 236 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** c 20 GLN ** c 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** i 194 GLN u 64 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7212 moved from start: 0.1143 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 74475 Z= 0.174 Angle : 0.520 11.484 101224 Z= 0.262 Chirality : 0.040 0.178 11172 Planarity : 0.004 0.061 13313 Dihedral : 4.355 51.559 10233 Min Nonbonded Distance : 2.127 Molprobity Statistics. All-atom Clashscore : 8.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % Rotamer: Outliers : 1.41 % Allowed : 11.66 % Favored : 86.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.96 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.19 (0.09), residues: 9336 helix: 1.82 (0.09), residues: 3572 sheet: -0.70 (0.13), residues: 1575 loop : -1.04 (0.09), residues: 4189 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP J 103 HIS 0.004 0.001 HIS Z 235 PHE 0.024 0.001 PHE B 21 TYR 0.025 0.001 TYR W 177 ARG 0.006 0.000 ARG i 160 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 18672 Ramachandran restraints generated. 9336 Oldfield, 0 Emsley, 9336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 18672 Ramachandran restraints generated. 9336 Oldfield, 0 Emsley, 9336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 647 residues out of total 7562 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 105 poor density : 542 time to evaluate : 6.712 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 716 MET cc_start: 0.7773 (mtt) cc_final: 0.7247 (mtm) REVERT: C 527 GLU cc_start: 0.5886 (OUTLIER) cc_final: 0.5568 (mp0) REVERT: D 53 VAL cc_start: 0.8306 (OUTLIER) cc_final: 0.8074 (p) REVERT: E 257 PHE cc_start: 0.5479 (OUTLIER) cc_final: 0.5242 (t80) REVERT: M 1 MET cc_start: 0.5407 (ptt) cc_final: 0.5067 (ptt) REVERT: Y 304 MET cc_start: 0.8245 (tmm) cc_final: 0.7975 (tmm) REVERT: k 144 GLU cc_start: 0.2936 (mp0) cc_final: 0.2413 (mp0) REVERT: u 62 GLU cc_start: 0.7714 (OUTLIER) cc_final: 0.6577 (mp0) outliers start: 105 outliers final: 66 residues processed: 618 average time/residue: 0.7310 time to fit residues: 790.7147 Evaluate side-chains 563 residues out of total 7562 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 493 time to evaluate : 6.471 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 LEU Chi-restraints excluded: chain A residue 113 ASP Chi-restraints excluded: chain A residue 176 SER Chi-restraints excluded: chain A residue 344 VAL Chi-restraints excluded: chain A residue 450 LEU Chi-restraints excluded: chain A residue 477 ILE Chi-restraints excluded: chain A residue 543 GLU Chi-restraints excluded: chain B residue 76 VAL Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 740 ILE Chi-restraints excluded: chain B residue 800 ILE Chi-restraints excluded: chain B residue 808 VAL Chi-restraints excluded: chain C residue 502 HIS Chi-restraints excluded: chain C residue 527 GLU Chi-restraints excluded: chain D residue 53 VAL Chi-restraints excluded: chain D residue 249 MET Chi-restraints excluded: chain E residue 257 PHE Chi-restraints excluded: chain E residue 368 SER Chi-restraints excluded: chain F residue 182 GLU Chi-restraints excluded: chain G residue 43 ASN Chi-restraints excluded: chain G residue 70 ILE Chi-restraints excluded: chain G residue 72 VAL Chi-restraints excluded: chain G residue 442 GLU Chi-restraints excluded: chain H residue 204 VAL Chi-restraints excluded: chain I residue 406 VAL Chi-restraints excluded: chain J residue 290 VAL Chi-restraints excluded: chain K residue 89 LEU Chi-restraints excluded: chain K residue 280 SER Chi-restraints excluded: chain K residue 405 VAL Chi-restraints excluded: chain L residue 50 VAL Chi-restraints excluded: chain L residue 405 VAL Chi-restraints excluded: chain M residue 10 THR Chi-restraints excluded: chain O residue 105 CYS Chi-restraints excluded: chain O residue 166 VAL Chi-restraints excluded: chain P residue 111 MET Chi-restraints excluded: chain P residue 112 LEU Chi-restraints excluded: chain Q residue 2 VAL Chi-restraints excluded: chain Q residue 8 ILE Chi-restraints excluded: chain Q residue 147 ILE Chi-restraints excluded: chain S residue 73 THR Chi-restraints excluded: chain S residue 87 MET Chi-restraints excluded: chain S residue 114 ASN Chi-restraints excluded: chain S residue 152 THR Chi-restraints excluded: chain T residue 87 MET Chi-restraints excluded: chain T residue 114 ASN Chi-restraints excluded: chain V residue 3 VAL Chi-restraints excluded: chain V residue 4 GLU Chi-restraints excluded: chain V residue 46 THR Chi-restraints excluded: chain W residue 65 HIS Chi-restraints excluded: chain W residue 80 ASP Chi-restraints excluded: chain W residue 110 THR Chi-restraints excluded: chain W residue 176 ILE Chi-restraints excluded: chain X residue 32 THR Chi-restraints excluded: chain X residue 154 THR Chi-restraints excluded: chain X residue 212 VAL Chi-restraints excluded: chain X residue 370 PHE Chi-restraints excluded: chain X residue 371 LYS Chi-restraints excluded: chain Y residue 178 VAL Chi-restraints excluded: chain Y residue 180 VAL Chi-restraints excluded: chain b residue 36 ILE Chi-restraints excluded: chain d residue 55 THR Chi-restraints excluded: chain k residue 75 ILE Chi-restraints excluded: chain k residue 92 ILE Chi-restraints excluded: chain k residue 225 ASP Chi-restraints excluded: chain u residue 62 GLU Chi-restraints excluded: chain v residue 18 THR Chi-restraints excluded: chain y residue 14 THR Chi-restraints excluded: chain y residue 22 ILE Chi-restraints excluded: chain z residue 18 ASN Chi-restraints excluded: chain z residue 37 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 932 random chunks: chunk 750 optimal weight: 4.9990 chunk 511 optimal weight: 6.9990 chunk 13 optimal weight: 0.9990 chunk 670 optimal weight: 2.9990 chunk 371 optimal weight: 0.8980 chunk 768 optimal weight: 1.9990 chunk 622 optimal weight: 1.9990 chunk 1 optimal weight: 3.9990 chunk 460 optimal weight: 1.9990 chunk 808 optimal weight: 0.0770 chunk 227 optimal weight: 0.0370 overall best weight: 0.8020 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 548 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 288 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 134 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 54 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 33 GLN ** V 47 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 158 HIS ** Y 236 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Z 158 HIS b 52 HIS ** b 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** c 20 GLN ** i 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** u 64 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7214 moved from start: 0.1285 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 74475 Z= 0.192 Angle : 0.523 11.321 101224 Z= 0.263 Chirality : 0.040 0.209 11172 Planarity : 0.004 0.062 13313 Dihedral : 4.259 52.285 10231 Min Nonbonded Distance : 2.093 Molprobity Statistics. All-atom Clashscore : 8.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer: Outliers : 1.85 % Allowed : 12.62 % Favored : 85.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.96 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.32 (0.09), residues: 9336 helix: 1.92 (0.09), residues: 3578 sheet: -0.63 (0.13), residues: 1579 loop : -0.96 (0.09), residues: 4179 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP v 59 HIS 0.004 0.001 HIS A 610 PHE 0.018 0.001 PHE B 550 TYR 0.025 0.001 TYR a 43 ARG 0.007 0.000 ARG i 160 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 18672 Ramachandran restraints generated. 9336 Oldfield, 0 Emsley, 9336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 18672 Ramachandran restraints generated. 9336 Oldfield, 0 Emsley, 9336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 659 residues out of total 7562 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 138 poor density : 521 time to evaluate : 6.591 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 716 MET cc_start: 0.7778 (mtt) cc_final: 0.7177 (mtm) REVERT: C 527 GLU cc_start: 0.5910 (OUTLIER) cc_final: 0.5527 (mp0) REVERT: E 279 MET cc_start: 0.6012 (mmt) cc_final: 0.5756 (mmt) REVERT: G 72 VAL cc_start: 0.8749 (OUTLIER) cc_final: 0.8490 (m) REVERT: J 185 TRP cc_start: 0.9265 (OUTLIER) cc_final: 0.8968 (t-100) REVERT: M 1 MET cc_start: 0.5361 (ptt) cc_final: 0.5040 (ptt) REVERT: T 104 MET cc_start: 0.6620 (mtm) cc_final: 0.5854 (mtm) REVERT: Y 304 MET cc_start: 0.8291 (tmm) cc_final: 0.8019 (tmm) REVERT: i 73 ILE cc_start: 0.9218 (OUTLIER) cc_final: 0.8885 (pt) REVERT: k 144 GLU cc_start: 0.3012 (mp0) cc_final: 0.2576 (mp0) REVERT: u 62 GLU cc_start: 0.7602 (OUTLIER) cc_final: 0.6413 (mp0) outliers start: 138 outliers final: 96 residues processed: 625 average time/residue: 0.6633 time to fit residues: 721.6852 Evaluate side-chains 605 residues out of total 7562 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 101 poor density : 504 time to evaluate : 6.383 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 LEU Chi-restraints excluded: chain A residue 113 ASP Chi-restraints excluded: chain A residue 176 SER Chi-restraints excluded: chain A residue 344 VAL Chi-restraints excluded: chain A residue 445 THR Chi-restraints excluded: chain A residue 450 LEU Chi-restraints excluded: chain A residue 477 ILE Chi-restraints excluded: chain A residue 678 LEU Chi-restraints excluded: chain A residue 740 ILE Chi-restraints excluded: chain B residue 35 CYS Chi-restraints excluded: chain B residue 76 VAL Chi-restraints excluded: chain B residue 82 ILE Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 708 LEU Chi-restraints excluded: chain B residue 740 ILE Chi-restraints excluded: chain B residue 800 ILE Chi-restraints excluded: chain B residue 808 VAL Chi-restraints excluded: chain C residue 502 HIS Chi-restraints excluded: chain C residue 527 GLU Chi-restraints excluded: chain D residue 53 VAL Chi-restraints excluded: chain D residue 249 MET Chi-restraints excluded: chain D residue 573 LEU Chi-restraints excluded: chain E residue 158 VAL Chi-restraints excluded: chain E residue 343 LEU Chi-restraints excluded: chain E residue 368 SER Chi-restraints excluded: chain F residue 158 VAL Chi-restraints excluded: chain F residue 182 GLU Chi-restraints excluded: chain F residue 278 PHE Chi-restraints excluded: chain F residue 343 LEU Chi-restraints excluded: chain F residue 368 SER Chi-restraints excluded: chain G residue 43 ASN Chi-restraints excluded: chain G residue 70 ILE Chi-restraints excluded: chain G residue 72 VAL Chi-restraints excluded: chain G residue 442 GLU Chi-restraints excluded: chain H residue 93 ILE Chi-restraints excluded: chain H residue 204 VAL Chi-restraints excluded: chain H residue 223 SER Chi-restraints excluded: chain I residue 280 VAL Chi-restraints excluded: chain I residue 290 VAL Chi-restraints excluded: chain I residue 406 VAL Chi-restraints excluded: chain J residue 185 TRP Chi-restraints excluded: chain J residue 290 VAL Chi-restraints excluded: chain K residue 89 LEU Chi-restraints excluded: chain K residue 280 SER Chi-restraints excluded: chain K residue 405 VAL Chi-restraints excluded: chain L residue 50 VAL Chi-restraints excluded: chain L residue 193 VAL Chi-restraints excluded: chain L residue 405 VAL Chi-restraints excluded: chain M residue 10 THR Chi-restraints excluded: chain O residue 7 ASN Chi-restraints excluded: chain O residue 147 ILE Chi-restraints excluded: chain O residue 166 VAL Chi-restraints excluded: chain P residue 112 LEU Chi-restraints excluded: chain Q residue 2 VAL Chi-restraints excluded: chain Q residue 8 ILE Chi-restraints excluded: chain Q residue 147 ILE Chi-restraints excluded: chain Q residue 180 VAL Chi-restraints excluded: chain R residue 144 VAL Chi-restraints excluded: chain S residue 73 THR Chi-restraints excluded: chain S residue 114 ASN Chi-restraints excluded: chain S residue 152 THR Chi-restraints excluded: chain T residue 87 MET Chi-restraints excluded: chain T residue 114 ASN Chi-restraints excluded: chain V residue 3 VAL Chi-restraints excluded: chain V residue 4 GLU Chi-restraints excluded: chain V residue 46 THR Chi-restraints excluded: chain W residue 65 HIS Chi-restraints excluded: chain W residue 80 ASP Chi-restraints excluded: chain W residue 110 THR Chi-restraints excluded: chain W residue 176 ILE Chi-restraints excluded: chain W residue 178 ASN Chi-restraints excluded: chain X residue 32 THR Chi-restraints excluded: chain X residue 60 LEU Chi-restraints excluded: chain X residue 154 THR Chi-restraints excluded: chain X residue 370 PHE Chi-restraints excluded: chain X residue 371 LYS Chi-restraints excluded: chain Y residue 178 VAL Chi-restraints excluded: chain Y residue 180 VAL Chi-restraints excluded: chain Z residue 162 VAL Chi-restraints excluded: chain Z residue 180 VAL Chi-restraints excluded: chain Z residue 220 VAL Chi-restraints excluded: chain b residue 36 ILE Chi-restraints excluded: chain c residue 53 ASN Chi-restraints excluded: chain d residue 45 LYS Chi-restraints excluded: chain d residue 55 THR Chi-restraints excluded: chain i residue 73 ILE Chi-restraints excluded: chain i residue 91 MET Chi-restraints excluded: chain i residue 124 ASP Chi-restraints excluded: chain k residue 75 ILE Chi-restraints excluded: chain k residue 92 ILE Chi-restraints excluded: chain k residue 162 ASN Chi-restraints excluded: chain k residue 166 LYS Chi-restraints excluded: chain k residue 225 ASP Chi-restraints excluded: chain s residue 382 ASN Chi-restraints excluded: chain u residue 62 GLU Chi-restraints excluded: chain v residue 18 THR Chi-restraints excluded: chain y residue 14 THR Chi-restraints excluded: chain y residue 22 ILE Chi-restraints excluded: chain z residue 6 ASP Chi-restraints excluded: chain z residue 18 ASN Chi-restraints excluded: chain z residue 37 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 932 random chunks: chunk 303 optimal weight: 2.9990 chunk 811 optimal weight: 2.9990 chunk 178 optimal weight: 0.0470 chunk 528 optimal weight: 0.9990 chunk 222 optimal weight: 5.9990 chunk 901 optimal weight: 2.9990 chunk 748 optimal weight: 0.3980 chunk 417 optimal weight: 6.9990 chunk 74 optimal weight: 4.9990 chunk 298 optimal weight: 0.0070 chunk 473 optimal weight: 2.9990 overall best weight: 0.8900 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 30 ASN ** B 548 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 288 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 183 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 54 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 47 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 158 HIS ** Y 236 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Z 158 HIS ** b 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** c 20 GLN ** c 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** u 64 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7216 moved from start: 0.1385 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 74475 Z= 0.200 Angle : 0.521 11.265 101224 Z= 0.262 Chirality : 0.040 0.194 11172 Planarity : 0.004 0.062 13313 Dihedral : 4.209 52.648 10231 Min Nonbonded Distance : 2.104 Molprobity Statistics. All-atom Clashscore : 8.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.31 % Favored : 96.69 % Rotamer: Outliers : 1.98 % Allowed : 13.08 % Favored : 84.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.96 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.38 (0.09), residues: 9336 helix: 1.95 (0.09), residues: 3585 sheet: -0.62 (0.13), residues: 1607 loop : -0.90 (0.10), residues: 4144 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP v 59 HIS 0.004 0.001 HIS A 610 PHE 0.018 0.001 PHE a 48 TYR 0.030 0.001 TYR a 43 ARG 0.008 0.000 ARG i 160 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 18672 Ramachandran restraints generated. 9336 Oldfield, 0 Emsley, 9336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 18672 Ramachandran restraints generated. 9336 Oldfield, 0 Emsley, 9336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 675 residues out of total 7562 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 148 poor density : 527 time to evaluate : 6.467 Fit side-chains revert: symmetry clash REVERT: B 716 MET cc_start: 0.7817 (mtt) cc_final: 0.7231 (mtm) REVERT: C 527 GLU cc_start: 0.5875 (OUTLIER) cc_final: 0.5528 (mp0) REVERT: G 72 VAL cc_start: 0.8716 (OUTLIER) cc_final: 0.8452 (m) REVERT: J 185 TRP cc_start: 0.9263 (OUTLIER) cc_final: 0.8950 (t-100) REVERT: T 104 MET cc_start: 0.6517 (mtm) cc_final: 0.5940 (mtm) REVERT: Y 304 MET cc_start: 0.8338 (tmm) cc_final: 0.8057 (tmm) REVERT: i 73 ILE cc_start: 0.9214 (OUTLIER) cc_final: 0.8874 (pt) REVERT: k 144 GLU cc_start: 0.2984 (mp0) cc_final: 0.2607 (mp0) REVERT: u 62 GLU cc_start: 0.7540 (OUTLIER) cc_final: 0.6354 (mp0) outliers start: 148 outliers final: 106 residues processed: 642 average time/residue: 0.6488 time to fit residues: 729.4444 Evaluate side-chains 612 residues out of total 7562 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 111 poor density : 501 time to evaluate : 6.452 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 ASN Chi-restraints excluded: chain A residue 44 LEU Chi-restraints excluded: chain A residue 113 ASP Chi-restraints excluded: chain A residue 176 SER Chi-restraints excluded: chain A residue 188 ILE Chi-restraints excluded: chain A residue 344 VAL Chi-restraints excluded: chain A residue 362 LEU Chi-restraints excluded: chain A residue 445 THR Chi-restraints excluded: chain A residue 450 LEU Chi-restraints excluded: chain A residue 477 ILE Chi-restraints excluded: chain A residue 543 GLU Chi-restraints excluded: chain A residue 740 ILE Chi-restraints excluded: chain B residue 76 VAL Chi-restraints excluded: chain B residue 82 ILE Chi-restraints excluded: chain B residue 113 ASP Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 708 LEU Chi-restraints excluded: chain B residue 740 ILE Chi-restraints excluded: chain B residue 800 ILE Chi-restraints excluded: chain B residue 808 VAL Chi-restraints excluded: chain C residue 502 HIS Chi-restraints excluded: chain C residue 527 GLU Chi-restraints excluded: chain D residue 53 VAL Chi-restraints excluded: chain D residue 249 MET Chi-restraints excluded: chain D residue 573 LEU Chi-restraints excluded: chain E residue 158 VAL Chi-restraints excluded: chain E residue 343 LEU Chi-restraints excluded: chain E residue 368 SER Chi-restraints excluded: chain F residue 158 VAL Chi-restraints excluded: chain F residue 182 GLU Chi-restraints excluded: chain F residue 278 PHE Chi-restraints excluded: chain F residue 343 LEU Chi-restraints excluded: chain F residue 368 SER Chi-restraints excluded: chain G residue 43 ASN Chi-restraints excluded: chain G residue 70 ILE Chi-restraints excluded: chain G residue 72 VAL Chi-restraints excluded: chain G residue 448 LEU Chi-restraints excluded: chain H residue 93 ILE Chi-restraints excluded: chain H residue 204 VAL Chi-restraints excluded: chain H residue 223 SER Chi-restraints excluded: chain I residue 158 LEU Chi-restraints excluded: chain I residue 216 THR Chi-restraints excluded: chain I residue 280 VAL Chi-restraints excluded: chain I residue 290 VAL Chi-restraints excluded: chain I residue 406 VAL Chi-restraints excluded: chain I residue 495 VAL Chi-restraints excluded: chain J residue 185 TRP Chi-restraints excluded: chain J residue 290 VAL Chi-restraints excluded: chain K residue 280 SER Chi-restraints excluded: chain K residue 405 VAL Chi-restraints excluded: chain L residue 50 VAL Chi-restraints excluded: chain L residue 193 VAL Chi-restraints excluded: chain L residue 405 VAL Chi-restraints excluded: chain M residue 10 THR Chi-restraints excluded: chain O residue 7 ASN Chi-restraints excluded: chain O residue 147 ILE Chi-restraints excluded: chain O residue 166 VAL Chi-restraints excluded: chain P residue 112 LEU Chi-restraints excluded: chain Q residue 2 VAL Chi-restraints excluded: chain Q residue 8 ILE Chi-restraints excluded: chain Q residue 147 ILE Chi-restraints excluded: chain Q residue 180 VAL Chi-restraints excluded: chain R residue 112 LEU Chi-restraints excluded: chain R residue 144 VAL Chi-restraints excluded: chain S residue 73 THR Chi-restraints excluded: chain S residue 114 ASN Chi-restraints excluded: chain S residue 116 ASP Chi-restraints excluded: chain S residue 152 THR Chi-restraints excluded: chain T residue 87 MET Chi-restraints excluded: chain T residue 114 ASN Chi-restraints excluded: chain V residue 3 VAL Chi-restraints excluded: chain V residue 4 GLU Chi-restraints excluded: chain V residue 46 THR Chi-restraints excluded: chain W residue 65 HIS Chi-restraints excluded: chain W residue 80 ASP Chi-restraints excluded: chain W residue 86 ASP Chi-restraints excluded: chain W residue 110 THR Chi-restraints excluded: chain W residue 176 ILE Chi-restraints excluded: chain X residue 32 THR Chi-restraints excluded: chain X residue 60 LEU Chi-restraints excluded: chain X residue 154 THR Chi-restraints excluded: chain X residue 370 PHE Chi-restraints excluded: chain X residue 371 LYS Chi-restraints excluded: chain Y residue 142 GLU Chi-restraints excluded: chain Y residue 178 VAL Chi-restraints excluded: chain Y residue 180 VAL Chi-restraints excluded: chain Z residue 162 VAL Chi-restraints excluded: chain Z residue 180 VAL Chi-restraints excluded: chain Z residue 220 VAL Chi-restraints excluded: chain a residue 9 VAL Chi-restraints excluded: chain b residue 36 ILE Chi-restraints excluded: chain b residue 68 VAL Chi-restraints excluded: chain c residue 53 ASN Chi-restraints excluded: chain d residue 55 THR Chi-restraints excluded: chain i residue 73 ILE Chi-restraints excluded: chain i residue 91 MET Chi-restraints excluded: chain i residue 124 ASP Chi-restraints excluded: chain k residue 75 ILE Chi-restraints excluded: chain k residue 92 ILE Chi-restraints excluded: chain k residue 137 THR Chi-restraints excluded: chain k residue 162 ASN Chi-restraints excluded: chain k residue 166 LYS Chi-restraints excluded: chain k residue 225 ASP Chi-restraints excluded: chain s residue 371 THR Chi-restraints excluded: chain u residue 62 GLU Chi-restraints excluded: chain v residue 18 THR Chi-restraints excluded: chain y residue 14 THR Chi-restraints excluded: chain y residue 22 ILE Chi-restraints excluded: chain z residue 6 ASP Chi-restraints excluded: chain z residue 18 ASN Chi-restraints excluded: chain z residue 37 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 932 random chunks: chunk 869 optimal weight: 3.9990 chunk 101 optimal weight: 0.0030 chunk 513 optimal weight: 5.9990 chunk 658 optimal weight: 1.9990 chunk 510 optimal weight: 6.9990 chunk 759 optimal weight: 0.8980 chunk 503 optimal weight: 0.9990 chunk 898 optimal weight: 0.5980 chunk 562 optimal weight: 2.9990 chunk 547 optimal weight: 3.9990 chunk 414 optimal weight: 3.9990 overall best weight: 0.8994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 548 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 94 ASN ** I 288 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 183 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 54 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 47 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 65 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Y 158 HIS ** Y 236 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Z 158 HIS ** b 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** c 20 GLN ** c 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** u 64 GLN v 64 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7216 moved from start: 0.1458 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 74475 Z= 0.203 Angle : 0.525 11.198 101224 Z= 0.265 Chirality : 0.040 0.194 11172 Planarity : 0.004 0.062 13313 Dihedral : 4.187 53.035 10231 Min Nonbonded Distance : 2.105 Molprobity Statistics. All-atom Clashscore : 8.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.48 % Favored : 96.52 % Rotamer: Outliers : 1.82 % Allowed : 14.09 % Favored : 84.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.96 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.43 (0.09), residues: 9336 helix: 1.98 (0.09), residues: 3577 sheet: -0.56 (0.13), residues: 1601 loop : -0.87 (0.10), residues: 4158 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP v 59 HIS 0.004 0.001 HIS b 52 PHE 0.017 0.001 PHE B 21 TYR 0.033 0.001 TYR a 43 ARG 0.004 0.000 ARG U 31 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 18672 Ramachandran restraints generated. 9336 Oldfield, 0 Emsley, 9336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 18672 Ramachandran restraints generated. 9336 Oldfield, 0 Emsley, 9336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 658 residues out of total 7562 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 136 poor density : 522 time to evaluate : 6.521 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 716 MET cc_start: 0.7779 (mtt) cc_final: 0.7197 (mtm) REVERT: C 527 GLU cc_start: 0.5881 (OUTLIER) cc_final: 0.5533 (mp0) REVERT: E 271 MET cc_start: 0.6021 (mmm) cc_final: 0.4775 (mmm) REVERT: G 72 VAL cc_start: 0.8706 (OUTLIER) cc_final: 0.8448 (m) REVERT: J 185 TRP cc_start: 0.9239 (OUTLIER) cc_final: 0.8963 (t-100) REVERT: K 424 VAL cc_start: 0.7189 (m) cc_final: 0.6966 (m) REVERT: T 104 MET cc_start: 0.6513 (mtm) cc_final: 0.6067 (mtm) REVERT: Y 304 MET cc_start: 0.8340 (tmm) cc_final: 0.8063 (tmm) REVERT: i 73 ILE cc_start: 0.9211 (OUTLIER) cc_final: 0.8872 (pt) REVERT: k 144 GLU cc_start: 0.3001 (mp0) cc_final: 0.2031 (mp0) REVERT: u 62 GLU cc_start: 0.7546 (OUTLIER) cc_final: 0.6344 (mp0) outliers start: 136 outliers final: 111 residues processed: 626 average time/residue: 0.6713 time to fit residues: 736.1446 Evaluate side-chains 617 residues out of total 7562 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 116 poor density : 501 time to evaluate : 6.596 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 ASN Chi-restraints excluded: chain A residue 27 GLU Chi-restraints excluded: chain A residue 44 LEU Chi-restraints excluded: chain A residue 113 ASP Chi-restraints excluded: chain A residue 176 SER Chi-restraints excluded: chain A residue 188 ILE Chi-restraints excluded: chain A residue 344 VAL Chi-restraints excluded: chain A residue 362 LEU Chi-restraints excluded: chain A residue 445 THR Chi-restraints excluded: chain A residue 450 LEU Chi-restraints excluded: chain A residue 740 ILE Chi-restraints excluded: chain B residue 35 CYS Chi-restraints excluded: chain B residue 76 VAL Chi-restraints excluded: chain B residue 82 ILE Chi-restraints excluded: chain B residue 113 ASP Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 708 LEU Chi-restraints excluded: chain B residue 709 THR Chi-restraints excluded: chain B residue 740 ILE Chi-restraints excluded: chain B residue 800 ILE Chi-restraints excluded: chain B residue 808 VAL Chi-restraints excluded: chain C residue 111 VAL Chi-restraints excluded: chain C residue 502 HIS Chi-restraints excluded: chain C residue 527 GLU Chi-restraints excluded: chain C residue 587 VAL Chi-restraints excluded: chain D residue 53 VAL Chi-restraints excluded: chain D residue 249 MET Chi-restraints excluded: chain D residue 573 LEU Chi-restraints excluded: chain E residue 158 VAL Chi-restraints excluded: chain E residue 343 LEU Chi-restraints excluded: chain E residue 368 SER Chi-restraints excluded: chain E residue 506 ASN Chi-restraints excluded: chain F residue 158 VAL Chi-restraints excluded: chain F residue 182 GLU Chi-restraints excluded: chain F residue 270 VAL Chi-restraints excluded: chain F residue 278 PHE Chi-restraints excluded: chain F residue 343 LEU Chi-restraints excluded: chain F residue 368 SER Chi-restraints excluded: chain G residue 43 ASN Chi-restraints excluded: chain G residue 70 ILE Chi-restraints excluded: chain G residue 72 VAL Chi-restraints excluded: chain G residue 448 LEU Chi-restraints excluded: chain H residue 93 ILE Chi-restraints excluded: chain H residue 204 VAL Chi-restraints excluded: chain I residue 158 LEU Chi-restraints excluded: chain I residue 216 THR Chi-restraints excluded: chain I residue 290 VAL Chi-restraints excluded: chain I residue 406 VAL Chi-restraints excluded: chain I residue 495 VAL Chi-restraints excluded: chain J residue 185 TRP Chi-restraints excluded: chain J residue 290 VAL Chi-restraints excluded: chain K residue 89 LEU Chi-restraints excluded: chain K residue 280 SER Chi-restraints excluded: chain K residue 405 VAL Chi-restraints excluded: chain L residue 50 VAL Chi-restraints excluded: chain L residue 193 VAL Chi-restraints excluded: chain L residue 405 VAL Chi-restraints excluded: chain M residue 10 THR Chi-restraints excluded: chain O residue 7 ASN Chi-restraints excluded: chain O residue 147 ILE Chi-restraints excluded: chain O residue 166 VAL Chi-restraints excluded: chain P residue 112 LEU Chi-restraints excluded: chain Q residue 2 VAL Chi-restraints excluded: chain Q residue 8 ILE Chi-restraints excluded: chain Q residue 147 ILE Chi-restraints excluded: chain Q residue 180 VAL Chi-restraints excluded: chain R residue 112 LEU Chi-restraints excluded: chain R residue 144 VAL Chi-restraints excluded: chain R residue 185 LEU Chi-restraints excluded: chain S residue 73 THR Chi-restraints excluded: chain S residue 114 ASN Chi-restraints excluded: chain S residue 116 ASP Chi-restraints excluded: chain S residue 152 THR Chi-restraints excluded: chain T residue 87 MET Chi-restraints excluded: chain T residue 114 ASN Chi-restraints excluded: chain V residue 3 VAL Chi-restraints excluded: chain V residue 35 THR Chi-restraints excluded: chain V residue 46 THR Chi-restraints excluded: chain W residue 65 HIS Chi-restraints excluded: chain W residue 80 ASP Chi-restraints excluded: chain W residue 86 ASP Chi-restraints excluded: chain W residue 110 THR Chi-restraints excluded: chain W residue 176 ILE Chi-restraints excluded: chain W residue 178 ASN Chi-restraints excluded: chain X residue 7 ILE Chi-restraints excluded: chain X residue 32 THR Chi-restraints excluded: chain X residue 60 LEU Chi-restraints excluded: chain X residue 154 THR Chi-restraints excluded: chain X residue 370 PHE Chi-restraints excluded: chain Y residue 142 GLU Chi-restraints excluded: chain Y residue 145 LEU Chi-restraints excluded: chain Y residue 178 VAL Chi-restraints excluded: chain Y residue 180 VAL Chi-restraints excluded: chain Z residue 162 VAL Chi-restraints excluded: chain Z residue 180 VAL Chi-restraints excluded: chain Z residue 220 VAL Chi-restraints excluded: chain b residue 36 ILE Chi-restraints excluded: chain b residue 68 VAL Chi-restraints excluded: chain c residue 53 ASN Chi-restraints excluded: chain d residue 55 THR Chi-restraints excluded: chain i residue 73 ILE Chi-restraints excluded: chain i residue 91 MET Chi-restraints excluded: chain i residue 124 ASP Chi-restraints excluded: chain k residue 75 ILE Chi-restraints excluded: chain k residue 92 ILE Chi-restraints excluded: chain k residue 137 THR Chi-restraints excluded: chain k residue 162 ASN Chi-restraints excluded: chain k residue 166 LYS Chi-restraints excluded: chain k residue 225 ASP Chi-restraints excluded: chain s residue 371 THR Chi-restraints excluded: chain u residue 62 GLU Chi-restraints excluded: chain v residue 18 THR Chi-restraints excluded: chain y residue 14 THR Chi-restraints excluded: chain y residue 22 ILE Chi-restraints excluded: chain z residue 18 ASN Chi-restraints excluded: chain z residue 37 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 932 random chunks: chunk 555 optimal weight: 3.9990 chunk 358 optimal weight: 2.9990 chunk 536 optimal weight: 2.9990 chunk 270 optimal weight: 4.9990 chunk 176 optimal weight: 0.9980 chunk 174 optimal weight: 10.0000 chunk 571 optimal weight: 1.9990 chunk 612 optimal weight: 3.9990 chunk 444 optimal weight: 9.9990 chunk 83 optimal weight: 0.0470 chunk 706 optimal weight: 10.0000 overall best weight: 1.8084 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 548 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 285 GLN ** G 329 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 288 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 183 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 54 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 47 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 65 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** W 178 ASN X 372 HIS Y 158 HIS ** Y 236 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Z 158 HIS ** b 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** c 20 GLN ** c 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 57 HIS i 162 GLN u 64 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7270 moved from start: 0.1509 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 74475 Z= 0.345 Angle : 0.590 11.252 101224 Z= 0.299 Chirality : 0.042 0.208 11172 Planarity : 0.004 0.060 13313 Dihedral : 4.418 54.695 10229 Min Nonbonded Distance : 2.052 Molprobity Statistics. All-atom Clashscore : 9.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.18 % Favored : 95.82 % Rotamer: Outliers : 2.05 % Allowed : 14.35 % Favored : 83.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.96 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.22 (0.09), residues: 9336 helix: 1.78 (0.09), residues: 3576 sheet: -0.67 (0.13), residues: 1623 loop : -0.95 (0.10), residues: 4137 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.050 0.002 TRP v 59 HIS 0.008 0.001 HIS b 57 PHE 0.022 0.002 PHE I 339 TYR 0.028 0.002 TYR a 43 ARG 0.012 0.000 ARG i 160 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 18672 Ramachandran restraints generated. 9336 Oldfield, 0 Emsley, 9336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 18672 Ramachandran restraints generated. 9336 Oldfield, 0 Emsley, 9336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 658 residues out of total 7562 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 153 poor density : 505 time to evaluate : 6.676 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 527 GLU cc_start: 0.5893 (OUTLIER) cc_final: 0.5552 (mp0) REVERT: E 279 MET cc_start: 0.6036 (mmp) cc_final: 0.5283 (mmt) REVERT: J 185 TRP cc_start: 0.9271 (OUTLIER) cc_final: 0.8981 (t-100) REVERT: W 48 CYS cc_start: 0.5569 (m) cc_final: 0.5218 (m) REVERT: Y 304 MET cc_start: 0.8299 (tmm) cc_final: 0.8033 (tmm) REVERT: i 73 ILE cc_start: 0.9221 (OUTLIER) cc_final: 0.8891 (pt) REVERT: k 144 GLU cc_start: 0.3547 (mp0) cc_final: 0.2632 (mp0) REVERT: u 62 GLU cc_start: 0.7585 (OUTLIER) cc_final: 0.6327 (mp0) outliers start: 153 outliers final: 127 residues processed: 625 average time/residue: 0.6618 time to fit residues: 723.6641 Evaluate side-chains 624 residues out of total 7562 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 131 poor density : 493 time to evaluate : 6.392 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 ASN Chi-restraints excluded: chain A residue 27 GLU Chi-restraints excluded: chain A residue 44 LEU Chi-restraints excluded: chain A residue 113 ASP Chi-restraints excluded: chain A residue 176 SER Chi-restraints excluded: chain A residue 188 ILE Chi-restraints excluded: chain A residue 199 LEU Chi-restraints excluded: chain A residue 344 VAL Chi-restraints excluded: chain A residue 362 LEU Chi-restraints excluded: chain A residue 445 THR Chi-restraints excluded: chain A residue 450 LEU Chi-restraints excluded: chain A residue 477 ILE Chi-restraints excluded: chain A residue 546 LEU Chi-restraints excluded: chain A residue 740 ILE Chi-restraints excluded: chain B residue 35 CYS Chi-restraints excluded: chain B residue 76 VAL Chi-restraints excluded: chain B residue 82 ILE Chi-restraints excluded: chain B residue 113 ASP Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 708 LEU Chi-restraints excluded: chain B residue 709 THR Chi-restraints excluded: chain B residue 740 ILE Chi-restraints excluded: chain B residue 800 ILE Chi-restraints excluded: chain B residue 808 VAL Chi-restraints excluded: chain C residue 111 VAL Chi-restraints excluded: chain C residue 502 HIS Chi-restraints excluded: chain C residue 527 GLU Chi-restraints excluded: chain C residue 587 VAL Chi-restraints excluded: chain D residue 53 VAL Chi-restraints excluded: chain D residue 73 VAL Chi-restraints excluded: chain D residue 249 MET Chi-restraints excluded: chain D residue 477 ASP Chi-restraints excluded: chain D residue 573 LEU Chi-restraints excluded: chain E residue 158 VAL Chi-restraints excluded: chain E residue 343 LEU Chi-restraints excluded: chain E residue 368 SER Chi-restraints excluded: chain E residue 506 ASN Chi-restraints excluded: chain F residue 158 VAL Chi-restraints excluded: chain F residue 182 GLU Chi-restraints excluded: chain F residue 261 VAL Chi-restraints excluded: chain F residue 270 VAL Chi-restraints excluded: chain F residue 278 PHE Chi-restraints excluded: chain F residue 343 LEU Chi-restraints excluded: chain F residue 368 SER Chi-restraints excluded: chain G residue 43 ASN Chi-restraints excluded: chain G residue 72 VAL Chi-restraints excluded: chain G residue 448 LEU Chi-restraints excluded: chain H residue 93 ILE Chi-restraints excluded: chain H residue 204 VAL Chi-restraints excluded: chain I residue 216 THR Chi-restraints excluded: chain I residue 290 VAL Chi-restraints excluded: chain I residue 406 VAL Chi-restraints excluded: chain I residue 495 VAL Chi-restraints excluded: chain J residue 185 TRP Chi-restraints excluded: chain J residue 290 VAL Chi-restraints excluded: chain J residue 495 VAL Chi-restraints excluded: chain K residue 89 LEU Chi-restraints excluded: chain K residue 280 SER Chi-restraints excluded: chain K residue 405 VAL Chi-restraints excluded: chain L residue 50 VAL Chi-restraints excluded: chain L residue 193 VAL Chi-restraints excluded: chain L residue 405 VAL Chi-restraints excluded: chain L residue 418 CYS Chi-restraints excluded: chain L residue 444 CYS Chi-restraints excluded: chain M residue 10 THR Chi-restraints excluded: chain O residue 7 ASN Chi-restraints excluded: chain O residue 147 ILE Chi-restraints excluded: chain O residue 166 VAL Chi-restraints excluded: chain P residue 112 LEU Chi-restraints excluded: chain Q residue 2 VAL Chi-restraints excluded: chain Q residue 8 ILE Chi-restraints excluded: chain Q residue 147 ILE Chi-restraints excluded: chain Q residue 180 VAL Chi-restraints excluded: chain R residue 112 LEU Chi-restraints excluded: chain R residue 144 VAL Chi-restraints excluded: chain R residue 185 LEU Chi-restraints excluded: chain S residue 73 THR Chi-restraints excluded: chain S residue 114 ASN Chi-restraints excluded: chain S residue 116 ASP Chi-restraints excluded: chain S residue 152 THR Chi-restraints excluded: chain T residue 87 MET Chi-restraints excluded: chain T residue 114 ASN Chi-restraints excluded: chain V residue 3 VAL Chi-restraints excluded: chain V residue 4 GLU Chi-restraints excluded: chain V residue 6 ILE Chi-restraints excluded: chain V residue 35 THR Chi-restraints excluded: chain V residue 46 THR Chi-restraints excluded: chain W residue 65 HIS Chi-restraints excluded: chain W residue 80 ASP Chi-restraints excluded: chain W residue 86 ASP Chi-restraints excluded: chain W residue 110 THR Chi-restraints excluded: chain W residue 176 ILE Chi-restraints excluded: chain X residue 7 ILE Chi-restraints excluded: chain X residue 32 THR Chi-restraints excluded: chain X residue 370 PHE Chi-restraints excluded: chain X residue 371 LYS Chi-restraints excluded: chain Y residue 142 GLU Chi-restraints excluded: chain Y residue 145 LEU Chi-restraints excluded: chain Y residue 178 VAL Chi-restraints excluded: chain Y residue 180 VAL Chi-restraints excluded: chain Z residue 162 VAL Chi-restraints excluded: chain Z residue 180 VAL Chi-restraints excluded: chain Z residue 220 VAL Chi-restraints excluded: chain a residue 9 VAL Chi-restraints excluded: chain b residue 36 ILE Chi-restraints excluded: chain b residue 68 VAL Chi-restraints excluded: chain c residue 20 GLN Chi-restraints excluded: chain c residue 53 ASN Chi-restraints excluded: chain d residue 55 THR Chi-restraints excluded: chain i residue 73 ILE Chi-restraints excluded: chain i residue 91 MET Chi-restraints excluded: chain i residue 124 ASP Chi-restraints excluded: chain i residue 145 THR Chi-restraints excluded: chain j residue 65 VAL Chi-restraints excluded: chain j residue 145 THR Chi-restraints excluded: chain k residue 75 ILE Chi-restraints excluded: chain k residue 92 ILE Chi-restraints excluded: chain k residue 162 ASN Chi-restraints excluded: chain k residue 166 LYS Chi-restraints excluded: chain k residue 224 ASN Chi-restraints excluded: chain k residue 225 ASP Chi-restraints excluded: chain s residue 371 THR Chi-restraints excluded: chain s residue 382 ASN Chi-restraints excluded: chain u residue 62 GLU Chi-restraints excluded: chain u residue 64 GLN Chi-restraints excluded: chain v residue 18 THR Chi-restraints excluded: chain y residue 14 THR Chi-restraints excluded: chain y residue 22 ILE Chi-restraints excluded: chain z residue 18 ASN Chi-restraints excluded: chain z residue 37 ILE Chi-restraints excluded: chain z residue 59 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 932 random chunks: chunk 817 optimal weight: 1.9990 chunk 860 optimal weight: 7.9990 chunk 785 optimal weight: 0.8980 chunk 837 optimal weight: 1.9990 chunk 503 optimal weight: 1.9990 chunk 364 optimal weight: 0.9980 chunk 657 optimal weight: 1.9990 chunk 256 optimal weight: 9.9990 chunk 756 optimal weight: 1.9990 chunk 791 optimal weight: 3.9990 chunk 834 optimal weight: 0.1980 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 30 ASN B 49 HIS ** B 548 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 329 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 288 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 183 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 54 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 47 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 65 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** X 372 HIS Y 158 HIS ** Y 236 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Z 158 HIS ** b 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 57 HIS u 64 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7247 moved from start: 0.1531 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 74475 Z= 0.253 Angle : 0.556 11.221 101224 Z= 0.281 Chirality : 0.041 0.198 11172 Planarity : 0.004 0.061 13313 Dihedral : 4.346 54.958 10229 Min Nonbonded Distance : 2.078 Molprobity Statistics. All-atom Clashscore : 8.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.73 % Favored : 96.27 % Rotamer: Outliers : 1.89 % Allowed : 14.64 % Favored : 83.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.96 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.31 (0.09), residues: 9336 helix: 1.84 (0.09), residues: 3581 sheet: -0.63 (0.13), residues: 1577 loop : -0.89 (0.10), residues: 4178 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.045 0.001 TRP v 59 HIS 0.005 0.001 HIS b 52 PHE 0.017 0.001 PHE D 521 TYR 0.020 0.001 TYR W 20 ARG 0.008 0.000 ARG u 66 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 18672 Ramachandran restraints generated. 9336 Oldfield, 0 Emsley, 9336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 18672 Ramachandran restraints generated. 9336 Oldfield, 0 Emsley, 9336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 648 residues out of total 7562 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 141 poor density : 507 time to evaluate : 6.461 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 527 GLU cc_start: 0.5851 (OUTLIER) cc_final: 0.5495 (mp0) REVERT: E 279 MET cc_start: 0.6054 (mmp) cc_final: 0.5246 (mmt) REVERT: J 185 TRP cc_start: 0.9238 (OUTLIER) cc_final: 0.8957 (t-100) REVERT: W 48 CYS cc_start: 0.5521 (m) cc_final: 0.5158 (m) REVERT: Y 304 MET cc_start: 0.8282 (tmm) cc_final: 0.8006 (tmm) REVERT: i 73 ILE cc_start: 0.9218 (OUTLIER) cc_final: 0.8881 (pt) REVERT: k 144 GLU cc_start: 0.3415 (mp0) cc_final: 0.2508 (mp0) REVERT: u 62 GLU cc_start: 0.7537 (OUTLIER) cc_final: 0.6380 (mp0) outliers start: 141 outliers final: 127 residues processed: 615 average time/residue: 0.6745 time to fit residues: 726.8152 Evaluate side-chains 631 residues out of total 7562 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 131 poor density : 500 time to evaluate : 6.420 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 ASN Chi-restraints excluded: chain A residue 27 GLU Chi-restraints excluded: chain A residue 44 LEU Chi-restraints excluded: chain A residue 113 ASP Chi-restraints excluded: chain A residue 176 SER Chi-restraints excluded: chain A residue 188 ILE Chi-restraints excluded: chain A residue 199 LEU Chi-restraints excluded: chain A residue 344 VAL Chi-restraints excluded: chain A residue 362 LEU Chi-restraints excluded: chain A residue 445 THR Chi-restraints excluded: chain A residue 450 LEU Chi-restraints excluded: chain A residue 477 ILE Chi-restraints excluded: chain A residue 546 LEU Chi-restraints excluded: chain A residue 708 LEU Chi-restraints excluded: chain A residue 740 ILE Chi-restraints excluded: chain B residue 35 CYS Chi-restraints excluded: chain B residue 76 VAL Chi-restraints excluded: chain B residue 82 ILE Chi-restraints excluded: chain B residue 113 ASP Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 708 LEU Chi-restraints excluded: chain B residue 709 THR Chi-restraints excluded: chain B residue 740 ILE Chi-restraints excluded: chain B residue 800 ILE Chi-restraints excluded: chain B residue 808 VAL Chi-restraints excluded: chain C residue 111 VAL Chi-restraints excluded: chain C residue 502 HIS Chi-restraints excluded: chain C residue 527 GLU Chi-restraints excluded: chain C residue 587 VAL Chi-restraints excluded: chain D residue 53 VAL Chi-restraints excluded: chain D residue 73 VAL Chi-restraints excluded: chain D residue 249 MET Chi-restraints excluded: chain D residue 573 LEU Chi-restraints excluded: chain E residue 158 VAL Chi-restraints excluded: chain E residue 343 LEU Chi-restraints excluded: chain E residue 368 SER Chi-restraints excluded: chain E residue 506 ASN Chi-restraints excluded: chain F residue 158 VAL Chi-restraints excluded: chain F residue 182 GLU Chi-restraints excluded: chain F residue 261 VAL Chi-restraints excluded: chain F residue 270 VAL Chi-restraints excluded: chain F residue 278 PHE Chi-restraints excluded: chain F residue 343 LEU Chi-restraints excluded: chain F residue 368 SER Chi-restraints excluded: chain G residue 43 ASN Chi-restraints excluded: chain G residue 70 ILE Chi-restraints excluded: chain G residue 72 VAL Chi-restraints excluded: chain G residue 448 LEU Chi-restraints excluded: chain H residue 93 ILE Chi-restraints excluded: chain H residue 204 VAL Chi-restraints excluded: chain I residue 216 THR Chi-restraints excluded: chain I residue 290 VAL Chi-restraints excluded: chain I residue 406 VAL Chi-restraints excluded: chain I residue 495 VAL Chi-restraints excluded: chain J residue 185 TRP Chi-restraints excluded: chain J residue 290 VAL Chi-restraints excluded: chain K residue 89 LEU Chi-restraints excluded: chain K residue 280 SER Chi-restraints excluded: chain K residue 405 VAL Chi-restraints excluded: chain K residue 418 CYS Chi-restraints excluded: chain L residue 50 VAL Chi-restraints excluded: chain L residue 193 VAL Chi-restraints excluded: chain L residue 405 VAL Chi-restraints excluded: chain L residue 444 CYS Chi-restraints excluded: chain M residue 10 THR Chi-restraints excluded: chain O residue 7 ASN Chi-restraints excluded: chain O residue 147 ILE Chi-restraints excluded: chain O residue 166 VAL Chi-restraints excluded: chain P residue 112 LEU Chi-restraints excluded: chain Q residue 2 VAL Chi-restraints excluded: chain Q residue 8 ILE Chi-restraints excluded: chain Q residue 147 ILE Chi-restraints excluded: chain Q residue 180 VAL Chi-restraints excluded: chain R residue 112 LEU Chi-restraints excluded: chain R residue 144 VAL Chi-restraints excluded: chain R residue 185 LEU Chi-restraints excluded: chain S residue 73 THR Chi-restraints excluded: chain S residue 87 MET Chi-restraints excluded: chain S residue 114 ASN Chi-restraints excluded: chain S residue 116 ASP Chi-restraints excluded: chain S residue 152 THR Chi-restraints excluded: chain T residue 87 MET Chi-restraints excluded: chain T residue 114 ASN Chi-restraints excluded: chain V residue 3 VAL Chi-restraints excluded: chain V residue 4 GLU Chi-restraints excluded: chain V residue 6 ILE Chi-restraints excluded: chain V residue 35 THR Chi-restraints excluded: chain V residue 46 THR Chi-restraints excluded: chain W residue 65 HIS Chi-restraints excluded: chain W residue 80 ASP Chi-restraints excluded: chain W residue 86 ASP Chi-restraints excluded: chain W residue 110 THR Chi-restraints excluded: chain W residue 176 ILE Chi-restraints excluded: chain X residue 7 ILE Chi-restraints excluded: chain X residue 32 THR Chi-restraints excluded: chain X residue 370 PHE Chi-restraints excluded: chain X residue 371 LYS Chi-restraints excluded: chain Y residue 142 GLU Chi-restraints excluded: chain Y residue 145 LEU Chi-restraints excluded: chain Y residue 178 VAL Chi-restraints excluded: chain Y residue 180 VAL Chi-restraints excluded: chain Z residue 162 VAL Chi-restraints excluded: chain Z residue 180 VAL Chi-restraints excluded: chain Z residue 220 VAL Chi-restraints excluded: chain a residue 9 VAL Chi-restraints excluded: chain b residue 36 ILE Chi-restraints excluded: chain b residue 68 VAL Chi-restraints excluded: chain c residue 53 ASN Chi-restraints excluded: chain d residue 55 THR Chi-restraints excluded: chain i residue 73 ILE Chi-restraints excluded: chain i residue 91 MET Chi-restraints excluded: chain i residue 124 ASP Chi-restraints excluded: chain i residue 145 THR Chi-restraints excluded: chain j residue 65 VAL Chi-restraints excluded: chain j residue 145 THR Chi-restraints excluded: chain k residue 75 ILE Chi-restraints excluded: chain k residue 92 ILE Chi-restraints excluded: chain k residue 129 VAL Chi-restraints excluded: chain k residue 162 ASN Chi-restraints excluded: chain k residue 166 LYS Chi-restraints excluded: chain k residue 225 ASP Chi-restraints excluded: chain s residue 371 THR Chi-restraints excluded: chain s residue 382 ASN Chi-restraints excluded: chain u residue 62 GLU Chi-restraints excluded: chain u residue 64 GLN Chi-restraints excluded: chain v residue 18 THR Chi-restraints excluded: chain y residue 14 THR Chi-restraints excluded: chain y residue 22 ILE Chi-restraints excluded: chain z residue 18 ASN Chi-restraints excluded: chain z residue 37 ILE Chi-restraints excluded: chain z residue 59 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 932 random chunks: chunk 549 optimal weight: 0.9990 chunk 885 optimal weight: 1.9990 chunk 540 optimal weight: 0.5980 chunk 419 optimal weight: 5.9990 chunk 615 optimal weight: 3.9990 chunk 928 optimal weight: 0.8980 chunk 854 optimal weight: 0.9980 chunk 739 optimal weight: 0.4980 chunk 76 optimal weight: 1.9990 chunk 571 optimal weight: 1.9990 chunk 453 optimal weight: 1.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 548 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 172 GLN G 329 GLN ** I 288 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 183 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 54 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 47 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 65 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** X 372 HIS Y 158 HIS ** Y 236 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Z 158 HIS ** b 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** c 20 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7219 moved from start: 0.1582 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 74475 Z= 0.194 Angle : 0.536 11.318 101224 Z= 0.270 Chirality : 0.040 0.205 11172 Planarity : 0.004 0.062 13313 Dihedral : 4.206 54.384 10229 Min Nonbonded Distance : 2.103 Molprobity Statistics. All-atom Clashscore : 8.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.48 % Favored : 96.52 % Rotamer: Outliers : 1.77 % Allowed : 14.96 % Favored : 83.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.96 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.44 (0.09), residues: 9336 helix: 1.96 (0.09), residues: 3580 sheet: -0.56 (0.13), residues: 1595 loop : -0.84 (0.10), residues: 4161 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.045 0.001 TRP v 59 HIS 0.005 0.001 HIS b 52 PHE 0.022 0.001 PHE a 48 TYR 0.057 0.001 TYR c 43 ARG 0.009 0.000 ARG u 66 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 18672 Ramachandran restraints generated. 9336 Oldfield, 0 Emsley, 9336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 18672 Ramachandran restraints generated. 9336 Oldfield, 0 Emsley, 9336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 650 residues out of total 7562 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 132 poor density : 518 time to evaluate : 6.497 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 35 CYS cc_start: 0.4971 (t) cc_final: 0.4768 (t) REVERT: C 527 GLU cc_start: 0.5810 (OUTLIER) cc_final: 0.5448 (mp0) REVERT: E 279 MET cc_start: 0.6052 (mmp) cc_final: 0.5201 (mmt) REVERT: G 72 VAL cc_start: 0.8706 (OUTLIER) cc_final: 0.8449 (m) REVERT: J 185 TRP cc_start: 0.9205 (OUTLIER) cc_final: 0.8993 (t-100) REVERT: Y 304 MET cc_start: 0.8332 (tmm) cc_final: 0.8063 (tmm) REVERT: i 73 ILE cc_start: 0.9211 (OUTLIER) cc_final: 0.8871 (pt) REVERT: k 144 GLU cc_start: 0.3293 (mp0) cc_final: 0.2348 (mp0) REVERT: s 379 LEU cc_start: 0.7327 (tp) cc_final: 0.7121 (tp) REVERT: u 40 MET cc_start: 0.6405 (tpp) cc_final: 0.6083 (tpp) REVERT: u 62 GLU cc_start: 0.7489 (OUTLIER) cc_final: 0.6369 (mp0) outliers start: 132 outliers final: 119 residues processed: 621 average time/residue: 0.6583 time to fit residues: 716.7438 Evaluate side-chains 624 residues out of total 7562 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 124 poor density : 500 time to evaluate : 6.526 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 GLU Chi-restraints excluded: chain A residue 44 LEU Chi-restraints excluded: chain A residue 113 ASP Chi-restraints excluded: chain A residue 176 SER Chi-restraints excluded: chain A residue 188 ILE Chi-restraints excluded: chain A residue 199 LEU Chi-restraints excluded: chain A residue 344 VAL Chi-restraints excluded: chain A residue 362 LEU Chi-restraints excluded: chain A residue 445 THR Chi-restraints excluded: chain A residue 450 LEU Chi-restraints excluded: chain A residue 546 LEU Chi-restraints excluded: chain A residue 708 LEU Chi-restraints excluded: chain A residue 740 ILE Chi-restraints excluded: chain B residue 35 CYS Chi-restraints excluded: chain B residue 76 VAL Chi-restraints excluded: chain B residue 82 ILE Chi-restraints excluded: chain B residue 113 ASP Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 708 LEU Chi-restraints excluded: chain B residue 709 THR Chi-restraints excluded: chain B residue 740 ILE Chi-restraints excluded: chain B residue 800 ILE Chi-restraints excluded: chain B residue 808 VAL Chi-restraints excluded: chain C residue 111 VAL Chi-restraints excluded: chain C residue 502 HIS Chi-restraints excluded: chain C residue 527 GLU Chi-restraints excluded: chain C residue 587 VAL Chi-restraints excluded: chain D residue 53 VAL Chi-restraints excluded: chain D residue 249 MET Chi-restraints excluded: chain D residue 573 LEU Chi-restraints excluded: chain E residue 158 VAL Chi-restraints excluded: chain E residue 343 LEU Chi-restraints excluded: chain E residue 368 SER Chi-restraints excluded: chain E residue 506 ASN Chi-restraints excluded: chain F residue 158 VAL Chi-restraints excluded: chain F residue 182 GLU Chi-restraints excluded: chain F residue 261 VAL Chi-restraints excluded: chain F residue 270 VAL Chi-restraints excluded: chain F residue 278 PHE Chi-restraints excluded: chain F residue 343 LEU Chi-restraints excluded: chain F residue 368 SER Chi-restraints excluded: chain G residue 43 ASN Chi-restraints excluded: chain G residue 70 ILE Chi-restraints excluded: chain G residue 72 VAL Chi-restraints excluded: chain G residue 448 LEU Chi-restraints excluded: chain H residue 93 ILE Chi-restraints excluded: chain H residue 204 VAL Chi-restraints excluded: chain I residue 158 LEU Chi-restraints excluded: chain I residue 216 THR Chi-restraints excluded: chain I residue 290 VAL Chi-restraints excluded: chain I residue 406 VAL Chi-restraints excluded: chain I residue 462 CYS Chi-restraints excluded: chain I residue 495 VAL Chi-restraints excluded: chain J residue 185 TRP Chi-restraints excluded: chain J residue 290 VAL Chi-restraints excluded: chain K residue 89 LEU Chi-restraints excluded: chain K residue 405 VAL Chi-restraints excluded: chain K residue 418 CYS Chi-restraints excluded: chain L residue 50 VAL Chi-restraints excluded: chain L residue 405 VAL Chi-restraints excluded: chain L residue 444 CYS Chi-restraints excluded: chain M residue 10 THR Chi-restraints excluded: chain O residue 7 ASN Chi-restraints excluded: chain O residue 147 ILE Chi-restraints excluded: chain O residue 166 VAL Chi-restraints excluded: chain P residue 112 LEU Chi-restraints excluded: chain Q residue 2 VAL Chi-restraints excluded: chain Q residue 8 ILE Chi-restraints excluded: chain Q residue 147 ILE Chi-restraints excluded: chain Q residue 180 VAL Chi-restraints excluded: chain R residue 112 LEU Chi-restraints excluded: chain R residue 144 VAL Chi-restraints excluded: chain R residue 185 LEU Chi-restraints excluded: chain S residue 73 THR Chi-restraints excluded: chain S residue 87 MET Chi-restraints excluded: chain S residue 114 ASN Chi-restraints excluded: chain S residue 116 ASP Chi-restraints excluded: chain S residue 152 THR Chi-restraints excluded: chain T residue 87 MET Chi-restraints excluded: chain T residue 114 ASN Chi-restraints excluded: chain V residue 3 VAL Chi-restraints excluded: chain V residue 4 GLU Chi-restraints excluded: chain V residue 35 THR Chi-restraints excluded: chain V residue 46 THR Chi-restraints excluded: chain W residue 65 HIS Chi-restraints excluded: chain W residue 80 ASP Chi-restraints excluded: chain W residue 110 THR Chi-restraints excluded: chain W residue 176 ILE Chi-restraints excluded: chain X residue 32 THR Chi-restraints excluded: chain X residue 154 THR Chi-restraints excluded: chain X residue 370 PHE Chi-restraints excluded: chain X residue 371 LYS Chi-restraints excluded: chain Y residue 142 GLU Chi-restraints excluded: chain Y residue 145 LEU Chi-restraints excluded: chain Y residue 178 VAL Chi-restraints excluded: chain Y residue 180 VAL Chi-restraints excluded: chain Z residue 162 VAL Chi-restraints excluded: chain Z residue 180 VAL Chi-restraints excluded: chain Z residue 220 VAL Chi-restraints excluded: chain a residue 9 VAL Chi-restraints excluded: chain a residue 37 GLU Chi-restraints excluded: chain b residue 36 ILE Chi-restraints excluded: chain b residue 68 VAL Chi-restraints excluded: chain c residue 20 GLN Chi-restraints excluded: chain c residue 53 ASN Chi-restraints excluded: chain d residue 55 THR Chi-restraints excluded: chain i residue 73 ILE Chi-restraints excluded: chain i residue 91 MET Chi-restraints excluded: chain i residue 124 ASP Chi-restraints excluded: chain k residue 75 ILE Chi-restraints excluded: chain k residue 92 ILE Chi-restraints excluded: chain k residue 129 VAL Chi-restraints excluded: chain k residue 137 THR Chi-restraints excluded: chain k residue 162 ASN Chi-restraints excluded: chain k residue 166 LYS Chi-restraints excluded: chain k residue 225 ASP Chi-restraints excluded: chain s residue 371 THR Chi-restraints excluded: chain s residue 382 ASN Chi-restraints excluded: chain u residue 62 GLU Chi-restraints excluded: chain v residue 18 THR Chi-restraints excluded: chain y residue 14 THR Chi-restraints excluded: chain y residue 22 ILE Chi-restraints excluded: chain z residue 18 ASN Chi-restraints excluded: chain z residue 37 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 932 random chunks: chunk 587 optimal weight: 0.4980 chunk 787 optimal weight: 0.0070 chunk 226 optimal weight: 0.9990 chunk 681 optimal weight: 3.9990 chunk 109 optimal weight: 30.0000 chunk 205 optimal weight: 0.8980 chunk 740 optimal weight: 0.3980 chunk 309 optimal weight: 4.9990 chunk 760 optimal weight: 3.9990 chunk 93 optimal weight: 5.9990 chunk 136 optimal weight: 0.7980 overall best weight: 0.5198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 272 ASN ** B 548 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 329 GLN ** I 288 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 54 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 47 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 65 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** X 372 HIS Y 158 HIS ** Y 236 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Z 158 HIS ** b 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** c 20 GLN v 64 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.072152 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3245 r_free = 0.3245 target = 0.058742 restraints weight = 250731.134| |-----------------------------------------------------------------------------| r_work (start): 0.3245 rms_B_bonded: 2.73 r_work: 0.3118 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work (final): 0.3118 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3130 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3130 r_free = 0.3130 target_work(ls_wunit_k1) = 0.055 | | occupancies: max = 1.00 min = 0.53 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3129 r_free = 0.3129 target_work(ls_wunit_k1) = 0.055 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.3129 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8240 moved from start: 0.1672 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 74475 Z= 0.161 Angle : 0.525 11.813 101224 Z= 0.264 Chirality : 0.040 0.183 11172 Planarity : 0.004 0.068 13313 Dihedral : 4.107 53.279 10229 Min Nonbonded Distance : 2.129 Molprobity Statistics. All-atom Clashscore : 8.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 1.65 % Allowed : 15.34 % Favored : 83.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.96 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.01 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.55 (0.09), residues: 9336 helix: 2.04 (0.09), residues: 3580 sheet: -0.46 (0.13), residues: 1583 loop : -0.77 (0.10), residues: 4173 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.044 0.001 TRP v 59 HIS 0.005 0.001 HIS b 52 PHE 0.020 0.001 PHE F 357 TYR 0.046 0.001 TYR a 34 ARG 0.008 0.000 ARG U 32 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 16249.71 seconds wall clock time: 287 minutes 33.08 seconds (17253.08 seconds total)