Starting phenix.real_space_refine on Fri Feb 23 04:25:52 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dbr_27303/02_2024/8dbr_27303_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dbr_27303/02_2024/8dbr_27303.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/8dbr_27303/02_2024/8dbr_27303.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dbr_27303/02_2024/8dbr_27303.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dbr_27303/02_2024/8dbr_27303_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dbr_27303/02_2024/8dbr_27303_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= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 16 5.49 5 Mg 5 5.21 5 S 179 5.16 5 C 23302 2.51 5 N 6263 2.21 5 O 6913 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 7": "OE1" <-> "OE2" Residue "A GLU 28": "OE1" <-> "OE2" Residue "A ASP 36": "OD1" <-> "OD2" Residue "A GLU 67": "OE1" <-> "OE2" Residue "A ASP 69": "OD1" <-> "OD2" Residue "A ARG 93": "NH1" <-> "NH2" Residue "A ASP 122": "OD1" <-> "OD2" Residue "A ARG 161": "NH1" <-> "NH2" Residue "A GLU 165": "OE1" <-> "OE2" Residue "A ASP 181": "OD1" <-> "OD2" Residue "A PHE 249": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 252": "NH1" <-> "NH2" Residue "A GLU 254": "OE1" <-> "OE2" Residue "A ASP 255": "OD1" <-> "OD2" Residue "A ASP 289": "OD1" <-> "OD2" Residue "A PHE 291": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 354": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 356": "OE1" <-> "OE2" Residue "A PHE 360": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 376": "NH1" <-> "NH2" Residue "A PHE 406": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 412": "OD1" <-> "OD2" Residue "A ASP 415": "OD1" <-> "OD2" Residue "A GLU 452": "OE1" <-> "OE2" Residue "A ASP 458": "OD1" <-> "OD2" Residue "A GLU 468": "OE1" <-> "OE2" Residue "A GLU 485": "OE1" <-> "OE2" Residue "A GLU 495": "OE1" <-> "OE2" Residue "A GLU 497": "OE1" <-> "OE2" Residue "B ARG 15": "NH1" <-> "NH2" Residue "B GLU 67": "OE1" <-> "OE2" Residue "B ARG 68": "NH1" <-> "NH2" Residue "B ASP 81": "OD1" <-> "OD2" Residue "B GLU 84": "OE1" <-> "OE2" Residue "B ASP 116": "OD1" <-> "OD2" Residue "B ASP 122": "OD1" <-> "OD2" Residue "B ASP 188": "OD1" <-> "OD2" Residue "B TYR 195": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 214": "OE1" <-> "OE2" Residue "B TYR 240": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 248": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 249": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 260": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 284": "OE1" <-> "OE2" Residue "B GLU 299": "OE1" <-> "OE2" Residue "B GLU 307": "OE1" <-> "OE2" Residue "B TYR 308": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 312": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 316": "OE1" <-> "OE2" Residue "B ASP 336": "OD1" <-> "OD2" Residue "B GLU 356": "OE1" <-> "OE2" Residue "B PHE 360": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 365": "NH1" <-> "NH2" Residue "B PHE 406": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 409": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 422": "OD1" <-> "OD2" Residue "B GLU 429": "OE1" <-> "OE2" Residue "B PHE 449": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 452": "OE1" <-> "OE2" Residue "B ARG 453": "NH1" <-> "NH2" Residue "B ASP 458": "OD1" <-> "OD2" Residue "B PHE 467": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 468": "OE1" <-> "OE2" Residue "B TYR 474": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 477": "NH1" <-> "NH2" Residue "B TYR 492": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 494": "OD1" <-> "OD2" Residue "B ASP 505": "OD1" <-> "OD2" Residue "B PHE 507": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 19": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 36": "OD1" <-> "OD2" Residue "C ASP 69": "OD1" <-> "OD2" Residue "C ASP 81": "OD1" <-> "OD2" Residue "C ASP 124": "OD1" <-> "OD2" Residue "C GLU 138": "OE1" <-> "OE2" Residue "C ASP 188": "OD1" <-> "OD2" Residue "C TYR 195": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 213": "OE1" <-> "OE2" Residue "C GLU 230": "OE1" <-> "OE2" Residue "C TYR 240": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 248": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 249": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 261": "OD1" <-> "OD2" Residue "C ASP 262": "OD1" <-> "OD2" Residue "C ARG 283": "NH1" <-> "NH2" Residue "C GLU 284": "OE1" <-> "OE2" Residue "C PHE 286": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 307": "OE1" <-> "OE2" Residue "C GLU 316": "OE1" <-> "OE2" Residue "C GLU 331": "OE1" <-> "OE2" Residue "C ASP 350": "OD1" <-> "OD2" Residue "C PHE 354": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 356": "OE1" <-> "OE2" Residue "C PHE 360": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 365": "NH1" <-> "NH2" Residue "C ARG 376": "NH1" <-> "NH2" Residue "C PHE 409": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 415": "OD1" <-> "OD2" Residue "C ARG 418": "NH1" <-> "NH2" Residue "C GLU 429": "OE1" <-> "OE2" Residue "C PHE 449": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 453": "NH1" <-> "NH2" Residue "C TYR 455": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 467": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 468": "OE1" <-> "OE2" Residue "C TYR 474": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 477": "NH1" <-> "NH2" Residue "C TYR 492": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 495": "OE1" <-> "OE2" Residue "C PHE 507": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 14": "OD1" <-> "OD2" Residue "D PHE 17": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 36": "OE1" <-> "OE2" Residue "D ASP 67": "OD1" <-> "OD2" Residue "D GLU 76": "OE1" <-> "OE2" Residue "D GLU 100": "OE1" <-> "OE2" Residue "D ASP 134": "OD1" <-> "OD2" Residue "D GLU 169": "OE1" <-> "OE2" Residue "D PHE 176": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 211": "OE1" <-> "OE2" Residue "D GLU 228": "OE1" <-> "OE2" Residue "D ASP 236": "OD1" <-> "OD2" Residue "D TYR 247": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 253": "OE1" <-> "OE2" Residue "D TYR 267": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 338": "OD1" <-> "OD2" Residue "D ASP 372": "OD1" <-> "OD2" Residue "D GLU 384": "OE1" <-> "OE2" Residue "D PHE 405": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 417": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 434": "OE1" <-> "OE2" Residue "D TYR 435": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 440": "OE1" <-> "OE2" Residue "D PHE 443": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 454": "OE1" <-> "OE2" Residue "E GLU 16": "OE1" <-> "OE2" Residue "E PHE 17": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 67": "OD1" <-> "OD2" Residue "E GLU 76": "OE1" <-> "OE2" Residue "E TYR 116": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 117": "OE1" <-> "OE2" Residue "E GLU 124": "OE1" <-> "OE2" Residue "E ASP 134": "OD1" <-> "OD2" Residue "E TYR 173": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 181": "OE1" <-> "OE2" Residue "E ASP 188": "OD1" <-> "OD2" Residue "E PHE 189": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 192": "OE1" <-> "OE2" Residue "E GLU 211": "OE1" <-> "OE2" Residue "E GLU 228": "OE1" <-> "OE2" Residue "E PHE 230": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 233": "OE1" <-> "OE2" Residue "E PHE 240": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 280": "OE1" <-> "OE2" Residue "E ASP 338": "OD1" <-> "OD2" Residue "E ARG 342": "NH1" <-> "NH2" Residue "E ASP 355": "OD1" <-> "OD2" Residue "E GLU 369": "OE1" <-> "OE2" Residue "E GLU 381": "OE1" <-> "OE2" Residue "E ASP 386": "OD1" <-> "OD2" Residue "E GLU 434": "OE1" <-> "OE2" Residue "E ASP 436": "OD1" <-> "OD2" Residue "E GLU 440": "OE1" <-> "OE2" Residue "E GLU 450": "OE1" <-> "OE2" Residue "E GLU 451": "OE1" <-> "OE2" Residue "F PHE 17": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 30": "OE1" <-> "OE2" Residue "F GLU 36": "OE1" <-> "OE2" Residue "F GLU 103": "OE1" <-> "OE2" Residue "F GLU 105": "OE1" <-> "OE2" Residue "F GLU 117": "OE1" <-> "OE2" Residue "F GLU 118": "OE1" <-> "OE2" Residue "F ASP 134": "OD1" <-> "OD2" Residue "F GLU 181": "OE1" <-> "OE2" Residue "F ASP 188": "OD1" <-> "OD2" Residue "F ASP 195": "OD1" <-> "OD2" Residue "F GLU 228": "OE1" <-> "OE2" Residue "F GLU 273": "OE1" <-> "OE2" Residue "F GLU 280": "OE1" <-> "OE2" Residue "F ASP 301": "OD1" <-> "OD2" Residue "F ASP 302": "OD1" <-> "OD2" Residue "F ASP 305": "OD1" <-> "OD2" Residue "F ASP 316": "OD1" <-> "OD2" Residue "F ASP 338": "OD1" <-> "OD2" Residue "F ASP 345": "OD1" <-> "OD2" Residue "F ASP 355": "OD1" <-> "OD2" Residue "F ASP 372": "OD1" <-> "OD2" Residue "F GLU 385": "OE1" <-> "OE2" Residue "F ASP 386": "OD1" <-> "OD2" Residue "F GLU 408": "OE1" <-> "OE2" Residue "F PHE 427": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 432": "OE1" <-> "OE2" Residue "F GLU 434": "OE1" <-> "OE2" Residue "F ASP 436": "OD1" <-> "OD2" Residue "F GLU 440": "OE1" <-> "OE2" Residue "F PHE 443": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 450": "OE1" <-> "OE2" Residue "F GLU 454": "OE1" <-> "OE2" Residue "G ASP 5": "OD1" <-> "OD2" Residue "G GLU 24": "OE1" <-> "OE2" Residue "G ARG 32": "NH1" <-> "NH2" Residue "G ASP 36": "OD1" <-> "OD2" Residue "G TYR 44": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ARG 49": "NH1" <-> "NH2" Residue "G GLU 61": "OE1" <-> "OE2" Residue "G GLU 68": "OE1" <-> "OE2" Residue "G TYR 77": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ARG 84": "NH1" <-> "NH2" Residue "G GLU 101": "OE1" <-> "OE2" Residue "G ASP 141": "OD1" <-> "OD2" Residue "G GLU 147": "OE1" <-> "OE2" Residue "G ASP 160": "OD1" <-> "OD2" Residue "G GLU 161": "OE1" <-> "OE2" Residue "G ASP 165": "OD1" <-> "OD2" Residue "G TYR 168": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 174": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 194": "OD1" <-> "OD2" Residue "G ASP 197": "OD1" <-> "OD2" Residue "G ASP 204": "OD1" <-> "OD2" Residue "G ASP 210": "OD1" <-> "OD2" Residue "G ASP 216": "OD1" <-> "OD2" Residue "G ARG 221": "NH1" <-> "NH2" Residue "G TYR 222": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 233": "OE1" <-> "OE2" Residue "G GLU 238": "OE1" <-> "OE2" Residue "G GLU 259": "OE1" <-> "OE2" Residue "G GLU 275": "OE1" <-> "OE2" Residue "G GLU 278": "OE1" <-> "OE2" Residue "H TYR 4": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 16": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 21": "OE1" <-> "OE2" Residue "H GLU 29": "OE1" <-> "OE2" Residue "H GLU 60": "OE1" <-> "OE2" Residue "H TYR 63": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 70": "OE1" <-> "OE2" Residue "H ASP 88": "OD1" <-> "OD2" Residue "H GLU 91": "OE1" <-> "OE2" Residue "H GLU 102": "OE1" <-> "OE2" Residue "H GLU 103": "OE1" <-> "OE2" Residue "I ASP 7": "OD1" <-> "OD2" Residue "I ASP 44": "OD1" <-> "OD2" Residue "I ARG 50": "NH1" <-> "NH2" Residue "J TYR 10": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J GLU 37": "OE1" <-> "OE2" Residue "J ARG 50": "NH1" <-> "NH2" Residue "L GLU 37": "OE1" <-> "OE2" Residue "L ASP 44": "OD1" <-> "OD2" Residue "L ARG 50": "NH1" <-> "NH2" Residue "M ASP 7": "OD1" <-> "OD2" Residue "M TYR 10": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M GLU 37": "OE1" <-> "OE2" Residue "M ARG 50": "NH1" <-> "NH2" Residue "N ASP 7": "OD1" <-> "OD2" Residue "N TYR 10": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N GLU 37": "OE1" <-> "OE2" Residue "N ARG 50": "NH1" <-> "NH2" Residue "N ASP 61": "OD1" <-> "OD2" Residue "O TYR 10": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O GLU 37": "OE1" <-> "OE2" Residue "O ARG 50": "NH1" <-> "NH2" Residue "P ASP 7": "OD1" <-> "OD2" Residue "P TYR 10": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P GLU 37": "OE1" <-> "OE2" Residue "P ARG 50": "NH1" <-> "NH2" Residue "Q TYR 10": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q ARG 50": "NH1" <-> "NH2" Residue "R TYR 10": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R GLU 37": "OE1" <-> "OE2" Residue "R ARG 41": "NH1" <-> "NH2" Residue "R ARG 50": "NH1" <-> "NH2" Residue "R TYR 73": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S TYR 10": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S ASP 44": "OD1" <-> "OD2" Residue "S ARG 50": "NH1" <-> "NH2" Residue "W PHE 15": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W PHE 17": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W ARG 26": "NH1" <-> "NH2" Residue "W ASP 29": "OD1" <-> "OD2" Residue "W PHE 33": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W GLU 41": "OE1" <-> "OE2" Residue "W GLU 45": "OE1" <-> "OE2" Residue "W GLU 54": "OE1" <-> "OE2" Residue "W PHE 60": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W ASP 69": "OD1" <-> "OD2" Residue "W ARG 77": "NH1" <-> "NH2" Residue "W GLU 93": "OE1" <-> "OE2" Residue "W PHE 95": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W GLU 103": "OE1" <-> "OE2" Residue "W ASP 143": "OD1" <-> "OD2" Residue "W ASP 160": "OD1" <-> "OD2" Residue "W ARG 164": "NH1" <-> "NH2" Residue "W ARG 166": "NH1" <-> "NH2" Residue "W GLU 168": "OE1" <-> "OE2" Residue "W ASP 172": "OD1" <-> "OD2" Residue "X PHE 20": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X GLU 39": "OE1" <-> "OE2" Residue "X ASP 42": "OD1" <-> "OD2" Residue "X GLU 48": "OE1" <-> "OE2" Residue "X GLU 71": "OE1" <-> "OE2" Residue "X GLU 77": "OE1" <-> "OE2" Residue "X ARG 83": "NH1" <-> "NH2" Residue "X ASP 88": "OD1" <-> "OD2" Residue "X GLU 89": "OE1" <-> "OE2" Residue "X GLU 95": "OE1" <-> "OE2" Residue "X GLU 97": "OE1" <-> "OE2" Residue "X ARG 98": "NH1" <-> "NH2" Residue "X GLU 110": "OE1" <-> "OE2" Residue "X ARG 115": "NH1" <-> "NH2" Residue "X ARG 117": "NH1" <-> "NH2" Residue "X ARG 138": "NH1" <-> "NH2" Residue "X ASP 141": "OD1" <-> "OD2" Residue "X ASP 147": "OD1" <-> "OD2" Residue "X ASP 150": "OD1" <-> "OD2" Residue "X GLU 155": "OE1" <-> "OE2" Residue "Y GLU 39": "OE1" <-> "OE2" Residue "Y ASP 42": "OD1" <-> "OD2" Residue "Y GLU 48": "OE1" <-> "OE2" Residue "Y ARG 83": "NH1" <-> "NH2" Residue "Y ARG 98": "NH1" <-> "NH2" Residue "Y ARG 113": "NH1" <-> "NH2" Residue "Y ARG 115": "NH1" <-> "NH2" Residue "Y ARG 117": "NH1" <-> "NH2" Residue "Y ARG 121": "NH1" <-> "NH2" Residue "Y GLU 133": "OE1" <-> "OE2" Residue "Y ARG 138": "NH1" <-> "NH2" Residue "a ASP 30": "OD1" <-> "OD2" Residue "a PHE 38": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a PHE 48": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a PHE 60": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a PHE 75": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a GLU 80": "OE1" <-> "OE2" Residue "a PHE 109": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a PHE 113": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a TYR 128": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a PHE 163": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a GLU 219": "OE1" <-> "OE2" Residue "a PHE 244": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a PHE 256": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a GLU 269": "OE1" <-> "OE2" Time to flip residues: 0.12s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 36678 Number of models: 1 Model: "" Number of chains: 28 Chain: "A" Number of atoms: 3826 Number of conformers: 1 Conformer: "" Number of residues, atoms: 508, 3826 Classifications: {'peptide': 508} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 489} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'PHE:plan': 1} Unresolved non-hydrogen planarities: 6 Chain: "B" Number of atoms: 3877 Number of conformers: 1 Conformer: "" Number of residues, atoms: 513, 3877 Classifications: {'peptide': 513} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 494} Chain: "C" Number of atoms: 3849 Number of conformers: 1 Conformer: "" Number of residues, atoms: 510, 3849 Classifications: {'peptide': 510} Link IDs: {'PTRANS': 18, 'TRANS': 491} Chain: "D" Number of atoms: 3520 Number of conformers: 1 Conformer: "" Number of residues, atoms: 458, 3520 Classifications: {'peptide': 458} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 437} Chain: "E" Number of atoms: 3533 Number of conformers: 1 Conformer: "" Number of residues, atoms: 460, 3533 Classifications: {'peptide': 460} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 439} Chain: "F" Number of atoms: 3533 Number of conformers: 1 Conformer: "" Number of residues, atoms: 460, 3533 Classifications: {'peptide': 460} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 439} Chain: "G" Number of atoms: 2186 Number of conformers: 1 Conformer: "" Number of residues, atoms: 284, 2186 Classifications: {'peptide': 284} Link IDs: {'PCIS': 2, 'PTRANS': 7, 'TRANS': 274} Chain: "H" Number of atoms: 772 Number of conformers: 1 Conformer: "" Number of residues, atoms: 101, 772 Classifications: {'peptide': 101} Link IDs: {'PTRANS': 4, 'TRANS': 96} Chain: "I" Number of atoms: 557 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 557 Classifications: {'peptide': 77} Link IDs: {'PTRANS': 3, 'TRANS': 73} Chain: "J" Number of atoms: 557 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 557 Classifications: {'peptide': 77} Link IDs: {'PTRANS': 3, 'TRANS': 73} Chain: "L" Number of atoms: 557 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 557 Classifications: {'peptide': 77} Link IDs: {'PTRANS': 3, 'TRANS': 73} Chain: "M" Number of atoms: 557 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 557 Classifications: {'peptide': 77} Link IDs: {'PTRANS': 3, 'TRANS': 73} Chain: "N" Number of atoms: 557 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 557 Classifications: {'peptide': 77} Link IDs: {'PTRANS': 3, 'TRANS': 73} Chain: "O" Number of atoms: 557 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 557 Classifications: {'peptide': 77} Link IDs: {'PTRANS': 3, 'TRANS': 73} Chain: "P" Number of atoms: 557 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 557 Classifications: {'peptide': 77} Link IDs: {'PTRANS': 3, 'TRANS': 73} Chain: "Q" Number of atoms: 557 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 557 Classifications: {'peptide': 77} Link IDs: {'PTRANS': 3, 'TRANS': 73} Chain: "R" Number of atoms: 552 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 552 Classifications: {'peptide': 76} Link IDs: {'PTRANS': 3, 'TRANS': 72} Chain: "S" Number of atoms: 557 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 557 Classifications: {'peptide': 77} Link IDs: {'PTRANS': 3, 'TRANS': 73} Chain: "W" Number of atoms: 1320 Number of conformers: 1 Conformer: "" Number of residues, atoms: 173, 1320 Classifications: {'peptide': 173} Link IDs: {'PTRANS': 3, 'TRANS': 169} Chain: "X" Number of atoms: 1200 Number of conformers: 1 Conformer: "" Number of residues, atoms: 156, 1200 Classifications: {'peptide': 156} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 2, 'TRANS': 153} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 10 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "Y" Number of atoms: 1210 Number of conformers: 1 Conformer: "" Number of residues, atoms: 156, 1210 Classifications: {'peptide': 156} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 153} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Chain: "a" Number of atoms: 2104 Number of conformers: 1 Conformer: "" Number of residues, atoms: 266, 2104 Classifications: {'peptide': 266} Link IDs: {'PCIS': 1, 'PTRANS': 14, 'TRANS': 250} Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 18.09, per 1000 atoms: 0.49 Number of scatterers: 36678 At special positions: 0 Unit cell: (185.588, 216.879, 133.796, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 179 16.00 P 16 15.00 Mg 5 11.99 O 6913 8.00 N 6263 7.00 C 23302 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 15.36 Conformation dependent library (CDL) restraints added in 7.0 seconds 9540 Ramachandran restraints generated. 4770 Oldfield, 0 Emsley, 4770 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8746 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 173 helices and 26 sheets defined 56.0% alpha, 10.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 6.68 Creating SS restraints... Processing helix chain 'A' and resid 5 through 18 Processing helix chain 'A' and resid 101 through 103 No H-bonds generated for 'chain 'A' and resid 101 through 103' Processing helix chain 'A' and resid 136 through 138 No H-bonds generated for 'chain 'A' and resid 136 through 138' Processing helix chain 'A' and resid 151 through 156 Processing helix chain 'A' and resid 175 through 188 removed outlier: 3.965A pdb=" N ARG A 187 " --> pdb=" O ILE A 183 " (cutoff:3.500A) removed outlier: 5.283A pdb=" N ASP A 188 " --> pdb=" O ILE A 184 " (cutoff:3.500A) Processing helix chain 'A' and resid 202 through 214 Processing helix chain 'A' and resid 218 through 220 No H-bonds generated for 'chain 'A' and resid 218 through 220' Processing helix chain 'A' and resid 232 through 252 Proline residue: A 239 - end of helix removed outlier: 3.871A pdb=" N PHE A 249 " --> pdb=" O MET A 245 " (cutoff:3.500A) Processing helix chain 'A' and resid 263 through 276 removed outlier: 3.583A pdb=" N ILE A 273 " --> pdb=" O ALA A 269 " (cutoff:3.500A) Processing helix chain 'A' and resid 288 through 300 removed outlier: 3.898A pdb=" N PHE A 291 " --> pdb=" O GLY A 288 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N SER A 295 " --> pdb=" O TYR A 292 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N ARG A 296 " --> pdb=" O LEU A 293 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N LEU A 298 " --> pdb=" O SER A 295 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N GLU A 299 " --> pdb=" O ARG A 296 " (cutoff:3.500A) Processing helix chain 'A' and resid 306 through 313 Processing helix chain 'A' and resid 333 through 335 No H-bonds generated for 'chain 'A' and resid 333 through 335' Processing helix chain 'A' and resid 340 through 346 Processing helix chain 'A' and resid 357 through 361 Processing helix chain 'A' and resid 378 through 381 Processing helix chain 'A' and resid 384 through 390 Processing helix chain 'A' and resid 393 through 407 removed outlier: 3.560A pdb=" N GLU A 402 " --> pdb=" O ALA A 398 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N ALA A 405 " --> pdb=" O ARG A 401 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 431 Processing helix chain 'A' and resid 441 through 452 removed outlier: 3.561A pdb=" N LEU A 446 " --> pdb=" O ALA A 442 " (cutoff:3.500A) Processing helix chain 'A' and resid 461 through 478 removed outlier: 4.530A pdb=" N GLY A 465 " --> pdb=" O LEU A 461 " (cutoff:3.500A) removed outlier: 5.450A pdb=" N SER A 466 " --> pdb=" O SER A 462 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N ARG A 477 " --> pdb=" O ALA A 473 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N ASP A 478 " --> pdb=" O TYR A 474 " (cutoff:3.500A) Processing helix chain 'A' and resid 480 through 488 Processing helix chain 'A' and resid 494 through 509 Processing helix chain 'B' and resid 3 through 18 removed outlier: 4.439A pdb=" N ILE B 8 " --> pdb=" O SER B 5 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N LYS B 13 " --> pdb=" O GLU B 10 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N GLN B 14 " --> pdb=" O LEU B 11 " (cutoff:3.500A) Processing helix chain 'B' and resid 101 through 103 No H-bonds generated for 'chain 'B' and resid 101 through 103' Processing helix chain 'B' and resid 136 through 138 No H-bonds generated for 'chain 'B' and resid 136 through 138' Processing helix chain 'B' and resid 151 through 156 Processing helix chain 'B' and resid 175 through 188 removed outlier: 3.512A pdb=" N ALA B 179 " --> pdb=" O LYS B 175 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N GLN B 186 " --> pdb=" O ALA B 182 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N ARG B 187 " --> pdb=" O ILE B 183 " (cutoff:3.500A) removed outlier: 5.385A pdb=" N ASP B 188 " --> pdb=" O ILE B 184 " (cutoff:3.500A) Processing helix chain 'B' and resid 202 through 214 Processing helix chain 'B' and resid 218 through 220 No H-bonds generated for 'chain 'B' and resid 218 through 220' Processing helix chain 'B' and resid 232 through 252 Proline residue: B 239 - end of helix removed outlier: 3.516A pdb=" N TYR B 248 " --> pdb=" O ALA B 244 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N PHE B 249 " --> pdb=" O MET B 245 " (cutoff:3.500A) Processing helix chain 'B' and resid 263 through 276 Processing helix chain 'B' and resid 283 through 285 No H-bonds generated for 'chain 'B' and resid 283 through 285' Processing helix chain 'B' and resid 288 through 300 removed outlier: 3.994A pdb=" N PHE B 291 " --> pdb=" O GLY B 288 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N SER B 295 " --> pdb=" O TYR B 292 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N ARG B 296 " --> pdb=" O LEU B 293 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N LEU B 298 " --> pdb=" O SER B 295 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N GLU B 299 " --> pdb=" O ARG B 296 " (cutoff:3.500A) Processing helix chain 'B' and resid 306 through 313 Processing helix chain 'B' and resid 340 through 348 Processing helix chain 'B' and resid 357 through 362 Processing helix chain 'B' and resid 378 through 381 Processing helix chain 'B' and resid 384 through 406 removed outlier: 4.886A pdb=" N GLY B 392 " --> pdb=" O LYS B 388 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N ILE B 393 " --> pdb=" O LEU B 389 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N ARG B 394 " --> pdb=" O SER B 390 " (cutoff:3.500A) removed outlier: 4.533A pdb=" N THR B 395 " --> pdb=" O GLY B 391 " (cutoff:3.500A) Processing helix chain 'B' and resid 415 through 430 removed outlier: 4.409A pdb=" N GLN B 425 " --> pdb=" O LEU B 421 " (cutoff:3.500A) Processing helix chain 'B' and resid 441 through 452 Processing helix chain 'B' and resid 461 through 478 removed outlier: 4.107A pdb=" N GLY B 465 " --> pdb=" O LEU B 461 " (cutoff:3.500A) removed outlier: 4.169A pdb=" N SER B 466 " --> pdb=" O SER B 462 " (cutoff:3.500A) Processing helix chain 'B' and resid 480 through 489 Processing helix chain 'B' and resid 494 through 510 Processing helix chain 'C' and resid 9 through 17 Processing helix chain 'C' and resid 21 through 23 No H-bonds generated for 'chain 'C' and resid 21 through 23' Processing helix chain 'C' and resid 151 through 156 Processing helix chain 'C' and resid 175 through 187 removed outlier: 3.858A pdb=" N ARG C 187 " --> pdb=" O ILE C 183 " (cutoff:3.500A) Processing helix chain 'C' and resid 202 through 214 Processing helix chain 'C' and resid 218 through 220 No H-bonds generated for 'chain 'C' and resid 218 through 220' Processing helix chain 'C' and resid 232 through 252 Proline residue: C 239 - end of helix removed outlier: 3.620A pdb=" N TYR C 248 " --> pdb=" O ALA C 244 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N PHE C 249 " --> pdb=" O MET C 245 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N ARG C 252 " --> pdb=" O TYR C 248 " (cutoff:3.500A) Processing helix chain 'C' and resid 263 through 276 Processing helix chain 'C' and resid 283 through 285 No H-bonds generated for 'chain 'C' and resid 283 through 285' Processing helix chain 'C' and resid 290 through 300 removed outlier: 3.646A pdb=" N HIS C 294 " --> pdb=" O VAL C 290 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N LEU C 297 " --> pdb=" O LEU C 293 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N ARG C 300 " --> pdb=" O ARG C 296 " (cutoff:3.500A) Processing helix chain 'C' and resid 306 through 312 Processing helix chain 'C' and resid 340 through 348 Processing helix chain 'C' and resid 357 through 362 Processing helix chain 'C' and resid 378 through 381 Processing helix chain 'C' and resid 384 through 409 removed outlier: 4.145A pdb=" N GLY C 391 " --> pdb=" O LYS C 387 " (cutoff:3.500A) removed outlier: 5.090A pdb=" N GLY C 392 " --> pdb=" O LYS C 388 " (cutoff:3.500A) removed outlier: 4.115A pdb=" N ILE C 393 " --> pdb=" O LEU C 389 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N GLU C 402 " --> pdb=" O ALA C 398 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N ALA C 405 " --> pdb=" O ARG C 401 " (cutoff:3.500A) removed outlier: 4.336A pdb=" N PHE C 406 " --> pdb=" O GLU C 402 " (cutoff:3.500A) removed outlier: 4.649A pdb=" N GLN C 408 " --> pdb=" O ALA C 404 " (cutoff:3.500A) removed outlier: 5.559A pdb=" N PHE C 409 " --> pdb=" O ALA C 405 " (cutoff:3.500A) Processing helix chain 'C' and resid 415 through 431 removed outlier: 3.761A pdb=" N LYS C 426 " --> pdb=" O ASP C 422 " (cutoff:3.500A) Processing helix chain 'C' and resid 441 through 452 Processing helix chain 'C' and resid 461 through 478 removed outlier: 3.724A pdb=" N ILE C 464 " --> pdb=" O LEU C 461 " (cutoff:3.500A) removed outlier: 5.270A pdb=" N GLY C 465 " --> pdb=" O SER C 462 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N GLU C 468 " --> pdb=" O GLY C 465 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N ALA C 469 " --> pdb=" O SER C 466 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N LEU C 472 " --> pdb=" O ALA C 469 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N VAL C 475 " --> pdb=" O LEU C 472 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ASP C 476 " --> pdb=" O ALA C 473 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N ASP C 478 " --> pdb=" O VAL C 475 " (cutoff:3.500A) Processing helix chain 'C' and resid 480 through 489 Processing helix chain 'C' and resid 494 through 508 removed outlier: 3.877A pdb=" N LYS C 499 " --> pdb=" O GLU C 495 " (cutoff:3.500A) Processing helix chain 'D' and resid 81 through 83 No H-bonds generated for 'chain 'D' and resid 81 through 83' Processing helix chain 'D' and resid 131 through 136 Processing helix chain 'D' and resid 155 through 169 removed outlier: 4.043A pdb=" N ILE D 168 " --> pdb=" O ARG D 164 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N GLU D 169 " --> pdb=" O ASN D 165 " (cutoff:3.500A) Processing helix chain 'D' and resid 183 through 195 Processing helix chain 'D' and resid 199 through 201 No H-bonds generated for 'chain 'D' and resid 199 through 201' Processing helix chain 'D' and resid 213 through 232 removed outlier: 4.651A pdb=" N ALA D 220 " --> pdb=" O ARG D 216 " (cutoff:3.500A) removed outlier: 4.785A pdb=" N LEU D 221 " --> pdb=" O LEU D 217 " (cutoff:3.500A) Processing helix chain 'D' and resid 244 through 255 removed outlier: 3.687A pdb=" N ALA D 250 " --> pdb=" O TYR D 247 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N GLU D 253 " --> pdb=" O ALA D 250 " (cutoff:3.500A) Processing helix chain 'D' and resid 271 through 281 removed outlier: 3.555A pdb=" N LEU D 278 " --> pdb=" O GLU D 274 " (cutoff:3.500A) removed outlier: 4.131A pdb=" N ARG D 281 " --> pdb=" O VAL D 277 " (cutoff:3.500A) Processing helix chain 'D' and resid 299 through 301 No H-bonds generated for 'chain 'D' and resid 299 through 301' Processing helix chain 'D' and resid 306 through 314 removed outlier: 4.226A pdb=" N ALA D 313 " --> pdb=" O ALA D 309 " (cutoff:3.500A) removed outlier: 4.171A pdb=" N HIS D 314 " --> pdb=" O THR D 310 " (cutoff:3.500A) Processing helix chain 'D' and resid 323 through 328 removed outlier: 3.640A pdb=" N LEU D 328 " --> pdb=" O GLN D 324 " (cutoff:3.500A) Processing helix chain 'D' and resid 346 through 349 No H-bonds generated for 'chain 'D' and resid 346 through 349' Processing helix chain 'D' and resid 351 through 377 removed outlier: 4.324A pdb=" N ASP D 372 " --> pdb=" O GLN D 368 " (cutoff:3.500A) removed outlier: 4.767A pdb=" N ILE D 373 " --> pdb=" O GLU D 369 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N ILE D 376 " --> pdb=" O ASP D 372 " (cutoff:3.500A) Processing helix chain 'D' and resid 379 through 381 No H-bonds generated for 'chain 'D' and resid 379 through 381' Processing helix chain 'D' and resid 386 through 399 removed outlier: 3.736A pdb=" N LYS D 395 " --> pdb=" O ALA D 391 " (cutoff:3.500A) Processing helix chain 'D' and resid 405 through 411 removed outlier: 3.754A pdb=" N GLU D 408 " --> pdb=" O PHE D 405 " (cutoff:3.500A) removed outlier: 4.399A pdb=" N VAL D 409 " --> pdb=" O VAL D 406 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N THR D 411 " --> pdb=" O GLU D 408 " (cutoff:3.500A) Processing helix chain 'D' and resid 420 through 431 Processing helix chain 'D' and resid 440 through 442 No H-bonds generated for 'chain 'D' and resid 440 through 442' Processing helix chain 'D' and resid 449 through 458 removed outlier: 3.863A pdb=" N LYS D 458 " --> pdb=" O GLU D 454 " (cutoff:3.500A) Processing helix chain 'E' and resid 81 through 83 No H-bonds generated for 'chain 'E' and resid 81 through 83' Processing helix chain 'E' and resid 116 through 118 No H-bonds generated for 'chain 'E' and resid 116 through 118' Processing helix chain 'E' and resid 131 through 136 Processing helix chain 'E' and resid 155 through 169 removed outlier: 3.691A pdb=" N ILE E 168 " --> pdb=" O ARG E 164 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N GLU E 169 " --> pdb=" O ASN E 165 " (cutoff:3.500A) Processing helix chain 'E' and resid 183 through 195 Processing helix chain 'E' and resid 199 through 201 No H-bonds generated for 'chain 'E' and resid 199 through 201' Processing helix chain 'E' and resid 213 through 232 removed outlier: 4.788A pdb=" N ALA E 220 " --> pdb=" O ARG E 216 " (cutoff:3.500A) removed outlier: 5.716A pdb=" N LEU E 221 " --> pdb=" O LEU E 217 " (cutoff:3.500A) Processing helix chain 'E' and resid 244 through 257 removed outlier: 3.657A pdb=" N THR E 248 " --> pdb=" O ILE E 244 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N ALA E 256 " --> pdb=" O THR E 252 " (cutoff:3.500A) removed outlier: 4.488A pdb=" N LEU E 257 " --> pdb=" O GLU E 253 " (cutoff:3.500A) Processing helix chain 'E' and resid 271 through 281 removed outlier: 4.365A pdb=" N ARG E 281 " --> pdb=" O VAL E 277 " (cutoff:3.500A) Processing helix chain 'E' and resid 299 through 301 No H-bonds generated for 'chain 'E' and resid 299 through 301' Processing helix chain 'E' and resid 306 through 314 removed outlier: 4.618A pdb=" N ALA E 313 " --> pdb=" O ALA E 309 " (cutoff:3.500A) removed outlier: 4.493A pdb=" N HIS E 314 " --> pdb=" O THR E 310 " (cutoff:3.500A) Processing helix chain 'E' and resid 323 through 328 removed outlier: 4.227A pdb=" N LEU E 328 " --> pdb=" O GLN E 324 " (cutoff:3.500A) Processing helix chain 'E' and resid 346 through 377 removed outlier: 7.767A pdb=" N GLN E 351 " --> pdb=" O LEU E 347 " (cutoff:3.500A) removed outlier: 8.191A pdb=" N GLU E 352 " --> pdb=" O VAL E 348 " (cutoff:3.500A) removed outlier: 4.328A pdb=" N HIS E 353 " --> pdb=" O VAL E 349 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N GLU E 369 " --> pdb=" O GLN E 365 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N ASP E 372 " --> pdb=" O GLN E 368 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N ILE E 373 " --> pdb=" O GLU E 369 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N ILE E 376 " --> pdb=" O ASP E 372 " (cutoff:3.500A) Processing helix chain 'E' and resid 379 through 381 No H-bonds generated for 'chain 'E' and resid 379 through 381' Processing helix chain 'E' and resid 384 through 399 removed outlier: 3.600A pdb=" N ARG E 398 " --> pdb=" O ARG E 394 " (cutoff:3.500A) Processing helix chain 'E' and resid 408 through 411 No H-bonds generated for 'chain 'E' and resid 408 through 411' Processing helix chain 'E' and resid 420 through 431 Processing helix chain 'E' and resid 433 through 435 No H-bonds generated for 'chain 'E' and resid 433 through 435' Processing helix chain 'E' and resid 449 through 458 removed outlier: 3.771A pdb=" N VAL E 453 " --> pdb=" O ILE E 449 " (cutoff:3.500A) removed outlier: 5.054A pdb=" N GLU E 454 " --> pdb=" O GLU E 450 " (cutoff:3.500A) Processing helix chain 'F' and resid 47 through 49 No H-bonds generated for 'chain 'F' and resid 47 through 49' Processing helix chain 'F' and resid 81 through 83 No H-bonds generated for 'chain 'F' and resid 81 through 83' Processing helix chain 'F' and resid 131 through 136 Processing helix chain 'F' and resid 155 through 168 Processing helix chain 'F' and resid 183 through 195 Processing helix chain 'F' and resid 199 through 201 No H-bonds generated for 'chain 'F' and resid 199 through 201' Processing helix chain 'F' and resid 213 through 233 removed outlier: 4.871A pdb=" N ALA F 220 " --> pdb=" O ARG F 216 " (cutoff:3.500A) removed outlier: 4.810A pdb=" N LEU F 221 " --> pdb=" O LEU F 217 " (cutoff:3.500A) Processing helix chain 'F' and resid 244 through 258 Processing helix chain 'F' and resid 264 through 266 No H-bonds generated for 'chain 'F' and resid 264 through 266' Processing helix chain 'F' and resid 271 through 279 removed outlier: 3.503A pdb=" N LEU F 278 " --> pdb=" O GLU F 274 " (cutoff:3.500A) Processing helix chain 'F' and resid 306 through 312 Processing helix chain 'F' and resid 323 through 328 removed outlier: 3.696A pdb=" N LEU F 328 " --> pdb=" O GLN F 324 " (cutoff:3.500A) Processing helix chain 'F' and resid 346 through 349 No H-bonds generated for 'chain 'F' and resid 346 through 349' Processing helix chain 'F' and resid 351 through 376 removed outlier: 4.096A pdb=" N ASP F 372 " --> pdb=" O GLN F 368 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N ILE F 373 " --> pdb=" O GLU F 369 " (cutoff:3.500A) Processing helix chain 'F' and resid 379 through 381 No H-bonds generated for 'chain 'F' and resid 379 through 381' Processing helix chain 'F' and resid 386 through 399 removed outlier: 3.512A pdb=" N LYS F 395 " --> pdb=" O ALA F 391 " (cutoff:3.500A) Processing helix chain 'F' and resid 408 through 411 No H-bonds generated for 'chain 'F' and resid 408 through 411' Processing helix chain 'F' and resid 420 through 432 Processing helix chain 'F' and resid 440 through 442 No H-bonds generated for 'chain 'F' and resid 440 through 442' Processing helix chain 'F' and resid 449 through 458 removed outlier: 3.891A pdb=" N GLU F 454 " --> pdb=" O GLU F 450 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N LYS F 458 " --> pdb=" O GLU F 454 " (cutoff:3.500A) Processing helix chain 'G' and resid 6 through 56 removed outlier: 3.561A pdb=" N ALA G 11 " --> pdb=" O ARG G 7 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N MET G 25 " --> pdb=" O LYS G 21 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N ARG G 32 " --> pdb=" O ALA G 28 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N ARG G 42 " --> pdb=" O MET G 38 " (cutoff:3.500A) Proline residue: G 43 - end of helix Processing helix chain 'G' and resid 90 through 107 Processing helix chain 'G' and resid 119 through 128 Processing helix chain 'G' and resid 145 through 160 removed outlier: 4.448A pdb=" N GLY G 150 " --> pdb=" O SER G 146 " (cutoff:3.500A) Proline residue: G 151 - end of helix Processing helix chain 'G' and resid 199 through 202 No H-bonds generated for 'chain 'G' and resid 199 through 202' Processing helix chain 'G' and resid 213 through 282 removed outlier: 3.695A pdb=" N LEU G 218 " --> pdb=" O LEU G 214 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N LYS G 258 " --> pdb=" O GLY G 254 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N GLU G 259 " --> pdb=" O SER G 255 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N ILE G 272 " --> pdb=" O ARG G 268 " (cutoff:3.500A) Processing helix chain 'H' and resid 55 through 57 No H-bonds generated for 'chain 'H' and resid 55 through 57' Processing helix chain 'H' and resid 89 through 102 removed outlier: 4.199A pdb=" N GLU H 96 " --> pdb=" O ARG H 93 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N ARG H 99 " --> pdb=" O GLU H 96 " (cutoff:3.500A) removed outlier: 4.463A pdb=" N LYS H 100 " --> pdb=" O ALA H 97 " (cutoff:3.500A) Processing helix chain 'I' and resid 4 through 41 removed outlier: 3.598A pdb=" N LEU I 9 " --> pdb=" O ASN I 5 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N MET I 11 " --> pdb=" O ASP I 7 " (cutoff:3.500A) Processing helix chain 'I' and resid 43 through 76 removed outlier: 3.595A pdb=" N ILE I 46 " --> pdb=" O PRO I 43 " (cutoff:3.500A) Proline residue: I 47 - end of helix removed outlier: 4.363A pdb=" N ARG I 50 " --> pdb=" O PRO I 47 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N VAL I 56 " --> pdb=" O PHE I 53 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N MET I 57 " --> pdb=" O PHE I 54 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N VAL I 60 " --> pdb=" O MET I 57 " (cutoff:3.500A) removed outlier: 4.388A pdb=" N ASP I 61 " --> pdb=" O GLY I 58 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ALA I 62 " --> pdb=" O LEU I 59 " (cutoff:3.500A) removed outlier: 4.150A pdb=" N ILE I 63 " --> pdb=" O VAL I 60 " (cutoff:3.500A) Proline residue: I 64 - end of helix removed outlier: 3.751A pdb=" N VAL I 68 " --> pdb=" O MET I 65 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N LEU I 70 " --> pdb=" O ALA I 67 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N TYR I 73 " --> pdb=" O LEU I 70 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N PHE I 76 " --> pdb=" O TYR I 73 " (cutoff:3.500A) Processing helix chain 'J' and resid 4 through 41 removed outlier: 3.990A pdb=" N LEU J 8 " --> pdb=" O LEU J 4 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N MET J 11 " --> pdb=" O ASP J 7 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N ALA J 25 " --> pdb=" O ALA J 21 " (cutoff:3.500A) Processing helix chain 'J' and resid 46 through 76 removed outlier: 3.697A pdb=" N LEU J 59 " --> pdb=" O ILE J 55 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ALA J 62 " --> pdb=" O GLY J 58 " (cutoff:3.500A) removed outlier: 4.919A pdb=" N ILE J 63 " --> pdb=" O LEU J 59 " (cutoff:3.500A) Proline residue: J 64 - end of helix Processing helix chain 'L' and resid 4 through 41 removed outlier: 3.765A pdb=" N LEU L 8 " --> pdb=" O ASN L 5 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N TYR L 10 " --> pdb=" O ASP L 7 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N ALA L 13 " --> pdb=" O TYR L 10 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N VAL L 15 " --> pdb=" O ALA L 12 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N MET L 16 " --> pdb=" O ALA L 13 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N MET L 17 " --> pdb=" O ALA L 14 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N GLY L 18 " --> pdb=" O VAL L 15 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N LEU L 19 " --> pdb=" O MET L 16 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N ALA L 20 " --> pdb=" O MET L 17 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ILE L 22 " --> pdb=" O LEU L 19 " (cutoff:3.500A) removed outlier: 4.305A pdb=" N ALA L 24 " --> pdb=" O ALA L 21 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N ALA L 25 " --> pdb=" O ILE L 22 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N ILE L 26 " --> pdb=" O GLY L 23 " (cutoff:3.500A) removed outlier: 4.512A pdb=" N GLY L 27 " --> pdb=" O ALA L 24 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N ILE L 28 " --> pdb=" O ALA L 25 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ILE L 30 " --> pdb=" O GLY L 27 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N LEU L 31 " --> pdb=" O ILE L 28 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N GLY L 32 " --> pdb=" O GLY L 29 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N GLY L 33 " --> pdb=" O ILE L 30 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N LYS L 34 " --> pdb=" O LEU L 31 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N LEU L 36 " --> pdb=" O GLY L 33 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N GLU L 37 " --> pdb=" O LYS L 34 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N ARG L 41 " --> pdb=" O GLY L 38 " (cutoff:3.500A) Processing helix chain 'L' and resid 43 through 76 removed outlier: 3.738A pdb=" N ILE L 46 " --> pdb=" O PRO L 43 " (cutoff:3.500A) Proline residue: L 47 - end of helix removed outlier: 4.320A pdb=" N ARG L 50 " --> pdb=" O PRO L 47 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N PHE L 54 " --> pdb=" O THR L 51 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N MET L 57 " --> pdb=" O PHE L 54 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N GLY L 58 " --> pdb=" O ILE L 55 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N VAL L 60 " --> pdb=" O MET L 57 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N ASP L 61 " --> pdb=" O GLY L 58 " (cutoff:3.500A) removed outlier: 4.466A pdb=" N ILE L 63 " --> pdb=" O VAL L 60 " (cutoff:3.500A) Proline residue: L 64 - end of helix removed outlier: 4.236A pdb=" N VAL L 68 " --> pdb=" O MET L 65 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N LEU L 70 " --> pdb=" O ALA L 67 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N GLY L 71 " --> pdb=" O VAL L 68 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N LEU L 72 " --> pdb=" O GLY L 69 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N VAL L 74 " --> pdb=" O GLY L 71 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N MET L 75 " --> pdb=" O LEU L 72 " (cutoff:3.500A) Processing helix chain 'M' and resid 4 through 41 removed outlier: 3.532A pdb=" N MET M 11 " --> pdb=" O ASP M 7 " (cutoff:3.500A) Processing helix chain 'M' and resid 43 through 76 removed outlier: 3.667A pdb=" N ILE M 46 " --> pdb=" O PRO M 43 " (cutoff:3.500A) Proline residue: M 47 - end of helix removed outlier: 4.185A pdb=" N ARG M 50 " --> pdb=" O PRO M 47 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N THR M 51 " --> pdb=" O LEU M 48 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N PHE M 53 " --> pdb=" O ARG M 50 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N MET M 57 " --> pdb=" O PHE M 54 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N GLY M 58 " --> pdb=" O ILE M 55 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N VAL M 60 " --> pdb=" O MET M 57 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ASP M 61 " --> pdb=" O GLY M 58 " (cutoff:3.500A) removed outlier: 4.355A pdb=" N ILE M 63 " --> pdb=" O VAL M 60 " (cutoff:3.500A) Proline residue: M 64 - end of helix removed outlier: 3.596A pdb=" N ALA M 67 " --> pdb=" O PRO M 64 " (cutoff:3.500A) removed outlier: 4.320A pdb=" N VAL M 68 " --> pdb=" O MET M 65 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N LEU M 72 " --> pdb=" O GLY M 69 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N PHE M 76 " --> pdb=" O TYR M 73 " (cutoff:3.500A) Processing helix chain 'N' and resid 4 through 41 removed outlier: 5.037A pdb=" N LEU N 9 " --> pdb=" O ASN N 5 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N TYR N 10 " --> pdb=" O MET N 6 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N MET N 11 " --> pdb=" O ASP N 7 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N MET N 16 " --> pdb=" O ALA N 12 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N ALA N 21 " --> pdb=" O MET N 17 " (cutoff:3.500A) Processing helix chain 'N' and resid 43 through 76 removed outlier: 3.751A pdb=" N ILE N 46 " --> pdb=" O PRO N 43 " (cutoff:3.500A) Proline residue: N 47 - end of helix removed outlier: 4.248A pdb=" N ARG N 50 " --> pdb=" O PRO N 47 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N MET N 57 " --> pdb=" O PHE N 54 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N GLY N 58 " --> pdb=" O ILE N 55 " (cutoff:3.500A) removed outlier: 4.178A pdb=" N ASP N 61 " --> pdb=" O GLY N 58 " (cutoff:3.500A) removed outlier: 4.336A pdb=" N ILE N 63 " --> pdb=" O VAL N 60 " (cutoff:3.500A) Proline residue: N 64 - end of helix removed outlier: 3.823A pdb=" N ALA N 67 " --> pdb=" O PRO N 64 " (cutoff:3.500A) removed outlier: 4.148A pdb=" N VAL N 68 " --> pdb=" O MET N 65 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N GLY N 71 " --> pdb=" O VAL N 68 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N LEU N 72 " --> pdb=" O GLY N 69 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N VAL N 74 " --> pdb=" O GLY N 71 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N PHE N 76 " --> pdb=" O TYR N 73 " (cutoff:3.500A) Processing helix chain 'O' and resid 5 through 41 removed outlier: 3.532A pdb=" N LEU O 9 " --> pdb=" O MET O 6 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N ALA O 12 " --> pdb=" O LEU O 9 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ALA O 13 " --> pdb=" O TYR O 10 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N VAL O 15 " --> pdb=" O ALA O 12 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N MET O 16 " --> pdb=" O ALA O 13 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N MET O 17 " --> pdb=" O ALA O 14 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N GLY O 18 " --> pdb=" O VAL O 15 " (cutoff:3.500A) removed outlier: 4.142A pdb=" N LEU O 19 " --> pdb=" O MET O 16 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N ALA O 20 " --> pdb=" O MET O 17 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N GLY O 23 " --> pdb=" O ALA O 20 " (cutoff:3.500A) removed outlier: 4.259A pdb=" N ALA O 24 " --> pdb=" O ALA O 21 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N ALA O 25 " --> pdb=" O ILE O 22 " (cutoff:3.500A) removed outlier: 4.146A pdb=" N ILE O 26 " --> pdb=" O GLY O 23 " (cutoff:3.500A) removed outlier: 4.447A pdb=" N GLY O 27 " --> pdb=" O ALA O 24 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N ILE O 28 " --> pdb=" O ALA O 25 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N ILE O 30 " --> pdb=" O GLY O 27 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N LEU O 31 " --> pdb=" O ILE O 28 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N GLY O 33 " --> pdb=" O ILE O 30 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N LYS O 34 " --> pdb=" O LEU O 31 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N GLU O 37 " --> pdb=" O LYS O 34 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N ALA O 40 " --> pdb=" O GLU O 37 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ARG O 41 " --> pdb=" O GLY O 38 " (cutoff:3.500A) Processing helix chain 'O' and resid 46 through 76 removed outlier: 3.796A pdb=" N THR O 51 " --> pdb=" O PRO O 47 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N PHE O 54 " --> pdb=" O ARG O 50 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N LEU O 59 " --> pdb=" O ILE O 55 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N ASP O 61 " --> pdb=" O MET O 57 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N ALA O 62 " --> pdb=" O GLY O 58 " (cutoff:3.500A) removed outlier: 4.678A pdb=" N ILE O 63 " --> pdb=" O LEU O 59 " (cutoff:3.500A) Proline residue: O 64 - end of helix Processing helix chain 'P' and resid 6 through 41 removed outlier: 3.694A pdb=" N ALA P 21 " --> pdb=" O MET P 17 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N LYS P 34 " --> pdb=" O ILE P 30 " (cutoff:3.500A) Processing helix chain 'P' and resid 46 through 76 removed outlier: 3.729A pdb=" N LEU P 59 " --> pdb=" O ILE P 55 " (cutoff:3.500A) removed outlier: 4.219A pdb=" N ILE P 63 " --> pdb=" O LEU P 59 " (cutoff:3.500A) Proline residue: P 64 - end of helix removed outlier: 3.793A pdb=" N ALA P 67 " --> pdb=" O ILE P 63 " (cutoff:3.500A) Processing helix chain 'Q' and resid 4 through 41 removed outlier: 3.726A pdb=" N LEU Q 8 " --> pdb=" O LEU Q 4 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N TYR Q 10 " --> pdb=" O MET Q 6 " (cutoff:3.500A) Processing helix chain 'Q' and resid 43 through 76 Proline residue: Q 47 - end of helix removed outlier: 4.335A pdb=" N ARG Q 50 " --> pdb=" O PRO Q 47 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N PHE Q 54 " --> pdb=" O THR Q 51 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N VAL Q 56 " --> pdb=" O PHE Q 53 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N MET Q 57 " --> pdb=" O PHE Q 54 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N VAL Q 60 " --> pdb=" O MET Q 57 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N ASP Q 61 " --> pdb=" O GLY Q 58 " (cutoff:3.500A) removed outlier: 4.262A pdb=" N ILE Q 63 " --> pdb=" O VAL Q 60 " (cutoff:3.500A) Proline residue: Q 64 - end of helix removed outlier: 3.756A pdb=" N ALA Q 67 " --> pdb=" O PRO Q 64 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N VAL Q 68 " --> pdb=" O MET Q 65 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N GLY Q 69 " --> pdb=" O ILE Q 66 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N LEU Q 70 " --> pdb=" O ALA Q 67 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N LEU Q 72 " --> pdb=" O GLY Q 69 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N TYR Q 73 " --> pdb=" O LEU Q 70 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N MET Q 75 " --> pdb=" O LEU Q 72 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N PHE Q 76 " --> pdb=" O TYR Q 73 " (cutoff:3.500A) Processing helix chain 'R' and resid 4 through 41 removed outlier: 3.817A pdb=" N LEU R 8 " --> pdb=" O LEU R 4 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N ALA R 21 " --> pdb=" O MET R 17 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N ILE R 28 " --> pdb=" O ALA R 24 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N LYS R 34 " --> pdb=" O ILE R 30 " (cutoff:3.500A) Processing helix chain 'R' and resid 46 through 76 removed outlier: 3.505A pdb=" N GLN R 52 " --> pdb=" O LEU R 48 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N LEU R 59 " --> pdb=" O ILE R 55 " (cutoff:3.500A) removed outlier: 4.524A pdb=" N ILE R 63 " --> pdb=" O LEU R 59 " (cutoff:3.500A) Proline residue: R 64 - end of helix Processing helix chain 'S' and resid 6 through 41 removed outlier: 4.582A pdb=" N TYR S 10 " --> pdb=" O ASP S 7 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N ALA S 12 " --> pdb=" O LEU S 9 " (cutoff:3.500A) removed outlier: 4.114A pdb=" N ALA S 13 " --> pdb=" O TYR S 10 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N ALA S 14 " --> pdb=" O MET S 11 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N VAL S 15 " --> pdb=" O ALA S 12 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N MET S 17 " --> pdb=" O ALA S 14 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N GLY S 18 " --> pdb=" O VAL S 15 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N LEU S 19 " --> pdb=" O MET S 16 " (cutoff:3.500A) removed outlier: 4.409A pdb=" N ALA S 20 " --> pdb=" O MET S 17 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N ILE S 22 " --> pdb=" O LEU S 19 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N GLY S 23 " --> pdb=" O ALA S 20 " (cutoff:3.500A) removed outlier: 4.180A pdb=" N ALA S 24 " --> pdb=" O ALA S 21 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N ALA S 25 " --> pdb=" O ILE S 22 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N ILE S 26 " --> pdb=" O GLY S 23 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N GLY S 27 " --> pdb=" O ALA S 24 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N ILE S 28 " --> pdb=" O ALA S 25 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N ILE S 30 " --> pdb=" O GLY S 27 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N LEU S 31 " --> pdb=" O ILE S 28 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N GLY S 32 " --> pdb=" O GLY S 29 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N GLY S 33 " --> pdb=" O ILE S 30 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N LYS S 34 " --> pdb=" O LEU S 31 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N GLU S 37 " --> pdb=" O LYS S 34 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N ALA S 39 " --> pdb=" O LEU S 36 " (cutoff:3.500A) Processing helix chain 'S' and resid 43 through 60 Proline residue: S 47 - end of helix removed outlier: 3.742A pdb=" N ARG S 50 " --> pdb=" O PRO S 47 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N PHE S 54 " --> pdb=" O THR S 51 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N ILE S 55 " --> pdb=" O GLN S 52 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N MET S 57 " --> pdb=" O PHE S 54 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N GLY S 58 " --> pdb=" O ILE S 55 " (cutoff:3.500A) Processing helix chain 'S' and resid 63 through 77 Processing helix chain 'W' and resid 4 through 20 removed outlier: 3.605A pdb=" N ARG W 8 " --> pdb=" O ILE W 4 " (cutoff:3.500A) Proline residue: W 9 - end of helix Processing helix chain 'W' and resid 24 through 39 removed outlier: 3.636A pdb=" N LYS W 39 " --> pdb=" O ALA W 35 " (cutoff:3.500A) Processing helix chain 'W' and resid 41 through 48 removed outlier: 3.666A pdb=" N GLU W 45 " --> pdb=" O GLU W 41 " (cutoff:3.500A) Processing helix chain 'W' and resid 53 through 63 removed outlier: 3.580A pdb=" N SER W 59 " --> pdb=" O THR W 55 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N VAL W 63 " --> pdb=" O SER W 59 " (cutoff:3.500A) Processing helix chain 'W' and resid 69 through 82 removed outlier: 4.385A pdb=" N ASN W 74 " --> pdb=" O GLU W 70 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N ASN W 82 " --> pdb=" O VAL W 78 " (cutoff:3.500A) Processing helix chain 'W' and resid 85 through 102 Proline residue: W 89 - end of helix removed outlier: 3.990A pdb=" N LEU W 92 " --> pdb=" O PRO W 89 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N GLN W 94 " --> pdb=" O VAL W 91 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ILE W 96 " --> pdb=" O GLU W 93 " (cutoff:3.500A) Processing helix chain 'W' and resid 118 through 132 removed outlier: 3.705A pdb=" N LYS W 130 " --> pdb=" O ALA W 126 " (cutoff:3.500A) Processing helix chain 'W' and resid 163 through 173 removed outlier: 4.273A pdb=" N VAL W 173 " --> pdb=" O ARG W 169 " (cutoff:3.500A) Processing helix chain 'X' and resid 5 through 23 removed outlier: 4.153A pdb=" N GLN X 10 " --> pdb=" O ILE X 7 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N PHE X 14 " --> pdb=" O ALA X 11 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N VAL X 15 " --> pdb=" O ILE X 12 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N LEU X 16 " --> pdb=" O ALA X 13 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N LEU X 19 " --> pdb=" O LEU X 16 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N PHE X 20 " --> pdb=" O PHE X 17 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N CYS X 21 " --> pdb=" O VAL X 18 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N LYS X 23 " --> pdb=" O PHE X 20 " (cutoff:3.500A) Processing helix chain 'X' and resid 25 through 125 removed outlier: 3.649A pdb=" N GLU X 39 " --> pdb=" O LYS X 35 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N GLN X 73 " --> pdb=" O LYS X 69 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N VAL X 74 " --> pdb=" O ALA X 70 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N GLN X 96 " --> pdb=" O ALA X 92 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N LYS X 100 " --> pdb=" O GLN X 96 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N ALA X 107 " --> pdb=" O ALA X 103 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ALA X 111 " --> pdb=" O ALA X 107 " (cutoff:3.500A) removed outlier: 4.131A pdb=" N LYS X 114 " --> pdb=" O GLU X 110 " (cutoff:3.500A) removed outlier: 4.347A pdb=" N GLU X 118 " --> pdb=" O LYS X 114 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N GLU X 119 " --> pdb=" O ARG X 115 " (cutoff:3.500A) removed outlier: 4.663A pdb=" N ALA X 125 " --> pdb=" O ARG X 121 " (cutoff:3.500A) Processing helix chain 'X' and resid 128 through 135 removed outlier: 3.744A pdb=" N LYS X 134 " --> pdb=" O ALA X 130 " (cutoff:3.500A) Processing helix chain 'X' and resid 147 through 155 Processing helix chain 'Y' and resid 3 through 24 removed outlier: 3.751A pdb=" N LYS Y 23 " --> pdb=" O LEU Y 19 " (cutoff:3.500A) Processing helix chain 'Y' and resid 26 through 137 removed outlier: 3.563A pdb=" N GLU Y 39 " --> pdb=" O LYS Y 35 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N ILE Y 40 " --> pdb=" O ARG Y 36 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N ASP Y 55 " --> pdb=" O HIS Y 51 " (cutoff:3.500A) removed outlier: 4.664A pdb=" N LYS Y 58 " --> pdb=" O LEU Y 54 " (cutoff:3.500A) removed outlier: 4.545A pdb=" N GLU Y 95 " --> pdb=" O LYS Y 91 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N ALA Y 103 " --> pdb=" O THR Y 99 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N ILE Y 126 " --> pdb=" O LYS Y 122 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N LEU Y 127 " --> pdb=" O GLN Y 123 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N LYS Y 134 " --> pdb=" O ALA Y 130 " (cutoff:3.500A) Processing helix chain 'Y' and resid 142 through 153 Processing helix chain 'a' and resid 8 through 16 removed outlier: 3.550A pdb=" N GLY a 13 " --> pdb=" O GLN a 9 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N LEU a 16 " --> pdb=" O ILE a 12 " (cutoff:3.500A) Processing helix chain 'a' and resid 43 through 64 Processing helix chain 'a' and resid 76 through 93 removed outlier: 3.525A pdb=" N VAL a 82 " --> pdb=" O ALA a 78 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N MET a 93 " --> pdb=" O SER a 89 " (cutoff:3.500A) Processing helix chain 'a' and resid 99 through 120 Proline residue: a 103 - end of helix removed outlier: 3.599A pdb=" N MET a 118 " --> pdb=" O LEU a 114 " (cutoff:3.500A) removed outlier: 4.451A pdb=" N ASP a 119 " --> pdb=" O MET a 115 " (cutoff:3.500A) removed outlier: 4.285A pdb=" N LEU a 120 " --> pdb=" O ASN a 116 " (cutoff:3.500A) Processing helix chain 'a' and resid 125 through 132 Processing helix chain 'a' and resid 147 through 180 removed outlier: 3.521A pdb=" N LYS a 169 " --> pdb=" O SER a 165 " (cutoff:3.500A) removed outlier: 7.053A pdb=" N ILE a 171 " --> pdb=" O LYS a 167 " (cutoff:3.500A) removed outlier: 9.596A pdb=" N GLY a 172 " --> pdb=" O MET a 168 " (cutoff:3.500A) Processing helix chain 'a' and resid 186 through 228 Proline residue: a 190 - end of helix removed outlier: 3.838A pdb=" N LEU a 193 " --> pdb=" O PRO a 190 " (cutoff:3.500A) removed outlier: 4.348A pdb=" N GLU a 196 " --> pdb=" O LEU a 193 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N GLY a 197 " --> pdb=" O ILE a 194 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N VAL a 198 " --> pdb=" O LEU a 195 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N SER a 199 " --> pdb=" O GLU a 196 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N LYS a 203 " --> pdb=" O LEU a 200 " (cutoff:3.500A) Proline residue: a 204 - end of helix removed outlier: 3.754A pdb=" N GLY a 208 " --> pdb=" O VAL a 205 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N LEU a 209 " --> pdb=" O SER a 206 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N ARG a 210 " --> pdb=" O LEU a 207 " (cutoff:3.500A) removed outlier: 4.108A pdb=" N PHE a 212 " --> pdb=" O LEU a 209 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N GLY a 213 " --> pdb=" O ARG a 210 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N ASN a 214 " --> pdb=" O LEU a 211 " (cutoff:3.500A) removed outlier: 4.120A pdb=" N TYR a 216 " --> pdb=" O GLY a 213 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N GLU a 219 " --> pdb=" O TYR a 216 " (cutoff:3.500A) removed outlier: 4.901A pdb=" N LEU a 220 " --> pdb=" O ALA a 217 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N ILE a 225 " --> pdb=" O PHE a 222 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N ALA a 226 " --> pdb=" O ILE a 223 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N LEU a 228 " --> pdb=" O ILE a 225 " (cutoff:3.500A) Processing helix chain 'a' and resid 231 through 268 removed outlier: 4.670A pdb=" N TRP a 235 " --> pdb=" O TRP a 231 " (cutoff:3.500A) removed outlier: 6.017A pdb=" N ILE a 236 " --> pdb=" O TRP a 232 " (cutoff:3.500A) removed outlier: 4.314A pdb=" N LEU a 237 " --> pdb=" O SER a 233 " (cutoff:3.500A) Proline residue: a 240 - end of helix removed outlier: 3.535A pdb=" N PHE a 244 " --> pdb=" O PRO a 240 " (cutoff:3.500A) removed outlier: 4.442A pdb=" N LEU a 247 " --> pdb=" O ILE a 243 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N THR a 250 " --> pdb=" O ILE a 246 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N PHE a 256 " --> pdb=" O GLN a 252 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N SER a 268 " --> pdb=" O LEU a 264 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 87 through 89 removed outlier: 6.713A pdb=" N ARG A 40 " --> pdb=" O VAL A 32 " (cutoff:3.500A) removed outlier: 4.568A pdb=" N VAL A 34 " --> pdb=" O VAL A 38 " (cutoff:3.500A) removed outlier: 6.876A pdb=" N VAL A 38 " --> pdb=" O VAL A 34 " (cutoff:3.500A) removed outlier: 6.953A pdb=" N VAL A 74 " --> pdb=" O ALA A 63 " (cutoff:3.500A) removed outlier: 5.800A pdb=" N ALA A 63 " --> pdb=" O VAL A 74 " (cutoff:3.500A) removed outlier: 4.329A pdb=" N ARG A 59 " --> pdb=" O LEU A 55 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 96 through 98 Processing sheet with id= C, first strand: chain 'A' and resid 107 through 109 removed outlier: 8.374A pdb=" N VAL A 108 " --> pdb=" O THR A 221 " (cutoff:3.500A) removed outlier: 6.300A pdb=" N VAL A 223 " --> pdb=" O VAL A 108 " (cutoff:3.500A) removed outlier: 6.891A pdb=" N ALA A 193 " --> pdb=" O ILE A 222 " (cutoff:3.500A) removed outlier: 8.107A pdb=" N VAL A 224 " --> pdb=" O ALA A 193 " (cutoff:3.500A) removed outlier: 6.339A pdb=" N TYR A 195 " --> pdb=" O VAL A 224 " (cutoff:3.500A) removed outlier: 7.647A pdb=" N ALA A 226 " --> pdb=" O TYR A 195 " (cutoff:3.500A) removed outlier: 6.203A pdb=" N ALA A 197 " --> pdb=" O ALA A 226 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ILE A 198 " --> pdb=" O ASP A 261 " (cutoff:3.500A) removed outlier: 6.417A pdb=" N SER A 323 " --> pdb=" O ALA A 256 " (cutoff:3.500A) removed outlier: 7.983A pdb=" N ILE A 258 " --> pdb=" O SER A 323 " (cutoff:3.500A) removed outlier: 6.576A pdb=" N THR A 325 " --> pdb=" O ILE A 258 " (cutoff:3.500A) removed outlier: 7.783A pdb=" N TYR A 260 " --> pdb=" O THR A 325 " (cutoff:3.500A) removed outlier: 6.618A pdb=" N LEU A 327 " --> pdb=" O TYR A 260 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 352 through 355 removed outlier: 6.541A pdb=" N LEU A 166 " --> pdb=" O ILE A 353 " (cutoff:3.500A) removed outlier: 7.243A pdb=" N LEU A 355 " --> pdb=" O LEU A 166 " (cutoff:3.500A) removed outlier: 6.687A pdb=" N ILE A 168 " --> pdb=" O LEU A 355 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 87 through 90 removed outlier: 4.351A pdb=" N ASN B 27 " --> pdb=" O ALA B 90 " (cutoff:3.500A) removed outlier: 6.449A pdb=" N ARG B 40 " --> pdb=" O VAL B 32 " (cutoff:3.500A) removed outlier: 4.510A pdb=" N VAL B 34 " --> pdb=" O VAL B 38 " (cutoff:3.500A) removed outlier: 6.764A pdb=" N VAL B 38 " --> pdb=" O VAL B 34 " (cutoff:3.500A) removed outlier: 6.914A pdb=" N VAL B 74 " --> pdb=" O ALA B 63 " (cutoff:3.500A) removed outlier: 5.822A pdb=" N ALA B 63 " --> pdb=" O VAL B 74 " (cutoff:3.500A) removed outlier: 4.115A pdb=" N ARG B 59 " --> pdb=" O LEU B 55 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 96 through 98 Processing sheet with id= G, first strand: chain 'B' and resid 107 through 109 removed outlier: 8.542A pdb=" N VAL B 108 " --> pdb=" O THR B 221 " (cutoff:3.500A) removed outlier: 6.341A pdb=" N VAL B 223 " --> pdb=" O VAL B 108 " (cutoff:3.500A) removed outlier: 6.585A pdb=" N ALA B 193 " --> pdb=" O ILE B 222 " (cutoff:3.500A) removed outlier: 7.848A pdb=" N VAL B 224 " --> pdb=" O ALA B 193 " (cutoff:3.500A) removed outlier: 6.231A pdb=" N TYR B 195 " --> pdb=" O VAL B 224 " (cutoff:3.500A) removed outlier: 7.659A pdb=" N ALA B 226 " --> pdb=" O TYR B 195 " (cutoff:3.500A) removed outlier: 6.439A pdb=" N ALA B 197 " --> pdb=" O ALA B 226 " (cutoff:3.500A) removed outlier: 6.547A pdb=" N SER B 323 " --> pdb=" O ALA B 256 " (cutoff:3.500A) removed outlier: 7.890A pdb=" N ILE B 258 " --> pdb=" O SER B 323 " (cutoff:3.500A) removed outlier: 6.337A pdb=" N THR B 325 " --> pdb=" O ILE B 258 " (cutoff:3.500A) removed outlier: 7.544A pdb=" N TYR B 260 " --> pdb=" O THR B 325 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 352 through 355 removed outlier: 6.641A pdb=" N LEU B 166 " --> pdb=" O ILE B 353 " (cutoff:3.500A) removed outlier: 7.416A pdb=" N LEU B 355 " --> pdb=" O LEU B 166 " (cutoff:3.500A) removed outlier: 6.387A pdb=" N ILE B 168 " --> pdb=" O LEU B 355 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'C' and resid 87 through 89 removed outlier: 6.327A pdb=" N ARG C 40 " --> pdb=" O VAL C 32 " (cutoff:3.500A) removed outlier: 4.523A pdb=" N VAL C 34 " --> pdb=" O VAL C 38 " (cutoff:3.500A) removed outlier: 6.892A pdb=" N VAL C 38 " --> pdb=" O VAL C 34 " (cutoff:3.500A) removed outlier: 7.012A pdb=" N VAL C 74 " --> pdb=" O ALA C 63 " (cutoff:3.500A) removed outlier: 5.945A pdb=" N ALA C 63 " --> pdb=" O VAL C 74 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'C' and resid 96 through 98 Processing sheet with id= K, first strand: chain 'C' and resid 107 through 109 removed outlier: 8.380A pdb=" N VAL C 108 " --> pdb=" O THR C 221 " (cutoff:3.500A) removed outlier: 6.368A pdb=" N VAL C 223 " --> pdb=" O VAL C 108 " (cutoff:3.500A) removed outlier: 6.731A pdb=" N ALA C 193 " --> pdb=" O ILE C 222 " (cutoff:3.500A) removed outlier: 7.968A pdb=" N VAL C 224 " --> pdb=" O ALA C 193 " (cutoff:3.500A) removed outlier: 6.370A pdb=" N TYR C 195 " --> pdb=" O VAL C 224 " (cutoff:3.500A) removed outlier: 7.812A pdb=" N ALA C 226 " --> pdb=" O TYR C 195 " (cutoff:3.500A) removed outlier: 6.539A pdb=" N ALA C 197 " --> pdb=" O ALA C 226 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N ILE C 198 " --> pdb=" O ASP C 261 " (cutoff:3.500A) removed outlier: 6.363A pdb=" N SER C 323 " --> pdb=" O ALA C 256 " (cutoff:3.500A) removed outlier: 7.798A pdb=" N ILE C 258 " --> pdb=" O SER C 323 " (cutoff:3.500A) removed outlier: 6.200A pdb=" N THR C 325 " --> pdb=" O ILE C 258 " (cutoff:3.500A) removed outlier: 7.530A pdb=" N TYR C 260 " --> pdb=" O THR C 325 " (cutoff:3.500A) removed outlier: 6.751A pdb=" N LEU C 327 " --> pdb=" O TYR C 260 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'C' and resid 351 through 355 Processing sheet with id= M, first strand: chain 'D' and resid 4 through 9 removed outlier: 6.462A pdb=" N ASP D 14 " --> pdb=" O VAL D 6 " (cutoff:3.500A) removed outlier: 4.462A pdb=" N VAL D 8 " --> pdb=" O VAL D 12 " (cutoff:3.500A) removed outlier: 6.773A pdb=" N VAL D 12 " --> pdb=" O VAL D 8 " (cutoff:3.500A) removed outlier: 6.399A pdb=" N ILE D 54 " --> pdb=" O VAL D 42 " (cutoff:3.500A) removed outlier: 5.657A pdb=" N VAL D 42 " --> pdb=" O ILE D 54 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'D' and resid 76 through 78 Processing sheet with id= O, first strand: chain 'D' and resid 317 through 320 removed outlier: 8.086A pdb=" N VAL D 145 " --> pdb=" O ILE D 290 " (cutoff:3.500A) removed outlier: 6.502A pdb=" N SER D 292 " --> pdb=" O VAL D 145 " (cutoff:3.500A) removed outlier: 7.886A pdb=" N LEU D 147 " --> pdb=" O SER D 292 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N GLN D 294 " --> pdb=" O LEU D 147 " (cutoff:3.500A) removed outlier: 7.880A pdb=" N GLY D 149 " --> pdb=" O GLN D 294 " (cutoff:3.500A) removed outlier: 6.106A pdb=" N VAL D 296 " --> pdb=" O GLY D 149 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'E' and resid 50 through 54 removed outlier: 3.505A pdb=" N GLN E 7 " --> pdb=" O ASP E 14 " (cutoff:3.500A) removed outlier: 6.285A pdb=" N GLU E 16 " --> pdb=" O ILE E 5 " (cutoff:3.500A) removed outlier: 5.968A pdb=" N ILE E 5 " --> pdb=" O GLU E 16 " (cutoff:3.500A) removed outlier: 6.452A pdb=" N VAL E 68 " --> pdb=" O THR E 2 " (cutoff:3.500A) removed outlier: 6.910A pdb=" N ASP E 67 " --> pdb=" O GLN E 32 " (cutoff:3.500A) removed outlier: 4.808A pdb=" N GLN E 32 " --> pdb=" O ASP E 67 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N GLU E 36 " --> pdb=" O ASN E 33 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N ARG E 52 " --> pdb=" O GLN E 43 " (cutoff:3.500A) removed outlier: 5.060A pdb=" N GLN E 45 " --> pdb=" O ILE E 50 " (cutoff:3.500A) removed outlier: 7.401A pdb=" N ILE E 50 " --> pdb=" O GLN E 45 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'E' and resid 76 through 78 Processing sheet with id= R, first strand: chain 'E' and resid 317 through 320 removed outlier: 7.949A pdb=" N VAL E 145 " --> pdb=" O ILE E 290 " (cutoff:3.500A) removed outlier: 6.509A pdb=" N SER E 292 " --> pdb=" O VAL E 145 " (cutoff:3.500A) removed outlier: 7.814A pdb=" N LEU E 147 " --> pdb=" O SER E 292 " (cutoff:3.500A) removed outlier: 6.910A pdb=" N GLN E 294 " --> pdb=" O LEU E 147 " (cutoff:3.500A) removed outlier: 7.832A pdb=" N GLY E 149 " --> pdb=" O GLN E 294 " (cutoff:3.500A) removed outlier: 5.902A pdb=" N VAL E 296 " --> pdb=" O GLY E 149 " (cutoff:3.500A) removed outlier: 6.454A pdb=" N VAL E 237 " --> pdb=" O THR E 291 " (cutoff:3.500A) removed outlier: 8.172A pdb=" N VAL E 293 " --> pdb=" O VAL E 237 " (cutoff:3.500A) removed outlier: 6.641A pdb=" N LEU E 239 " --> pdb=" O VAL E 293 " (cutoff:3.500A) removed outlier: 7.934A pdb=" N ALA E 295 " --> pdb=" O LEU E 239 " (cutoff:3.500A) removed outlier: 6.950A pdb=" N VAL E 241 " --> pdb=" O ALA E 295 " (cutoff:3.500A) removed outlier: 8.439A pdb=" N TYR E 297 " --> pdb=" O VAL E 241 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'F' and resid 3 through 9 removed outlier: 6.530A pdb=" N ASP F 14 " --> pdb=" O VAL F 6 " (cutoff:3.500A) removed outlier: 4.526A pdb=" N VAL F 8 " --> pdb=" O VAL F 12 " (cutoff:3.500A) removed outlier: 6.936A pdb=" N VAL F 12 " --> pdb=" O VAL F 8 " (cutoff:3.500A) removed outlier: 6.372A pdb=" N ILE F 54 " --> pdb=" O VAL F 42 " (cutoff:3.500A) removed outlier: 5.597A pdb=" N VAL F 42 " --> pdb=" O ILE F 54 " (cutoff:3.500A) removed outlier: 4.509A pdb=" N ASP F 27 " --> pdb=" O VAL F 42 " (cutoff:3.500A) removed outlier: 5.636A pdb=" N HIS F 73 " --> pdb=" O ALA F 28 " (cutoff:3.500A) removed outlier: 6.969A pdb=" N GLU F 30 " --> pdb=" O LEU F 71 " (cutoff:3.500A) removed outlier: 6.813A pdb=" N LEU F 71 " --> pdb=" O GLU F 30 " (cutoff:3.500A) removed outlier: 8.576A pdb=" N GLN F 32 " --> pdb=" O LYS F 69 " (cutoff:3.500A) removed outlier: 9.649A pdb=" N LYS F 69 " --> pdb=" O GLN F 32 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'F' and resid 76 through 79 removed outlier: 3.534A pdb=" N VAL F 79 " --> pdb=" O GLU F 105 " (cutoff:3.500A) removed outlier: 4.729A pdb=" N GLU F 105 " --> pdb=" O VAL F 79 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'F' and resid 317 through 319 removed outlier: 8.729A pdb=" N VAL F 145 " --> pdb=" O ILE F 290 " (cutoff:3.500A) removed outlier: 6.592A pdb=" N SER F 292 " --> pdb=" O VAL F 145 " (cutoff:3.500A) removed outlier: 7.492A pdb=" N LEU F 147 " --> pdb=" O SER F 292 " (cutoff:3.500A) removed outlier: 6.572A pdb=" N GLN F 294 " --> pdb=" O LEU F 147 " (cutoff:3.500A) removed outlier: 6.693A pdb=" N TYR F 173 " --> pdb=" O LEU F 238 " (cutoff:3.500A) removed outlier: 8.116A pdb=" N PHE F 240 " --> pdb=" O TYR F 173 " (cutoff:3.500A) removed outlier: 6.763A pdb=" N VAL F 175 " --> pdb=" O PHE F 240 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'G' and resid 180 through 188 removed outlier: 6.468A pdb=" N LEU G 167 " --> pdb=" O LEU G 187 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N LYS G 166 " --> pdb=" O ARG G 74 " (cutoff:3.500A) removed outlier: 5.928A pdb=" N ASN G 172 " --> pdb=" O VAL G 80 " (cutoff:3.500A) removed outlier: 6.282A pdb=" N GLN G 111 " --> pdb=" O VAL G 75 " (cutoff:3.500A) removed outlier: 8.038A pdb=" N TYR G 77 " --> pdb=" O GLN G 111 " (cutoff:3.500A) removed outlier: 6.437A pdb=" N ASP G 113 " --> pdb=" O TYR G 77 " (cutoff:3.500A) removed outlier: 7.954A pdb=" N VAL G 79 " --> pdb=" O ASP G 113 " (cutoff:3.500A) removed outlier: 6.724A pdb=" N ALA G 115 " --> pdb=" O VAL G 79 " (cutoff:3.500A) removed outlier: 7.266A pdb=" N MET G 116 " --> pdb=" O VAL G 133 " (cutoff:3.500A) removed outlier: 4.111A pdb=" N GLN G 135 " --> pdb=" O MET G 116 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'H' and resid 41 through 45 removed outlier: 3.652A pdb=" N GLY H 67 " --> pdb=" O ILE H 45 " (cutoff:3.500A) removed outlier: 5.934A pdb=" N HIS H 5 " --> pdb=" O VAL H 76 " (cutoff:3.500A) removed outlier: 7.642A pdb=" N VAL H 78 " --> pdb=" O HIS H 5 " (cutoff:3.500A) removed outlier: 6.796A pdb=" N ASP H 7 " --> pdb=" O VAL H 78 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N TYR H 4 " --> pdb=" O VAL H 20 " (cutoff:3.500A) removed outlier: 6.445A pdb=" N SER H 10 " --> pdb=" O GLN H 14 " (cutoff:3.500A) removed outlier: 4.658A pdb=" N GLN H 14 " --> pdb=" O SER H 10 " (cutoff:3.500A) removed outlier: 7.059A pdb=" N VAL H 53 " --> pdb=" O GLU H 21 " (cutoff:3.500A) removed outlier: 4.629A pdb=" N ILE H 23 " --> pdb=" O ARG H 51 " (cutoff:3.500A) removed outlier: 6.878A pdb=" N ARG H 51 " --> pdb=" O ILE H 23 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain 'H' and resid 22 through 26 Processing sheet with id= Y, first strand: chain 'W' and resid 135 through 140 Processing sheet with id= Z, first strand: chain 'a' and resid 20 through 22 1840 hydrogen bonds defined for protein. 4929 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: 12.24 Time building geometry restraints manager: 16.40 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.31: 6370 1.31 - 1.44: 8683 1.44 - 1.57: 21794 1.57 - 1.69: 26 1.69 - 1.82: 358 Bond restraints: 37231 Sorted by residual: bond pdb=" C VAL a 50 " pdb=" N VAL a 51 " ideal model delta sigma weight residual 1.334 1.471 -0.137 1.26e-02 6.30e+03 1.19e+02 bond pdb=" C4 ATP D 502 " pdb=" C5 ATP D 502 " ideal model delta sigma weight residual 1.388 1.463 -0.075 1.00e-02 1.00e+04 5.57e+01 bond pdb=" C4 ATP C 600 " pdb=" C5 ATP C 600 " ideal model delta sigma weight residual 1.388 1.457 -0.069 1.00e-02 1.00e+04 4.71e+01 bond pdb=" C4 ATP B 600 " pdb=" C5 ATP B 600 " ideal model delta sigma weight residual 1.388 1.456 -0.068 1.00e-02 1.00e+04 4.60e+01 bond pdb=" C4 ATP A 600 " pdb=" C5 ATP A 600 " ideal model delta sigma weight residual 1.388 1.456 -0.068 1.00e-02 1.00e+04 4.57e+01 ... (remaining 37226 not shown) Histogram of bond angle deviations from ideal: 97.28 - 105.09: 821 105.09 - 112.91: 18939 112.91 - 120.73: 18306 120.73 - 128.55: 12146 128.55 - 136.37: 187 Bond angle restraints: 50399 Sorted by residual: angle pdb=" PB ATP D 502 " pdb=" O3B ATP D 502 " pdb=" PG ATP D 502 " ideal model delta sigma weight residual 139.87 113.95 25.92 1.00e+00 1.00e+00 6.72e+02 angle pdb=" PB ATP C 600 " pdb=" O3B ATP C 600 " pdb=" PG ATP C 600 " ideal model delta sigma weight residual 139.87 117.03 22.84 1.00e+00 1.00e+00 5.22e+02 angle pdb=" PB ATP A 600 " pdb=" O3B ATP A 600 " pdb=" PG ATP A 600 " ideal model delta sigma weight residual 139.87 119.18 20.69 1.00e+00 1.00e+00 4.28e+02 angle pdb=" PB ATP B 600 " pdb=" O3B ATP B 600 " pdb=" PG ATP B 600 " ideal model delta sigma weight residual 139.87 120.53 19.34 1.00e+00 1.00e+00 3.74e+02 angle pdb=" PA ATP D 502 " pdb=" O3A ATP D 502 " pdb=" PB ATP D 502 " ideal model delta sigma weight residual 136.83 119.43 17.40 1.00e+00 1.00e+00 3.03e+02 ... (remaining 50394 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 28.24: 21833 28.24 - 56.48: 674 56.48 - 84.73: 108 84.73 - 112.97: 16 112.97 - 141.21: 3 Dihedral angle restraints: 22634 sinusoidal: 8960 harmonic: 13674 Sorted by residual: dihedral pdb=" O1B ADP F 500 " pdb=" O3A ADP F 500 " pdb=" PB ADP F 500 " pdb=" PA ADP F 500 " ideal model delta sinusoidal sigma weight residual 300.00 158.79 141.21 1 2.00e+01 2.50e-03 4.27e+01 dihedral pdb=" O1B ADP E 501 " pdb=" O3A ADP E 501 " pdb=" PB ADP E 501 " pdb=" PA ADP E 501 " ideal model delta sinusoidal sigma weight residual -60.00 65.76 -125.76 1 2.00e+01 2.50e-03 3.80e+01 dihedral pdb=" C5' ADP E 501 " pdb=" O5' ADP E 501 " pdb=" PA ADP E 501 " pdb=" O2A ADP E 501 " ideal model delta sinusoidal sigma weight residual -60.00 -179.08 119.08 1 2.00e+01 2.50e-03 3.57e+01 ... (remaining 22631 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.091: 4951 0.091 - 0.182: 807 0.182 - 0.274: 92 0.274 - 0.365: 18 0.365 - 0.456: 7 Chirality restraints: 5875 Sorted by residual: chirality pdb=" CB ILE Q 63 " pdb=" CA ILE Q 63 " pdb=" CG1 ILE Q 63 " pdb=" CG2 ILE Q 63 " both_signs ideal model delta sigma weight residual False 2.64 2.19 0.46 2.00e-01 2.50e+01 5.20e+00 chirality pdb=" CB ILE E 330 " pdb=" CA ILE E 330 " pdb=" CG1 ILE E 330 " pdb=" CG2 ILE E 330 " both_signs ideal model delta sigma weight residual False 2.64 2.23 0.42 2.00e-01 2.50e+01 4.32e+00 chirality pdb=" CB ILE P 63 " pdb=" CA ILE P 63 " pdb=" CG1 ILE P 63 " pdb=" CG2 ILE P 63 " both_signs ideal model delta sigma weight residual False 2.64 2.25 0.39 2.00e-01 2.50e+01 3.80e+00 ... (remaining 5872 not shown) Planarity restraints: 6501 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG X 36 " -0.130 9.50e-02 1.11e+02 7.68e-02 3.32e+01 pdb=" NE ARG X 36 " 0.040 2.00e-02 2.50e+03 pdb=" CZ ARG X 36 " -0.095 2.00e-02 2.50e+03 pdb=" NH1 ARG X 36 " 0.034 2.00e-02 2.50e+03 pdb=" NH2 ARG X 36 " 0.027 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG D 281 " -0.126 9.50e-02 1.11e+02 6.98e-02 2.29e+01 pdb=" NE ARG D 281 " 0.034 2.00e-02 2.50e+03 pdb=" CZ ARG D 281 " -0.078 2.00e-02 2.50e+03 pdb=" NH1 ARG D 281 " 0.028 2.00e-02 2.50e+03 pdb=" NH2 ARG D 281 " 0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL A 268 " -0.022 2.00e-02 2.50e+03 4.35e-02 1.89e+01 pdb=" C VAL A 268 " 0.075 2.00e-02 2.50e+03 pdb=" O VAL A 268 " -0.028 2.00e-02 2.50e+03 pdb=" N ALA A 269 " -0.025 2.00e-02 2.50e+03 ... (remaining 6498 not shown) Histogram of nonbonded interaction distances: 1.89 - 2.49: 51 2.49 - 3.09: 27015 3.09 - 3.70: 54496 3.70 - 4.30: 82595 4.30 - 4.90: 137358 Nonbonded interactions: 301515 Sorted by model distance: nonbonded pdb=" O2G ATP B 600 " pdb="MG MG B 601 " model vdw 1.890 2.170 nonbonded pdb=" O2G ATP C 600 " pdb="MG MG C 601 " model vdw 1.899 2.170 nonbonded pdb=" O2G ATP A 600 " pdb="MG MG A 601 " model vdw 1.899 2.170 nonbonded pdb="MG MG D 501 " pdb=" O1G ATP D 502 " model vdw 1.930 2.170 nonbonded pdb=" O2B ATP A 600 " pdb="MG MG A 601 " model vdw 2.033 2.170 ... (remaining 301510 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' and (resid 4 through 408 or (resid 409 through 410 and (name N or nam \ e CA or name C or name O or name CB )) or resid 411 through 511 or resid 600 thr \ ough 601)) selection = (chain 'C' and (resid 4 through 408 or (resid 409 through 410 and (name N or nam \ e CA or name C or name O or name CB )) or resid 411 through 511 or resid 600 thr \ ough 601)) } ncs_group { reference = (chain 'D' and resid 2 through 459) selection = (chain 'E' and resid 2 through 459) selection = (chain 'F' and resid 2 through 459) } ncs_group { reference = (chain 'I' and resid 3 through 78) selection = (chain 'J' and resid 3 through 78) selection = (chain 'L' and resid 3 through 78) selection = (chain 'M' and resid 3 through 78) selection = (chain 'N' and resid 3 through 78) selection = (chain 'O' and resid 3 through 78) selection = (chain 'P' and resid 3 through 78) selection = (chain 'Q' and resid 3 through 78) selection = chain 'R' selection = (chain 'S' and resid 3 through 78) } ncs_group { reference = chain 'X' selection = (chain 'Y' and (resid 1 through 80 or (resid 81 through 82 and (name N or name C \ A or name C or name O or name CB )) or resid 83 through 156)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.740 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.030 Extract box with map and model: 11.790 Check model and map are aligned: 0.510 Set scattering table: 0.310 Process input model: 93.980 Find NCS groups from input model: 2.460 Set up NCS constraints: 0.220 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.770 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 113.830 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8326 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 : 0.010 0.137 37231 Z= 0.665 Angle : 1.284 25.924 50399 Z= 0.833 Chirality : 0.070 0.456 5875 Planarity : 0.008 0.110 6501 Dihedral : 14.490 141.209 13888 Min Nonbonded Distance : 1.890 Molprobity Statistics. All-atom Clashscore : 2.78 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.68 % Favored : 97.25 % Rotamer: Outliers : 0.74 % Allowed : 4.34 % Favored : 94.93 % Cbeta Deviations : 0.02 % Peptide Plane: Cis-proline : 4.47 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.64 (0.11), residues: 4770 helix: -1.39 (0.09), residues: 2557 sheet: 0.24 (0.21), residues: 525 loop : -0.70 (0.14), residues: 1688 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.047 0.005 TRP a 111 HIS 0.016 0.003 HIS W 21 PHE 0.059 0.005 PHE O 54 TYR 0.042 0.007 TYR D 26 ARG 0.097 0.011 ARG X 36 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9540 Ramachandran restraints generated. 4770 Oldfield, 0 Emsley, 4770 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9540 Ramachandran restraints generated. 4770 Oldfield, 0 Emsley, 4770 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 599 residues out of total 3810 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 571 time to evaluate : 3.969 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 236 TYR cc_start: 0.9336 (OUTLIER) cc_final: 0.8388 (t80) REVERT: A 289 ASP cc_start: 0.7697 (t0) cc_final: 0.7121 (t0) REVERT: A 468 GLU cc_start: 0.8603 (tt0) cc_final: 0.8360 (tm-30) REVERT: B 456 LEU cc_start: 0.9226 (mt) cc_final: 0.9021 (pp) REVERT: E 88 MET cc_start: 0.8814 (mtm) cc_final: 0.8604 (mtm) REVERT: E 159 MET cc_start: 0.8849 (ttp) cc_final: 0.8633 (ttm) REVERT: E 226 MET cc_start: 0.8728 (mtt) cc_final: 0.8526 (mtp) REVERT: E 445 MET cc_start: 0.8245 (mtt) cc_final: 0.7947 (mpp) REVERT: F 445 MET cc_start: 0.8906 (mmt) cc_final: 0.8680 (mmt) REVERT: G 59 ASN cc_start: 0.4574 (OUTLIER) cc_final: 0.4102 (p0) REVERT: H 24 GLN cc_start: 0.8291 (tt0) cc_final: 0.8074 (tm-30) REVERT: H 61 PHE cc_start: 0.8012 (m-80) cc_final: 0.7801 (m-10) REVERT: H 63 TYR cc_start: 0.8235 (t80) cc_final: 0.8013 (t80) REVERT: H 70 GLU cc_start: 0.8431 (pt0) cc_final: 0.8199 (pp20) REVERT: I 11 MET cc_start: 0.7130 (tpp) cc_final: 0.6728 (tpt) REVERT: I 17 MET cc_start: 0.5177 (ptp) cc_final: 0.4707 (ptm) REVERT: J 54 PHE cc_start: 0.6336 (m-10) cc_final: 0.5758 (t80) REVERT: L 16 MET cc_start: 0.4808 (mtm) cc_final: 0.4137 (mtp) REVERT: L 26 ILE cc_start: 0.4828 (mt) cc_final: 0.4600 (mm) REVERT: M 6 MET cc_start: 0.7059 (mtt) cc_final: 0.6750 (ppp) REVERT: M 53 PHE cc_start: 0.8292 (t80) cc_final: 0.7821 (t80) REVERT: N 16 MET cc_start: -0.2031 (mtp) cc_final: -0.2761 (tpp) REVERT: N 17 MET cc_start: 0.1364 (mtp) cc_final: 0.0916 (tpt) REVERT: N 78 VAL cc_start: 0.0246 (m) cc_final: -0.0303 (t) REVERT: O 37 GLU cc_start: 0.8762 (tt0) cc_final: 0.8547 (tt0) REVERT: P 44 ASP cc_start: 0.8114 (m-30) cc_final: 0.7792 (p0) REVERT: P 49 LEU cc_start: 0.9006 (mt) cc_final: 0.8553 (tp) REVERT: Q 16 MET cc_start: 0.5495 (ttt) cc_final: 0.4756 (tpp) REVERT: R 6 MET cc_start: 0.5680 (mmt) cc_final: 0.5144 (tpp) REVERT: W 68 LEU cc_start: 0.9002 (OUTLIER) cc_final: 0.8684 (tt) REVERT: W 102 SER cc_start: 0.8394 (t) cc_final: 0.8139 (p) REVERT: W 111 ILE cc_start: 0.9102 (mt) cc_final: 0.8846 (mm) REVERT: X 74 VAL cc_start: 0.8951 (m) cc_final: 0.8601 (p) REVERT: X 135 ILE cc_start: 0.6838 (OUTLIER) cc_final: 0.6400 (pp) REVERT: X 147 ASP cc_start: 0.7804 (OUTLIER) cc_final: 0.7588 (m-30) REVERT: Y 39 GLU cc_start: 0.7956 (tt0) cc_final: 0.7604 (tm-30) REVERT: a 177 GLU cc_start: 0.4972 (mt-10) cc_final: 0.4595 (tm-30) REVERT: a 219 GLU cc_start: 0.6480 (tt0) cc_final: 0.6199 (tt0) outliers start: 28 outliers final: 5 residues processed: 594 average time/residue: 0.5252 time to fit residues: 490.5279 Evaluate side-chains 350 residues out of total 3810 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 340 time to evaluate : 4.292 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 236 TYR Chi-restraints excluded: chain A residue 422 ASP Chi-restraints excluded: chain C residue 236 TYR Chi-restraints excluded: chain D residue 205 VAL Chi-restraints excluded: chain G residue 59 ASN Chi-restraints excluded: chain W residue 68 LEU Chi-restraints excluded: chain X residue 135 ILE Chi-restraints excluded: chain X residue 136 ILE Chi-restraints excluded: chain X residue 147 ASP Chi-restraints excluded: chain a residue 20 GLN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 470 random chunks: chunk 396 optimal weight: 9.9990 chunk 356 optimal weight: 20.0000 chunk 197 optimal weight: 0.8980 chunk 121 optimal weight: 2.9990 chunk 240 optimal weight: 2.9990 chunk 190 optimal weight: 0.9990 chunk 368 optimal weight: 8.9990 chunk 142 optimal weight: 2.9990 chunk 224 optimal weight: 0.9990 chunk 274 optimal weight: 1.9990 chunk 426 optimal weight: 3.9990 overall best weight: 1.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 147 GLN A 186 GLN B 58 ASN C 147 GLN C 344 ASN C 399 GLN E 368 GLN F 19 GLN F 45 GLN F 365 GLN F 368 GLN H 5 HIS H 55 GLN H 75 ASN I 52 GLN M 5 ASN O 3 ASN O 42 GLN O 52 GLN P 42 GLN Q 52 GLN R 3 ASN S 3 ASN S 5 ASN ** S 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 52 GLN ** W 67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 37 GLN X 51 HIS ** a 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 17 ASN a 20 GLN ** a 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 42 ASN ** a 252 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 30 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8342 moved from start: 0.2420 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 37231 Z= 0.229 Angle : 0.641 8.883 50399 Z= 0.336 Chirality : 0.045 0.438 5875 Planarity : 0.004 0.045 6501 Dihedral : 7.755 131.300 5344 Min Nonbonded Distance : 1.964 Molprobity Statistics. All-atom Clashscore : 6.53 Ramachandran Plot: Outliers : 0.02 % Allowed : 1.36 % Favored : 98.62 % Rotamer: Outliers : 1.81 % Allowed : 8.09 % Favored : 90.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.47 % 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: 0.23 (0.12), residues: 4770 helix: 0.36 (0.10), residues: 2588 sheet: 0.73 (0.21), residues: 508 loop : -0.13 (0.15), residues: 1674 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP X 26 HIS 0.013 0.001 HIS a 14 PHE 0.020 0.002 PHE P 53 TYR 0.032 0.002 TYR R 10 ARG 0.012 0.001 ARG H 93 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9540 Ramachandran restraints generated. 4770 Oldfield, 0 Emsley, 4770 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9540 Ramachandran restraints generated. 4770 Oldfield, 0 Emsley, 4770 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 449 residues out of total 3810 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 380 time to evaluate : 4.317 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 236 TYR cc_start: 0.9363 (OUTLIER) cc_final: 0.8204 (t80) REVERT: A 289 ASP cc_start: 0.7694 (t70) cc_final: 0.7301 (t0) REVERT: B 76 MET cc_start: 0.8723 (OUTLIER) cc_final: 0.8355 (mtp) REVERT: E 159 MET cc_start: 0.8865 (ttp) cc_final: 0.8621 (ttm) REVERT: E 275 MET cc_start: 0.8705 (tpp) cc_final: 0.8412 (ttp) REVERT: F 242 ASP cc_start: 0.7334 (t0) cc_final: 0.6650 (t0) REVERT: F 445 MET cc_start: 0.8801 (mmt) cc_final: 0.8458 (mmt) REVERT: H 13 GLN cc_start: 0.8506 (pt0) cc_final: 0.8154 (pm20) REVERT: H 31 GLU cc_start: 0.6280 (pm20) cc_final: 0.5663 (pm20) REVERT: H 70 GLU cc_start: 0.8395 (pt0) cc_final: 0.7875 (pp20) REVERT: J 53 PHE cc_start: 0.6791 (t80) cc_final: 0.5908 (t80) REVERT: L 16 MET cc_start: 0.4328 (mtm) cc_final: 0.4124 (mpp) REVERT: L 54 PHE cc_start: 0.5915 (m-80) cc_final: 0.4275 (t80) REVERT: M 6 MET cc_start: 0.7213 (mtt) cc_final: 0.6938 (ppp) REVERT: N 17 MET cc_start: 0.1809 (mtp) cc_final: 0.1549 (tpt) REVERT: P 6 MET cc_start: 0.3034 (ppp) cc_final: 0.2585 (ppp) REVERT: P 31 LEU cc_start: 0.8681 (tp) cc_final: 0.8173 (mt) REVERT: P 44 ASP cc_start: 0.7796 (m-30) cc_final: 0.7473 (p0) REVERT: P 49 LEU cc_start: 0.8983 (mt) cc_final: 0.8518 (tp) REVERT: Q 16 MET cc_start: 0.5279 (ttt) cc_final: 0.4897 (ttm) REVERT: Q 75 MET cc_start: 0.1185 (ttm) cc_final: 0.0805 (ttm) REVERT: R 11 MET cc_start: 0.6143 (tpp) cc_final: 0.4788 (mmt) REVERT: R 28 ILE cc_start: 0.7653 (mm) cc_final: 0.7343 (tt) REVERT: S 16 MET cc_start: 0.5823 (ttm) cc_final: 0.5591 (ttt) REVERT: W 102 SER cc_start: 0.8597 (t) cc_final: 0.8269 (p) REVERT: W 109 ASP cc_start: 0.8158 (t70) cc_final: 0.7554 (t0) REVERT: W 137 LYS cc_start: 0.8153 (tmtt) cc_final: 0.7599 (tmtt) REVERT: X 74 VAL cc_start: 0.8905 (m) cc_final: 0.8515 (p) REVERT: X 78 GLN cc_start: 0.9335 (mm110) cc_final: 0.9128 (mm-40) REVERT: a 61 ARG cc_start: 0.5811 (tpt170) cc_final: 0.5230 (mmm160) REVERT: a 177 GLU cc_start: 0.4926 (mt-10) cc_final: 0.4642 (tm-30) outliers start: 69 outliers final: 27 residues processed: 431 average time/residue: 0.4963 time to fit residues: 350.2556 Evaluate side-chains 342 residues out of total 3810 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 313 time to evaluate : 4.285 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 236 TYR Chi-restraints excluded: chain A residue 406 PHE Chi-restraints excluded: chain A residue 504 LEU Chi-restraints excluded: chain B residue 76 MET Chi-restraints excluded: chain B residue 413 LEU Chi-restraints excluded: chain B residue 448 LEU Chi-restraints excluded: chain C residue 48 MET Chi-restraints excluded: chain C residue 236 TYR Chi-restraints excluded: chain C residue 409 PHE Chi-restraints excluded: chain D residue 338 ASP Chi-restraints excluded: chain D residue 348 VAL Chi-restraints excluded: chain F residue 14 ASP Chi-restraints excluded: chain F residue 265 VAL Chi-restraints excluded: chain G residue 132 VAL Chi-restraints excluded: chain H residue 29 GLU Chi-restraints excluded: chain H residue 56 HIS Chi-restraints excluded: chain H residue 77 THR Chi-restraints excluded: chain I residue 30 ILE Chi-restraints excluded: chain L residue 6 MET Chi-restraints excluded: chain L residue 78 VAL Chi-restraints excluded: chain M residue 59 LEU Chi-restraints excluded: chain Q residue 5 ASN Chi-restraints excluded: chain R residue 72 LEU Chi-restraints excluded: chain S residue 3 ASN Chi-restraints excluded: chain X residue 88 ASP Chi-restraints excluded: chain X residue 129 VAL Chi-restraints excluded: chain Y residue 15 VAL Chi-restraints excluded: chain Y residue 141 ASP Chi-restraints excluded: chain a residue 140 ARG Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 470 random chunks: chunk 237 optimal weight: 6.9990 chunk 132 optimal weight: 6.9990 chunk 355 optimal weight: 9.9990 chunk 290 optimal weight: 0.8980 chunk 117 optimal weight: 5.9990 chunk 427 optimal weight: 5.9990 chunk 461 optimal weight: 0.8980 chunk 380 optimal weight: 8.9990 chunk 424 optimal weight: 7.9990 chunk 145 optimal weight: 1.9990 chunk 343 optimal weight: 7.9990 overall best weight: 3.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 358 ASN D 32 GLN ** D 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 73 HIS E 365 GLN F 19 GLN G 131 ASN M 5 ASN ** P 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 3 ASN ** S 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 9 GLN ** a 116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8443 moved from start: 0.3373 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.070 37231 Z= 0.321 Angle : 0.625 12.008 50399 Z= 0.322 Chirality : 0.044 0.281 5875 Planarity : 0.004 0.049 6501 Dihedral : 7.160 119.141 5328 Min Nonbonded Distance : 1.805 Molprobity Statistics. All-atom Clashscore : 7.34 Ramachandran Plot: Outliers : 0.02 % Allowed : 1.97 % Favored : 98.01 % Rotamer: Outliers : 2.10 % Allowed : 9.57 % Favored : 88.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.47 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.72 (0.12), residues: 4770 helix: 0.89 (0.10), residues: 2599 sheet: 0.76 (0.21), residues: 524 loop : -0.10 (0.16), residues: 1647 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP X 26 HIS 0.006 0.001 HIS a 14 PHE 0.023 0.002 PHE M 54 TYR 0.018 0.002 TYR A 236 ARG 0.006 0.001 ARG E 323 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9540 Ramachandran restraints generated. 4770 Oldfield, 0 Emsley, 4770 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9540 Ramachandran restraints generated. 4770 Oldfield, 0 Emsley, 4770 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 414 residues out of total 3810 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 80 poor density : 334 time to evaluate : 4.323 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 236 TYR cc_start: 0.9438 (OUTLIER) cc_final: 0.8299 (t80) REVERT: A 289 ASP cc_start: 0.7919 (t0) cc_final: 0.7567 (t0) REVERT: E 159 MET cc_start: 0.8905 (ttp) cc_final: 0.8680 (ttm) REVERT: F 136 MET cc_start: 0.9057 (mmm) cc_final: 0.8825 (mmm) REVERT: F 445 MET cc_start: 0.8913 (mmt) cc_final: 0.8509 (mmt) REVERT: H 13 GLN cc_start: 0.8496 (pt0) cc_final: 0.8218 (pm20) REVERT: H 22 LYS cc_start: 0.8590 (ptpp) cc_final: 0.8375 (ptpt) REVERT: H 70 GLU cc_start: 0.8499 (pt0) cc_final: 0.7837 (pp20) REVERT: H 95 MET cc_start: 0.8205 (ptt) cc_final: 0.7814 (ptp) REVERT: L 54 PHE cc_start: 0.6051 (m-80) cc_final: 0.4435 (t80) REVERT: M 6 MET cc_start: 0.7268 (mtt) cc_final: 0.7011 (ppp) REVERT: M 54 PHE cc_start: 0.5927 (m-10) cc_final: 0.4737 (t80) REVERT: M 65 MET cc_start: 0.6830 (tpp) cc_final: 0.6326 (ptp) REVERT: P 17 MET cc_start: 0.5533 (ttm) cc_final: 0.5004 (tpp) REVERT: P 44 ASP cc_start: 0.7884 (m-30) cc_final: 0.7539 (p0) REVERT: P 65 MET cc_start: 0.2978 (mmp) cc_final: 0.2559 (mmt) REVERT: Q 16 MET cc_start: 0.4970 (ttt) cc_final: 0.4285 (tpp) REVERT: Q 65 MET cc_start: 0.6107 (mtt) cc_final: 0.5891 (mmp) REVERT: W 137 LYS cc_start: 0.8389 (tmtt) cc_final: 0.7980 (tmtt) REVERT: a 119 ASP cc_start: 0.6993 (t0) cc_final: 0.6394 (m-30) REVERT: a 177 GLU cc_start: 0.4875 (mt-10) cc_final: 0.4469 (tm-30) REVERT: a 215 MET cc_start: 0.6584 (mmp) cc_final: 0.6380 (mmp) REVERT: a 269 GLU cc_start: 0.5761 (OUTLIER) cc_final: 0.4770 (mm-30) outliers start: 80 outliers final: 45 residues processed: 395 average time/residue: 0.4767 time to fit residues: 312.6426 Evaluate side-chains 345 residues out of total 3810 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 298 time to evaluate : 4.335 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 VAL Chi-restraints excluded: chain A residue 110 THR Chi-restraints excluded: chain A residue 236 TYR Chi-restraints excluded: chain A residue 395 THR Chi-restraints excluded: chain A residue 406 PHE Chi-restraints excluded: chain A residue 415 ASP Chi-restraints excluded: chain A residue 422 ASP Chi-restraints excluded: chain A residue 504 LEU Chi-restraints excluded: chain B residue 110 THR Chi-restraints excluded: chain B residue 413 LEU Chi-restraints excluded: chain B residue 448 LEU Chi-restraints excluded: chain C residue 48 MET Chi-restraints excluded: chain C residue 187 ARG Chi-restraints excluded: chain C residue 236 TYR Chi-restraints excluded: chain D residue 205 VAL Chi-restraints excluded: chain D residue 348 VAL Chi-restraints excluded: chain E residue 390 VAL Chi-restraints excluded: chain F residue 19 GLN Chi-restraints excluded: chain F residue 215 ASN Chi-restraints excluded: chain G residue 114 LEU Chi-restraints excluded: chain G residue 132 VAL Chi-restraints excluded: chain H residue 29 GLU Chi-restraints excluded: chain H residue 56 HIS Chi-restraints excluded: chain H residue 62 ILE Chi-restraints excluded: chain H residue 77 THR Chi-restraints excluded: chain I residue 26 ILE Chi-restraints excluded: chain I residue 30 ILE Chi-restraints excluded: chain I residue 51 THR Chi-restraints excluded: chain L residue 6 MET Chi-restraints excluded: chain L residue 15 VAL Chi-restraints excluded: chain L residue 60 VAL Chi-restraints excluded: chain L residue 78 VAL Chi-restraints excluded: chain M residue 59 LEU Chi-restraints excluded: chain N residue 78 VAL Chi-restraints excluded: chain O residue 3 ASN Chi-restraints excluded: chain O residue 9 LEU Chi-restraints excluded: chain P residue 15 VAL Chi-restraints excluded: chain Q residue 63 ILE Chi-restraints excluded: chain S residue 44 ASP Chi-restraints excluded: chain W residue 145 SER Chi-restraints excluded: chain X residue 18 VAL Chi-restraints excluded: chain X residue 129 VAL Chi-restraints excluded: chain X residue 140 VAL Chi-restraints excluded: chain Y residue 124 VAL Chi-restraints excluded: chain Y residue 141 ASP Chi-restraints excluded: chain a residue 140 ARG Chi-restraints excluded: chain a residue 269 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 470 random chunks: chunk 422 optimal weight: 10.0000 chunk 321 optimal weight: 6.9990 chunk 221 optimal weight: 5.9990 chunk 47 optimal weight: 0.0870 chunk 204 optimal weight: 4.9990 chunk 287 optimal weight: 10.0000 chunk 429 optimal weight: 0.6980 chunk 454 optimal weight: 30.0000 chunk 224 optimal weight: 2.9990 chunk 406 optimal weight: 0.8980 chunk 122 optimal weight: 0.0050 overall best weight: 0.9374 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 14 GLN M 5 ASN ** P 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 104 GLN ** a 42 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 238 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8407 moved from start: 0.3696 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 37231 Z= 0.162 Angle : 0.540 9.311 50399 Z= 0.276 Chirality : 0.041 0.259 5875 Planarity : 0.004 0.050 6501 Dihedral : 6.751 119.880 5328 Min Nonbonded Distance : 1.978 Molprobity Statistics. All-atom Clashscore : 7.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.57 % Favored : 98.43 % Rotamer: Outliers : 1.34 % Allowed : 10.93 % Favored : 87.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.47 % 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: 0.95 (0.12), residues: 4770 helix: 1.16 (0.10), residues: 2602 sheet: 0.86 (0.21), residues: 520 loop : -0.17 (0.16), residues: 1648 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP G 203 HIS 0.005 0.001 HIS a 14 PHE 0.020 0.001 PHE R 53 TYR 0.018 0.001 TYR L 73 ARG 0.009 0.000 ARG X 115 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9540 Ramachandran restraints generated. 4770 Oldfield, 0 Emsley, 4770 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9540 Ramachandran restraints generated. 4770 Oldfield, 0 Emsley, 4770 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 378 residues out of total 3810 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 327 time to evaluate : 4.231 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: A 236 TYR cc_start: 0.9388 (OUTLIER) cc_final: 0.8276 (t80) REVERT: A 289 ASP cc_start: 0.7855 (t0) cc_final: 0.7494 (t0) REVERT: E 56 MET cc_start: 0.9100 (mmt) cc_final: 0.8706 (mmt) REVERT: F 445 MET cc_start: 0.8833 (mmt) cc_final: 0.8413 (mmt) REVERT: H 70 GLU cc_start: 0.8376 (pt0) cc_final: 0.7785 (pp20) REVERT: H 95 MET cc_start: 0.8256 (ptt) cc_final: 0.7922 (ptp) REVERT: L 54 PHE cc_start: 0.6066 (m-80) cc_final: 0.4445 (t80) REVERT: M 6 MET cc_start: 0.7360 (mtt) cc_final: 0.7106 (ppp) REVERT: M 31 LEU cc_start: 0.6117 (tp) cc_final: 0.5691 (mt) REVERT: M 54 PHE cc_start: 0.5959 (m-10) cc_final: 0.4760 (t80) REVERT: M 65 MET cc_start: 0.7392 (tpp) cc_final: 0.6968 (ptm) REVERT: N 41 ARG cc_start: 0.7898 (mtt90) cc_final: 0.7604 (ttp-170) REVERT: O 75 MET cc_start: 0.2684 (ttt) cc_final: 0.2286 (tmm) REVERT: P 17 MET cc_start: 0.4913 (ttm) cc_final: 0.4429 (tpp) REVERT: P 44 ASP cc_start: 0.8207 (m-30) cc_final: 0.7746 (p0) REVERT: Q 16 MET cc_start: 0.4801 (ttt) cc_final: 0.4313 (tpp) REVERT: Q 63 ILE cc_start: 0.3178 (OUTLIER) cc_final: 0.2818 (tp) REVERT: Q 65 MET cc_start: 0.6127 (mtt) cc_final: 0.5920 (mmp) REVERT: R 11 MET cc_start: 0.6134 (tpp) cc_final: 0.4641 (mmt) REVERT: R 28 ILE cc_start: 0.7684 (mm) cc_final: 0.7259 (tt) REVERT: R 65 MET cc_start: 0.3770 (mtt) cc_final: 0.3546 (mtm) REVERT: S 75 MET cc_start: 0.3536 (tmm) cc_final: 0.3277 (tmt) REVERT: W 137 LYS cc_start: 0.8308 (tmtt) cc_final: 0.8015 (tmtt) REVERT: X 26 TRP cc_start: 0.4009 (m100) cc_final: 0.3000 (m100) REVERT: X 78 GLN cc_start: 0.9451 (mm110) cc_final: 0.9193 (mm-40) REVERT: Y 150 ASP cc_start: 0.8039 (m-30) cc_final: 0.7728 (t0) REVERT: a 6 MET cc_start: 0.0874 (ppp) cc_final: 0.0114 (ppp) REVERT: a 119 ASP cc_start: 0.7168 (t0) cc_final: 0.6753 (m-30) REVERT: a 167 LYS cc_start: 0.6889 (tttt) cc_final: 0.6672 (tptt) REVERT: a 177 GLU cc_start: 0.4864 (mt-10) cc_final: 0.4462 (tm-30) REVERT: a 257 MET cc_start: 0.7573 (ppp) cc_final: 0.7331 (ppp) outliers start: 51 outliers final: 30 residues processed: 363 average time/residue: 0.4684 time to fit residues: 284.9774 Evaluate side-chains 334 residues out of total 3810 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 302 time to evaluate : 4.382 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 110 THR Chi-restraints excluded: chain A residue 236 TYR Chi-restraints excluded: chain A residue 406 PHE Chi-restraints excluded: chain A residue 422 ASP Chi-restraints excluded: chain A residue 504 LEU Chi-restraints excluded: chain B residue 52 MET Chi-restraints excluded: chain B residue 413 LEU Chi-restraints excluded: chain C residue 48 MET Chi-restraints excluded: chain C residue 110 THR Chi-restraints excluded: chain C residue 187 ARG Chi-restraints excluded: chain C residue 236 TYR Chi-restraints excluded: chain C residue 409 PHE Chi-restraints excluded: chain D residue 205 VAL Chi-restraints excluded: chain D residue 338 ASP Chi-restraints excluded: chain D residue 348 VAL Chi-restraints excluded: chain E residue 46 LEU Chi-restraints excluded: chain E residue 88 MET Chi-restraints excluded: chain F residue 265 VAL Chi-restraints excluded: chain G residue 114 LEU Chi-restraints excluded: chain H residue 29 GLU Chi-restraints excluded: chain J residue 66 ILE Chi-restraints excluded: chain L residue 6 MET Chi-restraints excluded: chain L residue 10 TYR Chi-restraints excluded: chain L residue 15 VAL Chi-restraints excluded: chain L residue 60 VAL Chi-restraints excluded: chain L residue 78 VAL Chi-restraints excluded: chain M residue 57 MET Chi-restraints excluded: chain M residue 59 LEU Chi-restraints excluded: chain O residue 3 ASN Chi-restraints excluded: chain Q residue 63 ILE Chi-restraints excluded: chain X residue 129 VAL Chi-restraints excluded: chain Y residue 141 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 470 random chunks: chunk 378 optimal weight: 5.9990 chunk 257 optimal weight: 2.9990 chunk 6 optimal weight: 0.8980 chunk 338 optimal weight: 10.0000 chunk 187 optimal weight: 0.9980 chunk 387 optimal weight: 0.2980 chunk 314 optimal weight: 7.9990 chunk 0 optimal weight: 10.0000 chunk 231 optimal weight: 10.0000 chunk 407 optimal weight: 7.9990 chunk 114 optimal weight: 7.9990 overall best weight: 2.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 3 ASN S 42 GLN Y 104 GLN ** a 42 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8439 moved from start: 0.3964 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 37231 Z= 0.233 Angle : 0.550 14.232 50399 Z= 0.280 Chirality : 0.041 0.250 5875 Planarity : 0.004 0.050 6501 Dihedral : 6.574 118.701 5328 Min Nonbonded Distance : 1.897 Molprobity Statistics. All-atom Clashscore : 7.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Rotamer: Outliers : 1.79 % Allowed : 11.25 % Favored : 86.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.47 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.07 (0.12), residues: 4770 helix: 1.30 (0.10), residues: 2581 sheet: 0.92 (0.22), residues: 518 loop : -0.17 (0.15), residues: 1671 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP a 235 HIS 0.004 0.001 HIS a 132 PHE 0.021 0.001 PHE R 53 TYR 0.020 0.001 TYR a 94 ARG 0.012 0.000 ARG a 140 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9540 Ramachandran restraints generated. 4770 Oldfield, 0 Emsley, 4770 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9540 Ramachandran restraints generated. 4770 Oldfield, 0 Emsley, 4770 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 389 residues out of total 3810 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 321 time to evaluate : 4.517 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 MET cc_start: 0.8882 (mtp) cc_final: 0.8612 (mtm) REVERT: A 236 TYR cc_start: 0.9444 (OUTLIER) cc_final: 0.8446 (t80) REVERT: A 289 ASP cc_start: 0.7897 (t0) cc_final: 0.7557 (t0) REVERT: D 224 LEU cc_start: 0.9432 (OUTLIER) cc_final: 0.9132 (tt) REVERT: E 56 MET cc_start: 0.9232 (mmt) cc_final: 0.8848 (mmt) REVERT: E 445 MET cc_start: 0.8287 (mmm) cc_final: 0.8055 (mmm) REVERT: F 445 MET cc_start: 0.8831 (mmt) cc_final: 0.8386 (mmt) REVERT: H 70 GLU cc_start: 0.8258 (pt0) cc_final: 0.7694 (pp20) REVERT: M 6 MET cc_start: 0.7476 (mtt) cc_final: 0.7217 (ppp) REVERT: M 16 MET cc_start: 0.6165 (mmm) cc_final: 0.5492 (mmm) REVERT: M 31 LEU cc_start: 0.6156 (tp) cc_final: 0.5735 (mt) REVERT: M 54 PHE cc_start: 0.6079 (m-10) cc_final: 0.4872 (t80) REVERT: M 65 MET cc_start: 0.7599 (tpp) cc_final: 0.7228 (ptm) REVERT: N 41 ARG cc_start: 0.7968 (mtt90) cc_final: 0.7610 (ttp-170) REVERT: O 75 MET cc_start: 0.3013 (ttt) cc_final: 0.2658 (tmm) REVERT: P 17 MET cc_start: 0.4591 (ttm) cc_final: 0.3986 (tpp) REVERT: P 44 ASP cc_start: 0.8330 (m-30) cc_final: 0.7847 (p0) REVERT: R 28 ILE cc_start: 0.7602 (mm) cc_final: 0.7195 (tt) REVERT: W 111 ILE cc_start: 0.9352 (OUTLIER) cc_final: 0.8723 (tp) REVERT: W 137 LYS cc_start: 0.8303 (tmtt) cc_final: 0.8059 (tptp) REVERT: X 26 TRP cc_start: 0.3946 (m100) cc_final: 0.3087 (m100) REVERT: X 30 MET cc_start: 0.2654 (mmt) cc_final: 0.1896 (mmt) REVERT: Y 150 ASP cc_start: 0.8025 (OUTLIER) cc_final: 0.7723 (t0) REVERT: a 6 MET cc_start: 0.0383 (ppp) cc_final: -0.0511 (ppp) REVERT: a 119 ASP cc_start: 0.7094 (t0) cc_final: 0.6746 (m-30) REVERT: a 168 MET cc_start: 0.5763 (mmt) cc_final: 0.5521 (mmt) REVERT: a 177 GLU cc_start: 0.4867 (mt-10) cc_final: 0.4460 (tm-30) REVERT: a 235 TRP cc_start: 0.3643 (p-90) cc_final: 0.3047 (p-90) REVERT: a 263 TYR cc_start: 0.6754 (m-10) cc_final: 0.6534 (m-10) REVERT: a 269 GLU cc_start: 0.5650 (OUTLIER) cc_final: 0.4711 (mm-30) outliers start: 68 outliers final: 41 residues processed: 372 average time/residue: 0.4861 time to fit residues: 301.9660 Evaluate side-chains 339 residues out of total 3810 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 293 time to evaluate : 4.299 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 110 THR Chi-restraints excluded: chain A residue 236 TYR Chi-restraints excluded: chain A residue 406 PHE Chi-restraints excluded: chain A residue 422 ASP Chi-restraints excluded: chain A residue 504 LEU Chi-restraints excluded: chain B residue 146 VAL Chi-restraints excluded: chain B residue 413 LEU Chi-restraints excluded: chain C residue 48 MET Chi-restraints excluded: chain C residue 110 THR Chi-restraints excluded: chain C residue 187 ARG Chi-restraints excluded: chain C residue 236 TYR Chi-restraints excluded: chain C residue 409 PHE Chi-restraints excluded: chain D residue 224 LEU Chi-restraints excluded: chain D residue 338 ASP Chi-restraints excluded: chain D residue 348 VAL Chi-restraints excluded: chain E residue 46 LEU Chi-restraints excluded: chain E residue 88 MET Chi-restraints excluded: chain E residue 215 ASN Chi-restraints excluded: chain E residue 411 THR Chi-restraints excluded: chain F residue 215 ASN Chi-restraints excluded: chain F residue 265 VAL Chi-restraints excluded: chain G residue 114 LEU Chi-restraints excluded: chain G residue 132 VAL Chi-restraints excluded: chain H residue 29 GLU Chi-restraints excluded: chain H residue 56 HIS Chi-restraints excluded: chain I residue 51 THR Chi-restraints excluded: chain L residue 6 MET Chi-restraints excluded: chain L residue 10 TYR Chi-restraints excluded: chain L residue 15 VAL Chi-restraints excluded: chain L residue 60 VAL Chi-restraints excluded: chain L residue 78 VAL Chi-restraints excluded: chain M residue 57 MET Chi-restraints excluded: chain M residue 59 LEU Chi-restraints excluded: chain O residue 3 ASN Chi-restraints excluded: chain O residue 66 ILE Chi-restraints excluded: chain Q residue 55 ILE Chi-restraints excluded: chain S residue 44 ASP Chi-restraints excluded: chain W residue 111 ILE Chi-restraints excluded: chain X residue 18 VAL Chi-restraints excluded: chain X residue 22 MET Chi-restraints excluded: chain X residue 129 VAL Chi-restraints excluded: chain X residue 140 VAL Chi-restraints excluded: chain Y residue 141 ASP Chi-restraints excluded: chain Y residue 150 ASP Chi-restraints excluded: chain a residue 247 LEU Chi-restraints excluded: chain a residue 269 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 470 random chunks: chunk 152 optimal weight: 5.9990 chunk 409 optimal weight: 3.9990 chunk 89 optimal weight: 0.7980 chunk 266 optimal weight: 6.9990 chunk 112 optimal weight: 4.9990 chunk 454 optimal weight: 20.0000 chunk 377 optimal weight: 20.0000 chunk 210 optimal weight: 9.9990 chunk 37 optimal weight: 10.0000 chunk 150 optimal weight: 6.9990 chunk 238 optimal weight: 5.9990 overall best weight: 4.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 425 GLN ** D 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 361 GLN G 135 GLN ** P 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 5 ASN X 123 GLN a 14 HIS ** a 42 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8497 moved from start: 0.4393 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.054 37231 Z= 0.393 Angle : 0.630 9.929 50399 Z= 0.322 Chirality : 0.044 0.244 5875 Planarity : 0.004 0.052 6501 Dihedral : 6.780 119.758 5328 Min Nonbonded Distance : 1.841 Molprobity Statistics. All-atom Clashscore : 8.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 2.13 % Allowed : 11.83 % Favored : 86.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.47 % 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: 0.91 (0.12), residues: 4770 helix: 1.22 (0.10), residues: 2597 sheet: 0.78 (0.22), residues: 511 loop : -0.33 (0.15), residues: 1662 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP G 203 HIS 0.006 0.001 HIS F 73 PHE 0.020 0.002 PHE R 53 TYR 0.020 0.002 TYR a 94 ARG 0.010 0.001 ARG A 401 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9540 Ramachandran restraints generated. 4770 Oldfield, 0 Emsley, 4770 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9540 Ramachandran restraints generated. 4770 Oldfield, 0 Emsley, 4770 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 383 residues out of total 3810 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 81 poor density : 302 time to evaluate : 4.734 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: A 52 MET cc_start: 0.8919 (mtp) cc_final: 0.8654 (mtm) REVERT: A 236 TYR cc_start: 0.9567 (OUTLIER) cc_final: 0.8982 (t80) REVERT: A 289 ASP cc_start: 0.8058 (t0) cc_final: 0.7817 (t0) REVERT: D 224 LEU cc_start: 0.9493 (OUTLIER) cc_final: 0.9237 (tt) REVERT: E 445 MET cc_start: 0.8371 (mmm) cc_final: 0.8034 (mmm) REVERT: F 445 MET cc_start: 0.8824 (mmt) cc_final: 0.8399 (mmt) REVERT: G 38 MET cc_start: 0.8950 (ttp) cc_final: 0.8622 (ttm) REVERT: G 106 THR cc_start: 0.8371 (OUTLIER) cc_final: 0.8130 (p) REVERT: G 203 TRP cc_start: 0.5982 (m-90) cc_final: 0.5626 (m-90) REVERT: H 70 GLU cc_start: 0.8157 (pt0) cc_final: 0.7568 (pp20) REVERT: H 93 ARG cc_start: 0.8638 (tpt170) cc_final: 0.8327 (tpp80) REVERT: I 75 MET cc_start: 0.2871 (OUTLIER) cc_final: 0.2421 (mtp) REVERT: M 6 MET cc_start: 0.7479 (mtt) cc_final: 0.7232 (ppp) REVERT: M 17 MET cc_start: 0.4353 (mtm) cc_final: 0.3877 (tmm) REVERT: M 54 PHE cc_start: 0.6330 (m-10) cc_final: 0.5156 (t80) REVERT: M 65 MET cc_start: 0.7510 (tpp) cc_final: 0.7164 (ptm) REVERT: N 37 GLU cc_start: 0.6486 (mp0) cc_final: 0.6247 (mp0) REVERT: N 41 ARG cc_start: 0.7950 (mtt90) cc_final: 0.7606 (ttp-170) REVERT: O 75 MET cc_start: 0.3115 (ttt) cc_final: 0.2740 (tmm) REVERT: P 17 MET cc_start: 0.4610 (ttm) cc_final: 0.4224 (tpp) REVERT: P 44 ASP cc_start: 0.8428 (m-30) cc_final: 0.7912 (p0) REVERT: W 111 ILE cc_start: 0.9389 (OUTLIER) cc_final: 0.8718 (tp) REVERT: W 137 LYS cc_start: 0.8215 (tmtt) cc_final: 0.7995 (tptp) REVERT: X 26 TRP cc_start: 0.4078 (m100) cc_final: 0.3256 (m100) REVERT: X 30 MET cc_start: 0.3022 (mmt) cc_final: 0.2261 (mmt) REVERT: Y 123 GLN cc_start: 0.8698 (mt0) cc_final: 0.8429 (mt0) REVERT: Y 150 ASP cc_start: 0.8241 (OUTLIER) cc_final: 0.7955 (t0) REVERT: a 6 MET cc_start: 0.0257 (ppp) cc_final: -0.0191 (ppp) REVERT: a 79 ILE cc_start: 0.3575 (OUTLIER) cc_final: 0.3341 (tt) REVERT: a 119 ASP cc_start: 0.7254 (t0) cc_final: 0.6872 (m-30) REVERT: a 177 GLU cc_start: 0.4760 (mt-10) cc_final: 0.4329 (tm-30) REVERT: a 215 MET cc_start: 0.6661 (mmp) cc_final: 0.6324 (mmp) REVERT: a 235 TRP cc_start: 0.3514 (p-90) cc_final: 0.2897 (p-90) REVERT: a 257 MET cc_start: 0.7697 (ppp) cc_final: 0.7464 (ppp) REVERT: a 269 GLU cc_start: 0.5594 (OUTLIER) cc_final: 0.4729 (mm-30) outliers start: 81 outliers final: 51 residues processed: 365 average time/residue: 0.4674 time to fit residues: 287.3781 Evaluate side-chains 347 residues out of total 3810 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 288 time to evaluate : 4.502 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 VAL Chi-restraints excluded: chain A residue 110 THR Chi-restraints excluded: chain A residue 236 TYR Chi-restraints excluded: chain A residue 406 PHE Chi-restraints excluded: chain A residue 422 ASP Chi-restraints excluded: chain A residue 425 GLN Chi-restraints excluded: chain A residue 468 GLU Chi-restraints excluded: chain A residue 504 LEU Chi-restraints excluded: chain B residue 110 THR Chi-restraints excluded: chain B residue 146 VAL Chi-restraints excluded: chain B residue 397 LEU Chi-restraints excluded: chain B residue 413 LEU Chi-restraints excluded: chain B residue 513 TRP Chi-restraints excluded: chain C residue 48 MET Chi-restraints excluded: chain C residue 110 THR Chi-restraints excluded: chain C residue 187 ARG Chi-restraints excluded: chain C residue 236 TYR Chi-restraints excluded: chain C residue 409 PHE Chi-restraints excluded: chain D residue 224 LEU Chi-restraints excluded: chain D residue 348 VAL Chi-restraints excluded: chain E residue 46 LEU Chi-restraints excluded: chain E residue 88 MET Chi-restraints excluded: chain E residue 411 THR Chi-restraints excluded: chain F residue 132 VAL Chi-restraints excluded: chain F residue 205 VAL Chi-restraints excluded: chain F residue 215 ASN Chi-restraints excluded: chain F residue 265 VAL Chi-restraints excluded: chain F residue 423 THR Chi-restraints excluded: chain G residue 106 THR Chi-restraints excluded: chain G residue 114 LEU Chi-restraints excluded: chain G residue 132 VAL Chi-restraints excluded: chain H residue 29 GLU Chi-restraints excluded: chain H residue 56 HIS Chi-restraints excluded: chain H residue 77 THR Chi-restraints excluded: chain I residue 51 THR Chi-restraints excluded: chain I residue 75 MET Chi-restraints excluded: chain J residue 66 ILE Chi-restraints excluded: chain L residue 10 TYR Chi-restraints excluded: chain L residue 15 VAL Chi-restraints excluded: chain L residue 60 VAL Chi-restraints excluded: chain L residue 78 VAL Chi-restraints excluded: chain M residue 57 MET Chi-restraints excluded: chain M residue 59 LEU Chi-restraints excluded: chain O residue 3 ASN Chi-restraints excluded: chain O residue 66 ILE Chi-restraints excluded: chain Q residue 55 ILE Chi-restraints excluded: chain Q residue 63 ILE Chi-restraints excluded: chain S residue 3 ASN Chi-restraints excluded: chain S residue 44 ASP Chi-restraints excluded: chain W residue 111 ILE Chi-restraints excluded: chain X residue 18 VAL Chi-restraints excluded: chain X residue 22 MET Chi-restraints excluded: chain X residue 129 VAL Chi-restraints excluded: chain X residue 140 VAL Chi-restraints excluded: chain Y residue 141 ASP Chi-restraints excluded: chain Y residue 150 ASP Chi-restraints excluded: chain a residue 79 ILE Chi-restraints excluded: chain a residue 247 LEU Chi-restraints excluded: chain a residue 269 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 470 random chunks: chunk 438 optimal weight: 9.9990 chunk 51 optimal weight: 0.7980 chunk 259 optimal weight: 2.9990 chunk 332 optimal weight: 7.9990 chunk 257 optimal weight: 5.9990 chunk 382 optimal weight: 20.0000 chunk 253 optimal weight: 0.1980 chunk 453 optimal weight: 30.0000 chunk 283 optimal weight: 0.7980 chunk 276 optimal weight: 1.9990 chunk 209 optimal weight: 6.9990 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 27 ASN ** D 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 3 ASN ** a 42 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8456 moved from start: 0.4519 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 37231 Z= 0.178 Angle : 0.550 10.169 50399 Z= 0.277 Chirality : 0.041 0.231 5875 Planarity : 0.004 0.051 6501 Dihedral : 6.461 118.039 5328 Min Nonbonded Distance : 1.956 Molprobity Statistics. All-atom Clashscore : 8.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 1.50 % Allowed : 12.43 % Favored : 86.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.47 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.09 (0.12), residues: 4770 helix: 1.38 (0.10), residues: 2589 sheet: 0.88 (0.22), residues: 511 loop : -0.27 (0.15), residues: 1670 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP G 203 HIS 0.003 0.001 HIS B 479 PHE 0.021 0.001 PHE O 53 TYR 0.022 0.001 TYR a 94 ARG 0.010 0.000 ARG X 115 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9540 Ramachandran restraints generated. 4770 Oldfield, 0 Emsley, 4770 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9540 Ramachandran restraints generated. 4770 Oldfield, 0 Emsley, 4770 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 370 residues out of total 3810 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 313 time to evaluate : 4.591 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 MET cc_start: 0.8870 (mtp) cc_final: 0.8603 (mtm) REVERT: A 236 TYR cc_start: 0.9499 (OUTLIER) cc_final: 0.8864 (t80) REVERT: A 289 ASP cc_start: 0.7914 (t0) cc_final: 0.7610 (t0) REVERT: D 224 LEU cc_start: 0.9408 (OUTLIER) cc_final: 0.9151 (tt) REVERT: D 340 THR cc_start: 0.8548 (m) cc_final: 0.8161 (p) REVERT: E 445 MET cc_start: 0.8286 (mmm) cc_final: 0.7980 (mmm) REVERT: G 200 HIS cc_start: 0.7382 (m170) cc_final: 0.7128 (m-70) REVERT: H 46 LYS cc_start: 0.8882 (mtmt) cc_final: 0.8583 (mtmm) REVERT: H 63 TYR cc_start: 0.8661 (t80) cc_final: 0.8400 (t80) REVERT: H 70 GLU cc_start: 0.8137 (pt0) cc_final: 0.7532 (pp20) REVERT: M 17 MET cc_start: 0.3966 (mtm) cc_final: 0.3631 (tmm) REVERT: M 31 LEU cc_start: 0.5811 (tp) cc_final: 0.5439 (mt) REVERT: M 54 PHE cc_start: 0.6568 (m-10) cc_final: 0.5363 (t80) REVERT: M 65 MET cc_start: 0.7632 (tpp) cc_final: 0.7339 (ptm) REVERT: N 37 GLU cc_start: 0.6539 (mp0) cc_final: 0.5745 (mp0) REVERT: N 41 ARG cc_start: 0.7837 (mtt90) cc_final: 0.7407 (ttp-170) REVERT: O 75 MET cc_start: 0.2920 (ttt) cc_final: 0.2631 (tmm) REVERT: P 17 MET cc_start: 0.4435 (ttm) cc_final: 0.3946 (tpp) REVERT: P 44 ASP cc_start: 0.8462 (m-30) cc_final: 0.7937 (p0) REVERT: Q 65 MET cc_start: 0.6538 (mmp) cc_final: 0.6240 (mpp) REVERT: R 28 ILE cc_start: 0.7553 (mm) cc_final: 0.7137 (tt) REVERT: W 111 ILE cc_start: 0.9379 (OUTLIER) cc_final: 0.8720 (tp) REVERT: W 137 LYS cc_start: 0.8225 (tmtt) cc_final: 0.7989 (tptp) REVERT: X 26 TRP cc_start: 0.4271 (m100) cc_final: 0.3237 (m100) REVERT: X 30 MET cc_start: 0.3070 (mmt) cc_final: 0.2383 (mmt) REVERT: Y 150 ASP cc_start: 0.8253 (OUTLIER) cc_final: 0.7966 (t0) REVERT: a 6 MET cc_start: 0.0478 (ppp) cc_final: 0.0061 (ppp) REVERT: a 177 GLU cc_start: 0.4842 (mt-10) cc_final: 0.4421 (tm-30) REVERT: a 235 TRP cc_start: 0.3538 (p-90) cc_final: 0.2944 (p-90) REVERT: a 269 GLU cc_start: 0.5581 (OUTLIER) cc_final: 0.4743 (mm-30) outliers start: 57 outliers final: 42 residues processed: 357 average time/residue: 0.4694 time to fit residues: 282.0432 Evaluate side-chains 345 residues out of total 3810 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 298 time to evaluate : 4.716 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 VAL Chi-restraints excluded: chain A residue 110 THR Chi-restraints excluded: chain A residue 236 TYR Chi-restraints excluded: chain A residue 406 PHE Chi-restraints excluded: chain A residue 415 ASP Chi-restraints excluded: chain A residue 422 ASP Chi-restraints excluded: chain A residue 504 LEU Chi-restraints excluded: chain B residue 52 MET Chi-restraints excluded: chain B residue 146 VAL Chi-restraints excluded: chain B residue 413 LEU Chi-restraints excluded: chain C residue 48 MET Chi-restraints excluded: chain C residue 110 THR Chi-restraints excluded: chain C residue 129 VAL Chi-restraints excluded: chain C residue 187 ARG Chi-restraints excluded: chain C residue 236 TYR Chi-restraints excluded: chain C residue 409 PHE Chi-restraints excluded: chain D residue 51 VAL Chi-restraints excluded: chain D residue 224 LEU Chi-restraints excluded: chain D residue 338 ASP Chi-restraints excluded: chain D residue 348 VAL Chi-restraints excluded: chain E residue 88 MET Chi-restraints excluded: chain F residue 132 VAL Chi-restraints excluded: chain F residue 205 VAL Chi-restraints excluded: chain F residue 265 VAL Chi-restraints excluded: chain G residue 23 MET Chi-restraints excluded: chain G residue 114 LEU Chi-restraints excluded: chain G residue 132 VAL Chi-restraints excluded: chain H residue 29 GLU Chi-restraints excluded: chain H residue 77 THR Chi-restraints excluded: chain J residue 66 ILE Chi-restraints excluded: chain L residue 10 TYR Chi-restraints excluded: chain L residue 60 VAL Chi-restraints excluded: chain L residue 78 VAL Chi-restraints excluded: chain M residue 57 MET Chi-restraints excluded: chain M residue 59 LEU Chi-restraints excluded: chain O residue 30 ILE Chi-restraints excluded: chain Q residue 55 ILE Chi-restraints excluded: chain Q residue 63 ILE Chi-restraints excluded: chain S residue 3 ASN Chi-restraints excluded: chain W residue 111 ILE Chi-restraints excluded: chain X residue 22 MET Chi-restraints excluded: chain X residue 129 VAL Chi-restraints excluded: chain X residue 140 VAL Chi-restraints excluded: chain Y residue 141 ASP Chi-restraints excluded: chain Y residue 150 ASP Chi-restraints excluded: chain a residue 247 LEU Chi-restraints excluded: chain a residue 269 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 470 random chunks: chunk 280 optimal weight: 2.9990 chunk 180 optimal weight: 8.9990 chunk 270 optimal weight: 1.9990 chunk 136 optimal weight: 2.9990 chunk 89 optimal weight: 0.7980 chunk 87 optimal weight: 0.0970 chunk 288 optimal weight: 9.9990 chunk 308 optimal weight: 20.0000 chunk 223 optimal weight: 7.9990 chunk 42 optimal weight: 2.9990 chunk 356 optimal weight: 6.9990 overall best weight: 1.7784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 425 GLN ** D 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 42 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 185 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8458 moved from start: 0.4659 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 37231 Z= 0.203 Angle : 0.557 11.598 50399 Z= 0.280 Chirality : 0.041 0.232 5875 Planarity : 0.004 0.052 6501 Dihedral : 6.318 116.469 5328 Min Nonbonded Distance : 1.932 Molprobity Statistics. All-atom Clashscore : 8.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 1.55 % Allowed : 12.64 % Favored : 85.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.47 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.13 (0.12), residues: 4770 helix: 1.44 (0.10), residues: 2589 sheet: 0.88 (0.22), residues: 509 loop : -0.30 (0.15), residues: 1672 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP G 203 HIS 0.004 0.001 HIS a 185 PHE 0.020 0.001 PHE R 53 TYR 0.021 0.001 TYR a 94 ARG 0.008 0.000 ARG Y 36 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9540 Ramachandran restraints generated. 4770 Oldfield, 0 Emsley, 4770 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9540 Ramachandran restraints generated. 4770 Oldfield, 0 Emsley, 4770 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 362 residues out of total 3810 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 303 time to evaluate : 4.287 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: A 52 MET cc_start: 0.8859 (mtp) cc_final: 0.8588 (mtm) REVERT: A 236 TYR cc_start: 0.9489 (OUTLIER) cc_final: 0.8732 (t80) REVERT: A 289 ASP cc_start: 0.7878 (t0) cc_final: 0.7593 (t0) REVERT: D 224 LEU cc_start: 0.9385 (OUTLIER) cc_final: 0.9086 (tt) REVERT: D 340 THR cc_start: 0.8544 (m) cc_final: 0.8156 (p) REVERT: E 445 MET cc_start: 0.8314 (mmm) cc_final: 0.8005 (mmm) REVERT: G 38 MET cc_start: 0.8843 (ttp) cc_final: 0.8488 (ttm) REVERT: G 200 HIS cc_start: 0.7345 (m170) cc_final: 0.7143 (m-70) REVERT: H 70 GLU cc_start: 0.8119 (pt0) cc_final: 0.7473 (pp20) REVERT: I 57 MET cc_start: 0.5844 (ttp) cc_final: 0.5555 (mtp) REVERT: I 75 MET cc_start: 0.2843 (OUTLIER) cc_final: 0.2303 (mtp) REVERT: M 31 LEU cc_start: 0.5868 (tp) cc_final: 0.5559 (mt) REVERT: M 54 PHE cc_start: 0.6533 (m-10) cc_final: 0.5329 (t80) REVERT: M 65 MET cc_start: 0.7672 (tpp) cc_final: 0.7339 (ptm) REVERT: N 41 ARG cc_start: 0.7924 (mtt90) cc_final: 0.7547 (ttp-170) REVERT: O 17 MET cc_start: 0.5253 (mtm) cc_final: 0.4921 (mtp) REVERT: O 75 MET cc_start: 0.3161 (ttt) cc_final: 0.2959 (tmm) REVERT: P 17 MET cc_start: 0.4419 (ttm) cc_final: 0.3845 (tpp) REVERT: R 28 ILE cc_start: 0.7636 (mm) cc_final: 0.7227 (tt) REVERT: W 111 ILE cc_start: 0.9390 (OUTLIER) cc_final: 0.8731 (tp) REVERT: W 137 LYS cc_start: 0.8029 (tmtt) cc_final: 0.7809 (tptp) REVERT: X 26 TRP cc_start: 0.4398 (m100) cc_final: 0.3289 (m100) REVERT: X 30 MET cc_start: 0.3221 (mmt) cc_final: 0.2434 (mmt) REVERT: Y 150 ASP cc_start: 0.8262 (OUTLIER) cc_final: 0.7976 (t0) REVERT: a 6 MET cc_start: 0.0592 (ppp) cc_final: 0.0173 (ppp) REVERT: a 83 ILE cc_start: 0.5289 (OUTLIER) cc_final: 0.4991 (mt) REVERT: a 177 GLU cc_start: 0.4846 (mt-10) cc_final: 0.4421 (tm-30) REVERT: a 235 TRP cc_start: 0.3492 (p-90) cc_final: 0.2925 (p-90) REVERT: a 257 MET cc_start: 0.7691 (ppp) cc_final: 0.7487 (ppp) REVERT: a 269 GLU cc_start: 0.5526 (OUTLIER) cc_final: 0.4676 (mm-30) outliers start: 59 outliers final: 45 residues processed: 346 average time/residue: 0.4659 time to fit residues: 271.3485 Evaluate side-chains 348 residues out of total 3810 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 296 time to evaluate : 4.298 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 VAL Chi-restraints excluded: chain A residue 110 THR Chi-restraints excluded: chain A residue 236 TYR Chi-restraints excluded: chain A residue 406 PHE Chi-restraints excluded: chain A residue 415 ASP Chi-restraints excluded: chain A residue 422 ASP Chi-restraints excluded: chain A residue 504 LEU Chi-restraints excluded: chain B residue 52 MET Chi-restraints excluded: chain B residue 146 VAL Chi-restraints excluded: chain B residue 413 LEU Chi-restraints excluded: chain C residue 48 MET Chi-restraints excluded: chain C residue 110 THR Chi-restraints excluded: chain C residue 129 VAL Chi-restraints excluded: chain C residue 187 ARG Chi-restraints excluded: chain C residue 236 TYR Chi-restraints excluded: chain C residue 409 PHE Chi-restraints excluded: chain D residue 51 VAL Chi-restraints excluded: chain D residue 224 LEU Chi-restraints excluded: chain D residue 338 ASP Chi-restraints excluded: chain D residue 348 VAL Chi-restraints excluded: chain E residue 46 LEU Chi-restraints excluded: chain E residue 88 MET Chi-restraints excluded: chain F residue 132 VAL Chi-restraints excluded: chain F residue 205 VAL Chi-restraints excluded: chain F residue 265 VAL Chi-restraints excluded: chain G residue 23 MET Chi-restraints excluded: chain G residue 114 LEU Chi-restraints excluded: chain G residue 132 VAL Chi-restraints excluded: chain G residue 169 ILE Chi-restraints excluded: chain H residue 29 GLU Chi-restraints excluded: chain H residue 56 HIS Chi-restraints excluded: chain H residue 77 THR Chi-restraints excluded: chain I residue 75 MET Chi-restraints excluded: chain J residue 66 ILE Chi-restraints excluded: chain L residue 10 TYR Chi-restraints excluded: chain L residue 60 VAL Chi-restraints excluded: chain L residue 78 VAL Chi-restraints excluded: chain M residue 53 PHE Chi-restraints excluded: chain M residue 57 MET Chi-restraints excluded: chain M residue 59 LEU Chi-restraints excluded: chain O residue 3 ASN Chi-restraints excluded: chain Q residue 55 ILE Chi-restraints excluded: chain Q residue 63 ILE Chi-restraints excluded: chain W residue 111 ILE Chi-restraints excluded: chain X residue 22 MET Chi-restraints excluded: chain X residue 129 VAL Chi-restraints excluded: chain X residue 140 VAL Chi-restraints excluded: chain Y residue 141 ASP Chi-restraints excluded: chain Y residue 150 ASP Chi-restraints excluded: chain a residue 83 ILE Chi-restraints excluded: chain a residue 247 LEU Chi-restraints excluded: chain a residue 269 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 470 random chunks: chunk 412 optimal weight: 9.9990 chunk 433 optimal weight: 9.9990 chunk 395 optimal weight: 7.9990 chunk 422 optimal weight: 6.9990 chunk 254 optimal weight: 0.0870 chunk 183 optimal weight: 4.9990 chunk 331 optimal weight: 9.9990 chunk 129 optimal weight: 0.0050 chunk 381 optimal weight: 20.0000 chunk 399 optimal weight: 1.9990 chunk 420 optimal weight: 10.0000 overall best weight: 2.8178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 425 GLN ** D 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 3 ASN ** a 42 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8478 moved from start: 0.4816 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 37231 Z= 0.270 Angle : 0.580 12.346 50399 Z= 0.291 Chirality : 0.042 0.229 5875 Planarity : 0.004 0.051 6501 Dihedral : 6.369 115.244 5328 Min Nonbonded Distance : 1.893 Molprobity Statistics. All-atom Clashscore : 8.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 1.66 % Allowed : 12.72 % Favored : 85.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.47 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.11 (0.12), residues: 4770 helix: 1.42 (0.10), residues: 2599 sheet: 0.84 (0.22), residues: 511 loop : -0.30 (0.15), residues: 1660 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP a 241 HIS 0.004 0.001 HIS F 73 PHE 0.017 0.001 PHE R 53 TYR 0.020 0.001 TYR a 94 ARG 0.008 0.000 ARG Y 36 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9540 Ramachandran restraints generated. 4770 Oldfield, 0 Emsley, 4770 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9540 Ramachandran restraints generated. 4770 Oldfield, 0 Emsley, 4770 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 375 residues out of total 3810 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 312 time to evaluate : 4.596 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 MET cc_start: 0.8888 (mtp) cc_final: 0.8623 (mtm) REVERT: A 236 TYR cc_start: 0.9530 (OUTLIER) cc_final: 0.8976 (t80) REVERT: A 289 ASP cc_start: 0.7909 (t0) cc_final: 0.7623 (t0) REVERT: D 224 LEU cc_start: 0.9407 (OUTLIER) cc_final: 0.9125 (tt) REVERT: D 340 THR cc_start: 0.8615 (m) cc_final: 0.8268 (p) REVERT: E 445 MET cc_start: 0.8337 (mmm) cc_final: 0.8000 (mmm) REVERT: G 38 MET cc_start: 0.8928 (ttp) cc_final: 0.8571 (ttm) REVERT: G 105 TRP cc_start: 0.8337 (m100) cc_final: 0.8004 (m100) REVERT: G 200 HIS cc_start: 0.7368 (m170) cc_final: 0.7105 (m-70) REVERT: H 70 GLU cc_start: 0.8179 (pt0) cc_final: 0.7521 (pp20) REVERT: I 75 MET cc_start: 0.2788 (OUTLIER) cc_final: 0.2242 (mtp) REVERT: M 31 LEU cc_start: 0.5912 (tp) cc_final: 0.5536 (mt) REVERT: M 54 PHE cc_start: 0.6360 (m-10) cc_final: 0.5159 (t80) REVERT: M 65 MET cc_start: 0.7536 (tpp) cc_final: 0.7305 (ptm) REVERT: N 41 ARG cc_start: 0.7918 (mtt90) cc_final: 0.7531 (ttp-170) REVERT: O 17 MET cc_start: 0.5259 (mtm) cc_final: 0.4839 (mtp) REVERT: P 17 MET cc_start: 0.4544 (ttm) cc_final: 0.3941 (tpp) REVERT: P 65 MET cc_start: 0.4041 (mmp) cc_final: 0.3534 (mmp) REVERT: Q 65 MET cc_start: 0.6515 (mmp) cc_final: 0.6313 (mpp) REVERT: R 28 ILE cc_start: 0.7671 (mm) cc_final: 0.7311 (tt) REVERT: S 3 ASN cc_start: 0.3366 (OUTLIER) cc_final: 0.3035 (p0) REVERT: X 26 TRP cc_start: 0.4446 (m100) cc_final: 0.3352 (m100) REVERT: X 30 MET cc_start: 0.3252 (mmt) cc_final: 0.2483 (mmt) REVERT: Y 150 ASP cc_start: 0.8288 (OUTLIER) cc_final: 0.8001 (t0) REVERT: a 6 MET cc_start: 0.0817 (ppp) cc_final: 0.0381 (ppp) REVERT: a 83 ILE cc_start: 0.5404 (OUTLIER) cc_final: 0.5110 (mt) REVERT: a 177 GLU cc_start: 0.4749 (mt-10) cc_final: 0.4318 (tm-30) REVERT: a 235 TRP cc_start: 0.3540 (p-90) cc_final: 0.2969 (p-90) REVERT: a 257 MET cc_start: 0.7723 (ppp) cc_final: 0.7209 (ppp) REVERT: a 269 GLU cc_start: 0.5566 (OUTLIER) cc_final: 0.4703 (mm-30) outliers start: 63 outliers final: 48 residues processed: 360 average time/residue: 0.4657 time to fit residues: 282.1269 Evaluate side-chains 357 residues out of total 3810 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 302 time to evaluate : 4.300 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 VAL Chi-restraints excluded: chain A residue 110 THR Chi-restraints excluded: chain A residue 236 TYR Chi-restraints excluded: chain A residue 406 PHE Chi-restraints excluded: chain A residue 422 ASP Chi-restraints excluded: chain A residue 425 GLN Chi-restraints excluded: chain A residue 504 LEU Chi-restraints excluded: chain B residue 52 MET Chi-restraints excluded: chain B residue 146 VAL Chi-restraints excluded: chain B residue 397 LEU Chi-restraints excluded: chain B residue 413 LEU Chi-restraints excluded: chain B residue 513 TRP Chi-restraints excluded: chain C residue 48 MET Chi-restraints excluded: chain C residue 110 THR Chi-restraints excluded: chain C residue 129 VAL Chi-restraints excluded: chain C residue 187 ARG Chi-restraints excluded: chain C residue 236 TYR Chi-restraints excluded: chain C residue 409 PHE Chi-restraints excluded: chain D residue 51 VAL Chi-restraints excluded: chain D residue 224 LEU Chi-restraints excluded: chain D residue 348 VAL Chi-restraints excluded: chain E residue 88 MET Chi-restraints excluded: chain E residue 215 ASN Chi-restraints excluded: chain F residue 132 VAL Chi-restraints excluded: chain F residue 205 VAL Chi-restraints excluded: chain F residue 215 ASN Chi-restraints excluded: chain F residue 265 VAL Chi-restraints excluded: chain F residue 423 THR Chi-restraints excluded: chain G residue 114 LEU Chi-restraints excluded: chain G residue 132 VAL Chi-restraints excluded: chain G residue 169 ILE Chi-restraints excluded: chain H residue 29 GLU Chi-restraints excluded: chain H residue 56 HIS Chi-restraints excluded: chain H residue 77 THR Chi-restraints excluded: chain I residue 75 MET Chi-restraints excluded: chain L residue 15 VAL Chi-restraints excluded: chain L residue 60 VAL Chi-restraints excluded: chain L residue 78 VAL Chi-restraints excluded: chain M residue 57 MET Chi-restraints excluded: chain M residue 59 LEU Chi-restraints excluded: chain O residue 3 ASN Chi-restraints excluded: chain O residue 30 ILE Chi-restraints excluded: chain Q residue 51 THR Chi-restraints excluded: chain Q residue 55 ILE Chi-restraints excluded: chain Q residue 63 ILE Chi-restraints excluded: chain S residue 3 ASN Chi-restraints excluded: chain X residue 22 MET Chi-restraints excluded: chain X residue 129 VAL Chi-restraints excluded: chain X residue 140 VAL Chi-restraints excluded: chain Y residue 141 ASP Chi-restraints excluded: chain Y residue 150 ASP Chi-restraints excluded: chain a residue 83 ILE Chi-restraints excluded: chain a residue 216 TYR Chi-restraints excluded: chain a residue 247 LEU Chi-restraints excluded: chain a residue 269 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 470 random chunks: chunk 277 optimal weight: 0.9990 chunk 446 optimal weight: 10.0000 chunk 272 optimal weight: 1.9990 chunk 211 optimal weight: 2.9990 chunk 310 optimal weight: 0.8980 chunk 468 optimal weight: 30.0000 chunk 430 optimal weight: 7.9990 chunk 372 optimal weight: 7.9990 chunk 38 optimal weight: 0.7980 chunk 288 optimal weight: 9.9990 chunk 228 optimal weight: 0.6980 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 425 GLN ** D 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 42 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8450 moved from start: 0.4906 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 37231 Z= 0.169 Angle : 0.569 12.981 50399 Z= 0.284 Chirality : 0.041 0.227 5875 Planarity : 0.004 0.055 6501 Dihedral : 6.189 112.653 5328 Min Nonbonded Distance : 1.959 Molprobity Statistics. All-atom Clashscore : 8.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 1.24 % Allowed : 13.40 % Favored : 85.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.47 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.16 (0.12), residues: 4770 helix: 1.46 (0.10), residues: 2592 sheet: 0.92 (0.22), residues: 508 loop : -0.28 (0.15), residues: 1670 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP a 241 HIS 0.003 0.001 HIS a 185 PHE 0.029 0.001 PHE P 35 TYR 0.024 0.001 TYR a 94 ARG 0.009 0.000 ARG Y 36 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9540 Ramachandran restraints generated. 4770 Oldfield, 0 Emsley, 4770 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9540 Ramachandran restraints generated. 4770 Oldfield, 0 Emsley, 4770 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 357 residues out of total 3810 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 310 time to evaluate : 4.291 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 MET cc_start: 0.8863 (mtp) cc_final: 0.8591 (mtm) REVERT: A 236 TYR cc_start: 0.9463 (OUTLIER) cc_final: 0.8832 (t80) REVERT: A 289 ASP cc_start: 0.7834 (t0) cc_final: 0.7564 (t0) REVERT: C 48 MET cc_start: 0.8518 (OUTLIER) cc_final: 0.8244 (ptp) REVERT: D 224 LEU cc_start: 0.9335 (OUTLIER) cc_final: 0.9031 (tt) REVERT: D 340 THR cc_start: 0.8523 (m) cc_final: 0.8119 (p) REVERT: E 445 MET cc_start: 0.8298 (mmm) cc_final: 0.7992 (mmm) REVERT: G 38 MET cc_start: 0.8833 (ttp) cc_final: 0.8473 (ttm) REVERT: G 105 TRP cc_start: 0.8289 (m100) cc_final: 0.8002 (m100) REVERT: G 200 HIS cc_start: 0.7359 (m170) cc_final: 0.7106 (m-70) REVERT: H 70 GLU cc_start: 0.8194 (pt0) cc_final: 0.7479 (pp20) REVERT: I 57 MET cc_start: 0.5796 (ttp) cc_final: 0.5465 (mtp) REVERT: I 75 MET cc_start: 0.2766 (OUTLIER) cc_final: 0.2238 (mtp) REVERT: M 31 LEU cc_start: 0.5893 (tp) cc_final: 0.5534 (mt) REVERT: M 54 PHE cc_start: 0.6356 (m-10) cc_final: 0.5167 (t80) REVERT: M 65 MET cc_start: 0.7513 (tpp) cc_final: 0.7296 (ptm) REVERT: N 41 ARG cc_start: 0.7902 (mtt90) cc_final: 0.7513 (ttp-170) REVERT: O 17 MET cc_start: 0.5170 (mtm) cc_final: 0.3057 (tpt) REVERT: P 17 MET cc_start: 0.4448 (ttm) cc_final: 0.4148 (tpp) REVERT: Q 65 MET cc_start: 0.6515 (mmp) cc_final: 0.6287 (mpp) REVERT: R 28 ILE cc_start: 0.7678 (mm) cc_final: 0.7314 (tt) REVERT: W 111 ILE cc_start: 0.9390 (pt) cc_final: 0.8812 (tp) REVERT: X 26 TRP cc_start: 0.4312 (m100) cc_final: 0.3271 (m100) REVERT: X 30 MET cc_start: 0.3232 (mmt) cc_final: 0.2562 (mmt) REVERT: X 137 GLU cc_start: 0.5381 (mp0) cc_final: 0.4847 (mp0) REVERT: Y 150 ASP cc_start: 0.8223 (OUTLIER) cc_final: 0.7935 (t0) REVERT: a 6 MET cc_start: 0.0793 (ppp) cc_final: 0.0339 (ppp) REVERT: a 115 MET cc_start: 0.3317 (ttt) cc_final: 0.2931 (ttt) REVERT: a 177 GLU cc_start: 0.4741 (mt-10) cc_final: 0.4312 (tm-30) REVERT: a 210 ARG cc_start: 0.9007 (ptt-90) cc_final: 0.8742 (mtm-85) REVERT: a 235 TRP cc_start: 0.3522 (p-90) cc_final: 0.2957 (p-90) REVERT: a 257 MET cc_start: 0.7720 (ppp) cc_final: 0.7205 (ppp) outliers start: 47 outliers final: 37 residues processed: 347 average time/residue: 0.4729 time to fit residues: 274.9370 Evaluate side-chains 345 residues out of total 3810 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 303 time to evaluate : 4.760 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 VAL Chi-restraints excluded: chain A residue 110 THR Chi-restraints excluded: chain A residue 236 TYR Chi-restraints excluded: chain A residue 406 PHE Chi-restraints excluded: chain A residue 422 ASP Chi-restraints excluded: chain A residue 425 GLN Chi-restraints excluded: chain A residue 504 LEU Chi-restraints excluded: chain B residue 146 VAL Chi-restraints excluded: chain B residue 413 LEU Chi-restraints excluded: chain C residue 48 MET Chi-restraints excluded: chain C residue 110 THR Chi-restraints excluded: chain C residue 129 VAL Chi-restraints excluded: chain C residue 187 ARG Chi-restraints excluded: chain C residue 236 TYR Chi-restraints excluded: chain C residue 409 PHE Chi-restraints excluded: chain D residue 51 VAL Chi-restraints excluded: chain D residue 224 LEU Chi-restraints excluded: chain D residue 348 VAL Chi-restraints excluded: chain E residue 277 VAL Chi-restraints excluded: chain F residue 132 VAL Chi-restraints excluded: chain F residue 215 ASN Chi-restraints excluded: chain F residue 265 VAL Chi-restraints excluded: chain F residue 423 THR Chi-restraints excluded: chain G residue 114 LEU Chi-restraints excluded: chain G residue 132 VAL Chi-restraints excluded: chain G residue 169 ILE Chi-restraints excluded: chain H residue 29 GLU Chi-restraints excluded: chain H residue 77 THR Chi-restraints excluded: chain I residue 51 THR Chi-restraints excluded: chain I residue 75 MET Chi-restraints excluded: chain L residue 60 VAL Chi-restraints excluded: chain M residue 57 MET Chi-restraints excluded: chain M residue 59 LEU Chi-restraints excluded: chain O residue 30 ILE Chi-restraints excluded: chain Q residue 55 ILE Chi-restraints excluded: chain Q residue 63 ILE Chi-restraints excluded: chain X residue 22 MET Chi-restraints excluded: chain X residue 129 VAL Chi-restraints excluded: chain X residue 140 VAL Chi-restraints excluded: chain Y residue 141 ASP Chi-restraints excluded: chain Y residue 150 ASP Chi-restraints excluded: chain a residue 247 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 470 random chunks: chunk 296 optimal weight: 4.9990 chunk 397 optimal weight: 4.9990 chunk 114 optimal weight: 0.9990 chunk 343 optimal weight: 40.0000 chunk 55 optimal weight: 0.9990 chunk 103 optimal weight: 9.9990 chunk 373 optimal weight: 5.9990 chunk 156 optimal weight: 6.9990 chunk 383 optimal weight: 7.9990 chunk 47 optimal weight: 4.9990 chunk 68 optimal weight: 5.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 425 GLN ** D 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 52 GLN ** P 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 42 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3813 r_free = 0.3813 target = 0.088255 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 83)----------------| | r_work = 0.2982 r_free = 0.2982 target = 0.052075 restraints weight = 123138.819| |-----------------------------------------------------------------------------| r_work (start): 0.2899 rms_B_bonded: 2.81 r_work: 0.2759 rms_B_bonded: 3.32 restraints_weight: 0.5000 r_work (final): 0.2759 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8614 moved from start: 0.5014 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 37231 Z= 0.324 Angle : 0.606 12.785 50399 Z= 0.305 Chirality : 0.042 0.224 5875 Planarity : 0.004 0.058 6501 Dihedral : 6.348 111.985 5328 Min Nonbonded Distance : 1.856 Molprobity Statistics. All-atom Clashscore : 9.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 1.47 % Allowed : 13.17 % Favored : 85.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.47 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.11 (0.12), residues: 4770 helix: 1.44 (0.10), residues: 2597 sheet: 0.86 (0.22), residues: 510 loop : -0.34 (0.15), residues: 1663 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP a 241 HIS 0.005 0.001 HIS F 73 PHE 0.021 0.001 PHE R 53 TYR 0.024 0.001 TYR a 94 ARG 0.009 0.000 ARG Y 36 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8460.32 seconds wall clock time: 153 minutes 12.55 seconds (9192.55 seconds total)