Starting phenix.real_space_refine on Fri Mar 15 15:09:35 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qsn_14139/03_2024/7qsn_14139_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qsn_14139/03_2024/7qsn_14139.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qsn_14139/03_2024/7qsn_14139_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.81 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qsn_14139/03_2024/7qsn_14139_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qsn_14139/03_2024/7qsn_14139_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qsn_14139/03_2024/7qsn_14139.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qsn_14139/03_2024/7qsn_14139.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qsn_14139/03_2024/7qsn_14139_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qsn_14139/03_2024/7qsn_14139_updated.pdb" } resolution = 2.81 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= -0.001 sd= 0.943 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: 9 Type Number sf(0) Gaussians K 1 8.98 5 Fe 28 7.16 5 Zn 1 6.06 5 P 56 5.49 5 Mg 1 5.21 5 S 469 5.16 5 C 44217 2.51 5 N 11215 2.21 5 O 13331 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 11": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 32": "OE1" <-> "OE2" Residue "A GLU 68": "OE1" <-> "OE2" Residue "A PHE 93": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 35": "OD1" <-> "OD2" Residue "B ARG 71": "NH1" <-> "NH2" Residue "B PHE 72": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 111": "NH1" <-> "NH2" Residue "B TYR 126": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 154": "OE1" <-> "OE2" Residue "B TYR 158": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 174": "NH1" <-> "NH2" Residue "B ARG 178": "NH1" <-> "NH2" Residue "C ARG 8": "NH1" <-> "NH2" Residue "C ARG 12": "NH1" <-> "NH2" Residue "C ASP 16": "OD1" <-> "OD2" Residue "C GLU 31": "OE1" <-> "OE2" Residue "C GLU 49": "OE1" <-> "OE2" Residue "C TYR 124": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 149": "NH1" <-> "NH2" Residue "C PHE 157": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 166": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 173": "OE1" <-> "OE2" Residue "C GLU 179": "OE1" <-> "OE2" Residue "C GLU 186": "OE1" <-> "OE2" Residue "C PHE 194": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 107": "OD1" <-> "OD2" Residue "D GLU 123": "OE1" <-> "OE2" Residue "D PHE 141": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 160": "OD1" <-> "OD2" Residue "D PHE 168": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 179": "OE1" <-> "OE2" Residue "D ARG 221": "NH1" <-> "NH2" Residue "D ARG 233": "NH1" <-> "NH2" Residue "D GLU 248": "OE1" <-> "OE2" Residue "D GLU 282": "OE1" <-> "OE2" Residue "D GLU 343": "OE1" <-> "OE2" Residue "D ASP 403": "OD1" <-> "OD2" Residue "D ASP 422": "OD1" <-> "OD2" Residue "D PHE 425": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 427": "OE1" <-> "OE2" Residue "E ASP 11": "OD1" <-> "OD2" Residue "E GLU 14": "OE1" <-> "OE2" Residue "E GLU 71": "OE1" <-> "OE2" Residue "E ASP 158": "OD1" <-> "OD2" Residue "E GLU 171": "OE1" <-> "OE2" Residue "E ARG 190": "NH1" <-> "NH2" Residue "E GLU 204": "OE1" <-> "OE2" Residue "F PHE 12": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 32": "NH1" <-> "NH2" Residue "F ASP 54": "OD1" <-> "OD2" Residue "F GLU 109": "OE1" <-> "OE2" Residue "F ARG 112": "NH1" <-> "NH2" Residue "F ASP 114": "OD1" <-> "OD2" Residue "F ARG 132": "NH1" <-> "NH2" Residue "F ARG 139": "NH1" <-> "NH2" Residue "F GLU 155": "OE1" <-> "OE2" Residue "F GLU 158": "OE1" <-> "OE2" Residue "F GLU 226": "OE1" <-> "OE2" Residue "F GLU 248": "OE1" <-> "OE2" Residue "F ARG 249": "NH1" <-> "NH2" Residue "F PHE 256": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 269": "OE1" <-> "OE2" Residue "F GLU 278": "OE1" <-> "OE2" Residue "F ARG 349": "NH1" <-> "NH2" Residue "F PHE 353": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 394": "OE1" <-> "OE2" Residue "F PHE 422": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 425": "OE1" <-> "OE2" Residue "F GLU 428": "OE1" <-> "OE2" Residue "F ARG 429": "NH1" <-> "NH2" Residue "G GLU 21": "OE1" <-> "OE2" Residue "G ARG 39": "NH1" <-> "NH2" Residue "G ARG 53": "NH1" <-> "NH2" Residue "G GLU 58": "OE1" <-> "OE2" Residue "G GLU 60": "OE1" <-> "OE2" Residue "G GLU 165": "OE1" <-> "OE2" Residue "G ARG 218": "NH1" <-> "NH2" Residue "G ARG 253": "NH1" <-> "NH2" Residue "G GLU 261": "OE1" <-> "OE2" Residue "G ARG 285": "NH1" <-> "NH2" Residue "G GLU 287": "OE1" <-> "OE2" Residue "G ARG 302": "NH1" <-> "NH2" Residue "G ASP 339": "OD1" <-> "OD2" Residue "G GLU 347": "OE1" <-> "OE2" Residue "G ARG 385": "NH1" <-> "NH2" Residue "G ARG 418": "NH1" <-> "NH2" Residue "G ASP 420": "OD1" <-> "OD2" Residue "G GLU 512": "OE1" <-> "OE2" Residue "G PHE 523": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 595": "OE1" <-> "OE2" Residue "G TYR 613": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 617": "OD1" <-> "OD2" Residue "G GLU 624": "OE1" <-> "OE2" Residue "G GLU 625": "OE1" <-> "OE2" Residue "G GLU 637": "OE1" <-> "OE2" Residue "G PHE 642": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 647": "OE1" <-> "OE2" Residue "G ASP 675": "OD1" <-> "OD2" Residue "H PHE 19": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ARG 25": "NH1" <-> "NH2" Residue "H ARG 34": "NH1" <-> "NH2" Residue "H TYR 142": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 143": "OE1" <-> "OE2" Residue "H GLU 170": "OE1" <-> "OE2" Residue "H GLU 192": "OE1" <-> "OE2" Residue "H PHE 224": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 280": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ARG 8": "NH1" <-> "NH2" Residue "I ARG 108": "NH1" <-> "NH2" Residue "J TYR 4": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 28": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 47": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 60": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J GLU 77": "OE1" <-> "OE2" Residue "J GLU 81": "OE1" <-> "OE2" Residue "J GLU 100": "OE1" <-> "OE2" Residue "J PHE 136": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J GLU 170": "OE1" <-> "OE2" Residue "J ARG 173": "NH1" <-> "NH2" Residue "K TYR 5": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K GLU 34": "OE1" <-> "OE2" Residue "K TYR 89": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L GLU 60": "OE1" <-> "OE2" Residue "L PHE 80": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 107": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 109": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L GLU 145": "OE1" <-> "OE2" Residue "L ARG 161": "NH1" <-> "NH2" Residue "L ARG 262": "NH1" <-> "NH2" Residue "L PHE 263": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L GLU 268": "OE1" <-> "OE2" Residue "L ASP 297": "OD1" <-> "OD2" Residue "L TYR 323": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L GLU 353": "OE1" <-> "OE2" Residue "L PHE 428": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L GLU 503": "OE1" <-> "OE2" Residue "L PHE 522": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L GLU 559": "OE1" <-> "OE2" Residue "L GLU 606": "OE1" <-> "OE2" Residue "M PHE 95": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M TYR 119": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M PHE 122": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M ARG 142": "NH1" <-> "NH2" Residue "M PHE 194": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M TYR 210": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M GLU 222": "OE1" <-> "OE2" Residue "M ARG 346": "NH1" <-> "NH2" Residue "M PHE 386": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M TYR 406": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M ARG 416": "NH1" <-> "NH2" Residue "M ARG 432": "NH1" <-> "NH2" Residue "M TYR 459": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N GLU 54": "OE1" <-> "OE2" Residue "N PHE 90": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N PHE 146": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N ARG 295": "NH1" <-> "NH2" Residue "N PHE 325": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O TYR 8": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O ARG 104": "NH1" <-> "NH2" Residue "O ARG 126": "NH1" <-> "NH2" Residue "O PHE 134": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O GLU 136": "OE1" <-> "OE2" Residue "O GLU 191": "OE1" <-> "OE2" Residue "O GLU 219": "OE1" <-> "OE2" Residue "O GLU 236": "OE1" <-> "OE2" Residue "O ASP 253": "OD1" <-> "OD2" Residue "O GLU 295": "OE1" <-> "OE2" Residue "O PHE 296": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O ARG 302": "NH1" <-> "NH2" Residue "O ARG 305": "NH1" <-> "NH2" Residue "O TYR 308": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O GLU 310": "OE1" <-> "OE2" Residue "P PHE 24": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P ARG 40": "NH1" <-> "NH2" Residue "P ARG 50": "NH1" <-> "NH2" Residue "P ASP 55": "OD1" <-> "OD2" Residue "P ASP 77": "OD1" <-> "OD2" Residue "P ARG 82": "NH1" <-> "NH2" Residue "P ARG 97": "NH1" <-> "NH2" Residue "P PHE 104": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P TYR 145": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P ARG 157": "NH1" <-> "NH2" Residue "P GLU 162": "OE1" <-> "OE2" Residue "P PHE 172": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P GLU 175": "OE1" <-> "OE2" Residue "P TYR 181": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P PHE 188": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P ARG 235": "NH1" <-> "NH2" Residue "P TYR 236": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P PHE 239": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P ARG 251": "NH1" <-> "NH2" Residue "P TYR 256": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P TYR 263": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P ARG 264": "NH1" <-> "NH2" Residue "P GLU 276": "OE1" <-> "OE2" Residue "P TYR 324": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q ARG 6": "NH1" <-> "NH2" Residue "Q ASP 18": "OD1" <-> "OD2" Residue "Q GLU 66": "OE1" <-> "OE2" Residue "Q TYR 103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q ASP 104": "OD1" <-> "OD2" Residue "Q GLU 106": "OE1" <-> "OE2" Residue "Q GLU 107": "OE1" <-> "OE2" Residue "R TYR 23": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R ARG 31": "NH1" <-> "NH2" Residue "R GLU 34": "OE1" <-> "OE2" Residue "R GLU 78": "OE1" <-> "OE2" Residue "S PHE 35": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S ASP 49": "OD1" <-> "OD2" Residue "S TYR 68": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T GLU 9": "OE1" <-> "OE2" Residue "T ASP 13": "OD1" <-> "OD2" Residue "T ARG 14": "NH1" <-> "NH2" Residue "T TYR 17": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T GLU 55": "OE1" <-> "OE2" Residue "T PHE 58": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T PHE 60": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T TYR 79": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U TYR 17": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U GLU 49": "OE1" <-> "OE2" Residue "U GLU 55": "OE1" <-> "OE2" Residue "U GLU 61": "OE1" <-> "OE2" Residue "U GLU 68": "OE1" <-> "OE2" Residue "U TYR 79": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V ARG 22": "NH1" <-> "NH2" Residue "V GLU 68": "OE1" <-> "OE2" Residue "V GLU 86": "OE1" <-> "OE2" Residue "V GLU 100": "OE1" <-> "OE2" Residue "V GLU 105": "OE1" <-> "OE2" Residue "W GLU 27": "OE1" <-> "OE2" Residue "W ARG 30": "NH1" <-> "NH2" Residue "W GLU 34": "OE1" <-> "OE2" Residue "W TYR 40": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W ASP 61": "OD1" <-> "OD2" Residue "W GLU 91": "OE1" <-> "OE2" Residue "W PHE 107": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W ARG 114": "NH1" <-> "NH2" Residue "X GLU 16": "OE1" <-> "OE2" Residue "X GLU 48": "OE1" <-> "OE2" Residue "X GLU 49": "OE1" <-> "OE2" Residue "X GLU 57": "OE1" <-> "OE2" Residue "X ARG 75": "NH1" <-> "NH2" Residue "X GLU 79": "OE1" <-> "OE2" Residue "X ARG 97": "NH1" <-> "NH2" Residue "X ARG 118": "NH1" <-> "NH2" Residue "X ASP 133": "OD1" <-> "OD2" Residue "X ARG 134": "NH1" <-> "NH2" Residue "X ARG 144": "NH1" <-> "NH2" Residue "X ARG 146": "NH1" <-> "NH2" Residue "Y TYR 22": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y PHE 69": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y ARG 80": "NH1" <-> "NH2" Residue "Y ASP 84": "OD1" <-> "OD2" Residue "Y ASP 85": "OD1" <-> "OD2" Residue "Y ARG 103": "NH1" <-> "NH2" Residue "Z ASP 20": "OD1" <-> "OD2" Residue "Z TYR 33": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z GLU 66": "OE1" <-> "OE2" Residue "Z GLU 94": "OE1" <-> "OE2" Residue "Z GLU 108": "OE1" <-> "OE2" Residue "a GLU 4": "OE1" <-> "OE2" Residue "a GLU 49": "OE1" <-> "OE2" Residue "a ASP 51": "OD1" <-> "OD2" Residue "a ARG 53": "NH1" <-> "NH2" Residue "a ARG 59": "NH1" <-> "NH2" Residue "a ASP 70": "OD1" <-> "OD2" Residue "b ARG 3": "NH1" <-> "NH2" Residue "b TYR 50": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b ARG 57": "NH1" <-> "NH2" Residue "b ASP 59": "OD1" <-> "OD2" Residue "c PHE 26": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c TYR 30": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c ASP 38": "OD1" <-> "OD2" Residue "c GLU 41": "OE1" <-> "OE2" Residue "c ARG 44": "NH1" <-> "NH2" Residue "d PHE 13": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d ARG 50": "NH1" <-> "NH2" Residue "d ARG 51": "NH1" <-> "NH2" Residue "d TYR 73": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d ARG 86": "NH1" <-> "NH2" Residue "d TYR 93": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d PHE 101": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d GLU 114": "OE1" <-> "OE2" Residue "d GLU 115": "OE1" <-> "OE2" Residue "e ARG 8": "NH1" <-> "NH2" Residue "e GLU 23": "OE1" <-> "OE2" Residue "e GLU 38": "OE1" <-> "OE2" Residue "e ARG 50": "NH1" <-> "NH2" Residue "e GLU 88": "OE1" <-> "OE2" Residue "f ASP 9": "OD1" <-> "OD2" Residue "f ARG 28": "NH1" <-> "NH2" Residue "f ARG 46": "NH1" <-> "NH2" Residue "g ARG 25": "NH1" <-> "NH2" Residue "g ASP 29": "OD1" <-> "OD2" Residue "g GLU 31": "OE1" <-> "OE2" Residue "g GLU 35": "OE1" <-> "OE2" Residue "g GLU 39": "OE1" <-> "OE2" Residue "g GLU 87": "OE1" <-> "OE2" Residue "g GLU 94": "OE1" <-> "OE2" Residue "g TYR 99": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "g GLU 101": "OE1" <-> "OE2" Residue "h PHE 16": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "h ARG 20": "NH1" <-> "NH2" Residue "h GLU 49": "OE1" <-> "OE2" Residue "h ARG 77": "NH1" <-> "NH2" Residue "h GLU 84": "OE1" <-> "OE2" Residue "h TYR 87": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "h ARG 112": "NH1" <-> "NH2" Residue "i ARG 18": "NH1" <-> "NH2" Residue "i ASP 52": "OD1" <-> "OD2" Residue "i PHE 69": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "i GLU 98": "OE1" <-> "OE2" Residue "i GLU 111": "OE1" <-> "OE2" Residue "i ASP 124": "OD1" <-> "OD2" Residue "j GLU 8": "OE1" <-> "OE2" Residue "j PHE 14": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "j PHE 40": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "j ASP 43": "OD1" <-> "OD2" Residue "j GLU 63": "OE1" <-> "OE2" Residue "k TYR 18": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "k ARG 38": "NH1" <-> "NH2" Residue "k ARG 41": "NH1" <-> "NH2" Residue "k ASP 42": "OD1" <-> "OD2" Residue "k TYR 52": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "k PHE 70": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "k PHE 74": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "k GLU 84": "OE1" <-> "OE2" Residue "l TYR 13": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "l GLU 19": "OE1" <-> "OE2" Residue "l ARG 30": "NH1" <-> "NH2" Residue "l GLU 32": "OE1" <-> "OE2" Residue "l ASP 40": "OD1" <-> "OD2" Residue "l ARG 53": "NH1" <-> "NH2" Residue "l GLU 57": "OE1" <-> "OE2" Residue "l GLU 75": "OE1" <-> "OE2" Residue "l GLU 120": "OE1" <-> "OE2" Residue "l GLU 141": "OE1" <-> "OE2" Residue "l ARG 142": "NH1" <-> "NH2" Residue "l GLU 149": "OE1" <-> "OE2" Residue "m ARG 39": "NH1" <-> "NH2" Residue "m ARG 55": "NH1" <-> "NH2" Residue "m GLU 60": "OE1" <-> "OE2" Residue "m ARG 71": "NH1" <-> "NH2" Residue "m PHE 92": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "m GLU 112": "OE1" <-> "OE2" Residue "m GLU 117": "OE1" <-> "OE2" Residue "m ASP 121": "OD1" <-> "OD2" Residue "n ARG 21": "NH1" <-> "NH2" Residue "n GLU 27": "OE1" <-> "OE2" Residue "n ARG 37": "NH1" <-> "NH2" Residue "n PHE 47": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "n ARG 64": "NH1" <-> "NH2" Residue "n GLU 67": "OE1" <-> "OE2" Residue "n GLU 69": "OE1" <-> "OE2" Residue "n GLU 83": "OE1" <-> "OE2" Residue "n GLU 91": "OE1" <-> "OE2" Residue "n ARG 92": "NH1" <-> "NH2" Residue "n ASP 105": "OD1" <-> "OD2" Residue "n TYR 117": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "n ARG 129": "NH1" <-> "NH2" Residue "n GLU 130": "OE1" <-> "OE2" Residue "n GLU 133": "OE1" <-> "OE2" Residue "n ARG 134": "NH1" <-> "NH2" Residue "n ARG 134": "NH1" <-> "NH2" Residue "n ARG 149": "NH1" <-> "NH2" Residue "n GLU 175": "OE1" <-> "OE2" Residue "o ARG 6": "NH1" <-> "NH2" Residue "o ARG 20": "NH1" <-> "NH2" Residue "o PHE 24": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "o GLU 35": "OE1" <-> "OE2" Residue "o ARG 36": "NH1" <-> "NH2" Residue "o GLU 44": "OE1" <-> "OE2" Residue "o ARG 64": "NH1" <-> "NH2" Residue "o ARG 97": "NH1" <-> "NH2" Residue "o GLU 102": "OE1" <-> "OE2" Residue "o ARG 103": "NH1" <-> "NH2" Residue "o ARG 105": "NH1" <-> "NH2" Residue "o ARG 106": "NH1" <-> "NH2" Residue "o ARG 113": "NH1" <-> "NH2" Residue "o ARG 117": "NH1" <-> "NH2" Residue "o ASP 120": "OD1" <-> "OD2" Residue "p TYR 31": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "p PHE 50": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "p TYR 62": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "p GLU 88": "OE1" <-> "OE2" Residue "p GLU 100": "OE1" <-> "OE2" Residue "p GLU 127": "OE1" <-> "OE2" Residue "q ARG 21": "NH1" <-> "NH2" Residue "q TYR 23": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "q ARG 29": "NH1" <-> "NH2" Residue "q GLU 41": "OE1" <-> "OE2" Residue "q TYR 49": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "q GLU 50": "OE1" <-> "OE2" Residue "q GLU 85": "OE1" <-> "OE2" Residue "q ARG 88": "NH1" <-> "NH2" Residue "q PHE 115": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "r ASP 18": "OD1" <-> "OD2" Residue "r ARG 59": "NH1" <-> "NH2" Residue "r GLU 104": "OE1" <-> "OE2" Residue "r ASP 108": "OD1" <-> "OD2" Residue "r GLU 109": "OE1" <-> "OE2" Residue "r TYR 111": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "s ASP 57": "OD1" <-> "OD2" Time to flip residues: 0.17s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 69319 Number of models: 1 Model: "" Number of chains: 116 Chain: "A" Number of atoms: 852 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 852 Classifications: {'peptide': 106} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 100} Chain breaks: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'FME:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "B" Number of atoms: 1247 Number of conformers: 1 Conformer: "" Number of residues, atoms: 156, 1247 Classifications: {'peptide': 156} Link IDs: {'PCIS': 2, 'PTRANS': 8, 'TRANS': 145} Chain: "C" Number of atoms: 1721 Number of conformers: 1 Conformer: "" Number of residues, atoms: 207, 1721 Classifications: {'peptide': 207} Link IDs: {'PTRANS': 16, 'TRANS': 190} Chain: "D" Number of atoms: 3262 Number of conformers: 1 Conformer: "" Number of residues, atoms: 404, 3262 Classifications: {'peptide': 404} Link IDs: {'PTRANS': 26, 'TRANS': 377} Chain breaks: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'2MR:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "E" Number of atoms: 1659 Number of conformers: 1 Conformer: "" Number of residues, atoms: 214, 1659 Classifications: {'peptide': 214} Link IDs: {'PCIS': 1, 'PTRANS': 20, 'TRANS': 192} Chain: "F" Number of atoms: 3336 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 432, 3326 Classifications: {'peptide': 432} Link IDs: {'PCIS': 2, 'PTRANS': 19, 'TRANS': 410} Conformer: "B" Number of residues, atoms: 432, 3326 Classifications: {'peptide': 432} Link IDs: {'PCIS': 2, 'PTRANS': 19, 'TRANS': 410} bond proxies already assigned to first conformer: 3389 Chain: "G" Number of atoms: 5298 Number of conformers: 1 Conformer: "" Number of residues, atoms: 691, 5298 Classifications: {'peptide': 691} Link IDs: {'PTRANS': 32, 'TRANS': 658} Chain: "H" Number of atoms: 2316 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 291, 2306 Classifications: {'peptide': 291} Link IDs: {'PCIS': 2, 'PTRANS': 18, 'TRANS': 270} Chain breaks: 2 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'FME:plan-2': 1} Unresolved non-hydrogen planarities: 1 Conformer: "B" Number of residues, atoms: 291, 2306 Classifications: {'peptide': 291} Link IDs: {'PCIS': 2, 'PTRANS': 18, 'TRANS': 270} Chain breaks: 2 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'FME:plan-2': 1} Unresolved non-hydrogen planarities: 1 bond proxies already assigned to first conformer: 2358 Chain: "I" Number of atoms: 1414 Number of conformers: 1 Conformer: "" Number of residues, atoms: 176, 1414 Classifications: {'peptide': 176} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 165} Chain: "J" Number of atoms: 1345 Number of conformers: 1 Conformer: "" Number of residues, atoms: 175, 1345 Classifications: {'peptide': 175} Link IDs: {'PTRANS': 3, 'TRANS': 171} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'FME:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "K" Number of atoms: 745 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 745 Classifications: {'peptide': 98} Link IDs: {'PTRANS': 1, 'TRANS': 96} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'FME:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "L" Number of atoms: 4802 Number of conformers: 1 Conformer: "" Number of residues, atoms: 606, 4802 Classifications: {'peptide': 606} Link IDs: {'PTRANS': 27, 'TRANS': 578} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'FME:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "M" Number of atoms: 3654 Number of conformers: 1 Conformer: "" Number of residues, atoms: 459, 3654 Classifications: {'peptide': 459} Link IDs: {'PCIS': 3, 'PTRANS': 17, 'TRANS': 438} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'FME:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "N" Number of atoms: 2733 Number of conformers: 1 Conformer: "" Number of residues, atoms: 347, 2733 Classifications: {'peptide': 347} Link IDs: {'PCIS': 2, 'PTRANS': 19, 'TRANS': 325} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'FME:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "O" Number of atoms: 2589 Number of conformers: 1 Conformer: "" Number of residues, atoms: 320, 2589 Classifications: {'peptide': 320} Link IDs: {'PTRANS': 15, 'TRANS': 304} Chain: "P" Number of atoms: 2623 Number of conformers: 1 Conformer: "" Number of residues, atoms: 327, 2623 Classifications: {'peptide': 327} Link IDs: {'PTRANS': 20, 'TRANS': 306} Chain breaks: 3 Chain: "Q" Number of atoms: 1049 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 1049 Classifications: {'peptide': 129} Link IDs: {'PTRANS': 6, 'TRANS': 122} Chain: "R" Number of atoms: 740 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 740 Classifications: {'peptide': 96} Link IDs: {'PTRANS': 3, 'TRANS': 92} Chain: "S" Number of atoms: 691 Number of conformers: 1 Conformer: "" Number of residues, atoms: 86, 691 Classifications: {'peptide': 86} Link IDs: {'PTRANS': 4, 'TRANS': 81} Chain: "T" Number of atoms: 688 Number of conformers: 1 Conformer: "" Number of residues, atoms: 85, 688 Classifications: {'peptide': 85} Link IDs: {'PTRANS': 4, 'TRANS': 80} Chain: "U" Number of atoms: 707 Number of conformers: 1 Conformer: "" Number of residues, atoms: 88, 707 Classifications: {'peptide': 88} Link IDs: {'PTRANS': 5, 'TRANS': 82} Chain: "V" Number of atoms: 923 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 923 Classifications: {'peptide': 114} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 105} Chain: "W" Number of atoms: 982 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 982 Classifications: {'peptide': 116} Link IDs: {'PTRANS': 6, 'TRANS': 109} Chain: "X" Number of atoms: 1402 Number of conformers: 1 Conformer: "" Number of residues, atoms: 171, 1402 Classifications: {'peptide': 171} Link IDs: {'PTRANS': 12, 'TRANS': 158} Chain: "Y" Number of atoms: 1030 Number of conformers: 1 Conformer: "" Number of residues, atoms: 140, 1030 Classifications: {'peptide': 140} Link IDs: {'PTRANS': 5, 'TRANS': 134} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'AYA:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "Z" Number of atoms: 1157 Number of conformers: 1 Conformer: "" Number of residues, atoms: 142, 1157 Classifications: {'peptide': 142} Link IDs: {'PTRANS': 7, 'TRANS': 134} Chain: "a" Number of atoms: 569 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 569 Classifications: {'peptide': 70} Link IDs: {'PTRANS': 3, 'TRANS': 66} Chain: "b" Number of atoms: 651 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 651 Classifications: {'peptide': 83} Link IDs: {'PTRANS': 11, 'TRANS': 71} Chain: "c" Number of atoms: 414 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 414 Classifications: {'peptide': 49} Link IDs: {'PTRANS': 3, 'TRANS': 45} Chain: "d" Number of atoms: 999 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 999 Classifications: {'peptide': 120} Link IDs: {'PTRANS': 9, 'TRANS': 110} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'AME:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "e" Number of atoms: 825 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 825 Classifications: {'peptide': 98} Link IDs: {'PTRANS': 5, 'TRANS': 92} Chain: "f" Number of atoms: 492 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 492 Classifications: {'peptide': 57} Link IDs: {'PTRANS': 2, 'TRANS': 54} Chain: "g" Number of atoms: 846 Number of conformers: 1 Conformer: "" Number of residues, atoms: 101, 846 Classifications: {'peptide': 101} Link IDs: {'PTRANS': 8, 'TRANS': 92} Chain: "h" Number of atoms: 1154 Number of conformers: 1 Conformer: "" Number of residues, atoms: 138, 1154 Classifications: {'peptide': 138} Link IDs: {'PTRANS': 10, 'TRANS': 127} Chain: "i" Number of atoms: 1097 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 1097 Classifications: {'peptide': 127} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 113} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'SAC:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "j" Number of atoms: 580 Number of conformers: 1 Conformer: "" Number of residues, atoms: 67, 580 Classifications: {'peptide': 67} Link IDs: {'PTRANS': 7, 'TRANS': 59} Chain: "k" Number of atoms: 653 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 653 Classifications: {'peptide': 81} Link IDs: {'PTRANS': 3, 'TRANS': 77} Chain: "l" Number of atoms: 1314 Number of conformers: 1 Conformer: "" Number of residues, atoms: 156, 1314 Classifications: {'peptide': 156} Link IDs: {'PTRANS': 20, 'TRANS': 135} Chain: "m" Number of atoms: 1067 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 1067 Classifications: {'peptide': 128} Link IDs: {'PTRANS': 8, 'TRANS': 119} Chain: "n" Number of atoms: 1498 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 171, 1487 Classifications: {'peptide': 171} Link IDs: {'PTRANS': 15, 'TRANS': 155} Conformer: "B" Number of residues, atoms: 171, 1487 Classifications: {'peptide': 171} Link IDs: {'PTRANS': 15, 'TRANS': 155} bond proxies already assigned to first conformer: 1528 Chain: "o" Number of atoms: 1048 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 1048 Classifications: {'peptide': 122} Link IDs: {'PCIS': 2, 'PTRANS': 5, 'TRANS': 114} Chain: "p" Number of atoms: 1450 Number of conformers: 1 Conformer: "" Number of residues, atoms: 173, 1450 Classifications: {'peptide': 173} Link IDs: {'PTRANS': 10, 'TRANS': 162} Chain: "q" Number of atoms: 1209 Number of conformers: 1 Conformer: "" Number of residues, atoms: 145, 1209 Classifications: {'peptide': 145} Link IDs: {'PTRANS': 11, 'TRANS': 133} Chain: "r" Number of atoms: 776 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 776 Classifications: {'peptide': 95} Link IDs: {'PTRANS': 11, 'TRANS': 83} Chain breaks: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'AYA:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "s" Number of atoms: 371 Number of conformers: 1 Conformer: "" Number of residues, atoms: 44, 371 Classifications: {'peptide': 44} Link IDs: {'PTRANS': 3, 'TRANS': 40} Chain: "A" Number of atoms: 97 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 97 Unusual residues: {'3PE': 1, 'PC1': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 8 Chain: "B" Number of atoms: 59 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 59 Unusual residues: {'PC1': 1, 'SF4': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 Chain: "E" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 4 Unusual residues: {'FES': 1} Classifications: {'undetermined': 1} Chain: "F" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 39 Unusual residues: {'FMN': 1, 'SF4': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "G" Number of atoms: 21 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 21 Unusual residues: {' K': 1, 'FES': 1, 'SF4': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "H" Number of atoms: 36 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 36 Unusual residues: {'3PE': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 15 Chain: "I" Number of atoms: 118 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 118 Unusual residues: {'3PE': 2, 'SF4': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "J" Number of atoms: 46 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 46 Unusual residues: {'PC1': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 8 Chain: "K" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'3PE': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 8 Chain: "L" Number of atoms: 229 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 229 Unusual residues: {'3PE': 3, 'CDL': 1, 'CHD': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 53 Unresolved non-hydrogen angles: 53 Unresolved non-hydrogen dihedrals: 53 Chain: "M" Number of atoms: 240 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 240 Unusual residues: {'3PE': 3, 'PC1': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 21 Unresolved non-hydrogen angles: 21 Unresolved non-hydrogen dihedrals: 21 Chain: "N" Number of atoms: 205 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 205 Unusual residues: {'3PE': 2, 'CDL': 1, 'PC1': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 51 Unresolved non-hydrogen angles: 51 Unresolved non-hydrogen dihedrals: 51 Chain: "O" Number of atoms: 69 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 69 Unusual residues: {' MG': 1, '3PE': 1, 'GTP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 15 Chain: "P" Number of atoms: 48 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 48 Unusual residues: {'NDP': 1} Classifications: {'undetermined': 1} Chain: "R" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "T" Number of atoms: 37 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 37 Unusual residues: {'EHZ': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 3 Chain: "U" Number of atoms: 37 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 37 Unusual residues: {'EHZ': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 3 Chain: "X" Number of atoms: 86 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 86 Unusual residues: {'CDL': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 14 Chain: "Y" Number of atoms: 211 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 211 Unusual residues: {'3PE': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 44 Unresolved non-hydrogen angles: 44 Unresolved non-hydrogen dihedrals: 44 Chain: "Z" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'3PE': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 8 Chain: "b" Number of atoms: 88 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 88 Unusual residues: {'3PE': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 14 Chain: "d" Number of atoms: 195 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 195 Unusual residues: {'3PE': 2, 'CDL': 1, 'PC1': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 61 Unresolved non-hydrogen angles: 61 Unresolved non-hydrogen dihedrals: 61 Chain: "f" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'3PE': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 20 Chain: "g" Number of atoms: 36 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 36 Unusual residues: {'3PE': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 15 Chain: "h" Number of atoms: 107 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 107 Unusual residues: {'3PE': 1, 'CDL': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 44 Unresolved non-hydrogen angles: 44 Unresolved non-hydrogen dihedrals: 44 Chain: "m" Number of atoms: 40 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 40 Unusual residues: {'3PE': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 11 Chain: "o" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 15 Unusual residues: {'MYR': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'MYR:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "r" Number of atoms: 64 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 64 Unusual residues: {'CDL': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 36 Unresolved non-hydrogen angles: 36 Unresolved non-hydrogen dihedrals: 36 Chain: "A" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 5 Classifications: {'water': 5} Link IDs: {None: 4} Chain: "B" Number of atoms: 37 Number of conformers: 1 Conformer: "" Number of residues, atoms: 37, 37 Classifications: {'water': 37} Link IDs: {None: 36} Chain: "C" Number of atoms: 58 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 58 Classifications: {'water': 58} Link IDs: {None: 57} Chain: "D" Number of atoms: 113 Number of conformers: 1 Conformer: "" Number of residues, atoms: 113, 113 Classifications: {'water': 113} Link IDs: {None: 112} Chain: "E" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 8 Classifications: {'water': 8} Link IDs: {None: 7} Chain: "F" Number of atoms: 30 Number of conformers: 1 Conformer: "" Number of residues, atoms: 30, 30 Classifications: {'water': 30} Link IDs: {None: 29} Chain: "G" Number of atoms: 157 Number of conformers: 1 Conformer: "" Number of residues, atoms: 157, 157 Classifications: {'water': 157} Link IDs: {None: 156} Chain: "H" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 39, 39 Classifications: {'water': 39} Link IDs: {None: 38} Chain: "I" Number of atoms: 65 Number of conformers: 1 Conformer: "" Number of residues, atoms: 65, 65 Classifications: {'water': 65} Link IDs: {None: 64} Chain: "J" Number of atoms: 18 Number of conformers: 1 Conformer: "" Number of residues, atoms: 18, 18 Classifications: {'water': 18} Link IDs: {None: 17} Chain: "K" Number of atoms: 10 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 10 Classifications: {'water': 10} Link IDs: {None: 9} Chain: "L" Number of atoms: 64 Number of conformers: 1 Conformer: "" Number of residues, atoms: 64, 64 Classifications: {'water': 64} Link IDs: {None: 63} Chain: "M" Number of atoms: 80 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 80 Classifications: {'water': 80} Link IDs: {None: 79} Chain: "N" Number of atoms: 48 Number of conformers: 1 Conformer: "" Number of residues, atoms: 48, 48 Classifications: {'water': 48} Link IDs: {None: 47} Chain: "O" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 8 Classifications: {'water': 8} Link IDs: {None: 7} Chain: "P" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 29 Classifications: {'water': 29} Link IDs: {None: 28} Chain: "Q" Number of atoms: 63 Number of conformers: 1 Conformer: "" Number of residues, atoms: 63, 63 Classifications: {'water': 63} Link IDs: {None: 62} Chain: "R" Number of atoms: 12 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 12 Classifications: {'water': 12} Link IDs: {None: 11} Chain: "S" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "U" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 8 Classifications: {'water': 8} Link IDs: {None: 7} Chain: "V" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 5 Classifications: {'water': 5} Link IDs: {None: 4} Chain: "W" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "X" Number of atoms: 13 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 13 Classifications: {'water': 13} Link IDs: {None: 12} Chain: "Y" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "Z" Number of atoms: 23 Number of conformers: 1 Conformer: "" Number of residues, atoms: 23, 23 Classifications: {'water': 23} Link IDs: {None: 22} Chain: "a" Number of atoms: 13 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 13 Classifications: {'water': 13} Link IDs: {None: 12} Chain: "b" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "c" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "d" Number of atoms: 16 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 16 Classifications: {'water': 16} Link IDs: {None: 15} Chain: "e" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 14 Classifications: {'water': 14} Link IDs: {None: 13} Chain: "f" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "g" Number of atoms: 12 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 12 Classifications: {'water': 12} Link IDs: {None: 11} Chain: "h" Number of atoms: 26 Number of conformers: 1 Conformer: "" Number of residues, atoms: 26, 26 Classifications: {'water': 26} Link IDs: {None: 25} Chain: "i" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 5 Classifications: {'water': 5} Link IDs: {None: 4} Chain: "j" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "l" Number of atoms: 13 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 13 Classifications: {'water': 13} Link IDs: {None: 12} Chain: "m" Number of atoms: 10 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 10 Classifications: {'water': 10} Link IDs: {None: 9} Chain: "n" Number of atoms: 23 Number of conformers: 1 Conformer: "" Number of residues, atoms: 23, 23 Classifications: {'water': 23} Link IDs: {None: 22} Chain: "o" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "p" Number of atoms: 22 Number of conformers: 1 Conformer: "" Number of residues, atoms: 22, 22 Classifications: {'water': 22} Link IDs: {None: 21} Chain: "q" Number of atoms: 19 Number of conformers: 1 Conformer: "" Number of residues, atoms: 19, 19 Classifications: {'water': 19} Link IDs: {None: 18} Chain: "r" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 14 Classifications: {'water': 14} Link IDs: {None: 13} Chain: "s" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 1605 SG CYS B 119 97.632 95.426 205.022 1.00 30.13 S ATOM 1835 SG CYS B 149 95.653 93.223 209.830 1.00 28.50 S ATOM 1101 SG CYS B 54 92.146 91.779 204.341 1.00 33.06 S ATOM 1107 SG CYS B 55 91.882 97.606 207.033 1.00 33.00 S ATOM 7890 SG CYS E 103 116.421 48.005 261.253 1.00 43.16 S ATOM 7924 SG CYS E 108 114.690 45.441 263.277 1.00 44.05 S ATOM 8204 SG CYS E 144 118.452 44.501 257.994 1.00 40.77 S ATOM 8227 SG CYS E 148 117.063 41.834 258.990 1.00 46.08 S ATOM 11462 SG CYS F 362 120.830 54.012 237.339 1.00 29.91 S ATOM 11482 SG CYS F 365 118.038 53.513 242.277 1.00 29.63 S ATOM 11806 SG CYS F 405 122.575 49.000 241.418 1.00 30.51 S ATOM 11443 SG CYS F 359 124.494 54.937 242.725 1.00 31.15 S ATOM 12903 SG CYS G 114 117.284 72.413 227.838 1.00 28.18 S ATOM 12842 SG CYS G 105 111.538 74.925 229.656 1.00 26.86 S ATOM 12863 SG CYS G 108 117.126 77.380 231.703 1.00 27.80 S ATOM 13235 SG CYS G 156 125.740 66.342 232.675 1.00 28.94 S ATOM 13212 SG CYS G 153 122.988 68.794 238.276 1.00 27.83 S ATOM 13259 SG CYS G 159 129.189 69.713 236.864 1.00 29.89 S ATOM 13589 SG CYS G 203 124.772 72.406 233.013 1.00 28.16 S ATOM 12348 SG CYS G 41 126.025 59.565 230.547 1.00 28.20 S ATOM 12434 SG CYS G 52 122.198 60.003 229.612 1.00 28.70 S ATOM 12459 SG CYS G 55 123.650 55.471 226.303 1.00 29.80 S ATOM 12560 SG CYS G 69 126.795 56.201 227.462 1.00 29.69 S ATOM 20645 SG CYS I 119 98.685 87.469 215.894 1.00 26.13 S ATOM 20619 SG CYS I 116 99.116 94.012 216.701 1.00 26.14 S ATOM 20666 SG CYS I 122 100.444 89.772 221.374 1.00 25.85 S ATOM 20393 SG CYS I 87 104.366 90.309 216.178 1.00 24.96 S ATOM 20695 SG CYS I 126 103.017 86.655 228.786 1.00 26.73 S ATOM 20324 SG CYS I 77 108.007 90.885 229.727 1.00 27.45 S ATOM 20366 SG CYS I 83 106.383 89.111 223.888 1.00 25.36 S ATOM 20343 SG CYS I 80 108.462 84.452 227.541 1.00 26.39 S ATOM 41104 SG CYS R 59 104.966 82.454 244.124 1.00 30.33 S ATOM 41282 SG CYS R 84 107.960 83.065 242.008 1.00 30.77 S ATOM 41304 SG CYS R 87 105.721 85.735 242.689 1.00 30.07 S Residues with excluded nonbonded symmetry interactions: 3 residue: pdb=" N AHIS F 356 " occ=0.50 ... (18 atoms not shown) pdb=" NE2BHIS F 356 " occ=0.50 residue: pdb=" N AHIS H 287 " occ=0.50 ... (18 atoms not shown) pdb=" NE2BHIS H 287 " occ=0.50 residue: pdb=" N AARG n 134 " occ=0.50 ... (20 atoms not shown) pdb=" NH2BARG n 134 " occ=0.50 Time building chain proxies: 30.44, per 1000 atoms: 0.44 Number of scatterers: 69319 At special positions: 0 Unit cell: (186.65, 203.142, 293.843, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 9 Type Number sf(0) Zn 1 29.99 Fe 28 26.01 K 1 19.00 S 469 16.00 P 56 15.00 Mg 1 11.99 O 13331 8.00 N 11215 7.00 C 44217 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=7, symmetry=0 Simple disulfide: pdb=" SG CYS X 45 " - pdb=" SG CYS X 55 " distance=2.03 Simple disulfide: pdb=" SG CYS X 87 " - pdb=" SG CYS X 99 " distance=2.03 Simple disulfide: pdb=" SG CYS Y 17 " - pdb=" SG CYS Y 74 " distance=2.03 Simple disulfide: pdb=" SG CYS Y 94 " - pdb=" SG CYS Y 114 " distance=2.03 Simple disulfide: pdb=" SG CYS e 32 " - pdb=" SG CYS e 65 " distance=2.04 Simple disulfide: pdb=" SG CYS e 42 " - pdb=" SG CYS e 55 " distance=2.04 Simple disulfide: pdb=" SG CYS p 112 " - pdb=" SG CYS p 124 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=4, symmetry=0 Number of additional bonds: simple=4, symmetry=0 Coordination: Other bonds: Time building additional restraints: 22.54 Conformation dependent library (CDL) restraints added in 10.0 seconds Dynamic metal coordination Iron sulfur cluster coordination pdb=" FES E 301 " pdb="FE1 FES E 301 " - pdb=" SG CYS E 103 " pdb="FE1 FES E 301 " - pdb=" SG CYS E 108 " pdb="FE2 FES E 301 " - pdb=" SG CYS E 148 " pdb="FE2 FES E 301 " - pdb=" SG CYS E 144 " pdb=" FES G 803 " pdb="FE1 FES G 803 " - pdb=" SG CYS G 52 " pdb="FE2 FES G 803 " - pdb=" SG CYS G 55 " pdb="FE2 FES G 803 " - pdb=" SG CYS G 69 " pdb="FE1 FES G 803 " - pdb=" SG CYS G 41 " pdb=" SF4 B 201 " pdb="FE1 SF4 B 201 " - pdb=" SG CYS B 119 " pdb="FE2 SF4 B 201 " - pdb=" SG CYS B 149 " pdb="FE3 SF4 B 201 " - pdb=" SG CYS B 54 " pdb="FE4 SF4 B 201 " - pdb=" SG CYS B 55 " pdb=" SF4 F 502 " pdb="FE2 SF4 F 502 " - pdb=" SG CYS F 365 " pdb="FE4 SF4 F 502 " - pdb=" SG CYS F 359 " pdb="FE3 SF4 F 502 " - pdb=" SG CYS F 405 " pdb="FE1 SF4 F 502 " - pdb=" SG CYS F 362 " pdb=" SF4 G 801 " pdb="FE3 SF4 G 801 " - pdb=" NE2 HIS G 101 " pdb="FE1 SF4 G 801 " - pdb=" SG CYS G 114 " pdb="FE2 SF4 G 801 " - pdb=" SG CYS G 105 " pdb="FE4 SF4 G 801 " - pdb=" SG CYS G 108 " pdb=" SF4 G 802 " pdb="FE3 SF4 G 802 " - pdb=" SG CYS G 159 " pdb="FE1 SF4 G 802 " - pdb=" SG CYS G 156 " pdb="FE2 SF4 G 802 " - pdb=" SG CYS G 153 " pdb="FE4 SF4 G 802 " - pdb=" SG CYS G 203 " pdb=" SF4 I 202 " pdb="FE2 SF4 I 202 " - pdb=" SG CYS I 116 " pdb="FE4 SF4 I 202 " - pdb=" SG CYS I 87 " pdb="FE3 SF4 I 202 " - pdb=" SG CYS I 122 " pdb="FE1 SF4 I 202 " - pdb=" SG CYS I 119 " pdb=" SF4 I 203 " pdb="FE3 SF4 I 203 " - pdb=" SG CYS I 83 " pdb="FE4 SF4 I 203 " - pdb=" SG CYS I 80 " pdb="FE2 SF4 I 203 " - pdb=" SG CYS I 77 " pdb="FE1 SF4 I 203 " - pdb=" SG CYS I 126 " Number of angles added : 81 Zn2+ tetrahedral coordination pdb=" ZN R 201 " pdb="ZN ZN R 201 " - pdb=" NE2 HIS R 68 " pdb="ZN ZN R 201 " - pdb=" SG CYS R 84 " pdb="ZN ZN R 201 " - pdb=" SG CYS R 87 " pdb="ZN ZN R 201 " - pdb=" SG CYS R 59 " Number of angles added : 3 16180 Ramachandran restraints generated. 8090 Oldfield, 0 Emsley, 8090 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 15420 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 356 helices and 28 sheets defined 53.6% alpha, 4.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 11.51 Creating SS restraints... Processing helix chain 'A' and resid 3 through 23 removed outlier: 3.592A pdb=" N ALA A 21 " --> pdb=" O LEU A 17 " (cutoff:3.500A) Processing helix chain 'A' and resid 25 through 27 No H-bonds generated for 'chain 'A' and resid 25 through 27' Processing helix chain 'A' and resid 53 through 80 removed outlier: 3.905A pdb=" N ALA A 59 " --> pdb=" O PHE A 55 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N LEU A 72 " --> pdb=" O GLU A 68 " (cutoff:3.500A) Proline residue: A 74 - end of helix removed outlier: 5.458A pdb=" N TRP A 77 " --> pdb=" O LEU A 73 " (cutoff:3.500A) removed outlier: 4.632A pdb=" N GLN A 80 " --> pdb=" O PRO A 76 " (cutoff:3.500A) Processing helix chain 'A' and resid 84 through 107 removed outlier: 3.546A pdb=" N LEU A 102 " --> pdb=" O LEU A 98 " (cutoff:3.500A) Processing helix chain 'B' and resid 26 through 42 Processing helix chain 'B' and resid 54 through 63 removed outlier: 3.713A pdb=" N GLU B 58 " --> pdb=" O CYS B 54 " (cutoff:3.500A) Processing helix chain 'B' and resid 69 through 72 Processing helix chain 'B' and resid 94 through 105 Proline residue: B 98 - end of helix Processing helix chain 'B' and resid 117 through 122 Processing helix chain 'B' and resid 124 through 126 No H-bonds generated for 'chain 'B' and resid 124 through 126' 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 153 through 168 Processing helix chain 'B' and resid 172 through 177 Processing helix chain 'C' and resid 16 through 32 Processing helix chain 'C' and resid 54 through 66 removed outlier: 4.647A pdb=" N ILE C 58 " --> pdb=" O ASP C 55 " (cutoff:3.500A) Proline residue: C 59 - end of helix Processing helix chain 'C' and resid 120 through 122 No H-bonds generated for 'chain 'C' and resid 120 through 122' Processing helix chain 'C' and resid 127 through 138 Processing helix chain 'C' and resid 207 through 209 No H-bonds generated for 'chain 'C' and resid 207 through 209' Processing helix chain 'D' and resid 8 through 14 removed outlier: 3.962A pdb=" N GLN D 13 " --> pdb=" O GLU D 9 " (cutoff:3.500A) removed outlier: 4.413A pdb=" N TYR D 14 " --> pdb=" O TRP D 10 " (cutoff:3.500A) Processing helix chain 'D' and resid 87 through 93 removed outlier: 3.987A pdb=" N GLU D 92 " --> pdb=" O GLU D 88 " (cutoff:3.500A) removed outlier: 4.099A pdb=" N TYR D 93 " --> pdb=" O LYS D 89 " (cutoff:3.500A) Processing helix chain 'D' and resid 100 through 104 removed outlier: 3.855A pdb=" N ASP D 104 " --> pdb=" O LEU D 100 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 100 through 104' Processing helix chain 'D' and resid 111 through 126 Processing helix chain 'D' and resid 132 through 161 removed outlier: 3.758A pdb=" N ILE D 161 " --> pdb=" O HIS D 157 " (cutoff:3.500A) Processing helix chain 'D' and resid 165 through 185 removed outlier: 3.661A pdb=" N GLU D 172 " --> pdb=" O PHE D 168 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N GLU D 173 " --> pdb=" O TRP D 169 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N LYS D 176 " --> pdb=" O GLU D 172 " (cutoff:3.500A) Processing helix chain 'D' and resid 207 through 229 removed outlier: 3.841A pdb=" N ASN D 217 " --> pdb=" O GLU D 213 " (cutoff:3.500A) removed outlier: 4.579A pdb=" N SER D 219 " --> pdb=" O SER D 215 " (cutoff:3.500A) removed outlier: 5.735A pdb=" N LEU D 220 " --> pdb=" O LYS D 216 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N ARG D 221 " --> pdb=" O ASN D 217 " (cutoff:3.500A) Processing helix chain 'D' and resid 233 through 237 Processing helix chain 'D' and resid 247 through 252 Processing helix chain 'D' and resid 257 through 263 removed outlier: 4.386A pdb=" N GLY D 262 " --> pdb=" O MET D 259 " (cutoff:3.500A) Processing helix chain 'D' and resid 269 through 272 No H-bonds generated for 'chain 'D' and resid 269 through 272' Processing helix chain 'D' and resid 278 through 280 No H-bonds generated for 'chain 'D' and resid 278 through 280' Processing helix chain 'D' and resid 293 through 317 Processing helix chain 'D' and resid 335 through 338 No H-bonds generated for 'chain 'D' and resid 335 through 338' Processing helix chain 'D' and resid 342 through 351 Processing helix chain 'D' and resid 394 through 405 removed outlier: 3.562A pdb=" N HIS D 398 " --> pdb=" O PRO D 394 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N LEU D 402 " --> pdb=" O HIS D 398 " (cutoff:3.500A) removed outlier: 4.885A pdb=" N ASP D 403 " --> pdb=" O LEU D 399 " (cutoff:3.500A) removed outlier: 5.215A pdb=" N LYS D 404 " --> pdb=" O ALA D 400 " (cutoff:3.500A) Processing helix chain 'D' and resid 411 through 421 removed outlier: 4.098A pdb=" N VAL D 415 " --> pdb=" O LEU D 411 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N ALA D 416 " --> pdb=" O ALA D 412 " (cutoff:3.500A) Processing helix chain 'D' and resid 425 through 429 Processing helix chain 'E' and resid 25 through 37 removed outlier: 3.771A pdb=" N ASN E 37 " --> pdb=" O ALA E 33 " (cutoff:3.500A) Processing helix chain 'E' and resid 43 through 58 removed outlier: 4.532A pdb=" N LEU E 48 " --> pdb=" O ALA E 45 " (cutoff:3.500A) Proline residue: E 49 - end of helix Processing helix chain 'E' and resid 63 through 73 Processing helix chain 'E' and resid 77 through 86 removed outlier: 3.525A pdb=" N VAL E 83 " --> pdb=" O ARG E 79 " (cutoff:3.500A) Processing helix chain 'E' and resid 106 through 110 Processing helix chain 'E' and resid 113 through 124 Processing helix chain 'E' and resid 148 through 150 No H-bonds generated for 'chain 'E' and resid 148 through 150' Processing helix chain 'E' and resid 166 through 178 Processing helix chain 'F' and resid 33 through 39 removed outlier: 3.603A pdb=" N SER F 38 " --> pdb=" O LYS F 34 " (cutoff:3.500A) Processing helix chain 'F' and resid 45 through 51 Processing helix chain 'F' and resid 53 through 62 Processing helix chain 'F' and resid 75 through 82 removed outlier: 3.901A pdb=" N PHE F 81 " --> pdb=" O LEU F 77 " (cutoff:3.500A) removed outlier: 4.728A pdb=" N MET F 82 " --> pdb=" O LYS F 78 " (cutoff:3.500A) Processing helix chain 'F' and resid 106 through 113 Processing helix chain 'F' and resid 115 through 128 Processing helix chain 'F' and resid 143 through 158 Processing helix chain 'F' and resid 166 through 168 No H-bonds generated for 'chain 'F' and resid 166 through 168' Processing helix chain 'F' and resid 184 through 187 Processing helix chain 'F' and resid 189 through 196 Processing helix chain 'F' and resid 215 through 217 No H-bonds generated for 'chain 'F' and resid 215 through 217' Processing helix chain 'F' and resid 225 through 237 removed outlier: 3.663A pdb=" N SER F 231 " --> pdb=" O THR F 227 " (cutoff:3.500A) Proline residue: F 232 - end of helix Processing helix chain 'F' and resid 239 through 244 Processing helix chain 'F' and resid 276 through 284 Processing helix chain 'F' and resid 291 through 293 No H-bonds generated for 'chain 'F' and resid 291 through 293' Processing helix chain 'F' and resid 311 through 313 No H-bonds generated for 'chain 'F' and resid 311 through 313' Processing helix chain 'F' and resid 319 through 323 Processing helix chain 'F' and resid 343 through 357 Processing helix chain 'F' and resid 363 through 381 removed outlier: 4.223A pdb=" N ASP F 370 " --> pdb=" O ARG F 366 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N ARG F 381 " --> pdb=" O ALA F 377 " (cutoff:3.500A) Processing helix chain 'F' and resid 386 through 399 Processing helix chain 'F' and resid 407 through 421 Proline residue: F 414 - end of helix Processing helix chain 'F' and resid 423 through 437 Processing helix chain 'G' and resid 26 through 33 removed outlier: 3.629A pdb=" N LYS G 32 " --> pdb=" O GLN G 28 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N VAL G 33 " --> pdb=" O ALA G 29 " (cutoff:3.500A) Processing helix chain 'G' and resid 84 through 99 Processing helix chain 'G' and resid 105 through 107 No H-bonds generated for 'chain 'G' and resid 105 through 107' Processing helix chain 'G' and resid 115 through 123 Processing helix chain 'G' and resid 150 through 152 No H-bonds generated for 'chain 'G' and resid 150 through 152' Processing helix chain 'G' and resid 158 through 165 Processing helix chain 'G' and resid 178 through 180 No H-bonds generated for 'chain 'G' and resid 178 through 180' Processing helix chain 'G' and resid 196 through 202 removed outlier: 4.026A pdb=" N ILE G 202 " --> pdb=" O ILE G 199 " (cutoff:3.500A) Processing helix chain 'G' and resid 219 through 221 No H-bonds generated for 'chain 'G' and resid 219 through 221' Processing helix chain 'G' and resid 265 through 269 Processing helix chain 'G' and resid 271 through 275 Processing helix chain 'G' and resid 296 through 309 removed outlier: 3.613A pdb=" N SER G 309 " --> pdb=" O GLY G 305 " (cutoff:3.500A) Processing helix chain 'G' and resid 312 through 314 No H-bonds generated for 'chain 'G' and resid 312 through 314' Processing helix chain 'G' and resid 325 through 338 removed outlier: 3.644A pdb=" N VAL G 338 " --> pdb=" O LEU G 334 " (cutoff:3.500A) Processing helix chain 'G' and resid 359 through 361 No H-bonds generated for 'chain 'G' and resid 359 through 361' Processing helix chain 'G' and resid 368 through 371 Processing helix chain 'G' and resid 384 through 387 No H-bonds generated for 'chain 'G' and resid 384 through 387' Processing helix chain 'G' and resid 389 through 401 Processing helix chain 'G' and resid 426 through 434 removed outlier: 3.539A pdb=" N ASP G 431 " --> pdb=" O ILE G 428 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N SER G 434 " --> pdb=" O ASP G 431 " (cutoff:3.500A) Processing helix chain 'G' and resid 438 through 445 removed outlier: 4.013A pdb=" N VAL G 442 " --> pdb=" O PRO G 438 " (cutoff:3.500A) Processing helix chain 'G' and resid 455 through 459 Processing helix chain 'G' and resid 463 through 478 Processing helix chain 'G' and resid 499 through 505 Processing helix chain 'G' and resid 512 through 516 Processing helix chain 'G' and resid 554 through 556 No H-bonds generated for 'chain 'G' and resid 554 through 556' Processing helix chain 'G' and resid 566 through 568 No H-bonds generated for 'chain 'G' and resid 566 through 568' Processing helix chain 'G' and resid 596 through 606 removed outlier: 3.582A pdb=" N ILE G 600 " --> pdb=" O ASP G 596 " (cutoff:3.500A) Processing helix chain 'G' and resid 616 through 626 removed outlier: 3.507A pdb=" N VAL G 626 " --> pdb=" O ARG G 622 " (cutoff:3.500A) Processing helix chain 'G' and resid 628 through 631 removed outlier: 3.588A pdb=" N VAL G 631 " --> pdb=" O PRO G 628 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 628 through 631' Processing helix chain 'G' and resid 642 through 650 Processing helix chain 'G' and resid 668 through 670 No H-bonds generated for 'chain 'G' and resid 668 through 670' Processing helix chain 'G' and resid 676 through 680 Processing helix chain 'G' and resid 682 through 692 Processing helix chain 'H' and resid 3 through 32 Proline residue: H 12 - end of helix removed outlier: 3.890A pdb=" N LEU H 22 " --> pdb=" O ALA H 18 " (cutoff:3.500A) Processing helix chain 'H' and resid 42 through 44 No H-bonds generated for 'chain 'H' and resid 42 through 44' Processing helix chain 'H' and resid 47 through 57 Processing helix chain 'H' and resid 68 through 86 Proline residue: H 75 - end of helix removed outlier: 4.473A pdb=" N TRP H 86 " --> pdb=" O ALA H 82 " (cutoff:3.500A) Processing helix chain 'H' and resid 101 through 123 removed outlier: 4.291A pdb=" N VAL H 113 " --> pdb=" O SER H 109 " (cutoff:3.500A) removed outlier: 4.701A pdb=" N TYR H 114 " --> pdb=" O SER H 110 " (cutoff:3.500A) removed outlier: 4.305A pdb=" N SER H 115 " --> pdb=" O LEU H 111 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N ILE H 116 " --> pdb=" O ALA H 112 " (cutoff:3.500A) Processing helix chain 'H' and resid 126 through 157 removed outlier: 4.258A pdb=" N THR H 145 " --> pdb=" O SER H 141 " (cutoff:3.500A) removed outlier: 4.199A pdb=" N MET H 156 " --> pdb=" O SER H 152 " (cutoff:3.500A) Processing helix chain 'H' and resid 163 through 168 removed outlier: 3.523A pdb=" N THR H 167 " --> pdb=" O SER H 163 " (cutoff:3.500A) Processing helix chain 'H' and resid 174 through 192 Proline residue: H 180 - end of helix removed outlier: 3.525A pdb=" N MET H 184 " --> pdb=" O PRO H 180 " (cutoff:3.500A) Processing helix chain 'H' and resid 225 through 242 Processing helix chain 'H' and resid 252 through 276 removed outlier: 3.588A pdb=" N SER H 276 " --> pdb=" O TRP H 272 " (cutoff:3.500A) Processing helix chain 'H' and resid 282 through 290 Processing helix chain 'H' and resid 293 through 311 Proline residue: H 308 - end of helix Processing helix chain 'I' and resid 14 through 26 Processing helix chain 'I' and resid 28 through 42 removed outlier: 3.586A pdb=" N GLY I 33 " --> pdb=" O GLU I 29 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N PHE I 42 " --> pdb=" O LEU I 38 " (cutoff:3.500A) Processing helix chain 'I' and resid 82 through 86 Processing helix chain 'I' and resid 121 through 125 Processing helix chain 'I' and resid 145 through 147 No H-bonds generated for 'chain 'I' and resid 145 through 147' Processing helix chain 'I' and resid 151 through 175 removed outlier: 5.525A pdb=" N ALA I 163 " --> pdb=" O ASP I 159 " (cutoff:3.500A) removed outlier: 6.067A pdb=" N GLU I 164 " --> pdb=" O LYS I 160 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N ALA I 167 " --> pdb=" O ALA I 163 " (cutoff:3.500A) removed outlier: 5.371A pdb=" N LEU I 174 " --> pdb=" O GLN I 170 " (cutoff:3.500A) removed outlier: 5.926A pdb=" N TYR I 175 " --> pdb=" O ALA I 171 " (cutoff:3.500A) Processing helix chain 'J' and resid 5 through 21 Processing helix chain 'J' and resid 26 through 47 Processing helix chain 'J' and resid 50 through 58 Processing helix chain 'J' and resid 64 through 74 Processing helix chain 'J' and resid 87 through 110 Processing helix chain 'J' and resid 125 through 127 No H-bonds generated for 'chain 'J' and resid 125 through 127' Processing helix chain 'J' and resid 138 through 148 removed outlier: 4.091A pdb=" N LEU J 146 " --> pdb=" O GLY J 142 " (cutoff:3.500A) removed outlier: 4.850A pdb=" N TYR J 147 " --> pdb=" O ILE J 143 " (cutoff:3.500A) removed outlier: 4.360A pdb=" N SER J 148 " --> pdb=" O ALA J 144 " (cutoff:3.500A) Processing helix chain 'J' and resid 151 through 171 Processing helix chain 'K' and resid 4 through 20 Processing helix chain 'K' and resid 26 through 51 removed outlier: 3.586A pdb=" N CYS K 32 " --> pdb=" O SER K 28 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N MET K 37 " --> pdb=" O LEU K 33 " (cutoff:3.500A) Processing helix chain 'K' and resid 54 through 85 removed outlier: 3.729A pdb=" N MET K 58 " --> pdb=" O LEU K 55 " (cutoff:3.500A) Proline residue: K 60 - end of helix removed outlier: 3.845A pdb=" N PHE K 66 " --> pdb=" O LEU K 63 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N ALA K 67 " --> pdb=" O LEU K 64 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N LEU K 75 " --> pdb=" O ALA K 72 " (cutoff:3.500A) Processing helix chain 'K' and resid 90 through 92 No H-bonds generated for 'chain 'K' and resid 90 through 92' Processing helix chain 'K' and resid 95 through 97 No H-bonds generated for 'chain 'K' and resid 95 through 97' Processing helix chain 'L' and resid 3 through 21 removed outlier: 4.063A pdb=" N LEU L 12 " --> pdb=" O SER L 8 " (cutoff:3.500A) Proline residue: L 18 - end of helix Processing helix chain 'L' and resid 32 through 57 removed outlier: 3.649A pdb=" N ILE L 49 " --> pdb=" O ILE L 45 " (cutoff:3.500A) Proline residue: L 50 - end of helix Processing helix chain 'L' and resid 84 through 107 Proline residue: L 91 - end of helix removed outlier: 3.814A pdb=" N TRP L 106 " --> pdb=" O GLU L 102 " (cutoff:3.500A) Processing helix chain 'L' and resid 114 through 133 Processing helix chain 'L' and resid 137 through 155 Processing helix chain 'L' and resid 162 through 193 removed outlier: 4.202A pdb=" N GLY L 181 " --> pdb=" O ILE L 177 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N PHE L 182 " --> pdb=" O GLY L 178 " (cutoff:3.500A) Processing helix chain 'L' and resid 198 through 204 Processing helix chain 'L' and resid 210 through 223 removed outlier: 3.584A pdb=" N GLY L 222 " --> pdb=" O LEU L 218 " (cutoff:3.500A) Processing helix chain 'L' and resid 231 through 237 removed outlier: 3.980A pdb=" N MET L 237 " --> pdb=" O LEU L 233 " (cutoff:3.500A) Processing helix chain 'L' and resid 241 through 250 removed outlier: 4.668A pdb=" N SER L 249 " --> pdb=" O ALA L 245 " (cutoff:3.500A) Processing helix chain 'L' and resid 253 through 262 removed outlier: 3.740A pdb=" N GLY L 256 " --> pdb=" O VAL L 253 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ILE L 261 " --> pdb=" O PHE L 258 " (cutoff:3.500A) Processing helix chain 'L' and resid 264 through 269 removed outlier: 4.498A pdb=" N ASN L 269 " --> pdb=" O PRO L 265 " (cutoff:3.500A) Processing helix chain 'L' and resid 271 through 294 removed outlier: 3.575A pdb=" N ILE L 276 " --> pdb=" O TYR L 272 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N LEU L 293 " --> pdb=" O ALA L 289 " (cutoff:3.500A) removed outlier: 4.366A pdb=" N THR L 294 " --> pdb=" O MET L 290 " (cutoff:3.500A) Processing helix chain 'L' and resid 298 through 319 removed outlier: 3.516A pdb=" N VAL L 315 " --> pdb=" O GLY L 311 " (cutoff:3.500A) Processing helix chain 'L' and resid 322 through 349 removed outlier: 3.813A pdb=" N PHE L 334 " --> pdb=" O CYS L 330 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N PHE L 335 " --> pdb=" O THR L 331 " (cutoff:3.500A) Processing helix chain 'L' and resid 356 through 358 No H-bonds generated for 'chain 'L' and resid 356 through 358' Processing helix chain 'L' and resid 362 through 365 No H-bonds generated for 'chain 'L' and resid 362 through 365' Processing helix chain 'L' and resid 367 through 381 Processing helix chain 'L' and resid 387 through 400 removed outlier: 3.606A pdb=" N TYR L 390 " --> pdb=" O THR L 387 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N SER L 391 " --> pdb=" O GLY L 388 " (cutoff:3.500A) removed outlier: 4.138A pdb=" N LYS L 392 " --> pdb=" O PHE L 389 " (cutoff:3.500A) removed outlier: 6.005A pdb=" N ASP L 393 " --> pdb=" O TYR L 390 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N LEU L 394 " --> pdb=" O SER L 391 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N ALA L 399 " --> pdb=" O ILE L 396 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N ASN L 400 " --> pdb=" O GLU L 397 " (cutoff:3.500A) Processing helix chain 'L' and resid 406 through 430 removed outlier: 3.837A pdb=" N ALA L 420 " --> pdb=" O THR L 416 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ILE L 421 " --> pdb=" O SER L 417 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N ILE L 426 " --> pdb=" O TYR L 422 " (cutoff:3.500A) Processing helix chain 'L' and resid 448 through 469 removed outlier: 6.199A pdb=" N GLY L 465 " --> pdb=" O SER L 461 " (cutoff:3.500A) removed outlier: 5.049A pdb=" N TYR L 466 " --> pdb=" O LEU L 462 " (cutoff:3.500A) Processing helix chain 'L' and resid 484 through 487 No H-bonds generated for 'chain 'L' and resid 484 through 487' Processing helix chain 'L' and resid 489 through 509 removed outlier: 3.509A pdb=" N THR L 494 " --> pdb=" O ALA L 490 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N THR L 508 " --> pdb=" O ILE L 504 " (cutoff:3.500A) removed outlier: 4.262A pdb=" N LYS L 509 " --> pdb=" O SER L 505 " (cutoff:3.500A) Processing helix chain 'L' and resid 518 through 524 Processing helix chain 'L' and resid 526 through 547 Proline residue: L 530 - end of helix removed outlier: 3.643A pdb=" N MET L 533 " --> pdb=" O PRO L 530 " (cutoff:3.500A) removed outlier: 4.609A pdb=" N HIS L 534 " --> pdb=" O THR L 531 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N LEU L 536 " --> pdb=" O MET L 533 " (cutoff:3.500A) removed outlier: 5.874A pdb=" N ALA L 537 " --> pdb=" O HIS L 534 " (cutoff:3.500A) Proline residue: L 538 - end of helix removed outlier: 3.698A pdb=" N LEU L 542 " --> pdb=" O TYR L 539 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N LYS L 547 " --> pdb=" O MET L 544 " (cutoff:3.500A) Processing helix chain 'L' and resid 557 through 560 No H-bonds generated for 'chain 'L' and resid 557 through 560' Processing helix chain 'L' and resid 563 through 578 Processing helix chain 'L' and resid 584 through 600 Processing helix chain 'M' and resid 5 through 17 removed outlier: 4.287A pdb=" N MET M 12 " --> pdb=" O THR M 8 " (cutoff:3.500A) Proline residue: M 13 - end of helix Processing helix chain 'M' and resid 20 through 42 removed outlier: 3.904A pdb=" N ILE M 23 " --> pdb=" O ASN M 20 " (cutoff:3.500A) removed outlier: 5.314A pdb=" N TRP M 24 " --> pdb=" O ASN M 21 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N ASN M 26 " --> pdb=" O ILE M 23 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N SER M 27 " --> pdb=" O TRP M 24 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N THR M 28 " --> pdb=" O VAL M 25 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ALA M 29 " --> pdb=" O ASN M 26 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N HIS M 30 " --> pdb=" O SER M 27 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N SER M 31 " --> pdb=" O THR M 28 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N LEU M 32 " --> pdb=" O ALA M 29 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N ILE M 34 " --> pdb=" O SER M 31 " (cutoff:3.500A) Processing helix chain 'M' and resid 60 through 80 Proline residue: M 64 - end of helix removed outlier: 3.706A pdb=" N LEU M 73 " --> pdb=" O THR M 69 " (cutoff:3.500A) Proline residue: M 74 - end of helix Processing helix chain 'M' and resid 89 through 111 Processing helix chain 'M' and resid 115 through 136 removed outlier: 4.547A pdb=" N LEU M 126 " --> pdb=" O PHE M 122 " (cutoff:3.500A) removed outlier: 4.226A pdb=" N VAL M 127 " --> pdb=" O GLU M 123 " (cutoff:3.500A) Proline residue: M 128 - end of helix Processing helix chain 'M' and resid 140 through 171 removed outlier: 3.694A pdb=" N LEU M 143 " --> pdb=" O THR M 140 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N PHE M 149 " --> pdb=" O GLY M 146 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N PHE M 151 " --> pdb=" O TYR M 148 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N TYR M 152 " --> pdb=" O PHE M 149 " (cutoff:3.500A) removed outlier: 4.224A pdb=" N LEU M 154 " --> pdb=" O PHE M 151 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N ALA M 155 " --> pdb=" O TYR M 152 " (cutoff:3.500A) removed outlier: 4.672A pdb=" N LEU M 158 " --> pdb=" O ALA M 155 " (cutoff:3.500A) Proline residue: M 159 - end of helix removed outlier: 3.641A pdb=" N ILE M 165 " --> pdb=" O VAL M 162 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N VAL M 171 " --> pdb=" O GLN M 168 " (cutoff:3.500A) Processing helix chain 'M' and resid 176 through 182 removed outlier: 3.834A pdb=" N TYR M 181 " --> pdb=" O LEU M 177 " (cutoff:3.500A) Processing helix chain 'M' and resid 190 through 204 removed outlier: 4.516A pdb=" N ALA M 202 " --> pdb=" O ALA M 198 " (cutoff:3.500A) removed outlier: 5.333A pdb=" N PHE M 203 " --> pdb=" O CYS M 199 " (cutoff:3.500A) Processing helix chain 'M' and resid 214 through 222 removed outlier: 4.009A pdb=" N LYS M 218 " --> pdb=" O LEU M 214 " (cutoff:3.500A) Processing helix chain 'M' and resid 225 through 233 Processing helix chain 'M' and resid 235 through 249 removed outlier: 4.174A pdb=" N GLY M 239 " --> pdb=" O LEU M 235 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N GLY M 240 " --> pdb=" O LEU M 236 " (cutoff:3.500A) removed outlier: 5.078A pdb=" N LEU M 248 " --> pdb=" O LEU M 244 " (cutoff:3.500A) removed outlier: 4.808A pdb=" N ILE M 249 " --> pdb=" O ARG M 245 " (cutoff:3.500A) Processing helix chain 'M' and resid 253 through 257 removed outlier: 3.790A pdb=" N MET M 257 " --> pdb=" O THR M 254 " (cutoff:3.500A) Processing helix chain 'M' and resid 259 through 278 removed outlier: 3.698A pdb=" N ILE M 270 " --> pdb=" O LEU M 266 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N LEU M 277 " --> pdb=" O SER M 273 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N ARG M 278 " --> pdb=" O SER M 274 " (cutoff:3.500A) Processing helix chain 'M' and resid 282 through 303 removed outlier: 3.615A pdb=" N SER M 290 " --> pdb=" O ILE M 286 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N VAL M 291 " --> pdb=" O ALA M 287 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N LEU M 296 " --> pdb=" O SER M 292 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N VAL M 297 " --> pdb=" O HIS M 293 " (cutoff:3.500A) Processing helix chain 'M' and resid 306 through 337 removed outlier: 3.968A pdb=" N ARG M 336 " --> pdb=" O SER M 332 " (cutoff:3.500A) Processing helix chain 'M' and resid 348 through 351 No H-bonds generated for 'chain 'M' and resid 348 through 351' Processing helix chain 'M' and resid 353 through 366 Processing helix chain 'M' and resid 373 through 388 Processing helix chain 'M' and resid 390 through 415 removed outlier: 3.657A pdb=" N MET M 396 " --> pdb=" O ILE M 393 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N VAL M 398 " --> pdb=" O LEU M 395 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ASN M 399 " --> pdb=" O MET M 396 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N THR M 403 " --> pdb=" O MET M 400 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N TYR M 406 " --> pdb=" O THR M 403 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N SER M 407 " --> pdb=" O ALA M 404 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N LEU M 408 " --> pdb=" O LEU M 405 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N TYR M 409 " --> pdb=" O TYR M 406 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N MET M 410 " --> pdb=" O SER M 407 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N ILE M 412 " --> pdb=" O TYR M 409 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N MET M 413 " --> pdb=" O MET M 410 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N THR M 414 " --> pdb=" O LEU M 411 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N GLN M 415 " --> pdb=" O ILE M 412 " (cutoff:3.500A) Processing helix chain 'M' and resid 431 through 448 removed outlier: 3.763A pdb=" N HIS M 440 " --> pdb=" O LEU M 436 " (cutoff:3.500A) Proline residue: M 443 - end of helix removed outlier: 3.933A pdb=" N THR M 448 " --> pdb=" O LEU M 444 " (cutoff:3.500A) Processing helix chain 'M' and resid 451 through 454 Processing helix chain 'N' and resid 3 through 22 Processing helix chain 'N' and resid 26 through 44 Proline residue: N 42 - end of helix Processing helix chain 'N' and resid 50 through 81 Processing helix chain 'N' and resid 92 through 106 Processing helix chain 'N' and resid 113 through 120 removed outlier: 4.137A pdb=" N GLU N 117 " --> pdb=" O PHE N 113 " (cutoff:3.500A) Processing helix chain 'N' and resid 124 through 131 Processing helix chain 'N' and resid 133 through 148 removed outlier: 4.224A pdb=" N ALA N 137 " --> pdb=" O GLN N 134 " (cutoff:3.500A) Proline residue: N 138 - end of helix removed outlier: 3.735A pdb=" N TYR N 143 " --> pdb=" O SER N 140 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N ILE N 145 " --> pdb=" O LEU N 142 " (cutoff:3.500A) removed outlier: 4.338A pdb=" N PHE N 146 " --> pdb=" O TYR N 143 " (cutoff:3.500A) Proline residue: N 147 - end of helix Processing helix chain 'N' and resid 151 through 171 removed outlier: 3.755A pdb=" N LEU N 170 " --> pdb=" O GLY N 166 " (cutoff:3.500A) removed outlier: 4.196A pdb=" N ASN N 171 " --> pdb=" O TRP N 167 " (cutoff:3.500A) Processing helix chain 'N' and resid 175 through 192 removed outlier: 3.748A pdb=" N TRP N 189 " --> pdb=" O ALA N 185 " (cutoff:3.500A) Processing helix chain 'N' and resid 198 through 222 removed outlier: 3.835A pdb=" N ASN N 222 " --> pdb=" O MET N 218 " (cutoff:3.500A) Processing helix chain 'N' and resid 227 through 235 removed outlier: 3.761A pdb=" N HIS N 232 " --> pdb=" O LEU N 228 " (cutoff:3.500A) removed outlier: 4.355A pdb=" N THR N 233 " --> pdb=" O SER N 229 " (cutoff:3.500A) removed outlier: 4.950A pdb=" N TRP N 234 " --> pdb=" O LEU N 230 " (cutoff:3.500A) removed outlier: 5.746A pdb=" N ASN N 235 " --> pdb=" O SER N 231 " (cutoff:3.500A) Processing helix chain 'N' and resid 238 through 251 removed outlier: 3.629A pdb=" N VAL N 242 " --> pdb=" O PRO N 238 " (cutoff:3.500A) Processing helix chain 'N' and resid 258 through 272 Proline residue: N 262 - end of helix removed outlier: 3.541A pdb=" N ILE N 266 " --> pdb=" O LYS N 263 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ILE N 267 " --> pdb=" O TRP N 264 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N THR N 271 " --> pdb=" O GLN N 268 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N LYS N 272 " --> pdb=" O GLU N 269 " (cutoff:3.500A) Processing helix chain 'N' and resid 277 through 300 removed outlier: 3.820A pdb=" N LEU N 287 " --> pdb=" O ALA N 283 " (cutoff:3.500A) removed outlier: 4.439A pdb=" N LEU N 288 " --> pdb=" O ILE N 284 " (cutoff:3.500A) removed outlier: 4.379A pdb=" N ASN N 289 " --> pdb=" O THR N 285 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N LEU N 296 " --> pdb=" O PHE N 292 " (cutoff:3.500A) Processing helix chain 'N' and resid 309 through 316 removed outlier: 3.691A pdb=" N GLN N 316 " --> pdb=" O MET N 313 " (cutoff:3.500A) Processing helix chain 'N' and resid 326 through 332 removed outlier: 3.515A pdb=" N VAL N 331 " --> pdb=" O PRO N 327 " (cutoff:3.500A) Processing helix chain 'N' and resid 337 through 346 Proline residue: N 341 - end of helix Processing helix chain 'O' and resid 5 through 9 Processing helix chain 'O' and resid 14 through 17 No H-bonds generated for 'chain 'O' and resid 14 through 17' Processing helix chain 'O' and resid 35 through 46 Processing helix chain 'O' and resid 58 through 62 removed outlier: 3.558A pdb=" N THR O 62 " --> pdb=" O TYR O 58 " (cutoff:3.500A) No H-bonds generated for 'chain 'O' and resid 58 through 62' Processing helix chain 'O' and resid 71 through 74 Processing helix chain 'O' and resid 80 through 84 Processing helix chain 'O' and resid 92 through 118 Processing helix chain 'O' and resid 131 through 140 removed outlier: 3.575A pdb=" N TYR O 139 " --> pdb=" O GLU O 136 " (cutoff:3.500A) Processing helix chain 'O' and resid 146 through 162 removed outlier: 4.664A pdb=" N CYS O 161 " --> pdb=" O LYS O 157 " (cutoff:3.500A) removed outlier: 5.485A pdb=" N GLU O 162 " --> pdb=" O VAL O 158 " (cutoff:3.500A) Processing helix chain 'O' and resid 176 through 186 Processing helix chain 'O' and resid 191 through 193 No H-bonds generated for 'chain 'O' and resid 191 through 193' Processing helix chain 'O' and resid 196 through 208 removed outlier: 3.616A pdb=" N GLU O 203 " --> pdb=" O LEU O 199 " (cutoff:3.500A) Processing helix chain 'O' and resid 210 through 215 Processing helix chain 'O' and resid 225 through 229 removed outlier: 3.761A pdb=" N GLN O 229 " --> pdb=" O ALA O 225 " (cutoff:3.500A) No H-bonds generated for 'chain 'O' and resid 225 through 229' Processing helix chain 'O' and resid 231 through 240 removed outlier: 3.659A pdb=" N TYR O 240 " --> pdb=" O GLU O 236 " (cutoff:3.500A) Processing helix chain 'O' and resid 247 through 249 No H-bonds generated for 'chain 'O' and resid 247 through 249' Processing helix chain 'O' and resid 253 through 264 removed outlier: 3.521A pdb=" N LEU O 262 " --> pdb=" O LYS O 258 " (cutoff:3.500A) Processing helix chain 'O' and resid 266 through 269 No H-bonds generated for 'chain 'O' and resid 266 through 269' Processing helix chain 'O' and resid 271 through 274 removed outlier: 4.043A pdb=" N SER O 274 " --> pdb=" O ASN O 271 " (cutoff:3.500A) No H-bonds generated for 'chain 'O' and resid 271 through 274' Processing helix chain 'O' and resid 286 through 298 Processing helix chain 'O' and resid 310 through 312 No H-bonds generated for 'chain 'O' and resid 310 through 312' Processing helix chain 'O' and resid 317 through 319 No H-bonds generated for 'chain 'O' and resid 317 through 319' Processing helix chain 'P' and resid 29 through 40 removed outlier: 4.140A pdb=" N TYR P 33 " --> pdb=" O PHE P 29 " (cutoff:3.500A) Processing helix chain 'P' and resid 53 through 62 removed outlier: 3.507A pdb=" N MET P 57 " --> pdb=" O TYR P 54 " (cutoff:3.500A) removed outlier: 4.670A pdb=" N HIS P 58 " --> pdb=" O ASP P 55 " (cutoff:3.500A) Proline residue: P 61 - end of helix Processing helix chain 'P' and resid 78 through 85 removed outlier: 3.595A pdb=" N ALA P 84 " --> pdb=" O SER P 80 " (cutoff:3.500A) Processing helix chain 'P' and resid 106 through 110 Processing helix chain 'P' and resid 112 through 124 Processing helix chain 'P' and resid 144 through 159 Processing helix chain 'P' and resid 179 through 187 removed outlier: 3.892A pdb=" N ILE P 185 " --> pdb=" O TYR P 181 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N ARG P 186 " --> pdb=" O PHE P 182 " (cutoff:3.500A) removed outlier: 5.098A pdb=" N TRP P 187 " --> pdb=" O ALA P 183 " (cutoff:3.500A) Processing helix chain 'P' and resid 207 through 219 Processing helix chain 'P' and resid 221 through 223 No H-bonds generated for 'chain 'P' and resid 221 through 223' Processing helix chain 'P' and resid 238 through 249 Processing helix chain 'P' and resid 264 through 272 removed outlier: 3.725A pdb=" N ILE P 272 " --> pdb=" O ARG P 268 " (cutoff:3.500A) Processing helix chain 'P' and resid 281 through 287 Processing helix chain 'P' and resid 300 through 303 No H-bonds generated for 'chain 'P' and resid 300 through 303' Processing helix chain 'P' and resid 310 through 312 No H-bonds generated for 'chain 'P' and resid 310 through 312' Processing helix chain 'P' and resid 314 through 320 removed outlier: 5.236A pdb=" N ARG P 320 " --> pdb=" O GLU P 316 " (cutoff:3.500A) Processing helix chain 'Q' and resid 28 through 31 No H-bonds generated for 'chain 'Q' and resid 28 through 31' Processing helix chain 'Q' and resid 89 through 98 Processing helix chain 'Q' and resid 118 through 122 Processing helix chain 'R' and resid 23 through 28 Processing helix chain 'R' and resid 40 through 46 removed outlier: 3.566A pdb=" N GLU R 46 " --> pdb=" O ASP R 42 " (cutoff:3.500A) Processing helix chain 'R' and resid 64 through 66 No H-bonds generated for 'chain 'R' and resid 64 through 66' Processing helix chain 'S' and resid 27 through 46 removed outlier: 5.225A pdb=" N GLY S 31 " --> pdb=" O GLY S 28 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N ARG S 39 " --> pdb=" O ILE S 36 " (cutoff:3.500A) removed outlier: 5.279A pdb=" N TYR S 40 " --> pdb=" O GLU S 37 " (cutoff:3.500A) removed outlier: 4.887A pdb=" N VAL S 41 " --> pdb=" O LYS S 38 " (cutoff:3.500A) Processing helix chain 'S' and resid 69 through 71 No H-bonds generated for 'chain 'S' and resid 69 through 71' Processing helix chain 'S' and resid 85 through 95 Processing helix chain 'T' and resid 8 through 21 Processing helix chain 'T' and resid 27 through 29 No H-bonds generated for 'chain 'T' and resid 27 through 29' Processing helix chain 'T' and resid 44 through 58 Processing helix chain 'T' and resid 64 through 69 removed outlier: 4.221A pdb=" N LYS T 69 " --> pdb=" O ILE T 65 " (cutoff:3.500A) Processing helix chain 'T' and resid 73 through 84 Processing helix chain 'U' and resid 8 through 21 Processing helix chain 'U' and resid 27 through 29 No H-bonds generated for 'chain 'U' and resid 27 through 29' Processing helix chain 'U' and resid 44 through 58 Processing helix chain 'U' and resid 64 through 69 removed outlier: 4.720A pdb=" N LYS U 69 " --> pdb=" O ILE U 65 " (cutoff:3.500A) Processing helix chain 'U' and resid 73 through 83 Processing helix chain 'V' and resid 19 through 36 removed outlier: 4.119A pdb=" N HIS V 36 " --> pdb=" O ASP V 32 " (cutoff:3.500A) Processing helix chain 'V' and resid 42 through 60 Processing helix chain 'V' and resid 64 through 71 removed outlier: 3.727A pdb=" N GLU V 69 " --> pdb=" O LYS V 65 " (cutoff:3.500A) Processing helix chain 'V' and resid 76 through 96 removed outlier: 3.782A pdb=" N GLN V 95 " --> pdb=" O ARG V 91 " (cutoff:3.500A) Processing helix chain 'W' and resid 25 through 49 Proline residue: W 44 - end of helix Processing helix chain 'W' and resid 56 through 68 Processing helix chain 'W' and resid 76 through 94 Processing helix chain 'W' and resid 100 through 106 removed outlier: 4.450A pdb=" N PHE W 106 " --> pdb=" O HIS W 102 " (cutoff:3.500A) Processing helix chain 'W' and resid 118 through 124 removed outlier: 3.516A pdb=" N VAL W 124 " --> pdb=" O SER W 120 " (cutoff:3.500A) Processing helix chain 'X' and resid 21 through 34 removed outlier: 4.743A pdb=" N HIS X 29 " --> pdb=" O LYS X 25 " (cutoff:3.500A) removed outlier: 5.609A pdb=" N HIS X 30 " --> pdb=" O ALA X 26 " (cutoff:3.500A) Processing helix chain 'X' and resid 36 through 49 Processing helix chain 'X' and resid 52 through 76 removed outlier: 3.707A pdb=" N CYS X 55 " --> pdb=" O PRO X 52 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N LEU X 56 " --> pdb=" O ARG X 53 " (cutoff:3.500A) removed outlier: 5.839A pdb=" N GLU X 57 " --> pdb=" O ARG X 54 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N GLU X 58 " --> pdb=" O CYS X 55 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N GLY X 59 " --> pdb=" O LEU X 56 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N VAL X 62 " --> pdb=" O GLY X 59 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N LEU X 67 " --> pdb=" O GLN X 64 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N GLU X 68 " --> pdb=" O CYS X 65 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N ILE X 73 " --> pdb=" O PHE X 70 " (cutoff:3.500A) Processing helix chain 'X' and resid 78 through 90 removed outlier: 3.540A pdb=" N CYS X 87 " --> pdb=" O GLU X 83 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N TYR X 90 " --> pdb=" O THR X 86 " (cutoff:3.500A) Processing helix chain 'X' and resid 100 through 113 Processing helix chain 'Y' and resid 3 through 10 Processing helix chain 'Y' and resid 17 through 42 Processing helix chain 'Y' and resid 48 through 79 Processing helix chain 'Y' and resid 86 through 104 Processing helix chain 'Y' and resid 107 through 130 Processing helix chain 'Z' and resid 32 through 97 removed outlier: 3.504A pdb=" N ARG Z 68 " --> pdb=" O ASP Z 64 " (cutoff:3.500A) Proline residue: Z 73 - end of helix Processing helix chain 'Z' and resid 121 through 124 No H-bonds generated for 'chain 'Z' and resid 121 through 124' Processing helix chain 'Z' and resid 130 through 142 removed outlier: 5.948A pdb=" N PHE Z 140 " --> pdb=" O ALA Z 136 " (cutoff:3.500A) removed outlier: 5.593A pdb=" N ILE Z 141 " --> pdb=" O THR Z 137 " (cutoff:3.500A) Processing helix chain 'a' and resid 2 through 29 Proline residue: a 7 - end of helix removed outlier: 3.566A pdb=" N VAL a 14 " --> pdb=" O VAL a 11 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N LEU a 16 " --> pdb=" O GLY a 13 " (cutoff:3.500A) Proline residue: a 19 - end of helix removed outlier: 3.540A pdb=" N ALA a 24 " --> pdb=" O MET a 21 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N HIS a 27 " --> pdb=" O ALA a 24 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ARG a 28 " --> pdb=" O ARG a 25 " (cutoff:3.500A) Processing helix chain 'a' and resid 42 through 55 Processing helix chain 'a' and resid 66 through 68 No H-bonds generated for 'chain 'a' and resid 66 through 68' Processing helix chain 'b' and resid 3 through 14 removed outlier: 3.546A pdb=" N PHE b 7 " --> pdb=" O ARG b 3 " (cutoff:3.500A) Processing helix chain 'b' and resid 16 through 34 Proline residue: b 32 - end of helix Processing helix chain 'b' and resid 38 through 46 removed outlier: 3.693A pdb=" N LEU b 42 " --> pdb=" O THR b 38 " (cutoff:3.500A) Processing helix chain 'b' and resid 78 through 82 Processing helix chain 'c' and resid 14 through 46 Processing helix chain 'd' and resid 16 through 20 Processing helix chain 'd' and resid 29 through 49 removed outlier: 3.653A pdb=" N ARG d 49 " --> pdb=" O ASP d 45 " (cutoff:3.500A) Processing helix chain 'd' and resid 58 through 96 removed outlier: 3.523A pdb=" N LEU d 63 " --> pdb=" O HIS d 59 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N TYR d 74 " --> pdb=" O PHE d 70 " (cutoff:3.500A) Processing helix chain 'e' and resid 5 through 9 Processing helix chain 'e' and resid 15 through 17 No H-bonds generated for 'chain 'e' and resid 15 through 17' Processing helix chain 'e' and resid 25 through 27 No H-bonds generated for 'chain 'e' and resid 25 through 27' Processing helix chain 'e' and resid 33 through 43 Processing helix chain 'e' and resid 48 through 54 removed outlier: 4.185A pdb=" N LYS e 53 " --> pdb=" O ILE e 49 " (cutoff:3.500A) Processing helix chain 'e' and resid 56 through 67 Processing helix chain 'e' and resid 69 through 87 Processing helix chain 'f' and resid 6 through 33 removed outlier: 5.886A pdb=" N VAL f 12 " --> pdb=" O ARG f 8 " (cutoff:3.500A) removed outlier: 6.373A pdb=" N HIS f 13 " --> pdb=" O ASP f 9 " (cutoff:3.500A) removed outlier: 4.888A pdb=" N VAL f 14 " --> pdb=" O HIS f 10 " (cutoff:3.500A) removed outlier: 4.580A pdb=" N LEU f 15 " --> pdb=" O TRP f 11 " (cutoff:3.500A) removed outlier: 4.799A pdb=" N VAL f 16 " --> pdb=" O VAL f 12 " (cutoff:3.500A) Proline residue: f 17 - end of helix removed outlier: 4.027A pdb=" N LYS f 33 " --> pdb=" O LYS f 29 " (cutoff:3.500A) Processing helix chain 'g' and resid 37 through 40 No H-bonds generated for 'chain 'g' and resid 37 through 40' Processing helix chain 'g' and resid 51 through 65 Processing helix chain 'g' and resid 69 through 78 Processing helix chain 'g' and resid 83 through 102 removed outlier: 3.684A pdb=" N GLN g 86 " --> pdb=" O TYR g 83 " (cutoff:3.500A) removed outlier: 5.851A pdb=" N GLU g 87 " --> pdb=" O ARG g 84 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N LYS g 98 " --> pdb=" O ARG g 95 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N ARG g 100 " --> pdb=" O VAL g 97 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N GLU g 101 " --> pdb=" O LYS g 98 " (cutoff:3.500A) Processing helix chain 'g' and resid 115 through 117 No H-bonds generated for 'chain 'g' and resid 115 through 117' Processing helix chain 'h' and resid 16 through 46 removed outlier: 4.047A pdb=" N THR h 32 " --> pdb=" O TYR h 28 " (cutoff:3.500A) Proline residue: h 35 - end of helix Processing helix chain 'h' and resid 63 through 66 removed outlier: 3.810A pdb=" N TYR h 66 " --> pdb=" O HIS h 63 " (cutoff:3.500A) No H-bonds generated for 'chain 'h' and resid 63 through 66' Processing helix chain 'h' and resid 70 through 78 Processing helix chain 'h' and resid 83 through 117 removed outlier: 3.557A pdb=" N ALA h 116 " --> pdb=" O ARG h 112 " (cutoff:3.500A) Processing helix chain 'h' and resid 130 through 132 No H-bonds generated for 'chain 'h' and resid 130 through 132' Processing helix chain 'i' and resid 5 through 25 Processing helix chain 'i' and resid 41 through 51 removed outlier: 3.561A pdb=" N PHE i 49 " --> pdb=" O PHE i 45 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N LEU i 50 " --> pdb=" O TRP i 46 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N GLN i 51 " --> pdb=" O ASN i 47 " (cutoff:3.500A) Processing helix chain 'i' and resid 57 through 73 removed outlier: 5.008A pdb=" N TYR i 61 " --> pdb=" O ASN i 58 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N TYR i 64 " --> pdb=" O TYR i 61 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N HIS i 66 " --> pdb=" O THR i 63 " (cutoff:3.500A) removed outlier: 4.297A pdb=" N PHE i 69 " --> pdb=" O HIS i 66 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N ALA i 70 " --> pdb=" O SER i 67 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N HIS i 73 " --> pdb=" O ALA i 70 " (cutoff:3.500A) Processing helix chain 'i' and resid 75 through 88 Processing helix chain 'j' and resid 19 through 48 removed outlier: 6.728A pdb=" N ASP j 45 " --> pdb=" O TRP j 41 " (cutoff:3.500A) removed outlier: 6.707A pdb=" N ALA j 46 " --> pdb=" O HIS j 42 " (cutoff:3.500A) removed outlier: 4.311A pdb=" N VAL j 47 " --> pdb=" O ASP j 43 " (cutoff:3.500A) Processing helix chain 'j' and resid 56 through 58 No H-bonds generated for 'chain 'j' and resid 56 through 58' Processing helix chain 'k' and resid 18 through 20 No H-bonds generated for 'chain 'k' and resid 18 through 20' Processing helix chain 'k' and resid 27 through 36 removed outlier: 3.571A pdb=" N VAL k 31 " --> pdb=" O PRO k 27 " (cutoff:3.500A) Processing helix chain 'k' and resid 45 through 52 removed outlier: 4.636A pdb=" N TRP k 50 " --> pdb=" O ASN k 47 " (cutoff:3.500A) Processing helix chain 'k' and resid 54 through 56 No H-bonds generated for 'chain 'k' and resid 54 through 56' Processing helix chain 'k' and resid 62 through 66 Processing helix chain 'k' and resid 70 through 90 Processing helix chain 'l' and resid 6 through 8 No H-bonds generated for 'chain 'l' and resid 6 through 8' Processing helix chain 'l' and resid 17 through 26 Processing helix chain 'l' and resid 55 through 57 No H-bonds generated for 'chain 'l' and resid 55 through 57' Processing helix chain 'l' and resid 81 through 84 No H-bonds generated for 'chain 'l' and resid 81 through 84' Processing helix chain 'l' and resid 98 through 121 Processing helix chain 'l' and resid 134 through 138 Processing helix chain 'm' and resid 15 through 17 No H-bonds generated for 'chain 'm' and resid 15 through 17' Processing helix chain 'm' and resid 19 through 22 No H-bonds generated for 'chain 'm' and resid 19 through 22' Processing helix chain 'm' and resid 26 through 50 removed outlier: 3.791A pdb=" N GLN m 49 " --> pdb=" O GLU m 45 " (cutoff:3.500A) Processing helix chain 'm' and resid 62 through 70 Processing helix chain 'm' and resid 76 through 78 No H-bonds generated for 'chain 'm' and resid 76 through 78' Processing helix chain 'm' and resid 83 through 93 Processing helix chain 'm' and resid 95 through 117 Processing helix chain 'n' and resid 11 through 30 Processing helix chain 'n' and resid 33 through 50 removed outlier: 4.564A pdb=" N HIS n 50 " --> pdb=" O ARG n 46 " (cutoff:3.500A) Processing helix chain 'n' and resid 56 through 73 removed outlier: 3.653A pdb=" N HIS n 72 " --> pdb=" O GLU n 68 " (cutoff:3.500A) Processing helix chain 'n' and resid 94 through 96 No H-bonds generated for 'chain 'n' and resid 94 through 96' Processing helix chain 'n' and resid 100 through 105 Processing helix chain 'n' and resid 108 through 113 removed outlier: 3.721A pdb=" N MET n 113 " --> pdb=" O SER n 109 " (cutoff:3.500A) Processing helix chain 'n' and resid 115 through 142 removed outlier: 3.582A pdb=" N GLN n 123 " --> pdb=" O ALA n 119 " (cutoff:3.500A) removed outlier: 4.682A pdb=" N GLU n 133 " --> pdb=" O ARG n 129 " (cutoff:3.500A) removed outlier: 5.318A pdb=" N AARG n 134 " --> pdb=" O GLU n 130 " (cutoff:3.500A) Processing helix chain 'n' and resid 167 through 170 No H-bonds generated for 'chain 'n' and resid 167 through 170' Processing helix chain 'o' and resid 2 through 8 removed outlier: 3.530A pdb=" N ARG o 7 " --> pdb=" O HIS o 3 " (cutoff:3.500A) Processing helix chain 'o' and resid 42 through 48 Processing helix chain 'o' and resid 52 through 54 No H-bonds generated for 'chain 'o' and resid 52 through 54' Processing helix chain 'o' and resid 59 through 71 Processing helix chain 'o' and resid 80 through 121 Processing helix chain 'p' and resid 28 through 39 Processing helix chain 'p' and resid 41 through 57 Processing helix chain 'p' and resid 73 through 75 No H-bonds generated for 'chain 'p' and resid 73 through 75' Processing helix chain 'p' and resid 81 through 123 removed outlier: 6.411A pdb=" N GLU p 118 " --> pdb=" O GLN p 114 " (cutoff:3.500A) removed outlier: 7.115A pdb=" N SER p 119 " --> pdb=" O ARG p 115 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N HIS p 120 " --> pdb=" O GLU p 116 " (cutoff:3.500A) removed outlier: 5.220A pdb=" N ARG p 121 " --> pdb=" O GLY p 117 " (cutoff:3.500A) removed outlier: 6.383A pdb=" N GLN p 122 " --> pdb=" O GLU p 118 " (cutoff:3.500A) Processing helix chain 'p' and resid 125 through 142 Processing helix chain 'p' and resid 151 through 174 removed outlier: 3.591A pdb=" N ALA p 172 " --> pdb=" O ALA p 168 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N ALA p 174 " --> pdb=" O LYS p 170 " (cutoff:3.500A) Processing helix chain 'q' and resid 2 through 16 removed outlier: 4.073A pdb=" N VAL q 14 " --> pdb=" O GLY q 10 " (cutoff:3.500A) Processing helix chain 'q' and resid 19 through 29 Processing helix chain 'q' and resid 79 through 81 No H-bonds generated for 'chain 'q' and resid 79 through 81' Processing helix chain 'q' and resid 84 through 90 removed outlier: 4.243A pdb=" N TRP q 89 " --> pdb=" O GLU q 85 " (cutoff:3.500A) Processing helix chain 'r' and resid 5 through 15 Processing helix chain 'r' and resid 53 through 56 Processing helix chain 'r' and resid 59 through 61 No H-bonds generated for 'chain 'r' and resid 59 through 61' Processing helix chain 's' and resid 42 through 44 No H-bonds generated for 'chain 's' and resid 42 through 44' Processing helix chain 's' and resid 50 through 60 removed outlier: 3.570A pdb=" N SER s 59 " --> pdb=" O ASN s 55 " (cutoff:3.500A) removed outlier: 4.969A pdb=" N LYS s 60 " --> pdb=" O LEU s 56 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'B' and resid 47 through 51 removed outlier: 6.657A pdb=" N VAL B 85 " --> pdb=" O MET B 48 " (cutoff:3.500A) removed outlier: 7.195A pdb=" N PHE B 50 " --> pdb=" O VAL B 85 " (cutoff:3.500A) removed outlier: 6.698A pdb=" N ILE B 87 " --> pdb=" O PHE B 50 " (cutoff:3.500A) removed outlier: 6.493A pdb=" N TYR B 112 " --> pdb=" O MET B 86 " (cutoff:3.500A) removed outlier: 7.663A pdb=" N VAL B 88 " --> pdb=" O TYR B 112 " (cutoff:3.500A) removed outlier: 6.883A pdb=" N VAL B 114 " --> pdb=" O VAL B 88 " (cutoff:3.500A) removed outlier: 6.271A pdb=" N ILE B 144 " --> pdb=" O SER B 115 " (cutoff:3.500A) No H-bonds generated for sheet with id= A Processing sheet with id= B, first strand: chain 'C' and resid 74 through 82 removed outlier: 6.689A pdb=" N ASN C 95 " --> pdb=" O ALA C 76 " (cutoff:3.500A) removed outlier: 4.293A pdb=" N LEU C 78 " --> pdb=" O VAL C 93 " (cutoff:3.500A) removed outlier: 6.655A pdb=" N VAL C 93 " --> pdb=" O LEU C 78 " (cutoff:3.500A) removed outlier: 4.249A pdb=" N ALA C 80 " --> pdb=" O GLU C 91 " (cutoff:3.500A) removed outlier: 6.316A pdb=" N GLU C 91 " --> pdb=" O ALA C 80 " (cutoff:3.500A) removed outlier: 6.524A pdb=" N LEU C 48 " --> pdb=" O ARG C 106 " (cutoff:3.500A) removed outlier: 7.750A pdb=" N LYS C 108 " --> pdb=" O LEU C 48 " (cutoff:3.500A) removed outlier: 6.384A pdb=" N ILE C 50 " --> pdb=" O LYS C 108 " (cutoff:3.500A) removed outlier: 8.684A pdb=" N TYR C 110 " --> pdb=" O ILE C 50 " (cutoff:3.500A) removed outlier: 8.691A pdb=" N ILE C 52 " --> pdb=" O TYR C 110 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'C' and resid 172 through 177 Processing sheet with id= D, first strand: chain 'D' and resid 361 through 369 Processing sheet with id= E, first strand: chain 'E' and resid 137 through 142 removed outlier: 6.707A pdb=" N TYR E 98 " --> pdb=" O THR E 138 " (cutoff:3.500A) removed outlier: 8.099A pdb=" N ILE E 140 " --> pdb=" O TYR E 98 " (cutoff:3.500A) removed outlier: 6.366A pdb=" N ILE E 100 " --> pdb=" O ILE E 140 " (cutoff:3.500A) removed outlier: 7.061A pdb=" N VAL E 142 " --> pdb=" O ILE E 100 " (cutoff:3.500A) removed outlier: 6.337A pdb=" N VAL E 102 " --> pdb=" O VAL E 142 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'F' and resid 220 through 224 removed outlier: 6.927A pdb=" N TYR F 92 " --> pdb=" O THR F 221 " (cutoff:3.500A) removed outlier: 8.098A pdb=" N ALA F 223 " --> pdb=" O TYR F 92 " (cutoff:3.500A) removed outlier: 6.199A pdb=" N VAL F 94 " --> pdb=" O ALA F 223 " (cutoff:3.500A) removed outlier: 6.446A pdb=" N ALA F 133 " --> pdb=" O LEU F 93 " (cutoff:3.500A) removed outlier: 7.674A pdb=" N VAL F 95 " --> pdb=" O ALA F 133 " (cutoff:3.500A) removed outlier: 6.584A pdb=" N TYR F 135 " --> pdb=" O VAL F 95 " (cutoff:3.500A) removed outlier: 7.013A pdb=" N ALA F 97 " --> pdb=" O TYR F 135 " (cutoff:3.500A) removed outlier: 6.602A pdb=" N TYR F 137 " --> pdb=" O ALA F 97 " (cutoff:3.500A) removed outlier: 6.386A pdb=" N ASP F 174 " --> pdb=" O ALA F 134 " (cutoff:3.500A) removed outlier: 7.534A pdb=" N ILE F 136 " --> pdb=" O ASP F 174 " (cutoff:3.500A) removed outlier: 6.677A pdb=" N PHE F 176 " --> pdb=" O ILE F 136 " (cutoff:3.500A) removed outlier: 7.532A pdb=" N ILE F 138 " --> pdb=" O PHE F 176 " (cutoff:3.500A) removed outlier: 6.227A pdb=" N VAL F 178 " --> pdb=" O ILE F 138 " (cutoff:3.500A) No H-bonds generated for sheet with id= F Processing sheet with id= G, first strand: chain 'F' and resid 266 through 271 Processing sheet with id= H, first strand: chain 'G' and resid 9 through 13 Processing sheet with id= I, first strand: chain 'G' and resid 146 through 148 Processing sheet with id= J, first strand: chain 'G' and resid 173 through 175 Processing sheet with id= K, first strand: chain 'G' and resid 223 through 228 removed outlier: 6.411A pdb=" N ARG G 243 " --> pdb=" O VAL G 247 " (cutoff:3.500A) removed outlier: 5.625A pdb=" N VAL G 247 " --> pdb=" O ARG G 243 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'G' and resid 283 through 285 Processing sheet with id= M, first strand: chain 'G' and resid 343 through 345 removed outlier: 8.330A pdb=" N CYS G 344 " --> pdb=" O VAL G 315 " (cutoff:3.500A) removed outlier: 6.273A pdb=" N ALA G 317 " --> pdb=" O CYS G 344 " (cutoff:3.500A) removed outlier: 6.348A pdb=" N MET G 521 " --> pdb=" O ALA G 316 " (cutoff:3.500A) removed outlier: 7.924A pdb=" N ILE G 318 " --> pdb=" O MET G 521 " (cutoff:3.500A) removed outlier: 6.409A pdb=" N PHE G 523 " --> pdb=" O ILE G 318 " (cutoff:3.500A) removed outlier: 6.263A pdb=" N PHE G 542 " --> pdb=" O LEU G 522 " (cutoff:3.500A) removed outlier: 7.274A pdb=" N LEU G 524 " --> pdb=" O PHE G 542 " (cutoff:3.500A) removed outlier: 6.382A pdb=" N VAL G 544 " --> pdb=" O LEU G 524 " (cutoff:3.500A) removed outlier: 6.483A pdb=" N VAL G 559 " --> pdb=" O TYR G 545 " (cutoff:3.500A) removed outlier: 7.984A pdb=" N GLY G 547 " --> pdb=" O VAL G 559 " (cutoff:3.500A) removed outlier: 6.177A pdb=" N LEU G 561 " --> pdb=" O GLY G 547 " (cutoff:3.500A) No H-bonds generated for sheet with id= M Processing sheet with id= N, first strand: chain 'G' and resid 490 through 493 removed outlier: 8.278A pdb=" N ASN G 491 " --> pdb=" O PRO G 449 " (cutoff:3.500A) removed outlier: 6.309A pdb=" N VAL G 451 " --> pdb=" O ASN G 491 " (cutoff:3.500A) removed outlier: 7.212A pdb=" N LEU G 493 " --> pdb=" O VAL G 451 " (cutoff:3.500A) removed outlier: 6.730A pdb=" N LEU G 453 " --> pdb=" O LEU G 493 " (cutoff:3.500A) removed outlier: 6.506A pdb=" N VAL G 376 " --> pdb=" O MET G 450 " (cutoff:3.500A) removed outlier: 7.742A pdb=" N ILE G 452 " --> pdb=" O VAL G 376 " (cutoff:3.500A) removed outlier: 6.315A pdb=" N LEU G 378 " --> pdb=" O ILE G 452 " (cutoff:3.500A) removed outlier: 7.568A pdb=" N GLY G 454 " --> pdb=" O LEU G 378 " (cutoff:3.500A) removed outlier: 7.508A pdb=" N VAL G 380 " --> pdb=" O GLY G 454 " (cutoff:3.500A) removed outlier: 6.498A pdb=" N LYS G 405 " --> pdb=" O VAL G 377 " (cutoff:3.500A) removed outlier: 7.780A pdb=" N LEU G 379 " --> pdb=" O LYS G 405 " (cutoff:3.500A) removed outlier: 6.464A pdb=" N ALA G 407 " --> pdb=" O LEU G 379 " (cutoff:3.500A) removed outlier: 6.338A pdb=" N ASP G 420 " --> pdb=" O LEU G 408 " (cutoff:3.500A) No H-bonds generated for sheet with id= N Processing sheet with id= O, first strand: chain 'G' and resid 572 through 574 Processing sheet with id= P, first strand: chain 'I' and resid 65 through 67 Processing sheet with id= Q, first strand: chain 'I' and resid 92 through 98 removed outlier: 6.078A pdb=" N GLU I 97 " --> pdb=" O THR I 106 " (cutoff:3.500A) removed outlier: 5.316A pdb=" N THR I 106 " --> pdb=" O GLU I 97 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'J' and resid 112 through 115 Processing sheet with id= S, first strand: chain 'L' and resid 69 through 71 Processing sheet with id= T, first strand: chain 'L' and resid 61 through 67 removed outlier: 3.509A pdb=" N ASN L 65 " --> pdb=" O LEU L 78 " (cutoff:3.500A) removed outlier: 6.913A pdb=" N LEU L 78 " --> pdb=" O ASN L 65 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'O' and resid 219 through 223 removed outlier: 3.555A pdb=" N VAL O 168 " --> pdb=" O LEU O 24 " (cutoff:3.500A) removed outlier: 6.145A pdb=" N VAL O 122 " --> pdb=" O ILE O 25 " (cutoff:3.500A) removed outlier: 7.699A pdb=" N VAL O 27 " --> pdb=" O VAL O 122 " (cutoff:3.500A) removed outlier: 6.638A pdb=" N LEU O 124 " --> pdb=" O VAL O 27 " (cutoff:3.500A) removed outlier: 6.637A pdb=" N LYS O 49 " --> pdb=" O VAL O 123 " (cutoff:3.500A) removed outlier: 8.355A pdb=" N GLU O 125 " --> pdb=" O LYS O 49 " (cutoff:3.500A) removed outlier: 8.227A pdb=" N PHE O 51 " --> pdb=" O GLU O 125 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'P' and resid 227 through 230 removed outlier: 6.496A pdb=" N ILE P 165 " --> pdb=" O PHE P 228 " (cutoff:3.500A) removed outlier: 7.537A pdb=" N PHE P 230 " --> pdb=" O ILE P 165 " (cutoff:3.500A) removed outlier: 6.468A pdb=" N LYS P 167 " --> pdb=" O PHE P 230 " (cutoff:3.500A) removed outlier: 6.388A pdb=" N GLN P 44 " --> pdb=" O ALA P 21 " (cutoff:3.500A) removed outlier: 7.446A pdb=" N VAL P 23 " --> pdb=" O GLN P 44 " (cutoff:3.500A) removed outlier: 6.769A pdb=" N ILE P 46 " --> pdb=" O VAL P 23 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'Q' and resid 102 through 105 Processing sheet with id= X, first strand: chain 'Q' and resid 64 through 66 Processing sheet with id= Y, first strand: chain 'R' and resid 50 through 52 Processing sheet with id= Z, first strand: chain 'R' and resid 56 through 59 Processing sheet with id= AA, first strand: chain 'S' and resid 51 through 56 removed outlier: 3.500A pdb=" N LEU S 22 " --> pdb=" O ARG S 55 " (cutoff:3.500A) removed outlier: 6.517A pdb=" N ARG S 67 " --> pdb=" O ARG S 16 " (cutoff:3.500A) removed outlier: 4.342A pdb=" N ILE S 18 " --> pdb=" O TRP S 65 " (cutoff:3.500A) removed outlier: 6.483A pdb=" N TRP S 65 " --> pdb=" O ILE S 18 " (cutoff:3.500A) removed outlier: 4.481A pdb=" N ILE S 20 " --> pdb=" O LYS S 63 " (cutoff:3.500A) removed outlier: 6.569A pdb=" N LYS S 63 " --> pdb=" O ILE S 20 " (cutoff:3.500A) Processing sheet with id= AB, first strand: chain 'q' and resid 60 through 63 removed outlier: 6.541A pdb=" N GLU q 50 " --> pdb=" O LEU q 38 " (cutoff:3.500A) removed outlier: 5.578A pdb=" N LEU q 38 " --> pdb=" O GLU q 50 " (cutoff:3.500A) 2831 hydrogen bonds defined for protein. 7767 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: 22.58 Time building geometry restraints manager: 24.66 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.40: 28079 1.40 - 1.63: 40864 1.63 - 1.85: 873 1.85 - 2.08: 0 2.08 - 2.30: 80 Bond restraints: 69896 Sorted by residual: bond pdb=" C15 CHD L 705 " pdb=" C16 CHD L 705 " ideal model delta sigma weight residual 1.541 1.724 -0.183 2.00e-02 2.50e+03 8.35e+01 bond pdb=" C5 GTP O 401 " pdb=" N7 GTP O 401 " ideal model delta sigma weight residual 1.350 1.520 -0.170 2.00e-02 2.50e+03 7.26e+01 bond pdb=" C6 GTP O 401 " pdb=" O6 GTP O 401 " ideal model delta sigma weight residual 1.230 1.395 -0.165 2.00e-02 2.50e+03 6.77e+01 bond pdb=" C11 CHD L 705 " pdb=" C12 CHD L 705 " ideal model delta sigma weight residual 1.533 1.669 -0.136 2.00e-02 2.50e+03 4.61e+01 bond pdb=" CA7 CDL X 201 " pdb=" OA8 CDL X 201 " ideal model delta sigma weight residual 1.334 1.404 -0.070 1.10e-02 8.26e+03 4.10e+01 ... (remaining 69891 not shown) Histogram of bond angle deviations from ideal: 72.61 - 84.91: 76 84.91 - 97.21: 1 97.21 - 109.52: 8272 109.52 - 121.82: 72895 121.82 - 134.13: 13148 Bond angle restraints: 94392 Sorted by residual: angle pdb=" C51 CDL h 201 " pdb=" CB5 CDL h 201 " pdb=" OB6 CDL h 201 " ideal model delta sigma weight residual 111.33 121.41 -10.08 1.32e+00 5.72e-01 5.82e+01 angle pdb=" C51 CDL N 902 " pdb=" CB5 CDL N 902 " pdb=" OB6 CDL N 902 " ideal model delta sigma weight residual 111.33 121.10 -9.77 1.32e+00 5.72e-01 5.46e+01 angle pdb=" C51 CDL L 702 " pdb=" CB5 CDL L 702 " pdb=" OB6 CDL L 702 " ideal model delta sigma weight residual 111.33 120.50 -9.17 1.32e+00 5.72e-01 4.82e+01 angle pdb=" C11 CDL r 201 " pdb=" CA5 CDL r 201 " pdb=" OA6 CDL r 201 " ideal model delta sigma weight residual 111.33 120.46 -9.13 1.32e+00 5.72e-01 4.77e+01 angle pdb=" C51 CDL X 201 " pdb=" CB5 CDL X 201 " pdb=" OB6 CDL X 201 " ideal model delta sigma weight residual 111.33 120.20 -8.87 1.32e+00 5.72e-01 4.50e+01 ... (remaining 94387 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.92: 41399 35.92 - 71.84: 1091 71.84 - 107.76: 116 107.76 - 143.68: 6 143.68 - 179.60: 3 Dihedral angle restraints: 42615 sinusoidal: 18700 harmonic: 23915 Sorted by residual: dihedral pdb=" CD BARG n 134 " pdb=" NE BARG n 134 " pdb=" CZ BARG n 134 " pdb=" NH1BARG n 134 " ideal model delta sinusoidal sigma weight residual 0.00 -179.60 179.60 1 1.00e+01 1.00e-02 1.92e+02 dihedral pdb=" C10 FMN F 501 " pdb=" C1' FMN F 501 " pdb=" N10 FMN F 501 " pdb=" C2' FMN F 501 " ideal model delta sinusoidal sigma weight residual 257.59 84.48 173.11 1 2.00e+01 2.50e-03 4.78e+01 dihedral pdb=" C5' FMN F 501 " pdb=" O5' FMN F 501 " pdb=" P FMN F 501 " pdb=" O1P FMN F 501 " ideal model delta sinusoidal sigma weight residual 75.26 -89.51 164.77 1 2.00e+01 2.50e-03 4.72e+01 ... (remaining 42612 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 4.259: 10143 4.259 - 8.518: 0 8.518 - 12.777: 0 12.777 - 17.036: 0 17.036 - 21.295: 16 Chirality restraints: 10159 Sorted by residual: chirality pdb="FE1 SF4 I 202 " pdb=" S2 SF4 I 202 " pdb=" S3 SF4 I 202 " pdb=" S4 SF4 I 202 " both_signs ideal model delta sigma weight residual False -10.55 10.74 -21.29 2.00e-01 2.50e+01 1.13e+04 chirality pdb="FE1 SF4 G 802 " pdb=" S2 SF4 G 802 " pdb=" S3 SF4 G 802 " pdb=" S4 SF4 G 802 " both_signs ideal model delta sigma weight residual False -10.55 10.73 -21.28 2.00e-01 2.50e+01 1.13e+04 chirality pdb="FE2 SF4 G 802 " pdb=" S1 SF4 G 802 " pdb=" S3 SF4 G 802 " pdb=" S4 SF4 G 802 " both_signs ideal model delta sigma weight residual False 10.55 -10.72 21.28 2.00e-01 2.50e+01 1.13e+04 ... (remaining 10156 not shown) Planarity restraints: 11738 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD 2MR D 85 " 0.049 2.00e-02 2.50e+03 8.45e-02 1.25e+02 pdb=" NE 2MR D 85 " -0.094 2.00e-02 2.50e+03 pdb=" CZ 2MR D 85 " -0.048 2.00e-02 2.50e+03 pdb=" NH1 2MR D 85 " -0.116 2.00e-02 2.50e+03 pdb=" NH2 2MR D 85 " 0.094 2.00e-02 2.50e+03 pdb=" CQ1 2MR D 85 " 0.119 2.00e-02 2.50e+03 pdb=" CQ2 2MR D 85 " -0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR B 125 " 0.044 2.00e-02 2.50e+03 3.21e-02 2.06e+01 pdb=" CG TYR B 125 " -0.076 2.00e-02 2.50e+03 pdb=" CD1 TYR B 125 " 0.016 2.00e-02 2.50e+03 pdb=" CD2 TYR B 125 " -0.001 2.00e-02 2.50e+03 pdb=" CE1 TYR B 125 " -0.009 2.00e-02 2.50e+03 pdb=" CE2 TYR B 125 " 0.008 2.00e-02 2.50e+03 pdb=" CZ TYR B 125 " 0.009 2.00e-02 2.50e+03 pdb=" OH TYR B 125 " 0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLY D 86 " 0.014 2.00e-02 2.50e+03 2.93e-02 8.57e+00 pdb=" C GLY D 86 " -0.051 2.00e-02 2.50e+03 pdb=" O GLY D 86 " 0.019 2.00e-02 2.50e+03 pdb=" N THR D 87 " 0.017 2.00e-02 2.50e+03 ... (remaining 11735 not shown) Histogram of nonbonded interaction distances: 1.85 - 2.51: 588 2.51 - 3.17: 60732 3.17 - 3.83: 139762 3.83 - 4.48: 212372 4.48 - 5.14: 325679 Nonbonded interactions: 739133 Sorted by model distance: nonbonded pdb=" O HOH G 986 " pdb=" O HOH G1010 " model vdw 1.853 2.440 nonbonded pdb=" O LYS Q 133 " pdb=" O HOH Q 201 " model vdw 1.873 2.440 nonbonded pdb=" O HOH Z 322 " pdb=" O HOH e 210 " model vdw 1.885 2.440 nonbonded pdb=" OD2 ASP F 98 " pdb=" O HOH F 601 " model vdw 1.896 2.440 nonbonded pdb=" O1B GTP O 401 " pdb="MG MG O 402 " model vdw 1.911 2.170 ... (remaining 739128 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 'T' selection = (chain 'U' and (resid 4 through 88 or resid 101)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.50 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: 12.480 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.050 Extract box with map and model: 52.180 Check model and map are aligned: 0.810 Set scattering table: 0.500 Process input model: 170.960 Find NCS groups from input model: 2.130 Set up NCS constraints: 0.260 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.020 Load rotamer database and sin/cos tables:8.950 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 248.340 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8408 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 : 0.008 0.183 69896 Z= 0.497 Angle : 0.919 15.178 94392 Z= 0.415 Chirality : 0.847 21.295 10159 Planarity : 0.004 0.085 11738 Dihedral : 16.027 179.598 27174 Min Nonbonded Distance : 1.853 Molprobity Statistics. All-atom Clashscore : 3.83 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.30 % Favored : 96.67 % Rotamer: Outliers : 0.01 % Allowed : 0.17 % Favored : 99.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % 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: -0.45 (0.09), residues: 8090 helix: -0.27 (0.08), residues: 4296 sheet: -0.08 (0.26), residues: 392 loop : -0.13 (0.11), residues: 3402 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.002 TRP P 73 HIS 0.011 0.001 HIS p 143 PHE 0.039 0.002 PHE K 53 TYR 0.076 0.002 TYR B 125 ARG 0.010 0.001 ARG p 141 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16180 Ramachandran restraints generated. 8090 Oldfield, 0 Emsley, 8090 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16180 Ramachandran restraints generated. 8090 Oldfield, 0 Emsley, 8090 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1155 residues out of total 7150 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 1155 time to evaluate : 6.433 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 102 LYS cc_start: 0.7947 (ttpp) cc_final: 0.7674 (tppt) REVERT: G 31 GLU cc_start: 0.7678 (mt-10) cc_final: 0.7155 (mm-30) REVERT: J 65 MET cc_start: 0.8479 (mmm) cc_final: 0.8229 (mmm) REVERT: K 37 MET cc_start: 0.7566 (tmm) cc_final: 0.7361 (tmm) REVERT: N 294 MET cc_start: 0.8253 (mmm) cc_final: 0.8028 (tpt) REVERT: P 57 MET cc_start: 0.8562 (mmm) cc_final: 0.7999 (mmt) REVERT: Q 17 LEU cc_start: 0.7895 (tp) cc_final: 0.7667 (mt) REVERT: T 71 MET cc_start: 0.6549 (mmm) cc_final: 0.6265 (mmt) REVERT: W 68 LYS cc_start: 0.7907 (mmtp) cc_final: 0.7694 (mptm) REVERT: X 36 ASP cc_start: 0.7621 (t70) cc_final: 0.7348 (t70) REVERT: Y 137 GLU cc_start: 0.7572 (tp30) cc_final: 0.7257 (mm-30) REVERT: a 28 ARG cc_start: 0.7415 (mtt90) cc_final: 0.7182 (mmt90) REVERT: b 15 GLU cc_start: 0.8108 (mm-30) cc_final: 0.7729 (mm-30) REVERT: e 80 ARG cc_start: 0.7665 (ttm110) cc_final: 0.7092 (ttm-80) REVERT: h 100 LYS cc_start: 0.8753 (mtmt) cc_final: 0.8536 (mtmp) REVERT: l 32 GLU cc_start: 0.7371 (mp0) cc_final: 0.7067 (mp0) REVERT: m 60 GLU cc_start: 0.7859 (tt0) cc_final: 0.7653 (tt0) REVERT: o 45 MET cc_start: 0.8888 (mtm) cc_final: 0.8644 (mtp) REVERT: p 112 CYS cc_start: 0.5949 (t) cc_final: 0.5725 (t) outliers start: 0 outliers final: 1 residues processed: 1155 average time/residue: 1.7424 time to fit residues: 2557.5375 Evaluate side-chains 809 residues out of total 7150 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 808 time to evaluate : 6.560 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 290 MET Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 799 random chunks: chunk 674 optimal weight: 0.9990 chunk 605 optimal weight: 6.9990 chunk 336 optimal weight: 1.9990 chunk 206 optimal weight: 0.8980 chunk 408 optimal weight: 3.9990 chunk 323 optimal weight: 1.9990 chunk 626 optimal weight: 6.9990 chunk 242 optimal weight: 2.9990 chunk 380 optimal weight: 4.9990 chunk 466 optimal weight: 0.9990 chunk 725 optimal weight: 1.9990 overall best weight: 1.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 108 GLN C 69 ASN D 150 HIS D 200 HIS G 237 ASN G 461 ASN G 581 GLN G 643 GLN H 138 GLN ** H 287 HIS A ** both conformations clash, **PLEASE CHECK MANUALLY** K 83 ASN L 135 ASN L 199 GLN M 139 GLN M 188 ASN O 50 HIS O 76 ASN O 287 HIS O 291 GLN P 321 HIS R 51 GLN S 72 GLN a 68 ASN ** d 117 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** e 69 GLN j 6 HIS l 147 ASN n 140 GLN ** n 159 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** o 116 GLN p 77 GLN r 72 GLN Total number of N/Q/H flips: 29 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8343 moved from start: 0.1561 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.275 69896 Z= 0.461 Angle : 1.308 50.570 94392 Z= 0.838 Chirality : 0.256 6.438 10159 Planarity : 0.005 0.048 11738 Dihedral : 14.248 176.850 10959 Min Nonbonded Distance : 2.030 Molprobity Statistics. All-atom Clashscore : 4.90 Ramachandran Plot: Outliers : 0.04 % Allowed : 1.98 % Favored : 97.98 % Rotamer: Outliers : 1.84 % Allowed : 7.35 % Favored : 90.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % 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: 0.66 (0.09), residues: 8090 helix: 0.89 (0.08), residues: 4330 sheet: 0.11 (0.27), residues: 346 loop : 0.04 (0.11), residues: 3414 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP L 144 HIS 0.007 0.001 HIS G 101 PHE 0.027 0.002 PHE L 24 TYR 0.041 0.001 TYR B 125 ARG 0.006 0.000 ARG F 339 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16180 Ramachandran restraints generated. 8090 Oldfield, 0 Emsley, 8090 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16180 Ramachandran restraints generated. 8090 Oldfield, 0 Emsley, 8090 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1007 residues out of total 7150 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 131 poor density : 876 time to evaluate : 6.338 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 50 PHE cc_start: 0.6514 (OUTLIER) cc_final: 0.5381 (t80) REVERT: B 102 LYS cc_start: 0.7922 (ttpp) cc_final: 0.7630 (tppt) REVERT: C 73 LYS cc_start: 0.9026 (OUTLIER) cc_final: 0.8255 (mptp) REVERT: C 211 GLN cc_start: 0.8175 (OUTLIER) cc_final: 0.7833 (mt0) REVERT: D 9 GLU cc_start: 0.7113 (OUTLIER) cc_final: 0.6808 (tt0) REVERT: D 342 MET cc_start: 0.8538 (tpt) cc_final: 0.8155 (tpt) REVERT: G 31 GLU cc_start: 0.7552 (mt-10) cc_final: 0.6982 (mm-30) REVERT: G 673 MET cc_start: 0.8288 (OUTLIER) cc_final: 0.7741 (mtm) REVERT: H 192 GLU cc_start: 0.7756 (tp30) cc_final: 0.7488 (tp30) REVERT: J 64 MET cc_start: 0.8285 (OUTLIER) cc_final: 0.7532 (ttm) REVERT: J 70 TYR cc_start: 0.8831 (t80) cc_final: 0.8523 (t80) REVERT: K 10 MET cc_start: 0.7779 (OUTLIER) cc_final: 0.7496 (tmm) REVERT: M 355 MET cc_start: 0.8379 (tpp) cc_final: 0.8008 (tpp) REVERT: O 311 ASP cc_start: 0.7721 (OUTLIER) cc_final: 0.7458 (p0) REVERT: P 57 MET cc_start: 0.8406 (mmm) cc_final: 0.7879 (mmt) REVERT: P 119 GLN cc_start: 0.7704 (OUTLIER) cc_final: 0.6781 (tm-30) REVERT: P 237 LEU cc_start: 0.8422 (mm) cc_final: 0.8065 (mt) REVERT: R 37 GLU cc_start: 0.7983 (OUTLIER) cc_final: 0.7442 (mp0) REVERT: S 39 ARG cc_start: 0.8230 (OUTLIER) cc_final: 0.7709 (mmm-85) REVERT: U 25 ILE cc_start: 0.8989 (OUTLIER) cc_final: 0.8721 (mp) REVERT: X 43 MET cc_start: 0.8953 (mmm) cc_final: 0.8681 (mmp) REVERT: Y 50 GLU cc_start: 0.6617 (tm-30) cc_final: 0.6384 (tm-30) REVERT: Y 82 LYS cc_start: 0.7939 (OUTLIER) cc_final: 0.7201 (mtpp) REVERT: Y 137 GLU cc_start: 0.7532 (tp30) cc_final: 0.7165 (mm-30) REVERT: Z 132 GLU cc_start: 0.7788 (OUTLIER) cc_final: 0.7110 (tp30) REVERT: a 60 SER cc_start: 0.9105 (OUTLIER) cc_final: 0.8771 (t) REVERT: b 15 GLU cc_start: 0.8043 (mm-30) cc_final: 0.7644 (mm-30) REVERT: e 56 LYS cc_start: 0.8850 (OUTLIER) cc_final: 0.8139 (tmtm) REVERT: e 80 ARG cc_start: 0.7606 (ttm110) cc_final: 0.7121 (ttm-80) REVERT: h 19 LYS cc_start: 0.8195 (ttmm) cc_final: 0.7940 (tttm) REVERT: i 16 GLU cc_start: 0.6376 (OUTLIER) cc_final: 0.6034 (tp30) REVERT: l 32 GLU cc_start: 0.7315 (mp0) cc_final: 0.7082 (mp0) REVERT: m 107 ASP cc_start: 0.8327 (t0) cc_final: 0.8000 (t70) REVERT: m 113 LYS cc_start: 0.7867 (OUTLIER) cc_final: 0.7613 (ttpp) REVERT: o 45 MET cc_start: 0.8916 (mtm) cc_final: 0.8678 (mtp) REVERT: p 72 ASP cc_start: 0.7806 (p0) cc_final: 0.7499 (p0) REVERT: p 123 ASN cc_start: 0.8306 (m-40) cc_final: 0.7935 (m110) REVERT: s 35 ASN cc_start: 0.7301 (t0) cc_final: 0.7090 (t0) outliers start: 131 outliers final: 35 residues processed: 938 average time/residue: 1.6787 time to fit residues: 2018.2164 Evaluate side-chains 843 residues out of total 7150 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 790 time to evaluate : 6.165 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 50 PHE Chi-restraints excluded: chain C residue 73 LYS Chi-restraints excluded: chain C residue 211 GLN Chi-restraints excluded: chain D residue 9 GLU Chi-restraints excluded: chain D residue 22 THR Chi-restraints excluded: chain E residue 134 ASP Chi-restraints excluded: chain G residue 436 SER Chi-restraints excluded: chain G residue 517 ASN Chi-restraints excluded: chain G residue 673 MET Chi-restraints excluded: chain J residue 64 MET Chi-restraints excluded: chain J residue 124 ASP Chi-restraints excluded: chain K residue 10 MET Chi-restraints excluded: chain L residue 197 ASP Chi-restraints excluded: chain M residue 72 LEU Chi-restraints excluded: chain N residue 98 MET Chi-restraints excluded: chain N residue 117 GLU Chi-restraints excluded: chain O residue 85 ASP Chi-restraints excluded: chain O residue 209 THR Chi-restraints excluded: chain O residue 252 ASN Chi-restraints excluded: chain O residue 311 ASP Chi-restraints excluded: chain P residue 119 GLN Chi-restraints excluded: chain P residue 185 ILE Chi-restraints excluded: chain Q residue 18 ASP Chi-restraints excluded: chain R residue 37 GLU Chi-restraints excluded: chain S residue 29 SER Chi-restraints excluded: chain S residue 39 ARG Chi-restraints excluded: chain S residue 49 ASP Chi-restraints excluded: chain S residue 95 SER Chi-restraints excluded: chain T residue 7 THR Chi-restraints excluded: chain U residue 25 ILE Chi-restraints excluded: chain V residue 39 LYS Chi-restraints excluded: chain W residue 16 SER Chi-restraints excluded: chain W residue 27 GLU Chi-restraints excluded: chain Y residue 10 ASP Chi-restraints excluded: chain Y residue 82 LYS Chi-restraints excluded: chain Z residue 20 ASP Chi-restraints excluded: chain Z residue 96 THR Chi-restraints excluded: chain Z residue 132 GLU Chi-restraints excluded: chain a residue 60 SER Chi-restraints excluded: chain c residue 29 ILE Chi-restraints excluded: chain e residue 56 LYS Chi-restraints excluded: chain g residue 37 LEU Chi-restraints excluded: chain i residue 16 GLU Chi-restraints excluded: chain i residue 63 THR Chi-restraints excluded: chain l residue 5 THR Chi-restraints excluded: chain m residue 91 LEU Chi-restraints excluded: chain m residue 113 LYS Chi-restraints excluded: chain n residue 145 VAL Chi-restraints excluded: chain n residue 161 ASP Chi-restraints excluded: chain o residue 23 THR Chi-restraints excluded: chain p residue 119 SER Chi-restraints excluded: chain q residue 142 THR Chi-restraints excluded: chain r residue 2 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 799 random chunks: chunk 403 optimal weight: 2.9990 chunk 225 optimal weight: 8.9990 chunk 603 optimal weight: 8.9990 chunk 494 optimal weight: 4.9990 chunk 200 optimal weight: 5.9990 chunk 726 optimal weight: 0.9990 chunk 785 optimal weight: 0.0370 chunk 647 optimal weight: 0.8980 chunk 720 optimal weight: 0.5980 chunk 247 optimal weight: 4.9990 chunk 583 optimal weight: 0.9980 overall best weight: 0.7060 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 157 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 287 HIS A ** both conformations clash, **PLEASE CHECK MANUALLY** L 579 ASN M 188 ASN N 204 ASN U 74 GLN V 95 GLN d 61 GLN ** d 117 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** j 6 HIS l 147 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8311 moved from start: 0.1981 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.248 69896 Z= 0.434 Angle : 1.282 50.753 94392 Z= 0.828 Chirality : 0.254 6.421 10159 Planarity : 0.004 0.047 11738 Dihedral : 13.441 179.078 10956 Min Nonbonded Distance : 2.062 Molprobity Statistics. All-atom Clashscore : 4.98 Ramachandran Plot: Outliers : 0.04 % Allowed : 2.14 % Favored : 97.82 % Rotamer: Outliers : 1.79 % Allowed : 9.21 % Favored : 89.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % 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: 1.12 (0.09), residues: 8090 helix: 1.35 (0.08), residues: 4304 sheet: 0.17 (0.26), residues: 381 loop : 0.16 (0.11), residues: 3405 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP L 144 HIS 0.004 0.001 HIS G 101 PHE 0.027 0.001 PHE P 275 TYR 0.025 0.001 TYR B 125 ARG 0.009 0.000 ARG C 14 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16180 Ramachandran restraints generated. 8090 Oldfield, 0 Emsley, 8090 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16180 Ramachandran restraints generated. 8090 Oldfield, 0 Emsley, 8090 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 984 residues out of total 7150 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 127 poor density : 857 time to evaluate : 6.495 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 50 PHE cc_start: 0.6524 (OUTLIER) cc_final: 0.5412 (t80) REVERT: B 67 TYR cc_start: 0.8296 (m-80) cc_final: 0.8001 (m-80) REVERT: B 102 LYS cc_start: 0.7911 (ttpp) cc_final: 0.7528 (tttm) REVERT: C 158 GLU cc_start: 0.7601 (OUTLIER) cc_final: 0.7107 (mt-10) REVERT: C 211 GLN cc_start: 0.8186 (OUTLIER) cc_final: 0.7814 (mt0) REVERT: D 410 MET cc_start: 0.8742 (OUTLIER) cc_final: 0.8158 (mtt) REVERT: G 31 GLU cc_start: 0.7575 (mt-10) cc_final: 0.7029 (mm-30) REVERT: G 673 MET cc_start: 0.8153 (OUTLIER) cc_final: 0.7587 (mtm) REVERT: H 79 LEU cc_start: 0.7496 (tp) cc_final: 0.7198 (tm) REVERT: H 121 TRP cc_start: 0.7901 (OUTLIER) cc_final: 0.6964 (t60) REVERT: H 192 GLU cc_start: 0.7731 (tp30) cc_final: 0.7507 (tp30) REVERT: J 64 MET cc_start: 0.8307 (OUTLIER) cc_final: 0.7417 (ttm) REVERT: J 70 TYR cc_start: 0.8660 (t80) cc_final: 0.8390 (t80) REVERT: L 22 MET cc_start: 0.7641 (mtp) cc_final: 0.7400 (mtp) REVERT: L 411 MET cc_start: 0.7119 (OUTLIER) cc_final: 0.6857 (mmt) REVERT: M 355 MET cc_start: 0.8406 (tpp) cc_final: 0.8068 (tpp) REVERT: M 378 GLU cc_start: 0.7541 (OUTLIER) cc_final: 0.7320 (tm-30) REVERT: M 400 MET cc_start: 0.7702 (OUTLIER) cc_final: 0.7372 (ttm) REVERT: O 192 MET cc_start: 0.7915 (OUTLIER) cc_final: 0.7154 (mpp) REVERT: O 311 ASP cc_start: 0.7672 (OUTLIER) cc_final: 0.7456 (p0) REVERT: P 57 MET cc_start: 0.8361 (mmm) cc_final: 0.7877 (mmt) REVERT: T 14 ARG cc_start: 0.7376 (mtm180) cc_final: 0.7014 (mtm180) REVERT: T 51 ILE cc_start: 0.8865 (mm) cc_final: 0.8320 (mm) REVERT: U 61 GLU cc_start: 0.8038 (tt0) cc_final: 0.7822 (tt0) REVERT: U 83 LYS cc_start: 0.8448 (OUTLIER) cc_final: 0.8165 (mptm) REVERT: X 43 MET cc_start: 0.8941 (mmm) cc_final: 0.8701 (mmp) REVERT: Y 137 GLU cc_start: 0.7464 (tp30) cc_final: 0.7117 (mm-30) REVERT: Z 132 GLU cc_start: 0.7777 (OUTLIER) cc_final: 0.7099 (tp30) REVERT: a 60 SER cc_start: 0.9086 (OUTLIER) cc_final: 0.8818 (t) REVERT: b 15 GLU cc_start: 0.8010 (mm-30) cc_final: 0.7618 (mm-30) REVERT: e 56 LYS cc_start: 0.8838 (OUTLIER) cc_final: 0.8064 (tmtm) REVERT: k 38 ARG cc_start: 0.8404 (OUTLIER) cc_final: 0.7459 (ttm110) REVERT: l 32 GLU cc_start: 0.7231 (mp0) cc_final: 0.7026 (mp0) REVERT: m 107 ASP cc_start: 0.8340 (t0) cc_final: 0.8016 (t70) REVERT: n 72 HIS cc_start: 0.7617 (t-170) cc_final: 0.7349 (t-170) REVERT: o 45 MET cc_start: 0.8920 (mtm) cc_final: 0.8660 (mtp) REVERT: p 72 ASP cc_start: 0.7643 (p0) cc_final: 0.7384 (p0) REVERT: q 21 ARG cc_start: 0.7769 (OUTLIER) cc_final: 0.7399 (ttm110) outliers start: 127 outliers final: 41 residues processed: 918 average time/residue: 1.6423 time to fit residues: 1942.5290 Evaluate side-chains 844 residues out of total 7150 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 785 time to evaluate : 6.236 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 30 VAL Chi-restraints excluded: chain B residue 50 PHE Chi-restraints excluded: chain B residue 54 CYS Chi-restraints excluded: chain B residue 70 ASP Chi-restraints excluded: chain C residue 158 GLU Chi-restraints excluded: chain C residue 211 GLN Chi-restraints excluded: chain D residue 22 THR Chi-restraints excluded: chain D residue 410 MET Chi-restraints excluded: chain E residue 19 THR Chi-restraints excluded: chain E residue 134 ASP Chi-restraints excluded: chain G residue 425 SER Chi-restraints excluded: chain G residue 436 SER Chi-restraints excluded: chain G residue 517 ASN Chi-restraints excluded: chain G residue 673 MET Chi-restraints excluded: chain H residue 121 TRP Chi-restraints excluded: chain J residue 64 MET Chi-restraints excluded: chain J residue 90 LEU Chi-restraints excluded: chain J residue 124 ASP Chi-restraints excluded: chain L residue 10 VAL Chi-restraints excluded: chain L residue 24 PHE Chi-restraints excluded: chain L residue 411 MET Chi-restraints excluded: chain M residue 378 GLU Chi-restraints excluded: chain M residue 400 MET Chi-restraints excluded: chain N residue 182 SER Chi-restraints excluded: chain O residue 85 ASP Chi-restraints excluded: chain O residue 192 MET Chi-restraints excluded: chain O residue 250 ASP Chi-restraints excluded: chain O residue 252 ASN Chi-restraints excluded: chain O residue 311 ASP Chi-restraints excluded: chain P residue 185 ILE Chi-restraints excluded: chain Q residue 17 LEU Chi-restraints excluded: chain S residue 29 SER Chi-restraints excluded: chain S residue 82 SER Chi-restraints excluded: chain S residue 90 LEU Chi-restraints excluded: chain T residue 7 THR Chi-restraints excluded: chain T residue 76 ILE Chi-restraints excluded: chain U residue 30 LEU Chi-restraints excluded: chain U residue 32 VAL Chi-restraints excluded: chain U residue 83 LYS Chi-restraints excluded: chain X residue 11 ASP Chi-restraints excluded: chain Y residue 10 ASP Chi-restraints excluded: chain Y residue 36 SER Chi-restraints excluded: chain Y residue 114 CYS Chi-restraints excluded: chain Z residue 20 ASP Chi-restraints excluded: chain Z residue 99 LYS Chi-restraints excluded: chain Z residue 132 GLU Chi-restraints excluded: chain a residue 60 SER Chi-restraints excluded: chain e residue 56 LYS Chi-restraints excluded: chain g residue 37 LEU Chi-restraints excluded: chain g residue 60 VAL Chi-restraints excluded: chain i residue 68 ILE Chi-restraints excluded: chain k residue 38 ARG Chi-restraints excluded: chain l residue 5 THR Chi-restraints excluded: chain m residue 91 LEU Chi-restraints excluded: chain o residue 11 ASP Chi-restraints excluded: chain o residue 23 THR Chi-restraints excluded: chain p residue 119 SER Chi-restraints excluded: chain q residue 21 ARG Chi-restraints excluded: chain r residue 68 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 799 random chunks: chunk 718 optimal weight: 5.9990 chunk 546 optimal weight: 4.9990 chunk 377 optimal weight: 0.9980 chunk 80 optimal weight: 4.9990 chunk 346 optimal weight: 2.9990 chunk 488 optimal weight: 6.9990 chunk 729 optimal weight: 0.9980 chunk 772 optimal weight: 0.6980 chunk 381 optimal weight: 0.9990 chunk 691 optimal weight: 0.0570 chunk 208 optimal weight: 3.9990 overall best weight: 0.7500 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 157 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 37 ASN F 150 GLN F 250 ASN G 640 ASN ** H 287 HIS A ** both conformations clash, **PLEASE CHECK MANUALLY** M 175 ASN N 152 ASN N 204 ASN P 87 HIS R 94 GLN T 33 ASN X 139 ASN d 117 HIS j 6 HIS l 147 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8304 moved from start: 0.2169 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.246 69896 Z= 0.430 Angle : 1.278 50.577 94392 Z= 0.826 Chirality : 0.254 6.395 10159 Planarity : 0.004 0.046 11738 Dihedral : 12.989 178.686 10956 Min Nonbonded Distance : 2.090 Molprobity Statistics. All-atom Clashscore : 5.40 Ramachandran Plot: Outliers : 0.02 % Allowed : 2.04 % Favored : 97.93 % Rotamer: Outliers : 1.94 % Allowed : 10.19 % Favored : 87.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.01 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.30 (0.09), residues: 8090 helix: 1.53 (0.08), residues: 4295 sheet: 0.20 (0.26), residues: 381 loop : 0.21 (0.11), residues: 3414 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP L 144 HIS 0.004 0.001 HIS G 101 PHE 0.032 0.001 PHE L 24 TYR 0.023 0.001 TYR L 422 ARG 0.007 0.000 ARG C 14 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16180 Ramachandran restraints generated. 8090 Oldfield, 0 Emsley, 8090 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16180 Ramachandran restraints generated. 8090 Oldfield, 0 Emsley, 8090 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 979 residues out of total 7150 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 138 poor density : 841 time to evaluate : 6.313 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 102 LYS cc_start: 0.7929 (ttpp) cc_final: 0.7544 (tttm) REVERT: B 116 MET cc_start: 0.8251 (ttt) cc_final: 0.8032 (ttt) REVERT: B 175 ILE cc_start: 0.9021 (OUTLIER) cc_final: 0.8622 (mp) REVERT: C 158 GLU cc_start: 0.7606 (OUTLIER) cc_final: 0.7106 (mt-10) REVERT: C 211 GLN cc_start: 0.8184 (OUTLIER) cc_final: 0.7789 (mt0) REVERT: G 31 GLU cc_start: 0.7613 (mt-10) cc_final: 0.7094 (mm-30) REVERT: G 673 MET cc_start: 0.8116 (OUTLIER) cc_final: 0.7526 (mtm) REVERT: H 79 LEU cc_start: 0.7558 (tp) cc_final: 0.7337 (tm) REVERT: H 121 TRP cc_start: 0.7973 (OUTLIER) cc_final: 0.7106 (t60) REVERT: J 64 MET cc_start: 0.8339 (OUTLIER) cc_final: 0.7429 (ttm) REVERT: J 70 TYR cc_start: 0.8610 (t80) cc_final: 0.8311 (t80) REVERT: K 70 GLU cc_start: 0.7386 (OUTLIER) cc_final: 0.6759 (tt0) REVERT: L 411 MET cc_start: 0.7141 (OUTLIER) cc_final: 0.6872 (mmt) REVERT: M 355 MET cc_start: 0.8402 (tpp) cc_final: 0.8089 (tpp) REVERT: M 378 GLU cc_start: 0.7573 (OUTLIER) cc_final: 0.7362 (tm-30) REVERT: M 400 MET cc_start: 0.7694 (OUTLIER) cc_final: 0.7368 (ttm) REVERT: O 192 MET cc_start: 0.7928 (OUTLIER) cc_final: 0.7565 (mtm) REVERT: P 57 MET cc_start: 0.8355 (mmm) cc_final: 0.7842 (mmt) REVERT: T 14 ARG cc_start: 0.7462 (mtm180) cc_final: 0.7201 (mtm180) REVERT: T 51 ILE cc_start: 0.8831 (mm) cc_final: 0.8299 (mm) REVERT: T 52 MET cc_start: 0.8000 (OUTLIER) cc_final: 0.7626 (ttm) REVERT: U 61 GLU cc_start: 0.8024 (tt0) cc_final: 0.7815 (tt0) REVERT: X 43 MET cc_start: 0.8945 (mmm) cc_final: 0.8692 (mmp) REVERT: Y 137 GLU cc_start: 0.7462 (tp30) cc_final: 0.7124 (mm-30) REVERT: a 60 SER cc_start: 0.9131 (OUTLIER) cc_final: 0.8869 (t) REVERT: b 15 GLU cc_start: 0.8005 (mm-30) cc_final: 0.7621 (mm-30) REVERT: e 4 ASP cc_start: 0.8215 (t70) cc_final: 0.7894 (t0) REVERT: e 56 LYS cc_start: 0.8844 (OUTLIER) cc_final: 0.8053 (tmtm) REVERT: i 12 GLN cc_start: 0.8240 (OUTLIER) cc_final: 0.7862 (tt0) REVERT: k 38 ARG cc_start: 0.8418 (OUTLIER) cc_final: 0.7477 (ttm110) REVERT: l 32 GLU cc_start: 0.7222 (mp0) cc_final: 0.7005 (mp0) REVERT: l 137 ASN cc_start: 0.8288 (t0) cc_final: 0.8069 (t0) REVERT: m 107 ASP cc_start: 0.8366 (t0) cc_final: 0.8044 (t70) REVERT: n 72 HIS cc_start: 0.7620 (t-170) cc_final: 0.7344 (t-170) REVERT: o 42 GLN cc_start: 0.8155 (mt0) cc_final: 0.7883 (mt0) REVERT: o 45 MET cc_start: 0.8910 (mtm) cc_final: 0.8653 (mtp) REVERT: p 72 ASP cc_start: 0.7615 (p0) cc_final: 0.7344 (p0) REVERT: q 21 ARG cc_start: 0.7783 (OUTLIER) cc_final: 0.7406 (ttm110) REVERT: r 29 GLU cc_start: 0.7756 (OUTLIER) cc_final: 0.7386 (pm20) outliers start: 138 outliers final: 60 residues processed: 917 average time/residue: 1.6372 time to fit residues: 1942.5339 Evaluate side-chains 865 residues out of total 7150 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 78 poor density : 787 time to evaluate : 6.275 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 96 ILE Chi-restraints excluded: chain B residue 30 VAL Chi-restraints excluded: chain B residue 50 PHE Chi-restraints excluded: chain B residue 54 CYS Chi-restraints excluded: chain B residue 175 ILE Chi-restraints excluded: chain C residue 17 VAL Chi-restraints excluded: chain C residue 158 GLU Chi-restraints excluded: chain C residue 211 GLN Chi-restraints excluded: chain D residue 22 THR Chi-restraints excluded: chain E residue 19 THR Chi-restraints excluded: chain E residue 114 ASP Chi-restraints excluded: chain G residue 18 VAL Chi-restraints excluded: chain G residue 425 SER Chi-restraints excluded: chain G residue 483 VAL Chi-restraints excluded: chain G residue 517 ASN Chi-restraints excluded: chain G residue 673 MET Chi-restraints excluded: chain H residue 4 ILE Chi-restraints excluded: chain H residue 121 TRP Chi-restraints excluded: chain J residue 64 MET Chi-restraints excluded: chain J residue 113 VAL Chi-restraints excluded: chain J residue 124 ASP Chi-restraints excluded: chain K residue 70 GLU Chi-restraints excluded: chain L residue 10 VAL Chi-restraints excluded: chain L residue 290 MET Chi-restraints excluded: chain L residue 411 MET Chi-restraints excluded: chain L residue 482 MET Chi-restraints excluded: chain M residue 72 LEU Chi-restraints excluded: chain M residue 378 GLU Chi-restraints excluded: chain M residue 385 THR Chi-restraints excluded: chain M residue 400 MET Chi-restraints excluded: chain N residue 38 LEU Chi-restraints excluded: chain N residue 222 ASN Chi-restraints excluded: chain O residue 85 ASP Chi-restraints excluded: chain O residue 192 MET Chi-restraints excluded: chain O residue 209 THR Chi-restraints excluded: chain O residue 252 ASN Chi-restraints excluded: chain P residue 266 ILE Chi-restraints excluded: chain Q residue 18 ASP Chi-restraints excluded: chain Q residue 104 ASP Chi-restraints excluded: chain R residue 7 THR Chi-restraints excluded: chain R residue 19 ASP Chi-restraints excluded: chain S residue 29 SER Chi-restraints excluded: chain S residue 90 LEU Chi-restraints excluded: chain T residue 7 THR Chi-restraints excluded: chain T residue 52 MET Chi-restraints excluded: chain T residue 76 ILE Chi-restraints excluded: chain U residue 32 VAL Chi-restraints excluded: chain V residue 4 LEU Chi-restraints excluded: chain W residue 116 LYS Chi-restraints excluded: chain X residue 8 SER Chi-restraints excluded: chain X residue 11 ASP Chi-restraints excluded: chain Y residue 10 ASP Chi-restraints excluded: chain Y residue 47 SER Chi-restraints excluded: chain Y residue 49 LEU Chi-restraints excluded: chain Y residue 114 CYS Chi-restraints excluded: chain Z residue 20 ASP Chi-restraints excluded: chain Z residue 99 LYS Chi-restraints excluded: chain a residue 60 SER Chi-restraints excluded: chain d residue 10 THR Chi-restraints excluded: chain d residue 90 MET Chi-restraints excluded: chain e residue 56 LYS Chi-restraints excluded: chain g residue 37 LEU Chi-restraints excluded: chain g residue 60 VAL Chi-restraints excluded: chain i residue 12 GLN Chi-restraints excluded: chain i residue 68 ILE Chi-restraints excluded: chain i residue 72 THR Chi-restraints excluded: chain k residue 38 ARG Chi-restraints excluded: chain l residue 4 ILE Chi-restraints excluded: chain l residue 153 VAL Chi-restraints excluded: chain m residue 91 LEU Chi-restraints excluded: chain n residue 145 VAL Chi-restraints excluded: chain o residue 23 THR Chi-restraints excluded: chain p residue 119 SER Chi-restraints excluded: chain q residue 21 ARG Chi-restraints excluded: chain q residue 142 THR Chi-restraints excluded: chain r residue 2 SER Chi-restraints excluded: chain r residue 29 GLU Chi-restraints excluded: chain r residue 68 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 799 random chunks: chunk 643 optimal weight: 5.9990 chunk 438 optimal weight: 0.9990 chunk 11 optimal weight: 1.9990 chunk 575 optimal weight: 0.7980 chunk 318 optimal weight: 2.9990 chunk 659 optimal weight: 7.9990 chunk 533 optimal weight: 9.9990 chunk 0 optimal weight: 10.0000 chunk 394 optimal weight: 7.9990 chunk 693 optimal weight: 5.9990 chunk 194 optimal weight: 9.9990 overall best weight: 2.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 287 HIS A ** both conformations clash, **PLEASE CHECK MANUALLY** M 44 GLN M 139 GLN N 204 ASN X 139 ASN h 143 ASN j 6 HIS l 147 ASN q 12 GLN q 91 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8352 moved from start: 0.2058 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.242 69896 Z= 0.482 Angle : 1.301 50.645 94392 Z= 0.834 Chirality : 0.257 6.497 10159 Planarity : 0.004 0.046 11738 Dihedral : 12.930 177.229 10956 Min Nonbonded Distance : 2.034 Molprobity Statistics. All-atom Clashscore : 5.75 Ramachandran Plot: Outliers : 0.02 % Allowed : 2.28 % Favored : 97.70 % Rotamer: Outliers : 2.15 % Allowed : 10.89 % Favored : 86.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % 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: 1.20 (0.09), residues: 8090 helix: 1.42 (0.08), residues: 4296 sheet: 0.23 (0.26), residues: 365 loop : 0.18 (0.11), residues: 3429 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP g 26 HIS 0.007 0.001 HIS C 160 PHE 0.029 0.002 PHE L 24 TYR 0.023 0.002 TYR I 118 ARG 0.008 0.000 ARG C 14 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16180 Ramachandran restraints generated. 8090 Oldfield, 0 Emsley, 8090 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16180 Ramachandran restraints generated. 8090 Oldfield, 0 Emsley, 8090 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 939 residues out of total 7150 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 153 poor density : 786 time to evaluate : 6.358 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 102 LYS cc_start: 0.7922 (ttpp) cc_final: 0.7516 (tttm) REVERT: B 175 ILE cc_start: 0.9052 (OUTLIER) cc_final: 0.8598 (mp) REVERT: C 73 LYS cc_start: 0.9071 (OUTLIER) cc_final: 0.8629 (mptp) REVERT: C 211 GLN cc_start: 0.8245 (OUTLIER) cc_final: 0.7850 (mt0) REVERT: D 164 MET cc_start: 0.7874 (OUTLIER) cc_final: 0.6371 (pmm) REVERT: G 31 GLU cc_start: 0.7608 (mt-10) cc_final: 0.6990 (mm-30) REVERT: G 673 MET cc_start: 0.8202 (OUTLIER) cc_final: 0.7750 (mtm) REVERT: H 79 LEU cc_start: 0.7627 (tp) cc_final: 0.7401 (tm) REVERT: H 121 TRP cc_start: 0.8122 (OUTLIER) cc_final: 0.7396 (t60) REVERT: J 64 MET cc_start: 0.8339 (OUTLIER) cc_final: 0.7441 (ttm) REVERT: K 70 GLU cc_start: 0.7452 (OUTLIER) cc_final: 0.6797 (tt0) REVERT: L 411 MET cc_start: 0.7216 (OUTLIER) cc_final: 0.6986 (mmt) REVERT: M 378 GLU cc_start: 0.7703 (OUTLIER) cc_final: 0.7472 (tm-30) REVERT: M 400 MET cc_start: 0.7714 (OUTLIER) cc_final: 0.7393 (ttm) REVERT: N 294 MET cc_start: 0.8211 (mmm) cc_final: 0.7990 (tpt) REVERT: O 192 MET cc_start: 0.7966 (OUTLIER) cc_final: 0.7283 (mtm) REVERT: P 57 MET cc_start: 0.8438 (mmm) cc_final: 0.7943 (mmt) REVERT: U 25 ILE cc_start: 0.8977 (OUTLIER) cc_final: 0.8728 (mp) REVERT: X 43 MET cc_start: 0.8969 (mmm) cc_final: 0.8692 (mmp) REVERT: Y 137 GLU cc_start: 0.7494 (tp30) cc_final: 0.7114 (mm-30) REVERT: Z 131 GLU cc_start: 0.7577 (OUTLIER) cc_final: 0.7137 (tt0) REVERT: a 60 SER cc_start: 0.9118 (OUTLIER) cc_final: 0.8854 (t) REVERT: b 15 GLU cc_start: 0.8030 (mm-30) cc_final: 0.7708 (mm-30) REVERT: d 114 GLU cc_start: 0.8035 (mt-10) cc_final: 0.7832 (mt-10) REVERT: e 4 ASP cc_start: 0.8301 (t70) cc_final: 0.7932 (t0) REVERT: e 56 LYS cc_start: 0.8848 (OUTLIER) cc_final: 0.8099 (tmtm) REVERT: h 19 LYS cc_start: 0.8287 (ttmm) cc_final: 0.8048 (tttm) REVERT: i 12 GLN cc_start: 0.8280 (OUTLIER) cc_final: 0.7919 (tt0) REVERT: k 38 ARG cc_start: 0.8463 (OUTLIER) cc_final: 0.7524 (ttm110) REVERT: l 32 GLU cc_start: 0.7217 (mp0) cc_final: 0.7003 (mp0) REVERT: m 107 ASP cc_start: 0.8364 (t0) cc_final: 0.8034 (t70) REVERT: n 72 HIS cc_start: 0.7649 (t-170) cc_final: 0.7363 (t-170) REVERT: o 42 GLN cc_start: 0.8170 (mt0) cc_final: 0.7884 (mt0) REVERT: o 45 MET cc_start: 0.8927 (mtm) cc_final: 0.8673 (mtp) REVERT: p 72 ASP cc_start: 0.7793 (p0) cc_final: 0.7449 (p0) outliers start: 153 outliers final: 82 residues processed: 871 average time/residue: 1.6648 time to fit residues: 1866.7420 Evaluate side-chains 873 residues out of total 7150 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 100 poor density : 773 time to evaluate : 6.232 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 THR Chi-restraints excluded: chain A residue 96 ILE Chi-restraints excluded: chain B residue 30 VAL Chi-restraints excluded: chain B residue 50 PHE Chi-restraints excluded: chain B residue 54 CYS Chi-restraints excluded: chain B residue 175 ILE Chi-restraints excluded: chain C residue 73 LYS Chi-restraints excluded: chain C residue 211 GLN Chi-restraints excluded: chain D residue 22 THR Chi-restraints excluded: chain D residue 164 MET Chi-restraints excluded: chain E residue 19 THR Chi-restraints excluded: chain E residue 58 ASN Chi-restraints excluded: chain E residue 113 SER Chi-restraints excluded: chain E residue 134 ASP Chi-restraints excluded: chain G residue 425 SER Chi-restraints excluded: chain G residue 436 SER Chi-restraints excluded: chain G residue 483 VAL Chi-restraints excluded: chain G residue 512 GLU Chi-restraints excluded: chain G residue 517 ASN Chi-restraints excluded: chain G residue 673 MET Chi-restraints excluded: chain H residue 121 TRP Chi-restraints excluded: chain I residue 37 THR Chi-restraints excluded: chain J residue 55 MET Chi-restraints excluded: chain J residue 64 MET Chi-restraints excluded: chain J residue 113 VAL Chi-restraints excluded: chain J residue 124 ASP Chi-restraints excluded: chain K residue 70 GLU Chi-restraints excluded: chain L residue 10 VAL Chi-restraints excluded: chain L residue 290 MET Chi-restraints excluded: chain L residue 411 MET Chi-restraints excluded: chain L residue 482 MET Chi-restraints excluded: chain M residue 72 LEU Chi-restraints excluded: chain M residue 378 GLU Chi-restraints excluded: chain M residue 385 THR Chi-restraints excluded: chain M residue 400 MET Chi-restraints excluded: chain N residue 98 MET Chi-restraints excluded: chain N residue 117 GLU Chi-restraints excluded: chain N residue 182 SER Chi-restraints excluded: chain N residue 218 MET Chi-restraints excluded: chain O residue 85 ASP Chi-restraints excluded: chain O residue 192 MET Chi-restraints excluded: chain O residue 209 THR Chi-restraints excluded: chain O residue 250 ASP Chi-restraints excluded: chain O residue 252 ASN Chi-restraints excluded: chain P residue 266 ILE Chi-restraints excluded: chain Q residue 15 GLU Chi-restraints excluded: chain Q residue 17 LEU Chi-restraints excluded: chain Q residue 18 ASP Chi-restraints excluded: chain Q residue 87 SER Chi-restraints excluded: chain Q residue 104 ASP Chi-restraints excluded: chain R residue 7 THR Chi-restraints excluded: chain R residue 19 ASP Chi-restraints excluded: chain S residue 29 SER Chi-restraints excluded: chain S residue 76 VAL Chi-restraints excluded: chain S residue 82 SER Chi-restraints excluded: chain S residue 90 LEU Chi-restraints excluded: chain T residue 7 THR Chi-restraints excluded: chain T residue 76 ILE Chi-restraints excluded: chain U residue 25 ILE Chi-restraints excluded: chain U residue 30 LEU Chi-restraints excluded: chain U residue 32 VAL Chi-restraints excluded: chain U residue 65 ILE Chi-restraints excluded: chain W residue 16 SER Chi-restraints excluded: chain W residue 116 LYS Chi-restraints excluded: chain Y residue 10 ASP Chi-restraints excluded: chain Y residue 36 SER Chi-restraints excluded: chain Y residue 46 THR Chi-restraints excluded: chain Y residue 47 SER Chi-restraints excluded: chain Y residue 49 LEU Chi-restraints excluded: chain Y residue 114 CYS Chi-restraints excluded: chain Z residue 20 ASP Chi-restraints excluded: chain Z residue 99 LYS Chi-restraints excluded: chain Z residue 131 GLU Chi-restraints excluded: chain a residue 60 SER Chi-restraints excluded: chain c residue 29 ILE Chi-restraints excluded: chain d residue 10 THR Chi-restraints excluded: chain d residue 90 MET Chi-restraints excluded: chain e residue 56 LYS Chi-restraints excluded: chain g residue 37 LEU Chi-restraints excluded: chain g residue 60 VAL Chi-restraints excluded: chain i residue 4 THR Chi-restraints excluded: chain i residue 12 GLN Chi-restraints excluded: chain i residue 47 ASN Chi-restraints excluded: chain i residue 68 ILE Chi-restraints excluded: chain i residue 72 THR Chi-restraints excluded: chain i residue 81 ILE Chi-restraints excluded: chain k residue 38 ARG Chi-restraints excluded: chain l residue 4 ILE Chi-restraints excluded: chain l residue 5 THR Chi-restraints excluded: chain l residue 121 THR Chi-restraints excluded: chain l residue 153 VAL Chi-restraints excluded: chain m residue 91 LEU Chi-restraints excluded: chain m residue 116 GLN Chi-restraints excluded: chain n residue 145 VAL Chi-restraints excluded: chain o residue 11 ASP Chi-restraints excluded: chain o residue 23 THR Chi-restraints excluded: chain p residue 119 SER Chi-restraints excluded: chain q residue 142 THR Chi-restraints excluded: chain r residue 2 SER Chi-restraints excluded: chain r residue 68 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 799 random chunks: chunk 259 optimal weight: 5.9990 chunk 695 optimal weight: 0.9990 chunk 152 optimal weight: 0.7980 chunk 453 optimal weight: 5.9990 chunk 190 optimal weight: 9.9990 chunk 773 optimal weight: 7.9990 chunk 641 optimal weight: 1.9990 chunk 357 optimal weight: 0.9980 chunk 64 optimal weight: 5.9990 chunk 255 optimal weight: 0.7980 chunk 405 optimal weight: 5.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 665 GLN ** H 287 HIS A ** both conformations clash, **PLEASE CHECK MANUALLY** M 188 ASN N 204 ASN R 94 GLN S 75 ASN h 143 ASN j 6 HIS l 147 ASN q 12 GLN q 17 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8323 moved from start: 0.2242 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.246 69896 Z= 0.435 Angle : 1.282 50.609 94392 Z= 0.827 Chirality : 0.254 6.418 10159 Planarity : 0.004 0.047 11738 Dihedral : 12.578 178.575 10956 Min Nonbonded Distance : 2.075 Molprobity Statistics. All-atom Clashscore : 5.77 Ramachandran Plot: Outliers : 0.02 % Allowed : 2.19 % Favored : 97.78 % Rotamer: Outliers : 2.05 % Allowed : 11.42 % Favored : 86.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % 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: 1.32 (0.09), residues: 8090 helix: 1.56 (0.08), residues: 4304 sheet: 0.04 (0.26), residues: 381 loop : 0.20 (0.11), residues: 3405 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP g 26 HIS 0.005 0.001 HIS q 87 PHE 0.027 0.001 PHE N 292 TYR 0.020 0.001 TYR L 422 ARG 0.010 0.000 ARG C 14 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16180 Ramachandran restraints generated. 8090 Oldfield, 0 Emsley, 8090 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16180 Ramachandran restraints generated. 8090 Oldfield, 0 Emsley, 8090 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 959 residues out of total 7150 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 146 poor density : 813 time to evaluate : 6.298 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 112 GLU cc_start: 0.7808 (mm-30) cc_final: 0.7306 (mp0) REVERT: B 102 LYS cc_start: 0.7871 (ttpp) cc_final: 0.7465 (tttm) REVERT: B 171 LYS cc_start: 0.8436 (mtmm) cc_final: 0.7669 (mtmt) REVERT: B 175 ILE cc_start: 0.9021 (OUTLIER) cc_final: 0.8578 (mp) REVERT: C 73 LYS cc_start: 0.9061 (OUTLIER) cc_final: 0.8310 (mptp) REVERT: C 211 GLN cc_start: 0.8227 (OUTLIER) cc_final: 0.7826 (mt0) REVERT: D 12 GLU cc_start: 0.7110 (pp20) cc_final: 0.6887 (pp20) REVERT: D 164 MET cc_start: 0.7711 (OUTLIER) cc_final: 0.6215 (pmm) REVERT: G 31 GLU cc_start: 0.7607 (mt-10) cc_final: 0.7072 (mm-30) REVERT: G 109 ASP cc_start: 0.7769 (OUTLIER) cc_final: 0.7490 (t0) REVERT: G 673 MET cc_start: 0.8112 (OUTLIER) cc_final: 0.7632 (mtm) REVERT: H 121 TRP cc_start: 0.8110 (OUTLIER) cc_final: 0.7407 (t60) REVERT: J 64 MET cc_start: 0.8313 (OUTLIER) cc_final: 0.7464 (ttm) REVERT: J 70 TYR cc_start: 0.8733 (t80) cc_final: 0.8482 (t80) REVERT: K 70 GLU cc_start: 0.7423 (OUTLIER) cc_final: 0.6816 (tt0) REVERT: M 378 GLU cc_start: 0.7634 (OUTLIER) cc_final: 0.7426 (tm-30) REVERT: M 400 MET cc_start: 0.7703 (OUTLIER) cc_final: 0.7392 (ttm) REVERT: N 222 ASN cc_start: 0.8036 (OUTLIER) cc_final: 0.7731 (t0) REVERT: O 192 MET cc_start: 0.7923 (OUTLIER) cc_final: 0.7610 (mtm) REVERT: P 57 MET cc_start: 0.8418 (mmm) cc_final: 0.7824 (mmt) REVERT: P 256 TYR cc_start: 0.5389 (OUTLIER) cc_final: 0.5033 (p90) REVERT: T 14 ARG cc_start: 0.7526 (mtm180) cc_final: 0.7259 (mtm180) REVERT: U 61 GLU cc_start: 0.7980 (tt0) cc_final: 0.7763 (tt0) REVERT: X 43 MET cc_start: 0.8952 (mmm) cc_final: 0.8688 (mmp) REVERT: Y 105 ARG cc_start: 0.7482 (OUTLIER) cc_final: 0.5757 (tpt170) REVERT: Y 137 GLU cc_start: 0.7457 (tp30) cc_final: 0.7090 (mm-30) REVERT: a 60 SER cc_start: 0.9104 (OUTLIER) cc_final: 0.8856 (t) REVERT: b 15 GLU cc_start: 0.7984 (mm-30) cc_final: 0.7580 (mm-30) REVERT: d 114 GLU cc_start: 0.7989 (mt-10) cc_final: 0.7778 (mt-10) REVERT: e 4 ASP cc_start: 0.8250 (t70) cc_final: 0.7926 (t0) REVERT: e 56 LYS cc_start: 0.8844 (OUTLIER) cc_final: 0.8074 (tmtm) REVERT: h 19 LYS cc_start: 0.8259 (ttmm) cc_final: 0.8016 (tttm) REVERT: k 38 ARG cc_start: 0.8459 (OUTLIER) cc_final: 0.7523 (ttm110) REVERT: l 137 ASN cc_start: 0.8310 (t0) cc_final: 0.8096 (t0) REVERT: m 107 ASP cc_start: 0.8339 (t0) cc_final: 0.8026 (t70) REVERT: n 72 HIS cc_start: 0.7651 (t-170) cc_final: 0.7368 (t-170) REVERT: o 42 GLN cc_start: 0.8141 (mt0) cc_final: 0.7886 (mt0) REVERT: o 45 MET cc_start: 0.8917 (mtm) cc_final: 0.8685 (mtp) REVERT: p 72 ASP cc_start: 0.7684 (p0) cc_final: 0.7390 (p0) REVERT: q 21 ARG cc_start: 0.7782 (OUTLIER) cc_final: 0.7399 (ttm110) REVERT: q 25 ARG cc_start: 0.7013 (OUTLIER) cc_final: 0.6233 (ttt90) REVERT: r 29 GLU cc_start: 0.7723 (OUTLIER) cc_final: 0.7323 (pm20) outliers start: 146 outliers final: 77 residues processed: 887 average time/residue: 1.6139 time to fit residues: 1845.9692 Evaluate side-chains 884 residues out of total 7150 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 98 poor density : 786 time to evaluate : 6.144 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 96 ILE Chi-restraints excluded: chain B residue 30 VAL Chi-restraints excluded: chain B residue 50 PHE Chi-restraints excluded: chain B residue 54 CYS Chi-restraints excluded: chain B residue 70 ASP Chi-restraints excluded: chain B residue 125 TYR Chi-restraints excluded: chain B residue 175 ILE Chi-restraints excluded: chain C residue 73 LYS Chi-restraints excluded: chain C residue 211 GLN Chi-restraints excluded: chain D residue 22 THR Chi-restraints excluded: chain D residue 164 MET Chi-restraints excluded: chain D residue 420 THR Chi-restraints excluded: chain E residue 19 THR Chi-restraints excluded: chain E residue 58 ASN Chi-restraints excluded: chain E residue 114 ASP Chi-restraints excluded: chain E residue 134 ASP Chi-restraints excluded: chain G residue 18 VAL Chi-restraints excluded: chain G residue 109 ASP Chi-restraints excluded: chain G residue 425 SER Chi-restraints excluded: chain G residue 436 SER Chi-restraints excluded: chain G residue 483 VAL Chi-restraints excluded: chain G residue 512 GLU Chi-restraints excluded: chain G residue 517 ASN Chi-restraints excluded: chain G residue 673 MET Chi-restraints excluded: chain H residue 4 ILE Chi-restraints excluded: chain H residue 121 TRP Chi-restraints excluded: chain I residue 37 THR Chi-restraints excluded: chain J residue 64 MET Chi-restraints excluded: chain J residue 113 VAL Chi-restraints excluded: chain J residue 124 ASP Chi-restraints excluded: chain K residue 70 GLU Chi-restraints excluded: chain L residue 10 VAL Chi-restraints excluded: chain L residue 197 ASP Chi-restraints excluded: chain L residue 290 MET Chi-restraints excluded: chain L residue 482 MET Chi-restraints excluded: chain M residue 72 LEU Chi-restraints excluded: chain M residue 378 GLU Chi-restraints excluded: chain M residue 385 THR Chi-restraints excluded: chain M residue 400 MET Chi-restraints excluded: chain N residue 38 LEU Chi-restraints excluded: chain N residue 98 MET Chi-restraints excluded: chain N residue 117 GLU Chi-restraints excluded: chain N residue 222 ASN Chi-restraints excluded: chain O residue 85 ASP Chi-restraints excluded: chain O residue 192 MET Chi-restraints excluded: chain O residue 209 THR Chi-restraints excluded: chain O residue 250 ASP Chi-restraints excluded: chain O residue 252 ASN Chi-restraints excluded: chain P residue 256 TYR Chi-restraints excluded: chain P residue 266 ILE Chi-restraints excluded: chain Q residue 15 GLU Chi-restraints excluded: chain Q residue 87 SER Chi-restraints excluded: chain Q residue 104 ASP Chi-restraints excluded: chain R residue 7 THR Chi-restraints excluded: chain R residue 19 ASP Chi-restraints excluded: chain S residue 29 SER Chi-restraints excluded: chain S residue 75 ASN Chi-restraints excluded: chain S residue 82 SER Chi-restraints excluded: chain S residue 90 LEU Chi-restraints excluded: chain T residue 7 THR Chi-restraints excluded: chain T residue 76 ILE Chi-restraints excluded: chain U residue 30 LEU Chi-restraints excluded: chain U residue 32 VAL Chi-restraints excluded: chain U residue 83 LYS Chi-restraints excluded: chain W residue 16 SER Chi-restraints excluded: chain W residue 116 LYS Chi-restraints excluded: chain X residue 8 SER Chi-restraints excluded: chain X residue 11 ASP Chi-restraints excluded: chain Y residue 46 THR Chi-restraints excluded: chain Y residue 105 ARG Chi-restraints excluded: chain Y residue 114 CYS Chi-restraints excluded: chain Z residue 20 ASP Chi-restraints excluded: chain a residue 60 SER Chi-restraints excluded: chain d residue 10 THR Chi-restraints excluded: chain d residue 90 MET Chi-restraints excluded: chain e residue 56 LYS Chi-restraints excluded: chain g residue 29 ASP Chi-restraints excluded: chain g residue 37 LEU Chi-restraints excluded: chain g residue 60 VAL Chi-restraints excluded: chain i residue 4 THR Chi-restraints excluded: chain i residue 6 GLU Chi-restraints excluded: chain i residue 68 ILE Chi-restraints excluded: chain i residue 72 THR Chi-restraints excluded: chain k residue 38 ARG Chi-restraints excluded: chain l residue 4 ILE Chi-restraints excluded: chain l residue 5 THR Chi-restraints excluded: chain m residue 91 LEU Chi-restraints excluded: chain n residue 145 VAL Chi-restraints excluded: chain o residue 11 ASP Chi-restraints excluded: chain o residue 23 THR Chi-restraints excluded: chain p residue 7 ASP Chi-restraints excluded: chain p residue 119 SER Chi-restraints excluded: chain q residue 21 ARG Chi-restraints excluded: chain q residue 25 ARG Chi-restraints excluded: chain q residue 142 THR Chi-restraints excluded: chain r residue 2 SER Chi-restraints excluded: chain r residue 29 GLU Chi-restraints excluded: chain r residue 68 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 799 random chunks: chunk 745 optimal weight: 0.0980 chunk 87 optimal weight: 4.9990 chunk 440 optimal weight: 8.9990 chunk 564 optimal weight: 0.8980 chunk 437 optimal weight: 6.9990 chunk 650 optimal weight: 7.9990 chunk 431 optimal weight: 4.9990 chunk 770 optimal weight: 8.9990 chunk 481 optimal weight: 1.9990 chunk 469 optimal weight: 0.4980 chunk 355 optimal weight: 4.9990 overall best weight: 1.6984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 653 ASN ** H 287 HIS A ** both conformations clash, **PLEASE CHECK MANUALLY** N 204 ASN h 143 ASN j 6 HIS l 147 ASN q 12 GLN ** s 44 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8334 moved from start: 0.2249 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.244 69896 Z= 0.451 Angle : 1.290 50.625 94392 Z= 0.830 Chirality : 0.255 6.443 10159 Planarity : 0.004 0.046 11738 Dihedral : 12.444 177.917 10956 Min Nonbonded Distance : 2.037 Molprobity Statistics. All-atom Clashscore : 5.92 Ramachandran Plot: Outliers : 0.02 % Allowed : 2.30 % Favored : 97.67 % Rotamer: Outliers : 1.90 % Allowed : 12.06 % Favored : 86.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % 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: 1.32 (0.09), residues: 8090 helix: 1.55 (0.08), residues: 4300 sheet: 0.17 (0.26), residues: 372 loop : 0.21 (0.11), residues: 3418 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP g 26 HIS 0.005 0.001 HIS q 87 PHE 0.038 0.001 PHE L 24 TYR 0.022 0.001 TYR T 79 ARG 0.010 0.000 ARG C 14 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16180 Ramachandran restraints generated. 8090 Oldfield, 0 Emsley, 8090 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16180 Ramachandran restraints generated. 8090 Oldfield, 0 Emsley, 8090 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 929 residues out of total 7150 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 135 poor density : 794 time to evaluate : 6.377 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 112 GLU cc_start: 0.7825 (mm-30) cc_final: 0.7349 (mp0) REVERT: B 102 LYS cc_start: 0.7901 (ttpp) cc_final: 0.7486 (tttm) REVERT: B 165 LYS cc_start: 0.8724 (OUTLIER) cc_final: 0.8498 (mttp) REVERT: B 171 LYS cc_start: 0.8448 (mtmm) cc_final: 0.7763 (mtmt) REVERT: B 175 ILE cc_start: 0.9027 (OUTLIER) cc_final: 0.8574 (mp) REVERT: C 73 LYS cc_start: 0.9055 (OUTLIER) cc_final: 0.8442 (mptp) REVERT: C 211 GLN cc_start: 0.8240 (OUTLIER) cc_final: 0.7833 (mt0) REVERT: D 12 GLU cc_start: 0.7155 (pp20) cc_final: 0.6917 (pp20) REVERT: D 164 MET cc_start: 0.7773 (OUTLIER) cc_final: 0.6240 (pmm) REVERT: G 31 GLU cc_start: 0.7581 (mt-10) cc_final: 0.7095 (mm-30) REVERT: G 109 ASP cc_start: 0.7805 (OUTLIER) cc_final: 0.7441 (t0) REVERT: G 673 MET cc_start: 0.8148 (OUTLIER) cc_final: 0.7708 (mtm) REVERT: H 79 LEU cc_start: 0.7678 (OUTLIER) cc_final: 0.7318 (tm) REVERT: H 121 TRP cc_start: 0.8159 (OUTLIER) cc_final: 0.7524 (t60) REVERT: H 289 LEU cc_start: 0.8905 (OUTLIER) cc_final: 0.8498 (tp) REVERT: J 64 MET cc_start: 0.8298 (OUTLIER) cc_final: 0.7489 (ttm) REVERT: J 70 TYR cc_start: 0.8770 (t80) cc_final: 0.8508 (t80) REVERT: K 70 GLU cc_start: 0.7422 (OUTLIER) cc_final: 0.6815 (tt0) REVERT: L 3 MET cc_start: 0.7686 (ttm) cc_final: 0.7403 (mmm) REVERT: L 411 MET cc_start: 0.7148 (OUTLIER) cc_final: 0.6888 (mmt) REVERT: M 378 GLU cc_start: 0.7663 (OUTLIER) cc_final: 0.7441 (tm-30) REVERT: M 400 MET cc_start: 0.7719 (OUTLIER) cc_final: 0.7411 (ttm) REVERT: N 222 ASN cc_start: 0.8041 (OUTLIER) cc_final: 0.7742 (t0) REVERT: O 85 ASP cc_start: 0.7239 (OUTLIER) cc_final: 0.7039 (p0) REVERT: O 192 MET cc_start: 0.7934 (OUTLIER) cc_final: 0.7275 (mtm) REVERT: P 57 MET cc_start: 0.8437 (mmm) cc_final: 0.7925 (mmt) REVERT: P 256 TYR cc_start: 0.5449 (OUTLIER) cc_final: 0.5083 (p90) REVERT: T 14 ARG cc_start: 0.7568 (mtm180) cc_final: 0.7347 (mtm180) REVERT: U 61 GLU cc_start: 0.8000 (tt0) cc_final: 0.7771 (tt0) REVERT: X 43 MET cc_start: 0.8965 (mmm) cc_final: 0.8698 (mmp) REVERT: Y 73 SER cc_start: 0.8588 (p) cc_final: 0.8247 (p) REVERT: Y 105 ARG cc_start: 0.7507 (OUTLIER) cc_final: 0.5787 (tpt170) REVERT: Y 117 MET cc_start: 0.7899 (mtp) cc_final: 0.7675 (mtt) REVERT: Y 137 GLU cc_start: 0.7476 (tp30) cc_final: 0.7106 (mm-30) REVERT: a 60 SER cc_start: 0.9124 (OUTLIER) cc_final: 0.8880 (t) REVERT: b 15 GLU cc_start: 0.7973 (mm-30) cc_final: 0.7591 (mm-30) REVERT: e 4 ASP cc_start: 0.8263 (t70) cc_final: 0.7955 (t0) REVERT: e 56 LYS cc_start: 0.8840 (OUTLIER) cc_final: 0.8082 (tmtm) REVERT: k 38 ARG cc_start: 0.8479 (OUTLIER) cc_final: 0.7548 (ttm110) REVERT: m 107 ASP cc_start: 0.8349 (t0) cc_final: 0.8037 (t70) REVERT: n 72 HIS cc_start: 0.7654 (t-170) cc_final: 0.7369 (t-170) REVERT: o 20 ARG cc_start: 0.7475 (OUTLIER) cc_final: 0.7087 (mpt180) REVERT: o 42 GLN cc_start: 0.8137 (mt0) cc_final: 0.7876 (mt0) REVERT: o 45 MET cc_start: 0.8915 (mtm) cc_final: 0.8674 (mtp) REVERT: p 72 ASP cc_start: 0.7724 (p0) cc_final: 0.7388 (p0) REVERT: q 21 ARG cc_start: 0.7816 (OUTLIER) cc_final: 0.7426 (ttm110) REVERT: q 25 ARG cc_start: 0.7024 (OUTLIER) cc_final: 0.6250 (ttt90) REVERT: r 29 GLU cc_start: 0.7718 (OUTLIER) cc_final: 0.7322 (pm20) outliers start: 135 outliers final: 74 residues processed: 871 average time/residue: 1.6484 time to fit residues: 1850.3604 Evaluate side-chains 886 residues out of total 7150 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 101 poor density : 785 time to evaluate : 6.183 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 96 ILE Chi-restraints excluded: chain B residue 30 VAL Chi-restraints excluded: chain B residue 50 PHE Chi-restraints excluded: chain B residue 54 CYS Chi-restraints excluded: chain B residue 125 TYR Chi-restraints excluded: chain B residue 165 LYS Chi-restraints excluded: chain B residue 175 ILE Chi-restraints excluded: chain C residue 17 VAL Chi-restraints excluded: chain C residue 73 LYS Chi-restraints excluded: chain C residue 211 GLN Chi-restraints excluded: chain D residue 22 THR Chi-restraints excluded: chain D residue 164 MET Chi-restraints excluded: chain D residue 420 THR Chi-restraints excluded: chain E residue 19 THR Chi-restraints excluded: chain E residue 58 ASN Chi-restraints excluded: chain E residue 114 ASP Chi-restraints excluded: chain E residue 134 ASP Chi-restraints excluded: chain G residue 18 VAL Chi-restraints excluded: chain G residue 109 ASP Chi-restraints excluded: chain G residue 425 SER Chi-restraints excluded: chain G residue 436 SER Chi-restraints excluded: chain G residue 483 VAL Chi-restraints excluded: chain G residue 512 GLU Chi-restraints excluded: chain G residue 517 ASN Chi-restraints excluded: chain G residue 673 MET Chi-restraints excluded: chain H residue 79 LEU Chi-restraints excluded: chain H residue 121 TRP Chi-restraints excluded: chain H residue 289 LEU Chi-restraints excluded: chain I residue 37 THR Chi-restraints excluded: chain J residue 64 MET Chi-restraints excluded: chain J residue 113 VAL Chi-restraints excluded: chain J residue 124 ASP Chi-restraints excluded: chain K residue 70 GLU Chi-restraints excluded: chain L residue 10 VAL Chi-restraints excluded: chain L residue 197 ASP Chi-restraints excluded: chain L residue 290 MET Chi-restraints excluded: chain L residue 411 MET Chi-restraints excluded: chain L residue 482 MET Chi-restraints excluded: chain M residue 72 LEU Chi-restraints excluded: chain M residue 126 LEU Chi-restraints excluded: chain M residue 378 GLU Chi-restraints excluded: chain M residue 385 THR Chi-restraints excluded: chain M residue 400 MET Chi-restraints excluded: chain N residue 117 GLU Chi-restraints excluded: chain N residue 222 ASN Chi-restraints excluded: chain O residue 85 ASP Chi-restraints excluded: chain O residue 192 MET Chi-restraints excluded: chain O residue 209 THR Chi-restraints excluded: chain O residue 250 ASP Chi-restraints excluded: chain O residue 252 ASN Chi-restraints excluded: chain O residue 279 LEU Chi-restraints excluded: chain P residue 256 TYR Chi-restraints excluded: chain P residue 266 ILE Chi-restraints excluded: chain Q residue 87 SER Chi-restraints excluded: chain Q residue 104 ASP Chi-restraints excluded: chain R residue 7 THR Chi-restraints excluded: chain R residue 19 ASP Chi-restraints excluded: chain S residue 29 SER Chi-restraints excluded: chain S residue 82 SER Chi-restraints excluded: chain S residue 90 LEU Chi-restraints excluded: chain T residue 7 THR Chi-restraints excluded: chain T residue 72 CYS Chi-restraints excluded: chain T residue 76 ILE Chi-restraints excluded: chain U residue 30 LEU Chi-restraints excluded: chain U residue 32 VAL Chi-restraints excluded: chain W residue 16 SER Chi-restraints excluded: chain W residue 116 LYS Chi-restraints excluded: chain X residue 8 SER Chi-restraints excluded: chain X residue 11 ASP Chi-restraints excluded: chain Y residue 46 THR Chi-restraints excluded: chain Y residue 47 SER Chi-restraints excluded: chain Y residue 105 ARG Chi-restraints excluded: chain Y residue 114 CYS Chi-restraints excluded: chain Z residue 20 ASP Chi-restraints excluded: chain a residue 60 SER Chi-restraints excluded: chain d residue 10 THR Chi-restraints excluded: chain d residue 90 MET Chi-restraints excluded: chain e residue 56 LYS Chi-restraints excluded: chain g residue 37 LEU Chi-restraints excluded: chain g residue 60 VAL Chi-restraints excluded: chain i residue 4 THR Chi-restraints excluded: chain i residue 6 GLU Chi-restraints excluded: chain i residue 68 ILE Chi-restraints excluded: chain i residue 72 THR Chi-restraints excluded: chain i residue 81 ILE Chi-restraints excluded: chain k residue 38 ARG Chi-restraints excluded: chain l residue 4 ILE Chi-restraints excluded: chain l residue 5 THR Chi-restraints excluded: chain m residue 91 LEU Chi-restraints excluded: chain n residue 145 VAL Chi-restraints excluded: chain o residue 11 ASP Chi-restraints excluded: chain o residue 20 ARG Chi-restraints excluded: chain o residue 23 THR Chi-restraints excluded: chain p residue 7 ASP Chi-restraints excluded: chain p residue 119 SER Chi-restraints excluded: chain q residue 21 ARG Chi-restraints excluded: chain q residue 25 ARG Chi-restraints excluded: chain q residue 142 THR Chi-restraints excluded: chain r residue 2 SER Chi-restraints excluded: chain r residue 29 GLU Chi-restraints excluded: chain r residue 68 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 799 random chunks: chunk 476 optimal weight: 4.9990 chunk 307 optimal weight: 2.9990 chunk 459 optimal weight: 0.5980 chunk 231 optimal weight: 3.9990 chunk 151 optimal weight: 0.6980 chunk 149 optimal weight: 3.9990 chunk 489 optimal weight: 0.6980 chunk 524 optimal weight: 6.9990 chunk 380 optimal weight: 7.9990 chunk 71 optimal weight: 2.9990 chunk 605 optimal weight: 5.9990 overall best weight: 1.5984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 287 HIS A ** both conformations clash, **PLEASE CHECK MANUALLY** N 204 ASN h 143 ASN j 6 HIS l 147 ASN s 44 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8332 moved from start: 0.2296 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.244 69896 Z= 0.447 Angle : 1.290 50.631 94392 Z= 0.830 Chirality : 0.255 6.447 10159 Planarity : 0.004 0.046 11738 Dihedral : 12.270 178.144 10956 Min Nonbonded Distance : 2.032 Molprobity Statistics. All-atom Clashscore : 5.89 Ramachandran Plot: Outliers : 0.02 % Allowed : 2.14 % Favored : 97.83 % Rotamer: Outliers : 1.83 % Allowed : 12.45 % Favored : 85.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % 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: 1.34 (0.09), residues: 8090 helix: 1.56 (0.08), residues: 4304 sheet: 0.16 (0.26), residues: 372 loop : 0.22 (0.11), residues: 3414 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP g 26 HIS 0.005 0.001 HIS q 87 PHE 0.026 0.001 PHE N 292 TYR 0.020 0.001 TYR L 422 ARG 0.011 0.000 ARG C 14 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16180 Ramachandran restraints generated. 8090 Oldfield, 0 Emsley, 8090 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16180 Ramachandran restraints generated. 8090 Oldfield, 0 Emsley, 8090 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 926 residues out of total 7150 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 130 poor density : 796 time to evaluate : 6.283 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 112 GLU cc_start: 0.7802 (mm-30) cc_final: 0.7338 (mp0) REVERT: B 102 LYS cc_start: 0.7904 (ttpp) cc_final: 0.7478 (tttm) REVERT: B 165 LYS cc_start: 0.8722 (OUTLIER) cc_final: 0.8496 (mttp) REVERT: B 171 LYS cc_start: 0.8439 (mtmm) cc_final: 0.7750 (mtmt) REVERT: B 175 ILE cc_start: 0.9024 (OUTLIER) cc_final: 0.8573 (mp) REVERT: C 73 LYS cc_start: 0.9063 (OUTLIER) cc_final: 0.8455 (mptp) REVERT: C 211 GLN cc_start: 0.8235 (OUTLIER) cc_final: 0.7829 (mt0) REVERT: D 12 GLU cc_start: 0.7177 (pp20) cc_final: 0.6925 (pp20) REVERT: D 164 MET cc_start: 0.7754 (OUTLIER) cc_final: 0.6240 (pmm) REVERT: G 31 GLU cc_start: 0.7578 (mt-10) cc_final: 0.7094 (mm-30) REVERT: G 109 ASP cc_start: 0.7786 (OUTLIER) cc_final: 0.7442 (t0) REVERT: G 673 MET cc_start: 0.8145 (OUTLIER) cc_final: 0.7698 (mtm) REVERT: H 79 LEU cc_start: 0.7703 (OUTLIER) cc_final: 0.7345 (tm) REVERT: H 121 TRP cc_start: 0.8186 (OUTLIER) cc_final: 0.7579 (t60) REVERT: J 70 TYR cc_start: 0.8764 (t80) cc_final: 0.8509 (t80) REVERT: K 70 GLU cc_start: 0.7413 (OUTLIER) cc_final: 0.6811 (tt0) REVERT: L 3 MET cc_start: 0.7698 (ttm) cc_final: 0.7424 (mmm) REVERT: L 411 MET cc_start: 0.7143 (OUTLIER) cc_final: 0.6880 (mmt) REVERT: M 378 GLU cc_start: 0.7665 (OUTLIER) cc_final: 0.7449 (tm-30) REVERT: M 400 MET cc_start: 0.7704 (OUTLIER) cc_final: 0.7394 (ttm) REVERT: N 222 ASN cc_start: 0.8033 (OUTLIER) cc_final: 0.7717 (t0) REVERT: O 192 MET cc_start: 0.7897 (OUTLIER) cc_final: 0.7245 (mtm) REVERT: P 57 MET cc_start: 0.8437 (mmm) cc_final: 0.7923 (mmt) REVERT: P 256 TYR cc_start: 0.5470 (OUTLIER) cc_final: 0.5104 (p90) REVERT: T 14 ARG cc_start: 0.7629 (mtm180) cc_final: 0.7382 (mtm180) REVERT: U 61 GLU cc_start: 0.8003 (tt0) cc_final: 0.7765 (tt0) REVERT: X 43 MET cc_start: 0.8963 (mmm) cc_final: 0.8698 (mmp) REVERT: Y 13 GLU cc_start: 0.7462 (OUTLIER) cc_final: 0.6659 (mp0) REVERT: Y 73 SER cc_start: 0.8615 (p) cc_final: 0.8229 (m) REVERT: Y 117 MET cc_start: 0.7881 (mtp) cc_final: 0.7671 (mtt) REVERT: Y 137 GLU cc_start: 0.7478 (tp30) cc_final: 0.7092 (mm-30) REVERT: a 60 SER cc_start: 0.9117 (OUTLIER) cc_final: 0.8879 (t) REVERT: b 15 GLU cc_start: 0.7963 (mm-30) cc_final: 0.7570 (mm-30) REVERT: e 4 ASP cc_start: 0.8248 (t70) cc_final: 0.7917 (t0) REVERT: e 56 LYS cc_start: 0.8842 (OUTLIER) cc_final: 0.8080 (tmtm) REVERT: k 38 ARG cc_start: 0.8483 (OUTLIER) cc_final: 0.7550 (ttm110) REVERT: m 107 ASP cc_start: 0.8344 (t0) cc_final: 0.8039 (t70) REVERT: n 72 HIS cc_start: 0.7653 (t-170) cc_final: 0.7382 (t-170) REVERT: o 20 ARG cc_start: 0.7473 (OUTLIER) cc_final: 0.7095 (mpt180) REVERT: o 42 GLN cc_start: 0.8122 (mt0) cc_final: 0.7857 (mt0) REVERT: o 45 MET cc_start: 0.8918 (mtm) cc_final: 0.8678 (mtp) REVERT: p 72 ASP cc_start: 0.7720 (p0) cc_final: 0.7382 (p0) REVERT: q 21 ARG cc_start: 0.7809 (OUTLIER) cc_final: 0.7425 (ttm110) REVERT: q 25 ARG cc_start: 0.7030 (OUTLIER) cc_final: 0.6555 (ttt90) REVERT: r 29 GLU cc_start: 0.7744 (OUTLIER) cc_final: 0.7383 (pm20) outliers start: 130 outliers final: 79 residues processed: 872 average time/residue: 1.6669 time to fit residues: 1869.5226 Evaluate side-chains 885 residues out of total 7150 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 103 poor density : 782 time to evaluate : 6.193 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 ILE Chi-restraints excluded: chain A residue 96 ILE Chi-restraints excluded: chain B residue 30 VAL Chi-restraints excluded: chain B residue 50 PHE Chi-restraints excluded: chain B residue 54 CYS Chi-restraints excluded: chain B residue 125 TYR Chi-restraints excluded: chain B residue 165 LYS Chi-restraints excluded: chain B residue 175 ILE Chi-restraints excluded: chain C residue 17 VAL Chi-restraints excluded: chain C residue 73 LYS Chi-restraints excluded: chain C residue 211 GLN Chi-restraints excluded: chain D residue 22 THR Chi-restraints excluded: chain D residue 164 MET Chi-restraints excluded: chain D residue 420 THR Chi-restraints excluded: chain E residue 19 THR Chi-restraints excluded: chain E residue 58 ASN Chi-restraints excluded: chain E residue 113 SER Chi-restraints excluded: chain E residue 114 ASP Chi-restraints excluded: chain E residue 134 ASP Chi-restraints excluded: chain G residue 18 VAL Chi-restraints excluded: chain G residue 109 ASP Chi-restraints excluded: chain G residue 425 SER Chi-restraints excluded: chain G residue 436 SER Chi-restraints excluded: chain G residue 483 VAL Chi-restraints excluded: chain G residue 512 GLU Chi-restraints excluded: chain G residue 517 ASN Chi-restraints excluded: chain G residue 673 MET Chi-restraints excluded: chain H residue 79 LEU Chi-restraints excluded: chain H residue 121 TRP Chi-restraints excluded: chain I residue 37 THR Chi-restraints excluded: chain J residue 55 MET Chi-restraints excluded: chain J residue 113 VAL Chi-restraints excluded: chain J residue 124 ASP Chi-restraints excluded: chain K residue 70 GLU Chi-restraints excluded: chain L residue 10 VAL Chi-restraints excluded: chain L residue 290 MET Chi-restraints excluded: chain L residue 411 MET Chi-restraints excluded: chain L residue 482 MET Chi-restraints excluded: chain M residue 378 GLU Chi-restraints excluded: chain M residue 385 THR Chi-restraints excluded: chain M residue 400 MET Chi-restraints excluded: chain N residue 38 LEU Chi-restraints excluded: chain N residue 98 MET Chi-restraints excluded: chain N residue 117 GLU Chi-restraints excluded: chain N residue 222 ASN Chi-restraints excluded: chain O residue 192 MET Chi-restraints excluded: chain O residue 209 THR Chi-restraints excluded: chain O residue 250 ASP Chi-restraints excluded: chain O residue 252 ASN Chi-restraints excluded: chain O residue 279 LEU Chi-restraints excluded: chain P residue 256 TYR Chi-restraints excluded: chain P residue 266 ILE Chi-restraints excluded: chain Q residue 87 SER Chi-restraints excluded: chain R residue 7 THR Chi-restraints excluded: chain R residue 19 ASP Chi-restraints excluded: chain S residue 29 SER Chi-restraints excluded: chain S residue 74 LYS Chi-restraints excluded: chain S residue 82 SER Chi-restraints excluded: chain S residue 90 LEU Chi-restraints excluded: chain T residue 7 THR Chi-restraints excluded: chain T residue 72 CYS Chi-restraints excluded: chain T residue 76 ILE Chi-restraints excluded: chain U residue 65 ILE Chi-restraints excluded: chain V residue 47 THR Chi-restraints excluded: chain W residue 16 SER Chi-restraints excluded: chain W residue 116 LYS Chi-restraints excluded: chain W residue 127 ASP Chi-restraints excluded: chain X residue 8 SER Chi-restraints excluded: chain X residue 11 ASP Chi-restraints excluded: chain Y residue 13 GLU Chi-restraints excluded: chain Y residue 46 THR Chi-restraints excluded: chain Y residue 114 CYS Chi-restraints excluded: chain Z residue 20 ASP Chi-restraints excluded: chain Z residue 99 LYS Chi-restraints excluded: chain a residue 60 SER Chi-restraints excluded: chain d residue 90 MET Chi-restraints excluded: chain e residue 56 LYS Chi-restraints excluded: chain g residue 37 LEU Chi-restraints excluded: chain g residue 60 VAL Chi-restraints excluded: chain i residue 4 THR Chi-restraints excluded: chain i residue 6 GLU Chi-restraints excluded: chain i residue 68 ILE Chi-restraints excluded: chain i residue 72 THR Chi-restraints excluded: chain i residue 81 ILE Chi-restraints excluded: chain k residue 38 ARG Chi-restraints excluded: chain l residue 4 ILE Chi-restraints excluded: chain l residue 5 THR Chi-restraints excluded: chain l residue 121 THR Chi-restraints excluded: chain m residue 91 LEU Chi-restraints excluded: chain n residue 145 VAL Chi-restraints excluded: chain o residue 11 ASP Chi-restraints excluded: chain o residue 20 ARG Chi-restraints excluded: chain o residue 23 THR Chi-restraints excluded: chain p residue 7 ASP Chi-restraints excluded: chain p residue 119 SER Chi-restraints excluded: chain q residue 21 ARG Chi-restraints excluded: chain q residue 25 ARG Chi-restraints excluded: chain q residue 142 THR Chi-restraints excluded: chain r residue 2 SER Chi-restraints excluded: chain r residue 29 GLU Chi-restraints excluded: chain r residue 34 THR Chi-restraints excluded: chain r residue 68 VAL Chi-restraints excluded: chain s residue 41 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 799 random chunks: chunk 700 optimal weight: 1.9990 chunk 737 optimal weight: 3.9990 chunk 673 optimal weight: 5.9990 chunk 717 optimal weight: 6.9990 chunk 431 optimal weight: 8.9990 chunk 312 optimal weight: 7.9990 chunk 563 optimal weight: 0.9990 chunk 220 optimal weight: 4.9990 chunk 648 optimal weight: 8.9990 chunk 678 optimal weight: 10.0000 chunk 715 optimal weight: 5.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 287 HIS A ** both conformations clash, **PLEASE CHECK MANUALLY** L 31 ASN N 152 ASN N 204 ASN O 76 ASN d 61 GLN h 124 HIS h 143 ASN j 6 HIS l 147 ASN m 116 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8378 moved from start: 0.2147 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.241 69896 Z= 0.538 Angle : 1.330 50.562 94392 Z= 0.845 Chirality : 0.258 6.544 10159 Planarity : 0.005 0.049 11738 Dihedral : 12.593 176.459 10956 Min Nonbonded Distance : 1.998 Molprobity Statistics. All-atom Clashscore : 6.37 Ramachandran Plot: Outliers : 0.04 % Allowed : 2.55 % Favored : 97.41 % Rotamer: Outliers : 1.86 % Allowed : 12.55 % Favored : 85.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % 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: 1.01 (0.09), residues: 8090 helix: 1.28 (0.08), residues: 4307 sheet: 0.12 (0.26), residues: 377 loop : 0.07 (0.11), residues: 3406 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP g 26 HIS 0.007 0.001 HIS p 143 PHE 0.042 0.002 PHE L 24 TYR 0.027 0.002 TYR I 118 ARG 0.013 0.001 ARG C 14 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16180 Ramachandran restraints generated. 8090 Oldfield, 0 Emsley, 8090 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16180 Ramachandran restraints generated. 8090 Oldfield, 0 Emsley, 8090 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 908 residues out of total 7150 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 132 poor density : 776 time to evaluate : 6.321 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 102 LYS cc_start: 0.7908 (ttpp) cc_final: 0.7466 (tttm) REVERT: B 165 LYS cc_start: 0.8781 (OUTLIER) cc_final: 0.8507 (mttp) REVERT: B 171 LYS cc_start: 0.8484 (mtmm) cc_final: 0.7798 (mtmt) REVERT: B 175 ILE cc_start: 0.9049 (OUTLIER) cc_final: 0.8561 (mp) REVERT: C 211 GLN cc_start: 0.8304 (OUTLIER) cc_final: 0.7896 (mt0) REVERT: D 12 GLU cc_start: 0.7211 (pp20) cc_final: 0.6964 (pp20) REVERT: D 164 MET cc_start: 0.7984 (OUTLIER) cc_final: 0.6513 (pmm) REVERT: G 31 GLU cc_start: 0.7573 (mt-10) cc_final: 0.7019 (mm-30) REVERT: H 79 LEU cc_start: 0.7717 (OUTLIER) cc_final: 0.7394 (tm) REVERT: H 121 TRP cc_start: 0.8232 (OUTLIER) cc_final: 0.7773 (t60) REVERT: K 70 GLU cc_start: 0.7504 (OUTLIER) cc_final: 0.6809 (tt0) REVERT: L 3 MET cc_start: 0.7933 (OUTLIER) cc_final: 0.7603 (mmm) REVERT: M 378 GLU cc_start: 0.7759 (OUTLIER) cc_final: 0.7519 (tm-30) REVERT: M 400 MET cc_start: 0.7687 (OUTLIER) cc_final: 0.7368 (ttm) REVERT: O 192 MET cc_start: 0.7932 (OUTLIER) cc_final: 0.7331 (mtm) REVERT: P 57 MET cc_start: 0.8455 (mmm) cc_final: 0.7940 (mmt) REVERT: U 30 LEU cc_start: 0.8296 (OUTLIER) cc_final: 0.8020 (tp) REVERT: X 36 ASP cc_start: 0.7605 (t70) cc_final: 0.7313 (t70) REVERT: Y 13 GLU cc_start: 0.7419 (OUTLIER) cc_final: 0.6667 (mp0) REVERT: Y 73 SER cc_start: 0.8571 (p) cc_final: 0.8124 (m) REVERT: Y 137 GLU cc_start: 0.7489 (tp30) cc_final: 0.7077 (mm-30) REVERT: a 60 SER cc_start: 0.9165 (OUTLIER) cc_final: 0.8877 (t) REVERT: b 15 GLU cc_start: 0.7989 (mm-30) cc_final: 0.7661 (mm-30) REVERT: e 4 ASP cc_start: 0.8339 (t70) cc_final: 0.8042 (t0) REVERT: e 56 LYS cc_start: 0.8863 (OUTLIER) cc_final: 0.8185 (tmtm) REVERT: h 19 LYS cc_start: 0.8345 (ttmm) cc_final: 0.8114 (tttm) REVERT: k 38 ARG cc_start: 0.8539 (OUTLIER) cc_final: 0.7659 (ttm110) REVERT: m 107 ASP cc_start: 0.8380 (t0) cc_final: 0.8045 (t70) REVERT: o 20 ARG cc_start: 0.7489 (OUTLIER) cc_final: 0.7109 (mpt180) REVERT: o 45 MET cc_start: 0.8918 (mtm) cc_final: 0.8696 (mtp) REVERT: p 72 ASP cc_start: 0.7870 (p0) cc_final: 0.7491 (p0) REVERT: q 25 ARG cc_start: 0.7049 (OUTLIER) cc_final: 0.6257 (ttt90) REVERT: r 29 GLU cc_start: 0.7731 (OUTLIER) cc_final: 0.7282 (pm20) REVERT: s 35 ASN cc_start: 0.7259 (t0) cc_final: 0.7059 (t0) outliers start: 132 outliers final: 82 residues processed: 851 average time/residue: 1.6703 time to fit residues: 1829.0513 Evaluate side-chains 866 residues out of total 7150 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 101 poor density : 765 time to evaluate : 6.225 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 THR Chi-restraints excluded: chain A residue 69 ILE Chi-restraints excluded: chain A residue 96 ILE Chi-restraints excluded: chain B residue 30 VAL Chi-restraints excluded: chain B residue 50 PHE Chi-restraints excluded: chain B residue 54 CYS Chi-restraints excluded: chain B residue 85 VAL Chi-restraints excluded: chain B residue 125 TYR Chi-restraints excluded: chain B residue 165 LYS Chi-restraints excluded: chain B residue 175 ILE Chi-restraints excluded: chain C residue 17 VAL Chi-restraints excluded: chain C residue 73 LYS Chi-restraints excluded: chain C residue 211 GLN Chi-restraints excluded: chain D residue 22 THR Chi-restraints excluded: chain D residue 164 MET Chi-restraints excluded: chain D residue 420 THR Chi-restraints excluded: chain E residue 19 THR Chi-restraints excluded: chain E residue 113 SER Chi-restraints excluded: chain E residue 134 ASP Chi-restraints excluded: chain G residue 18 VAL Chi-restraints excluded: chain G residue 109 ASP Chi-restraints excluded: chain G residue 425 SER Chi-restraints excluded: chain G residue 436 SER Chi-restraints excluded: chain G residue 483 VAL Chi-restraints excluded: chain G residue 512 GLU Chi-restraints excluded: chain G residue 517 ASN Chi-restraints excluded: chain H residue 79 LEU Chi-restraints excluded: chain H residue 121 TRP Chi-restraints excluded: chain I residue 37 THR Chi-restraints excluded: chain J residue 113 VAL Chi-restraints excluded: chain J residue 124 ASP Chi-restraints excluded: chain K residue 70 GLU Chi-restraints excluded: chain L residue 3 MET Chi-restraints excluded: chain L residue 10 VAL Chi-restraints excluded: chain L residue 21 MET Chi-restraints excluded: chain L residue 290 MET Chi-restraints excluded: chain L residue 482 MET Chi-restraints excluded: chain M residue 72 LEU Chi-restraints excluded: chain M residue 378 GLU Chi-restraints excluded: chain M residue 385 THR Chi-restraints excluded: chain M residue 400 MET Chi-restraints excluded: chain N residue 38 LEU Chi-restraints excluded: chain N residue 98 MET Chi-restraints excluded: chain N residue 117 GLU Chi-restraints excluded: chain N residue 222 ASN Chi-restraints excluded: chain O residue 85 ASP Chi-restraints excluded: chain O residue 192 MET Chi-restraints excluded: chain O residue 209 THR Chi-restraints excluded: chain O residue 250 ASP Chi-restraints excluded: chain O residue 252 ASN Chi-restraints excluded: chain P residue 266 ILE Chi-restraints excluded: chain Q residue 87 SER Chi-restraints excluded: chain Q residue 104 ASP Chi-restraints excluded: chain R residue 7 THR Chi-restraints excluded: chain R residue 19 ASP Chi-restraints excluded: chain S residue 29 SER Chi-restraints excluded: chain S residue 74 LYS Chi-restraints excluded: chain S residue 76 VAL Chi-restraints excluded: chain S residue 82 SER Chi-restraints excluded: chain S residue 90 LEU Chi-restraints excluded: chain T residue 72 CYS Chi-restraints excluded: chain T residue 76 ILE Chi-restraints excluded: chain U residue 30 LEU Chi-restraints excluded: chain V residue 47 THR Chi-restraints excluded: chain W residue 16 SER Chi-restraints excluded: chain W residue 127 ASP Chi-restraints excluded: chain X residue 8 SER Chi-restraints excluded: chain X residue 11 ASP Chi-restraints excluded: chain Y residue 13 GLU Chi-restraints excluded: chain Y residue 46 THR Chi-restraints excluded: chain Y residue 114 CYS Chi-restraints excluded: chain Z residue 20 ASP Chi-restraints excluded: chain a residue 60 SER Chi-restraints excluded: chain c residue 29 ILE Chi-restraints excluded: chain d residue 90 MET Chi-restraints excluded: chain e residue 56 LYS Chi-restraints excluded: chain g residue 29 ASP Chi-restraints excluded: chain g residue 37 LEU Chi-restraints excluded: chain g residue 60 VAL Chi-restraints excluded: chain h residue 57 GLU Chi-restraints excluded: chain i residue 4 THR Chi-restraints excluded: chain i residue 6 GLU Chi-restraints excluded: chain i residue 47 ASN Chi-restraints excluded: chain i residue 72 THR Chi-restraints excluded: chain i residue 81 ILE Chi-restraints excluded: chain k residue 38 ARG Chi-restraints excluded: chain l residue 4 ILE Chi-restraints excluded: chain l residue 5 THR Chi-restraints excluded: chain l residue 121 THR Chi-restraints excluded: chain m residue 91 LEU Chi-restraints excluded: chain n residue 145 VAL Chi-restraints excluded: chain o residue 20 ARG Chi-restraints excluded: chain o residue 23 THR Chi-restraints excluded: chain p residue 7 ASP Chi-restraints excluded: chain q residue 25 ARG Chi-restraints excluded: chain q residue 142 THR Chi-restraints excluded: chain r residue 2 SER Chi-restraints excluded: chain r residue 29 GLU Chi-restraints excluded: chain r residue 34 THR Chi-restraints excluded: chain r residue 68 VAL Chi-restraints excluded: chain s residue 41 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 799 random chunks: chunk 471 optimal weight: 5.9990 chunk 758 optimal weight: 0.0030 chunk 463 optimal weight: 0.7980 chunk 359 optimal weight: 4.9990 chunk 527 optimal weight: 6.9990 chunk 796 optimal weight: 6.9990 chunk 732 optimal weight: 0.8980 chunk 633 optimal weight: 5.9990 chunk 65 optimal weight: 7.9990 chunk 489 optimal weight: 4.9990 chunk 388 optimal weight: 1.9990 overall best weight: 1.7394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 653 ASN ** H 287 HIS A ** both conformations clash, **PLEASE CHECK MANUALLY** N 152 ASN N 204 ASN O 76 ASN ** S 75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** h 143 ASN j 6 HIS l 147 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8344 moved from start: 0.2308 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.244 69896 Z= 0.453 Angle : 1.299 50.632 94392 Z= 0.834 Chirality : 0.255 6.444 10159 Planarity : 0.004 0.050 11738 Dihedral : 12.293 178.396 10956 Min Nonbonded Distance : 2.031 Molprobity Statistics. All-atom Clashscore : 6.33 Ramachandran Plot: Outliers : 0.02 % Allowed : 2.10 % Favored : 97.87 % Rotamer: Outliers : 1.45 % Allowed : 13.29 % Favored : 85.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % 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: 1.19 (0.09), residues: 8090 helix: 1.44 (0.08), residues: 4309 sheet: 0.09 (0.26), residues: 371 loop : 0.14 (0.11), residues: 3410 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP g 26 HIS 0.005 0.001 HIS T 35 PHE 0.026 0.001 PHE N 292 TYR 0.020 0.001 TYR L 422 ARG 0.014 0.000 ARG C 14 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16180 Ramachandran restraints generated. 8090 Oldfield, 0 Emsley, 8090 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16180 Ramachandran restraints generated. 8090 Oldfield, 0 Emsley, 8090 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 889 residues out of total 7150 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 103 poor density : 786 time to evaluate : 6.355 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 112 GLU cc_start: 0.7820 (mm-30) cc_final: 0.7432 (mp0) REVERT: B 102 LYS cc_start: 0.7901 (ttpp) cc_final: 0.7449 (tttm) REVERT: B 165 LYS cc_start: 0.8745 (OUTLIER) cc_final: 0.8513 (mttp) REVERT: B 171 LYS cc_start: 0.8415 (mtmm) cc_final: 0.7734 (mtmt) REVERT: B 175 ILE cc_start: 0.9027 (OUTLIER) cc_final: 0.8565 (mp) REVERT: C 73 LYS cc_start: 0.9105 (OUTLIER) cc_final: 0.8596 (mptp) REVERT: C 211 GLN cc_start: 0.8280 (OUTLIER) cc_final: 0.7872 (mt0) REVERT: D 12 GLU cc_start: 0.7176 (pp20) cc_final: 0.6928 (pp20) REVERT: D 72 MET cc_start: 0.8687 (mmt) cc_final: 0.8404 (mmt) REVERT: D 164 MET cc_start: 0.7802 (OUTLIER) cc_final: 0.6226 (pmm) REVERT: G 31 GLU cc_start: 0.7583 (mt-10) cc_final: 0.7059 (mm-30) REVERT: G 109 ASP cc_start: 0.7778 (OUTLIER) cc_final: 0.7449 (t0) REVERT: H 79 LEU cc_start: 0.7661 (OUTLIER) cc_final: 0.7340 (tm) REVERT: J 77 GLU cc_start: 0.7150 (mm-30) cc_final: 0.6760 (mm-30) REVERT: K 70 GLU cc_start: 0.7455 (OUTLIER) cc_final: 0.6810 (tt0) REVERT: L 3 MET cc_start: 0.7769 (OUTLIER) cc_final: 0.7525 (mmm) REVERT: L 411 MET cc_start: 0.7169 (mmm) cc_final: 0.6936 (mmt) REVERT: M 378 GLU cc_start: 0.7647 (OUTLIER) cc_final: 0.7439 (tm-30) REVERT: M 400 MET cc_start: 0.7672 (OUTLIER) cc_final: 0.7359 (ttm) REVERT: N 222 ASN cc_start: 0.8051 (OUTLIER) cc_final: 0.7731 (t0) REVERT: O 192 MET cc_start: 0.7893 (OUTLIER) cc_final: 0.7268 (mtm) REVERT: P 57 MET cc_start: 0.8447 (mmm) cc_final: 0.7860 (mmt) REVERT: R 3 ARG cc_start: 0.7950 (ttp80) cc_final: 0.7612 (ttp-110) REVERT: U 30 LEU cc_start: 0.8207 (OUTLIER) cc_final: 0.7932 (tp) REVERT: U 61 GLU cc_start: 0.8023 (tt0) cc_final: 0.7768 (tt0) REVERT: X 36 ASP cc_start: 0.7562 (t70) cc_final: 0.7310 (t70) REVERT: X 43 MET cc_start: 0.8955 (mmm) cc_final: 0.8708 (mmp) REVERT: Y 73 SER cc_start: 0.8527 (p) cc_final: 0.8100 (m) REVERT: Y 137 GLU cc_start: 0.7460 (tp30) cc_final: 0.7059 (mm-30) REVERT: Z 131 GLU cc_start: 0.7589 (OUTLIER) cc_final: 0.7135 (tm-30) REVERT: a 60 SER cc_start: 0.9132 (OUTLIER) cc_final: 0.8863 (t) REVERT: b 15 GLU cc_start: 0.7974 (mm-30) cc_final: 0.7648 (mm-30) REVERT: d 106 LYS cc_start: 0.8468 (tttp) cc_final: 0.8240 (tttt) REVERT: e 4 ASP cc_start: 0.8281 (t70) cc_final: 0.8023 (t0) REVERT: e 56 LYS cc_start: 0.8858 (OUTLIER) cc_final: 0.8147 (tmtm) REVERT: m 107 ASP cc_start: 0.8355 (t0) cc_final: 0.8031 (t70) REVERT: n 72 HIS cc_start: 0.7685 (t-170) cc_final: 0.7431 (t-170) REVERT: o 20 ARG cc_start: 0.7444 (OUTLIER) cc_final: 0.7110 (mpt180) REVERT: o 42 GLN cc_start: 0.8113 (mt0) cc_final: 0.7806 (mt0) REVERT: o 45 MET cc_start: 0.8913 (mtm) cc_final: 0.8667 (mtp) REVERT: p 72 ASP cc_start: 0.7728 (p0) cc_final: 0.7397 (p0) REVERT: q 25 ARG cc_start: 0.7051 (OUTLIER) cc_final: 0.6563 (ttt90) REVERT: r 29 GLU cc_start: 0.7732 (OUTLIER) cc_final: 0.7319 (pm20) outliers start: 103 outliers final: 71 residues processed: 852 average time/residue: 1.6431 time to fit residues: 1801.2398 Evaluate side-chains 857 residues out of total 7150 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 91 poor density : 766 time to evaluate : 6.150 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 ILE Chi-restraints excluded: chain A residue 96 ILE Chi-restraints excluded: chain B residue 30 VAL Chi-restraints excluded: chain B residue 50 PHE Chi-restraints excluded: chain B residue 54 CYS Chi-restraints excluded: chain B residue 85 VAL Chi-restraints excluded: chain B residue 125 TYR Chi-restraints excluded: chain B residue 165 LYS Chi-restraints excluded: chain B residue 175 ILE Chi-restraints excluded: chain C residue 17 VAL Chi-restraints excluded: chain C residue 73 LYS Chi-restraints excluded: chain C residue 211 GLN Chi-restraints excluded: chain D residue 22 THR Chi-restraints excluded: chain D residue 164 MET Chi-restraints excluded: chain D residue 420 THR Chi-restraints excluded: chain E residue 19 THR Chi-restraints excluded: chain E residue 134 ASP Chi-restraints excluded: chain G residue 18 VAL Chi-restraints excluded: chain G residue 109 ASP Chi-restraints excluded: chain G residue 425 SER Chi-restraints excluded: chain G residue 436 SER Chi-restraints excluded: chain G residue 483 VAL Chi-restraints excluded: chain G residue 517 ASN Chi-restraints excluded: chain H residue 79 LEU Chi-restraints excluded: chain I residue 37 THR Chi-restraints excluded: chain J residue 113 VAL Chi-restraints excluded: chain J residue 124 ASP Chi-restraints excluded: chain K residue 70 GLU Chi-restraints excluded: chain L residue 3 MET Chi-restraints excluded: chain L residue 10 VAL Chi-restraints excluded: chain L residue 214 ILE Chi-restraints excluded: chain L residue 290 MET Chi-restraints excluded: chain M residue 378 GLU Chi-restraints excluded: chain M residue 385 THR Chi-restraints excluded: chain M residue 400 MET Chi-restraints excluded: chain N residue 38 LEU Chi-restraints excluded: chain N residue 117 GLU Chi-restraints excluded: chain N residue 222 ASN Chi-restraints excluded: chain O residue 85 ASP Chi-restraints excluded: chain O residue 192 MET Chi-restraints excluded: chain O residue 209 THR Chi-restraints excluded: chain O residue 250 ASP Chi-restraints excluded: chain O residue 252 ASN Chi-restraints excluded: chain P residue 266 ILE Chi-restraints excluded: chain Q residue 87 SER Chi-restraints excluded: chain Q residue 104 ASP Chi-restraints excluded: chain R residue 7 THR Chi-restraints excluded: chain R residue 19 ASP Chi-restraints excluded: chain S residue 29 SER Chi-restraints excluded: chain S residue 74 LYS Chi-restraints excluded: chain S residue 76 VAL Chi-restraints excluded: chain S residue 82 SER Chi-restraints excluded: chain T residue 65 ILE Chi-restraints excluded: chain T residue 72 CYS Chi-restraints excluded: chain T residue 76 ILE Chi-restraints excluded: chain U residue 30 LEU Chi-restraints excluded: chain V residue 47 THR Chi-restraints excluded: chain W residue 16 SER Chi-restraints excluded: chain X residue 8 SER Chi-restraints excluded: chain X residue 11 ASP Chi-restraints excluded: chain Y residue 10 ASP Chi-restraints excluded: chain Y residue 46 THR Chi-restraints excluded: chain Y residue 114 CYS Chi-restraints excluded: chain Z residue 20 ASP Chi-restraints excluded: chain Z residue 131 GLU Chi-restraints excluded: chain a residue 60 SER Chi-restraints excluded: chain c residue 29 ILE Chi-restraints excluded: chain d residue 90 MET Chi-restraints excluded: chain e residue 56 LYS Chi-restraints excluded: chain g residue 29 ASP Chi-restraints excluded: chain g residue 37 LEU Chi-restraints excluded: chain g residue 60 VAL Chi-restraints excluded: chain i residue 4 THR Chi-restraints excluded: chain i residue 6 GLU Chi-restraints excluded: chain i residue 72 THR Chi-restraints excluded: chain i residue 81 ILE Chi-restraints excluded: chain l residue 5 THR Chi-restraints excluded: chain l residue 121 THR Chi-restraints excluded: chain m residue 91 LEU Chi-restraints excluded: chain n residue 145 VAL Chi-restraints excluded: chain o residue 11 ASP Chi-restraints excluded: chain o residue 20 ARG Chi-restraints excluded: chain o residue 23 THR Chi-restraints excluded: chain p residue 7 ASP Chi-restraints excluded: chain q residue 25 ARG Chi-restraints excluded: chain q residue 142 THR Chi-restraints excluded: chain r residue 2 SER Chi-restraints excluded: chain r residue 29 GLU Chi-restraints excluded: chain r residue 34 THR Chi-restraints excluded: chain r residue 68 VAL Chi-restraints excluded: chain s residue 41 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 799 random chunks: chunk 503 optimal weight: 0.0770 chunk 675 optimal weight: 0.9990 chunk 194 optimal weight: 6.9990 chunk 584 optimal weight: 0.9990 chunk 93 optimal weight: 10.0000 chunk 176 optimal weight: 5.9990 chunk 634 optimal weight: 0.0870 chunk 265 optimal weight: 0.8980 chunk 651 optimal weight: 9.9990 chunk 80 optimal weight: 8.9990 chunk 116 optimal weight: 0.9990 overall best weight: 0.6120 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 157 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 287 HIS A ** both conformations clash, **PLEASE CHECK MANUALLY** N 204 ASN R 94 GLN ** S 75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** h 143 ASN j 6 HIS l 147 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.087758 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3113 r_free = 0.3113 target = 0.074863 restraints weight = 169858.832| |-----------------------------------------------------------------------------| r_work (start): 0.3107 rms_B_bonded: 1.63 r_work: 0.3014 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.2904 rms_B_bonded: 3.82 restraints_weight: 0.2500 r_work (final): 0.2904 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2904 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2904 r_free = 0.2904 target_work(ls_wunit_k1) = 0.065 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2904 r_free = 0.2904 target_work(ls_wunit_k1) = 0.065 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2904 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8625 moved from start: 0.2466 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.246 69896 Z= 0.431 Angle : 1.289 50.591 94392 Z= 0.830 Chirality : 0.254 6.384 10159 Planarity : 0.004 0.050 11738 Dihedral : 11.924 179.128 10956 Min Nonbonded Distance : 2.042 Molprobity Statistics. All-atom Clashscore : 6.17 Ramachandran Plot: Outliers : 0.02 % Allowed : 2.09 % Favored : 97.88 % Rotamer: Outliers : 1.23 % Allowed : 13.49 % Favored : 85.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % 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: 1.39 (0.09), residues: 8090 helix: 1.62 (0.08), residues: 4303 sheet: 0.03 (0.26), residues: 371 loop : 0.24 (0.11), residues: 3416 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP L 144 HIS 0.004 0.001 HIS q 87 PHE 0.035 0.001 PHE L 24 TYR 0.021 0.001 TYR L 422 ARG 0.013 0.000 ARG C 14 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 28460.28 seconds wall clock time: 494 minutes 24.50 seconds (29664.50 seconds total)