Starting phenix.real_space_refine on Fri Mar 15 13:15:03 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7r41_14251/03_2024/7r41_14251_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7r41_14251/03_2024/7r41_14251.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7r41_14251/03_2024/7r41_14251_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7r41_14251/03_2024/7r41_14251_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7r41_14251/03_2024/7r41_14251_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7r41_14251/03_2024/7r41_14251.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7r41_14251/03_2024/7r41_14251.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7r41_14251/03_2024/7r41_14251_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7r41_14251/03_2024/7r41_14251_updated.pdb" } resolution = 2.3 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.004 sd= 1.021 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: 11 Type Number sf(0) Gaussians I 1 10.91 5 K 1 8.98 5 Fe 28 7.16 5 Zn 1 6.06 5 P 37 5.49 5 Mg 1 5.21 5 S 468 5.16 5 Cl 1 4.86 5 C 43886 2.51 5 N 11170 2.21 5 O 13544 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 32": "OE1" <-> "OE2" Residue "A PHE 41": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 51": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 55": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 56": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 68": "OE1" <-> "OE2" Residue "A PHE 93": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 105": "OE1" <-> "OE2" Residue "A GLU 112": "OE1" <-> "OE2" Residue "A GLU 115": "OE1" <-> "OE2" Residue "B GLU 27": "OE1" <-> "OE2" Residue "B ASP 35": "OD1" <-> "OD2" Residue "B ARG 71": "NH1" <-> "NH2" Residue "B GLU 109": "OE1" <-> "OE2" Residue "B ARG 111": "NH1" <-> "NH2" Residue "B TYR 126": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 154": "OE1" <-> "OE2" Residue "C ARG 8": "NH1" <-> "NH2" Residue "C ARG 12": "NH1" <-> "NH2" Residue "C ASP 16": "OD1" <-> "OD2" Residue "C PHE 45": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 77": "OD1" <-> "OD2" Residue "C GLU 91": "OE1" <-> "OE2" Residue "C ARG 149": "NH1" <-> "NH2" Residue "C PHE 157": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 158": "OE1" <-> "OE2" Residue "C PHE 166": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 179": "OE1" <-> "OE2" Residue "C GLU 186": "OE1" <-> "OE2" Residue "C ASP 198": "OD1" <-> "OD2" Residue "D ARG 2": "NH1" <-> "NH2" Residue "D GLU 12": "OE1" <-> "OE2" Residue "D GLU 24": "OE1" <-> "OE2" Residue "D PHE 51": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 123": "OE1" <-> "OE2" Residue "D ASP 160": "OD1" <-> "OD2" Residue "D GLU 175": "OE1" <-> "OE2" Residue "D GLU 179": "OE1" <-> "OE2" Residue "D ASP 210": "OD1" <-> "OD2" Residue "D ARG 221": "NH1" <-> "NH2" Residue "D ARG 233": "NH1" <-> "NH2" Residue "D GLU 303": "OE1" <-> "OE2" Residue "D GLU 343": "OE1" <-> "OE2" Residue "D PHE 425": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 429": "OD1" <-> "OD2" Residue "E GLU 26": "OE1" <-> "OE2" Residue "E TYR 28": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 52": "OD1" <-> "OD2" Residue "E GLU 71": "OE1" <-> "OE2" Residue "E GLU 82": "OE1" <-> "OE2" Residue "E GLU 162": "OE1" <-> "OE2" Residue "E GLU 170": "OE1" <-> "OE2" Residue "E ARG 190": "NH1" <-> "NH2" Residue "E GLU 204": "OE1" <-> "OE2" Residue "F ARG 32": "NH1" <-> "NH2" Residue "F GLU 101": "OE1" <-> "OE2" Residue "F GLU 109": "OE1" <-> "OE2" Residue "F ARG 112": "NH1" <-> "NH2" Residue "F ARG 132": "NH1" <-> "NH2" Residue "F ARG 139": "NH1" <-> "NH2" Residue "F GLU 189": "OE1" <-> "OE2" Residue "F GLU 194": "OE1" <-> "OE2" Residue "F ARG 249": "NH1" <-> "NH2" Residue "F PHE 256": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 278": "OE1" <-> "OE2" Residue "F GLU 313": "OE1" <-> "OE2" Residue "F ASP 338": "OD1" <-> "OD2" Residue "F ARG 349": "NH1" <-> "NH2" Residue "F GLU 352": "OE1" <-> "OE2" Residue "F GLU 357": "OE1" <-> "OE2" Residue "F ASP 370": "OD1" <-> "OD2" Residue "F GLU 428": "OE1" <-> "OE2" Residue "F ARG 429": "NH1" <-> "NH2" Residue "G GLU 10": "OE1" <-> "OE2" Residue "G ARG 39": "NH1" <-> "NH2" Residue "G ARG 53": "NH1" <-> "NH2" Residue "G GLU 60": "OE1" <-> "OE2" Residue "G GLU 95": "OE1" <-> "OE2" Residue "G GLU 165": "OE1" <-> "OE2" Residue "G ARG 218": "NH1" <-> "NH2" Residue "G ASP 232": "OD1" <-> "OD2" Residue "G ARG 243": "NH1" <-> "NH2" Residue "G GLU 246": "OE1" <-> "OE2" Residue "G ARG 253": "NH1" <-> "NH2" Residue "G GLU 261": "OE1" <-> "OE2" Residue "G GLU 281": "OE1" <-> "OE2" Residue "G ARG 285": "NH1" <-> "NH2" Residue "G GLU 287": "OE1" <-> "OE2" Residue "G ARG 302": "NH1" <-> "NH2" Residue "G ASP 314": "OD1" <-> "OD2" Residue "G ASP 341": "OD1" <-> "OD2" Residue "G GLU 346": "OE1" <-> "OE2" Residue "G GLU 347": "OE1" <-> "OE2" Residue "G ASP 357": "OD1" <-> "OD2" Residue "G ASP 375": "OD1" <-> "OD2" Residue "G ARG 385": "NH1" <-> "NH2" Residue "G ASP 414": "OD1" <-> "OD2" Residue "G ARG 418": "NH1" <-> "NH2" Residue "G ASP 536": "OD1" <-> "OD2" Residue "G ASP 558": "OD1" <-> "OD2" Residue "G ASP 614": "OD1" <-> "OD2" Residue "G ASP 617": "OD1" <-> "OD2" Residue "G GLU 625": "OE1" <-> "OE2" Residue "G ASP 634": "OD1" <-> "OD2" Residue "G GLU 637": "OE1" <-> "OE2" Residue "G PHE 642": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 693": "OE1" <-> "OE2" Residue "H ARG 25": "NH1" <-> "NH2" Residue "H ARG 34": "NH1" <-> "NH2" Residue "H ARG 62": "NH1" <-> "NH2" Residue "H GLU 170": "OE1" <-> "OE2" Residue "H GLU 192": "OE1" <-> "OE2" Residue "H GLU 202": "OE1" <-> "OE2" Residue "H GLU 204": "OE1" <-> "OE2" Residue "H PHE 211": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 214": "OE1" <-> "OE2" Residue "H PHE 224": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 253": "OE1" <-> "OE2" Residue "I ARG 8": "NH1" <-> "NH2" Residue "I GLU 9": "OE1" <-> "OE2" Residue "I ASP 13": "OD1" <-> "OD2" Residue "I TYR 50": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I GLU 95": "OE1" <-> "OE2" Residue "I ARG 108": "NH1" <-> "NH2" Residue "I GLU 133": "OE1" <-> "OE2" Residue "I GLU 146": "OE1" <-> "OE2" Residue "J TYR 4": "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 101": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J GLU 114": "OE1" <-> "OE2" Residue "J GLU 118": "OE1" <-> "OE2" Residue "J TYR 128": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ASP 129": "OD1" <-> "OD2" Residue "J PHE 135": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J GLU 139": "OE1" <-> "OE2" Residue "J ARG 173": "NH1" <-> "NH2" Residue "K GLU 34": "OE1" <-> "OE2" Residue "L GLU 60": "OE1" <-> "OE2" Residue "L PHE 89": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L GLU 102": "OE1" <-> "OE2" Residue "L PHE 103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 109": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ARG 161": "NH1" <-> "NH2" Residue "L ASP 179": "OD1" <-> "OD2" Residue "L ASP 208": "OD1" <-> "OD2" Residue "L PHE 258": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ARG 262": "NH1" <-> "NH2" Residue "L PHE 263": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L GLU 268": "OE1" <-> "OE2" Residue "L TYR 323": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L GLU 353": "OE1" <-> "OE2" Residue "L ASP 393": "OD1" <-> "OD2" Residue "L TYR 484": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 485": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L GLU 503": "OE1" <-> "OE2" Residue "L GLU 559": "OE1" <-> "OE2" Residue "L GLU 606": "OE1" <-> "OE2" Residue "M ASP 59": "OD1" <-> "OD2" Residue "M PHE 95": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M PHE 122": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M GLU 141": "OE1" <-> "OE2" Residue "M ARG 142": "NH1" <-> "NH2" Residue "M TYR 166": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M GLU 222": "OE1" <-> "OE2" Residue "M PHE 256": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M GLU 378": "OE1" <-> "OE2" Residue "M TYR 419": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M ARG 432": "NH1" <-> "NH2" Residue "N GLU 34": "OE1" <-> "OE2" Residue "N GLU 54": "OE1" <-> "OE2" Residue "N GLU 117": "OE1" <-> "OE2" Residue "N TYR 143": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N PHE 281": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N ARG 295": "NH1" <-> "NH2" Residue "N PHE 325": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N GLU 347": "OE1" <-> "OE2" Residue "O GLU 12": "OE1" <-> "OE2" Residue "O GLU 53": "OE1" <-> "OE2" Residue "O ASP 85": "OD1" <-> "OD2" Residue "O PHE 132": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O GLU 232": "OE1" <-> "OE2" Residue "O ASP 237": "OD1" <-> "OD2" Residue "O ASP 244": "OD1" <-> "OD2" Residue "O ARG 302": "NH1" <-> "NH2" Residue "O ARG 305": "NH1" <-> "NH2" Residue "O GLU 310": "OE1" <-> "OE2" Residue "P ARG 40": "NH1" <-> "NH2" Residue "P ARG 50": "NH1" <-> "NH2" Residue "P GLU 52": "OE1" <-> "OE2" Residue "P PHE 70": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P ARG 82": "NH1" <-> "NH2" Residue "P ARG 97": "NH1" <-> "NH2" Residue "P GLU 98": "OE1" <-> "OE2" Residue "P PHE 104": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P GLU 107": "OE1" <-> "OE2" Residue "P GLU 127": "OE1" <-> "OE2" Residue "P ARG 147": "NH1" <-> "NH2" Residue "P GLU 153": "OE1" <-> "OE2" Residue "P ARG 157": "NH1" <-> "NH2" Residue "P GLU 158": "OE1" <-> "OE2" Residue "P GLU 162": "OE1" <-> "OE2" Residue "P GLU 170": "OE1" <-> "OE2" Residue "P PHE 172": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P GLU 175": "OE1" <-> "OE2" Residue "P PHE 188": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P ARG 235": "NH1" <-> "NH2" Residue "P ARG 251": "NH1" <-> "NH2" Residue "P TYR 256": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P PHE 261": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P PHE 270": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P GLU 276": "OE1" <-> "OE2" Residue "P GLU 285": "OE1" <-> "OE2" Residue "P GLU 306": "OE1" <-> "OE2" Residue "P GLU 316": "OE1" <-> "OE2" Residue "P ARG 325": "NH1" <-> "NH2" Residue "Q GLU 15": "OE1" <-> "OE2" Residue "Q GLU 27": "OE1" <-> "OE2" Residue "Q TYR 103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q GLU 106": "OE1" <-> "OE2" Residue "Q GLU 107": "OE1" <-> "OE2" Residue "R ASP 19": "OD1" <-> "OD2" Residue "R ASP 20": "OD1" <-> "OD2" Residue "R TYR 23": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R ARG 31": "NH1" <-> "NH2" Residue "R GLU 34": "OE1" <-> "OE2" Residue "R GLU 37": "OE1" <-> "OE2" Residue "R GLU 46": "OE1" <-> "OE2" Residue "S GLU 42": "OE1" <-> "OE2" Residue "S ASP 49": "OD1" <-> "OD2" Residue "S GLU 56": "OE1" <-> "OE2" Residue "S TYR 68": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S ASP 84": "OD1" <-> "OD2" Residue "S GLU 91": "OE1" <-> "OE2" Residue "T GLU 9": "OE1" <-> "OE2" Residue "T TYR 17": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T ASP 23": "OD1" <-> "OD2" Residue "T ASP 26": "OD1" <-> "OD2" Residue "T GLU 28": "OE1" <-> "OE2" Residue "T ASP 43": "OD1" <-> "OD2" Residue "T ASP 66": "OD1" <-> "OD2" Residue "T GLU 68": "OE1" <-> "OE2" Residue "T GLU 75": "OE1" <-> "OE2" Residue "T ASP 78": "OD1" <-> "OD2" Residue "U GLU 9": "OE1" <-> "OE2" Residue "U ASP 39": "OD1" <-> "OD2" Residue "U ASP 43": "OD1" <-> "OD2" 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 GLU 75": "OE1" <-> "OE2" Residue "U GLU 88": "OE1" <-> "OE2" Residue "V GLU 21": "OE1" <-> "OE2" Residue "V ARG 22": "NH1" <-> "NH2" Residue "V ASP 32": "OD1" <-> "OD2" Residue "V ASP 63": "OD1" <-> "OD2" Residue "V GLU 69": "OE1" <-> "OE2" Residue "V GLU 78": "OE1" <-> "OE2" Residue "V GLU 86": "OE1" <-> "OE2" Residue "V GLU 104": "OE1" <-> "OE2" Residue "W GLU 27": "OE1" <-> "OE2" Residue "W GLU 42": "OE1" <-> "OE2" Residue "W ASP 53": "OD1" <-> "OD2" Residue "W GLU 65": "OE1" <-> "OE2" Residue "W GLU 89": "OE1" <-> "OE2" Residue "W GLU 111": "OE1" <-> "OE2" Residue "X GLU 16": "OE1" <-> "OE2" Residue "X GLU 41": "OE1" <-> "OE2" Residue "X GLU 48": "OE1" <-> "OE2" Residue "X GLU 49": "OE1" <-> "OE2" Residue "X PHE 69": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X GLU 79": "OE1" <-> "OE2" Residue "X ARG 97": "NH1" <-> "NH2" Residue "X GLU 108": "OE1" <-> "OE2" Residue "X ASP 112": "OD1" <-> "OD2" Residue "X ARG 118": "NH1" <-> "NH2" Residue "X ARG 134": "NH1" <-> "NH2" Residue "X GLU 138": "OE1" <-> "OE2" Residue "X ARG 144": "NH1" <-> "NH2" Residue "X ARG 146": "NH1" <-> "NH2" Residue "X GLU 154": "OE1" <-> "OE2" Residue "Y ASP 10": "OD1" <-> "OD2" Residue "Y GLU 13": "OE1" <-> "OE2" Residue "Y GLU 16": "OE1" <-> "OE2" Residue "Y TYR 22": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y ARG 57": "NH1" <-> "NH2" Residue "Y GLU 81": "OE1" <-> "OE2" Residue "Y ASP 84": "OD1" <-> "OD2" Residue "Y ARG 103": "NH1" <-> "NH2" Residue "Z TYR 21": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z GLU 63": "OE1" <-> "OE2" Residue "Z GLU 78": "OE1" <-> "OE2" Residue "Z ARG 82": "NH1" <-> "NH2" Residue "Z GLU 89": "OE1" <-> "OE2" Residue "Z GLU 123": "OE1" <-> "OE2" Residue "Z GLU 131": "OE1" <-> "OE2" Residue "Z GLU 132": "OE1" <-> "OE2" Residue "a ARG 59": "NH1" <-> "NH2" Residue "a ASP 70": "OD1" <-> "OD2" Residue "b ARG 3": "NH1" <-> "NH2" Residue "b TYR 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b ARG 57": "NH1" <-> "NH2" Residue "b ASP 64": "OD1" <-> "OD2" Residue "b GLU 78": "OE1" <-> "OE2" Residue "c GLU 6": "OE1" <-> "OE2" Residue "c ARG 44": "NH1" <-> "NH2" Residue "d ARG 51": "NH1" <-> "NH2" Residue "d GLU 99": "OE1" <-> "OE2" Residue "d PHE 101": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d GLU 111": "OE1" <-> "OE2" Residue "d GLU 114": "OE1" <-> "OE2" Residue "e ARG 8": "NH1" <-> "NH2" Residue "e GLU 38": "OE1" <-> "OE2" Residue "e GLU 41": "OE1" <-> "OE2" Residue "e ARG 50": "NH1" <-> "NH2" Residue "e GLU 52": "OE1" <-> "OE2" Residue "e GLU 60": "OE1" <-> "OE2" Residue "e GLU 83": "OE1" <-> "OE2" Residue "e GLU 88": "OE1" <-> "OE2" Residue "f ASP 9": "OD1" <-> "OD2" Residue "f ASP 27": "OD1" <-> "OD2" Residue "f ARG 28": "NH1" <-> "NH2" Residue "f ARG 46": "NH1" <-> "NH2" Residue "f GLU 52": "OE1" <-> "OE2" Residue "f GLU 53": "OE1" <-> "OE2" Residue "g ASP 29": "OD1" <-> "OD2" Residue "g GLU 33": "OE1" <-> "OE2" Residue "g ASP 34": "OD1" <-> "OD2" Residue "g ASP 48": "OD1" <-> "OD2" Residue "g PHE 76": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "g TYR 99": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "g GLU 109": "OE1" <-> "OE2" Residue "g ASP 114": "OD1" <-> "OD2" Residue "h PHE 9": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "h ARG 20": "NH1" <-> "NH2" Residue "h GLU 54": "OE1" <-> "OE2" Residue "h GLU 57": "OE1" <-> "OE2" Residue "h TYR 59": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "h GLU 62": "OE1" <-> "OE2" Residue "h GLU 65": "OE1" <-> "OE2" Residue "h ARG 77": "NH1" <-> "NH2" Residue "h TYR 87": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "h GLU 88": "OE1" <-> "OE2" Residue "h GLU 99": "OE1" <-> "OE2" Residue "h GLU 102": "OE1" <-> "OE2" Residue "h ARG 112": "NH1" <-> "NH2" Residue "i GLU 6": "OE1" <-> "OE2" Residue "i ARG 18": "NH1" <-> "NH2" Residue "i GLU 98": "OE1" <-> "OE2" Residue "j GLU 8": "OE1" <-> "OE2" Residue "j PHE 14": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "j GLU 26": "OE1" <-> "OE2" Residue "j ASP 55": "OD1" <-> "OD2" Residue "j GLU 71": "OE1" <-> "OE2" Residue "k GLU 14": "OE1" <-> "OE2" Residue "k ASP 17": "OD1" <-> "OD2" Residue "k GLU 24": "OE1" <-> "OE2" Residue "k GLU 29": "OE1" <-> "OE2" Residue "k GLU 33": "OE1" <-> "OE2" Residue "k ARG 38": "NH1" <-> "NH2" Residue "k ARG 41": "NH1" <-> "NH2" Residue "k TYR 52": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "k PHE 70": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "k TYR 86": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "l ASP 7": "OD1" <-> "OD2" Residue "l TYR 13": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "l ARG 30": "NH1" <-> "NH2" Residue "l ASP 52": "OD1" <-> "OD2" Residue "l GLU 75": "OE1" <-> "OE2" Residue "l PHE 108": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "l ARG 142": "NH1" <-> "NH2" Residue "l GLU 151": "OE1" <-> "OE2" Residue "l GLU 157": "OE1" <-> "OE2" Residue "m GLU 6": "OE1" <-> "OE2" Residue "m ASP 23": "OD1" <-> "OD2" Residue "m GLU 27": "OE1" <-> "OE2" Residue "m GLU 34": "OE1" <-> "OE2" Residue "m ARG 39": "NH1" <-> "NH2" Residue "m GLU 45": "OE1" <-> "OE2" Residue "m GLU 60": "OE1" <-> "OE2" Residue "m ARG 71": "NH1" <-> "NH2" Residue "m ASP 109": "OD1" <-> "OD2" Residue "m ASP 121": "OD1" <-> "OD2" Residue "n ARG 21": "NH1" <-> "NH2" Residue "n GLU 27": "OE1" <-> "OE2" Residue "n GLU 53": "OE1" <-> "OE2" Residue "n ASP 55": "OD1" <-> "OD2" Residue "n ARG 64": "NH1" <-> "NH2" Residue "n GLU 67": "OE1" <-> "OE2" Residue "n GLU 68": "OE1" <-> "OE2" Residue "n GLU 69": "OE1" <-> "OE2" Residue "n GLU 91": "OE1" <-> "OE2" Residue "n ARG 92": "NH1" <-> "NH2" Residue "n TYR 93": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "n GLU 94": "OE1" <-> "OE2" Residue "n TYR 96": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "n GLU 133": "OE1" <-> "OE2" Residue "n ARG 134": "NH1" <-> "NH2" Residue "n ARG 149": "NH1" <-> "NH2" Residue "n GLU 151": "OE1" <-> "OE2" Residue "o ARG 6": "NH1" <-> "NH2" Residue "o PHE 24": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "o ASP 27": "OD1" <-> "OD2" Residue "o TYR 28": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "o ARG 36": "NH1" <-> "NH2" Residue "o GLU 37": "OE1" <-> "OE2" Residue "o ARG 97": "NH1" <-> "NH2" Residue "o ARG 103": "NH1" <-> "NH2" Residue "o ARG 105": "NH1" <-> "NH2" Residue "o ARG 106": "NH1" <-> "NH2" Residue "p TYR 31": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "p ASP 37": "OD1" <-> "OD2" Residue "p ASP 72": "OD1" <-> "OD2" Residue "p GLU 75": "OE1" <-> "OE2" Residue "p GLU 86": "OE1" <-> "OE2" Residue "p GLU 100": "OE1" <-> "OE2" Residue "p GLU 116": "OE1" <-> "OE2" Residue "p GLU 129": "OE1" <-> "OE2" Residue "q ARG 21": "NH1" <-> "NH2" Residue "q ARG 29": "NH1" <-> "NH2" Residue "q GLU 67": "OE1" <-> "OE2" Residue "q ASP 78": "OD1" <-> "OD2" Residue "q ARG 88": "NH1" <-> "NH2" Residue "q ASP 96": "OD1" <-> "OD2" Residue "q GLU 136": "OE1" <-> "OE2" Residue "r TYR 27": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "r GLU 29": "OE1" <-> "OE2" Residue "r ARG 59": "NH1" <-> "NH2" Residue "r GLU 61": "OE1" <-> "OE2" 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 PHE 33": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.16s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 69138 Number of models: 1 Model: "" Number of chains: 111 Chain: "A" Number of atoms: 921 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 921 Classifications: {'peptide': 115} Link IDs: {'PTRANS': 6, 'TRANS': 108} 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: 1241 Number of conformers: 1 Conformer: "" Number of residues, atoms: 155, 1241 Classifications: {'peptide': 155} Link IDs: {'PCIS': 2, 'PTRANS': 8, 'TRANS': 144} 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: 3459 Number of conformers: 1 Conformer: "" Number of residues, atoms: 430, 3459 Classifications: {'peptide': 430} Link IDs: {'PCIS': 1, 'PTRANS': 27, 'TRANS': 401} 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: 1655 Number of conformers: 1 Conformer: "" Number of residues, atoms: 213, 1655 Classifications: {'peptide': 213} Link IDs: {'PCIS': 1, 'PTRANS': 20, 'TRANS': 191} Chain: "F" Number of atoms: 3310 Number of conformers: 1 Conformer: "" Number of residues, atoms: 430, 3310 Classifications: {'peptide': 430} Link IDs: {'PCIS': 2, 'PTRANS': 19, 'TRANS': 408} Chain: "G" Number of atoms: 5279 Number of conformers: 1 Conformer: "" Number of residues, atoms: 688, 5279 Classifications: {'peptide': 688} Link IDs: {'PTRANS': 32, 'TRANS': 655} Chain: "H" Number of atoms: 2509 Number of conformers: 1 Conformer: "" Number of residues, atoms: 318, 2509 Classifications: {'peptide': 318} Link IDs: {'PCIS': 2, 'PTRANS': 20, 'TRANS': 295} 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: "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: 1337 Number of conformers: 1 Conformer: "" Number of residues, atoms: 174, 1337 Classifications: {'peptide': 174} Link IDs: {'PTRANS': 3, 'TRANS': 170} 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: 4791 Number of conformers: 1 Conformer: "" Number of residues, atoms: 606, 4791 Classifications: {'peptide': 606} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 27, 'TRANS': 578} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 17 Unresolved non-hydrogen dihedrals: 12 Planarities with less than four sites: {'FME:plan-2': 1, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 8 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: 2747 Number of conformers: 1 Conformer: "" Number of residues, atoms: 341, 2747 Classifications: {'peptide': 341} Link IDs: {'PTRANS': 22, 'TRANS': 318} Chain: "Q" Number of atoms: 1016 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 1016 Classifications: {'peptide': 125} Link IDs: {'PTRANS': 6, 'TRANS': 118} Chain: "R" Number of atoms: 730 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 730 Classifications: {'peptide': 95} Link IDs: {'PTRANS': 3, 'TRANS': 91} Chain: "S" Number of atoms: 677 Number of conformers: 1 Conformer: "" Number of residues, atoms: 84, 677 Classifications: {'peptide': 84} Link IDs: {'PTRANS': 4, 'TRANS': 79} Chain: "T" Number of atoms: 612 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 612 Classifications: {'peptide': 76} Link IDs: {'PTRANS': 3, 'TRANS': 72} Chain: "U" Number of atoms: 693 Number of conformers: 1 Conformer: "" Number of residues, atoms: 86, 693 Classifications: {'peptide': 86} Link IDs: {'PTRANS': 5, 'TRANS': 80} Chain: "V" Number of atoms: 911 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 911 Classifications: {'peptide': 112} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 103} Chain: "W" Number of atoms: 971 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 971 Classifications: {'peptide': 114} Link IDs: {'PTRANS': 6, 'TRANS': 107} 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: 1146 Number of conformers: 1 Conformer: "" Number of residues, atoms: 140, 1146 Classifications: {'peptide': 140} Link IDs: {'PTRANS': 7, 'TRANS': 132} 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: 646 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 646 Classifications: {'peptide': 82} Link IDs: {'PTRANS': 11, 'TRANS': 70} Chain: "c" Number of atoms: 405 Number of conformers: 1 Conformer: "" Number of residues, atoms: 48, 405 Classifications: {'peptide': 48} Link IDs: {'PTRANS': 3, 'TRANS': 44} Chain: "d" Number of atoms: 945 Number of conformers: 1 Conformer: "" Number of residues, atoms: 113, 945 Classifications: {'peptide': 113} Link IDs: {'PTRANS': 9, 'TRANS': 103} Chain: "e" Number of atoms: 819 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 819 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 5, 'TRANS': 91} Chain: "f" Number of atoms: 451 Number of conformers: 1 Conformer: "" Number of residues, atoms: 52, 451 Classifications: {'peptide': 52} Link IDs: {'PTRANS': 2, 'TRANS': 49} Chain: "g" Number of atoms: 824 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 824 Classifications: {'peptide': 98} Link IDs: {'PTRANS': 8, 'TRANS': 89} 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: 879 Number of conformers: 1 Conformer: "" Number of residues, atoms: 102, 879 Classifications: {'peptide': 102} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 89} Chain breaks: 1 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: 638 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 638 Classifications: {'peptide': 79} Link IDs: {'PTRANS': 3, 'TRANS': 75} Chain: "l" Number of atoms: 1304 Number of conformers: 1 Conformer: "" Number of residues, atoms: 155, 1304 Classifications: {'peptide': 155} Link IDs: {'PTRANS': 20, 'TRANS': 134} Chain: "m" Number of atoms: 1061 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 1061 Classifications: {'peptide': 127} Link IDs: {'PTRANS': 8, 'TRANS': 118} Chain: "n" Number of atoms: 1492 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 1492 Classifications: {'peptide': 172} Link IDs: {'PTRANS': 15, 'TRANS': 156} Chain: "o" Number of atoms: 1035 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 1035 Classifications: {'peptide': 120} Link IDs: {'PCIS': 2, 'PTRANS': 5, 'TRANS': 112} Chain: "p" Number of atoms: 1443 Number of conformers: 1 Conformer: "" Number of residues, atoms: 171, 1443 Classifications: {'peptide': 171} Link IDs: {'PTRANS': 10, 'TRANS': 160} 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: 767 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 767 Classifications: {'peptide': 94} Link IDs: {'PTRANS': 11, 'TRANS': 82} 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: 91 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 91 Unusual residues: {'LMT': 2, 'PC1': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 33 Unresolved non-hydrogen angles: 34 Unresolved non-hydrogen dihedrals: 32 Planarities with less than four sites: {'PC1:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "B" Number of atoms: 97 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 97 Unusual residues: {'PC1': 2, 'SF4': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 19 Unresolved non-hydrogen angles: 19 Unresolved non-hydrogen dihedrals: 19 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: 78 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 78 Unusual residues: {'3PE': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 24 Unresolved non-hydrogen angles: 25 Unresolved non-hydrogen dihedrals: 23 Planarities with less than four sites: {'3PE:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "I" Number of atoms: 67 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 67 Unusual residues: {'3PE': 1, 'SF4': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "J" Number of atoms: 97 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 97 Unusual residues: {'CDL': 1, 'LMT': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 38 Unresolved non-hydrogen angles: 38 Unresolved non-hydrogen dihedrals: 38 Chain: "K" Number of atoms: 71 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 71 Unusual residues: {'CDL': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 29 Unresolved non-hydrogen angles: 29 Unresolved non-hydrogen dihedrals: 29 Chain: "L" Number of atoms: 317 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 317 Unusual residues: {'3PE': 2, 'CDL': 1, 'LMT': 3, 'PC1': 1} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 44 Unresolved non-hydrogen angles: 44 Unresolved non-hydrogen dihedrals: 44 Chain: "M" Number of atoms: 202 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 202 Unusual residues: {'3PE': 2, 'LMT': 3} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 5 Chain: "N" Number of atoms: 173 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 173 Unusual residues: {'3PE': 3, 'I49': 1, 'LMT': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 32 Unresolved non-hydrogen angles: 32 Unresolved non-hydrogen dihedrals: 32 Chain: "O" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {' MG': 1, 'GTP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "P" Number of atoms: 85 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 85 Unusual residues: {'3PE': 1, 'NDP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 14 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: 51 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 51 Unusual residues: {'3PE': 1} Classifications: {'undetermined': 1} Chain: "Y" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 140 Unusual residues: {'3PE': 1, 'LMT': 3} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 16 Chain: "d" Number of atoms: 51 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 51 Unusual residues: {'3PE': 1} Classifications: {'undetermined': 1} Chain: "h" Number of atoms: 102 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 102 Unusual residues: {'CDL': 1, 'LMT': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 33 Unresolved non-hydrogen angles: 33 Unresolved non-hydrogen dihedrals: 33 Chain: "j" Number of atoms: 35 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 35 Unusual residues: {'LMT': 1} Classifications: {'undetermined': 1} Chain: "l" Number of atoms: 35 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 35 Unusual residues: {'LMT': 1} Classifications: {'undetermined': 1} Chain: "o" Number of atoms: 6 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 6 Unusual residues: {'MYR': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'MYR:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "q" Number of atoms: 76 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 76 Unusual residues: {'CDL': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 24 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 24 Chain: "A" Number of atoms: 21 Number of conformers: 1 Conformer: "" Number of residues, atoms: 21, 21 Classifications: {'water': 21} Link IDs: {None: 20} Chain: "B" Number of atoms: 62 Number of conformers: 1 Conformer: "" Number of residues, atoms: 62, 62 Classifications: {'water': 62} Link IDs: {None: 61} Chain: "C" Number of atoms: 83 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 83 Classifications: {'water': 83} Link IDs: {None: 82} Chain: "D" Number of atoms: 155 Number of conformers: 1 Conformer: "" Number of residues, atoms: 155, 155 Classifications: {'water': 155} Link IDs: {None: 154} Chain: "E" Number of atoms: 13 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 13 Classifications: {'water': 13} Link IDs: {None: 12} Chain: "F" Number of atoms: 59 Number of conformers: 1 Conformer: "" Number of residues, atoms: 59, 59 Classifications: {'water': 59} Link IDs: {None: 58} Chain: "G" Number of atoms: 183 Number of conformers: 1 Conformer: "" Number of residues, atoms: 183, 183 Classifications: {'water': 183} Link IDs: {None: 182} Chain: "H" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 61, 61 Classifications: {'water': 61} Link IDs: {None: 60} Chain: "I" Number of atoms: 91 Number of conformers: 1 Conformer: "" Number of residues, atoms: 91, 91 Classifications: {'water': 91} Link IDs: {None: 90} Chain: "J" Number of atoms: 21 Number of conformers: 1 Conformer: "" Number of residues, atoms: 21, 21 Classifications: {'water': 21} Link IDs: {None: 20} Chain: "K" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 15 Classifications: {'water': 15} Link IDs: {None: 14} Chain: "L" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 31, 31 Classifications: {'water': 31} Link IDs: {None: 30} Chain: "M" Number of atoms: 49 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 49 Classifications: {'water': 49} Link IDs: {None: 48} Chain: "N" Number of atoms: 49 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 49 Classifications: {'water': 49} Link IDs: {None: 48} Chain: "O" Number of atoms: 21 Number of conformers: 1 Conformer: "" Number of residues, atoms: 21, 21 Classifications: {'water': 21} Link IDs: {None: 20} Chain: "P" Number of atoms: 58 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 58 Classifications: {'water': 58} Link IDs: {None: 57} Chain: "Q" Number of atoms: 59 Number of conformers: 1 Conformer: "" Number of residues, atoms: 59, 59 Classifications: {'water': 59} Link IDs: {None: 58} Chain: "R" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 39, 39 Classifications: {'water': 39} Link IDs: {None: 38} Chain: "S" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "V" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 15 Classifications: {'water': 15} Link IDs: {None: 14} Chain: "W" Number of atoms: 10 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 10 Classifications: {'water': 10} Link IDs: {None: 9} Chain: "X" Number of atoms: 23 Number of conformers: 1 Conformer: "" Number of residues, atoms: 23, 23 Classifications: {'water': 23} Link IDs: {None: 22} Chain: "Y" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "Z" Number of atoms: 24 Number of conformers: 1 Conformer: "" Number of residues, atoms: 24, 24 Classifications: {'water': 24} Link IDs: {None: 23} Chain: "a" Number of atoms: 11 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 11 Classifications: {'water': 11} Link IDs: {None: 10} Chain: "b" Number of atoms: 7 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 7 Classifications: {'water': 7} Link IDs: {None: 6} Chain: "d" Number of atoms: 9 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 9 Classifications: {'water': 9} Link IDs: {None: 8} Chain: "e" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 15 Classifications: {'water': 15} Link IDs: {None: 14} 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: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Classifications: {'water': 4} Link IDs: {None: 3} Chain: "h" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 15 Classifications: {'water': 15} Link IDs: {None: 14} Chain: "i" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "j" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "k" 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: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "m" Number of atoms: 7 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 7 Classifications: {'water': 7} Link IDs: {None: 6} Chain: "n" Number of atoms: 9 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 9 Classifications: {'water': 9} Link IDs: {None: 8} Chain: "p" Number of atoms: 10 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 10 Classifications: {'water': 10} Link IDs: {None: 9} Chain: "q" Number of atoms: 35 Number of conformers: 1 Conformer: "" Number of residues, atoms: 35, 35 Classifications: {'water': 35} Link IDs: {None: 34} Chain: "r" Number of atoms: 25 Number of conformers: 1 Conformer: "" Number of residues, atoms: 25, 25 Classifications: {'water': 25} Link IDs: {None: 24} Chain: "s" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Classifications: {'water': 4} Link IDs: {None: 3} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 1668 SG CYS B 119 96.033 94.690 204.236 1.00 25.29 S ATOM 1898 SG CYS B 149 93.806 92.106 208.891 1.00 24.29 S ATOM 1164 SG CYS B 54 90.559 91.134 203.193 1.00 28.02 S ATOM 1170 SG CYS B 55 90.088 96.662 206.343 1.00 27.20 S ATOM 8146 SG CYS E 103 114.507 44.407 258.130 1.00 46.60 S ATOM 8180 SG CYS E 108 112.933 41.685 259.982 1.00 46.25 S ATOM 8460 SG CYS E 144 116.716 41.236 254.597 1.00 43.95 S ATOM 8483 SG CYS E 148 115.498 38.438 255.567 1.00 47.61 S ATOM 11701 SG CYS F 362 119.252 51.910 234.684 1.00 29.29 S ATOM 11721 SG CYS F 365 116.415 51.180 239.552 1.00 31.38 S ATOM 12045 SG CYS F 405 121.031 46.764 238.498 1.00 32.64 S ATOM 11682 SG CYS F 359 122.890 52.647 240.151 1.00 32.55 S ATOM 13133 SG CYS G 114 115.498 70.788 225.946 1.00 27.37 S ATOM 13072 SG CYS G 105 109.635 73.108 227.988 1.00 26.20 S ATOM 13093 SG CYS G 108 115.189 75.558 230.181 1.00 26.84 S ATOM 13465 SG CYS G 156 123.982 64.576 230.641 1.00 28.24 S ATOM 13442 SG CYS G 153 121.182 66.681 236.339 1.00 28.28 S ATOM 13489 SG CYS G 159 127.235 67.679 234.885 1.00 30.54 S ATOM 13819 SG CYS G 203 122.750 70.606 231.135 1.00 28.83 S ATOM 12578 SG CYS G 41 124.409 57.894 228.132 1.00 28.81 S ATOM 12664 SG CYS G 52 120.609 58.415 227.245 1.00 28.40 S ATOM 12689 SG CYS G 55 122.141 54.036 223.770 1.00 30.28 S ATOM 12790 SG CYS G 69 125.381 54.729 224.920 1.00 30.79 S ATOM 21049 SG CYS I 119 96.947 86.088 214.709 1.00 23.61 S ATOM 21023 SG CYS I 116 97.237 92.593 215.691 1.00 23.97 S ATOM 21070 SG CYS I 122 98.514 88.058 220.224 1.00 24.92 S ATOM 20797 SG CYS I 87 102.552 88.992 215.061 1.00 23.79 S ATOM 21099 SG CYS I 126 101.139 84.639 227.624 1.00 25.71 S ATOM 20728 SG CYS I 77 106.020 88.915 228.748 1.00 26.65 S ATOM 20770 SG CYS I 83 104.507 87.338 222.758 1.00 24.91 S ATOM 20747 SG CYS I 80 106.670 82.627 226.093 1.00 25.99 S ATOM 41580 SG CYS R 59 103.070 79.633 242.692 1.00 33.76 S ATOM 41758 SG CYS R 84 105.998 80.410 240.499 1.00 33.51 S ATOM 41780 SG CYS R 87 103.739 83.080 241.399 1.00 31.86 S Time building chain proxies: 26.97, per 1000 atoms: 0.39 Number of scatterers: 69138 At special positions: 0 Unit cell: (185.674, 198.832, 291.669, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 11 Type Number sf(0) I 1 52.95 Zn 1 29.99 Fe 28 26.01 K 1 19.00 Cl 1 17.00 S 468 16.00 P 37 15.00 Mg 1 11.99 O 13544 8.00 N 11170 7.00 C 43886 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 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=2.04 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=2.03 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=2.03 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=3, symmetry=0 Number of additional bonds: simple=3, symmetry=0 Coordination: Other bonds: Time building additional restraints: 22.11 Conformation dependent library (CDL) restraints added in 8.5 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 144 " pdb="FE2 FES E 301 " - pdb=" SG CYS E 148 " 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="FE1 FES G 803 " - pdb=" SG CYS G 41 " pdb="FE2 FES G 803 " - pdb=" SG CYS G 69 " 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="FE4 SF4 B 201 " - pdb=" SG CYS B 55 " pdb="FE3 SF4 B 201 " - pdb=" SG CYS B 54 " 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="FE2 SF4 G 801 " - pdb=" SG CYS G 105 " pdb="FE4 SF4 G 801 " - pdb=" SG CYS G 108 " pdb="FE1 SF4 G 801 " - pdb=" SG CYS G 114 " pdb=" SF4 G 802 " pdb="FE3 SF4 G 802 " - pdb=" SG CYS G 159 " pdb="FE2 SF4 G 802 " - pdb=" SG CYS G 153 " pdb="FE4 SF4 G 802 " - pdb=" SG CYS G 203 " pdb="FE1 SF4 G 802 " - pdb=" SG CYS G 156 " pdb=" SF4 I 202 " pdb="FE3 SF4 I 202 " - pdb=" SG CYS I 122 " pdb="FE2 SF4 I 202 " - pdb=" SG CYS I 116 " pdb="FE4 SF4 I 202 " - pdb=" SG CYS I 87 " 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="FE2 SF4 I 203 " - pdb=" SG CYS I 77 " pdb="FE1 SF4 I 203 " - pdb=" SG CYS I 126 " pdb="FE4 SF4 I 203 " - pdb=" SG CYS I 80 " 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 16174 Ramachandran restraints generated. 8087 Oldfield, 0 Emsley, 8087 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 15398 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 366 helices and 30 sheets defined 54.4% alpha, 4.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 8.86 Creating SS restraints... Processing helix chain 'A' and resid 3 through 23 Processing helix chain 'A' and resid 31 through 34 No H-bonds generated for 'chain 'A' and resid 31 through 34' Processing helix chain 'A' and resid 56 through 80 removed outlier: 3.509A pdb=" N LEU A 63 " --> pdb=" O ALA A 59 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ILE A 69 " --> pdb=" O PHE A 65 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N ALA A 70 " --> pdb=" O ASP A 66 " (cutoff:3.500A) Proline residue: A 74 - end of helix removed outlier: 5.400A pdb=" N TRP A 77 " --> pdb=" O LEU A 73 " (cutoff:3.500A) removed outlier: 4.158A pdb=" N GLN A 80 " --> pdb=" O PRO A 76 " (cutoff:3.500A) Processing helix chain 'A' and resid 84 through 107 Processing helix chain 'B' and resid 26 through 44 Processing helix chain 'B' and resid 54 through 63 Processing helix chain 'B' and resid 69 through 72 Processing helix chain 'B' and resid 80 through 82 No H-bonds generated for 'chain 'B' and resid 80 through 82' 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 169 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: 4.815A pdb=" N ILE C 58 " --> pdb=" O ASP C 55 " (cutoff:3.500A) Proline residue: C 59 - end of helix removed outlier: 3.627A pdb=" N THR C 62 " --> pdb=" O PRO C 59 " (cutoff:3.500A) Processing helix chain 'C' and resid 125 through 138 removed outlier: 3.787A pdb=" N TRP C 129 " --> pdb=" O ALA C 126 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N MET C 137 " --> pdb=" O ILE C 134 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N PHE C 138 " --> pdb=" O TRP C 135 " (cutoff:3.500A) 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: 3.796A pdb=" N GLN D 13 " --> pdb=" O GLU D 9 " (cutoff:3.500A) removed outlier: 4.482A pdb=" N TYR D 14 " --> pdb=" O TRP D 10 " (cutoff:3.500A) Processing helix chain 'D' and resid 23 through 25 No H-bonds generated for 'chain 'D' and resid 23 through 25' Processing helix chain 'D' and resid 87 through 93 removed outlier: 3.852A pdb=" N GLU D 92 " --> pdb=" O GLU D 88 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N TYR D 93 " --> pdb=" O LYS D 89 " (cutoff:3.500A) Processing helix chain 'D' and resid 96 through 104 Proline residue: D 101 - end of helix removed outlier: 3.961A pdb=" N ASP D 104 " --> pdb=" O LEU D 100 " (cutoff:3.500A) Processing helix chain 'D' and resid 111 through 126 Processing helix chain 'D' and resid 132 through 161 Processing helix chain 'D' and resid 165 through 185 removed outlier: 3.502A pdb=" N GLU D 172 " --> pdb=" O PHE D 168 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N GLU D 173 " --> pdb=" O TRP D 169 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N PHE D 180 " --> pdb=" O LYS D 176 " (cutoff:3.500A) Processing helix chain 'D' and resid 207 through 229 removed outlier: 3.685A pdb=" N ASN D 217 " --> pdb=" O GLU D 213 " (cutoff:3.500A) removed outlier: 4.540A pdb=" N SER D 219 " --> pdb=" O SER D 215 " (cutoff:3.500A) removed outlier: 5.665A pdb=" N LEU D 220 " --> pdb=" O LYS D 216 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N ARG D 221 " --> pdb=" O ASN D 217 " (cutoff:3.500A) Processing helix chain 'D' and resid 233 through 239 Processing helix chain 'D' and resid 247 through 252 Processing helix chain 'D' and resid 257 through 263 removed outlier: 4.718A 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 316 removed outlier: 3.513A pdb=" N GLN D 313 " --> pdb=" O ARG D 309 " (cutoff:3.500A) 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 353 Processing helix chain 'D' and resid 394 through 405 removed outlier: 3.505A pdb=" N LEU D 402 " --> pdb=" O HIS D 398 " (cutoff:3.500A) removed outlier: 4.797A pdb=" N ASP D 403 " --> pdb=" O LEU D 399 " (cutoff:3.500A) removed outlier: 5.233A pdb=" N LYS D 404 " --> pdb=" O ALA D 400 " (cutoff:3.500A) Processing helix chain 'D' and resid 411 through 421 Processing helix chain 'D' and resid 425 through 429 Processing helix chain 'E' and resid 25 through 37 removed outlier: 3.538A pdb=" N LYS E 29 " --> pdb=" O PRO E 25 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N ASN E 37 " --> pdb=" O ALA E 33 " (cutoff:3.500A) Processing helix chain 'E' and resid 43 through 58 removed outlier: 4.341A pdb=" N LEU E 48 " --> pdb=" O ALA E 45 " (cutoff:3.500A) Proline residue: E 49 - end of helix removed outlier: 3.580A pdb=" N GLN E 57 " --> pdb=" O ALA E 54 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ASN E 58 " --> pdb=" O GLN E 55 " (cutoff:3.500A) Processing helix chain 'E' and resid 63 through 72 Processing helix chain 'E' and resid 77 through 86 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 38 Processing helix chain 'F' and resid 45 through 51 Processing helix chain 'F' and resid 53 through 63 Processing helix chain 'F' and resid 75 through 82 removed outlier: 3.857A pdb=" N PHE F 81 " --> pdb=" O LEU F 77 " (cutoff:3.500A) removed outlier: 4.812A pdb=" N MET F 82 " --> pdb=" O LYS F 78 " (cutoff:3.500A) Processing helix chain 'F' and resid 106 through 113 removed outlier: 3.587A pdb=" N ILE F 110 " --> pdb=" O LYS F 106 " (cutoff:3.500A) Processing helix chain 'F' and resid 115 through 129 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 229 Processing helix chain 'F' and resid 231 through 237 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 309 through 312 No H-bonds generated for 'chain 'F' and resid 309 through 312' Processing helix chain 'F' and resid 319 through 324 Processing helix chain 'F' and resid 343 through 357 Processing helix chain 'F' and resid 363 through 381 removed outlier: 4.219A pdb=" N ASP F 370 " --> pdb=" O ARG F 366 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N ARG F 381 " --> pdb=" O ALA F 377 " (cutoff:3.500A) Processing helix chain 'F' and resid 386 through 399 removed outlier: 3.627A pdb=" N ASP F 390 " --> pdb=" O ALA F 387 " (cutoff:3.500A) Processing helix chain 'F' and resid 407 through 436 Proline residue: F 414 - end of helix removed outlier: 3.649A pdb=" N ARG F 423 " --> pdb=" O ILE F 419 " (cutoff:3.500A) Proline residue: F 424 - end of helix Processing helix chain 'G' and resid 26 through 33 removed outlier: 3.837A 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: 3.698A 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 275 removed outlier: 5.135A pdb=" N TYR G 271 " --> pdb=" O THR G 267 " (cutoff:3.500A) removed outlier: 6.533A pdb=" N ASP G 272 " --> pdb=" O ARG G 268 " (cutoff:3.500A) removed outlier: 5.433A pdb=" N GLY G 273 " --> pdb=" O PHE G 269 " (cutoff:3.500A) removed outlier: 4.241A pdb=" N LEU G 274 " --> pdb=" O ALA G 270 " (cutoff:3.500A) removed outlier: 4.348A pdb=" N LYS G 275 " --> pdb=" O TYR G 271 " (cutoff:3.500A) Processing helix chain 'G' and resid 296 through 309 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: 3.675A pdb=" N VAL G 338 " --> pdb=" O LEU G 334 " (cutoff:3.500A) Processing helix chain 'G' and resid 359 through 362 Processing helix chain 'G' and resid 369 through 373 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 Processing helix chain 'G' and resid 438 through 445 Processing helix chain 'G' and resid 455 through 459 Processing helix chain 'G' and resid 463 through 479 Processing helix chain 'G' and resid 499 through 505 Processing helix chain 'G' and resid 512 through 516 Processing helix chain 'G' and resid 534 through 536 No H-bonds generated for 'chain 'G' and resid 534 through 536' 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 Processing helix chain 'G' and resid 616 through 626 Processing helix chain 'G' and resid 628 through 631 removed outlier: 3.664A 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: 3.613A 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: 4.207A pdb=" N TRP H 86 " --> pdb=" O ALA H 82 " (cutoff:3.500A) Processing helix chain 'H' and resid 101 through 123 removed outlier: 3.532A pdb=" N VAL H 113 " --> pdb=" O SER H 109 " (cutoff:3.500A) removed outlier: 4.135A pdb=" N TYR H 114 " --> pdb=" O SER H 110 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N SER H 115 " --> pdb=" O LEU H 111 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N ILE H 116 " --> pdb=" O ALA H 112 " (cutoff:3.500A) Processing helix chain 'H' and resid 126 through 157 removed outlier: 5.034A pdb=" N VAL H 144 " --> pdb=" O ILE H 140 " (cutoff:3.500A) removed outlier: 5.053A pdb=" N THR H 145 " --> pdb=" O SER H 141 " (cutoff:3.500A) removed outlier: 4.187A pdb=" N MET H 156 " --> pdb=" O SER H 152 " (cutoff:3.500A) Processing helix chain 'H' and resid 162 through 168 removed outlier: 4.017A pdb=" N ILE H 166 " --> pdb=" O LEU H 162 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N THR H 167 " --> pdb=" O SER H 163 " (cutoff:3.500A) Processing helix chain 'H' and resid 174 through 177 No H-bonds generated for 'chain 'H' and resid 174 through 177' Processing helix chain 'H' and resid 179 through 192 Processing helix chain 'H' and resid 204 through 207 No H-bonds generated for 'chain 'H' and resid 204 through 207' Processing helix chain 'H' and resid 210 through 212 No H-bonds generated for 'chain 'H' and resid 210 through 212' Processing helix chain 'H' and resid 217 through 242 removed outlier: 3.586A pdb=" N PHE H 223 " --> pdb=" O PRO H 219 " (cutoff:3.500A) Processing helix chain 'H' and resid 252 through 274 Processing helix chain 'H' and resid 282 through 291 Processing helix chain 'H' and resid 293 through 310 Proline residue: H 308 - end of helix Processing helix chain 'I' and resid 14 through 26 Processing helix chain 'I' and resid 28 through 41 removed outlier: 3.520A pdb=" N THR I 37 " --> pdb=" O GLY I 33 " (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: 5.571A pdb=" N ALA I 163 " --> pdb=" O ASP I 159 " (cutoff:3.500A) removed outlier: 6.187A pdb=" N GLU I 164 " --> pdb=" O LYS I 160 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N ALA I 167 " --> pdb=" O ALA I 163 " (cutoff:3.500A) removed outlier: 5.341A pdb=" N LEU I 174 " --> pdb=" O GLN I 170 " (cutoff:3.500A) removed outlier: 5.896A 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 74 Processing helix chain 'J' and resid 87 through 110 Processing helix chain 'J' and resid 124 through 127 removed outlier: 3.624A pdb=" N ILE J 127 " --> pdb=" O ASP J 124 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 124 through 127' Processing helix chain 'J' and resid 138 through 147 removed outlier: 4.052A pdb=" N LEU J 146 " --> pdb=" O GLY J 142 " (cutoff:3.500A) removed outlier: 4.867A pdb=" N TYR J 147 " --> pdb=" O ILE J 143 " (cutoff:3.500A) Processing helix chain 'J' and resid 151 through 171 Processing helix chain 'K' and resid 3 through 20 removed outlier: 3.773A pdb=" N ASN K 7 " --> pdb=" O MET K 3 " (cutoff:3.500A) Processing helix chain 'K' and resid 26 through 51 Processing helix chain 'K' and resid 54 through 85 removed outlier: 3.674A pdb=" N MET K 58 " --> pdb=" O LEU K 55 " (cutoff:3.500A) Proline residue: K 60 - end of helix removed outlier: 3.633A pdb=" N CYS K 69 " --> pdb=" O PHE K 66 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N ALA K 72 " --> pdb=" O CYS K 69 " (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 23 removed outlier: 4.120A pdb=" N LEU L 12 " --> pdb=" O SER L 8 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N THR L 16 " --> pdb=" O LEU L 12 " (cutoff:3.500A) Proline residue: L 18 - end of helix Processing helix chain 'L' and resid 29 through 57 removed outlier: 4.111A pdb=" N TYR L 32 " --> pdb=" O PRO L 29 " (cutoff:3.500A) Proline residue: L 33 - end of helix removed outlier: 3.592A pdb=" N ILE L 49 " --> pdb=" O THR L 46 " (cutoff:3.500A) Proline residue: L 50 - end of helix removed outlier: 3.702A pdb=" N SER L 57 " --> pdb=" O PHE L 54 " (cutoff:3.500A) Processing helix chain 'L' and resid 84 through 107 Proline residue: L 91 - end of helix removed outlier: 3.734A 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 removed outlier: 3.503A pdb=" N GLY L 143 " --> pdb=" O GLN L 139 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N GLY L 148 " --> pdb=" O TRP L 144 " (cutoff:3.500A) Processing helix chain 'L' and resid 162 through 193 removed outlier: 4.404A pdb=" N GLY L 181 " --> pdb=" O ILE L 177 " (cutoff:3.500A) removed outlier: 3.658A 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 224 Processing helix chain 'L' and resid 231 through 238 removed outlier: 3.816A pdb=" N MET L 237 " --> pdb=" O LEU L 233 " (cutoff:3.500A) removed outlier: 5.004A pdb=" N GLU L 238 " --> pdb=" O PRO L 234 " (cutoff:3.500A) Processing helix chain 'L' and resid 241 through 249 Processing helix chain 'L' and resid 251 through 262 removed outlier: 3.818A pdb=" N ALA L 255 " --> pdb=" O THR L 251 " (cutoff:3.500A) removed outlier: 4.264A pdb=" N GLY L 256 " --> pdb=" O MET L 252 " (cutoff:3.500A) removed outlier: 4.620A pdb=" N ILE L 257 " --> pdb=" O VAL L 253 " (cutoff:3.500A) Processing helix chain 'L' and resid 264 through 269 removed outlier: 4.392A pdb=" N ASN L 269 " --> pdb=" O PRO L 265 " (cutoff:3.500A) Processing helix chain 'L' and resid 271 through 294 removed outlier: 4.724A pdb=" N THR L 294 " --> pdb=" O MET L 290 " (cutoff:3.500A) Processing helix chain 'L' and resid 298 through 319 Processing helix chain 'L' and resid 322 through 349 removed outlier: 3.921A pdb=" N PHE L 334 " --> pdb=" O CYS L 330 " (cutoff:3.500A) removed outlier: 3.890A 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 380 Processing helix chain 'L' and resid 387 through 400 removed outlier: 4.383A pdb=" N SER L 391 " --> pdb=" O THR L 387 " (cutoff:3.500A) removed outlier: 4.519A pdb=" N LEU L 394 " --> pdb=" O TYR L 390 " (cutoff:3.500A) Processing helix chain 'L' and resid 406 through 430 removed outlier: 3.633A pdb=" N ALA L 420 " --> pdb=" O THR L 416 " (cutoff:3.500A) Processing helix chain 'L' and resid 448 through 469 removed outlier: 3.542A pdb=" N LEU L 457 " --> pdb=" O SER L 453 " (cutoff:3.500A) removed outlier: 5.935A pdb=" N GLY L 465 " --> pdb=" O SER L 461 " (cutoff:3.500A) removed outlier: 5.205A 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: 3.750A pdb=" N THR L 508 " --> pdb=" O ILE L 504 " (cutoff:3.500A) removed outlier: 4.294A 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: 3.868A pdb=" N MET L 533 " --> pdb=" O PRO L 530 " (cutoff:3.500A) removed outlier: 4.235A pdb=" N HIS L 534 " --> pdb=" O THR L 531 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N LEU L 536 " --> pdb=" O MET L 533 " (cutoff:3.500A) removed outlier: 5.726A pdb=" N ALA L 537 " --> pdb=" O HIS L 534 " (cutoff:3.500A) Proline residue: L 538 - end of helix removed outlier: 3.711A pdb=" N ASN L 541 " --> pdb=" O PRO L 538 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N LEU L 542 " --> pdb=" O TYR L 539 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N SER L 543 " --> pdb=" O MET L 540 " (cutoff:3.500A) removed outlier: 3.774A 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: 4.261A 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 23 through 42 removed outlier: 4.059A pdb=" N LEU M 39 " --> pdb=" O SER M 35 " (cutoff:3.500A) removed outlier: 4.851A pdb=" N LEU M 40 " --> pdb=" O PHE M 36 " (cutoff:3.500A) removed outlier: 4.713A pdb=" N LEU M 41 " --> pdb=" O THR M 37 " (cutoff:3.500A) removed outlier: 4.715A pdb=" N MET M 42 " --> pdb=" O SER M 38 " (cutoff:3.500A) Processing helix chain 'M' and resid 60 through 80 Proline residue: M 64 - end of helix removed outlier: 3.508A 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 109 Processing helix chain 'M' and resid 115 through 136 removed outlier: 4.676A pdb=" N LEU M 126 " --> pdb=" O PHE M 122 " (cutoff:3.500A) removed outlier: 4.486A 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: 3.565A pdb=" N PHE M 151 " --> pdb=" O TYR M 148 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N TYR M 152 " --> pdb=" O PHE M 149 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N LEU M 154 " --> pdb=" O PHE M 151 " (cutoff:3.500A) removed outlier: 4.624A pdb=" N LEU M 158 " --> pdb=" O ALA M 155 " (cutoff:3.500A) Proline residue: M 159 - end of helix removed outlier: 3.505A pdb=" N LEU M 164 " --> pdb=" O LEU M 161 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N VAL M 171 " --> pdb=" O GLN M 168 " (cutoff:3.500A) Processing helix chain 'M' and resid 176 through 182 removed outlier: 3.780A pdb=" N TYR M 181 " --> pdb=" O LEU M 177 " (cutoff:3.500A) Processing helix chain 'M' and resid 190 through 206 removed outlier: 4.514A pdb=" N ALA M 202 " --> pdb=" O ALA M 198 " (cutoff:3.500A) removed outlier: 5.174A pdb=" N PHE M 203 " --> pdb=" O CYS M 199 " (cutoff:3.500A) Processing helix chain 'M' and resid 214 through 222 removed outlier: 3.836A 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 250 removed outlier: 4.200A pdb=" N GLY M 239 " --> pdb=" O LEU M 235 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N GLY M 240 " --> pdb=" O LEU M 236 " (cutoff:3.500A) removed outlier: 4.938A pdb=" N LEU M 248 " --> pdb=" O LEU M 244 " (cutoff:3.500A) removed outlier: 4.945A pdb=" N ILE M 249 " --> pdb=" O ARG M 245 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N LEU M 250 " --> pdb=" O ILE M 246 " (cutoff:3.500A) Processing helix chain 'M' and resid 253 through 257 removed outlier: 3.898A pdb=" N MET M 257 " --> pdb=" O THR M 254 " (cutoff:3.500A) Processing helix chain 'M' and resid 259 through 278 removed outlier: 3.920A pdb=" N ILE M 270 " --> pdb=" O LEU M 266 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N LEU M 277 " --> pdb=" O SER M 273 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N ARG M 278 " --> pdb=" O SER M 274 " (cutoff:3.500A) Processing helix chain 'M' and resid 282 through 303 removed outlier: 3.785A pdb=" N LEU M 296 " --> pdb=" O SER M 292 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N VAL M 297 " --> pdb=" O HIS M 293 " (cutoff:3.500A) Processing helix chain 'M' and resid 306 through 337 removed outlier: 3.589A pdb=" N ARG M 336 " --> pdb=" O SER M 332 " (cutoff:3.500A) Processing helix chain 'M' and resid 348 through 350 No H-bonds generated for 'chain 'M' and resid 348 through 350' 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: 3.525A pdb=" N MET M 396 " --> pdb=" O ILE M 393 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N THR M 403 " --> pdb=" O MET M 400 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N TYR M 406 " --> pdb=" O THR M 403 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N LEU M 408 " --> pdb=" O LEU M 405 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N TYR M 409 " --> pdb=" O TYR M 406 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N MET M 410 " --> pdb=" O SER M 407 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N MET M 413 " --> pdb=" O MET M 410 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N THR M 414 " --> pdb=" O LEU M 411 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N GLN M 415 " --> pdb=" O ILE M 412 " (cutoff:3.500A) Processing helix chain 'M' and resid 431 through 454 Proline residue: M 443 - end of helix removed outlier: 4.125A pdb=" N THR M 448 " --> pdb=" O LEU M 444 " (cutoff:3.500A) removed outlier: 4.345A pdb=" N LEU M 449 " --> pdb=" O LEU M 445 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N ASN M 450 " --> pdb=" O LEU M 446 " (cutoff:3.500A) Proline residue: M 451 - end of helix removed outlier: 5.134A pdb=" N ILE M 454 " --> pdb=" O ASN M 450 " (cutoff:3.500A) Processing helix chain 'N' and resid 3 through 22 Processing helix chain 'N' and resid 26 through 47 removed outlier: 3.583A pdb=" N ILE N 41 " --> pdb=" O MET N 37 " (cutoff:3.500A) Proline residue: N 42 - end of helix removed outlier: 5.417A pdb=" N ASN N 47 " --> pdb=" O ILE N 43 " (cutoff:3.500A) Processing helix chain 'N' and resid 50 through 79 Processing helix chain 'N' and resid 92 through 106 Processing helix chain 'N' and resid 113 through 121 removed outlier: 4.046A 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: 4.428A pdb=" N ALA N 137 " --> pdb=" O TRP N 133 " (cutoff:3.500A) Proline residue: N 138 - end of helix removed outlier: 3.697A pdb=" N GLN N 144 " --> pdb=" O SER N 140 " (cutoff:3.500A) Proline residue: N 147 - end of helix Processing helix chain 'N' and resid 151 through 171 removed outlier: 3.759A pdb=" N LEU N 170 " --> pdb=" O GLY N 166 " (cutoff:3.500A) removed outlier: 4.230A pdb=" N ASN N 171 " --> pdb=" O TRP N 167 " (cutoff:3.500A) Processing helix chain 'N' and resid 175 through 192 removed outlier: 3.857A pdb=" N TRP N 189 " --> pdb=" O ALA N 185 " (cutoff:3.500A) Processing helix chain 'N' and resid 198 through 222 Processing helix chain 'N' and resid 227 through 236 removed outlier: 3.664A pdb=" N HIS N 232 " --> pdb=" O LEU N 228 " (cutoff:3.500A) removed outlier: 4.422A pdb=" N THR N 233 " --> pdb=" O SER N 229 " (cutoff:3.500A) removed outlier: 5.009A pdb=" N TRP N 234 " --> pdb=" O LEU N 230 " (cutoff:3.500A) removed outlier: 5.547A pdb=" N ASN N 235 " --> pdb=" O SER N 231 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N LYS N 236 " --> pdb=" O HIS N 232 " (cutoff:3.500A) Processing helix chain 'N' and resid 238 through 251 removed outlier: 3.565A 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: 3.674A pdb=" N ILE N 266 " --> pdb=" O LYS N 263 " (cutoff:3.500A) Processing helix chain 'N' and resid 277 through 300 removed outlier: 3.648A pdb=" N LEU N 287 " --> pdb=" O ALA N 283 " (cutoff:3.500A) removed outlier: 4.360A pdb=" N LEU N 288 " --> pdb=" O ILE N 284 " (cutoff:3.500A) removed outlier: 4.241A pdb=" N ASN N 289 " --> pdb=" O THR N 285 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N LEU N 296 " --> pdb=" O PHE N 292 " (cutoff:3.500A) Processing helix chain 'N' and resid 309 through 316 Processing helix chain 'N' and resid 326 through 334 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 Processing helix chain 'O' and resid 71 through 74 Processing helix chain 'O' and resid 79 through 84 Processing helix chain 'O' and resid 92 through 118 Processing helix chain 'O' and resid 131 through 140 removed outlier: 3.521A pdb=" N ALA O 137 " --> pdb=" O PHE O 134 " (cutoff:3.500A) Processing helix chain 'O' and resid 146 through 157 Processing helix chain 'O' and resid 160 through 162 No H-bonds generated for 'chain 'O' and resid 160 through 162' 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 Processing helix chain 'O' and resid 210 through 216 removed outlier: 3.895A pdb=" N GLU O 216 " --> pdb=" O PRO O 212 " (cutoff:3.500A) Processing helix chain 'O' and resid 227 through 229 No H-bonds generated for 'chain 'O' and resid 227 through 229' Processing helix chain 'O' and resid 231 through 240 removed outlier: 3.609A pdb=" N TYR O 240 " --> pdb=" O GLU O 236 " (cutoff:3.500A) Processing helix chain 'O' and resid 247 through 250 Processing helix chain 'O' and resid 253 through 263 removed outlier: 3.524A pdb=" N LYS O 258 " --> pdb=" O ARG O 254 " (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: 3.759A 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 3 through 5 No H-bonds generated for 'chain 'P' and resid 3 through 5' Processing helix chain 'P' and resid 29 through 41 removed outlier: 4.122A pdb=" N TYR P 33 " --> pdb=" O PHE P 29 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N MET P 41 " --> pdb=" O HIS P 37 " (cutoff:3.500A) Processing helix chain 'P' and resid 53 through 62 removed outlier: 5.197A 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: 3.606A 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 123 Processing helix chain 'P' and resid 144 through 159 Processing helix chain 'P' and resid 179 through 188 removed outlier: 4.289A pdb=" N ARG P 186 " --> pdb=" O PHE P 182 " (cutoff:3.500A) removed outlier: 5.287A pdb=" N TRP P 187 " --> pdb=" O ALA P 183 " (cutoff:3.500A) removed outlier: 5.072A pdb=" N PHE P 188 " --> pdb=" O ASN P 184 " (cutoff:3.500A) Processing helix chain 'P' and resid 194 through 197 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 248 Processing helix chain 'P' and resid 260 through 272 removed outlier: 3.742A pdb=" N ILE P 272 " --> pdb=" O ARG P 268 " (cutoff:3.500A) Processing helix chain 'P' and resid 281 through 288 Processing helix 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 321 removed outlier: 5.883A pdb=" N ARG P 320 " --> pdb=" O GLU P 316 " (cutoff:3.500A) removed outlier: 5.156A pdb=" N HIS P 321 " --> pdb=" O VAL P 317 " (cutoff:3.500A) Processing helix chain 'P' and resid 324 through 326 No H-bonds generated for 'chain 'P' and resid 324 through 326' Processing helix chain 'P' and resid 331 through 333 No H-bonds generated for 'chain 'P' and resid 331 through 333' Processing helix chain 'Q' and resid 27 through 29 No H-bonds generated for 'chain 'Q' and resid 27 through 29' Processing helix chain 'Q' and resid 50 through 52 No H-bonds generated for 'chain 'Q' and resid 50 through 52' Processing helix chain 'Q' and resid 89 through 99 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: 3.622A pdb=" N ALA R 45 " --> pdb=" O ILE R 41 " (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: 5.041A pdb=" N GLY S 31 " --> pdb=" O GLY S 28 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N ILE S 36 " --> pdb=" O ARG S 33 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N ARG S 39 " --> pdb=" O ILE S 36 " (cutoff:3.500A) removed outlier: 5.693A pdb=" N TYR S 40 " --> pdb=" O GLU S 37 " (cutoff:3.500A) removed outlier: 4.886A pdb=" N VAL S 41 " --> pdb=" O LYS S 38 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N GLU S 42 " --> pdb=" O ARG S 39 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N LYS S 44 " --> pdb=" O VAL S 41 " (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 83 through 95 Processing helix chain 'T' and resid 8 through 21 removed outlier: 3.540A pdb=" N LYS T 12 " --> pdb=" O LEU T 8 " (cutoff:3.500A) removed outlier: 4.166A pdb=" N ASP T 13 " --> pdb=" O GLU T 9 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N LEU T 16 " --> pdb=" O LYS T 12 " (cutoff:3.500A) 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 44A through 57 Processing helix chain 'T' and resid 64 through 69 removed outlier: 4.488A pdb=" N LYS T 69 " --> pdb=" O ILE T 65 " (cutoff:3.500A) Processing helix chain 'T' and resid 73 through 81 Processing helix chain 'U' and resid 8 through 21 Processing helix chain 'U' and resid 44A through 58 Processing helix chain 'U' and resid 64 through 69 removed outlier: 4.595A 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: 4.172A 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 Processing helix chain 'V' and resid 76 through 96 removed outlier: 3.916A pdb=" N GLN V 95 " --> pdb=" O ARG V 91 " (cutoff:3.500A) Processing helix chain 'W' and resid 25 through 50 removed outlier: 3.591A pdb=" N ARG W 30 " --> pdb=" O ASN W 26 " (cutoff:3.500A) Proline residue: W 44 - end of helix Processing helix chain 'W' and resid 56 through 70 removed outlier: 4.220A pdb=" N ASN W 70 " --> pdb=" O MET W 66 " (cutoff:3.500A) Processing helix chain 'W' and resid 76 through 94 Processing helix chain 'W' and resid 100 through 107 removed outlier: 4.458A pdb=" N PHE W 106 " --> pdb=" O HIS W 102 " (cutoff:3.500A) removed outlier: 4.882A pdb=" N PHE W 107 " --> pdb=" O VAL W 103 " (cutoff:3.500A) Processing helix chain 'W' and resid 118 through 124 removed outlier: 3.598A pdb=" N VAL W 124 " --> pdb=" O SER W 120 " (cutoff:3.500A) Processing helix chain 'X' and resid 21 through 26 Processing helix chain 'X' and resid 28 through 34 Processing helix chain 'X' and resid 36 through 49 Processing helix chain 'X' and resid 52 through 90 removed outlier: 4.194A pdb=" N LEU X 56 " --> pdb=" O ARG X 53 " (cutoff:3.500A) removed outlier: 5.907A pdb=" N GLU X 57 " --> pdb=" O ARG X 54 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N GLN X 64 " --> pdb=" O LEU X 61 " (cutoff:3.500A) removed outlier: 4.367A pdb=" N CYS X 77 " --> pdb=" O LYS X 74 " (cutoff:3.500A) removed outlier: 5.387A pdb=" N ALA X 78 " --> pdb=" O ARG X 75 " (cutoff:3.500A) removed outlier: 6.223A pdb=" N GLU X 79 " --> pdb=" O HIS X 76 " (cutoff:3.500A) Proline residue: X 80 - end of helix removed outlier: 3.661A pdb=" N GLU X 83 " --> pdb=" O PRO X 80 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N TRP X 85 " --> pdb=" O THR X 82 " (cutoff:3.500A) Processing helix chain 'X' and resid 96 through 98 No H-bonds generated for 'chain 'X' and resid 96 through 98' Processing helix chain 'X' and resid 100 through 114 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 80 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 Proline residue: Z 73 - end of helix removed outlier: 3.746A pdb=" N THR Z 96 " --> pdb=" O GLU Z 92 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N VAL Z 97 " --> pdb=" O GLU Z 93 " (cutoff:3.500A) 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 138 Processing helix chain 'a' and resid 2 through 31 Proline residue: a 7 - end of helix Proline residue: a 19 - end of helix removed outlier: 3.542A pdb=" N THR a 23 " --> pdb=" O GLY a 20 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ILE a 26 " --> pdb=" O THR a 23 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N HIS a 27 " --> pdb=" O ALA a 24 " (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 Processing helix chain 'b' and resid 16 through 34 Proline residue: b 32 - end of helix Processing helix chain 'b' and resid 38 through 47 removed outlier: 4.006A pdb=" N LEU b 42 " --> pdb=" O THR b 38 " (cutoff:3.500A) Processing helix chain 'b' and resid 78 through 81 No H-bonds generated for 'chain 'b' and resid 78 through 81' Processing helix chain 'c' and resid 14 through 45 Processing helix chain 'd' and resid 16 through 20 Processing helix chain 'd' and resid 29 through 48 Processing helix chain 'd' and resid 58 through 96 removed outlier: 3.613A pdb=" N TYR d 74 " --> pdb=" O PHE d 70 " (cutoff:3.500A) Processing helix chain 'd' and resid 98 through 100 No H-bonds generated for 'chain 'd' and resid 98 through 100' 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: 4.272A 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 12 through 33 removed outlier: 3.607A pdb=" N LEU f 15 " --> pdb=" O VAL f 12 " (cutoff:3.500A) removed outlier: 4.884A pdb=" N VAL f 16 " --> pdb=" O HIS f 13 " (cutoff:3.500A) Proline residue: f 17 - end of helix 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 103 removed outlier: 3.810A pdb=" N GLN g 86 " --> pdb=" O TYR g 83 " (cutoff:3.500A) removed outlier: 5.755A pdb=" N GLU g 87 " --> pdb=" O ARG g 84 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N TRP g 88 " --> pdb=" O MET g 85 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N ALA g 89 " --> pdb=" O GLN g 86 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N LYS g 98 " --> pdb=" O ARG g 95 " (cutoff:3.500A) removed outlier: 3.778A 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: 4.101A 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: 3.960A 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 79 Processing helix chain 'h' and resid 83 through 117 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 62 through 73 Processing helix chain 'i' and resid 75 through 87 Processing helix chain 'j' and resid 19 through 42 Processing helix chain 'j' and resid 44 through 48 Processing helix chain 'j' and resid 56 through 58 No H-bonds generated for 'chain 'j' and resid 56 through 58' Processing helix chain 'j' and resid 61 through 64 No H-bonds generated for 'chain 'j' and resid 61 through 64' 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 38 removed outlier: 3.927A pdb=" N ARG k 38 " --> pdb=" O LYS k 34 " (cutoff:3.500A) Processing helix chain 'k' and resid 45 through 51 removed outlier: 5.104A 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 89 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 142 removed outlier: 5.641A pdb=" N LEU l 140 " --> pdb=" O ASN l 136 " (cutoff:3.500A) removed outlier: 6.498A pdb=" N GLU l 141 " --> pdb=" O ASN l 137 " (cutoff:3.500A) 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 21 No H-bonds generated for 'chain 'm' and resid 19 through 21' Processing helix chain 'm' and resid 26 through 50 removed outlier: 3.653A 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: 3.856A pdb=" N HIS n 50 " --> pdb=" O ARG n 46 " (cutoff:3.500A) Processing helix chain 'n' and resid 56 through 73 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 142 removed outlier: 3.846A pdb=" N MET n 113 " --> pdb=" O SER n 109 " (cutoff:3.500A) removed outlier: 4.308A pdb=" N TYR n 114 " --> pdb=" O GLU n 110 " (cutoff:3.500A) Proline residue: n 115 - end of helix removed outlier: 4.486A pdb=" N GLU n 133 " --> pdb=" O ARG n 129 " (cutoff:3.500A) removed outlier: 4.930A pdb=" N ARG 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 9 Processing helix chain 'o' and resid 12 through 14 No H-bonds generated for 'chain 'o' and resid 12 through 14' 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 72 Processing helix chain 'o' and resid 80 through 119 removed outlier: 3.898A pdb=" N GLU o 118 " --> pdb=" O ARG o 114 " (cutoff:3.500A) Processing helix chain 'p' and resid 28 through 39 Processing helix chain 'p' and resid 41 through 56 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: 3.684A pdb=" N GLU p 86 " --> pdb=" O LEU p 82 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N GLY p 117 " --> pdb=" O GLN p 113 " (cutoff:3.500A) removed outlier: 6.476A pdb=" N GLU p 118 " --> pdb=" O GLN p 114 " (cutoff:3.500A) removed outlier: 7.278A pdb=" N SER p 119 " --> pdb=" O ARG p 115 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N HIS p 120 " --> pdb=" O GLU p 116 " (cutoff:3.500A) removed outlier: 5.236A pdb=" N ARG p 121 " --> pdb=" O GLY p 117 " (cutoff:3.500A) removed outlier: 6.325A 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 171 Processing helix chain 'q' and resid 2 through 16 removed outlier: 3.831A pdb=" N VAL q 14 " --> pdb=" O GLY q 10 " (cutoff:3.500A) Processing helix chain 'q' and resid 20 through 30 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: 4.308A 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 55 No H-bonds generated for 'chain 'r' and resid 53 through 55' 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 45 Processing helix chain 's' and resid 50 through 61 removed outlier: 3.566A pdb=" N SER s 59 " --> pdb=" O ASN s 55 " (cutoff:3.500A) removed outlier: 4.821A pdb=" N LYS s 60 " --> pdb=" O LEU s 56 " (cutoff:3.500A) removed outlier: 5.041A pdb=" N PHE s 61 " --> pdb=" O ASP s 57 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'B' and resid 85 through 89 removed outlier: 6.661A pdb=" N TYR B 112 " --> pdb=" O MET B 86 " (cutoff:3.500A) removed outlier: 7.492A pdb=" N VAL B 88 " --> pdb=" O TYR B 112 " (cutoff:3.500A) removed outlier: 6.957A pdb=" N VAL B 114 " --> pdb=" O VAL B 88 " (cutoff:3.500A) removed outlier: 6.375A 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: 6.763A pdb=" N ASN C 95 " --> pdb=" O ALA C 76 " (cutoff:3.500A) removed outlier: 4.264A pdb=" N LEU C 78 " --> pdb=" O VAL C 93 " (cutoff:3.500A) removed outlier: 6.622A pdb=" N VAL C 93 " --> pdb=" O LEU C 78 " (cutoff:3.500A) removed outlier: 4.328A pdb=" N ALA C 80 " --> pdb=" O GLU C 91 " (cutoff:3.500A) removed outlier: 6.453A pdb=" N GLU C 91 " --> pdb=" O ALA C 80 " (cutoff:3.500A) removed outlier: 4.910A pdb=" N LEU C 48 " --> pdb=" O ARG C 104 " (cutoff:3.500A) removed outlier: 4.783A pdb=" N TYR C 110 " --> pdb=" O ILE C 52 " (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 47 through 51 removed outlier: 6.459A pdb=" N SER D 69 " --> pdb=" O VAL D 73 " (cutoff:3.500A) removed outlier: 5.390A pdb=" N VAL D 73 " --> pdb=" O SER D 69 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'D' and resid 361 through 369 Processing sheet with id= F, first strand: chain 'E' and resid 137 through 142 removed outlier: 6.441A pdb=" N TYR E 98 " --> pdb=" O THR E 138 " (cutoff:3.500A) removed outlier: 7.786A pdb=" N ILE E 140 " --> pdb=" O TYR E 98 " (cutoff:3.500A) removed outlier: 6.411A pdb=" N ILE E 100 " --> pdb=" O ILE E 140 " (cutoff:3.500A) removed outlier: 7.110A pdb=" N VAL E 142 " --> pdb=" O ILE E 100 " (cutoff:3.500A) removed outlier: 6.097A pdb=" N VAL E 102 " --> pdb=" O VAL E 142 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'F' and resid 220 through 224 removed outlier: 7.004A pdb=" N TYR F 92 " --> pdb=" O THR F 221 " (cutoff:3.500A) removed outlier: 8.057A pdb=" N ALA F 223 " --> pdb=" O TYR F 92 " (cutoff:3.500A) removed outlier: 6.347A pdb=" N VAL F 94 " --> pdb=" O ALA F 223 " (cutoff:3.500A) removed outlier: 6.344A pdb=" N ALA F 133 " --> pdb=" O LEU F 93 " (cutoff:3.500A) removed outlier: 7.648A pdb=" N VAL F 95 " --> pdb=" O ALA F 133 " (cutoff:3.500A) removed outlier: 6.617A pdb=" N TYR F 135 " --> pdb=" O VAL F 95 " (cutoff:3.500A) removed outlier: 6.953A pdb=" N ALA F 97 " --> pdb=" O TYR F 135 " (cutoff:3.500A) removed outlier: 6.383A pdb=" N TYR F 137 " --> pdb=" O ALA F 97 " (cutoff:3.500A) removed outlier: 6.312A pdb=" N ASP F 174 " --> pdb=" O ALA F 134 " (cutoff:3.500A) removed outlier: 7.578A pdb=" N ILE F 136 " --> pdb=" O ASP F 174 " (cutoff:3.500A) removed outlier: 6.774A pdb=" N PHE F 176 " --> pdb=" O ILE F 136 " (cutoff:3.500A) removed outlier: 7.527A pdb=" N ILE F 138 " --> pdb=" O PHE F 176 " (cutoff:3.500A) removed outlier: 6.253A pdb=" N VAL F 178 " --> pdb=" O ILE F 138 " (cutoff:3.500A) No H-bonds generated for sheet with id= G Processing sheet with id= H, first strand: chain 'F' and resid 266 through 271 Processing sheet with id= I, first strand: chain 'G' and resid 9 through 13 Processing sheet with id= J, first strand: chain 'G' and resid 146 through 148 Processing sheet with id= K, first strand: chain 'G' and resid 173 through 175 Processing sheet with id= L, first strand: chain 'G' and resid 223 through 228 removed outlier: 6.184A pdb=" N ARG G 243 " --> pdb=" O VAL G 247 " (cutoff:3.500A) removed outlier: 5.369A pdb=" N VAL G 247 " --> pdb=" O ARG G 243 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'G' and resid 283 through 285 Processing sheet with id= N, first strand: chain 'G' and resid 342 through 345 removed outlier: 4.722A pdb=" N THR G 342 " --> pdb=" O VAL G 315 " (cutoff:3.500A) removed outlier: 6.337A pdb=" N MET G 521 " --> pdb=" O ALA G 316 " (cutoff:3.500A) removed outlier: 7.947A pdb=" N ILE G 318 " --> pdb=" O MET G 521 " (cutoff:3.500A) removed outlier: 6.442A pdb=" N PHE G 523 " --> pdb=" O ILE G 318 " (cutoff:3.500A) removed outlier: 6.448A pdb=" N PHE G 542 " --> pdb=" O LEU G 522 " (cutoff:3.500A) removed outlier: 7.369A pdb=" N LEU G 524 " --> pdb=" O PHE G 542 " (cutoff:3.500A) removed outlier: 6.492A pdb=" N VAL G 544 " --> pdb=" O LEU G 524 " (cutoff:3.500A) removed outlier: 6.427A pdb=" N VAL G 559 " --> pdb=" O TYR G 545 " (cutoff:3.500A) removed outlier: 7.843A pdb=" N GLY G 547 " --> pdb=" O VAL G 559 " (cutoff:3.500A) removed outlier: 6.140A pdb=" N LEU G 561 " --> pdb=" O GLY G 547 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'G' and resid 490 through 493 removed outlier: 8.077A pdb=" N ASN G 491 " --> pdb=" O PRO G 449 " (cutoff:3.500A) removed outlier: 6.460A pdb=" N VAL G 451 " --> pdb=" O ASN G 491 " (cutoff:3.500A) removed outlier: 7.155A pdb=" N LEU G 493 " --> pdb=" O VAL G 451 " (cutoff:3.500A) removed outlier: 6.656A pdb=" N LEU G 453 " --> pdb=" O LEU G 493 " (cutoff:3.500A) removed outlier: 6.579A pdb=" N VAL G 376 " --> pdb=" O MET G 450 " (cutoff:3.500A) removed outlier: 7.655A pdb=" N ILE G 452 " --> pdb=" O VAL G 376 " (cutoff:3.500A) removed outlier: 6.286A pdb=" N LEU G 378 " --> pdb=" O ILE G 452 " (cutoff:3.500A) removed outlier: 7.440A pdb=" N GLY G 454 " --> pdb=" O LEU G 378 " (cutoff:3.500A) removed outlier: 7.560A pdb=" N VAL G 380 " --> pdb=" O GLY G 454 " (cutoff:3.500A) removed outlier: 6.429A pdb=" N LYS G 405 " --> pdb=" O VAL G 377 " (cutoff:3.500A) removed outlier: 7.520A pdb=" N LEU G 379 " --> pdb=" O LYS G 405 " (cutoff:3.500A) removed outlier: 6.385A pdb=" N ALA G 407 " --> pdb=" O LEU G 379 " (cutoff:3.500A) removed outlier: 6.661A pdb=" N ASP G 420 " --> pdb=" O LEU G 408 " (cutoff:3.500A) No H-bonds generated for sheet with id= O Processing sheet with id= P, first strand: chain 'G' and resid 572 through 574 Processing sheet with id= Q, first strand: chain 'I' and resid 65 through 67 Processing sheet with id= R, first strand: chain 'I' and resid 92 through 98 removed outlier: 5.991A pdb=" N GLU I 97 " --> pdb=" O THR I 106 " (cutoff:3.500A) removed outlier: 5.304A pdb=" N THR I 106 " --> pdb=" O GLU I 97 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'J' and resid 112 through 115 Processing sheet with id= T, first strand: chain 'L' and resid 69 through 71 Processing sheet with id= U, first strand: chain 'L' and resid 61 through 67 removed outlier: 7.012A pdb=" N LEU L 78 " --> pdb=" O ASN L 65 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'O' and resid 219 through 224 removed outlier: 6.247A pdb=" N VAL O 122 " --> pdb=" O ILE O 25 " (cutoff:3.500A) removed outlier: 7.787A pdb=" N VAL O 27 " --> pdb=" O VAL O 122 " (cutoff:3.500A) removed outlier: 6.593A pdb=" N LEU O 124 " --> pdb=" O VAL O 27 " (cutoff:3.500A) removed outlier: 8.579A pdb=" N GLY O 29 " --> pdb=" O LEU O 124 " (cutoff:3.500A) removed outlier: 6.464A pdb=" N LYS O 49 " --> pdb=" O VAL O 123 " (cutoff:3.500A) removed outlier: 8.251A pdb=" N GLU O 125 " --> pdb=" O LYS O 49 " (cutoff:3.500A) removed outlier: 8.374A pdb=" N PHE O 51 " --> pdb=" O GLU O 125 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'P' and resid 227 through 230 removed outlier: 6.565A pdb=" N ILE P 165 " --> pdb=" O PHE P 228 " (cutoff:3.500A) removed outlier: 7.458A pdb=" N PHE P 230 " --> pdb=" O ILE P 165 " (cutoff:3.500A) removed outlier: 6.472A pdb=" N LYS P 167 " --> pdb=" O PHE P 230 " (cutoff:3.500A) removed outlier: 6.486A pdb=" N GLN P 44 " --> pdb=" O ALA P 21 " (cutoff:3.500A) removed outlier: 7.462A pdb=" N VAL P 23 " --> pdb=" O GLN P 44 " (cutoff:3.500A) removed outlier: 6.603A pdb=" N ILE P 46 " --> pdb=" O VAL P 23 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain 'P' and resid 191 through 194 Processing sheet with id= Y, first strand: chain 'Q' and resid 102 through 105 Processing sheet with id= Z, first strand: chain 'Q' and resid 64 through 66 Processing sheet with id= AA, first strand: chain 'R' and resid 50 through 52 Processing sheet with id= AB, first strand: chain 'R' and resid 56 through 59 Processing sheet with id= AC, first strand: chain 'S' and resid 51 through 56 removed outlier: 6.488A pdb=" N ARG S 67 " --> pdb=" O ARG S 16 " (cutoff:3.500A) removed outlier: 4.292A pdb=" N ILE S 18 " --> pdb=" O TRP S 65 " (cutoff:3.500A) removed outlier: 6.536A pdb=" N TRP S 65 " --> pdb=" O ILE S 18 " (cutoff:3.500A) removed outlier: 4.436A pdb=" N ILE S 20 " --> pdb=" O LYS S 63 " (cutoff:3.500A) removed outlier: 6.549A pdb=" N LYS S 63 " --> pdb=" O ILE S 20 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N GLN S 72 " --> pdb=" O TYR S 68 " (cutoff:3.500A) Processing sheet with id= AD, first strand: chain 'q' and resid 60 through 63 removed outlier: 6.645A pdb=" N GLU q 50 " --> pdb=" O LEU q 38 " (cutoff:3.500A) removed outlier: 5.646A pdb=" N LEU q 38 " --> pdb=" O GLU q 50 " (cutoff:3.500A) 2917 hydrogen bonds defined for protein. 7866 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: 22.22 Time building geometry restraints manager: 24.11 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.40: 27858 1.40 - 1.63: 40770 1.63 - 1.85: 831 1.85 - 2.08: 0 2.08 - 2.30: 81 Bond restraints: 69540 Sorted by residual: 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 7.19e+01 bond pdb=" C6 GTP O 401 " pdb=" O6 GTP O 401 " ideal model delta sigma weight residual 1.230 1.393 -0.163 2.00e-02 2.50e+03 6.60e+01 bond pdb=" CB7 CDL L 703 " pdb=" OB8 CDL L 703 " ideal model delta sigma weight residual 1.334 1.402 -0.068 1.10e-02 8.26e+03 3.84e+01 bond pdb=" CB7 CDL K 401 " pdb=" OB8 CDL K 401 " ideal model delta sigma weight residual 1.334 1.401 -0.067 1.10e-02 8.26e+03 3.70e+01 bond pdb=" C 2MR D 85 " pdb=" O 2MR D 85 " ideal model delta sigma weight residual 1.231 1.352 -0.121 2.00e-02 2.50e+03 3.66e+01 ... (remaining 69535 not shown) Histogram of bond angle deviations from ideal: 72.60 - 84.92: 76 84.92 - 97.23: 1 97.23 - 109.54: 8008 109.54 - 121.85: 73047 121.85 - 134.16: 12946 Bond angle restraints: 94078 Sorted by residual: angle pdb=" C51 CDL J 701 " pdb=" CB5 CDL J 701 " pdb=" OB6 CDL J 701 " ideal model delta sigma weight residual 111.33 122.09 -10.76 1.32e+00 5.72e-01 6.62e+01 angle pdb=" O 2MR D 85 " pdb=" C 2MR D 85 " pdb=" N GLY D 86 " ideal model delta sigma weight residual 123.00 111.62 11.38 1.60e+00 3.91e-01 5.06e+01 angle pdb=" C51 CDL h1001 " pdb=" CB5 CDL h1001 " pdb=" OB6 CDL h1001 " ideal model delta sigma weight residual 111.33 120.70 -9.37 1.32e+00 5.72e-01 5.02e+01 angle pdb=" C11 CDL J 701 " pdb=" CA5 CDL J 701 " pdb=" OA6 CDL J 701 " ideal model delta sigma weight residual 111.33 120.26 -8.93 1.32e+00 5.72e-01 4.56e+01 angle pdb=" C11 CDL h1001 " pdb=" CA5 CDL h1001 " pdb=" OA6 CDL h1001 " ideal model delta sigma weight residual 111.33 120.24 -8.91 1.32e+00 5.72e-01 4.54e+01 ... (remaining 94073 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.90: 40813 34.90 - 69.80: 1600 69.80 - 104.69: 217 104.69 - 139.59: 24 139.59 - 174.49: 5 Dihedral angle restraints: 42659 sinusoidal: 18773 harmonic: 23886 Sorted by residual: 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 83.10 174.49 1 2.00e+01 2.50e-03 4.79e+01 dihedral pdb=" O5' GTP O 401 " pdb=" O3A GTP O 401 " pdb=" PA GTP O 401 " pdb=" PB GTP O 401 " ideal model delta sinusoidal sigma weight residual 274.12 119.01 155.11 1 2.00e+01 2.50e-03 4.58e+01 dihedral pdb=" O3B GTP O 401 " pdb=" O3A GTP O 401 " pdb=" PB GTP O 401 " pdb=" PA GTP O 401 " ideal model delta sinusoidal sigma weight residual -68.92 81.93 -150.85 1 2.00e+01 2.50e-03 4.50e+01 ... (remaining 42656 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 4.263: 10264 4.263 - 8.526: 0 8.526 - 12.789: 0 12.789 - 17.052: 0 17.052 - 21.315: 16 Chirality restraints: 10280 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 10.76 -21.31 2.00e-01 2.50e+01 1.14e+04 chirality pdb="FE2 SF4 I 202 " pdb=" S1 SF4 I 202 " pdb=" S3 SF4 I 202 " pdb=" S4 SF4 I 202 " both_signs ideal model delta sigma weight residual False 10.55 -10.75 21.30 2.00e-01 2.50e+01 1.13e+04 chirality pdb="FE1 SF4 G 801 " pdb=" S2 SF4 G 801 " pdb=" S3 SF4 G 801 " pdb=" S4 SF4 G 801 " both_signs ideal model delta sigma weight residual False -10.55 10.74 -21.29 2.00e-01 2.50e+01 1.13e+04 ... (remaining 10277 not shown) Planarity restraints: 11693 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C08 I49 N1305 " -0.039 2.00e-02 2.50e+03 5.20e-01 5.41e+03 pdb=" C14 I49 N1305 " -0.129 2.00e-02 2.50e+03 pdb=" C15 I49 N1305 " -0.041 2.00e-02 2.50e+03 pdb=" N01 I49 N1305 " -0.517 2.00e-02 2.50e+03 pdb=" N02 I49 N1305 " -0.647 2.00e-02 2.50e+03 pdb=" N03 I49 N1305 " 0.709 2.00e-02 2.50e+03 pdb=" N04 I49 N1305 " 0.938 2.00e-02 2.50e+03 pdb=" N05 I49 N1305 " -0.274 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA 2MR D 85 " 0.077 2.00e-02 2.50e+03 1.43e-01 2.04e+02 pdb=" C 2MR D 85 " -0.247 2.00e-02 2.50e+03 pdb=" O 2MR D 85 " 0.082 2.00e-02 2.50e+03 pdb=" N GLY D 86 " 0.088 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C THR e 92 " -0.046 5.00e-02 4.00e+02 6.90e-02 7.61e+00 pdb=" N PRO e 93 " 0.119 5.00e-02 4.00e+02 pdb=" CA PRO e 93 " -0.036 5.00e-02 4.00e+02 pdb=" CD PRO e 93 " -0.038 5.00e-02 4.00e+02 ... (remaining 11690 not shown) Histogram of nonbonded interaction distances: 1.90 - 2.55: 714 2.55 - 3.20: 65735 3.20 - 3.85: 147736 3.85 - 4.49: 214204 4.49 - 5.14: 323808 Nonbonded interactions: 752197 Sorted by model distance: nonbonded pdb=" OG SER e 21 " pdb=" OE1 GLU e 36 " model vdw 1.904 2.440 nonbonded pdb=" O HOH B 351 " pdb=" O HOH B 361 " model vdw 1.927 2.440 nonbonded pdb=" O1G GTP O 401 " pdb="MG MG O 402 " model vdw 1.928 2.170 nonbonded pdb=" O2B LMT j 101 " pdb=" O3' LMT j 101 " model vdw 1.937 2.440 nonbonded pdb=" O HOH I 365 " pdb=" O HOH I 375 " model vdw 1.940 2.440 ... (remaining 752192 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 7 through 82 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=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 14.220 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: 57.590 Check model and map are aligned: 0.760 Set scattering table: 0.480 Process input model: 159.760 Find NCS groups from input model: 2.030 Set up NCS constraints: 0.240 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:11.760 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 246.910 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8758 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 0.170 69540 Z= 0.508 Angle : 0.851 15.682 94078 Z= 0.385 Chirality : 0.840 21.315 10280 Planarity : 0.006 0.520 11693 Dihedral : 18.228 174.491 27243 Min Nonbonded Distance : 1.904 Molprobity Statistics. All-atom Clashscore : 3.40 Ramachandran Plot: Outliers : 0.02 % Allowed : 2.44 % Favored : 97.54 % Rotamer: Outliers : 1.01 % Allowed : 11.49 % Favored : 87.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.66 % 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: 0.57 (0.09), residues: 8087 helix: 0.63 (0.08), residues: 4298 sheet: 0.15 (0.26), residues: 370 loop : 0.28 (0.11), residues: 3419 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP N 84 HIS 0.008 0.001 HIS N 112 PHE 0.024 0.002 PHE D 425 TYR 0.031 0.002 TYR B 125 ARG 0.007 0.000 ARG o 20 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16174 Ramachandran restraints generated. 8087 Oldfield, 0 Emsley, 8087 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16174 Ramachandran restraints generated. 8087 Oldfield, 0 Emsley, 8087 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1061 residues out of total 7148 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 989 time to evaluate : 6.497 Fit side-chains REVERT: A 85 ASN cc_start: 0.8104 (m-40) cc_final: 0.7733 (m-40) REVERT: H 227 GLU cc_start: 0.7756 (mm-30) cc_final: 0.7514 (mm-30) REVERT: J 118 GLU cc_start: 0.6366 (mp0) cc_final: 0.6139 (mp0) REVERT: L 442 ASN cc_start: 0.8364 (t0) cc_final: 0.8117 (t0) REVERT: T 11 ILE cc_start: 0.7450 (mt) cc_final: 0.7056 (mm) REVERT: Z 76 GLN cc_start: 0.8886 (tp40) cc_final: 0.8554 (tm-30) REVERT: b 61 ASN cc_start: 0.8143 (OUTLIER) cc_final: 0.7904 (p0) REVERT: d 45 ASP cc_start: 0.8813 (t70) cc_final: 0.8501 (t0) REVERT: e 48 SER cc_start: 0.8543 (m) cc_final: 0.8341 (p) REVERT: l 114 PHE cc_start: 0.8734 (t80) cc_final: 0.8490 (t80) REVERT: n 61 GLN cc_start: 0.8020 (tm-30) cc_final: 0.7790 (tm-30) REVERT: n 72 HIS cc_start: 0.8354 (t-90) cc_final: 0.8112 (t-170) REVERT: s 33 PHE cc_start: 0.8049 (t80) cc_final: 0.7838 (t80) outliers start: 72 outliers final: 64 residues processed: 1043 average time/residue: 1.7233 time to fit residues: 2282.3592 Evaluate side-chains 1015 residues out of total 7148 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 950 time to evaluate : 6.003 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 54 CYS Chi-restraints excluded: chain B residue 91 THR Chi-restraints excluded: chain D residue 44 VAL Chi-restraints excluded: chain D residue 61 VAL Chi-restraints excluded: chain E residue 40 GLU Chi-restraints excluded: chain E residue 203 THR Chi-restraints excluded: chain F residue 11 SER Chi-restraints excluded: chain F residue 86 SER Chi-restraints excluded: chain F residue 307 ILE Chi-restraints excluded: chain G residue 84 GLU Chi-restraints excluded: chain G residue 174 THR Chi-restraints excluded: chain G residue 292 THR Chi-restraints excluded: chain G residue 609 MET Chi-restraints excluded: chain G residue 659 ASP Chi-restraints excluded: chain H residue 103 LEU Chi-restraints excluded: chain I residue 1 THR Chi-restraints excluded: chain J residue 133 SER Chi-restraints excluded: chain K residue 46 LEU Chi-restraints excluded: chain L residue 254 VAL Chi-restraints excluded: chain L residue 262 ARG Chi-restraints excluded: chain L residue 551 SER Chi-restraints excluded: chain L residue 568 LEU Chi-restraints excluded: chain M residue 72 LEU Chi-restraints excluded: chain M residue 80 SER Chi-restraints excluded: chain M residue 116 ILE Chi-restraints excluded: chain M residue 393 ILE Chi-restraints excluded: chain M residue 427 SER Chi-restraints excluded: chain N residue 250 SER Chi-restraints excluded: chain O residue 196 SER Chi-restraints excluded: chain O residue 224 SER Chi-restraints excluded: chain O residue 250 ASP Chi-restraints excluded: chain R residue 2 VAL Chi-restraints excluded: chain R residue 4 THR Chi-restraints excluded: chain S residue 91 GLU Chi-restraints excluded: chain T residue 31 SER Chi-restraints excluded: chain W residue 81 LEU Chi-restraints excluded: chain X residue 11 ASP Chi-restraints excluded: chain X residue 154 GLU Chi-restraints excluded: chain Y residue 5 LEU Chi-restraints excluded: chain Y residue 11 ILE Chi-restraints excluded: chain Y residue 76 SER Chi-restraints excluded: chain Z residue 106 VAL Chi-restraints excluded: chain Z residue 130 SER Chi-restraints excluded: chain b residue 33 THR Chi-restraints excluded: chain b residue 61 ASN Chi-restraints excluded: chain c residue 11 SER Chi-restraints excluded: chain d residue 10 THR Chi-restraints excluded: chain e residue 18 THR Chi-restraints excluded: chain f residue 30 ASN Chi-restraints excluded: chain g residue 34 ASP Chi-restraints excluded: chain g residue 109 GLU Chi-restraints excluded: chain g residue 116 SER Chi-restraints excluded: chain h residue 32 THR Chi-restraints excluded: chain i residue 8 LYS Chi-restraints excluded: chain j residue 40 PHE Chi-restraints excluded: chain j residue 44 SER Chi-restraints excluded: chain k residue 78 VAL Chi-restraints excluded: chain l residue 4 ILE Chi-restraints excluded: chain l residue 154 VAL Chi-restraints excluded: chain m residue 26 SER Chi-restraints excluded: chain n residue 84 SER Chi-restraints excluded: chain o residue 112 LYS Chi-restraints excluded: chain p residue 24 SER Chi-restraints excluded: chain q residue 26 VAL Chi-restraints excluded: chain q residue 145 LYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 800 random chunks: chunk 675 optimal weight: 0.8980 chunk 606 optimal weight: 7.9990 chunk 336 optimal weight: 3.9990 chunk 207 optimal weight: 9.9990 chunk 409 optimal weight: 0.9980 chunk 323 optimal weight: 0.9990 chunk 627 optimal weight: 1.9990 chunk 242 optimal weight: 7.9990 chunk 381 optimal weight: 0.9990 chunk 466 optimal weight: 5.9990 chunk 726 optimal weight: 2.9990 overall best weight: 1.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 79 HIS F 257 ASN M 139 GLN M 175 ASN N 316 GLN P 87 HIS P 296 HIS S 85 GLN Z 85 GLN e 69 GLN j 6 HIS l 99 ASN m 32 GLN n 140 GLN n 159 GLN o 43 GLN o 53 GLN o 116 GLN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8656 moved from start: 0.0984 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.276 69540 Z= 0.459 Angle : 1.306 50.516 94078 Z= 0.836 Chirality : 0.255 6.498 10280 Planarity : 0.004 0.059 11693 Dihedral : 14.116 173.470 11165 Min Nonbonded Distance : 1.976 Molprobity Statistics. All-atom Clashscore : 3.63 Ramachandran Plot: Outliers : 0.01 % Allowed : 1.56 % Favored : 98.43 % Rotamer: Outliers : 1.82 % Allowed : 11.28 % Favored : 86.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.66 % 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: 1.35 (0.09), residues: 8087 helix: 1.44 (0.08), residues: 4309 sheet: 0.10 (0.25), residues: 371 loop : 0.43 (0.11), residues: 3407 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP H 179 HIS 0.006 0.001 HIS G 101 PHE 0.026 0.001 PHE N 292 TYR 0.021 0.001 TYR I 118 ARG 0.004 0.000 ARG S 25 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16174 Ramachandran restraints generated. 8087 Oldfield, 0 Emsley, 8087 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16174 Ramachandran restraints generated. 8087 Oldfield, 0 Emsley, 8087 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1151 residues out of total 7148 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 130 poor density : 1021 time to evaluate : 6.145 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 31 SER cc_start: 0.8830 (OUTLIER) cc_final: 0.8526 (t) REVERT: A 81 THR cc_start: 0.8659 (t) cc_final: 0.8391 (p) REVERT: A 85 ASN cc_start: 0.7916 (OUTLIER) cc_final: 0.7596 (m-40) REVERT: G 16 GLN cc_start: 0.8289 (OUTLIER) cc_final: 0.7610 (tm-30) REVERT: G 536 ASP cc_start: 0.8398 (OUTLIER) cc_final: 0.7950 (m-30) REVERT: H 85 MET cc_start: 0.8965 (mmm) cc_final: 0.8745 (mmm) REVERT: H 202 GLU cc_start: 0.7486 (OUTLIER) cc_final: 0.7154 (tt0) REVERT: I 36 MET cc_start: 0.8868 (tpp) cc_final: 0.8570 (tpp) REVERT: J 118 GLU cc_start: 0.6319 (mp0) cc_final: 0.6093 (mp0) REVERT: L 14 LEU cc_start: 0.9023 (OUTLIER) cc_final: 0.8791 (tt) REVERT: L 26 THR cc_start: 0.5871 (OUTLIER) cc_final: 0.5546 (p) REVERT: L 442 ASN cc_start: 0.8362 (t0) cc_final: 0.8121 (t0) REVERT: O 20 GLU cc_start: 0.7424 (OUTLIER) cc_final: 0.7095 (mm-30) REVERT: O 182 ARG cc_start: 0.8538 (OUTLIER) cc_final: 0.8206 (mtt180) REVERT: P 268 ARG cc_start: 0.6836 (OUTLIER) cc_final: 0.6220 (ttp80) REVERT: T 11 ILE cc_start: 0.7576 (mt) cc_final: 0.7197 (mm) REVERT: T 14 ARG cc_start: 0.7769 (mmm-85) cc_final: 0.7397 (mtt180) REVERT: X 154 GLU cc_start: 0.6990 (OUTLIER) cc_final: 0.6097 (pp20) REVERT: Y 105 ARG cc_start: 0.6917 (OUTLIER) cc_final: 0.6132 (mpt90) REVERT: Z 76 GLN cc_start: 0.8778 (tp40) cc_final: 0.8407 (tm-30) REVERT: c 6 GLU cc_start: 0.7492 (OUTLIER) cc_final: 0.7162 (tt0) REVERT: e 97 HIS cc_start: 0.5895 (OUTLIER) cc_final: 0.5539 (m-70) REVERT: j 19 ARG cc_start: 0.7086 (mmm160) cc_final: 0.6591 (mmm160) REVERT: k 12 LYS cc_start: 0.5955 (OUTLIER) cc_final: 0.5544 (tmmt) REVERT: l 114 PHE cc_start: 0.8659 (t80) cc_final: 0.8367 (t80) REVERT: p 23 THR cc_start: 0.8701 (OUTLIER) cc_final: 0.8453 (p) REVERT: s 33 PHE cc_start: 0.8025 (t80) cc_final: 0.7819 (t80) outliers start: 130 outliers final: 33 residues processed: 1101 average time/residue: 1.6893 time to fit residues: 2372.2567 Evaluate side-chains 1015 residues out of total 7148 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 966 time to evaluate : 5.864 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 SER Chi-restraints excluded: chain A residue 85 ASN Chi-restraints excluded: chain B residue 54 CYS Chi-restraints excluded: chain D residue 44 VAL Chi-restraints excluded: chain D residue 61 VAL Chi-restraints excluded: chain D residue 109 VAL Chi-restraints excluded: chain F residue 105 CYS Chi-restraints excluded: chain G residue 16 GLN Chi-restraints excluded: chain G residue 84 GLU Chi-restraints excluded: chain G residue 484 THR Chi-restraints excluded: chain G residue 536 ASP Chi-restraints excluded: chain G residue 659 ASP Chi-restraints excluded: chain H residue 202 GLU Chi-restraints excluded: chain K residue 46 LEU Chi-restraints excluded: chain L residue 14 LEU Chi-restraints excluded: chain L residue 26 THR Chi-restraints excluded: chain L residue 254 VAL Chi-restraints excluded: chain L residue 551 SER Chi-restraints excluded: chain M residue 72 LEU Chi-restraints excluded: chain M residue 365 THR Chi-restraints excluded: chain N residue 320 MET Chi-restraints excluded: chain O residue 19 THR Chi-restraints excluded: chain O residue 20 GLU Chi-restraints excluded: chain O residue 182 ARG Chi-restraints excluded: chain O residue 250 ASP Chi-restraints excluded: chain P residue 170 GLU Chi-restraints excluded: chain P residue 268 ARG Chi-restraints excluded: chain R residue 2 VAL Chi-restraints excluded: chain S residue 59 ASP Chi-restraints excluded: chain U residue 37 MET Chi-restraints excluded: chain V residue 6 LYS Chi-restraints excluded: chain W residue 96 VAL Chi-restraints excluded: chain X residue 154 GLU Chi-restraints excluded: chain Y residue 11 ILE Chi-restraints excluded: chain Y residue 105 ARG Chi-restraints excluded: chain Y residue 114 CYS Chi-restraints excluded: chain a residue 70 ASP Chi-restraints excluded: chain b residue 33 THR Chi-restraints excluded: chain c residue 6 GLU Chi-restraints excluded: chain e residue 97 HIS Chi-restraints excluded: chain i residue 34 LEU Chi-restraints excluded: chain j residue 40 PHE Chi-restraints excluded: chain k residue 12 LYS Chi-restraints excluded: chain l residue 16 THR Chi-restraints excluded: chain n residue 84 SER Chi-restraints excluded: chain o residue 112 LYS Chi-restraints excluded: chain p residue 23 THR Chi-restraints excluded: chain q residue 141 SER Chi-restraints excluded: chain q residue 145 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 800 random chunks: chunk 403 optimal weight: 10.0000 chunk 225 optimal weight: 2.9990 chunk 604 optimal weight: 5.9990 chunk 494 optimal weight: 4.9990 chunk 200 optimal weight: 0.0770 chunk 727 optimal weight: 6.9990 chunk 786 optimal weight: 3.9990 chunk 648 optimal weight: 0.8980 chunk 721 optimal weight: 5.9990 chunk 248 optimal weight: 5.9990 chunk 583 optimal weight: 10.0000 overall best weight: 2.5944 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 29 HIS F 432 GLN G 475 GLN M 139 GLN M 304 GLN N 222 ASN P 296 HIS S 92 ASN X 64 GLN Y 7 GLN Z 85 GLN b 10 ASN e 69 GLN e 81 GLN g 119 GLN k 90 GLN l 99 ASN n 140 GLN n 159 GLN o 43 GLN o 53 GLN Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8676 moved from start: 0.1037 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.248 69540 Z= 0.486 Angle : 1.309 50.533 94078 Z= 0.837 Chirality : 0.257 6.578 10280 Planarity : 0.004 0.056 11693 Dihedral : 12.914 173.528 11092 Min Nonbonded Distance : 1.932 Molprobity Statistics. All-atom Clashscore : 3.80 Ramachandran Plot: Outliers : 0.01 % Allowed : 2.14 % Favored : 97.85 % Rotamer: Outliers : 1.78 % Allowed : 11.99 % Favored : 86.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.66 % 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: 1.40 (0.09), residues: 8087 helix: 1.52 (0.08), residues: 4303 sheet: 0.10 (0.26), residues: 359 loop : 0.42 (0.11), residues: 3425 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP X 85 HIS 0.006 0.001 HIS G 101 PHE 0.026 0.002 PHE N 292 TYR 0.022 0.002 TYR H 282 ARG 0.006 0.000 ARG W 30 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16174 Ramachandran restraints generated. 8087 Oldfield, 0 Emsley, 8087 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16174 Ramachandran restraints generated. 8087 Oldfield, 0 Emsley, 8087 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1109 residues out of total 7148 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 127 poor density : 982 time to evaluate : 6.787 Fit side-chains REVERT: A 31 SER cc_start: 0.8843 (OUTLIER) cc_final: 0.8542 (t) REVERT: A 81 THR cc_start: 0.8627 (t) cc_final: 0.8397 (p) REVERT: G 16 GLN cc_start: 0.8278 (OUTLIER) cc_final: 0.7619 (tm-30) REVERT: G 536 ASP cc_start: 0.8463 (OUTLIER) cc_final: 0.8011 (m-30) REVERT: H 202 GLU cc_start: 0.7544 (OUTLIER) cc_final: 0.7208 (tt0) REVERT: I 36 MET cc_start: 0.8957 (tpp) cc_final: 0.8601 (tpp) REVERT: J 118 GLU cc_start: 0.6398 (mp0) cc_final: 0.6124 (mp0) REVERT: L 14 LEU cc_start: 0.9031 (OUTLIER) cc_final: 0.8801 (tt) REVERT: L 26 THR cc_start: 0.5963 (OUTLIER) cc_final: 0.5746 (p) REVERT: L 442 ASN cc_start: 0.8328 (t0) cc_final: 0.8110 (t0) REVERT: N 263 LYS cc_start: 0.8640 (OUTLIER) cc_final: 0.8277 (tmmm) REVERT: O 182 ARG cc_start: 0.8574 (OUTLIER) cc_final: 0.8245 (mtt180) REVERT: P 268 ARG cc_start: 0.6810 (OUTLIER) cc_final: 0.6226 (ttp80) REVERT: T 11 ILE cc_start: 0.7591 (mt) cc_final: 0.7204 (mm) REVERT: T 14 ARG cc_start: 0.7678 (mmm-85) cc_final: 0.7441 (mtt180) REVERT: X 154 GLU cc_start: 0.7007 (OUTLIER) cc_final: 0.6129 (pp20) REVERT: Y 105 ARG cc_start: 0.6954 (OUTLIER) cc_final: 0.6168 (mpt90) REVERT: Z 64 ASP cc_start: 0.7980 (OUTLIER) cc_final: 0.7598 (t70) REVERT: Z 76 GLN cc_start: 0.8797 (tp40) cc_final: 0.8422 (tm-30) REVERT: b 64 ASP cc_start: 0.7233 (OUTLIER) cc_final: 0.7017 (p0) REVERT: c 6 GLU cc_start: 0.7484 (OUTLIER) cc_final: 0.7147 (tt0) REVERT: e 97 HIS cc_start: 0.5924 (OUTLIER) cc_final: 0.5459 (m-70) REVERT: j 19 ARG cc_start: 0.7043 (mmm160) cc_final: 0.6559 (mmm160) REVERT: k 12 LYS cc_start: 0.6073 (OUTLIER) cc_final: 0.5604 (tmmt) REVERT: k 32 GLN cc_start: 0.8913 (tp-100) cc_final: 0.8675 (tp-100) REVERT: k 41 ARG cc_start: 0.7925 (mtp85) cc_final: 0.7652 (mtp85) REVERT: l 114 PHE cc_start: 0.8669 (t80) cc_final: 0.8376 (t80) REVERT: p 23 THR cc_start: 0.8745 (OUTLIER) cc_final: 0.8478 (p) REVERT: s 33 PHE cc_start: 0.8042 (t80) cc_final: 0.7821 (t80) outliers start: 127 outliers final: 52 residues processed: 1054 average time/residue: 1.7349 time to fit residues: 2326.6920 Evaluate side-chains 1020 residues out of total 7148 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 951 time to evaluate : 5.889 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 SER Chi-restraints excluded: chain B residue 34 ASP Chi-restraints excluded: chain B residue 54 CYS Chi-restraints excluded: chain D residue 44 VAL Chi-restraints excluded: chain D residue 61 VAL Chi-restraints excluded: chain D residue 109 VAL Chi-restraints excluded: chain D residue 376 VAL Chi-restraints excluded: chain F residue 105 CYS Chi-restraints excluded: chain G residue 16 GLN Chi-restraints excluded: chain G residue 84 GLU Chi-restraints excluded: chain G residue 536 ASP Chi-restraints excluded: chain G residue 609 MET Chi-restraints excluded: chain G residue 653 ASN Chi-restraints excluded: chain G residue 659 ASP Chi-restraints excluded: chain H residue 202 GLU Chi-restraints excluded: chain H residue 289 LEU Chi-restraints excluded: chain I residue 37 THR Chi-restraints excluded: chain J residue 133 SER Chi-restraints excluded: chain K residue 2 SER Chi-restraints excluded: chain K residue 46 LEU Chi-restraints excluded: chain L residue 14 LEU Chi-restraints excluded: chain L residue 26 THR Chi-restraints excluded: chain L residue 235 SER Chi-restraints excluded: chain L residue 254 VAL Chi-restraints excluded: chain L residue 568 LEU Chi-restraints excluded: chain M residue 72 LEU Chi-restraints excluded: chain N residue 263 LYS Chi-restraints excluded: chain O residue 19 THR Chi-restraints excluded: chain O residue 182 ARG Chi-restraints excluded: chain O residue 196 SER Chi-restraints excluded: chain P residue 139 ILE Chi-restraints excluded: chain P residue 170 GLU Chi-restraints excluded: chain P residue 268 ARG Chi-restraints excluded: chain P residue 272 ILE Chi-restraints excluded: chain Q residue 110 VAL Chi-restraints excluded: chain R residue 2 VAL Chi-restraints excluded: chain R residue 4 THR Chi-restraints excluded: chain S residue 59 ASP Chi-restraints excluded: chain T residue 31 SER Chi-restraints excluded: chain U residue 37 MET Chi-restraints excluded: chain X residue 3 ILE Chi-restraints excluded: chain X residue 11 ASP Chi-restraints excluded: chain X residue 154 GLU Chi-restraints excluded: chain Y residue 11 ILE Chi-restraints excluded: chain Y residue 105 ARG Chi-restraints excluded: chain Y residue 109 ILE Chi-restraints excluded: chain Z residue 64 ASP Chi-restraints excluded: chain a residue 70 ASP Chi-restraints excluded: chain b residue 33 THR Chi-restraints excluded: chain b residue 64 ASP Chi-restraints excluded: chain c residue 6 GLU Chi-restraints excluded: chain c residue 25 VAL Chi-restraints excluded: chain d residue 25 LYS Chi-restraints excluded: chain e residue 48 SER Chi-restraints excluded: chain e residue 97 HIS Chi-restraints excluded: chain f residue 30 ASN Chi-restraints excluded: chain g residue 109 GLU Chi-restraints excluded: chain i residue 34 LEU Chi-restraints excluded: chain j residue 40 PHE Chi-restraints excluded: chain k residue 12 LYS Chi-restraints excluded: chain l residue 16 THR Chi-restraints excluded: chain l residue 154 VAL Chi-restraints excluded: chain m residue 11 SER Chi-restraints excluded: chain o residue 34 LYS Chi-restraints excluded: chain o residue 112 LYS Chi-restraints excluded: chain p residue 20 SER Chi-restraints excluded: chain p residue 23 THR Chi-restraints excluded: chain q residue 141 SER Chi-restraints excluded: chain q residue 145 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 800 random chunks: chunk 719 optimal weight: 2.9990 chunk 547 optimal weight: 10.0000 chunk 377 optimal weight: 3.9990 chunk 80 optimal weight: 0.9990 chunk 347 optimal weight: 0.9990 chunk 488 optimal weight: 9.9990 chunk 730 optimal weight: 4.9990 chunk 773 optimal weight: 2.9990 chunk 381 optimal weight: 4.9990 chunk 692 optimal weight: 1.9990 chunk 208 optimal weight: 10.0000 overall best weight: 1.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 475 GLN K 97 GLN M 139 GLN P 296 HIS S 85 GLN S 92 ASN X 64 GLN Y 7 GLN Z 85 GLN b 10 ASN e 69 GLN g 119 GLN l 99 ASN n 140 GLN n 159 GLN o 43 GLN o 53 GLN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8662 moved from start: 0.1185 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.245 69540 Z= 0.466 Angle : 1.296 50.500 94078 Z= 0.833 Chirality : 0.255 6.507 10280 Planarity : 0.004 0.053 11693 Dihedral : 12.335 172.957 11088 Min Nonbonded Distance : 1.984 Molprobity Statistics. All-atom Clashscore : 4.11 Ramachandran Plot: Outliers : 0.01 % Allowed : 1.71 % Favored : 98.28 % Rotamer: Outliers : 1.82 % Allowed : 12.52 % Favored : 85.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.66 % 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: 1.47 (0.09), residues: 8087 helix: 1.58 (0.08), residues: 4304 sheet: 0.10 (0.26), residues: 360 loop : 0.44 (0.11), residues: 3423 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP X 85 HIS 0.006 0.001 HIS G 101 PHE 0.027 0.001 PHE N 292 TYR 0.019 0.001 TYR H 282 ARG 0.005 0.000 ARG W 30 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16174 Ramachandran restraints generated. 8087 Oldfield, 0 Emsley, 8087 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16174 Ramachandran restraints generated. 8087 Oldfield, 0 Emsley, 8087 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1103 residues out of total 7148 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 130 poor density : 973 time to evaluate : 6.765 Fit side-chains revert: symmetry clash REVERT: A 31 SER cc_start: 0.8842 (OUTLIER) cc_final: 0.8548 (t) REVERT: A 85 ASN cc_start: 0.7935 (OUTLIER) cc_final: 0.7569 (m-40) REVERT: G 536 ASP cc_start: 0.8448 (OUTLIER) cc_final: 0.7985 (m-30) REVERT: H 202 GLU cc_start: 0.7517 (OUTLIER) cc_final: 0.7189 (tt0) REVERT: J 118 GLU cc_start: 0.6332 (mp0) cc_final: 0.6062 (mp0) REVERT: J 138 GLU cc_start: 0.8342 (OUTLIER) cc_final: 0.8042 (mt-10) REVERT: L 14 LEU cc_start: 0.9024 (OUTLIER) cc_final: 0.8743 (tt) REVERT: L 442 ASN cc_start: 0.8343 (t0) cc_final: 0.8130 (t0) REVERT: L 544 MET cc_start: 0.7859 (tmm) cc_final: 0.7640 (tmm) REVERT: N 263 LYS cc_start: 0.8616 (OUTLIER) cc_final: 0.8246 (tmmm) REVERT: O 206 TYR cc_start: 0.8883 (OUTLIER) cc_final: 0.8403 (m-80) REVERT: P 268 ARG cc_start: 0.6851 (OUTLIER) cc_final: 0.6247 (ttp80) REVERT: S 88 ARG cc_start: 0.7952 (mtm-85) cc_final: 0.7735 (mtm110) REVERT: T 11 ILE cc_start: 0.7598 (mt) cc_final: 0.7195 (mm) REVERT: T 14 ARG cc_start: 0.7672 (mmm-85) cc_final: 0.7423 (mtt180) REVERT: X 154 GLU cc_start: 0.7016 (OUTLIER) cc_final: 0.6118 (pp20) REVERT: Y 105 ARG cc_start: 0.6927 (OUTLIER) cc_final: 0.6146 (mpt90) REVERT: Z 64 ASP cc_start: 0.7939 (OUTLIER) cc_final: 0.7561 (t70) REVERT: Z 76 GLN cc_start: 0.8777 (tp40) cc_final: 0.8402 (tm-30) REVERT: c 6 GLU cc_start: 0.7488 (OUTLIER) cc_final: 0.7158 (tt0) REVERT: e 17 MET cc_start: 0.8547 (OUTLIER) cc_final: 0.8262 (ttm) REVERT: e 36 GLU cc_start: 0.7728 (tt0) cc_final: 0.7240 (tt0) REVERT: e 97 HIS cc_start: 0.5946 (OUTLIER) cc_final: 0.5544 (m-70) REVERT: h 136 SER cc_start: 0.8640 (m) cc_final: 0.8408 (p) REVERT: j 19 ARG cc_start: 0.7037 (mmm160) cc_final: 0.6631 (mmm160) REVERT: k 12 LYS cc_start: 0.5952 (OUTLIER) cc_final: 0.5443 (tmmt) REVERT: k 41 ARG cc_start: 0.7938 (mtp85) cc_final: 0.7662 (ttt-90) REVERT: l 114 PHE cc_start: 0.8658 (t80) cc_final: 0.8367 (t80) REVERT: m 36 LEU cc_start: 0.8878 (OUTLIER) cc_final: 0.8556 (tt) REVERT: p 23 THR cc_start: 0.8734 (OUTLIER) cc_final: 0.8483 (p) REVERT: s 33 PHE cc_start: 0.8035 (t80) cc_final: 0.7806 (t80) outliers start: 130 outliers final: 51 residues processed: 1052 average time/residue: 1.7179 time to fit residues: 2300.6614 Evaluate side-chains 1006 residues out of total 7148 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 937 time to evaluate : 5.943 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 SER Chi-restraints excluded: chain A residue 85 ASN Chi-restraints excluded: chain B residue 34 ASP Chi-restraints excluded: chain B residue 54 CYS Chi-restraints excluded: chain D residue 44 VAL Chi-restraints excluded: chain D residue 61 VAL Chi-restraints excluded: chain D residue 109 VAL Chi-restraints excluded: chain F residue 105 CYS Chi-restraints excluded: chain G residue 84 GLU Chi-restraints excluded: chain G residue 536 ASP Chi-restraints excluded: chain G residue 588 THR Chi-restraints excluded: chain G residue 653 ASN Chi-restraints excluded: chain G residue 659 ASP Chi-restraints excluded: chain H residue 103 LEU Chi-restraints excluded: chain H residue 202 GLU Chi-restraints excluded: chain H residue 289 LEU Chi-restraints excluded: chain J residue 133 SER Chi-restraints excluded: chain J residue 138 GLU Chi-restraints excluded: chain K residue 2 SER Chi-restraints excluded: chain K residue 46 LEU Chi-restraints excluded: chain L residue 14 LEU Chi-restraints excluded: chain L residue 235 SER Chi-restraints excluded: chain L residue 254 VAL Chi-restraints excluded: chain M residue 304 GLN Chi-restraints excluded: chain M residue 365 THR Chi-restraints excluded: chain N residue 263 LYS Chi-restraints excluded: chain O residue 19 THR Chi-restraints excluded: chain O residue 206 TYR Chi-restraints excluded: chain O residue 250 ASP Chi-restraints excluded: chain P residue 139 ILE Chi-restraints excluded: chain P residue 170 GLU Chi-restraints excluded: chain P residue 268 ARG Chi-restraints excluded: chain P residue 272 ILE Chi-restraints excluded: chain Q residue 110 VAL Chi-restraints excluded: chain R residue 2 VAL Chi-restraints excluded: chain S residue 59 ASP Chi-restraints excluded: chain S residue 90 LEU Chi-restraints excluded: chain S residue 91 GLU Chi-restraints excluded: chain T residue 31 SER Chi-restraints excluded: chain U residue 37 MET Chi-restraints excluded: chain V residue 6 LYS Chi-restraints excluded: chain X residue 3 ILE Chi-restraints excluded: chain X residue 11 ASP Chi-restraints excluded: chain X residue 130 VAL Chi-restraints excluded: chain X residue 154 GLU Chi-restraints excluded: chain Y residue 11 ILE Chi-restraints excluded: chain Y residue 105 ARG Chi-restraints excluded: chain Y residue 109 ILE Chi-restraints excluded: chain Y residue 114 CYS Chi-restraints excluded: chain Z residue 64 ASP Chi-restraints excluded: chain a residue 70 ASP Chi-restraints excluded: chain b residue 33 THR Chi-restraints excluded: chain c residue 6 GLU Chi-restraints excluded: chain e residue 17 MET Chi-restraints excluded: chain e residue 48 SER Chi-restraints excluded: chain e residue 97 HIS Chi-restraints excluded: chain f residue 30 ASN Chi-restraints excluded: chain g residue 34 ASP Chi-restraints excluded: chain g residue 109 GLU Chi-restraints excluded: chain i residue 34 LEU Chi-restraints excluded: chain j residue 40 PHE Chi-restraints excluded: chain k residue 12 LYS Chi-restraints excluded: chain l residue 16 THR Chi-restraints excluded: chain l residue 154 VAL Chi-restraints excluded: chain m residue 11 SER Chi-restraints excluded: chain m residue 36 LEU Chi-restraints excluded: chain o residue 34 LYS Chi-restraints excluded: chain p residue 20 SER Chi-restraints excluded: chain p residue 23 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 800 random chunks: chunk 644 optimal weight: 5.9990 chunk 438 optimal weight: 3.9990 chunk 11 optimal weight: 10.0000 chunk 575 optimal weight: 10.0000 chunk 319 optimal weight: 4.9990 chunk 659 optimal weight: 8.9990 chunk 534 optimal weight: 6.9990 chunk 0 optimal weight: 10.0000 chunk 394 optimal weight: 4.9990 chunk 694 optimal weight: 8.9990 chunk 195 optimal weight: 0.7980 overall best weight: 4.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 97 GLN L 170 GLN ** L 479 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 139 GLN M 304 GLN P 296 HIS Q 29 HIS S 92 ASN X 64 GLN Y 7 GLN Z 85 GLN b 10 ASN e 69 GLN g 119 GLN l 99 ASN l 137 ASN n 140 GLN n 159 GLN o 43 GLN o 53 GLN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8692 moved from start: 0.1052 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.241 69540 Z= 0.548 Angle : 1.329 50.419 94078 Z= 0.845 Chirality : 0.259 6.654 10280 Planarity : 0.005 0.054 11693 Dihedral : 12.503 174.369 11078 Min Nonbonded Distance : 1.938 Molprobity Statistics. All-atom Clashscore : 4.25 Ramachandran Plot: Outliers : 0.01 % Allowed : 2.10 % Favored : 97.89 % Rotamer: Outliers : 2.07 % Allowed : 12.45 % Favored : 85.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.66 % 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: 1.28 (0.09), residues: 8087 helix: 1.41 (0.08), residues: 4311 sheet: 0.19 (0.25), residues: 376 loop : 0.36 (0.11), residues: 3400 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP X 85 HIS 0.008 0.001 HIS N 112 PHE 0.028 0.002 PHE N 292 TYR 0.023 0.002 TYR O 94 ARG 0.005 0.001 ARG S 25 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16174 Ramachandran restraints generated. 8087 Oldfield, 0 Emsley, 8087 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16174 Ramachandran restraints generated. 8087 Oldfield, 0 Emsley, 8087 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1090 residues out of total 7148 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 148 poor density : 942 time to evaluate : 5.978 Fit side-chains revert: symmetry clash REVERT: A 85 ASN cc_start: 0.7995 (OUTLIER) cc_final: 0.7621 (m-40) REVERT: F 77 LEU cc_start: 0.8847 (OUTLIER) cc_final: 0.8379 (tp) REVERT: G 536 ASP cc_start: 0.8485 (OUTLIER) cc_final: 0.8036 (m-30) REVERT: H 202 GLU cc_start: 0.7614 (OUTLIER) cc_final: 0.7251 (tt0) REVERT: J 118 GLU cc_start: 0.6426 (mp0) cc_final: 0.6206 (mp0) REVERT: L 442 ASN cc_start: 0.8340 (t0) cc_final: 0.8122 (t0) REVERT: N 263 LYS cc_start: 0.8650 (OUTLIER) cc_final: 0.8277 (tmmm) REVERT: O 182 ARG cc_start: 0.8486 (OUTLIER) cc_final: 0.8230 (mtt180) REVERT: O 206 TYR cc_start: 0.8908 (OUTLIER) cc_final: 0.8473 (m-80) REVERT: P 102 GLN cc_start: 0.8084 (OUTLIER) cc_final: 0.7836 (mt0) REVERT: P 268 ARG cc_start: 0.6915 (OUTLIER) cc_final: 0.6337 (ttp80) REVERT: T 11 ILE cc_start: 0.7583 (mt) cc_final: 0.7204 (mm) REVERT: T 14 ARG cc_start: 0.7712 (mmm-85) cc_final: 0.7453 (mtt180) REVERT: X 154 GLU cc_start: 0.6987 (OUTLIER) cc_final: 0.6135 (pp20) REVERT: Y 105 ARG cc_start: 0.6977 (OUTLIER) cc_final: 0.6176 (mpt90) REVERT: Z 64 ASP cc_start: 0.8041 (OUTLIER) cc_final: 0.7669 (t70) REVERT: Z 76 GLN cc_start: 0.8837 (tp40) cc_final: 0.8461 (tm-30) REVERT: c 6 GLU cc_start: 0.7473 (OUTLIER) cc_final: 0.7132 (tt0) REVERT: c 34 GLN cc_start: 0.8546 (OUTLIER) cc_final: 0.7772 (tp40) REVERT: e 17 MET cc_start: 0.8544 (OUTLIER) cc_final: 0.8286 (ttm) REVERT: e 97 HIS cc_start: 0.5948 (OUTLIER) cc_final: 0.5459 (m-70) REVERT: j 19 ARG cc_start: 0.7046 (mmm160) cc_final: 0.6646 (mmm160) REVERT: k 12 LYS cc_start: 0.5922 (OUTLIER) cc_final: 0.5352 (tmmt) REVERT: k 32 GLN cc_start: 0.8898 (tp40) cc_final: 0.8656 (tp-100) REVERT: k 41 ARG cc_start: 0.7935 (mtp85) cc_final: 0.7645 (mtp85) REVERT: l 114 PHE cc_start: 0.8677 (t80) cc_final: 0.8373 (t80) REVERT: m 36 LEU cc_start: 0.8903 (OUTLIER) cc_final: 0.8566 (tt) REVERT: n 8 TYR cc_start: 0.6194 (OUTLIER) cc_final: 0.5875 (p90) REVERT: o 118 GLU cc_start: 0.7507 (OUTLIER) cc_final: 0.7262 (mp0) REVERT: p 23 THR cc_start: 0.8748 (OUTLIER) cc_final: 0.8485 (p) REVERT: s 33 PHE cc_start: 0.8024 (t80) cc_final: 0.7785 (t80) outliers start: 148 outliers final: 79 residues processed: 1028 average time/residue: 1.7140 time to fit residues: 2237.1705 Evaluate side-chains 1027 residues out of total 7148 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 100 poor density : 927 time to evaluate : 5.936 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 SER Chi-restraints excluded: chain A residue 85 ASN Chi-restraints excluded: chain B residue 34 ASP Chi-restraints excluded: chain B residue 54 CYS Chi-restraints excluded: chain D residue 44 VAL Chi-restraints excluded: chain D residue 61 VAL Chi-restraints excluded: chain D residue 109 VAL Chi-restraints excluded: chain E residue 40 GLU Chi-restraints excluded: chain E residue 192 SER Chi-restraints excluded: chain E residue 203 THR Chi-restraints excluded: chain F residue 77 LEU Chi-restraints excluded: chain F residue 105 CYS Chi-restraints excluded: chain F residue 431 GLN Chi-restraints excluded: chain G residue 32 LYS Chi-restraints excluded: chain G residue 84 GLU Chi-restraints excluded: chain G residue 292 THR Chi-restraints excluded: chain G residue 382 THR Chi-restraints excluded: chain G residue 536 ASP Chi-restraints excluded: chain G residue 609 MET Chi-restraints excluded: chain G residue 653 ASN Chi-restraints excluded: chain G residue 659 ASP Chi-restraints excluded: chain H residue 103 LEU Chi-restraints excluded: chain H residue 202 GLU Chi-restraints excluded: chain H residue 289 LEU Chi-restraints excluded: chain I residue 9 GLU Chi-restraints excluded: chain I residue 122 CYS Chi-restraints excluded: chain J residue 133 SER Chi-restraints excluded: chain J residue 148 SER Chi-restraints excluded: chain K residue 2 SER Chi-restraints excluded: chain K residue 46 LEU Chi-restraints excluded: chain L residue 235 SER Chi-restraints excluded: chain L residue 254 VAL Chi-restraints excluded: chain L residue 440 LEU Chi-restraints excluded: chain L residue 568 LEU Chi-restraints excluded: chain L residue 597 ILE Chi-restraints excluded: chain M residue 139 GLN Chi-restraints excluded: chain M residue 365 THR Chi-restraints excluded: chain N residue 223 SER Chi-restraints excluded: chain N residue 263 LYS Chi-restraints excluded: chain O residue 1 LEU Chi-restraints excluded: chain O residue 19 THR Chi-restraints excluded: chain O residue 182 ARG Chi-restraints excluded: chain O residue 196 SER Chi-restraints excluded: chain O residue 206 TYR Chi-restraints excluded: chain O residue 250 ASP Chi-restraints excluded: chain P residue 102 GLN Chi-restraints excluded: chain P residue 139 ILE Chi-restraints excluded: chain P residue 170 GLU Chi-restraints excluded: chain P residue 268 ARG Chi-restraints excluded: chain Q residue 110 VAL Chi-restraints excluded: chain R residue 2 VAL Chi-restraints excluded: chain R residue 4 THR Chi-restraints excluded: chain S residue 59 ASP Chi-restraints excluded: chain S residue 63 LYS Chi-restraints excluded: chain S residue 90 LEU Chi-restraints excluded: chain S residue 91 GLU Chi-restraints excluded: chain T residue 31 SER Chi-restraints excluded: chain T residue 72 CYS Chi-restraints excluded: chain U residue 32 VAL Chi-restraints excluded: chain U residue 37 MET Chi-restraints excluded: chain V residue 6 LYS Chi-restraints excluded: chain X residue 3 ILE Chi-restraints excluded: chain X residue 11 ASP Chi-restraints excluded: chain X residue 130 VAL Chi-restraints excluded: chain X residue 154 GLU Chi-restraints excluded: chain Y residue 11 ILE Chi-restraints excluded: chain Y residue 105 ARG Chi-restraints excluded: chain Y residue 109 ILE Chi-restraints excluded: chain Y residue 114 CYS Chi-restraints excluded: chain Z residue 64 ASP Chi-restraints excluded: chain Z residue 106 VAL Chi-restraints excluded: chain a residue 70 ASP Chi-restraints excluded: chain b residue 33 THR Chi-restraints excluded: chain c residue 6 GLU Chi-restraints excluded: chain c residue 34 GLN Chi-restraints excluded: chain d residue 25 LYS Chi-restraints excluded: chain e residue 17 MET Chi-restraints excluded: chain e residue 18 THR Chi-restraints excluded: chain e residue 48 SER Chi-restraints excluded: chain e residue 97 HIS Chi-restraints excluded: chain f residue 7 VAL Chi-restraints excluded: chain f residue 30 ASN Chi-restraints excluded: chain g residue 34 ASP Chi-restraints excluded: chain g residue 109 GLU Chi-restraints excluded: chain i residue 34 LEU Chi-restraints excluded: chain i residue 110 LEU Chi-restraints excluded: chain j residue 40 PHE Chi-restraints excluded: chain k residue 12 LYS Chi-restraints excluded: chain l residue 16 THR Chi-restraints excluded: chain l residue 154 VAL Chi-restraints excluded: chain m residue 11 SER Chi-restraints excluded: chain m residue 36 LEU Chi-restraints excluded: chain m residue 75 ILE Chi-restraints excluded: chain m residue 91 LEU Chi-restraints excluded: chain n residue 8 TYR Chi-restraints excluded: chain o residue 118 GLU Chi-restraints excluded: chain p residue 20 SER Chi-restraints excluded: chain p residue 23 THR Chi-restraints excluded: chain q residue 26 VAL Chi-restraints excluded: chain q residue 141 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 800 random chunks: chunk 260 optimal weight: 1.9990 chunk 696 optimal weight: 3.9990 chunk 152 optimal weight: 5.9990 chunk 454 optimal weight: 0.9990 chunk 190 optimal weight: 1.9990 chunk 774 optimal weight: 8.9990 chunk 642 optimal weight: 4.9990 chunk 358 optimal weight: 0.9980 chunk 64 optimal weight: 2.9990 chunk 256 optimal weight: 5.9990 chunk 406 optimal weight: 0.9990 overall best weight: 1.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 475 GLN K 97 GLN ** L 479 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 139 GLN P 296 HIS S 85 GLN S 92 ASN Y 7 GLN Z 85 GLN b 10 ASN e 69 GLN g 119 GLN l 99 ASN n 140 GLN n 159 GLN o 43 GLN o 53 GLN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8654 moved from start: 0.1300 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.246 69540 Z= 0.452 Angle : 1.290 50.531 94078 Z= 0.831 Chirality : 0.254 6.467 10280 Planarity : 0.004 0.054 11693 Dihedral : 11.973 172.658 11078 Min Nonbonded Distance : 2.008 Molprobity Statistics. All-atom Clashscore : 4.38 Ramachandran Plot: Outliers : 0.01 % Allowed : 1.64 % Favored : 98.34 % Rotamer: Outliers : 1.68 % Allowed : 13.08 % Favored : 85.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.66 % 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: 1.53 (0.09), residues: 8087 helix: 1.63 (0.08), residues: 4295 sheet: 0.07 (0.25), residues: 380 loop : 0.47 (0.11), residues: 3412 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP X 85 HIS 0.006 0.001 HIS G 101 PHE 0.027 0.001 PHE N 292 TYR 0.020 0.001 TYR L 422 ARG 0.009 0.000 ARG o 117 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16174 Ramachandran restraints generated. 8087 Oldfield, 0 Emsley, 8087 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16174 Ramachandran restraints generated. 8087 Oldfield, 0 Emsley, 8087 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1078 residues out of total 7148 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 120 poor density : 958 time to evaluate : 6.364 Fit side-chains revert: symmetry clash REVERT: A 31 SER cc_start: 0.8835 (OUTLIER) cc_final: 0.8537 (t) REVERT: G 16 GLN cc_start: 0.8299 (OUTLIER) cc_final: 0.7559 (tm-30) REVERT: G 536 ASP cc_start: 0.8450 (OUTLIER) cc_final: 0.7986 (m-30) REVERT: J 138 GLU cc_start: 0.8328 (OUTLIER) cc_final: 0.8037 (mt-10) REVERT: L 140 LEU cc_start: 0.9219 (OUTLIER) cc_final: 0.8920 (tt) REVERT: L 442 ASN cc_start: 0.8342 (t0) cc_final: 0.8124 (t0) REVERT: N 263 LYS cc_start: 0.8599 (OUTLIER) cc_final: 0.8230 (tmmm) REVERT: O 206 TYR cc_start: 0.8879 (OUTLIER) cc_final: 0.8391 (m-80) REVERT: T 11 ILE cc_start: 0.7611 (mt) cc_final: 0.7236 (mm) REVERT: T 14 ARG cc_start: 0.7695 (mmm-85) cc_final: 0.7365 (mtt180) REVERT: X 154 GLU cc_start: 0.7009 (OUTLIER) cc_final: 0.6111 (pp20) REVERT: Y 105 ARG cc_start: 0.6932 (OUTLIER) cc_final: 0.6153 (mpt90) REVERT: Z 64 ASP cc_start: 0.7901 (OUTLIER) cc_final: 0.7512 (t70) REVERT: Z 76 GLN cc_start: 0.8770 (tp40) cc_final: 0.8410 (tm-30) REVERT: Z 108 GLU cc_start: 0.8187 (OUTLIER) cc_final: 0.7909 (tt0) REVERT: b 46 ARG cc_start: 0.7706 (ttp80) cc_final: 0.7425 (ttp-170) REVERT: c 6 GLU cc_start: 0.7487 (OUTLIER) cc_final: 0.7160 (tt0) REVERT: e 17 MET cc_start: 0.8559 (OUTLIER) cc_final: 0.8266 (ttm) REVERT: e 36 GLU cc_start: 0.7701 (tt0) cc_final: 0.7207 (tt0) REVERT: e 97 HIS cc_start: 0.5968 (OUTLIER) cc_final: 0.5550 (m-70) REVERT: h 136 SER cc_start: 0.8633 (m) cc_final: 0.8430 (p) REVERT: j 19 ARG cc_start: 0.7026 (mmm160) cc_final: 0.6584 (mmm160) REVERT: k 12 LYS cc_start: 0.5893 (OUTLIER) cc_final: 0.5372 (tmmt) REVERT: k 41 ARG cc_start: 0.7926 (mtp85) cc_final: 0.7659 (ttt-90) REVERT: l 114 PHE cc_start: 0.8642 (t80) cc_final: 0.8348 (t80) REVERT: m 36 LEU cc_start: 0.8843 (OUTLIER) cc_final: 0.8504 (tt) REVERT: p 23 THR cc_start: 0.8750 (OUTLIER) cc_final: 0.8515 (p) REVERT: s 33 PHE cc_start: 0.8025 (t80) cc_final: 0.7808 (t80) outliers start: 120 outliers final: 57 residues processed: 1025 average time/residue: 1.7487 time to fit residues: 2275.2040 Evaluate side-chains 1010 residues out of total 7148 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 936 time to evaluate : 5.992 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 SER Chi-restraints excluded: chain B residue 34 ASP Chi-restraints excluded: chain B residue 54 CYS Chi-restraints excluded: chain D residue 44 VAL Chi-restraints excluded: chain D residue 61 VAL Chi-restraints excluded: chain D residue 109 VAL Chi-restraints excluded: chain E residue 203 THR Chi-restraints excluded: chain F residue 105 CYS Chi-restraints excluded: chain F residue 431 GLN Chi-restraints excluded: chain G residue 16 GLN Chi-restraints excluded: chain G residue 84 GLU Chi-restraints excluded: chain G residue 536 ASP Chi-restraints excluded: chain G residue 588 THR Chi-restraints excluded: chain G residue 609 MET Chi-restraints excluded: chain H residue 103 LEU Chi-restraints excluded: chain H residue 289 LEU Chi-restraints excluded: chain J residue 113 VAL Chi-restraints excluded: chain J residue 138 GLU Chi-restraints excluded: chain K residue 46 LEU Chi-restraints excluded: chain L residue 140 LEU Chi-restraints excluded: chain L residue 235 SER Chi-restraints excluded: chain L residue 254 VAL Chi-restraints excluded: chain L residue 440 LEU Chi-restraints excluded: chain L residue 597 ILE Chi-restraints excluded: chain N residue 263 LYS Chi-restraints excluded: chain O residue 19 THR Chi-restraints excluded: chain O residue 196 SER Chi-restraints excluded: chain O residue 206 TYR Chi-restraints excluded: chain O residue 250 ASP Chi-restraints excluded: chain P residue 94 LEU Chi-restraints excluded: chain P residue 139 ILE Chi-restraints excluded: chain P residue 170 GLU Chi-restraints excluded: chain R residue 2 VAL Chi-restraints excluded: chain R residue 4 THR Chi-restraints excluded: chain S residue 59 ASP Chi-restraints excluded: chain S residue 63 LYS Chi-restraints excluded: chain S residue 91 GLU Chi-restraints excluded: chain T residue 31 SER Chi-restraints excluded: chain T residue 72 CYS Chi-restraints excluded: chain U residue 37 MET Chi-restraints excluded: chain V residue 6 LYS Chi-restraints excluded: chain X residue 3 ILE Chi-restraints excluded: chain X residue 11 ASP Chi-restraints excluded: chain X residue 130 VAL Chi-restraints excluded: chain X residue 154 GLU Chi-restraints excluded: chain Y residue 11 ILE Chi-restraints excluded: chain Y residue 105 ARG Chi-restraints excluded: chain Y residue 109 ILE Chi-restraints excluded: chain Y residue 114 CYS Chi-restraints excluded: chain Z residue 64 ASP Chi-restraints excluded: chain Z residue 106 VAL Chi-restraints excluded: chain Z residue 108 GLU Chi-restraints excluded: chain a residue 70 ASP Chi-restraints excluded: chain b residue 33 THR Chi-restraints excluded: chain c residue 6 GLU Chi-restraints excluded: chain e residue 17 MET Chi-restraints excluded: chain e residue 18 THR Chi-restraints excluded: chain e residue 48 SER Chi-restraints excluded: chain e residue 97 HIS Chi-restraints excluded: chain f residue 30 ASN Chi-restraints excluded: chain g residue 34 ASP Chi-restraints excluded: chain g residue 109 GLU Chi-restraints excluded: chain i residue 34 LEU Chi-restraints excluded: chain j residue 40 PHE Chi-restraints excluded: chain k residue 12 LYS Chi-restraints excluded: chain l residue 16 THR Chi-restraints excluded: chain l residue 154 VAL Chi-restraints excluded: chain m residue 11 SER Chi-restraints excluded: chain m residue 36 LEU Chi-restraints excluded: chain m residue 75 ILE Chi-restraints excluded: chain p residue 20 SER Chi-restraints excluded: chain p residue 23 THR Chi-restraints excluded: chain q residue 26 VAL Chi-restraints excluded: chain q residue 141 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 800 random chunks: chunk 746 optimal weight: 5.9990 chunk 87 optimal weight: 0.9980 chunk 441 optimal weight: 0.8980 chunk 565 optimal weight: 7.9990 chunk 437 optimal weight: 1.9990 chunk 651 optimal weight: 4.9990 chunk 432 optimal weight: 5.9990 chunk 771 optimal weight: 3.9990 chunk 482 optimal weight: 3.9990 chunk 470 optimal weight: 4.9990 chunk 355 optimal weight: 2.9990 overall best weight: 2.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 97 GLN L 135 ASN L 199 GLN ** L 479 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 139 GLN M 188 ASN P 296 HIS X 64 GLN Y 7 GLN Z 85 GLN b 10 ASN e 69 GLN g 119 GLN k 58 ASN n 140 GLN o 43 GLN o 53 GLN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8664 moved from start: 0.1279 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.244 69540 Z= 0.473 Angle : 1.298 50.472 94078 Z= 0.833 Chirality : 0.255 6.515 10280 Planarity : 0.004 0.053 11693 Dihedral : 11.846 172.744 11076 Min Nonbonded Distance : 1.985 Molprobity Statistics. All-atom Clashscore : 4.35 Ramachandran Plot: Outliers : 0.01 % Allowed : 1.89 % Favored : 98.10 % Rotamer: Outliers : 1.64 % Allowed : 13.29 % Favored : 85.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.66 % 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: 1.53 (0.09), residues: 8087 helix: 1.62 (0.08), residues: 4299 sheet: 0.11 (0.25), residues: 380 loop : 0.48 (0.11), residues: 3408 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP X 85 HIS 0.006 0.001 HIS G 101 PHE 0.027 0.001 PHE N 292 TYR 0.021 0.001 TYR k 85 ARG 0.006 0.000 ARG W 30 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16174 Ramachandran restraints generated. 8087 Oldfield, 0 Emsley, 8087 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16174 Ramachandran restraints generated. 8087 Oldfield, 0 Emsley, 8087 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1062 residues out of total 7148 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 117 poor density : 945 time to evaluate : 6.130 Fit side-chains revert: symmetry clash REVERT: A 31 SER cc_start: 0.8839 (OUTLIER) cc_final: 0.8543 (t) REVERT: F 77 LEU cc_start: 0.8820 (OUTLIER) cc_final: 0.8365 (tp) REVERT: G 16 GLN cc_start: 0.8301 (OUTLIER) cc_final: 0.7563 (tm-30) REVERT: G 536 ASP cc_start: 0.8455 (OUTLIER) cc_final: 0.8012 (m-30) REVERT: J 138 GLU cc_start: 0.8334 (OUTLIER) cc_final: 0.8045 (mt-10) REVERT: L 140 LEU cc_start: 0.9224 (OUTLIER) cc_final: 0.8914 (tt) REVERT: L 442 ASN cc_start: 0.8356 (t0) cc_final: 0.8135 (t0) REVERT: N 263 LYS cc_start: 0.8610 (OUTLIER) cc_final: 0.8248 (tmmm) REVERT: O 206 TYR cc_start: 0.8884 (OUTLIER) cc_final: 0.8408 (m-80) REVERT: T 11 ILE cc_start: 0.7628 (mt) cc_final: 0.7251 (mm) REVERT: T 14 ARG cc_start: 0.7674 (mmm-85) cc_final: 0.7408 (mtt180) REVERT: X 154 GLU cc_start: 0.7019 (OUTLIER) cc_final: 0.6119 (pp20) REVERT: Y 105 ARG cc_start: 0.6927 (OUTLIER) cc_final: 0.6148 (mpt90) REVERT: Z 64 ASP cc_start: 0.7948 (OUTLIER) cc_final: 0.7569 (t70) REVERT: Z 76 GLN cc_start: 0.8789 (tp40) cc_final: 0.8433 (tm-30) REVERT: c 6 GLU cc_start: 0.7498 (OUTLIER) cc_final: 0.7167 (tt0) REVERT: e 17 MET cc_start: 0.8545 (OUTLIER) cc_final: 0.8263 (ttm) REVERT: e 36 GLU cc_start: 0.7730 (tt0) cc_final: 0.7225 (tt0) REVERT: e 97 HIS cc_start: 0.5987 (OUTLIER) cc_final: 0.5573 (m-70) REVERT: h 136 SER cc_start: 0.8639 (m) cc_final: 0.8431 (p) REVERT: j 19 ARG cc_start: 0.7023 (mmm160) cc_final: 0.6617 (mmm160) REVERT: k 12 LYS cc_start: 0.5836 (OUTLIER) cc_final: 0.5289 (tmmt) REVERT: k 41 ARG cc_start: 0.7925 (mtp85) cc_final: 0.7639 (ttt-90) REVERT: k 85 TYR cc_start: 0.6974 (t80) cc_final: 0.6669 (t80) REVERT: l 114 PHE cc_start: 0.8631 (t80) cc_final: 0.8341 (t80) REVERT: m 36 LEU cc_start: 0.8857 (OUTLIER) cc_final: 0.8521 (tt) REVERT: p 23 THR cc_start: 0.8765 (OUTLIER) cc_final: 0.8533 (p) REVERT: s 33 PHE cc_start: 0.8018 (t80) cc_final: 0.7773 (t80) outliers start: 117 outliers final: 67 residues processed: 1020 average time/residue: 1.7486 time to fit residues: 2265.2645 Evaluate side-chains 1013 residues out of total 7148 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 84 poor density : 929 time to evaluate : 5.897 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 SER Chi-restraints excluded: chain B residue 34 ASP Chi-restraints excluded: chain B residue 54 CYS Chi-restraints excluded: chain D residue 44 VAL Chi-restraints excluded: chain D residue 61 VAL Chi-restraints excluded: chain D residue 109 VAL Chi-restraints excluded: chain E residue 203 THR Chi-restraints excluded: chain F residue 77 LEU Chi-restraints excluded: chain F residue 105 CYS Chi-restraints excluded: chain F residue 431 GLN Chi-restraints excluded: chain G residue 16 GLN Chi-restraints excluded: chain G residue 382 THR Chi-restraints excluded: chain G residue 536 ASP Chi-restraints excluded: chain G residue 588 THR Chi-restraints excluded: chain G residue 609 MET Chi-restraints excluded: chain G residue 659 ASP Chi-restraints excluded: chain H residue 103 LEU Chi-restraints excluded: chain H residue 289 LEU Chi-restraints excluded: chain I residue 37 THR Chi-restraints excluded: chain J residue 67 VAL Chi-restraints excluded: chain J residue 113 VAL Chi-restraints excluded: chain J residue 133 SER Chi-restraints excluded: chain J residue 138 GLU Chi-restraints excluded: chain K residue 46 LEU Chi-restraints excluded: chain L residue 140 LEU Chi-restraints excluded: chain L residue 235 SER Chi-restraints excluded: chain L residue 254 VAL Chi-restraints excluded: chain L residue 387 THR Chi-restraints excluded: chain L residue 440 LEU Chi-restraints excluded: chain L residue 540 MET Chi-restraints excluded: chain L residue 568 LEU Chi-restraints excluded: chain L residue 597 ILE Chi-restraints excluded: chain M residue 72 LEU Chi-restraints excluded: chain N residue 263 LYS Chi-restraints excluded: chain O residue 19 THR Chi-restraints excluded: chain O residue 196 SER Chi-restraints excluded: chain O residue 206 TYR Chi-restraints excluded: chain O residue 250 ASP Chi-restraints excluded: chain P residue 139 ILE Chi-restraints excluded: chain P residue 170 GLU Chi-restraints excluded: chain R residue 2 VAL Chi-restraints excluded: chain R residue 4 THR Chi-restraints excluded: chain S residue 63 LYS Chi-restraints excluded: chain S residue 91 GLU Chi-restraints excluded: chain T residue 31 SER Chi-restraints excluded: chain T residue 72 CYS Chi-restraints excluded: chain U residue 32 VAL Chi-restraints excluded: chain U residue 37 MET Chi-restraints excluded: chain V residue 6 LYS Chi-restraints excluded: chain X residue 3 ILE Chi-restraints excluded: chain X residue 11 ASP Chi-restraints excluded: chain X residue 130 VAL Chi-restraints excluded: chain X residue 154 GLU Chi-restraints excluded: chain Y residue 11 ILE Chi-restraints excluded: chain Y residue 105 ARG Chi-restraints excluded: chain Y residue 109 ILE Chi-restraints excluded: chain Y residue 114 CYS Chi-restraints excluded: chain Z residue 64 ASP Chi-restraints excluded: chain Z residue 106 VAL Chi-restraints excluded: chain a residue 70 ASP Chi-restraints excluded: chain b residue 33 THR Chi-restraints excluded: chain c residue 6 GLU Chi-restraints excluded: chain e residue 17 MET Chi-restraints excluded: chain e residue 18 THR Chi-restraints excluded: chain e residue 48 SER Chi-restraints excluded: chain e residue 97 HIS Chi-restraints excluded: chain f residue 30 ASN Chi-restraints excluded: chain g residue 34 ASP Chi-restraints excluded: chain g residue 109 GLU Chi-restraints excluded: chain i residue 34 LEU Chi-restraints excluded: chain i residue 110 LEU Chi-restraints excluded: chain j residue 40 PHE Chi-restraints excluded: chain k residue 12 LYS Chi-restraints excluded: chain l residue 16 THR Chi-restraints excluded: chain l residue 154 VAL Chi-restraints excluded: chain m residue 11 SER Chi-restraints excluded: chain m residue 36 LEU Chi-restraints excluded: chain m residue 75 ILE Chi-restraints excluded: chain m residue 91 LEU Chi-restraints excluded: chain n residue 84 SER Chi-restraints excluded: chain p residue 20 SER Chi-restraints excluded: chain p residue 23 THR Chi-restraints excluded: chain q residue 26 VAL Chi-restraints excluded: chain q residue 141 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 800 random chunks: chunk 477 optimal weight: 2.9990 chunk 307 optimal weight: 6.9990 chunk 460 optimal weight: 6.9990 chunk 232 optimal weight: 0.7980 chunk 151 optimal weight: 5.9990 chunk 149 optimal weight: 6.9990 chunk 490 optimal weight: 2.9990 chunk 525 optimal weight: 8.9990 chunk 381 optimal weight: 0.8980 chunk 71 optimal weight: 5.9990 chunk 606 optimal weight: 0.4980 overall best weight: 1.6384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 475 GLN K 97 GLN ** L 479 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 139 GLN M 188 ASN P 296 HIS S 85 GLN Y 7 GLN Z 85 GLN b 10 ASN e 69 GLN g 119 GLN k 32 GLN k 58 ASN l 99 ASN n 140 GLN o 43 GLN o 53 GLN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8651 moved from start: 0.1392 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.245 69540 Z= 0.457 Angle : 1.290 50.504 94078 Z= 0.830 Chirality : 0.254 6.477 10280 Planarity : 0.004 0.054 11693 Dihedral : 11.515 172.350 11073 Min Nonbonded Distance : 1.999 Molprobity Statistics. All-atom Clashscore : 4.30 Ramachandran Plot: Outliers : 0.01 % Allowed : 1.66 % Favored : 98.33 % Rotamer: Outliers : 1.57 % Allowed : 13.52 % Favored : 84.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.66 % 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: 1.61 (0.09), residues: 8087 helix: 1.69 (0.08), residues: 4300 sheet: 0.13 (0.25), residues: 380 loop : 0.52 (0.11), residues: 3407 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP X 85 HIS 0.006 0.001 HIS G 101 PHE 0.030 0.001 PHE c 26 TYR 0.021 0.001 TYR k 85 ARG 0.007 0.000 ARG W 30 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16174 Ramachandran restraints generated. 8087 Oldfield, 0 Emsley, 8087 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16174 Ramachandran restraints generated. 8087 Oldfield, 0 Emsley, 8087 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1062 residues out of total 7148 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 112 poor density : 950 time to evaluate : 6.106 Fit side-chains revert: symmetry clash REVERT: A 31 SER cc_start: 0.8841 (OUTLIER) cc_final: 0.8544 (t) REVERT: F 77 LEU cc_start: 0.8786 (OUTLIER) cc_final: 0.8333 (tp) REVERT: G 16 GLN cc_start: 0.8294 (OUTLIER) cc_final: 0.7561 (tm-30) REVERT: G 536 ASP cc_start: 0.8440 (OUTLIER) cc_final: 0.8006 (m-30) REVERT: J 138 GLU cc_start: 0.8326 (OUTLIER) cc_final: 0.8037 (mt-10) REVERT: L 140 LEU cc_start: 0.9215 (OUTLIER) cc_final: 0.8901 (tt) REVERT: L 442 ASN cc_start: 0.8351 (t0) cc_final: 0.8131 (t0) REVERT: L 544 MET cc_start: 0.7852 (tmm) cc_final: 0.7637 (tmm) REVERT: N 263 LYS cc_start: 0.8588 (OUTLIER) cc_final: 0.8219 (tmmm) REVERT: O 206 TYR cc_start: 0.8869 (OUTLIER) cc_final: 0.8480 (m-80) REVERT: P 254 LEU cc_start: 0.8703 (OUTLIER) cc_final: 0.8503 (mm) REVERT: T 11 ILE cc_start: 0.7643 (mt) cc_final: 0.7268 (mm) REVERT: T 14 ARG cc_start: 0.7677 (mmm-85) cc_final: 0.7406 (mtt180) REVERT: X 154 GLU cc_start: 0.7008 (OUTLIER) cc_final: 0.6105 (pp20) REVERT: Y 105 ARG cc_start: 0.6904 (OUTLIER) cc_final: 0.6142 (mpt90) REVERT: Z 64 ASP cc_start: 0.7908 (OUTLIER) cc_final: 0.7528 (t70) REVERT: Z 76 GLN cc_start: 0.8776 (tp40) cc_final: 0.8424 (tm-30) REVERT: c 6 GLU cc_start: 0.7488 (OUTLIER) cc_final: 0.7165 (tt0) REVERT: e 17 MET cc_start: 0.8554 (OUTLIER) cc_final: 0.8265 (ttm) REVERT: e 36 GLU cc_start: 0.7704 (tt0) cc_final: 0.7237 (tt0) REVERT: e 97 HIS cc_start: 0.5934 (OUTLIER) cc_final: 0.5468 (m-70) REVERT: j 19 ARG cc_start: 0.7019 (mmm160) cc_final: 0.6608 (mmm160) REVERT: k 12 LYS cc_start: 0.5860 (OUTLIER) cc_final: 0.5322 (tmmt) REVERT: l 114 PHE cc_start: 0.8624 (t80) cc_final: 0.8330 (t80) REVERT: m 36 LEU cc_start: 0.8838 (OUTLIER) cc_final: 0.8497 (tt) REVERT: m 113 LYS cc_start: 0.8417 (ttmt) cc_final: 0.8191 (ttmt) REVERT: p 23 THR cc_start: 0.8753 (OUTLIER) cc_final: 0.8525 (p) REVERT: s 33 PHE cc_start: 0.8021 (t80) cc_final: 0.7798 (t80) outliers start: 112 outliers final: 62 residues processed: 1020 average time/residue: 1.8439 time to fit residues: 2434.0232 Evaluate side-chains 1009 residues out of total 7148 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 80 poor density : 929 time to evaluate : 6.094 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 SER Chi-restraints excluded: chain B residue 34 ASP Chi-restraints excluded: chain B residue 54 CYS Chi-restraints excluded: chain D residue 44 VAL Chi-restraints excluded: chain D residue 61 VAL Chi-restraints excluded: chain D residue 109 VAL Chi-restraints excluded: chain E residue 203 THR Chi-restraints excluded: chain F residue 77 LEU Chi-restraints excluded: chain F residue 431 GLN Chi-restraints excluded: chain G residue 16 GLN Chi-restraints excluded: chain G residue 84 GLU Chi-restraints excluded: chain G residue 382 THR Chi-restraints excluded: chain G residue 536 ASP Chi-restraints excluded: chain G residue 588 THR Chi-restraints excluded: chain G residue 609 MET Chi-restraints excluded: chain G residue 659 ASP Chi-restraints excluded: chain H residue 103 LEU Chi-restraints excluded: chain H residue 289 LEU Chi-restraints excluded: chain J residue 67 VAL Chi-restraints excluded: chain J residue 113 VAL Chi-restraints excluded: chain J residue 138 GLU Chi-restraints excluded: chain K residue 46 LEU Chi-restraints excluded: chain L residue 140 LEU Chi-restraints excluded: chain L residue 235 SER Chi-restraints excluded: chain L residue 254 VAL Chi-restraints excluded: chain L residue 387 THR Chi-restraints excluded: chain L residue 440 LEU Chi-restraints excluded: chain L residue 597 ILE Chi-restraints excluded: chain M residue 437 MET Chi-restraints excluded: chain N residue 263 LYS Chi-restraints excluded: chain O residue 19 THR Chi-restraints excluded: chain O residue 196 SER Chi-restraints excluded: chain O residue 206 TYR Chi-restraints excluded: chain O residue 250 ASP Chi-restraints excluded: chain P residue 139 ILE Chi-restraints excluded: chain P residue 170 GLU Chi-restraints excluded: chain P residue 254 LEU Chi-restraints excluded: chain R residue 2 VAL Chi-restraints excluded: chain R residue 4 THR Chi-restraints excluded: chain S residue 59 ASP Chi-restraints excluded: chain S residue 63 LYS Chi-restraints excluded: chain S residue 91 GLU Chi-restraints excluded: chain T residue 31 SER Chi-restraints excluded: chain T residue 72 CYS Chi-restraints excluded: chain U residue 32 VAL Chi-restraints excluded: chain U residue 37 MET Chi-restraints excluded: chain V residue 6 LYS Chi-restraints excluded: chain X residue 3 ILE Chi-restraints excluded: chain X residue 11 ASP Chi-restraints excluded: chain X residue 130 VAL Chi-restraints excluded: chain X residue 154 GLU Chi-restraints excluded: chain Y residue 11 ILE Chi-restraints excluded: chain Y residue 105 ARG Chi-restraints excluded: chain Y residue 109 ILE Chi-restraints excluded: chain Y residue 114 CYS Chi-restraints excluded: chain Z residue 64 ASP Chi-restraints excluded: chain Z residue 106 VAL Chi-restraints excluded: chain b residue 33 THR Chi-restraints excluded: chain c residue 6 GLU Chi-restraints excluded: chain e residue 17 MET Chi-restraints excluded: chain e residue 18 THR Chi-restraints excluded: chain e residue 48 SER Chi-restraints excluded: chain e residue 97 HIS Chi-restraints excluded: chain f residue 30 ASN Chi-restraints excluded: chain g residue 34 ASP Chi-restraints excluded: chain g residue 109 GLU Chi-restraints excluded: chain i residue 34 LEU Chi-restraints excluded: chain j residue 40 PHE Chi-restraints excluded: chain k residue 12 LYS Chi-restraints excluded: chain l residue 16 THR Chi-restraints excluded: chain l residue 154 VAL Chi-restraints excluded: chain m residue 11 SER Chi-restraints excluded: chain m residue 36 LEU Chi-restraints excluded: chain m residue 75 ILE Chi-restraints excluded: chain m residue 91 LEU Chi-restraints excluded: chain n residue 84 SER Chi-restraints excluded: chain p residue 20 SER Chi-restraints excluded: chain p residue 23 THR Chi-restraints excluded: chain q residue 26 VAL Chi-restraints excluded: chain q residue 141 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 800 random chunks: chunk 701 optimal weight: 5.9990 chunk 738 optimal weight: 6.9990 chunk 673 optimal weight: 1.9990 chunk 718 optimal weight: 1.9990 chunk 432 optimal weight: 3.9990 chunk 313 optimal weight: 4.9990 chunk 564 optimal weight: 2.9990 chunk 220 optimal weight: 4.9990 chunk 649 optimal weight: 9.9990 chunk 679 optimal weight: 0.9980 chunk 716 optimal weight: 1.9990 overall best weight: 1.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 432 GLN K 97 GLN ** L 479 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 139 GLN M 188 ASN P 296 HIS X 64 GLN Y 7 GLN Z 85 GLN b 10 ASN e 69 GLN g 119 GLN k 58 ASN l 99 ASN n 140 GLN o 43 GLN o 53 GLN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8658 moved from start: 0.1363 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.244 69540 Z= 0.467 Angle : 1.296 50.486 94078 Z= 0.833 Chirality : 0.255 6.505 10280 Planarity : 0.004 0.053 11693 Dihedral : 11.444 172.550 11073 Min Nonbonded Distance : 1.980 Molprobity Statistics. All-atom Clashscore : 4.31 Ramachandran Plot: Outliers : 0.02 % Allowed : 1.83 % Favored : 98.15 % Rotamer: Outliers : 1.46 % Allowed : 13.77 % Favored : 84.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.66 % 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: 1.60 (0.09), residues: 8087 helix: 1.67 (0.08), residues: 4302 sheet: 0.14 (0.25), residues: 380 loop : 0.53 (0.11), residues: 3405 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP X 85 HIS 0.006 0.001 HIS G 101 PHE 0.027 0.001 PHE N 292 TYR 0.024 0.001 TYR k 85 ARG 0.008 0.000 ARG W 30 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16174 Ramachandran restraints generated. 8087 Oldfield, 0 Emsley, 8087 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16174 Ramachandran restraints generated. 8087 Oldfield, 0 Emsley, 8087 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1046 residues out of total 7148 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 104 poor density : 942 time to evaluate : 6.177 Fit side-chains revert: symmetry clash REVERT: A 31 SER cc_start: 0.8837 (OUTLIER) cc_final: 0.8543 (t) REVERT: F 77 LEU cc_start: 0.8810 (OUTLIER) cc_final: 0.8352 (tp) REVERT: G 16 GLN cc_start: 0.8303 (OUTLIER) cc_final: 0.7565 (tm-30) REVERT: G 536 ASP cc_start: 0.8448 (OUTLIER) cc_final: 0.8011 (m-30) REVERT: J 138 GLU cc_start: 0.8329 (OUTLIER) cc_final: 0.8040 (mt-10) REVERT: L 140 LEU cc_start: 0.9223 (OUTLIER) cc_final: 0.8906 (tt) REVERT: L 442 ASN cc_start: 0.8355 (t0) cc_final: 0.8136 (t0) REVERT: L 544 MET cc_start: 0.7862 (tmm) cc_final: 0.7642 (tmm) REVERT: N 263 LYS cc_start: 0.8609 (OUTLIER) cc_final: 0.8250 (tmmm) REVERT: O 182 ARG cc_start: 0.8526 (OUTLIER) cc_final: 0.8276 (mtt180) REVERT: O 206 TYR cc_start: 0.8877 (OUTLIER) cc_final: 0.8497 (m-80) REVERT: T 11 ILE cc_start: 0.7639 (mt) cc_final: 0.7258 (mm) REVERT: X 154 GLU cc_start: 0.6998 (OUTLIER) cc_final: 0.6079 (pp20) REVERT: Y 105 ARG cc_start: 0.6904 (OUTLIER) cc_final: 0.6138 (mpt90) REVERT: Z 64 ASP cc_start: 0.7940 (OUTLIER) cc_final: 0.7562 (t70) REVERT: Z 76 GLN cc_start: 0.8789 (tp40) cc_final: 0.8438 (tm-30) REVERT: c 6 GLU cc_start: 0.7489 (OUTLIER) cc_final: 0.7160 (tt0) REVERT: c 34 GLN cc_start: 0.8509 (OUTLIER) cc_final: 0.7727 (tp40) REVERT: c 41 GLU cc_start: 0.8844 (tp30) cc_final: 0.8624 (tp30) REVERT: e 17 MET cc_start: 0.8556 (OUTLIER) cc_final: 0.8276 (ttm) REVERT: e 36 GLU cc_start: 0.7725 (tt0) cc_final: 0.7274 (tt0) REVERT: e 97 HIS cc_start: 0.5937 (OUTLIER) cc_final: 0.5436 (m-70) REVERT: j 19 ARG cc_start: 0.7005 (mmm160) cc_final: 0.6594 (mmm160) REVERT: k 12 LYS cc_start: 0.5842 (OUTLIER) cc_final: 0.5291 (tmmt) REVERT: k 41 ARG cc_start: 0.7924 (mtp85) cc_final: 0.7650 (ttt-90) REVERT: l 100 LEU cc_start: 0.9049 (tp) cc_final: 0.8835 (tt) REVERT: l 114 PHE cc_start: 0.8628 (t80) cc_final: 0.8340 (t80) REVERT: m 36 LEU cc_start: 0.8844 (OUTLIER) cc_final: 0.8507 (tt) REVERT: m 113 LYS cc_start: 0.8421 (ttmt) cc_final: 0.8192 (ttmt) REVERT: p 23 THR cc_start: 0.8760 (OUTLIER) cc_final: 0.8536 (p) REVERT: s 33 PHE cc_start: 0.8019 (t80) cc_final: 0.7806 (t80) outliers start: 104 outliers final: 68 residues processed: 1009 average time/residue: 1.7526 time to fit residues: 2247.0167 Evaluate side-chains 1016 residues out of total 7148 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 87 poor density : 929 time to evaluate : 5.927 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 SER Chi-restraints excluded: chain B residue 34 ASP Chi-restraints excluded: chain B residue 54 CYS Chi-restraints excluded: chain D residue 44 VAL Chi-restraints excluded: chain D residue 61 VAL Chi-restraints excluded: chain D residue 109 VAL Chi-restraints excluded: chain E residue 40 GLU Chi-restraints excluded: chain E residue 203 THR Chi-restraints excluded: chain F residue 77 LEU Chi-restraints excluded: chain F residue 105 CYS Chi-restraints excluded: chain G residue 16 GLN Chi-restraints excluded: chain G residue 84 GLU Chi-restraints excluded: chain G residue 382 THR Chi-restraints excluded: chain G residue 536 ASP Chi-restraints excluded: chain G residue 588 THR Chi-restraints excluded: chain G residue 609 MET Chi-restraints excluded: chain G residue 659 ASP Chi-restraints excluded: chain H residue 103 LEU Chi-restraints excluded: chain H residue 289 LEU Chi-restraints excluded: chain I residue 37 THR Chi-restraints excluded: chain J residue 67 VAL Chi-restraints excluded: chain J residue 113 VAL Chi-restraints excluded: chain J residue 133 SER Chi-restraints excluded: chain J residue 138 GLU Chi-restraints excluded: chain K residue 46 LEU Chi-restraints excluded: chain L residue 140 LEU Chi-restraints excluded: chain L residue 235 SER Chi-restraints excluded: chain L residue 254 VAL Chi-restraints excluded: chain L residue 387 THR Chi-restraints excluded: chain L residue 440 LEU Chi-restraints excluded: chain L residue 540 MET Chi-restraints excluded: chain L residue 597 ILE Chi-restraints excluded: chain M residue 72 LEU Chi-restraints excluded: chain M residue 437 MET Chi-restraints excluded: chain N residue 263 LYS Chi-restraints excluded: chain O residue 19 THR Chi-restraints excluded: chain O residue 182 ARG Chi-restraints excluded: chain O residue 196 SER Chi-restraints excluded: chain O residue 206 TYR Chi-restraints excluded: chain O residue 250 ASP Chi-restraints excluded: chain P residue 139 ILE Chi-restraints excluded: chain P residue 170 GLU Chi-restraints excluded: chain R residue 2 VAL Chi-restraints excluded: chain R residue 4 THR Chi-restraints excluded: chain S residue 59 ASP Chi-restraints excluded: chain S residue 63 LYS Chi-restraints excluded: chain S residue 91 GLU Chi-restraints excluded: chain T residue 19 LEU Chi-restraints excluded: chain T residue 31 SER Chi-restraints excluded: chain T residue 72 CYS Chi-restraints excluded: chain U residue 32 VAL Chi-restraints excluded: chain U residue 37 MET Chi-restraints excluded: chain V residue 6 LYS Chi-restraints excluded: chain X residue 3 ILE Chi-restraints excluded: chain X residue 11 ASP Chi-restraints excluded: chain X residue 130 VAL Chi-restraints excluded: chain X residue 154 GLU Chi-restraints excluded: chain Y residue 11 ILE Chi-restraints excluded: chain Y residue 105 ARG Chi-restraints excluded: chain Y residue 109 ILE Chi-restraints excluded: chain Y residue 114 CYS Chi-restraints excluded: chain Z residue 64 ASP Chi-restraints excluded: chain Z residue 106 VAL Chi-restraints excluded: chain b residue 33 THR Chi-restraints excluded: chain c residue 6 GLU Chi-restraints excluded: chain c residue 34 GLN Chi-restraints excluded: chain e residue 17 MET Chi-restraints excluded: chain e residue 18 THR Chi-restraints excluded: chain e residue 48 SER Chi-restraints excluded: chain e residue 97 HIS Chi-restraints excluded: chain g residue 34 ASP Chi-restraints excluded: chain g residue 109 GLU Chi-restraints excluded: chain i residue 34 LEU Chi-restraints excluded: chain i residue 67 SER Chi-restraints excluded: chain j residue 40 PHE Chi-restraints excluded: chain k residue 12 LYS Chi-restraints excluded: chain l residue 16 THR Chi-restraints excluded: chain l residue 154 VAL Chi-restraints excluded: chain m residue 11 SER Chi-restraints excluded: chain m residue 36 LEU Chi-restraints excluded: chain m residue 75 ILE Chi-restraints excluded: chain m residue 91 LEU Chi-restraints excluded: chain n residue 84 SER Chi-restraints excluded: chain p residue 20 SER Chi-restraints excluded: chain p residue 23 THR Chi-restraints excluded: chain q residue 26 VAL Chi-restraints excluded: chain q residue 141 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 800 random chunks: chunk 471 optimal weight: 1.9990 chunk 759 optimal weight: 5.9990 chunk 463 optimal weight: 4.9990 chunk 360 optimal weight: 7.9990 chunk 528 optimal weight: 1.9990 chunk 797 optimal weight: 9.9990 chunk 733 optimal weight: 8.9990 chunk 634 optimal weight: 1.9990 chunk 65 optimal weight: 1.9990 chunk 490 optimal weight: 4.9990 chunk 389 optimal weight: 3.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 432 GLN G 475 GLN K 97 GLN ** L 479 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 139 GLN M 188 ASN P 296 HIS Y 7 GLN Z 85 GLN b 10 ASN e 69 GLN g 36 ASN g 119 GLN k 58 ASN l 99 ASN n 140 GLN o 43 GLN o 53 GLN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8665 moved from start: 0.1330 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.245 69540 Z= 0.479 Angle : 1.302 50.469 94078 Z= 0.835 Chirality : 0.256 6.524 10280 Planarity : 0.004 0.053 11693 Dihedral : 11.467 173.227 11073 Min Nonbonded Distance : 1.968 Molprobity Statistics. All-atom Clashscore : 4.32 Ramachandran Plot: Outliers : 0.02 % Allowed : 1.85 % Favored : 98.12 % Rotamer: Outliers : 1.39 % Allowed : 13.92 % Favored : 84.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.66 % 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: 1.54 (0.09), residues: 8087 helix: 1.62 (0.08), residues: 4313 sheet: 0.13 (0.25), residues: 378 loop : 0.51 (0.11), residues: 3396 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP X 85 HIS 0.006 0.001 HIS G 101 PHE 0.032 0.002 PHE c 26 TYR 0.024 0.002 TYR k 85 ARG 0.008 0.000 ARG T 14 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16174 Ramachandran restraints generated. 8087 Oldfield, 0 Emsley, 8087 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16174 Ramachandran restraints generated. 8087 Oldfield, 0 Emsley, 8087 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1036 residues out of total 7148 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 99 poor density : 937 time to evaluate : 6.196 Fit side-chains revert: symmetry clash REVERT: A 31 SER cc_start: 0.8846 (OUTLIER) cc_final: 0.8551 (t) REVERT: A 85 ASN cc_start: 0.7931 (OUTLIER) cc_final: 0.7622 (m-40) REVERT: F 77 LEU cc_start: 0.8828 (OUTLIER) cc_final: 0.8369 (tp) REVERT: G 16 GLN cc_start: 0.8305 (OUTLIER) cc_final: 0.7571 (tm-30) REVERT: G 536 ASP cc_start: 0.8448 (OUTLIER) cc_final: 0.7999 (m-30) REVERT: J 138 GLU cc_start: 0.8339 (OUTLIER) cc_final: 0.8048 (mt-10) REVERT: L 140 LEU cc_start: 0.9225 (OUTLIER) cc_final: 0.8909 (tt) REVERT: L 442 ASN cc_start: 0.8381 (t0) cc_final: 0.8161 (t0) REVERT: L 544 MET cc_start: 0.7850 (tmm) cc_final: 0.7630 (tmm) REVERT: O 182 ARG cc_start: 0.8540 (OUTLIER) cc_final: 0.8280 (mtt180) REVERT: O 206 TYR cc_start: 0.8886 (OUTLIER) cc_final: 0.8413 (m-80) REVERT: T 11 ILE cc_start: 0.7634 (mt) cc_final: 0.7253 (mm) REVERT: X 154 GLU cc_start: 0.7003 (OUTLIER) cc_final: 0.6078 (pp20) REVERT: Y 105 ARG cc_start: 0.6909 (OUTLIER) cc_final: 0.6128 (mpt90) REVERT: Z 64 ASP cc_start: 0.7958 (OUTLIER) cc_final: 0.7578 (t70) REVERT: Z 76 GLN cc_start: 0.8796 (tp40) cc_final: 0.8435 (tm-30) REVERT: c 6 GLU cc_start: 0.7495 (OUTLIER) cc_final: 0.7167 (tt0) REVERT: c 34 GLN cc_start: 0.8525 (OUTLIER) cc_final: 0.7739 (tp40) REVERT: e 17 MET cc_start: 0.8561 (OUTLIER) cc_final: 0.8289 (ttm) REVERT: e 36 GLU cc_start: 0.7736 (tt0) cc_final: 0.7265 (tt0) REVERT: e 97 HIS cc_start: 0.5961 (OUTLIER) cc_final: 0.5433 (m-70) REVERT: j 19 ARG cc_start: 0.7013 (mmm160) cc_final: 0.6605 (mmm160) REVERT: k 12 LYS cc_start: 0.5822 (OUTLIER) cc_final: 0.5253 (tmmt) REVERT: k 41 ARG cc_start: 0.7936 (mtp85) cc_final: 0.7645 (ttt-90) REVERT: l 114 PHE cc_start: 0.8636 (t80) cc_final: 0.8355 (t80) REVERT: l 115 MET cc_start: 0.8480 (mmm) cc_final: 0.8227 (mmm) REVERT: m 36 LEU cc_start: 0.8854 (OUTLIER) cc_final: 0.8520 (tt) REVERT: p 23 THR cc_start: 0.8760 (OUTLIER) cc_final: 0.8535 (p) REVERT: s 33 PHE cc_start: 0.8018 (t80) cc_final: 0.7803 (t80) outliers start: 99 outliers final: 68 residues processed: 999 average time/residue: 1.7431 time to fit residues: 2211.8574 Evaluate side-chains 1014 residues out of total 7148 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 87 poor density : 927 time to evaluate : 6.050 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 SER Chi-restraints excluded: chain A residue 85 ASN Chi-restraints excluded: chain B residue 34 ASP Chi-restraints excluded: chain B residue 54 CYS Chi-restraints excluded: chain D residue 44 VAL Chi-restraints excluded: chain D residue 61 VAL Chi-restraints excluded: chain D residue 109 VAL Chi-restraints excluded: chain E residue 40 GLU Chi-restraints excluded: chain E residue 203 THR Chi-restraints excluded: chain F residue 77 LEU Chi-restraints excluded: chain F residue 105 CYS Chi-restraints excluded: chain G residue 16 GLN Chi-restraints excluded: chain G residue 84 GLU Chi-restraints excluded: chain G residue 382 THR Chi-restraints excluded: chain G residue 536 ASP Chi-restraints excluded: chain G residue 609 MET Chi-restraints excluded: chain G residue 659 ASP Chi-restraints excluded: chain H residue 103 LEU Chi-restraints excluded: chain H residue 289 LEU Chi-restraints excluded: chain I residue 37 THR Chi-restraints excluded: chain J residue 67 VAL Chi-restraints excluded: chain J residue 113 VAL Chi-restraints excluded: chain J residue 133 SER Chi-restraints excluded: chain J residue 138 GLU Chi-restraints excluded: chain K residue 46 LEU Chi-restraints excluded: chain L residue 140 LEU Chi-restraints excluded: chain L residue 235 SER Chi-restraints excluded: chain L residue 254 VAL Chi-restraints excluded: chain L residue 387 THR Chi-restraints excluded: chain L residue 440 LEU Chi-restraints excluded: chain L residue 540 MET Chi-restraints excluded: chain L residue 568 LEU Chi-restraints excluded: chain L residue 597 ILE Chi-restraints excluded: chain M residue 72 LEU Chi-restraints excluded: chain M residue 365 THR Chi-restraints excluded: chain M residue 437 MET Chi-restraints excluded: chain N residue 223 SER Chi-restraints excluded: chain O residue 19 THR Chi-restraints excluded: chain O residue 182 ARG Chi-restraints excluded: chain O residue 196 SER Chi-restraints excluded: chain O residue 206 TYR Chi-restraints excluded: chain O residue 250 ASP Chi-restraints excluded: chain P residue 139 ILE Chi-restraints excluded: chain P residue 170 GLU Chi-restraints excluded: chain R residue 2 VAL Chi-restraints excluded: chain R residue 4 THR Chi-restraints excluded: chain S residue 59 ASP Chi-restraints excluded: chain S residue 63 LYS Chi-restraints excluded: chain S residue 91 GLU Chi-restraints excluded: chain T residue 31 SER Chi-restraints excluded: chain T residue 72 CYS Chi-restraints excluded: chain U residue 32 VAL Chi-restraints excluded: chain U residue 37 MET Chi-restraints excluded: chain V residue 6 LYS Chi-restraints excluded: chain X residue 3 ILE Chi-restraints excluded: chain X residue 11 ASP Chi-restraints excluded: chain X residue 130 VAL Chi-restraints excluded: chain X residue 154 GLU Chi-restraints excluded: chain Y residue 11 ILE Chi-restraints excluded: chain Y residue 105 ARG Chi-restraints excluded: chain Y residue 109 ILE Chi-restraints excluded: chain Y residue 114 CYS Chi-restraints excluded: chain Z residue 64 ASP Chi-restraints excluded: chain Z residue 106 VAL Chi-restraints excluded: chain b residue 33 THR Chi-restraints excluded: chain c residue 6 GLU Chi-restraints excluded: chain c residue 34 GLN Chi-restraints excluded: chain e residue 17 MET Chi-restraints excluded: chain e residue 18 THR Chi-restraints excluded: chain e residue 48 SER Chi-restraints excluded: chain e residue 97 HIS Chi-restraints excluded: chain g residue 109 GLU Chi-restraints excluded: chain i residue 34 LEU Chi-restraints excluded: chain i residue 67 SER Chi-restraints excluded: chain j residue 40 PHE Chi-restraints excluded: chain k residue 12 LYS Chi-restraints excluded: chain l residue 16 THR Chi-restraints excluded: chain l residue 154 VAL Chi-restraints excluded: chain m residue 11 SER Chi-restraints excluded: chain m residue 36 LEU Chi-restraints excluded: chain m residue 75 ILE Chi-restraints excluded: chain m residue 91 LEU Chi-restraints excluded: chain n residue 84 SER Chi-restraints excluded: chain p residue 20 SER Chi-restraints excluded: chain p residue 23 THR Chi-restraints excluded: chain q residue 26 VAL Chi-restraints excluded: chain q residue 141 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 800 random chunks: chunk 504 optimal weight: 2.9990 chunk 676 optimal weight: 0.0370 chunk 194 optimal weight: 7.9990 chunk 585 optimal weight: 10.0000 chunk 93 optimal weight: 1.9990 chunk 176 optimal weight: 4.9990 chunk 635 optimal weight: 7.9990 chunk 266 optimal weight: 4.9990 chunk 652 optimal weight: 2.9990 chunk 80 optimal weight: 0.9980 chunk 117 optimal weight: 0.6980 overall best weight: 1.3462 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 432 GLN K 97 GLN ** L 479 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 139 GLN M 188 ASN P 296 HIS W 70 ASN X 64 GLN Y 7 GLN Z 85 GLN b 10 ASN e 69 GLN g 119 GLN k 58 ASN l 99 ASN n 140 GLN o 43 GLN o 53 GLN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.094943 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3019 r_free = 0.3019 target = 0.077787 restraints weight = 70963.696| |-----------------------------------------------------------------------------| r_work (start): 0.3015 rms_B_bonded: 1.09 r_work: 0.2928 rms_B_bonded: 1.51 restraints_weight: 0.5000 r_work: 0.2836 rms_B_bonded: 2.51 restraints_weight: 0.2500 r_work (final): 0.2836 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8883 moved from start: 0.1482 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.246 69540 Z= 0.452 Angle : 1.288 50.490 94078 Z= 0.830 Chirality : 0.254 6.503 10280 Planarity : 0.004 0.054 11693 Dihedral : 11.176 172.074 11073 Min Nonbonded Distance : 2.011 Molprobity Statistics. All-atom Clashscore : 4.67 Ramachandran Plot: Outliers : 0.02 % Allowed : 1.77 % Favored : 98.21 % Rotamer: Outliers : 1.27 % Allowed : 14.16 % Favored : 84.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.66 % 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: 1.68 (0.09), residues: 8087 helix: 1.74 (0.08), residues: 4294 sheet: 0.08 (0.25), residues: 391 loop : 0.58 (0.11), residues: 3402 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP X 85 HIS 0.006 0.001 HIS G 101 PHE 0.027 0.001 PHE N 292 TYR 0.024 0.001 TYR k 85 ARG 0.011 0.000 ARG W 30 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 31510.56 seconds wall clock time: 546 minutes 14.82 seconds (32774.82 seconds total)