Starting phenix.real_space_refine on Fri Mar 15 14:16:33 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7r48_14287/03_2024/7r48_14287_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7r48_14287/03_2024/7r48_14287.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7r48_14287/03_2024/7r48_14287_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/7r48_14287/03_2024/7r48_14287_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7r48_14287/03_2024/7r48_14287_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7r48_14287/03_2024/7r48_14287.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7r48_14287/03_2024/7r48_14287.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7r48_14287/03_2024/7r48_14287_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7r48_14287/03_2024/7r48_14287_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= 0.010 sd= 1.076 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 2 10.91 5 K 1 8.98 5 Fe 28 7.16 5 Zn 1 6.06 5 P 36 5.49 5 Mg 1 5.21 5 S 466 5.16 5 Cl 2 4.86 5 C 43412 2.51 5 N 11066 2.21 5 O 14232 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 11": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 32": "OE1" <-> "OE2" Residue "A PHE 93": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 115": "OE1" <-> "OE2" Residue "B ASP 34": "OD1" <-> "OD2" Residue "B ASP 35": "OD1" <-> "OD2" Residue "B ARG 71": "NH1" <-> "NH2" Residue "B PHE 72": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 109": "OE1" <-> "OE2" Residue "B ARG 111": "NH1" <-> "NH2" Residue "B TYR 112": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 126": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 154": "OE1" <-> "OE2" Residue "B GLU 170": "OE1" <-> "OE2" Residue "C ARG 8": "NH1" <-> "NH2" Residue "C ARG 12": "NH1" <-> "NH2" Residue "C GLU 27": "OE1" <-> "OE2" Residue "C GLU 31": "OE1" <-> "OE2" Residue "C ARG 149": "NH1" <-> "NH2" Residue "C PHE 157": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 158": "OE1" <-> "OE2" Residue "C GLU 173": "OE1" <-> "OE2" Residue "C GLU 179": "OE1" <-> "OE2" Residue "C GLU 186": "OE1" <-> "OE2" Residue "D ARG 2": "NH1" <-> "NH2" Residue "D ASP 7": "OD1" <-> "OD2" Residue "D TYR 20": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 67": "OE1" <-> "OE2" Residue "D GLU 71": "OE1" <-> "OE2" Residue "D GLU 123": "OE1" <-> "OE2" Residue "D PHE 167": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 179": "OE1" <-> "OE2" Residue "D ARG 221": "NH1" <-> "NH2" Residue "D GLU 226": "OE1" <-> "OE2" Residue "D ARG 233": "NH1" <-> "NH2" Residue "D GLU 248": "OE1" <-> "OE2" Residue "D GLU 282": "OE1" <-> "OE2" Residue "D GLU 303": "OE1" <-> "OE2" Residue "D GLU 343": "OE1" <-> "OE2" Residue "D GLU 427": "OE1" <-> "OE2" Residue "E GLU 14": "OE1" <-> "OE2" Residue "E GLU 18": "OE1" <-> "OE2" Residue "E GLU 32": "OE1" <-> "OE2" Residue "E GLU 118": "OE1" <-> "OE2" Residue "E ASP 134": "OD1" <-> "OD2" Residue "E ASP 158": "OD1" <-> "OD2" Residue "E GLU 162": "OE1" <-> "OE2" Residue "E ASP 168": "OD1" <-> "OD2" Residue "E GLU 175": "OE1" <-> "OE2" Residue "E ARG 190": "NH1" <-> "NH2" Residue "E GLU 204": "OE1" <-> "OE2" Residue "F ARG 32": "NH1" <-> "NH2" Residue "F GLU 99": "OE1" <-> "OE2" Residue "F GLU 109": "OE1" <-> "OE2" Residue "F ARG 112": "NH1" <-> "NH2" Residue "F ARG 132": "NH1" <-> "NH2" Residue "F TYR 135": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 139": "NH1" <-> "NH2" Residue "F GLU 155": "OE1" <-> "OE2" Residue "F GLU 189": "OE1" <-> "OE2" Residue "F GLU 194": "OE1" <-> "OE2" Residue "F GLU 226": "OE1" <-> "OE2" Residue "F GLU 248": "OE1" <-> "OE2" Residue "F ARG 249": "NH1" <-> "NH2" Residue "F GLU 269": "OE1" <-> "OE2" Residue "F GLU 270": "OE1" <-> "OE2" Residue "F GLU 278": "OE1" <-> "OE2" Residue "F ASP 292": "OD1" <-> "OD2" Residue "F ASP 318": "OD1" <-> "OD2" Residue "F ARG 349": "NH1" <-> "NH2" Residue "F GLU 352": "OE1" <-> "OE2" Residue "F GLU 367": "OE1" <-> "OE2" Residue "F GLU 394": "OE1" <-> "OE2" Residue "F GLU 425": "OE1" <-> "OE2" Residue "F ARG 429": "NH1" <-> "NH2" Residue "F PHE 433": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 12": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 14": "OD1" <-> "OD2" Residue "G ARG 39": "NH1" <-> "NH2" Residue "G ARG 53": "NH1" <-> "NH2" Residue "G GLU 58": "OE1" <-> "OE2" Residue "G GLU 60": "OE1" <-> "OE2" Residue "G GLU 165": "OE1" <-> "OE2" Residue "G ASP 180": "OD1" <-> "OD2" Residue "G GLU 188": "OE1" <-> "OE2" Residue "G ARG 218": "NH1" <-> "NH2" Residue "G ARG 243": "NH1" <-> "NH2" Residue "G ARG 253": "NH1" <-> "NH2" Residue "G GLU 261": "OE1" <-> "OE2" Residue "G ARG 285": "NH1" <-> "NH2" Residue "G GLU 287": "OE1" <-> "OE2" Residue "G ARG 302": "NH1" <-> "NH2" Residue "G ASP 339": "OD1" <-> "OD2" Residue "G ASP 341": "OD1" <-> "OD2" Residue "G GLU 347": "OE1" <-> "OE2" Residue "G GLU 372": "OE1" <-> "OE2" Residue "G ARG 385": "NH1" <-> "NH2" Residue "G ARG 418": "NH1" <-> "NH2" Residue "G ASP 420": "OD1" <-> "OD2" Residue "G GLU 512": "OE1" <-> "OE2" Residue "G ASP 540": "OD1" <-> "OD2" Residue "G GLU 577": "OE1" <-> "OE2" Residue "G ASP 617": "OD1" <-> "OD2" Residue "G GLU 624": "OE1" <-> "OE2" Residue "G GLU 625": "OE1" <-> "OE2" Residue "G GLU 637": "OE1" <-> "OE2" Residue "G GLU 693": "OE1" <-> "OE2" Residue "H GLU 24": "OE1" <-> "OE2" Residue "H ARG 25": "NH1" <-> "NH2" Residue "H ARG 34": "NH1" <-> "NH2" Residue "H PHE 56": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ARG 62": "NH1" <-> "NH2" Residue "H TYR 142": "CD1" <-> "CD2" "CE1" <-> "CE2" 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 TYR 215": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 227": "OE1" <-> "OE2" Residue "H PHE 259": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 280": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ARG 8": "NH1" <-> "NH2" Residue "I ARG 108": "NH1" <-> "NH2" Residue "I PHE 137": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 28": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 47": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 79": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J GLU 100": "OE1" <-> "OE2" Residue "J PHE 101": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 106": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ASP 110": "OD1" <-> "OD2" Residue "J GLU 112": "OE1" <-> "OE2" Residue "J GLU 114": "OE1" <-> "OE2" Residue "J GLU 118": "OE1" <-> "OE2" Residue "J ASP 129": "OD1" <-> "OD2" Residue "J GLU 139": "OE1" <-> "OE2" Residue "J GLU 170": "OE1" <-> "OE2" Residue "J ARG 173": "NH1" <-> "NH2" Residue "K TYR 89": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L GLU 60": "OE1" <-> "OE2" Residue "L TYR 107": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 109": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ARG 161": "NH1" <-> "NH2" Residue "L ASP 197": "OD1" <-> "OD2" Residue "L ARG 262": "NH1" <-> "NH2" Residue "L PHE 263": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L GLU 268": "OE1" <-> "OE2" Residue "L GLU 353": "OE1" <-> "OE2" Residue "L ASP 393": "OD1" <-> "OD2" Residue "L GLU 445": "OE1" <-> "OE2" Residue "L TYR 466": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L GLU 503": "OE1" <-> "OE2" Residue "M GLU 87": "OE1" <-> "OE2" Residue "M PHE 95": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M GLU 114": "OE1" <-> "OE2" Residue "M PHE 118": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M PHE 122": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M GLU 123": "OE1" <-> "OE2" Residue "M ARG 142": "NH1" <-> "NH2" Residue "M TYR 210": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M ASP 255": "OD1" <-> "OD2" Residue "M PHE 256": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M GLU 335": "OE1" <-> "OE2" Residue "M ARG 346": "NH1" <-> "NH2" Residue "M GLU 378": "OE1" <-> "OE2" Residue "M ARG 432": "NH1" <-> "NH2" Residue "M TYR 459": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N GLU 54": "OE1" <-> "OE2" Residue "N GLU 117": "OE1" <-> "OE2" Residue "N PHE 281": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N ARG 295": "NH1" <-> "NH2" Residue "N PHE 325": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O GLU 12": "OE1" <-> "OE2" Residue "O GLU 20": "OE1" <-> "OE2" Residue "O ARG 104": "NH1" <-> "NH2" Residue "O ASP 110": "OD1" <-> "OD2" Residue "O GLU 113": "OE1" <-> "OE2" Residue "O ARG 126": "NH1" <-> "NH2" Residue "O ASP 131": "OD1" <-> "OD2" Residue "O GLU 136": "OE1" <-> "OE2" Residue "O GLU 178": "OE1" <-> "OE2" Residue "O GLU 203": "OE1" <-> "OE2" Residue "O GLU 213": "OE1" <-> "OE2" Residue "O GLU 219": "OE1" <-> "OE2" Residue "O GLU 232": "OE1" <-> "OE2" Residue "O GLU 236": "OE1" <-> "OE2" Residue "O ASP 237": "OD1" <-> "OD2" Residue "O GLU 239": "OE1" <-> "OE2" Residue "O TYR 240": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O ASP 244": "OD1" <-> "OD2" Residue "O ASP 253": "OD1" <-> "OD2" Residue "O GLU 268": "OE1" <-> "OE2" Residue "O GLU 295": "OE1" <-> "OE2" Residue "O ARG 302": "NH1" <-> "NH2" Residue "O ARG 305": "NH1" <-> "NH2" Residue "O TYR 308": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O GLU 310": "OE1" <-> "OE2" Residue "P ARG 40": "NH1" <-> "NH2" Residue "P ARG 50": "NH1" <-> "NH2" Residue "P GLU 52": "OE1" <-> "OE2" Residue "P ASP 79": "OD1" <-> "OD2" Residue "P ARG 82": "NH1" <-> "NH2" Residue "P GLU 86": "OE1" <-> "OE2" Residue "P ARG 97": "NH1" <-> "NH2" Residue "P GLU 107": "OE1" <-> "OE2" Residue "P GLU 123": "OE1" <-> "OE2" Residue "P GLU 127": "OE1" <-> "OE2" Residue "P ARG 147": "NH1" <-> "NH2" Residue "P GLU 155": "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 GLU 175": "OE1" <-> "OE2" Residue "P TYR 181": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P ARG 235": "NH1" <-> "NH2" Residue "P PHE 246": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P ARG 251": "NH1" <-> "NH2" Residue "P GLU 301": "OE1" <-> "OE2" Residue "P GLU 306": "OE1" <-> "OE2" Residue "P TYR 324": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q ASP 14": "OD1" <-> "OD2" Residue "Q GLU 58": "OE1" <-> "OE2" Residue "Q PHE 59": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q GLU 66": "OE1" <-> "OE2" Residue "Q GLU 97": "OE1" <-> "OE2" Residue "Q TYR 103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q ASP 104": "OD1" <-> "OD2" Residue "Q GLU 106": "OE1" <-> "OE2" Residue "R ASP 19": "OD1" <-> "OD2" Residue "R TYR 23": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R ARG 31": "NH1" <-> "NH2" Residue "R GLU 46": "OE1" <-> "OE2" Residue "R GLU 78": "OE1" <-> "OE2" Residue "S PHE 35": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S GLU 37": "OE1" <-> "OE2" Residue "S GLU 42": "OE1" <-> "OE2" Residue "S ASP 49": "OD1" <-> "OD2" Residue "T GLU 9": "OE1" <-> "OE2" Residue "T ASP 13": "OD1" <-> "OD2" Residue "T TYR 17": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T TYR 22": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T ASP 26": "OD1" <-> "OD2" Residue "T ASP 39": "OD1" <-> "OD2" Residue "T GLU 75": "OE1" <-> "OE2" Residue "T ASP 78": "OD1" <-> "OD2" Residue "U GLU 9": "OE1" <-> "OE2" Residue "U TYR 17": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U GLU 28": "OE1" <-> "OE2" 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 "V GLU 17": "OE1" <-> "OE2" Residue "V ARG 22": "NH1" <-> "NH2" Residue "V ASP 32": "OD1" <-> "OD2" Residue "V ASP 63": "OD1" <-> "OD2" Residue "V GLU 68": "OE1" <-> "OE2" Residue "V GLU 69": "OE1" <-> "OE2" Residue "V GLU 78": "OE1" <-> "OE2" Residue "V GLU 86": "OE1" <-> "OE2" Residue "V GLU 100": "OE1" <-> "OE2" Residue "V GLU 105": "OE1" <-> "OE2" Residue "W GLU 27": "OE1" <-> "OE2" Residue "W ARG 30": "NH1" <-> "NH2" Residue "W ASP 61": "OD1" <-> "OD2" Residue "W GLU 65": "OE1" <-> "OE2" Residue "W GLU 111": "OE1" <-> "OE2" Residue "W ASP 117": "OD1" <-> "OD2" Residue "X GLU 5": "OE1" <-> "OE2" Residue "X ASP 36": "OD1" <-> "OD2" Residue "X GLU 48": "OE1" <-> "OE2" Residue "X GLU 49": "OE1" <-> "OE2" Residue "X GLU 57": "OE1" <-> "OE2" Residue "X ARG 97": "NH1" <-> "NH2" 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 148": "OE1" <-> "OE2" Residue "X ASP 156": "OD1" <-> "OD2" Residue "Y TYR 22": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y GLU 50": "OE1" <-> "OE2" Residue "Y ARG 57": "NH1" <-> "NH2" Residue "Y ARG 103": "NH1" <-> "NH2" Residue "Z ARG 82": "NH1" <-> "NH2" Residue "Z GLU 92": "OE1" <-> "OE2" Residue "Z ASP 100": "OD1" <-> "OD2" Residue "Z GLU 108": "OE1" <-> "OE2" Residue "Z GLU 131": "OE1" <-> "OE2" Residue "Z GLU 132": "OE1" <-> "OE2" Residue "a GLU 4": "OE1" <-> "OE2" Residue "a GLU 35": "OE1" <-> "OE2" Residue "a ASP 51": "OD1" <-> "OD2" Residue "a ARG 59": "NH1" <-> "NH2" Residue "b ARG 3": "NH1" <-> "NH2" Residue "b GLU 15": "OE1" <-> "OE2" Residue "b TYR 50": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b ARG 57": "NH1" <-> "NH2" Residue "c GLU 6": "OE1" <-> "OE2" Residue "c PHE 26": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c TYR 30": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c GLU 37": "OE1" <-> "OE2" Residue "c GLU 41": "OE1" <-> "OE2" Residue "c ARG 44": "NH1" <-> "NH2" Residue "d PHE 13": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d ASP 16": "OD1" <-> "OD2" Residue "d ARG 51": "NH1" <-> "NH2" Residue "d ARG 86": "NH1" <-> "NH2" Residue "d GLU 103": "OE1" <-> "OE2" Residue "d GLU 111": "OE1" <-> "OE2" Residue "d GLU 114": "OE1" <-> "OE2" Residue "e ASP 4": "OD1" <-> "OD2" Residue "e ARG 8": "NH1" <-> "NH2" Residue "e GLU 23": "OE1" <-> "OE2" Residue "e GLU 36": "OE1" <-> "OE2" Residue "e GLU 38": "OE1" <-> "OE2" Residue "e ARG 50": "NH1" <-> "NH2" Residue "e GLU 52": "OE1" <-> "OE2" Residue "e GLU 83": "OE1" <-> "OE2" Residue "f ASP 9": "OD1" <-> "OD2" Residue "f ARG 28": "NH1" <-> "NH2" Residue "f GLU 32": "OE1" <-> "OE2" Residue "f ARG 46": "NH1" <-> "NH2" Residue "f GLU 52": "OE1" <-> "OE2" Residue "f GLU 53": "OE1" <-> "OE2" Residue "g ARG 25": "NH1" <-> "NH2" Residue "g GLU 31": "OE1" <-> "OE2" Residue "g ASP 34": "OD1" <-> "OD2" Residue "g GLU 35": "OE1" <-> "OE2" Residue "g GLU 39": "OE1" <-> "OE2" Residue "g ASP 43": "OD1" <-> "OD2" Residue "g GLU 94": "OE1" <-> "OE2" Residue "g GLU 101": "OE1" <-> "OE2" Residue "g ASP 114": "OD1" <-> "OD2" Residue "g GLU 122": "OE1" <-> "OE2" Residue "h PHE 9": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "h PHE 16": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "h ARG 20": "NH1" <-> "NH2" Residue "h GLU 49": "OE1" <-> "OE2" Residue "h GLU 51": "OE1" <-> "OE2" Residue "h GLU 62": "OE1" <-> "OE2" Residue "h GLU 65": "OE1" <-> "OE2" Residue "h ARG 77": "NH1" <-> "NH2" Residue "h GLU 84": "OE1" <-> "OE2" Residue "h GLU 99": "OE1" <-> "OE2" Residue "h GLU 102": "OE1" <-> "OE2" Residue "h ARG 112": "NH1" <-> "NH2" Residue "i GLU 16": "OE1" <-> "OE2" Residue "i ARG 18": "NH1" <-> "NH2" Residue "i GLU 26": "OE1" <-> "OE2" Residue "i TYR 64": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "i GLU 98": "OE1" <-> "OE2" Residue "i GLU 111": "OE1" <-> "OE2" Residue "i GLU 114": "OE1" <-> "OE2" Residue "j PHE 14": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "j PHE 40": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "j ASP 43": "OD1" <-> "OD2" Residue "j ASP 45": "OD1" <-> "OD2" Residue "j GLU 63": "OE1" <-> "OE2" Residue "j ASP 69": "OD1" <-> "OD2" Residue "k GLU 14": "OE1" <-> "OE2" Residue "k TYR 18": "CD1" <-> "CD2" "CE1" <-> "CE2" 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 ASP 42": "OD1" <-> "OD2" Residue "k GLU 84": "OE1" <-> "OE2" Residue "k TYR 86": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "k GLU 88": "OE1" <-> "OE2" Residue "l TYR 13": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "l GLU 18": "OE1" <-> "OE2" Residue "l GLU 19": "OE1" <-> "OE2" Residue "l ARG 30": "NH1" <-> "NH2" Residue "l GLU 32": "OE1" <-> "OE2" Residue "l ASP 40": "OD1" <-> "OD2" Residue "l GLU 57": "OE1" <-> "OE2" Residue "l GLU 75": "OE1" <-> "OE2" Residue "l GLU 120": "OE1" <-> "OE2" Residue "l GLU 141": "OE1" <-> "OE2" Residue "l ARG 142": "NH1" <-> "NH2" Residue "l GLU 149": "OE1" <-> "OE2" Residue "l GLU 157": "OE1" <-> "OE2" Residue "m TYR 22": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "m GLU 27": "OE1" <-> "OE2" Residue "m ARG 39": "NH1" <-> "NH2" Residue "m ARG 55": "NH1" <-> "NH2" Residue "m GLU 60": "OE1" <-> "OE2" Residue "m ARG 71": "NH1" <-> "NH2" Residue "m ASP 107": "OD1" <-> "OD2" Residue "n ARG 21": "NH1" <-> "NH2" Residue "n ARG 37": "NH1" <-> "NH2" Residue "n ASP 48": "OD1" <-> "OD2" Residue "n GLU 49": "OE1" <-> "OE2" Residue "n GLU 53": "OE1" <-> "OE2" Residue "n ARG 64": "NH1" <-> "NH2" Residue "n GLU 65": "OE1" <-> "OE2" Residue "n GLU 69": "OE1" <-> "OE2" Residue "n GLU 83": "OE1" <-> "OE2" Residue "n GLU 91": "OE1" <-> "OE2" Residue "n ARG 92": "NH1" <-> "NH2" Residue "n GLU 130": "OE1" <-> "OE2" Residue "n ARG 149": "NH1" <-> "NH2" Residue "n GLU 175": "OE1" <-> "OE2" Residue "o ARG 6": "NH1" <-> "NH2" Residue "o TYR 28": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "o GLU 32": "OE1" <-> "OE2" Residue "o GLU 35": "OE1" <-> "OE2" Residue "o ARG 36": "NH1" <-> "NH2" Residue "o GLU 37": "OE1" <-> "OE2" Residue "o GLU 44": "OE1" <-> "OE2" Residue "o ASP 93": "OD1" <-> "OD2" Residue "o ARG 97": "NH1" <-> "NH2" Residue "o GLU 102": "OE1" <-> "OE2" Residue "o ARG 103": "NH1" <-> "NH2" Residue "o ARG 105": "NH1" <-> "NH2" Residue "o ARG 106": "NH1" <-> "NH2" Residue "o GLU 118": "OE1" <-> "OE2" Residue "p ASP 7": "OD1" <-> "OD2" Residue "p GLU 11": "OE1" <-> "OE2" Residue "p PHE 36": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "p ASP 41": "OD1" <-> "OD2" Residue "p TYR 61": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "p GLU 86": "OE1" <-> "OE2" Residue "p GLU 100": "OE1" <-> "OE2" Residue "p GLU 116": "OE1" <-> "OE2" Residue "p GLU 127": "OE1" <-> "OE2" Residue "p GLU 129": "OE1" <-> "OE2" Residue "p GLU 171": "OE1" <-> "OE2" Residue "q GLU 2": "OE1" <-> "OE2" Residue "q ARG 21": "NH1" <-> "NH2" Residue "q PHE 28": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "q ARG 29": "NH1" <-> "NH2" Residue "q GLU 41": "OE1" <-> "OE2" Residue "q ASP 76": "OD1" <-> "OD2" Residue "q ASP 78": "OD1" <-> "OD2" Residue "q GLU 85": "OE1" <-> "OE2" Residue "q ARG 88": "NH1" <-> "NH2" Residue "q ASP 95": "OD1" <-> "OD2" Residue "q ASP 96": "OD1" <-> "OD2" Residue "q GLU 136": "OE1" <-> "OE2" 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 GLU 109": "OE1" <-> "OE2" Residue "s ASP 34": "OD1" <-> "OD2" Residue "s GLU 71": "OE1" <-> "OE2" Time to flip residues: 0.18s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 69247 Number of models: 1 Model: "" Number of chains: 115 Chain: "A" Number of atoms: 836 Number of conformers: 1 Conformer: "" Number of residues, atoms: 104, 836 Classifications: {'peptide': 104} Link IDs: {'PTRANS': 4, 'TRANS': 99} Chain breaks: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'FME:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "B" Number of atoms: 1247 Number of conformers: 1 Conformer: "" Number of residues, atoms: 156, 1247 Classifications: {'peptide': 156} Link IDs: {'PCIS': 2, 'PTRANS': 8, 'TRANS': 145} Chain: "C" Number of atoms: 1714 Number of conformers: 1 Conformer: "" Number of residues, atoms: 206, 1714 Classifications: {'peptide': 206} Link IDs: {'PTRANS': 16, 'TRANS': 189} Chain: "D" Number of atoms: 3373 Number of conformers: 1 Conformer: "" Number of residues, atoms: 419, 3373 Classifications: {'peptide': 419} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 27, 'TRANS': 391} Chain breaks: 2 Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'2MR:plan-2': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 6 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: 3319 Number of conformers: 1 Conformer: "" Number of residues, atoms: 431, 3319 Classifications: {'peptide': 431} Link IDs: {'PCIS': 2, 'PTRANS': 19, 'TRANS': 409} 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: 2457 Number of conformers: 1 Conformer: "" Number of residues, atoms: 311, 2457 Classifications: {'peptide': 311} Link IDs: {'PCIS': 2, 'PTRANS': 20, 'TRANS': 288} Chain breaks: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'FME:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "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: 4786 Number of conformers: 1 Conformer: "" Number of residues, atoms: 606, 4786 Classifications: {'peptide': 606} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 27, 'TRANS': 578} Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'FME:plan-2': 1, 'TYR:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 11 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: 2353 Number of conformers: 1 Conformer: "" Number of residues, atoms: 295, 2353 Classifications: {'peptide': 295} Link IDs: {'PTRANS': 16, 'TRANS': 278} Chain breaks: 3 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: 691 Number of conformers: 1 Conformer: "" Number of residues, atoms: 86, 691 Classifications: {'peptide': 86} Link IDs: {'PTRANS': 4, 'TRANS': 81} Chain: "T" Number of atoms: 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: 681 Number of conformers: 1 Conformer: "" Number of residues, atoms: 84, 681 Classifications: {'peptide': 84} Link IDs: {'PTRANS': 3, 'TRANS': 80} Chain: "V" Number of atoms: 923 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 923 Classifications: {'peptide': 114} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 105} Chain: "W" Number of atoms: 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: 1152 Number of conformers: 1 Conformer: "" Number of residues, atoms: 141, 1152 Classifications: {'peptide': 141} Link IDs: {'PTRANS': 7, 'TRANS': 133} Chain: "a" Number of atoms: 561 Number of conformers: 1 Conformer: "" Number of residues, atoms: 69, 561 Classifications: {'peptide': 69} Link IDs: {'PTRANS': 3, 'TRANS': 65} Chain: "b" Number of atoms: 651 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 651 Classifications: {'peptide': 83} Link IDs: {'PTRANS': 11, 'TRANS': 71} Chain: "c" Number of atoms: 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: 934 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 934 Classifications: {'peptide': 112} Link IDs: {'PTRANS': 9, 'TRANS': 102} Chain: "e" Number of atoms: 799 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 799 Classifications: {'peptide': 95} Link IDs: {'PTRANS': 5, 'TRANS': 89} Chain: "f" Number of atoms: 444 Number of conformers: 1 Conformer: "" Number of residues, atoms: 51, 444 Classifications: {'peptide': 51} Link IDs: {'PTRANS': 2, 'TRANS': 48} 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: 892 Number of conformers: 1 Conformer: "" Number of residues, atoms: 104, 892 Classifications: {'peptide': 104} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 91} 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: 1050 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 1050 Classifications: {'peptide': 126} Link IDs: {'PTRANS': 7, 'TRANS': 118} Chain: "n" Number of atoms: 1487 Number of conformers: 1 Conformer: "" Number of residues, atoms: 171, 1487 Classifications: {'peptide': 171} Link IDs: {'PTRANS': 15, 'TRANS': 155} 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: 1435 Number of conformers: 1 Conformer: "" Number of residues, atoms: 170, 1435 Classifications: {'peptide': 170} Link IDs: {'PTRANS': 10, 'TRANS': 159} 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: 118 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 118 Unusual residues: {'3PE': 1, 'LMT': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 Chain: "B" Number of atoms: 78 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 78 Unusual residues: {'LMT': 1, 'PC1': 1, '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: 95 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 95 Unusual residues: {'3PE': 2, 'I49': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} 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: 106 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 106 Unusual residues: {'CDL': 1, 'LMT': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 29 Unresolved non-hydrogen angles: 29 Unresolved non-hydrogen dihedrals: 29 Chain: "L" Number of atoms: 227 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 227 Unusual residues: {'3PE': 3, 'CDL': 1, 'LMT': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 61 Unresolved non-hydrogen angles: 61 Unresolved non-hydrogen dihedrals: 61 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: 158 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 158 Unusual residues: {'3PE': 1, 'CDL': 1, 'I49': 1, 'LMT': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 45 Unresolved non-hydrogen angles: 45 Unresolved non-hydrogen dihedrals: 45 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: 48 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 48 Unusual residues: {'NDP': 1} Classifications: {'undetermined': 1} Chain: "R" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "T" Number of atoms: 37 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 37 Unusual residues: {'EHZ': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 3 Chain: "U" Number of atoms: 37 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 37 Unusual residues: {'EHZ': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 3 Chain: "Y" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 70 Unusual residues: {'3PE': 1, 'LMT': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 16 Chain: "d" Number of atoms: 120 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 120 Unusual residues: {'3PE': 1, 'CDL': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 31 Unresolved non-hydrogen angles: 31 Unresolved non-hydrogen dihedrals: 31 Chain: "f" Number of atoms: 35 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 35 Unusual residues: {'LMT': 1} Classifications: {'undetermined': 1} Chain: "g" Number of atoms: 49 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 49 Unusual residues: {'PC1': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 5 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: "k" 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: "m" Number of atoms: 76 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 76 Unusual residues: {'3PE': 1, 'LMT': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 10 Chain: "o" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 15 Unusual residues: {'MYR': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'MYR:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "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: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 15 Classifications: {'water': 15} Link IDs: {None: 14} Chain: "B" Number of atoms: 63 Number of conformers: 1 Conformer: "" Number of residues, atoms: 63, 63 Classifications: {'water': 63} Link IDs: {None: 62} Chain: "C" Number of atoms: 113 Number of conformers: 1 Conformer: "" Number of residues, atoms: 113, 113 Classifications: {'water': 113} Link IDs: {None: 112} Chain: "D" Number of atoms: 184 Number of conformers: 1 Conformer: "" Number of residues, atoms: 184, 184 Classifications: {'water': 184} Link IDs: {None: 183} Chain: "E" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 38, 38 Classifications: {'water': 38} Link IDs: {None: 37} Chain: "F" Number of atoms: 92 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 92 Classifications: {'water': 92} Link IDs: {None: 91} Chain: "G" Number of atoms: 248 Number of conformers: 1 Conformer: "" Number of residues, atoms: 248, 248 Classifications: {'water': 248} Link IDs: {None: 247} 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: 111 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 111 Classifications: {'water': 111} Link IDs: {None: 110} Chain: "J" Number of atoms: 20 Number of conformers: 1 Conformer: "" Number of residues, atoms: 20, 20 Classifications: {'water': 20} Link IDs: {None: 19} Chain: "K" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 14 Classifications: {'water': 14} Link IDs: {None: 13} Chain: "L" Number of atoms: 100 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 100 Classifications: {'water': 100} Link IDs: {None: 99} Chain: "M" Number of atoms: 110 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 110 Classifications: {'water': 110} Link IDs: {None: 109} Chain: "N" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 61, 61 Classifications: {'water': 61} Link IDs: {None: 60} Chain: "O" Number of atoms: 36 Number of conformers: 1 Conformer: "" Number of residues, atoms: 36, 36 Classifications: {'water': 36} Link IDs: {None: 35} Chain: "P" Number of atoms: 67 Number of conformers: 1 Conformer: "" Number of residues, atoms: 67, 67 Classifications: {'water': 67} Link IDs: {None: 66} Chain: "Q" Number of atoms: 98 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 98 Classifications: {'water': 98} Link IDs: {None: 97} Chain: "R" Number of atoms: 53 Number of conformers: 1 Conformer: "" Number of residues, atoms: 53, 53 Classifications: {'water': 53} Link IDs: {None: 52} Chain: "S" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "T" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "U" Number of atoms: 22 Number of conformers: 1 Conformer: "" Number of residues, atoms: 22, 22 Classifications: {'water': 22} Link IDs: {None: 21} Chain: "V" Number of atoms: 20 Number of conformers: 1 Conformer: "" Number of residues, atoms: 20, 20 Classifications: {'water': 20} Link IDs: {None: 19} Chain: "W" Number of atoms: 26 Number of conformers: 1 Conformer: "" Number of residues, atoms: 26, 26 Classifications: {'water': 26} Link IDs: {None: 25} Chain: "X" Number of atoms: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 44, 44 Classifications: {'water': 44} Link IDs: {None: 43} 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: 30 Number of conformers: 1 Conformer: "" Number of residues, atoms: 30, 30 Classifications: {'water': 30} Link IDs: {None: 29} Chain: "a" Number of atoms: 22 Number of conformers: 1 Conformer: "" Number of residues, atoms: 22, 22 Classifications: {'water': 22} Link IDs: {None: 21} Chain: "b" Number of atoms: 13 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 13 Classifications: {'water': 13} Link IDs: {None: 12} Chain: "d" Number of atoms: 16 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 16 Classifications: {'water': 16} Link IDs: {None: 15} Chain: "e" Number of atoms: 30 Number of conformers: 1 Conformer: "" Number of residues, atoms: 30, 30 Classifications: {'water': 30} Link IDs: {None: 29} Chain: "f" Number of atoms: 10 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 10 Classifications: {'water': 10} Link IDs: {None: 9} Chain: "g" Number of atoms: 30 Number of conformers: 1 Conformer: "" Number of residues, atoms: 30, 30 Classifications: {'water': 30} Link IDs: {None: 29} Chain: "h" Number of atoms: 34 Number of conformers: 1 Conformer: "" Number of residues, atoms: 34, 34 Classifications: {'water': 34} Link IDs: {None: 33} Chain: "i" Number of atoms: 19 Number of conformers: 1 Conformer: "" Number of residues, atoms: 19, 19 Classifications: {'water': 19} Link IDs: {None: 18} Chain: "j" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Classifications: {'water': 4} Link IDs: {None: 3} Chain: "k" Number of atoms: 17 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 17 Classifications: {'water': 17} Link IDs: {None: 16} Chain: "l" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 42, 42 Classifications: {'water': 42} Link IDs: {None: 41} Chain: "m" Number of atoms: 26 Number of conformers: 1 Conformer: "" Number of residues, atoms: 26, 26 Classifications: {'water': 26} Link IDs: {None: 25} Chain: "n" Number of atoms: 52 Number of conformers: 1 Conformer: "" Number of residues, atoms: 52, 52 Classifications: {'water': 52} Link IDs: {None: 51} Chain: "o" Number of atoms: 35 Number of conformers: 1 Conformer: "" Number of residues, atoms: 35, 35 Classifications: {'water': 35} Link IDs: {None: 34} Chain: "p" Number of atoms: 55 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 55 Classifications: {'water': 55} Link IDs: {None: 54} Chain: "q" Number of atoms: 41 Number of conformers: 1 Conformer: "" Number of residues, atoms: 41, 41 Classifications: {'water': 41} Link IDs: {None: 40} Chain: "r" Number of atoms: 34 Number of conformers: 1 Conformer: "" Number of residues, atoms: 34, 34 Classifications: {'water': 34} Link IDs: {None: 33} Chain: "s" Number of atoms: 10 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 10 Classifications: {'water': 10} Link IDs: {None: 9} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 1589 SG CYS B 119 96.079 94.150 205.660 1.00 23.33 S ATOM 1819 SG CYS B 149 93.811 91.830 210.443 1.00 21.98 S ATOM 1085 SG CYS B 54 90.485 90.789 204.769 1.00 25.70 S ATOM 1091 SG CYS B 55 90.267 96.473 207.703 1.00 25.45 S ATOM 7974 SG CYS E 103 113.183 45.649 261.569 1.00 42.26 S ATOM 8008 SG CYS E 108 111.496 43.039 263.564 1.00 43.09 S ATOM 8288 SG CYS E 144 115.293 42.252 258.181 1.00 39.95 S ATOM 8311 SG CYS E 148 114.004 39.540 259.313 1.00 44.26 S ATOM 11529 SG CYS F 362 118.040 51.901 237.821 1.00 26.91 S ATOM 11549 SG CYS F 365 115.263 51.489 242.725 1.00 28.70 S ATOM 11873 SG CYS F 405 119.713 46.808 241.896 1.00 29.97 S ATOM 11510 SG CYS F 359 121.782 52.701 243.252 1.00 30.51 S ATOM 12970 SG CYS G 114 114.847 70.435 228.390 1.00 23.14 S ATOM 12909 SG CYS G 105 109.040 73.040 230.265 1.00 22.06 S ATOM 12930 SG CYS G 108 114.767 75.373 232.383 1.00 22.71 S ATOM 13302 SG CYS G 156 123.138 64.207 233.277 1.00 24.94 S ATOM 13279 SG CYS G 153 120.499 66.551 238.948 1.00 24.56 S ATOM 13326 SG CYS G 159 126.663 67.301 237.414 1.00 27.58 S ATOM 13656 SG CYS G 203 122.147 70.176 233.600 1.00 25.91 S ATOM 12415 SG CYS G 41 123.381 57.376 231.131 1.00 25.40 S ATOM 12501 SG CYS G 52 119.554 57.923 230.146 1.00 25.01 S ATOM 12526 SG CYS G 55 120.901 53.372 226.888 1.00 26.71 S ATOM 12627 SG CYS G 69 124.200 53.997 227.974 1.00 28.15 S ATOM 20834 SG CYS I 119 96.777 85.907 216.432 1.00 20.71 S ATOM 20808 SG CYS I 116 97.301 92.470 217.265 1.00 21.01 S ATOM 20855 SG CYS I 122 98.395 88.053 221.963 1.00 20.76 S ATOM 20582 SG CYS I 87 102.477 88.570 216.730 1.00 20.15 S ATOM 20884 SG CYS I 126 100.983 84.796 229.455 1.00 22.31 S ATOM 20513 SG CYS I 77 105.999 88.992 230.361 1.00 23.29 S ATOM 20555 SG CYS I 83 104.246 87.205 224.435 1.00 21.17 S ATOM 20532 SG CYS I 80 106.412 82.597 228.065 1.00 21.78 S ATOM 40966 SG CYS R 59 102.716 80.476 244.664 1.00 30.12 S ATOM 41144 SG CYS R 84 105.768 81.095 242.528 1.00 29.98 S ATOM 41166 SG CYS R 87 103.503 83.793 243.335 1.00 28.98 S Time building chain proxies: 28.32, per 1000 atoms: 0.41 Number of scatterers: 69247 At special positions: 0 Unit cell: (184.943, 198.832, 294.593, 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 2 52.95 Zn 1 29.99 Fe 28 26.01 K 1 19.00 Cl 2 17.00 S 466 16.00 P 36 15.00 Mg 1 11.99 O 14232 8.00 N 11066 7.00 C 43412 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS X 45 " - pdb=" SG CYS X 55 " distance=2.04 Simple disulfide: pdb=" SG CYS Y 94 " - pdb=" SG CYS Y 114 " distance=2.04 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 o 68 " - pdb=" SG CYS o 79 " distance=2.04 Simple disulfide: pdb=" SG CYS p 112 " - pdb=" SG CYS p 124 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=3, symmetry=0 Number of additional bonds: simple=3, symmetry=0 Coordination: Other bonds: Time building additional restraints: 23.03 Conformation dependent library (CDL) restraints added in 8.3 seconds Dynamic metal coordination Iron sulfur cluster coordination pdb=" FES E 301 " pdb="FE1 FES E 301 " - pdb=" SG CYS E 103 " pdb="FE1 FES E 301 " - pdb=" SG CYS E 108 " pdb="FE2 FES E 301 " - pdb=" SG CYS E 148 " pdb="FE2 FES E 301 " - pdb=" SG CYS E 144 " pdb=" FES G 803 " pdb="FE1 FES G 803 " - pdb=" SG CYS G 52 " pdb="FE1 FES G 803 " - pdb=" SG CYS G 41 " pdb="FE2 FES G 803 " - pdb=" SG CYS G 55 " 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="FE3 SF4 B 201 " - pdb=" SG CYS B 54 " pdb="FE4 SF4 B 201 " - pdb=" SG CYS B 55 " pdb=" SF4 F 502 " pdb="FE2 SF4 F 502 " - pdb=" SG CYS F 365 " pdb="FE4 SF4 F 502 " - pdb=" SG CYS F 359 " pdb="FE1 SF4 F 502 " - pdb=" SG CYS F 362 " pdb="FE3 SF4 F 502 " - pdb=" SG CYS F 405 " pdb=" SF4 G 801 " pdb="FE3 SF4 G 801 " - pdb=" NE2 HIS G 101 " pdb="FE1 SF4 G 801 " - pdb=" SG CYS G 114 " pdb="FE4 SF4 G 801 " - pdb=" SG CYS G 108 " pdb="FE2 SF4 G 801 " - pdb=" SG CYS G 105 " 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="FE4 SF4 I 203 " - pdb=" SG CYS I 80 " pdb="FE2 SF4 I 203 " - pdb=" SG CYS I 77 " pdb="FE1 SF4 I 203 " - pdb=" SG CYS I 126 " Number of angles added : 81 Zn2+ tetrahedral coordination pdb=" ZN R 201 " pdb="ZN ZN R 201 " - pdb=" NE2 HIS R 68 " pdb="ZN ZN R 201 " - pdb=" SG CYS R 84 " pdb="ZN ZN R 201 " - pdb=" SG CYS R 87 " pdb="ZN ZN R 201 " - pdb=" SG CYS R 59 " Number of angles added : 3 15994 Ramachandran restraints generated. 7997 Oldfield, 0 Emsley, 7997 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 15256 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 361 helices and 29 sheets defined 54.5% alpha, 4.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 9.78 Creating SS restraints... Processing helix chain 'A' and resid 3 through 22 Processing helix chain 'A' and resid 53 through 80 Proline residue: A 74 - end of helix removed outlier: 5.418A pdb=" N TRP A 77 " --> pdb=" O LEU A 73 " (cutoff:3.500A) removed outlier: 4.436A 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 25 through 43 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 106 Proline residue: B 98 - end of helix Processing helix chain 'B' and resid 117 through 122 Processing helix chain 'B' and resid 124 through 126 No H-bonds generated for 'chain 'B' and resid 124 through 126' Processing helix chain 'B' and resid 136 through 138 No H-bonds generated for 'chain 'B' and resid 136 through 138' Processing helix chain 'B' and resid 153 through 168 Processing helix chain 'B' and resid 172 through 177 Processing helix chain 'C' and resid 16 through 32 Processing helix chain 'C' and resid 54 through 66 removed outlier: 4.679A pdb=" N ILE C 58 " --> pdb=" O ASP C 55 " (cutoff:3.500A) Proline residue: C 59 - end of helix removed outlier: 3.533A pdb=" N THR C 62 " --> pdb=" O PRO C 59 " (cutoff:3.500A) Processing helix chain 'C' and resid 125 through 138 removed outlier: 3.845A pdb=" N TRP C 129 " --> pdb=" O ALA C 126 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N MET C 137 " --> pdb=" O ILE C 134 " (cutoff:3.500A) removed outlier: 3.868A 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: 3.981A pdb=" N GLN D 13 " --> pdb=" O GLU D 9 " (cutoff:3.500A) removed outlier: 4.592A pdb=" N TYR D 14 " --> pdb=" O TRP D 10 " (cutoff:3.500A) Processing helix chain 'D' and resid 87 through 93 removed outlier: 3.835A pdb=" N GLU D 92 " --> pdb=" O GLU D 88 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N TYR D 93 " --> pdb=" O LYS D 89 " (cutoff:3.500A) Processing helix chain 'D' and resid 96 through 105 Proline residue: D 101 - end of helix removed outlier: 3.946A pdb=" N ASP D 104 " --> pdb=" O LEU D 100 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N ARG D 105 " --> pdb=" O PRO D 101 " (cutoff:3.500A) Processing helix chain 'D' and resid 111 through 126 Processing helix chain 'D' and resid 132 through 161 removed outlier: 3.709A pdb=" N ILE D 161 " --> pdb=" O HIS D 157 " (cutoff:3.500A) Processing helix chain 'D' and resid 165 through 185 removed outlier: 3.868A pdb=" N GLU D 173 " --> pdb=" O TRP D 169 " (cutoff:3.500A) Processing helix chain 'D' and resid 207 through 229 removed outlier: 3.785A pdb=" N ASN D 217 " --> pdb=" O GLU D 213 " (cutoff:3.500A) removed outlier: 4.455A pdb=" N SER D 219 " --> pdb=" O SER D 215 " (cutoff:3.500A) removed outlier: 5.857A pdb=" N LEU D 220 " --> pdb=" O LYS D 216 " (cutoff:3.500A) removed outlier: 3.766A 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: 4.706A pdb=" N GLY D 262 " --> pdb=" O MET D 259 " (cutoff:3.500A) Processing helix chain 'D' and resid 269 through 272 No H-bonds generated for 'chain 'D' and resid 269 through 272' Processing helix chain 'D' and resid 278 through 280 No H-bonds generated for 'chain 'D' and resid 278 through 280' Processing helix chain 'D' and resid 293 through 317 Processing helix chain 'D' and resid 335 through 338 No H-bonds generated for 'chain 'D' and resid 335 through 338' Processing helix chain 'D' and resid 342 through 353 Processing helix chain 'D' and resid 394 through 405 removed outlier: 3.579A pdb=" N LEU D 402 " --> pdb=" O HIS D 398 " (cutoff:3.500A) removed outlier: 4.887A pdb=" N ASP D 403 " --> pdb=" O LEU D 399 " (cutoff:3.500A) removed outlier: 5.339A pdb=" N LYS D 404 " --> pdb=" O ALA D 400 " (cutoff:3.500A) Processing helix chain 'D' and resid 411 through 421 removed outlier: 4.024A pdb=" N VAL D 415 " --> pdb=" O LEU D 411 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N ALA D 416 " --> pdb=" O ALA D 412 " (cutoff:3.500A) Processing helix chain 'D' and resid 425 through 429 Processing helix chain 'E' and resid 25 through 37 removed outlier: 3.517A pdb=" N ASN E 37 " --> pdb=" O ALA E 33 " (cutoff:3.500A) Processing helix chain 'E' and resid 43 through 58 removed outlier: 4.340A pdb=" N LEU E 48 " --> pdb=" O ALA E 45 " (cutoff:3.500A) Proline residue: E 49 - end of helix Processing helix chain 'E' and resid 63 through 73 Processing helix chain 'E' and resid 77 through 86 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 17 through 19 No H-bonds generated for 'chain 'F' and resid 17 through 19' Processing helix chain 'F' and resid 33 through 39 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: 3.607A pdb=" N PHE F 81 " --> pdb=" O LEU F 77 " (cutoff:3.500A) removed outlier: 4.657A pdb=" N MET F 82 " --> pdb=" O LYS F 78 " (cutoff:3.500A) Processing helix chain 'F' and resid 106 through 113 Processing helix chain 'F' and resid 115 through 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 283 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 313 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: 4.287A pdb=" N ASP F 370 " --> pdb=" O ARG F 366 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N ARG F 381 " --> pdb=" O ALA F 377 " (cutoff:3.500A) Processing helix chain 'F' and resid 386 through 399 removed outlier: 3.637A pdb=" N ASP F 390 " --> pdb=" O ALA F 387 " (cutoff:3.500A) Processing helix chain 'F' and resid 406 through 436 Proline residue: F 414 - end of helix removed outlier: 3.625A 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: 3.888A 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: 3.612A 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: 5.301A pdb=" N TYR G 271 " --> pdb=" O THR G 267 " (cutoff:3.500A) removed outlier: 6.551A pdb=" N ASP G 272 " --> pdb=" O ARG G 268 " (cutoff:3.500A) removed outlier: 5.488A pdb=" N GLY G 273 " --> pdb=" O PHE G 269 " (cutoff:3.500A) removed outlier: 4.270A pdb=" N LEU G 274 " --> pdb=" O ALA G 270 " (cutoff:3.500A) removed outlier: 4.285A pdb=" N LYS G 275 " --> pdb=" O TYR G 271 " (cutoff:3.500A) Processing helix chain 'G' and resid 296 through 309 removed outlier: 3.556A pdb=" N SER G 309 " --> pdb=" O GLY G 305 " (cutoff:3.500A) Processing helix chain 'G' and resid 312 through 314 No H-bonds generated for 'chain 'G' and resid 312 through 314' Processing helix chain 'G' and resid 325 through 338 removed outlier: 3.594A 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 372 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 457 through 459 No H-bonds generated for 'chain 'G' and resid 457 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 Processing helix chain 'G' and resid 642 through 650 removed outlier: 3.541A pdb=" N LYS G 650 " --> pdb=" O SER G 646 " (cutoff:3.500A) 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 679 No H-bonds generated for 'chain 'G' and resid 676 through 679' 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: 3.781A 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 56 Processing helix chain 'H' and resid 68 through 86 Proline residue: H 75 - end of helix removed outlier: 4.153A pdb=" N TRP H 86 " --> pdb=" O ALA H 82 " (cutoff:3.500A) Processing helix chain 'H' and resid 101 through 122 removed outlier: 3.537A pdb=" N LEU H 111 " --> pdb=" O ALA H 107 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N ALA H 112 " --> pdb=" O MET H 108 " (cutoff:3.500A) removed outlier: 4.396A pdb=" N VAL H 113 " --> pdb=" O SER H 109 " (cutoff:3.500A) removed outlier: 5.236A pdb=" N TYR H 114 " --> pdb=" O SER H 110 " (cutoff:3.500A) removed outlier: 4.477A pdb=" N SER H 115 " --> pdb=" O LEU H 111 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N ILE H 116 " --> pdb=" O ALA H 112 " (cutoff:3.500A) Processing helix chain 'H' and resid 126 through 157 removed outlier: 4.172A pdb=" N THR H 145 " --> pdb=" O SER H 141 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N MET H 156 " --> pdb=" O SER H 152 " (cutoff:3.500A) Processing helix chain 'H' and resid 162 through 168 removed outlier: 3.990A pdb=" N ILE H 166 " --> pdb=" O LEU H 162 " (cutoff:3.500A) removed outlier: 3.508A 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 200 through 206 Processing helix chain 'H' and resid 217 through 242 Processing helix chain 'H' and resid 252 through 274 Processing helix chain 'H' and resid 282 through 290 Processing helix chain 'H' and resid 293 through 311 Proline residue: H 308 - end of helix Processing helix chain 'I' and resid 14 through 26 Processing helix chain 'I' and resid 28 through 41 removed outlier: 3.511A 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: 5.700A pdb=" N ALA I 163 " --> pdb=" O ASP I 159 " (cutoff:3.500A) removed outlier: 6.186A pdb=" N GLU I 164 " --> pdb=" O LYS I 160 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N ALA I 167 " --> pdb=" O ALA I 163 " (cutoff:3.500A) removed outlier: 5.536A pdb=" N LEU I 174 " --> pdb=" O GLN I 170 " (cutoff:3.500A) removed outlier: 5.849A 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 removed outlier: 3.598A pdb=" N PHE J 47 " --> pdb=" O ILE J 43 " (cutoff:3.500A) Processing helix chain 'J' and resid 50 through 58 Processing helix chain 'J' and resid 64 through 75 Processing helix chain 'J' and resid 87 through 110 Processing helix chain 'J' and resid 124 through 127 Processing helix chain 'J' and resid 138 through 146 removed outlier: 3.899A pdb=" N LEU J 146 " --> pdb=" O GLY J 142 " (cutoff:3.500A) Processing helix chain 'J' and resid 151 through 173 Processing helix chain 'K' and resid 3 through 20 removed outlier: 3.928A 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 55 through 85 removed outlier: 3.818A pdb=" N MET K 58 " --> pdb=" O LEU K 55 " (cutoff:3.500A) Proline residue: K 60 - end of helix removed outlier: 3.527A pdb=" N PHE K 66 " --> pdb=" O LEU K 63 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N TYR K 85 " --> pdb=" O SER K 82 " (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: 3.781A pdb=" N LEU L 12 " --> pdb=" O SER L 8 " (cutoff:3.500A) Proline residue: L 18 - end of helix removed outlier: 4.148A pdb=" N SER L 23 " --> pdb=" O ILE L 19 " (cutoff:3.500A) Processing helix chain 'L' and resid 29 through 57 removed outlier: 3.830A pdb=" N TYR L 32 " --> pdb=" O PRO L 29 " (cutoff:3.500A) Proline residue: L 33 - end of helix removed outlier: 3.524A pdb=" N VAL L 36 " --> pdb=" O PRO L 33 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ILE L 49 " --> pdb=" O THR L 46 " (cutoff:3.500A) Proline residue: L 50 - end of helix removed outlier: 3.645A pdb=" N HIS L 56 " --> pdb=" O MET L 53 " (cutoff:3.500A) removed outlier: 3.830A 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: 3.770A 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: 3.518A pdb=" N GLY L 148 " --> pdb=" O TRP L 144 " (cutoff:3.500A) Processing helix chain 'L' and resid 162 through 193 removed outlier: 4.142A pdb=" N GLY L 181 " --> pdb=" O ILE L 177 " (cutoff:3.500A) Processing helix chain 'L' and resid 198 through 204 Processing helix chain 'L' and resid 210 through 223 Processing helix chain 'L' and resid 231 through 238 removed outlier: 4.095A pdb=" N MET L 237 " --> pdb=" O LEU L 233 " (cutoff:3.500A) removed outlier: 5.262A 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 252 through 262 removed outlier: 4.275A pdb=" N GLY L 256 " --> pdb=" O MET L 252 " (cutoff:3.500A) removed outlier: 4.450A pdb=" N ILE L 257 " --> pdb=" O VAL L 253 " (cutoff:3.500A) Processing helix chain 'L' and resid 264 through 269 removed outlier: 4.598A pdb=" N ASN L 269 " --> pdb=" O PRO L 265 " (cutoff:3.500A) Processing helix chain 'L' and resid 271 through 294 removed outlier: 4.431A pdb=" N THR L 294 " --> pdb=" O MET L 290 " (cutoff:3.500A) Processing helix chain 'L' and resid 298 through 318 Processing helix chain 'L' and resid 322 through 349 removed outlier: 3.923A pdb=" N PHE L 334 " --> pdb=" O CYS L 330 " (cutoff:3.500A) removed outlier: 3.866A 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 367 through 381 Processing helix chain 'L' and resid 387 through 400 removed outlier: 3.936A pdb=" N LYS L 392 " --> pdb=" O PHE L 389 " (cutoff:3.500A) removed outlier: 5.727A pdb=" N ASP L 393 " --> pdb=" O TYR L 390 " (cutoff:3.500A) Processing helix chain 'L' and resid 406 through 431 removed outlier: 3.607A pdb=" N ALA L 420 " --> pdb=" O THR L 416 " (cutoff:3.500A) Processing helix chain 'L' and resid 448 through 469 removed outlier: 6.155A pdb=" N GLY L 465 " --> pdb=" O SER L 461 " (cutoff:3.500A) removed outlier: 5.192A 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: 3.587A pdb=" N THR L 508 " --> pdb=" O ILE L 504 " (cutoff:3.500A) removed outlier: 4.244A 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: 3.816A pdb=" N MET L 533 " --> pdb=" O PRO L 530 " (cutoff:3.500A) removed outlier: 4.486A pdb=" N HIS L 534 " --> pdb=" O THR L 531 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N LEU L 536 " --> pdb=" O MET L 533 " (cutoff:3.500A) removed outlier: 5.456A pdb=" N ALA L 537 " --> pdb=" O HIS L 534 " (cutoff:3.500A) Proline residue: L 538 - end of helix removed outlier: 3.510A pdb=" N MET L 544 " --> pdb=" O ASN L 541 " (cutoff:3.500A) removed outlier: 3.643A 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 16 removed outlier: 4.193A pdb=" N MET M 12 " --> pdb=" O THR M 8 " (cutoff:3.500A) Proline residue: M 13 - end of helix Processing helix chain 'M' and resid 20 through 42 removed outlier: 4.088A pdb=" N ILE M 23 " --> pdb=" O ASN M 20 " (cutoff:3.500A) removed outlier: 5.224A pdb=" N TRP M 24 " --> pdb=" O ASN M 21 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N ASN M 26 " --> pdb=" O ILE M 23 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N SER M 27 " --> pdb=" O TRP M 24 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N THR M 28 " --> pdb=" O VAL M 25 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N HIS M 30 " --> pdb=" O SER M 27 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N SER M 31 " --> pdb=" O THR M 28 " (cutoff:3.500A) Processing helix chain 'M' and resid 60 through 80 Proline residue: M 64 - end of helix removed outlier: 3.568A pdb=" N LEU M 73 " --> pdb=" O THR M 69 " (cutoff:3.500A) Proline residue: M 74 - end of helix Processing helix chain 'M' and resid 89 through 111 Processing helix chain 'M' and resid 115 through 136 removed outlier: 4.705A pdb=" N LEU M 126 " --> pdb=" O PHE M 122 " (cutoff:3.500A) removed outlier: 4.457A 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: 3.586A pdb=" N PHE M 151 " --> pdb=" O TYR M 148 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N TYR M 152 " --> pdb=" O PHE M 149 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N LEU M 154 " --> pdb=" O PHE M 151 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N ALA M 155 " --> pdb=" O TYR M 152 " (cutoff:3.500A) removed outlier: 4.616A pdb=" N LEU M 158 " --> pdb=" O ALA M 155 " (cutoff:3.500A) Proline residue: M 159 - end of helix 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: 3.884A pdb=" N TYR M 181 " --> pdb=" O LEU M 177 " (cutoff:3.500A) Processing helix chain 'M' and resid 190 through 206 removed outlier: 4.745A pdb=" N ALA M 202 " --> pdb=" O ALA M 198 " (cutoff:3.500A) removed outlier: 5.325A pdb=" N PHE M 203 " --> pdb=" O CYS M 199 " (cutoff:3.500A) Processing helix chain 'M' and resid 214 through 222 removed outlier: 3.809A pdb=" N LYS M 218 " --> pdb=" O LEU M 214 " (cutoff:3.500A) Processing helix chain 'M' and resid 225 through 233 Processing helix chain 'M' and resid 235 through 249 removed outlier: 4.227A pdb=" N GLY M 239 " --> pdb=" O LEU M 235 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N GLY M 240 " --> pdb=" O LEU M 236 " (cutoff:3.500A) removed outlier: 4.810A pdb=" N LEU M 248 " --> pdb=" O LEU M 244 " (cutoff:3.500A) removed outlier: 4.860A pdb=" N ILE M 249 " --> pdb=" O ARG M 245 " (cutoff:3.500A) Processing helix chain 'M' and resid 253 through 257 removed outlier: 3.725A pdb=" N MET M 257 " --> pdb=" O THR M 254 " (cutoff:3.500A) Processing helix chain 'M' and resid 259 through 278 removed outlier: 3.919A pdb=" N ILE M 270 " --> pdb=" O LEU M 266 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N LEU M 277 " --> pdb=" O SER M 273 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N ARG M 278 " --> pdb=" O SER M 274 " (cutoff:3.500A) Processing helix chain 'M' and resid 282 through 303 removed outlier: 3.762A pdb=" N LEU M 296 " --> pdb=" O SER M 292 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N VAL M 297 " --> pdb=" O HIS M 293 " (cutoff:3.500A) Processing helix chain 'M' and resid 306 through 337 removed outlier: 3.806A pdb=" N ARG M 336 " --> pdb=" O SER M 332 " (cutoff:3.500A) Processing helix chain 'M' and resid 348 through 351 No H-bonds generated for 'chain 'M' and resid 348 through 351' Processing helix chain 'M' and resid 353 through 366 Processing helix chain 'M' and resid 373 through 388 removed outlier: 3.510A pdb=" N SER M 387 " --> pdb=" O MET M 383 " (cutoff:3.500A) Processing helix chain 'M' and resid 390 through 415 removed outlier: 3.609A pdb=" N GLY M 397 " --> pdb=" O ILE M 394 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N TYR M 406 " --> pdb=" O THR M 403 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N LEU M 408 " --> pdb=" O LEU M 405 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N MET M 410 " --> pdb=" O SER M 407 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N MET M 413 " --> pdb=" O MET M 410 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N THR M 414 " --> pdb=" O LEU M 411 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N GLN M 415 " --> pdb=" O ILE M 412 " (cutoff:3.500A) Processing helix chain 'M' and resid 431 through 449 removed outlier: 3.524A pdb=" N HIS M 440 " --> pdb=" O LEU M 436 " (cutoff:3.500A) Proline residue: M 443 - end of helix removed outlier: 3.991A pdb=" N THR M 448 " --> pdb=" O LEU M 444 " (cutoff:3.500A) removed outlier: 4.175A pdb=" N LEU M 449 " --> pdb=" O LEU M 445 " (cutoff:3.500A) Processing helix chain 'M' and resid 451 through 454 Processing helix chain 'N' and resid 3 through 22 Processing helix chain 'N' and resid 26 through 44 removed outlier: 3.556A pdb=" N ILE N 41 " --> pdb=" O MET N 37 " (cutoff:3.500A) Proline residue: N 42 - end of helix Processing helix chain 'N' and resid 50 through 81 Processing helix chain 'N' and resid 92 through 106 Processing helix chain 'N' and resid 113 through 120 removed outlier: 4.062A 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: 4.338A pdb=" N ALA N 137 " --> pdb=" O GLN N 134 " (cutoff:3.500A) Proline residue: N 138 - end of helix removed outlier: 3.827A pdb=" N TYR N 143 " --> pdb=" O SER N 140 " (cutoff:3.500A) removed outlier: 4.533A pdb=" N PHE N 146 " --> pdb=" O TYR N 143 " (cutoff:3.500A) Proline residue: N 147 - end of helix Processing helix chain 'N' and resid 151 through 171 removed outlier: 3.659A pdb=" N LEU N 170 " --> pdb=" O GLY N 166 " (cutoff:3.500A) removed outlier: 4.208A pdb=" N ASN N 171 " --> pdb=" O TRP N 167 " (cutoff:3.500A) Processing helix chain 'N' and resid 175 through 194 removed outlier: 3.633A pdb=" N TRP N 189 " --> pdb=" O ALA N 185 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N LEU N 194 " --> pdb=" O MET N 190 " (cutoff:3.500A) Processing helix chain 'N' and resid 198 through 222 removed outlier: 3.629A pdb=" N ASN N 222 " --> pdb=" O MET N 218 " (cutoff:3.500A) Processing helix chain 'N' and resid 227 through 235 removed outlier: 3.654A pdb=" N HIS N 232 " --> pdb=" O LEU N 228 " (cutoff:3.500A) removed outlier: 4.306A pdb=" N THR N 233 " --> pdb=" O SER N 229 " (cutoff:3.500A) removed outlier: 4.898A pdb=" N TRP N 234 " --> pdb=" O LEU N 230 " (cutoff:3.500A) removed outlier: 5.560A pdb=" N ASN N 235 " --> pdb=" O SER N 231 " (cutoff:3.500A) Processing helix chain 'N' and resid 238 through 251 Processing helix chain 'N' and resid 258 through 273 Proline residue: N 262 - end of helix Processing helix chain 'N' and resid 277 through 300 removed outlier: 3.685A pdb=" N LEU N 287 " --> pdb=" O ALA N 283 " (cutoff:3.500A) removed outlier: 4.282A pdb=" N LEU N 288 " --> pdb=" O ILE N 284 " (cutoff:3.500A) removed outlier: 4.286A pdb=" N ASN N 289 " --> pdb=" O THR N 285 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N LEU N 296 " --> pdb=" O PHE N 292 " (cutoff:3.500A) Processing helix chain 'N' and resid 310 through 316 Processing helix chain 'N' and resid 326 through 332 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: 3.504A pdb=" N ARG O 140 " --> pdb=" O ALA O 137 " (cutoff:3.500A) Processing helix chain 'O' and resid 146 through 162 removed outlier: 4.046A pdb=" N CYS O 161 " --> pdb=" O LYS O 157 " (cutoff:3.500A) removed outlier: 5.333A pdb=" N GLU O 162 " --> pdb=" O VAL O 158 " (cutoff:3.500A) Processing helix chain 'O' and resid 176 through 186 Processing helix chain 'O' and resid 191 through 193 No H-bonds generated for 'chain 'O' and resid 191 through 193' Processing helix chain 'O' and resid 196 through 208 Processing helix chain 'O' and resid 210 through 217 removed outlier: 3.593A pdb=" N GLU O 216 " --> pdb=" O PRO O 212 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N LYS O 217 " --> pdb=" O GLU O 213 " (cutoff:3.500A) Processing helix chain 'O' and resid 225 through 229 Processing helix chain 'O' and resid 231 through 240 Processing helix chain 'O' and resid 247 through 249 No H-bonds generated for 'chain 'O' and resid 247 through 249' Processing helix chain 'O' and resid 253 through 264 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: 3.741A 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 removed outlier: 3.523A pdb=" N GLU O 298 " --> pdb=" O GLN O 294 " (cutoff:3.500A) 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: 4.103A pdb=" N TYR P 33 " --> pdb=" O PHE P 29 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N MET P 41 " --> pdb=" O HIS P 37 " (cutoff:3.500A) Processing helix chain 'P' and resid 53 through 62 removed outlier: 3.559A pdb=" N MET P 57 " --> pdb=" O TYR P 54 " (cutoff:3.500A) removed outlier: 4.907A 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 Processing helix chain 'P' and resid 106 through 110 Processing helix chain 'P' and resid 112 through 124 Processing helix chain 'P' and resid 144 through 159 Processing helix chain 'P' and resid 179 through 183 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 281 through 287 Processing helix chain 'P' and resid 301 through 303 No H-bonds generated for 'chain 'P' and resid 301 through 303' Processing helix chain 'P' and resid 310 through 321 removed outlier: 5.078A pdb=" N ILE P 315 " --> pdb=" O GLU P 311 " (cutoff:3.500A) removed outlier: 5.529A pdb=" N GLU P 316 " --> pdb=" O LEU P 312 " (cutoff:3.500A) removed outlier: 5.520A pdb=" N ARG P 320 " --> pdb=" O GLU P 316 " (cutoff:3.500A) removed outlier: 5.089A pdb=" N HIS P 321 " --> pdb=" O VAL P 317 " (cutoff:3.500A) Processing helix chain 'Q' and resid 20 through 22 No H-bonds generated for 'chain 'Q' and resid 20 through 22' Processing helix chain 'Q' and resid 27 through 31 removed outlier: 3.833A pdb=" N LYS Q 31 " --> pdb=" O GLU Q 28 " (cutoff:3.500A) 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: 3.513A pdb=" N ALA R 45 " --> pdb=" O ILE R 41 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N GLU R 46 " --> pdb=" O ASP R 42 " (cutoff:3.500A) Processing helix chain 'R' and resid 64 through 66 No H-bonds generated for 'chain 'R' and resid 64 through 66' Processing helix chain 'S' and resid 27 through 46 removed outlier: 4.817A pdb=" N GLY S 31 " --> pdb=" O GLY S 28 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N ARG S 39 " --> pdb=" O ILE S 36 " (cutoff:3.500A) removed outlier: 5.668A pdb=" N TYR S 40 " --> pdb=" O GLU S 37 " (cutoff:3.500A) removed outlier: 5.523A pdb=" N VAL S 41 " --> pdb=" O LYS S 38 " (cutoff:3.500A) Processing helix chain 'S' and resid 69 through 71 No H-bonds generated for 'chain 'S' and resid 69 through 71' Processing helix chain 'S' and resid 83 through 94 Processing helix chain 'T' and resid 8 through 21 Processing helix chain 'T' and resid 44 through 58 Processing helix chain 'T' and resid 64 through 69 removed outlier: 4.163A pdb=" N LYS T 69 " --> pdb=" O ILE T 65 " (cutoff:3.500A) Processing helix chain 'T' and resid 73 through 80 Processing helix chain 'U' and resid 8 through 21 Processing helix chain 'U' and resid 44 through 58 Processing helix chain 'U' and resid 64 through 69 removed outlier: 4.504A 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: 4.036A pdb=" N HIS V 36 " --> pdb=" O ASP V 32 " (cutoff:3.500A) Processing helix chain 'V' and resid 42 through 59 Processing helix chain 'V' and resid 64 through 71 Processing helix chain 'V' and resid 76 through 96 removed outlier: 3.866A pdb=" N GLN V 95 " --> pdb=" O ARG V 91 " (cutoff:3.500A) Processing helix chain 'W' and resid 25 through 49 removed outlier: 3.505A pdb=" N ARG W 31 " --> pdb=" O GLU W 27 " (cutoff:3.500A) Proline residue: W 44 - end of helix Processing helix chain 'W' and resid 56 through 70 removed outlier: 4.237A 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 106 removed outlier: 4.414A pdb=" N PHE W 106 " --> pdb=" O HIS W 102 " (cutoff:3.500A) Processing helix chain 'W' and resid 118 through 124 Processing helix chain 'X' and resid 10 through 12 No H-bonds generated for 'chain 'X' and resid 10 through 12' 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 76 removed outlier: 3.523A pdb=" N CYS X 55 " --> pdb=" O PRO X 52 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N LEU X 56 " --> pdb=" O ARG X 53 " (cutoff:3.500A) removed outlier: 5.663A pdb=" N GLU X 57 " --> pdb=" O ARG X 54 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N CYS X 65 " --> pdb=" O VAL X 62 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N ILE X 73 " --> pdb=" O PHE X 70 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N LYS X 74 " --> pdb=" O ARG X 71 " (cutoff:3.500A) Processing helix chain 'X' and resid 78 through 90 removed outlier: 3.505A pdb=" N TYR X 90 " --> pdb=" O THR X 86 " (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 103 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 Processing helix chain 'Z' and resid 121 through 124 No H-bonds generated for 'chain 'Z' and resid 121 through 124' Processing helix chain 'Z' and resid 130 through 142 removed outlier: 5.700A pdb=" N PHE Z 140 " --> pdb=" O ALA Z 136 " (cutoff:3.500A) removed outlier: 5.412A pdb=" N ILE Z 141 " --> pdb=" O THR Z 137 " (cutoff:3.500A) Processing helix chain 'a' and resid 2 through 30 Proline residue: a 7 - end of helix removed outlier: 3.621A pdb=" N ILE a 18 " --> pdb=" O CYS a 15 " (cutoff:3.500A) Proline residue: a 19 - end of helix removed outlier: 3.604A pdb=" N THR a 23 " --> pdb=" O GLY a 20 " (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 2 through 14 removed outlier: 3.528A pdb=" N ASN b 10 " --> pdb=" O ALA b 6 " (cutoff:3.500A) Processing helix chain 'b' and resid 16 through 34 Proline residue: b 32 - end of helix Processing helix chain 'b' and resid 38 through 47 removed outlier: 3.893A pdb=" N LEU b 42 " --> pdb=" O THR b 38 " (cutoff:3.500A) Processing helix chain 'b' and resid 78 through 82 Processing helix chain 'c' and resid 14 through 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: 3.656A 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 42 Processing helix chain 'e' and resid 48 through 54 removed outlier: 4.152A 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 88 Processing helix chain 'f' and resid 11 through 33 removed outlier: 4.706A pdb=" N VAL f 16 " --> pdb=" O HIS f 13 " (cutoff:3.500A) Proline residue: f 17 - end of helix removed outlier: 3.536A pdb=" N PHE f 22 " --> pdb=" O GLY f 19 " (cutoff:3.500A) Processing helix chain 'g' and resid 37 through 40 No H-bonds generated for 'chain 'g' and resid 37 through 40' Processing helix chain 'g' and resid 51 through 65 Processing helix chain 'g' and resid 69 through 79 Processing helix chain 'g' and resid 83 through 102 removed outlier: 3.751A pdb=" N GLN g 86 " --> pdb=" O TYR g 83 " (cutoff:3.500A) removed outlier: 5.924A pdb=" N GLU g 87 " --> pdb=" O ARG g 84 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N LYS g 98 " --> pdb=" O ARG g 95 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ARG g 100 " --> pdb=" O VAL g 97 " (cutoff:3.500A) removed outlier: 3.595A 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: 4.028A 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: 3.619A 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 60 through 73 removed outlier: 3.661A pdb=" N ARG i 65 " --> pdb=" O TYR i 61 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N HIS i 66 " --> pdb=" O LYS i 62 " (cutoff:3.500A) 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 '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 37 Processing helix chain 'k' and resid 46 through 52 removed outlier: 5.234A 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 138 Processing helix chain 'm' and resid 15 through 17 No H-bonds generated for 'chain 'm' and resid 15 through 17' Processing helix chain 'm' and resid 19 through 21 No H-bonds generated for 'chain 'm' and resid 19 through 21' Processing helix chain 'm' and resid 26 through 50 removed outlier: 3.699A 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 73 through 78 Proline residue: m 77 - end of helix No H-bonds generated for 'chain 'm' and resid 73 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: 3.947A 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: 3.863A pdb=" N MET n 113 " --> pdb=" O SER n 109 " (cutoff:3.500A) removed outlier: 4.218A pdb=" N TYR n 114 " --> pdb=" O GLU n 110 " (cutoff:3.500A) Proline residue: n 115 - end of helix removed outlier: 4.784A pdb=" N GLU n 133 " --> pdb=" O ARG n 129 " (cutoff:3.500A) removed outlier: 5.316A 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 8 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 47 Processing helix chain 'o' and resid 52 through 54 No H-bonds generated for 'chain 'o' and resid 52 through 54' Processing helix chain 'o' and resid 59 through 71 Processing helix chain 'o' and resid 80 through 119 removed outlier: 3.933A pdb=" N ALA o 119 " --> pdb=" O GLU o 115 " (cutoff:3.500A) Processing helix chain 'p' and resid 28 through 39 Processing helix chain 'p' and resid 41 through 57 Processing helix chain 'p' and resid 73 through 75 No H-bonds generated for 'chain 'p' and resid 73 through 75' Processing helix chain 'p' and resid 81 through 123 removed outlier: 3.737A pdb=" N GLU p 86 " --> pdb=" O LEU p 82 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N GLY p 117 " --> pdb=" O GLN p 113 " (cutoff:3.500A) removed outlier: 6.487A pdb=" N GLU p 118 " --> pdb=" O GLN p 114 " (cutoff:3.500A) removed outlier: 7.237A pdb=" N SER p 119 " --> pdb=" O ARG p 115 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N HIS p 120 " --> pdb=" O GLU p 116 " (cutoff:3.500A) removed outlier: 5.352A pdb=" N ARG p 121 " --> pdb=" O GLY p 117 " (cutoff:3.500A) removed outlier: 6.289A 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: 3.834A pdb=" N VAL q 14 " --> pdb=" O GLY q 10 " (cutoff:3.500A) Processing helix chain 'q' and resid 19 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: 4.224A 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 19 through 22 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 58 through 61 No H-bonds generated for 'chain 'r' and resid 58 through 61' Processing helix chain 's' and resid 42 through 45 Processing helix chain 's' and resid 50 through 61 removed outlier: 4.593A pdb=" N LYS s 60 " --> pdb=" O LEU s 56 " (cutoff:3.500A) removed outlier: 4.876A pdb=" N PHE s 61 " --> pdb=" O ASP s 57 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'B' and resid 47 through 51 removed outlier: 6.396A pdb=" N VAL B 85 " --> pdb=" O MET B 48 " (cutoff:3.500A) removed outlier: 7.271A pdb=" N PHE B 50 " --> pdb=" O VAL B 85 " (cutoff:3.500A) removed outlier: 6.581A pdb=" N ILE B 87 " --> pdb=" O PHE B 50 " (cutoff:3.500A) removed outlier: 6.531A pdb=" N TYR B 112 " --> pdb=" O MET B 86 " (cutoff:3.500A) removed outlier: 7.638A pdb=" N VAL B 88 " --> pdb=" O TYR B 112 " (cutoff:3.500A) removed outlier: 6.867A pdb=" N VAL B 114 " --> pdb=" O VAL B 88 " (cutoff:3.500A) removed outlier: 6.185A 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: 6.698A pdb=" N ASN C 95 " --> pdb=" O ALA C 76 " (cutoff:3.500A) removed outlier: 4.292A pdb=" N LEU C 78 " --> pdb=" O VAL C 93 " (cutoff:3.500A) removed outlier: 6.696A pdb=" N VAL C 93 " --> pdb=" O LEU C 78 " (cutoff:3.500A) removed outlier: 4.243A pdb=" N ALA C 80 " --> pdb=" O GLU C 91 " (cutoff:3.500A) removed outlier: 6.373A pdb=" N GLU C 91 " --> pdb=" O ALA C 80 " (cutoff:3.500A) removed outlier: 4.898A pdb=" N LEU C 48 " --> pdb=" O ARG C 104 " (cutoff:3.500A) removed outlier: 4.814A 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 49 removed outlier: 6.480A pdb=" N SER D 69 " --> pdb=" O VAL D 73 " (cutoff:3.500A) removed outlier: 5.687A 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: 6.357A pdb=" N TYR E 98 " --> pdb=" O THR E 138 " (cutoff:3.500A) removed outlier: 7.759A pdb=" N ILE E 140 " --> pdb=" O TYR E 98 " (cutoff:3.500A) removed outlier: 6.355A pdb=" N ILE E 100 " --> pdb=" O ILE E 140 " (cutoff:3.500A) removed outlier: 7.068A pdb=" N VAL E 142 " --> pdb=" O ILE E 100 " (cutoff:3.500A) removed outlier: 6.025A pdb=" N VAL E 102 " --> pdb=" O VAL E 142 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'F' and resid 219 through 224 removed outlier: 6.398A pdb=" N ALA F 133 " --> pdb=" O LEU F 93 " (cutoff:3.500A) removed outlier: 7.666A pdb=" N VAL F 95 " --> pdb=" O ALA F 133 " (cutoff:3.500A) removed outlier: 6.548A pdb=" N TYR F 135 " --> pdb=" O VAL F 95 " (cutoff:3.500A) removed outlier: 6.878A pdb=" N ALA F 97 " --> pdb=" O TYR F 135 " (cutoff:3.500A) removed outlier: 6.302A pdb=" N TYR F 137 " --> pdb=" O ALA F 97 " (cutoff:3.500A) removed outlier: 6.425A pdb=" N ASP F 174 " --> pdb=" O ALA F 134 " (cutoff:3.500A) removed outlier: 7.569A pdb=" N ILE F 136 " --> pdb=" O ASP F 174 " (cutoff:3.500A) removed outlier: 6.642A pdb=" N PHE F 176 " --> pdb=" O ILE F 136 " (cutoff:3.500A) removed outlier: 7.474A pdb=" N ILE F 138 " --> pdb=" O PHE F 176 " (cutoff:3.500A) removed outlier: 6.314A pdb=" N VAL F 178 " --> pdb=" O ILE F 138 " (cutoff:3.500A) 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: 3.577A pdb=" N ARG G 249 " --> pdb=" O SER G 241 " (cutoff:3.500A) removed outlier: 6.230A pdb=" N ARG G 243 " --> pdb=" O VAL G 247 " (cutoff:3.500A) removed outlier: 5.404A 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: 4.709A pdb=" N THR G 342 " --> pdb=" O VAL G 315 " (cutoff:3.500A) removed outlier: 6.435A pdb=" N MET G 521 " --> pdb=" O ALA G 316 " (cutoff:3.500A) removed outlier: 8.023A pdb=" N ILE G 318 " --> pdb=" O MET G 521 " (cutoff:3.500A) removed outlier: 6.443A pdb=" N PHE G 523 " --> pdb=" O ILE G 318 " (cutoff:3.500A) removed outlier: 6.399A pdb=" N PHE G 542 " --> pdb=" O LEU G 522 " (cutoff:3.500A) removed outlier: 7.412A pdb=" N LEU G 524 " --> pdb=" O PHE G 542 " (cutoff:3.500A) removed outlier: 6.424A pdb=" N VAL G 544 " --> pdb=" O LEU G 524 " (cutoff:3.500A) removed outlier: 6.301A pdb=" N VAL G 559 " --> pdb=" O TYR G 545 " (cutoff:3.500A) removed outlier: 7.764A pdb=" N GLY G 547 " --> pdb=" O VAL G 559 " (cutoff:3.500A) removed outlier: 6.042A 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: 8.102A pdb=" N ASN G 491 " --> pdb=" O PRO G 449 " (cutoff:3.500A) removed outlier: 6.365A pdb=" N VAL G 451 " --> pdb=" O ASN G 491 " (cutoff:3.500A) removed outlier: 7.131A pdb=" N LEU G 493 " --> pdb=" O VAL G 451 " (cutoff:3.500A) removed outlier: 6.619A pdb=" N LEU G 453 " --> pdb=" O LEU G 493 " (cutoff:3.500A) removed outlier: 6.426A pdb=" N VAL G 376 " --> pdb=" O MET G 450 " (cutoff:3.500A) removed outlier: 7.726A pdb=" N ILE G 452 " --> pdb=" O VAL G 376 " (cutoff:3.500A) removed outlier: 6.386A pdb=" N LEU G 378 " --> pdb=" O ILE G 452 " (cutoff:3.500A) removed outlier: 7.492A pdb=" N GLY G 454 " --> pdb=" O LEU G 378 " (cutoff:3.500A) removed outlier: 7.553A pdb=" N VAL G 380 " --> pdb=" O GLY G 454 " (cutoff:3.500A) removed outlier: 6.438A pdb=" N LYS G 405 " --> pdb=" O VAL G 377 " (cutoff:3.500A) removed outlier: 7.623A pdb=" N LEU G 379 " --> pdb=" O LYS G 405 " (cutoff:3.500A) removed outlier: 6.485A pdb=" N ALA G 407 " --> pdb=" O LEU G 379 " (cutoff:3.500A) removed outlier: 6.486A 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: 5.950A pdb=" N GLU I 97 " --> pdb=" O THR I 106 " (cutoff:3.500A) removed outlier: 5.278A 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: 6.857A 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: 6.171A pdb=" N VAL O 122 " --> pdb=" O ILE O 25 " (cutoff:3.500A) removed outlier: 7.763A pdb=" N VAL O 27 " --> pdb=" O VAL O 122 " (cutoff:3.500A) removed outlier: 6.632A pdb=" N LEU O 124 " --> pdb=" O VAL O 27 " (cutoff:3.500A) removed outlier: 8.612A pdb=" N GLY O 29 " --> pdb=" O LEU O 124 " (cutoff:3.500A) removed outlier: 6.590A pdb=" N LYS O 49 " --> pdb=" O VAL O 123 " (cutoff:3.500A) removed outlier: 8.394A pdb=" N GLU O 125 " --> pdb=" O LYS O 49 " (cutoff:3.500A) removed outlier: 8.389A 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: 6.603A pdb=" N ILE P 165 " --> pdb=" O PHE P 228 " (cutoff:3.500A) removed outlier: 7.594A pdb=" N PHE P 230 " --> pdb=" O ILE P 165 " (cutoff:3.500A) removed outlier: 6.433A pdb=" N LYS P 167 " --> pdb=" O PHE P 230 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ILE P 132 " --> pdb=" O ASN P 93 " (cutoff:3.500A) removed outlier: 6.392A pdb=" N GLN P 44 " --> pdb=" O ALA P 21 " (cutoff:3.500A) removed outlier: 7.389A pdb=" N VAL P 23 " --> pdb=" O GLN P 44 " (cutoff:3.500A) removed outlier: 6.699A pdb=" N ILE P 46 " --> pdb=" O VAL P 23 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain 'Q' and resid 102 through 105 Processing sheet with id= Y, first strand: chain 'Q' and resid 64 through 66 Processing sheet with id= Z, first strand: chain 'R' and resid 50 through 52 Processing sheet with id= AA, first strand: chain 'R' and resid 56 through 59 Processing sheet with id= AB, first strand: chain 'S' and resid 51 through 56 removed outlier: 3.580A pdb=" N LEU S 22 " --> pdb=" O ARG S 55 " (cutoff:3.500A) removed outlier: 6.650A pdb=" N ARG S 67 " --> pdb=" O ARG S 16 " (cutoff:3.500A) removed outlier: 4.463A pdb=" N ILE S 18 " --> pdb=" O TRP S 65 " (cutoff:3.500A) removed outlier: 6.646A pdb=" N TRP S 65 " --> pdb=" O ILE S 18 " (cutoff:3.500A) removed outlier: 4.528A pdb=" N ILE S 20 " --> pdb=" O LYS S 63 " (cutoff:3.500A) removed outlier: 6.573A pdb=" N LYS S 63 " --> pdb=" O ILE S 20 " (cutoff:3.500A) Processing sheet with id= AC, first strand: chain 'q' and resid 60 through 63 removed outlier: 3.570A pdb=" N GLY q 40 " --> pdb=" O TYR q 48 " (cutoff:3.500A) removed outlier: 6.609A pdb=" N GLU q 50 " --> pdb=" O LEU q 38 " (cutoff:3.500A) removed outlier: 5.660A pdb=" N LEU q 38 " --> pdb=" O GLU q 50 " (cutoff:3.500A) 2923 hydrogen bonds defined for protein. 7815 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: 22.23 Time building geometry restraints manager: 24.88 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.40: 27595 1.40 - 1.63: 40288 1.63 - 1.85: 827 1.85 - 2.08: 0 2.08 - 2.31: 82 Bond restraints: 68792 Sorted by residual: bond pdb=" C5 GTP O 401 " pdb=" N7 GTP O 401 " ideal model delta sigma weight residual 1.350 1.518 -0.168 2.00e-02 2.50e+03 7.09e+01 bond pdb=" C6 GTP O 401 " pdb=" O6 GTP O 401 " ideal model delta sigma weight residual 1.230 1.394 -0.164 2.00e-02 2.50e+03 6.70e+01 bond pdb=" C SAC i 1 " pdb=" O SAC i 1 " ideal model delta sigma weight residual 1.231 1.362 -0.131 2.00e-02 2.50e+03 4.31e+01 bond pdb=" CB7 CDL d1202 " pdb=" OB8 CDL d1202 " ideal model delta sigma weight residual 1.334 1.401 -0.067 1.10e-02 8.26e+03 3.71e+01 bond pdb=" CB7 CDL N 503 " pdb=" OB8 CDL N 503 " ideal model delta sigma weight residual 1.334 1.401 -0.067 1.10e-02 8.26e+03 3.69e+01 ... (remaining 68787 not shown) Histogram of bond angle deviations from ideal: 72.63 - 84.92: 76 84.92 - 97.21: 2 97.21 - 109.50: 7553 109.50 - 121.79: 72265 121.79 - 134.08: 13149 Bond angle restraints: 93045 Sorted by residual: angle pdb=" O SAC i 1 " pdb=" C SAC i 1 " pdb=" N GLY i 2 " ideal model delta sigma weight residual 123.00 91.36 31.64 1.60e+00 3.91e-01 3.91e+02 angle pdb=" C51 CDL h1001 " pdb=" CB5 CDL h1001 " pdb=" OB6 CDL h1001 " ideal model delta sigma weight residual 111.33 121.48 -10.15 1.32e+00 5.72e-01 5.90e+01 angle pdb=" O 2MR D 85 " pdb=" C 2MR D 85 " pdb=" N GLY D 86 " ideal model delta sigma weight residual 123.00 111.71 11.29 1.60e+00 3.91e-01 4.98e+01 angle pdb=" C51 CDL N 503 " pdb=" CB5 CDL N 503 " pdb=" OB6 CDL N 503 " ideal model delta sigma weight residual 111.33 120.42 -9.09 1.32e+00 5.72e-01 4.73e+01 angle pdb=" C11 CDL N 503 " pdb=" CA5 CDL N 503 " pdb=" OA6 CDL N 503 " ideal model delta sigma weight residual 111.33 120.32 -8.99 1.32e+00 5.72e-01 4.62e+01 ... (remaining 93040 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.10: 40340 35.10 - 70.20: 1548 70.20 - 105.29: 226 105.29 - 140.39: 59 140.39 - 175.49: 5 Dihedral angle restraints: 42178 sinusoidal: 18520 harmonic: 23658 Sorted by residual: dihedral pdb=" CA TYR D 275 " pdb=" C TYR D 275 " pdb=" N ASP D 276 " pdb=" CA ASP D 276 " ideal model delta harmonic sigma weight residual -180.00 -130.06 -49.94 0 5.00e+00 4.00e-02 9.98e+01 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 82.10 175.49 1 2.00e+01 2.50e-03 4.79e+01 dihedral pdb=" C5' FMN F 501 " pdb=" O5' FMN F 501 " pdb=" P FMN F 501 " pdb=" O1P FMN F 501 " ideal model delta sinusoidal sigma weight residual 75.26 -79.03 154.28 1 2.00e+01 2.50e-03 4.56e+01 ... (remaining 42175 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 4.283: 10165 4.283 - 8.566: 0 8.566 - 12.850: 0 12.850 - 17.133: 0 17.133 - 21.416: 16 Chirality restraints: 10181 Sorted by residual: chirality pdb="FE2 SF4 G 801 " pdb=" S1 SF4 G 801 " pdb=" S3 SF4 G 801 " pdb=" S4 SF4 G 801 " both_signs ideal model delta sigma weight residual False 10.55 -10.86 21.42 2.00e-01 2.50e+01 1.15e+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 -10.84 21.40 2.00e-01 2.50e+01 1.14e+04 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 10.84 -21.40 2.00e-01 2.50e+01 1.14e+04 ... (remaining 10178 not shown) Planarity restraints: 11563 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C08 I49 H 403 " -0.535 2.00e-02 2.50e+03 5.66e-01 6.41e+03 pdb=" C14 I49 H 403 " 0.327 2.00e-02 2.50e+03 pdb=" C15 I49 H 403 " 0.033 2.00e-02 2.50e+03 pdb=" N01 I49 H 403 " 0.063 2.00e-02 2.50e+03 pdb=" N02 I49 H 403 " 0.875 2.00e-02 2.50e+03 pdb=" N03 I49 H 403 " 0.126 2.00e-02 2.50e+03 pdb=" N04 I49 H 403 " -1.147 2.00e-02 2.50e+03 pdb=" N05 I49 H 403 " 0.258 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C08 I49 N 504 " 0.576 2.00e-02 2.50e+03 5.34e-01 5.70e+03 pdb=" C14 I49 N 504 " -0.340 2.00e-02 2.50e+03 pdb=" C15 I49 N 504 " -0.005 2.00e-02 2.50e+03 pdb=" N01 I49 N 504 " 0.057 2.00e-02 2.50e+03 pdb=" N02 I49 N 504 " -0.809 2.00e-02 2.50e+03 pdb=" N03 I49 N 504 " -0.358 2.00e-02 2.50e+03 pdb=" N04 I49 N 504 " -0.135 2.00e-02 2.50e+03 pdb=" N05 I49 N 504 " 1.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SAC i 1 " 0.136 2.00e-02 2.50e+03 2.20e-01 4.84e+02 pdb=" C SAC i 1 " -0.381 2.00e-02 2.50e+03 pdb=" O SAC i 1 " 0.119 2.00e-02 2.50e+03 pdb=" N GLY i 2 " 0.126 2.00e-02 2.50e+03 ... (remaining 11560 not shown) Histogram of nonbonded interaction distances: 1.92 - 2.57: 895 2.57 - 3.21: 68003 3.21 - 3.85: 152397 3.85 - 4.50: 217042 4.50 - 5.14: 325790 Nonbonded interactions: 764127 Sorted by model distance: nonbonded pdb=" OG SER J 25 " pdb=" OE1 GLU J 77 " model vdw 1.924 2.440 nonbonded pdb=" OD1 ASP l 40 " pdb=" OG1 THR l 42 " model vdw 1.955 2.440 nonbonded pdb=" OG1 THR l 5 " pdb=" OD1 ASP l 7 " model vdw 1.983 2.440 nonbonded pdb=" O HOH H 547 " pdb=" O HOH b 111 " model vdw 2.011 2.440 nonbonded pdb=" O HOH L 811 " pdb=" O HOH o 323 " model vdw 2.014 2.440 ... (remaining 764122 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: 13.620 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: 0.040 Extract box with map and model: 57.620 Check model and map are aligned: 0.790 Set scattering table: 0.490 Process input model: 162.590 Find NCS groups from input model: 2.050 Set up NCS constraints: 0.310 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:10.130 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 247.650 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8809 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 0.168 68792 Z= 0.512 Angle : 0.848 31.644 93045 Z= 0.390 Chirality : 0.846 21.416 10181 Planarity : 0.008 0.566 11563 Dihedral : 18.869 175.489 26904 Min Nonbonded Distance : 1.924 Molprobity Statistics. All-atom Clashscore : 2.56 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.11 % Favored : 97.86 % Rotamer: Outliers : 1.24 % Allowed : 10.97 % Favored : 87.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.54 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.01 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.80 (0.09), residues: 7997 helix: 0.88 (0.08), residues: 4328 sheet: 0.16 (0.25), residues: 390 loop : 0.30 (0.11), residues: 3279 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP N 84 HIS 0.008 0.001 HIS C 160 PHE 0.023 0.002 PHE D 103 TYR 0.021 0.002 TYR I 118 ARG 0.008 0.000 ARG F 339 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15994 Ramachandran restraints generated. 7997 Oldfield, 0 Emsley, 7997 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15994 Ramachandran restraints generated. 7997 Oldfield, 0 Emsley, 7997 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1072 residues out of total 7080 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 88 poor density : 984 time to evaluate : 5.995 Fit side-chains REVERT: M 19 LYS cc_start: 0.8481 (mmtm) cc_final: 0.7788 (mppt) REVERT: b 9 LYS cc_start: 0.8621 (OUTLIER) cc_final: 0.8105 (ttmt) REVERT: d 77 LYS cc_start: 0.8886 (mtpp) cc_final: 0.8675 (ttpt) REVERT: g 49 LYS cc_start: 0.8396 (mtmm) cc_final: 0.8162 (mttp) REVERT: l 103 LYS cc_start: 0.8765 (mttp) cc_final: 0.8536 (mttm) outliers start: 88 outliers final: 74 residues processed: 1056 average time/residue: 1.7996 time to fit residues: 2401.2941 Evaluate side-chains 1037 residues out of total 7080 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 962 time to evaluate : 5.925 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 29 VAL Chi-restraints excluded: chain B residue 54 CYS Chi-restraints excluded: chain B residue 79 SER Chi-restraints excluded: chain B residue 91 THR Chi-restraints excluded: chain B residue 161 LEU Chi-restraints excluded: chain D residue 76 CYS Chi-restraints excluded: chain D residue 219 SER Chi-restraints excluded: chain E residue 14 GLU Chi-restraints excluded: chain F residue 54 ASP Chi-restraints excluded: chain G residue 17 SER Chi-restraints excluded: chain G residue 193 SER Chi-restraints excluded: chain G residue 364 LEU Chi-restraints excluded: chain G residue 398 SER Chi-restraints excluded: chain G residue 456 SER Chi-restraints excluded: chain G residue 471 SER Chi-restraints excluded: chain G residue 533 THR Chi-restraints excluded: chain G residue 646 SER Chi-restraints excluded: chain H residue 66 SER Chi-restraints excluded: chain H residue 163 SER Chi-restraints excluded: chain H residue 222 LEU Chi-restraints excluded: chain J residue 148 SER Chi-restraints excluded: chain K residue 46 LEU Chi-restraints excluded: chain L residue 10 VAL Chi-restraints excluded: chain L residue 30 SER Chi-restraints excluded: chain L residue 393 ASP Chi-restraints excluded: chain L residue 469 SER Chi-restraints excluded: chain M residue 72 LEU Chi-restraints excluded: chain N residue 67 SER Chi-restraints excluded: chain O residue 1 LEU Chi-restraints excluded: chain O residue 2 GLN Chi-restraints excluded: chain O residue 60 ASP Chi-restraints excluded: chain O residue 289 SER Chi-restraints excluded: chain O residue 310 GLU Chi-restraints excluded: chain P residue 43 SER Chi-restraints excluded: chain P residue 142 SER Chi-restraints excluded: chain P residue 199 LYS Chi-restraints excluded: chain P residue 290 THR Chi-restraints excluded: chain Q residue 66 GLU Chi-restraints excluded: chain Q residue 110 VAL Chi-restraints excluded: chain Q residue 115 SER Chi-restraints excluded: chain R residue 79 THR Chi-restraints excluded: chain R residue 95 HIS Chi-restraints excluded: chain S residue 39 ARG Chi-restraints excluded: chain S residue 90 LEU Chi-restraints excluded: chain T residue 11 ILE Chi-restraints excluded: chain T residue 32 VAL Chi-restraints excluded: chain T residue 82 ASP Chi-restraints excluded: chain W residue 49 LEU Chi-restraints excluded: chain X residue 11 ASP Chi-restraints excluded: chain X residue 17 VAL Chi-restraints excluded: chain X residue 77 CYS Chi-restraints excluded: chain X residue 132 THR Chi-restraints excluded: chain X residue 148 GLU Chi-restraints excluded: chain Y residue 25 THR Chi-restraints excluded: chain Y residue 75 ILE Chi-restraints excluded: chain Y residue 109 ILE Chi-restraints excluded: chain Y residue 114 CYS Chi-restraints excluded: chain Z residue 144 THR Chi-restraints excluded: chain a residue 30 SER Chi-restraints excluded: chain b residue 4 VAL Chi-restraints excluded: chain b residue 9 LYS Chi-restraints excluded: chain b residue 67 SER Chi-restraints excluded: chain e residue 18 THR Chi-restraints excluded: chain g residue 122 GLU Chi-restraints excluded: chain k residue 58 ASN Chi-restraints excluded: chain m residue 8 SER Chi-restraints excluded: chain n residue 57 VAL Chi-restraints excluded: chain n residue 122 GLU Chi-restraints excluded: chain o residue 30 PHE Chi-restraints excluded: chain p residue 119 SER Chi-restraints excluded: chain p residue 134 VAL Chi-restraints excluded: chain q residue 4 LEU Chi-restraints excluded: chain q residue 15 SER Chi-restraints excluded: chain r residue 66 SER Chi-restraints excluded: chain s residue 57 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 791 random chunks: chunk 667 optimal weight: 0.8980 chunk 599 optimal weight: 0.8980 chunk 332 optimal weight: 1.9990 chunk 204 optimal weight: 9.9990 chunk 404 optimal weight: 4.9990 chunk 320 optimal weight: 2.9990 chunk 619 optimal weight: 0.9990 chunk 239 optimal weight: 0.9990 chunk 376 optimal weight: 2.9990 chunk 461 optimal weight: 2.9990 chunk 718 optimal weight: 3.9990 overall best weight: 1.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 69 ASN C 211 GLN F 257 ASN F 435 GLN G 444 GLN J 46 ASN J 120 ASN L 546 GLN N 268 GLN V 72 GLN V 95 GLN W 51 GLN Y 7 GLN Y 88 ASN b 10 ASN j 6 HIS n 61 GLN n 140 GLN n 159 GLN o 116 GLN p 22 GLN q 112 ASN Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8706 moved from start: 0.0853 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.288 68792 Z= 0.472 Angle : 1.311 51.019 93045 Z= 0.840 Chirality : 0.256 6.667 10181 Planarity : 0.004 0.043 11563 Dihedral : 14.907 176.771 10993 Min Nonbonded Distance : 2.119 Molprobity Statistics. All-atom Clashscore : 3.08 Ramachandran Plot: Outliers : 0.01 % Allowed : 1.41 % Favored : 98.57 % Rotamer: Outliers : 1.80 % Allowed : 10.66 % Favored : 87.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.54 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.01 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.46 (0.09), residues: 7997 helix: 1.59 (0.08), residues: 4317 sheet: 0.24 (0.26), residues: 375 loop : 0.37 (0.11), residues: 3305 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP L 144 HIS 0.006 0.001 HIS G 101 PHE 0.028 0.001 PHE N 292 TYR 0.021 0.001 TYR O 94 ARG 0.008 0.000 ARG g 95 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15994 Ramachandran restraints generated. 7997 Oldfield, 0 Emsley, 7997 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15994 Ramachandran restraints generated. 7997 Oldfield, 0 Emsley, 7997 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1112 residues out of total 7080 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 127 poor density : 985 time to evaluate : 6.049 Fit side-chains revert: symmetry clash REVERT: A 26 GLN cc_start: 0.7270 (OUTLIER) cc_final: 0.6394 (mt0) REVERT: B 35 ASP cc_start: 0.8375 (m-30) cc_final: 0.8064 (m-30) REVERT: E 114 ASP cc_start: 0.7680 (OUTLIER) cc_final: 0.7256 (m-30) REVERT: E 134 ASP cc_start: 0.7998 (OUTLIER) cc_final: 0.7562 (p0) REVERT: F 249 ARG cc_start: 0.8389 (OUTLIER) cc_final: 0.7732 (mtp-110) REVERT: G 653 ASN cc_start: 0.8219 (t0) cc_final: 0.7879 (t0) REVERT: G 655 GLN cc_start: 0.7845 (OUTLIER) cc_final: 0.7538 (mp10) REVERT: K 46 LEU cc_start: 0.9056 (OUTLIER) cc_final: 0.8715 (mp) REVERT: L 179 ASP cc_start: 0.8427 (m-30) cc_final: 0.8205 (m-30) REVERT: L 445 GLU cc_start: 0.8731 (pt0) cc_final: 0.8399 (pt0) REVERT: O 20 GLU cc_start: 0.7225 (pp20) cc_final: 0.6807 (pm20) REVERT: R 3 ARG cc_start: 0.7361 (OUTLIER) cc_final: 0.7045 (ttp80) REVERT: R 51 GLN cc_start: 0.8666 (OUTLIER) cc_final: 0.7988 (mp10) REVERT: R 95 HIS cc_start: 0.5973 (OUTLIER) cc_final: 0.4999 (t-90) REVERT: S 90 LEU cc_start: 0.9113 (OUTLIER) cc_final: 0.8819 (mm) REVERT: V 69 GLU cc_start: 0.7756 (OUTLIER) cc_final: 0.7382 (tt0) REVERT: X 148 GLU cc_start: 0.7874 (OUTLIER) cc_final: 0.7372 (mp0) REVERT: X 152 GLU cc_start: 0.6483 (OUTLIER) cc_final: 0.6171 (tt0) REVERT: d 77 LYS cc_start: 0.8820 (mtpp) cc_final: 0.8585 (mtpt) REVERT: g 49 LYS cc_start: 0.8376 (mtmm) cc_final: 0.8120 (mttp) REVERT: l 83 MET cc_start: 0.9265 (ttp) cc_final: 0.9015 (ttp) REVERT: n 149 ARG cc_start: 0.7754 (OUTLIER) cc_final: 0.7545 (mtt-85) REVERT: p 121 ARG cc_start: 0.8218 (OUTLIER) cc_final: 0.7793 (ttp-170) outliers start: 127 outliers final: 50 residues processed: 1059 average time/residue: 1.8127 time to fit residues: 2418.2143 Evaluate side-chains 1026 residues out of total 7080 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 961 time to evaluate : 6.121 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 GLN Chi-restraints excluded: chain B residue 54 CYS Chi-restraints excluded: chain D residue 7 ASP Chi-restraints excluded: chain D residue 61 VAL Chi-restraints excluded: chain D residue 109 VAL Chi-restraints excluded: chain E residue 114 ASP Chi-restraints excluded: chain E residue 134 ASP Chi-restraints excluded: chain F residue 54 ASP Chi-restraints excluded: chain F residue 248 GLU Chi-restraints excluded: chain F residue 249 ARG Chi-restraints excluded: chain G residue 193 SER Chi-restraints excluded: chain G residue 364 LEU Chi-restraints excluded: chain G residue 651 LEU Chi-restraints excluded: chain G residue 655 GLN Chi-restraints excluded: chain G residue 659 ASP Chi-restraints excluded: chain H residue 121 TRP Chi-restraints excluded: chain H residue 194 ASN Chi-restraints excluded: chain K residue 46 LEU Chi-restraints excluded: chain L residue 10 VAL Chi-restraints excluded: chain L residue 393 ASP Chi-restraints excluded: chain M residue 72 LEU Chi-restraints excluded: chain M residue 114 GLU Chi-restraints excluded: chain M residue 398 VAL Chi-restraints excluded: chain O residue 1 LEU Chi-restraints excluded: chain O residue 2 GLN Chi-restraints excluded: chain O residue 19 THR Chi-restraints excluded: chain O residue 60 ASP Chi-restraints excluded: chain P residue 109 VAL Chi-restraints excluded: chain P residue 290 THR Chi-restraints excluded: chain Q residue 110 VAL Chi-restraints excluded: chain Q residue 115 SER Chi-restraints excluded: chain R residue 3 ARG Chi-restraints excluded: chain R residue 51 GLN Chi-restraints excluded: chain R residue 79 THR Chi-restraints excluded: chain R residue 95 HIS Chi-restraints excluded: chain S residue 90 LEU Chi-restraints excluded: chain T residue 7 THR Chi-restraints excluded: chain T residue 82 ASP Chi-restraints excluded: chain V residue 69 GLU Chi-restraints excluded: chain W residue 49 LEU Chi-restraints excluded: chain W residue 99 GLN Chi-restraints excluded: chain X residue 11 ASP Chi-restraints excluded: chain X residue 13 LYS Chi-restraints excluded: chain X residue 17 VAL Chi-restraints excluded: chain X residue 132 THR Chi-restraints excluded: chain X residue 148 GLU Chi-restraints excluded: chain X residue 152 GLU Chi-restraints excluded: chain Y residue 94 CYS Chi-restraints excluded: chain Y residue 109 ILE Chi-restraints excluded: chain Y residue 114 CYS Chi-restraints excluded: chain b residue 4 VAL Chi-restraints excluded: chain f residue 14 VAL Chi-restraints excluded: chain g residue 122 GLU Chi-restraints excluded: chain k residue 85 TYR Chi-restraints excluded: chain n residue 64 ARG Chi-restraints excluded: chain n residue 122 GLU Chi-restraints excluded: chain n residue 145 VAL Chi-restraints excluded: chain n residue 149 ARG Chi-restraints excluded: chain o residue 30 PHE Chi-restraints excluded: chain o residue 37 GLU Chi-restraints excluded: chain o residue 69 LYS Chi-restraints excluded: chain p residue 121 ARG Chi-restraints excluded: chain q residue 4 LEU Chi-restraints excluded: chain q residue 96 ASP Chi-restraints excluded: chain s residue 57 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 791 random chunks: chunk 399 optimal weight: 6.9990 chunk 222 optimal weight: 0.7980 chunk 597 optimal weight: 5.9990 chunk 489 optimal weight: 9.9990 chunk 198 optimal weight: 10.0000 chunk 719 optimal weight: 0.8980 chunk 777 optimal weight: 1.9990 chunk 640 optimal weight: 3.9990 chunk 713 optimal weight: 0.8980 chunk 245 optimal weight: 1.9990 chunk 577 optimal weight: 9.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 85 ASN C 211 GLN F 324 GLN G 444 GLN J 46 ASN J 120 ASN M 293 HIS V 49 GLN V 95 GLN W 51 GLN Y 88 ASN b 10 ASN j 6 HIS n 61 GLN n 140 GLN n 159 GLN p 22 GLN q 112 ASN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8697 moved from start: 0.1090 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.250 68792 Z= 0.462 Angle : 1.294 50.505 93045 Z= 0.834 Chirality : 0.256 6.517 10181 Planarity : 0.004 0.048 11563 Dihedral : 12.663 173.819 10929 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 3.26 Ramachandran Plot: Outliers : 0.01 % Allowed : 1.68 % Favored : 98.31 % Rotamer: Outliers : 1.67 % Allowed : 11.14 % Favored : 87.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.54 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.01 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.62 (0.09), residues: 7997 helix: 1.72 (0.08), residues: 4330 sheet: 0.24 (0.26), residues: 374 loop : 0.43 (0.11), residues: 3293 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP N 84 HIS 0.006 0.001 HIS N 112 PHE 0.028 0.001 PHE N 292 TYR 0.019 0.001 TYR L 422 ARG 0.008 0.000 ARG g 95 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15994 Ramachandran restraints generated. 7997 Oldfield, 0 Emsley, 7997 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15994 Ramachandran restraints generated. 7997 Oldfield, 0 Emsley, 7997 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1115 residues out of total 7080 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 118 poor density : 997 time to evaluate : 6.099 Fit side-chains revert: symmetry clash REVERT: E 114 ASP cc_start: 0.7642 (OUTLIER) cc_final: 0.7199 (m-30) REVERT: E 134 ASP cc_start: 0.7994 (OUTLIER) cc_final: 0.7553 (p0) REVERT: F 249 ARG cc_start: 0.8361 (OUTLIER) cc_final: 0.7657 (mtp-110) REVERT: G 447 LYS cc_start: 0.8381 (OUTLIER) cc_final: 0.8178 (mptp) REVERT: G 653 ASN cc_start: 0.8226 (t0) cc_final: 0.7886 (t0) REVERT: H 8 MET cc_start: 0.8117 (OUTLIER) cc_final: 0.7643 (mtt) REVERT: L 128 MET cc_start: 0.8962 (tpt) cc_final: 0.8742 (tpt) REVERT: O 20 GLU cc_start: 0.7205 (pp20) cc_final: 0.6794 (pm20) REVERT: R 3 ARG cc_start: 0.7346 (OUTLIER) cc_final: 0.7052 (ttp80) REVERT: R 95 HIS cc_start: 0.5960 (OUTLIER) cc_final: 0.5076 (t-90) REVERT: V 6 LYS cc_start: 0.8277 (OUTLIER) cc_final: 0.7892 (ttpt) REVERT: V 69 GLU cc_start: 0.7717 (OUTLIER) cc_final: 0.7332 (tt0) REVERT: X 148 GLU cc_start: 0.7857 (OUTLIER) cc_final: 0.7307 (mp0) REVERT: X 152 GLU cc_start: 0.6555 (OUTLIER) cc_final: 0.6243 (tt0) REVERT: Y 109 ILE cc_start: 0.8053 (OUTLIER) cc_final: 0.7829 (mp) REVERT: b 39 LYS cc_start: 0.8415 (OUTLIER) cc_final: 0.8143 (pttm) REVERT: c 1 LYS cc_start: 0.7446 (OUTLIER) cc_final: 0.7068 (mppt) REVERT: d 77 LYS cc_start: 0.8829 (mtpp) cc_final: 0.8586 (mtpt) REVERT: g 49 LYS cc_start: 0.8353 (mtmm) cc_final: 0.8100 (mttp) REVERT: h 57 GLU cc_start: 0.7498 (OUTLIER) cc_final: 0.7021 (tm-30) REVERT: j 40 PHE cc_start: 0.8539 (t80) cc_final: 0.8125 (t80) REVERT: l 83 MET cc_start: 0.9280 (ttp) cc_final: 0.9029 (ttp) REVERT: o 120 ASP cc_start: 0.5938 (m-30) cc_final: 0.5376 (m-30) outliers start: 118 outliers final: 38 residues processed: 1059 average time/residue: 1.7981 time to fit residues: 2400.6351 Evaluate side-chains 1011 residues out of total 7080 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 958 time to evaluate : 5.940 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 54 CYS Chi-restraints excluded: chain D residue 61 VAL Chi-restraints excluded: chain E residue 14 GLU Chi-restraints excluded: chain E residue 114 ASP Chi-restraints excluded: chain E residue 134 ASP Chi-restraints excluded: chain F residue 54 ASP Chi-restraints excluded: chain F residue 231 SER Chi-restraints excluded: chain F residue 249 ARG Chi-restraints excluded: chain G residue 193 SER Chi-restraints excluded: chain G residue 351 THR Chi-restraints excluded: chain G residue 447 LYS Chi-restraints excluded: chain G residue 659 ASP Chi-restraints excluded: chain H residue 8 MET Chi-restraints excluded: chain H residue 121 TRP Chi-restraints excluded: chain L residue 10 VAL Chi-restraints excluded: chain L residue 349 SER Chi-restraints excluded: chain L residue 597 ILE Chi-restraints excluded: chain O residue 1 LEU Chi-restraints excluded: chain O residue 2 GLN Chi-restraints excluded: chain O residue 60 ASP Chi-restraints excluded: chain P residue 199 LYS Chi-restraints excluded: chain Q residue 66 GLU Chi-restraints excluded: chain R residue 3 ARG Chi-restraints excluded: chain R residue 20 ASP Chi-restraints excluded: chain R residue 95 HIS Chi-restraints excluded: chain S residue 39 ARG Chi-restraints excluded: chain T residue 82 ASP Chi-restraints excluded: chain V residue 6 LYS Chi-restraints excluded: chain V residue 69 GLU Chi-restraints excluded: chain W residue 49 LEU Chi-restraints excluded: chain X residue 13 LYS Chi-restraints excluded: chain X residue 148 GLU Chi-restraints excluded: chain X residue 152 GLU Chi-restraints excluded: chain Y residue 94 CYS Chi-restraints excluded: chain Y residue 109 ILE Chi-restraints excluded: chain Y residue 114 CYS Chi-restraints excluded: chain Z residue 99 LYS Chi-restraints excluded: chain b residue 39 LYS Chi-restraints excluded: chain c residue 1 LYS Chi-restraints excluded: chain e residue 56 LYS Chi-restraints excluded: chain f residue 14 VAL Chi-restraints excluded: chain g residue 122 GLU Chi-restraints excluded: chain h residue 57 GLU Chi-restraints excluded: chain k residue 85 TYR Chi-restraints excluded: chain n residue 64 ARG Chi-restraints excluded: chain n residue 122 GLU Chi-restraints excluded: chain n residue 145 VAL Chi-restraints excluded: chain o residue 30 PHE Chi-restraints excluded: chain o residue 37 GLU Chi-restraints excluded: chain q residue 96 ASP Chi-restraints excluded: chain q residue 134 ILE Chi-restraints excluded: chain r residue 68 VAL Chi-restraints excluded: chain s residue 57 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 791 random chunks: chunk 710 optimal weight: 3.9990 chunk 541 optimal weight: 4.9990 chunk 373 optimal weight: 0.7980 chunk 79 optimal weight: 5.9990 chunk 343 optimal weight: 4.9990 chunk 483 optimal weight: 4.9990 chunk 722 optimal weight: 6.9990 chunk 764 optimal weight: 3.9990 chunk 377 optimal weight: 2.9990 chunk 684 optimal weight: 3.9990 chunk 206 optimal weight: 0.9980 overall best weight: 2.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 85 ASN C 211 GLN G 444 GLN ** H 317 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 46 ASN J 120 ASN M 293 HIS V 95 GLN W 51 GLN Y 18 HIS Y 88 ASN b 10 ASN j 6 HIS n 61 GLN n 140 GLN n 159 GLN p 22 GLN q 112 ASN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8720 moved from start: 0.0981 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.241 68792 Z= 0.496 Angle : 1.311 50.545 93045 Z= 0.841 Chirality : 0.258 6.611 10181 Planarity : 0.004 0.045 11563 Dihedral : 12.264 175.533 10908 Min Nonbonded Distance : 2.143 Molprobity Statistics. All-atom Clashscore : 3.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % Rotamer: Outliers : 1.87 % Allowed : 11.15 % Favored : 86.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.54 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.01 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.55 (0.09), residues: 7997 helix: 1.67 (0.08), residues: 4319 sheet: 0.17 (0.26), residues: 386 loop : 0.40 (0.11), residues: 3292 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP N 84 HIS 0.007 0.001 HIS C 160 PHE 0.026 0.002 PHE N 292 TYR 0.021 0.002 TYR I 118 ARG 0.007 0.000 ARG g 95 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15994 Ramachandran restraints generated. 7997 Oldfield, 0 Emsley, 7997 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15994 Ramachandran restraints generated. 7997 Oldfield, 0 Emsley, 7997 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1093 residues out of total 7080 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 132 poor density : 961 time to evaluate : 6.176 Fit side-chains revert: symmetry clash REVERT: A 26 GLN cc_start: 0.7289 (OUTLIER) cc_final: 0.5970 (mt0) REVERT: E 114 ASP cc_start: 0.7654 (OUTLIER) cc_final: 0.7255 (m-30) REVERT: E 134 ASP cc_start: 0.7991 (OUTLIER) cc_final: 0.7559 (p0) REVERT: F 249 ARG cc_start: 0.8367 (OUTLIER) cc_final: 0.7701 (mtp-110) REVERT: G 445 GLU cc_start: 0.7399 (mt-10) cc_final: 0.7180 (mt-10) REVERT: G 447 LYS cc_start: 0.8392 (OUTLIER) cc_final: 0.8174 (mptp) REVERT: K 46 LEU cc_start: 0.9059 (OUTLIER) cc_final: 0.8697 (mp) REVERT: M 454 ILE cc_start: 0.9361 (OUTLIER) cc_final: 0.8802 (pp) REVERT: O 20 GLU cc_start: 0.7245 (pp20) cc_final: 0.6772 (pm20) REVERT: P 119 GLN cc_start: 0.8592 (OUTLIER) cc_final: 0.8277 (tt0) REVERT: R 95 HIS cc_start: 0.5933 (OUTLIER) cc_final: 0.5052 (t-90) REVERT: S 90 LEU cc_start: 0.9116 (OUTLIER) cc_final: 0.8839 (mm) REVERT: V 69 GLU cc_start: 0.7734 (OUTLIER) cc_final: 0.7356 (tt0) REVERT: X 148 GLU cc_start: 0.7852 (OUTLIER) cc_final: 0.7276 (mp0) REVERT: X 152 GLU cc_start: 0.6579 (OUTLIER) cc_final: 0.6277 (tt0) REVERT: Y 109 ILE cc_start: 0.8055 (OUTLIER) cc_final: 0.7825 (mp) REVERT: Z 7 LYS cc_start: 0.8372 (ttpt) cc_final: 0.8018 (tttp) REVERT: b 9 LYS cc_start: 0.8487 (OUTLIER) cc_final: 0.7996 (ttmt) REVERT: b 39 LYS cc_start: 0.8481 (OUTLIER) cc_final: 0.8157 (pttm) REVERT: c 1 LYS cc_start: 0.7497 (OUTLIER) cc_final: 0.7091 (mppt) REVERT: d 77 LYS cc_start: 0.8842 (mtpp) cc_final: 0.8614 (ttpt) REVERT: g 49 LYS cc_start: 0.8368 (mtmm) cc_final: 0.8128 (mttp) REVERT: h 57 GLU cc_start: 0.7552 (OUTLIER) cc_final: 0.7016 (tm-30) REVERT: i 121 GLU cc_start: 0.7131 (OUTLIER) cc_final: 0.6757 (mp0) REVERT: j 40 PHE cc_start: 0.8570 (t80) cc_final: 0.8136 (t80) REVERT: l 83 MET cc_start: 0.9259 (ttp) cc_final: 0.9011 (ttp) REVERT: o 120 ASP cc_start: 0.5922 (OUTLIER) cc_final: 0.5338 (m-30) REVERT: p 121 ARG cc_start: 0.8253 (OUTLIER) cc_final: 0.7797 (ttp-170) outliers start: 132 outliers final: 61 residues processed: 1029 average time/residue: 1.8591 time to fit residues: 2406.2238 Evaluate side-chains 1041 residues out of total 7080 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 82 poor density : 959 time to evaluate : 6.035 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 GLN Chi-restraints excluded: chain B residue 29 VAL Chi-restraints excluded: chain B residue 54 CYS Chi-restraints excluded: chain B residue 161 LEU Chi-restraints excluded: chain D residue 61 VAL Chi-restraints excluded: chain D residue 109 VAL Chi-restraints excluded: chain E residue 14 GLU Chi-restraints excluded: chain E residue 114 ASP Chi-restraints excluded: chain E residue 134 ASP Chi-restraints excluded: chain F residue 54 ASP Chi-restraints excluded: chain F residue 231 SER Chi-restraints excluded: chain F residue 248 GLU Chi-restraints excluded: chain F residue 249 ARG Chi-restraints excluded: chain G residue 193 SER Chi-restraints excluded: chain G residue 351 THR Chi-restraints excluded: chain G residue 447 LYS Chi-restraints excluded: chain G residue 659 ASP Chi-restraints excluded: chain H residue 121 TRP Chi-restraints excluded: chain H residue 194 ASN Chi-restraints excluded: chain J residue 82 ILE Chi-restraints excluded: chain K residue 46 LEU Chi-restraints excluded: chain L residue 10 VAL Chi-restraints excluded: chain L residue 349 SER Chi-restraints excluded: chain L residue 393 ASP Chi-restraints excluded: chain L residue 554 ASP Chi-restraints excluded: chain M residue 72 LEU Chi-restraints excluded: chain M residue 114 GLU Chi-restraints excluded: chain M residue 454 ILE Chi-restraints excluded: chain N residue 320 MET Chi-restraints excluded: chain N residue 322 LYS Chi-restraints excluded: chain O residue 1 LEU Chi-restraints excluded: chain O residue 2 GLN Chi-restraints excluded: chain O residue 19 THR Chi-restraints excluded: chain O residue 60 ASP Chi-restraints excluded: chain P residue 109 VAL Chi-restraints excluded: chain P residue 119 GLN Chi-restraints excluded: chain P residue 199 LYS Chi-restraints excluded: chain Q residue 66 GLU Chi-restraints excluded: chain R residue 4 THR Chi-restraints excluded: chain R residue 95 HIS Chi-restraints excluded: chain S residue 39 ARG Chi-restraints excluded: chain S residue 90 LEU Chi-restraints excluded: chain T residue 7 THR Chi-restraints excluded: chain T residue 82 ASP Chi-restraints excluded: chain V residue 6 LYS Chi-restraints excluded: chain V residue 69 GLU Chi-restraints excluded: chain W residue 49 LEU Chi-restraints excluded: chain X residue 11 ASP Chi-restraints excluded: chain X residue 13 LYS Chi-restraints excluded: chain X residue 17 VAL Chi-restraints excluded: chain X residue 148 GLU Chi-restraints excluded: chain X residue 152 GLU Chi-restraints excluded: chain Y residue 36 SER Chi-restraints excluded: chain Y residue 94 CYS Chi-restraints excluded: chain Y residue 109 ILE Chi-restraints excluded: chain Y residue 114 CYS Chi-restraints excluded: chain Z residue 99 LYS Chi-restraints excluded: chain Z residue 144 THR Chi-restraints excluded: chain b residue 9 LYS Chi-restraints excluded: chain b residue 39 LYS Chi-restraints excluded: chain b residue 42 LEU Chi-restraints excluded: chain c residue 1 LYS Chi-restraints excluded: chain c residue 19 LEU Chi-restraints excluded: chain e residue 56 LYS Chi-restraints excluded: chain g residue 122 GLU Chi-restraints excluded: chain h residue 57 GLU Chi-restraints excluded: chain i residue 121 GLU Chi-restraints excluded: chain k residue 85 TYR Chi-restraints excluded: chain m residue 23 ASP Chi-restraints excluded: chain n residue 64 ARG Chi-restraints excluded: chain n residue 122 GLU Chi-restraints excluded: chain n residue 145 VAL Chi-restraints excluded: chain o residue 30 PHE Chi-restraints excluded: chain o residue 37 GLU Chi-restraints excluded: chain o residue 69 LYS Chi-restraints excluded: chain o residue 120 ASP Chi-restraints excluded: chain p residue 38 LEU Chi-restraints excluded: chain p residue 121 ARG Chi-restraints excluded: chain q residue 4 LEU Chi-restraints excluded: chain q residue 134 ILE Chi-restraints excluded: chain r residue 68 VAL Chi-restraints excluded: chain s residue 57 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 791 random chunks: chunk 636 optimal weight: 3.9990 chunk 434 optimal weight: 6.9990 chunk 11 optimal weight: 0.9990 chunk 569 optimal weight: 0.7980 chunk 315 optimal weight: 0.7980 chunk 652 optimal weight: 4.9990 chunk 528 optimal weight: 0.6980 chunk 0 optimal weight: 10.0000 chunk 390 optimal weight: 0.9990 chunk 686 optimal weight: 0.9990 chunk 192 optimal weight: 0.7980 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 85 ASN C 211 GLN D 114 ASN E 37 ASN G 444 GLN ** H 317 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 23 GLN J 46 ASN J 120 ASN M 293 HIS V 95 GLN W 51 GLN Y 18 HIS Y 88 ASN Z 76 GLN b 10 ASN j 6 HIS n 61 GLN n 140 GLN n 159 GLN p 22 GLN q 112 ASN r 24 GLN s 55 ASN Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8678 moved from start: 0.1295 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.245 68792 Z= 0.449 Angle : 1.283 50.548 93045 Z= 0.830 Chirality : 0.254 6.454 10181 Planarity : 0.004 0.045 11563 Dihedral : 11.489 173.531 10908 Min Nonbonded Distance : 2.146 Molprobity Statistics. All-atom Clashscore : 3.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.55 % Favored : 98.45 % Rotamer: Outliers : 1.53 % Allowed : 11.63 % Favored : 86.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.54 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.01 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.71 (0.09), residues: 7997 helix: 1.82 (0.08), residues: 4310 sheet: 0.12 (0.26), residues: 387 loop : 0.47 (0.11), residues: 3300 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP X 85 HIS 0.006 0.001 HIS N 112 PHE 0.029 0.001 PHE N 292 TYR 0.020 0.001 TYR L 422 ARG 0.008 0.000 ARG g 95 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15994 Ramachandran restraints generated. 7997 Oldfield, 0 Emsley, 7997 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15994 Ramachandran restraints generated. 7997 Oldfield, 0 Emsley, 7997 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1099 residues out of total 7080 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 108 poor density : 991 time to evaluate : 6.006 Fit side-chains REVERT: A 26 GLN cc_start: 0.7215 (OUTLIER) cc_final: 0.5834 (mt0) REVERT: E 134 ASP cc_start: 0.7993 (OUTLIER) cc_final: 0.7551 (p0) REVERT: F 249 ARG cc_start: 0.8354 (OUTLIER) cc_final: 0.7550 (mtp-110) REVERT: G 653 ASN cc_start: 0.8185 (t0) cc_final: 0.7859 (t0) REVERT: G 655 GLN cc_start: 0.7844 (OUTLIER) cc_final: 0.7552 (mp10) REVERT: H 234 MET cc_start: 0.8174 (mmt) cc_final: 0.7733 (mmt) REVERT: M 454 ILE cc_start: 0.9336 (OUTLIER) cc_final: 0.8840 (pp) REVERT: O 1 LEU cc_start: 0.7139 (OUTLIER) cc_final: 0.6808 (tt) REVERT: O 20 GLU cc_start: 0.7196 (pp20) cc_final: 0.6745 (pm20) REVERT: P 119 GLN cc_start: 0.8565 (OUTLIER) cc_final: 0.8266 (tt0) REVERT: R 95 HIS cc_start: 0.5927 (OUTLIER) cc_final: 0.5148 (t-90) REVERT: T 57 GLU cc_start: 0.7035 (OUTLIER) cc_final: 0.6793 (tp30) REVERT: V 6 LYS cc_start: 0.8286 (OUTLIER) cc_final: 0.7902 (ttpt) REVERT: V 69 GLU cc_start: 0.7698 (OUTLIER) cc_final: 0.7312 (tt0) REVERT: W 26 ASN cc_start: 0.8182 (m-40) cc_final: 0.7882 (m110) REVERT: b 39 LYS cc_start: 0.8386 (OUTLIER) cc_final: 0.8076 (pttt) REVERT: c 1 LYS cc_start: 0.7496 (OUTLIER) cc_final: 0.7097 (mppt) REVERT: d 77 LYS cc_start: 0.8804 (mtpp) cc_final: 0.8582 (ttpt) REVERT: g 49 LYS cc_start: 0.8346 (mtmm) cc_final: 0.8099 (mttp) REVERT: g 122 GLU cc_start: 0.7333 (OUTLIER) cc_final: 0.6619 (tt0) REVERT: h 57 GLU cc_start: 0.7504 (OUTLIER) cc_final: 0.6991 (tm-30) REVERT: i 121 GLU cc_start: 0.7126 (OUTLIER) cc_final: 0.6767 (mp0) REVERT: j 40 PHE cc_start: 0.8518 (t80) cc_final: 0.8079 (t80) REVERT: l 83 MET cc_start: 0.9295 (ttp) cc_final: 0.8960 (ttp) REVERT: o 116 GLN cc_start: 0.7483 (mm-40) cc_final: 0.7181 (tp40) REVERT: o 120 ASP cc_start: 0.5942 (m-30) cc_final: 0.5239 (m-30) REVERT: p 14 ARG cc_start: 0.6723 (tpp80) cc_final: 0.6387 (tpt170) REVERT: p 121 ARG cc_start: 0.8176 (OUTLIER) cc_final: 0.7743 (ttp-170) outliers start: 108 outliers final: 40 residues processed: 1051 average time/residue: 1.8178 time to fit residues: 2406.3298 Evaluate side-chains 1020 residues out of total 7080 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 963 time to evaluate : 5.972 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 GLN Chi-restraints excluded: chain B residue 54 CYS Chi-restraints excluded: chain D residue 61 VAL Chi-restraints excluded: chain D residue 100 LEU Chi-restraints excluded: chain D residue 109 VAL Chi-restraints excluded: chain E residue 14 GLU Chi-restraints excluded: chain E residue 134 ASP Chi-restraints excluded: chain F residue 231 SER Chi-restraints excluded: chain F residue 248 GLU Chi-restraints excluded: chain F residue 249 ARG Chi-restraints excluded: chain G residue 351 THR Chi-restraints excluded: chain G residue 655 GLN Chi-restraints excluded: chain G residue 659 ASP Chi-restraints excluded: chain H residue 121 TRP Chi-restraints excluded: chain L residue 10 VAL Chi-restraints excluded: chain L residue 349 SER Chi-restraints excluded: chain L residue 393 ASP Chi-restraints excluded: chain L residue 554 ASP Chi-restraints excluded: chain M residue 78 MET Chi-restraints excluded: chain M residue 113 MET Chi-restraints excluded: chain M residue 114 GLU Chi-restraints excluded: chain M residue 454 ILE Chi-restraints excluded: chain O residue 1 LEU Chi-restraints excluded: chain O residue 2 GLN Chi-restraints excluded: chain O residue 19 THR Chi-restraints excluded: chain P residue 109 VAL Chi-restraints excluded: chain P residue 119 GLN Chi-restraints excluded: chain Q residue 66 GLU Chi-restraints excluded: chain R residue 95 HIS Chi-restraints excluded: chain T residue 57 GLU Chi-restraints excluded: chain V residue 6 LYS Chi-restraints excluded: chain V residue 69 GLU Chi-restraints excluded: chain W residue 49 LEU Chi-restraints excluded: chain X residue 11 ASP Chi-restraints excluded: chain X residue 13 LYS Chi-restraints excluded: chain X residue 132 THR Chi-restraints excluded: chain Y residue 36 SER Chi-restraints excluded: chain Y residue 114 CYS Chi-restraints excluded: chain Z residue 144 THR Chi-restraints excluded: chain b residue 39 LYS Chi-restraints excluded: chain b residue 42 LEU Chi-restraints excluded: chain c residue 1 LYS Chi-restraints excluded: chain c residue 40 LEU Chi-restraints excluded: chain f residue 14 VAL Chi-restraints excluded: chain g residue 122 GLU Chi-restraints excluded: chain h residue 57 GLU Chi-restraints excluded: chain i residue 121 GLU Chi-restraints excluded: chain k residue 85 TYR Chi-restraints excluded: chain n residue 122 GLU Chi-restraints excluded: chain n residue 145 VAL Chi-restraints excluded: chain o residue 30 PHE Chi-restraints excluded: chain o residue 37 GLU Chi-restraints excluded: chain p residue 38 LEU Chi-restraints excluded: chain p residue 121 ARG Chi-restraints excluded: chain q residue 134 ILE Chi-restraints excluded: chain r residue 68 VAL Chi-restraints excluded: chain s residue 57 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 791 random chunks: chunk 257 optimal weight: 3.9990 chunk 688 optimal weight: 6.9990 chunk 151 optimal weight: 3.9990 chunk 448 optimal weight: 9.9990 chunk 188 optimal weight: 2.9990 chunk 765 optimal weight: 9.9990 chunk 635 optimal weight: 9.9990 chunk 354 optimal weight: 8.9990 chunk 63 optimal weight: 0.9990 chunk 253 optimal weight: 7.9990 chunk 401 optimal weight: 3.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 85 ASN C 211 GLN ** H 317 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 199 GLN M 88 ASN M 169 ASN M 293 HIS V 95 GLN W 51 GLN Y 18 HIS Y 88 ASN b 10 ASN e 76 HIS j 6 HIS n 61 GLN n 140 GLN n 159 GLN p 22 GLN q 112 ASN r 24 GLN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8727 moved from start: 0.1005 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.241 68792 Z= 0.523 Angle : 1.320 50.466 93045 Z= 0.844 Chirality : 0.260 6.647 10181 Planarity : 0.004 0.048 11563 Dihedral : 11.673 176.038 10896 Min Nonbonded Distance : 2.145 Molprobity Statistics. All-atom Clashscore : 3.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.75 % Favored : 98.25 % Rotamer: Outliers : 1.74 % Allowed : 11.69 % Favored : 86.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.54 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.01 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.52 (0.09), residues: 7997 helix: 1.65 (0.08), residues: 4321 sheet: 0.17 (0.26), residues: 388 loop : 0.39 (0.11), residues: 3288 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP N 84 HIS 0.008 0.001 HIS e 76 PHE 0.025 0.002 PHE N 292 TYR 0.023 0.002 TYR I 118 ARG 0.008 0.000 ARG g 95 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15994 Ramachandran restraints generated. 7997 Oldfield, 0 Emsley, 7997 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15994 Ramachandran restraints generated. 7997 Oldfield, 0 Emsley, 7997 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1092 residues out of total 7080 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 123 poor density : 969 time to evaluate : 6.043 Fit side-chains revert: symmetry clash REVERT: A 26 GLN cc_start: 0.7301 (OUTLIER) cc_final: 0.5978 (mt0) REVERT: E 134 ASP cc_start: 0.7986 (OUTLIER) cc_final: 0.7551 (p0) REVERT: F 249 ARG cc_start: 0.8357 (OUTLIER) cc_final: 0.7661 (mtp-110) REVERT: G 427 LYS cc_start: 0.8323 (OUTLIER) cc_final: 0.8123 (mtmt) REVERT: K 46 LEU cc_start: 0.9064 (OUTLIER) cc_final: 0.8698 (mp) REVERT: O 20 GLU cc_start: 0.7229 (pp20) cc_final: 0.6763 (pm20) REVERT: P 119 GLN cc_start: 0.8608 (OUTLIER) cc_final: 0.8260 (tt0) REVERT: R 95 HIS cc_start: 0.5899 (OUTLIER) cc_final: 0.5112 (t-90) REVERT: S 90 LEU cc_start: 0.9108 (OUTLIER) cc_final: 0.8828 (mm) REVERT: V 69 GLU cc_start: 0.7751 (OUTLIER) cc_final: 0.7378 (tt0) REVERT: X 148 GLU cc_start: 0.7862 (OUTLIER) cc_final: 0.7187 (mp0) REVERT: X 152 GLU cc_start: 0.6614 (OUTLIER) cc_final: 0.6279 (tt0) REVERT: b 39 LYS cc_start: 0.8483 (OUTLIER) cc_final: 0.8140 (pttm) REVERT: c 1 LYS cc_start: 0.7509 (OUTLIER) cc_final: 0.7099 (mppt) REVERT: d 77 LYS cc_start: 0.8845 (mtpp) cc_final: 0.8622 (ttpt) REVERT: h 57 GLU cc_start: 0.7539 (OUTLIER) cc_final: 0.7005 (tm-30) REVERT: i 121 GLU cc_start: 0.7135 (OUTLIER) cc_final: 0.6766 (mp0) REVERT: j 32 MET cc_start: 0.9112 (ttp) cc_final: 0.8736 (ttp) REVERT: j 40 PHE cc_start: 0.8579 (t80) cc_final: 0.8153 (t80) REVERT: o 120 ASP cc_start: 0.5874 (OUTLIER) cc_final: 0.5283 (m-30) REVERT: p 121 ARG cc_start: 0.8270 (OUTLIER) cc_final: 0.7807 (ttp-170) outliers start: 123 outliers final: 61 residues processed: 1035 average time/residue: 1.8285 time to fit residues: 2380.5833 Evaluate side-chains 1034 residues out of total 7080 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 78 poor density : 956 time to evaluate : 5.922 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 GLN Chi-restraints excluded: chain B residue 54 CYS Chi-restraints excluded: chain B residue 161 LEU Chi-restraints excluded: chain D residue 61 VAL Chi-restraints excluded: chain D residue 109 VAL Chi-restraints excluded: chain E residue 14 GLU Chi-restraints excluded: chain E residue 134 ASP Chi-restraints excluded: chain F residue 54 ASP Chi-restraints excluded: chain F residue 105 CYS Chi-restraints excluded: chain F residue 231 SER Chi-restraints excluded: chain F residue 249 ARG Chi-restraints excluded: chain G residue 351 THR Chi-restraints excluded: chain G residue 427 LYS Chi-restraints excluded: chain G residue 483 VAL Chi-restraints excluded: chain G residue 659 ASP Chi-restraints excluded: chain H residue 121 TRP Chi-restraints excluded: chain J residue 82 ILE Chi-restraints excluded: chain K residue 46 LEU Chi-restraints excluded: chain L residue 10 VAL Chi-restraints excluded: chain L residue 30 SER Chi-restraints excluded: chain L residue 349 SER Chi-restraints excluded: chain L residue 393 ASP Chi-restraints excluded: chain L residue 554 ASP Chi-restraints excluded: chain M residue 72 LEU Chi-restraints excluded: chain M residue 113 MET Chi-restraints excluded: chain M residue 114 GLU Chi-restraints excluded: chain N residue 320 MET Chi-restraints excluded: chain O residue 1 LEU Chi-restraints excluded: chain O residue 2 GLN Chi-restraints excluded: chain O residue 19 THR Chi-restraints excluded: chain P residue 109 VAL Chi-restraints excluded: chain P residue 119 GLN Chi-restraints excluded: chain P residue 199 LYS Chi-restraints excluded: chain Q residue 66 GLU Chi-restraints excluded: chain R residue 95 HIS Chi-restraints excluded: chain S residue 39 ARG Chi-restraints excluded: chain S residue 90 LEU Chi-restraints excluded: chain T residue 32 VAL Chi-restraints excluded: chain T residue 82 ASP Chi-restraints excluded: chain V residue 6 LYS Chi-restraints excluded: chain V residue 69 GLU Chi-restraints excluded: chain W residue 49 LEU Chi-restraints excluded: chain X residue 11 ASP Chi-restraints excluded: chain X residue 13 LYS Chi-restraints excluded: chain X residue 17 VAL Chi-restraints excluded: chain X residue 132 THR Chi-restraints excluded: chain X residue 148 GLU Chi-restraints excluded: chain X residue 152 GLU Chi-restraints excluded: chain Y residue 36 SER Chi-restraints excluded: chain Y residue 94 CYS Chi-restraints excluded: chain Y residue 109 ILE Chi-restraints excluded: chain Y residue 114 CYS Chi-restraints excluded: chain Z residue 99 LYS Chi-restraints excluded: chain Z residue 144 THR Chi-restraints excluded: chain b residue 14 LYS Chi-restraints excluded: chain b residue 39 LYS Chi-restraints excluded: chain b residue 42 LEU Chi-restraints excluded: chain c residue 1 LYS Chi-restraints excluded: chain e residue 56 LYS Chi-restraints excluded: chain f residue 14 VAL Chi-restraints excluded: chain g residue 122 GLU Chi-restraints excluded: chain h residue 57 GLU Chi-restraints excluded: chain i residue 121 GLU Chi-restraints excluded: chain k residue 78 VAL Chi-restraints excluded: chain k residue 85 TYR Chi-restraints excluded: chain m residue 23 ASP Chi-restraints excluded: chain n residue 122 GLU Chi-restraints excluded: chain n residue 145 VAL Chi-restraints excluded: chain o residue 30 PHE Chi-restraints excluded: chain o residue 37 GLU Chi-restraints excluded: chain o residue 69 LYS Chi-restraints excluded: chain o residue 120 ASP Chi-restraints excluded: chain p residue 38 LEU Chi-restraints excluded: chain p residue 121 ARG Chi-restraints excluded: chain p residue 134 VAL Chi-restraints excluded: chain q residue 134 ILE Chi-restraints excluded: chain r residue 68 VAL Chi-restraints excluded: chain s residue 57 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 791 random chunks: chunk 737 optimal weight: 3.9990 chunk 86 optimal weight: 9.9990 chunk 436 optimal weight: 0.9980 chunk 558 optimal weight: 0.9980 chunk 433 optimal weight: 6.9990 chunk 644 optimal weight: 5.9990 chunk 427 optimal weight: 0.7980 chunk 762 optimal weight: 6.9990 chunk 477 optimal weight: 1.9990 chunk 464 optimal weight: 7.9990 chunk 351 optimal weight: 2.9990 overall best weight: 1.5584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 85 ASN C 211 GLN ** H 317 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 46 ASN M 293 HIS V 95 GLN W 51 GLN Y 18 HIS Y 88 ASN b 10 ASN j 6 HIS n 61 GLN n 140 GLN n 159 GLN p 22 GLN q 112 ASN r 24 GLN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8703 moved from start: 0.1155 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.244 68792 Z= 0.465 Angle : 1.295 50.538 93045 Z= 0.835 Chirality : 0.256 6.511 10181 Planarity : 0.004 0.045 11563 Dihedral : 11.361 175.129 10896 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 3.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.64 % Favored : 98.36 % Rotamer: Outliers : 1.37 % Allowed : 12.14 % Favored : 86.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.54 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.01 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.61 (0.09), residues: 7997 helix: 1.74 (0.08), residues: 4320 sheet: 0.13 (0.26), residues: 384 loop : 0.41 (0.11), residues: 3293 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP X 85 HIS 0.006 0.001 HIS N 112 PHE 0.028 0.001 PHE N 292 TYR 0.019 0.001 TYR L 422 ARG 0.009 0.000 ARG g 95 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15994 Ramachandran restraints generated. 7997 Oldfield, 0 Emsley, 7997 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15994 Ramachandran restraints generated. 7997 Oldfield, 0 Emsley, 7997 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1071 residues out of total 7080 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 97 poor density : 974 time to evaluate : 5.940 Fit side-chains revert: symmetry clash REVERT: A 26 GLN cc_start: 0.7265 (OUTLIER) cc_final: 0.5885 (mt0) REVERT: F 249 ARG cc_start: 0.8362 (OUTLIER) cc_final: 0.7616 (mtp-110) REVERT: G 427 LYS cc_start: 0.8297 (OUTLIER) cc_final: 0.8096 (mtmt) REVERT: G 653 ASN cc_start: 0.8248 (t0) cc_final: 0.7891 (t0) REVERT: M 454 ILE cc_start: 0.9348 (OUTLIER) cc_final: 0.8813 (pp) REVERT: O 20 GLU cc_start: 0.7220 (pp20) cc_final: 0.6760 (pm20) REVERT: P 119 GLN cc_start: 0.8565 (OUTLIER) cc_final: 0.8146 (tt0) REVERT: R 95 HIS cc_start: 0.5904 (OUTLIER) cc_final: 0.5174 (t-90) REVERT: S 90 LEU cc_start: 0.9088 (OUTLIER) cc_final: 0.8832 (mm) REVERT: V 69 GLU cc_start: 0.7720 (OUTLIER) cc_final: 0.7340 (tt0) REVERT: X 152 GLU cc_start: 0.6546 (OUTLIER) cc_final: 0.6227 (tt0) REVERT: b 39 LYS cc_start: 0.8419 (OUTLIER) cc_final: 0.8090 (pttm) REVERT: c 1 LYS cc_start: 0.7504 (OUTLIER) cc_final: 0.7100 (mppt) REVERT: d 77 LYS cc_start: 0.8822 (mtpp) cc_final: 0.8584 (ttpt) REVERT: g 49 LYS cc_start: 0.8354 (mtmm) cc_final: 0.8106 (mttp) REVERT: g 122 GLU cc_start: 0.7323 (OUTLIER) cc_final: 0.6610 (tt0) REVERT: h 57 GLU cc_start: 0.7528 (OUTLIER) cc_final: 0.7013 (tm-30) REVERT: i 121 GLU cc_start: 0.7113 (OUTLIER) cc_final: 0.6761 (mp0) REVERT: j 32 MET cc_start: 0.9101 (ttp) cc_final: 0.8700 (ttp) REVERT: j 40 PHE cc_start: 0.8549 (t80) cc_final: 0.8128 (t80) REVERT: o 116 GLN cc_start: 0.7502 (mm-40) cc_final: 0.7228 (tp40) REVERT: o 120 ASP cc_start: 0.5909 (OUTLIER) cc_final: 0.5021 (m-30) REVERT: p 121 ARG cc_start: 0.8211 (OUTLIER) cc_final: 0.7768 (ttp-170) outliers start: 97 outliers final: 53 residues processed: 1025 average time/residue: 1.8339 time to fit residues: 2359.9430 Evaluate side-chains 1036 residues out of total 7080 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 967 time to evaluate : 5.887 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 GLN Chi-restraints excluded: chain B residue 29 VAL Chi-restraints excluded: chain B residue 54 CYS Chi-restraints excluded: chain B residue 161 LEU Chi-restraints excluded: chain D residue 61 VAL Chi-restraints excluded: chain D residue 100 LEU Chi-restraints excluded: chain D residue 109 VAL Chi-restraints excluded: chain E residue 14 GLU Chi-restraints excluded: chain F residue 54 ASP Chi-restraints excluded: chain F residue 105 CYS Chi-restraints excluded: chain F residue 231 SER Chi-restraints excluded: chain F residue 248 GLU Chi-restraints excluded: chain F residue 249 ARG Chi-restraints excluded: chain G residue 351 THR Chi-restraints excluded: chain G residue 427 LYS Chi-restraints excluded: chain G residue 659 ASP Chi-restraints excluded: chain H residue 121 TRP Chi-restraints excluded: chain H residue 194 ASN Chi-restraints excluded: chain L residue 10 VAL Chi-restraints excluded: chain L residue 349 SER Chi-restraints excluded: chain L residue 393 ASP Chi-restraints excluded: chain L residue 554 ASP Chi-restraints excluded: chain M residue 113 MET Chi-restraints excluded: chain M residue 114 GLU Chi-restraints excluded: chain M residue 454 ILE Chi-restraints excluded: chain N residue 320 MET Chi-restraints excluded: chain O residue 1 LEU Chi-restraints excluded: chain O residue 2 GLN Chi-restraints excluded: chain O residue 19 THR Chi-restraints excluded: chain P residue 109 VAL Chi-restraints excluded: chain P residue 119 GLN Chi-restraints excluded: chain P residue 199 LYS Chi-restraints excluded: chain Q residue 66 GLU Chi-restraints excluded: chain R residue 95 HIS Chi-restraints excluded: chain S residue 90 LEU Chi-restraints excluded: chain T residue 32 VAL Chi-restraints excluded: chain V residue 69 GLU Chi-restraints excluded: chain W residue 49 LEU Chi-restraints excluded: chain X residue 11 ASP Chi-restraints excluded: chain X residue 13 LYS Chi-restraints excluded: chain X residue 132 THR Chi-restraints excluded: chain X residue 152 GLU Chi-restraints excluded: chain Y residue 36 SER Chi-restraints excluded: chain Y residue 94 CYS Chi-restraints excluded: chain Y residue 109 ILE Chi-restraints excluded: chain Y residue 114 CYS Chi-restraints excluded: chain Z residue 97 VAL Chi-restraints excluded: chain Z residue 144 THR Chi-restraints excluded: chain b residue 39 LYS Chi-restraints excluded: chain b residue 42 LEU Chi-restraints excluded: chain c residue 1 LYS Chi-restraints excluded: chain e residue 56 LYS Chi-restraints excluded: chain f residue 14 VAL Chi-restraints excluded: chain g residue 122 GLU Chi-restraints excluded: chain h residue 57 GLU Chi-restraints excluded: chain i residue 121 GLU Chi-restraints excluded: chain k residue 85 TYR Chi-restraints excluded: chain m residue 23 ASP Chi-restraints excluded: chain n residue 122 GLU Chi-restraints excluded: chain n residue 145 VAL Chi-restraints excluded: chain o residue 30 PHE Chi-restraints excluded: chain o residue 37 GLU Chi-restraints excluded: chain o residue 69 LYS Chi-restraints excluded: chain o residue 120 ASP Chi-restraints excluded: chain p residue 38 LEU Chi-restraints excluded: chain p residue 121 ARG Chi-restraints excluded: chain q residue 134 ILE Chi-restraints excluded: chain r residue 68 VAL Chi-restraints excluded: chain s residue 57 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 791 random chunks: chunk 471 optimal weight: 0.9990 chunk 304 optimal weight: 0.8980 chunk 455 optimal weight: 0.4980 chunk 229 optimal weight: 2.9990 chunk 149 optimal weight: 9.9990 chunk 147 optimal weight: 0.9980 chunk 484 optimal weight: 0.8980 chunk 519 optimal weight: 5.9990 chunk 376 optimal weight: 0.8980 chunk 71 optimal weight: 0.4980 chunk 599 optimal weight: 0.0070 overall best weight: 0.5598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 85 ASN C 211 GLN H 5 ASN J 46 ASN M 44 GLN M 88 ASN V 95 GLN W 51 GLN Y 18 HIS Y 88 ASN b 10 ASN j 6 HIS n 61 GLN n 140 GLN n 159 GLN p 22 GLN q 112 ASN r 24 GLN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8660 moved from start: 0.1471 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.246 68792 Z= 0.447 Angle : 1.279 50.616 93045 Z= 0.829 Chirality : 0.254 6.419 10181 Planarity : 0.004 0.044 11563 Dihedral : 10.731 172.338 10896 Min Nonbonded Distance : 2.149 Molprobity Statistics. All-atom Clashscore : 4.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.71 % Favored : 98.29 % Rotamer: Outliers : 1.24 % Allowed : 12.45 % Favored : 86.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.54 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.01 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.78 (0.09), residues: 7997 helix: 1.88 (0.08), residues: 4317 sheet: 0.15 (0.25), residues: 409 loop : 0.49 (0.11), residues: 3271 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP L 144 HIS 0.005 0.001 HIS N 112 PHE 0.030 0.001 PHE N 292 TYR 0.022 0.001 TYR L 422 ARG 0.008 0.000 ARG g 95 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15994 Ramachandran restraints generated. 7997 Oldfield, 0 Emsley, 7997 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15994 Ramachandran restraints generated. 7997 Oldfield, 0 Emsley, 7997 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1074 residues out of total 7080 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 88 poor density : 986 time to evaluate : 6.087 Fit side-chains REVERT: A 26 GLN cc_start: 0.7165 (OUTLIER) cc_final: 0.5744 (mt0) REVERT: G 430 GLN cc_start: 0.8086 (mt0) cc_final: 0.7641 (mt0) REVERT: G 653 ASN cc_start: 0.8200 (t0) cc_final: 0.7869 (t0) REVERT: G 655 GLN cc_start: 0.7833 (OUTLIER) cc_final: 0.7579 (mp10) REVERT: H 234 MET cc_start: 0.8155 (mmt) cc_final: 0.7720 (mmt) REVERT: K 46 LEU cc_start: 0.9011 (OUTLIER) cc_final: 0.8723 (mp) REVERT: O 1 LEU cc_start: 0.7057 (OUTLIER) cc_final: 0.6834 (tt) REVERT: O 20 GLU cc_start: 0.7171 (pp20) cc_final: 0.6692 (pm20) REVERT: O 237 ASP cc_start: 0.8023 (m-30) cc_final: 0.7805 (m-30) REVERT: R 95 HIS cc_start: 0.5809 (OUTLIER) cc_final: 0.5232 (t-90) REVERT: V 69 GLU cc_start: 0.7669 (OUTLIER) cc_final: 0.7291 (tt0) REVERT: Z 7 LYS cc_start: 0.8417 (ttpt) cc_final: 0.8111 (tttp) REVERT: c 1 LYS cc_start: 0.7492 (OUTLIER) cc_final: 0.7088 (mppt) REVERT: d 77 LYS cc_start: 0.8811 (OUTLIER) cc_final: 0.8579 (ttpt) REVERT: f 29 LYS cc_start: 0.8381 (mtpt) cc_final: 0.7937 (mtpp) REVERT: g 49 LYS cc_start: 0.8308 (mtmm) cc_final: 0.8069 (mttp) REVERT: g 122 GLU cc_start: 0.7291 (OUTLIER) cc_final: 0.6626 (tt0) REVERT: h 57 GLU cc_start: 0.7515 (OUTLIER) cc_final: 0.6971 (tm-30) REVERT: j 40 PHE cc_start: 0.8500 (t80) cc_final: 0.8050 (t80) REVERT: p 14 ARG cc_start: 0.6707 (tpp80) cc_final: 0.6279 (tpt170) outliers start: 88 outliers final: 38 residues processed: 1034 average time/residue: 1.8333 time to fit residues: 2392.8595 Evaluate side-chains 1013 residues out of total 7080 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 965 time to evaluate : 5.907 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 GLN Chi-restraints excluded: chain B residue 29 VAL Chi-restraints excluded: chain B residue 54 CYS Chi-restraints excluded: chain D residue 61 VAL Chi-restraints excluded: chain D residue 109 VAL Chi-restraints excluded: chain E residue 14 GLU Chi-restraints excluded: chain F residue 54 ASP Chi-restraints excluded: chain F residue 105 CYS Chi-restraints excluded: chain F residue 231 SER Chi-restraints excluded: chain G residue 18 VAL Chi-restraints excluded: chain G residue 351 THR Chi-restraints excluded: chain G residue 655 GLN Chi-restraints excluded: chain G residue 659 ASP Chi-restraints excluded: chain H residue 121 TRP Chi-restraints excluded: chain K residue 46 LEU Chi-restraints excluded: chain L residue 10 VAL Chi-restraints excluded: chain L residue 349 SER Chi-restraints excluded: chain L residue 393 ASP Chi-restraints excluded: chain L residue 554 ASP Chi-restraints excluded: chain M residue 113 MET Chi-restraints excluded: chain M residue 393 ILE Chi-restraints excluded: chain O residue 1 LEU Chi-restraints excluded: chain O residue 19 THR Chi-restraints excluded: chain R residue 95 HIS Chi-restraints excluded: chain S residue 39 ARG Chi-restraints excluded: chain T residue 7 THR Chi-restraints excluded: chain T residue 32 VAL Chi-restraints excluded: chain V residue 69 GLU Chi-restraints excluded: chain W residue 49 LEU Chi-restraints excluded: chain X residue 13 LYS Chi-restraints excluded: chain X residue 132 THR Chi-restraints excluded: chain Y residue 36 SER Chi-restraints excluded: chain Y residue 114 CYS Chi-restraints excluded: chain b residue 14 LYS Chi-restraints excluded: chain b residue 42 LEU Chi-restraints excluded: chain c residue 1 LYS Chi-restraints excluded: chain d residue 77 LYS Chi-restraints excluded: chain g residue 122 GLU Chi-restraints excluded: chain h residue 57 GLU Chi-restraints excluded: chain k residue 85 TYR Chi-restraints excluded: chain n residue 122 GLU Chi-restraints excluded: chain n residue 145 VAL Chi-restraints excluded: chain o residue 30 PHE Chi-restraints excluded: chain o residue 37 GLU Chi-restraints excluded: chain o residue 120 ASP Chi-restraints excluded: chain p residue 38 LEU Chi-restraints excluded: chain r residue 104 GLU Chi-restraints excluded: chain s residue 57 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 791 random chunks: chunk 693 optimal weight: 6.9990 chunk 730 optimal weight: 0.7980 chunk 666 optimal weight: 0.8980 chunk 710 optimal weight: 0.5980 chunk 427 optimal weight: 9.9990 chunk 309 optimal weight: 2.9990 chunk 557 optimal weight: 3.9990 chunk 218 optimal weight: 0.8980 chunk 641 optimal weight: 0.0970 chunk 671 optimal weight: 9.9990 chunk 707 optimal weight: 8.9990 overall best weight: 0.6578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 85 ASN C 211 GLN L 135 ASN M 88 ASN V 95 GLN W 51 GLN Y 18 HIS Y 88 ASN b 10 ASN j 6 HIS n 140 GLN n 159 GLN p 22 GLN q 112 ASN r 24 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8661 moved from start: 0.1518 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.245 68792 Z= 0.448 Angle : 1.281 50.582 93045 Z= 0.829 Chirality : 0.254 6.517 10181 Planarity : 0.004 0.044 11563 Dihedral : 10.523 172.263 10893 Min Nonbonded Distance : 2.150 Molprobity Statistics. All-atom Clashscore : 4.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.65 % Favored : 98.35 % Rotamer: Outliers : 0.92 % Allowed : 13.06 % Favored : 86.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.54 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.01 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.83 (0.09), residues: 7997 helix: 1.92 (0.08), residues: 4319 sheet: 0.17 (0.25), residues: 409 loop : 0.53 (0.11), residues: 3269 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP X 85 HIS 0.006 0.001 HIS N 112 PHE 0.028 0.001 PHE N 292 TYR 0.021 0.001 TYR L 422 ARG 0.009 0.000 ARG g 95 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15994 Ramachandran restraints generated. 7997 Oldfield, 0 Emsley, 7997 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15994 Ramachandran restraints generated. 7997 Oldfield, 0 Emsley, 7997 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1040 residues out of total 7080 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 975 time to evaluate : 6.091 Fit side-chains REVERT: A 26 GLN cc_start: 0.7133 (OUTLIER) cc_final: 0.5612 (mt0) REVERT: E 134 ASP cc_start: 0.8011 (OUTLIER) cc_final: 0.7554 (p0) REVERT: G 653 ASN cc_start: 0.8182 (t0) cc_final: 0.7853 (t0) REVERT: G 655 GLN cc_start: 0.7840 (OUTLIER) cc_final: 0.7585 (mp10) REVERT: H 234 MET cc_start: 0.8153 (mmt) cc_final: 0.7720 (mmt) REVERT: K 46 LEU cc_start: 0.9019 (OUTLIER) cc_final: 0.8741 (mp) REVERT: O 20 GLU cc_start: 0.7174 (pp20) cc_final: 0.6692 (pm20) REVERT: O 237 ASP cc_start: 0.8000 (m-30) cc_final: 0.7778 (m-30) REVERT: R 95 HIS cc_start: 0.5754 (OUTLIER) cc_final: 0.5212 (t-90) REVERT: V 69 GLU cc_start: 0.7669 (OUTLIER) cc_final: 0.7291 (tt0) REVERT: X 148 GLU cc_start: 0.7829 (OUTLIER) cc_final: 0.7207 (mp0) REVERT: X 152 GLU cc_start: 0.6470 (OUTLIER) cc_final: 0.6186 (tt0) REVERT: Y 99 ILE cc_start: 0.8665 (mm) cc_final: 0.8393 (mt) REVERT: Z 7 LYS cc_start: 0.8431 (ttpt) cc_final: 0.8123 (tttp) REVERT: c 1 LYS cc_start: 0.7447 (OUTLIER) cc_final: 0.7043 (mppt) REVERT: d 77 LYS cc_start: 0.8815 (OUTLIER) cc_final: 0.8582 (ttpt) REVERT: f 29 LYS cc_start: 0.8385 (mtpt) cc_final: 0.7944 (mtpp) REVERT: g 49 LYS cc_start: 0.8305 (mtmm) cc_final: 0.8064 (mttp) REVERT: g 122 GLU cc_start: 0.7286 (OUTLIER) cc_final: 0.6612 (tt0) REVERT: h 57 GLU cc_start: 0.7496 (OUTLIER) cc_final: 0.6962 (tm-30) REVERT: j 32 MET cc_start: 0.9028 (ttp) cc_final: 0.8643 (ttp) REVERT: j 40 PHE cc_start: 0.8498 (t80) cc_final: 0.8011 (t80) REVERT: o 120 ASP cc_start: 0.5716 (OUTLIER) cc_final: 0.5356 (m-30) REVERT: p 14 ARG cc_start: 0.6708 (tpp80) cc_final: 0.6390 (tpt-90) outliers start: 65 outliers final: 40 residues processed: 1013 average time/residue: 1.8476 time to fit residues: 2353.6923 Evaluate side-chains 1015 residues out of total 7080 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 962 time to evaluate : 6.085 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 GLN Chi-restraints excluded: chain B residue 54 CYS Chi-restraints excluded: chain B residue 161 LEU Chi-restraints excluded: chain D residue 61 VAL Chi-restraints excluded: chain D residue 109 VAL Chi-restraints excluded: chain E residue 14 GLU Chi-restraints excluded: chain E residue 134 ASP Chi-restraints excluded: chain F residue 54 ASP Chi-restraints excluded: chain F residue 105 CYS Chi-restraints excluded: chain F residue 231 SER Chi-restraints excluded: chain G residue 18 VAL Chi-restraints excluded: chain G residue 351 THR Chi-restraints excluded: chain G residue 655 GLN Chi-restraints excluded: chain G residue 659 ASP Chi-restraints excluded: chain H residue 121 TRP Chi-restraints excluded: chain K residue 46 LEU Chi-restraints excluded: chain L residue 10 VAL Chi-restraints excluded: chain L residue 349 SER Chi-restraints excluded: chain L residue 393 ASP Chi-restraints excluded: chain L residue 554 ASP Chi-restraints excluded: chain M residue 113 MET Chi-restraints excluded: chain M residue 393 ILE Chi-restraints excluded: chain O residue 19 THR Chi-restraints excluded: chain O residue 60 ASP Chi-restraints excluded: chain R residue 95 HIS Chi-restraints excluded: chain S residue 39 ARG Chi-restraints excluded: chain S residue 90 LEU Chi-restraints excluded: chain T residue 7 THR Chi-restraints excluded: chain T residue 32 VAL Chi-restraints excluded: chain V residue 69 GLU Chi-restraints excluded: chain W residue 49 LEU Chi-restraints excluded: chain X residue 11 ASP Chi-restraints excluded: chain X residue 132 THR Chi-restraints excluded: chain X residue 148 GLU Chi-restraints excluded: chain X residue 152 GLU Chi-restraints excluded: chain Y residue 36 SER Chi-restraints excluded: chain Y residue 109 ILE Chi-restraints excluded: chain Y residue 114 CYS Chi-restraints excluded: chain b residue 14 LYS Chi-restraints excluded: chain b residue 42 LEU Chi-restraints excluded: chain c residue 1 LYS Chi-restraints excluded: chain d residue 77 LYS Chi-restraints excluded: chain g residue 122 GLU Chi-restraints excluded: chain h residue 57 GLU Chi-restraints excluded: chain k residue 85 TYR Chi-restraints excluded: chain n residue 122 GLU Chi-restraints excluded: chain n residue 145 VAL Chi-restraints excluded: chain o residue 30 PHE Chi-restraints excluded: chain o residue 37 GLU Chi-restraints excluded: chain o residue 120 ASP Chi-restraints excluded: chain p residue 38 LEU Chi-restraints excluded: chain r residue 104 GLU Chi-restraints excluded: chain s residue 57 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 791 random chunks: chunk 466 optimal weight: 0.8980 chunk 751 optimal weight: 0.5980 chunk 458 optimal weight: 0.8980 chunk 356 optimal weight: 0.0980 chunk 522 optimal weight: 0.8980 chunk 788 optimal weight: 10.0000 chunk 725 optimal weight: 0.0020 chunk 627 optimal weight: 8.9990 chunk 65 optimal weight: 3.9990 chunk 484 optimal weight: 8.9990 chunk 384 optimal weight: 0.9990 overall best weight: 0.4988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 85 ASN C 211 GLN M 88 ASN V 95 GLN W 51 GLN Y 18 HIS Y 88 ASN b 10 ASN j 6 HIS n 140 GLN p 22 GLN q 112 ASN r 24 GLN s 44 HIS Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8641 moved from start: 0.1668 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.246 68792 Z= 0.447 Angle : 1.277 50.573 93045 Z= 0.828 Chirality : 0.254 6.417 10181 Planarity : 0.004 0.047 11563 Dihedral : 10.112 171.823 10891 Min Nonbonded Distance : 2.150 Molprobity Statistics. All-atom Clashscore : 4.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.70 % Favored : 98.30 % Rotamer: Outliers : 0.85 % Allowed : 13.24 % Favored : 85.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.54 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.01 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.90 (0.10), residues: 7997 helix: 1.97 (0.08), residues: 4314 sheet: 0.16 (0.25), residues: 414 loop : 0.57 (0.11), residues: 3269 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP L 144 HIS 0.006 0.001 HIS N 112 PHE 0.029 0.001 PHE N 292 TYR 0.024 0.001 TYR i 61 ARG 0.010 0.000 ARG g 95 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15994 Ramachandran restraints generated. 7997 Oldfield, 0 Emsley, 7997 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15994 Ramachandran restraints generated. 7997 Oldfield, 0 Emsley, 7997 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1052 residues out of total 7080 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 992 time to evaluate : 6.409 Fit side-chains revert: symmetry clash REVERT: E 134 ASP cc_start: 0.8026 (OUTLIER) cc_final: 0.7561 (p0) REVERT: G 653 ASN cc_start: 0.8152 (t0) cc_final: 0.7838 (t0) REVERT: H 234 MET cc_start: 0.8141 (mmt) cc_final: 0.7733 (mmt) REVERT: K 46 LEU cc_start: 0.9008 (OUTLIER) cc_final: 0.8764 (mp) REVERT: M 19 LYS cc_start: 0.8137 (mttm) cc_final: 0.7543 (mppt) REVERT: N 21 MET cc_start: 0.8736 (mtt) cc_final: 0.8381 (mtt) REVERT: O 2 GLN cc_start: 0.7072 (OUTLIER) cc_final: 0.6661 (pt0) REVERT: O 20 GLU cc_start: 0.7163 (pp20) cc_final: 0.6704 (pm20) REVERT: R 95 HIS cc_start: 0.5750 (OUTLIER) cc_final: 0.5078 (t-90) REVERT: T 16 LEU cc_start: 0.8117 (mm) cc_final: 0.7895 (mm) REVERT: V 69 GLU cc_start: 0.7648 (OUTLIER) cc_final: 0.7265 (tt0) REVERT: X 148 GLU cc_start: 0.7825 (OUTLIER) cc_final: 0.7214 (mp0) REVERT: X 152 GLU cc_start: 0.6452 (OUTLIER) cc_final: 0.6175 (tt0) REVERT: Y 99 ILE cc_start: 0.8689 (mm) cc_final: 0.8435 (mt) REVERT: Z 7 LYS cc_start: 0.8404 (ttpt) cc_final: 0.8099 (tttp) REVERT: a 59 ARG cc_start: 0.8007 (mmt-90) cc_final: 0.7746 (mmp80) REVERT: c 1 LYS cc_start: 0.7439 (OUTLIER) cc_final: 0.7042 (mppt) REVERT: d 77 LYS cc_start: 0.8816 (OUTLIER) cc_final: 0.8586 (ttpt) REVERT: d 111 GLU cc_start: 0.8207 (OUTLIER) cc_final: 0.7989 (mt-10) REVERT: f 29 LYS cc_start: 0.8350 (mtpt) cc_final: 0.7922 (mtpp) REVERT: g 49 LYS cc_start: 0.8302 (mtmm) cc_final: 0.8062 (mttp) REVERT: g 122 GLU cc_start: 0.7170 (OUTLIER) cc_final: 0.6560 (tt0) REVERT: i 64 TYR cc_start: 0.6804 (t80) cc_final: 0.6533 (t80) REVERT: j 40 PHE cc_start: 0.8474 (t80) cc_final: 0.8017 (t80) REVERT: n 61 GLN cc_start: 0.8284 (tp40) cc_final: 0.8054 (tm130) REVERT: o 117 ARG cc_start: 0.7248 (ttp80) cc_final: 0.7000 (ttp-170) REVERT: p 14 ARG cc_start: 0.6716 (tpp80) cc_final: 0.6404 (tpt-90) outliers start: 60 outliers final: 36 residues processed: 1029 average time/residue: 1.7989 time to fit residues: 2334.3235 Evaluate side-chains 1009 residues out of total 7080 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 962 time to evaluate : 5.939 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 GLN Chi-restraints excluded: chain A residue 28 ASN Chi-restraints excluded: chain B residue 54 CYS Chi-restraints excluded: chain B residue 161 LEU Chi-restraints excluded: chain D residue 61 VAL Chi-restraints excluded: chain D residue 109 VAL Chi-restraints excluded: chain D residue 275 TYR Chi-restraints excluded: chain E residue 134 ASP Chi-restraints excluded: chain F residue 54 ASP Chi-restraints excluded: chain F residue 105 CYS Chi-restraints excluded: chain F residue 231 SER Chi-restraints excluded: chain G residue 18 VAL Chi-restraints excluded: chain G residue 351 THR Chi-restraints excluded: chain G residue 659 ASP Chi-restraints excluded: chain H residue 121 TRP Chi-restraints excluded: chain K residue 46 LEU Chi-restraints excluded: chain L residue 10 VAL Chi-restraints excluded: chain L residue 349 SER Chi-restraints excluded: chain L residue 393 ASP Chi-restraints excluded: chain L residue 554 ASP Chi-restraints excluded: chain M residue 113 MET Chi-restraints excluded: chain M residue 393 ILE Chi-restraints excluded: chain O residue 2 GLN Chi-restraints excluded: chain O residue 19 THR Chi-restraints excluded: chain O residue 60 ASP Chi-restraints excluded: chain R residue 95 HIS Chi-restraints excluded: chain S residue 39 ARG Chi-restraints excluded: chain S residue 90 LEU Chi-restraints excluded: chain T residue 32 VAL Chi-restraints excluded: chain V residue 69 GLU Chi-restraints excluded: chain W residue 49 LEU Chi-restraints excluded: chain X residue 132 THR Chi-restraints excluded: chain X residue 148 GLU Chi-restraints excluded: chain X residue 152 GLU Chi-restraints excluded: chain Y residue 36 SER Chi-restraints excluded: chain Y residue 109 ILE Chi-restraints excluded: chain Y residue 114 CYS Chi-restraints excluded: chain c residue 1 LYS Chi-restraints excluded: chain d residue 77 LYS Chi-restraints excluded: chain d residue 111 GLU Chi-restraints excluded: chain g residue 122 GLU Chi-restraints excluded: chain k residue 85 TYR Chi-restraints excluded: chain n residue 122 GLU Chi-restraints excluded: chain n residue 145 VAL Chi-restraints excluded: chain o residue 30 PHE Chi-restraints excluded: chain p residue 38 LEU Chi-restraints excluded: chain s residue 57 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 791 random chunks: chunk 498 optimal weight: 0.8980 chunk 668 optimal weight: 5.9990 chunk 192 optimal weight: 6.9990 chunk 578 optimal weight: 10.0000 chunk 92 optimal weight: 5.9990 chunk 174 optimal weight: 0.9990 chunk 628 optimal weight: 0.8980 chunk 263 optimal weight: 4.9990 chunk 645 optimal weight: 4.9990 chunk 79 optimal weight: 0.9980 chunk 115 optimal weight: 7.9990 overall best weight: 1.7584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 85 ASN C 211 GLN F 432 GLN G 643 GLN ** H 317 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 7 ASN M 88 ASN V 95 GLN W 51 GLN Y 18 HIS Y 88 ASN j 6 HIS j 58 GLN n 140 GLN p 22 GLN q 112 ASN r 24 GLN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3229 r_free = 0.3229 target = 0.096171 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2900 r_free = 0.2900 target = 0.076952 restraints weight = 61185.454| |-----------------------------------------------------------------------------| r_work (start): 0.2892 rms_B_bonded: 1.04 r_work: 0.2792 rms_B_bonded: 1.47 restraints_weight: 0.5000 r_work: 0.2690 rms_B_bonded: 2.42 restraints_weight: 0.2500 r_work (final): 0.2690 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8969 moved from start: 0.1381 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.242 68792 Z= 0.471 Angle : 1.297 50.544 93045 Z= 0.835 Chirality : 0.257 6.541 10181 Planarity : 0.004 0.047 11563 Dihedral : 10.366 174.257 10891 Min Nonbonded Distance : 2.035 Molprobity Statistics. All-atom Clashscore : 4.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.69 % Favored : 98.31 % Rotamer: Outliers : 0.89 % Allowed : 13.44 % Favored : 85.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.54 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.01 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.80 (0.09), residues: 7997 helix: 1.88 (0.08), residues: 4319 sheet: 0.21 (0.25), residues: 407 loop : 0.53 (0.11), residues: 3271 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP M 71 HIS 0.006 0.001 HIS G 101 PHE 0.029 0.002 PHE T 60 TYR 0.020 0.002 TYR I 118 ARG 0.009 0.000 ARG g 95 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 32538.37 seconds wall clock time: 563 minutes 50.09 seconds (33830.09 seconds total)