Starting phenix.real_space_refine on Fri Mar 15 02:18:06 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7r45_14272/03_2024/7r45_14272_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7r45_14272/03_2024/7r45_14272.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7r45_14272/03_2024/7r45_14272_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7r45_14272/03_2024/7r45_14272_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7r45_14272/03_2024/7r45_14272_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7r45_14272/03_2024/7r45_14272.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7r45_14272/03_2024/7r45_14272.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7r45_14272/03_2024/7r45_14272_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7r45_14272/03_2024/7r45_14272_updated.pdb" } resolution = 2.4 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= 0.009 sd= 1.063 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 35 5.49 5 Mg 1 5.21 5 S 465 5.16 5 Cl 2 4.86 5 C 43242 2.51 5 N 11036 2.21 5 O 13382 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 51": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 93": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 105": "OE1" <-> "OE2" Residue "B ASP 34": "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 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 49": "OE1" <-> "OE2" Residue "C ARG 149": "NH1" <-> "NH2" Residue "C PHE 166": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 173": "OE1" <-> "OE2" Residue "C GLU 179": "OE1" <-> "OE2" Residue "C GLU 186": "OE1" <-> "OE2" Residue "C GLU 204": "OE1" <-> "OE2" Residue "D ARG 2": "NH1" <-> "NH2" Residue "D GLU 9": "OE1" <-> "OE2" Residue "D GLU 67": "OE1" <-> "OE2" Residue "D ASP 77": "OD1" <-> "OD2" Residue "D GLU 88": "OE1" <-> "OE2" Residue "D GLU 123": "OE1" <-> "OE2" 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 ASP 241": "OD1" <-> "OD2" Residue "D GLU 248": "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 ASP 134": "OD1" <-> "OD2" Residue "E PHE 137": "CD1" <-> "CD2" "CE1" <-> "CE2" 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 "F PHE 12": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 18": "OE1" <-> "OE2" Residue "F ARG 32": "NH1" <-> "NH2" Residue "F PHE 73": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 87": "OD1" <-> "OD2" 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 158": "OE1" <-> "OE2" Residue "F GLU 189": "OE1" <-> "OE2" Residue "F GLU 194": "OE1" <-> "OE2" Residue "F PHE 209": "CD1" <-> "CD2" "CE1" <-> "CE2" 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 ASP 338": "OD1" <-> "OD2" Residue "F ARG 349": "NH1" <-> "NH2" Residue "F GLU 352": "OE1" <-> "OE2" Residue "F GLU 367": "OE1" <-> "OE2" Residue "F ASP 370": "OD1" <-> "OD2" Residue "F ASP 390": "OD1" <-> "OD2" Residue "F GLU 394": "OE1" <-> "OE2" Residue "F GLU 425": "OE1" <-> "OE2" Residue "F ARG 429": "NH1" <-> "NH2" 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 84": "OE1" <-> "OE2" Residue "G GLU 165": "OE1" <-> "OE2" Residue "G ASP 180": "OD1" <-> "OD2" Residue "G ARG 218": "NH1" <-> "NH2" Residue "G ARG 243": "NH1" <-> "NH2" Residue "G GLU 246": "OE1" <-> "OE2" Residue "G ARG 253": "NH1" <-> "NH2" Residue "G GLU 261": "OE1" <-> "OE2" Residue "G ARG 285": "NH1" <-> "NH2" Residue "G GLU 297": "OE1" <-> "OE2" Residue "G ARG 302": "NH1" <-> "NH2" Residue "G ASP 339": "OD1" <-> "OD2" Residue "G GLU 347": "OE1" <-> "OE2" Residue "G GLU 373": "OE1" <-> "OE2" Residue "G ARG 385": "NH1" <-> "NH2" Residue "G ARG 418": "NH1" <-> "NH2" Residue "G ASP 420": "OD1" <-> "OD2" Residue "G GLU 445": "OE1" <-> "OE2" Residue "G PHE 523": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 540": "OD1" <-> "OD2" Residue "G ASP 558": "OD1" <-> "OD2" 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 647": "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 GLU 59": "OE1" <-> "OE2" Residue "H ARG 62": "NH1" <-> "NH2" Residue "H TYR 127": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 142": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 192": "OE1" <-> "OE2" Residue "H GLU 202": "OE1" <-> "OE2" Residue "H TYR 215": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 259": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 280": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ARG 8": "NH1" <-> "NH2" Residue "I ASP 13": "OD1" <-> "OD2" Residue "I ASP 19": "OD1" <-> "OD2" Residue "I ARG 108": "NH1" <-> "NH2" Residue "J TYR 28": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 47": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 60": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J GLU 81": "OE1" <-> "OE2" Residue "J GLU 100": "OE1" <-> "OE2" Residue "J GLU 112": "OE1" <-> "OE2" Residue "J GLU 114": "OE1" <-> "OE2" Residue "J GLU 118": "OE1" <-> "OE2" Residue "J PHE 119": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ASP 124": "OD1" <-> "OD2" Residue "J ASP 129": "OD1" <-> "OD2" Residue "J GLU 138": "OE1" <-> "OE2" Residue "J GLU 139": "OE1" <-> "OE2" Residue "J ARG 173": "NH1" <-> "NH2" Residue "K PHE 66": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K GLU 70": "OE1" <-> "OE2" Residue "L PHE 24": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L GLU 60": "OE1" <-> "OE2" Residue "L GLU 102": "OE1" <-> "OE2" Residue "L TYR 107": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 109": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L GLU 145": "OE1" <-> "OE2" Residue "L ARG 161": "NH1" <-> "NH2" Residue "L ASP 197": "OD1" <-> "OD2" Residue "L ASP 208": "OD1" <-> "OD2" Residue "L ARG 262": "NH1" <-> "NH2" 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 484": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L GLU 503": "OE1" <-> "OE2" Residue "L TYR 515": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 588": "CD1" <-> "CD2" "CE1" <-> "CE2" 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 GLU 141": "OE1" <-> "OE2" Residue "M ARG 142": "NH1" <-> "NH2" Residue "M TYR 210": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M GLU 222": "OE1" <-> "OE2" Residue "M ASP 255": "OD1" <-> "OD2" Residue "M PHE 256": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M ARG 346": "NH1" <-> "NH2" Residue "M ARG 432": "NH1" <-> "NH2" Residue "M TYR 459": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N GLU 34": "OE1" <-> "OE2" Residue "N GLU 54": "OE1" <-> "OE2" Residue "N GLU 117": "OE1" <-> "OE2" Residue "N ARG 295": "NH1" <-> "NH2" Residue "O GLU 12": "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 162": "OE1" <-> "OE2" Residue "O GLU 178": "OE1" <-> "OE2" Residue "O GLU 203": "OE1" <-> "OE2" Residue "O GLU 216": "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 ASP 244": "OD1" <-> "OD2" Residue "O ASP 250": "OD1" <-> "OD2" Residue "O ASP 253": "OD1" <-> "OD2" Residue "O GLU 268": "OE1" <-> "OE2" Residue "O GLU 295": "OE1" <-> "OE2" Residue "O PHE 296": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O ARG 302": "NH1" <-> "NH2" Residue "O ARG 305": "NH1" <-> "NH2" Residue "O TYR 308": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O GLU 310": "OE1" <-> "OE2" Residue "P 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 ARG 97": "NH1" <-> "NH2" Residue "P GLU 107": "OE1" <-> "OE2" Residue "P GLU 123": "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 PHE 172": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P GLU 175": "OE1" <-> "OE2" Residue "P TYR 181": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P ASP 220": "OD1" <-> "OD2" Residue "P ARG 235": "NH1" <-> "NH2" Residue "P PHE 246": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P ARG 251": "NH1" <-> "NH2" Residue "P ASP 282": "OD1" <-> "OD2" Residue "P GLU 285": "OE1" <-> "OE2" Residue "P GLU 301": "OE1" <-> "OE2" Residue "P ASP 302": "OD1" <-> "OD2" Residue "P TYR 324": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q GLU 15": "OE1" <-> "OE2" Residue "Q ASP 18": "OD1" <-> "OD2" Residue "Q GLU 28": "OE1" <-> "OE2" Residue "Q GLU 66": "OE1" <-> "OE2" Residue "Q ASP 91": "OD1" <-> "OD2" Residue "Q TYR 103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q ASP 104": "OD1" <-> "OD2" Residue "Q GLU 106": "OE1" <-> "OE2" Residue "Q GLU 107": "OE1" <-> "OE2" Residue "R ASP 19": "OD1" <-> "OD2" Residue "R TYR 23": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R ARG 31": "NH1" <-> "NH2" 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 "S ASP 84": "OD1" <-> "OD2" Residue "S GLU 91": "OE1" <-> "OE2" Residue "T GLU 9": "OE1" <-> "OE2" Residue "T TYR 17": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T TYR 22": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T ASP 23": "OD1" <-> "OD2" Residue "T ASP 26": "OD1" <-> "OD2" Residue "T ASP 39": "OD1" <-> "OD2" Residue "T GLU 61": "OE1" <-> "OE2" Residue "T GLU 68": "OE1" <-> "OE2" Residue "T GLU 75": "OE1" <-> "OE2" Residue "T ASP 78": "OD1" <-> "OD2" Residue "T ASP 82": "OD1" <-> "OD2" 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 ASP 66": "OD1" <-> "OD2" Residue "U GLU 68": "OE1" <-> "OE2" Residue "U GLU 75": "OE1" <-> "OE2" Residue "U TYR 87": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U GLU 88": "OE1" <-> "OE2" Residue "V GLU 17": "OE1" <-> "OE2" Residue "V ARG 22": "NH1" <-> "NH2" Residue "V ASP 63": "OD1" <-> "OD2" Residue "V GLU 68": "OE1" <-> "OE2" Residue "V GLU 78": "OE1" <-> "OE2" Residue "V GLU 86": "OE1" <-> "OE2" Residue "V GLU 104": "OE1" <-> "OE2" Residue "V GLU 105": "OE1" <-> "OE2" Residue "W GLU 27": "OE1" <-> "OE2" Residue "W ARG 30": "NH1" <-> "NH2" Residue "W PHE 50": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W ASP 61": "OD1" <-> "OD2" Residue "W GLU 109": "OE1" <-> "OE2" Residue "X GLU 5": "OE1" <-> "OE2" Residue "X GLU 48": "OE1" <-> "OE2" Residue "X GLU 49": "OE1" <-> "OE2" Residue "X GLU 68": "OE1" <-> "OE2" Residue "X ARG 97": "NH1" <-> "NH2" Residue "X ARG 118": "NH1" <-> "NH2" Residue "X ARG 134": "NH1" <-> "NH2" Residue "X ARG 144": "NH1" <-> "NH2" Residue "X ARG 146": "NH1" <-> "NH2" Residue "Y GLU 13": "OE1" <-> "OE2" Residue "Y GLU 16": "OE1" <-> "OE2" Residue "Y TYR 22": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y GLU 50": "OE1" <-> "OE2" Residue "Y ARG 57": "NH1" <-> "NH2" Residue "Y ASP 84": "OD1" <-> "OD2" Residue "Y ASP 85": "OD1" <-> "OD2" Residue "Y ARG 103": "NH1" <-> "NH2" Residue "Z ASP 80": "OD1" <-> "OD2" Residue "Z ARG 82": "NH1" <-> "NH2" Residue "Z GLU 89": "OE1" <-> "OE2" Residue "Z GLU 93": "OE1" <-> "OE2" Residue "Z ASP 100": "OD1" <-> "OD2" Residue "Z GLU 108": "OE1" <-> "OE2" Residue "Z GLU 131": "OE1" <-> "OE2" Residue "a GLU 35": "OE1" <-> "OE2" Residue "a GLU 49": "OE1" <-> "OE2" Residue "a ASP 51": "OD1" <-> "OD2" Residue "a ARG 59": "NH1" <-> "NH2" Residue "b GLU 2": "OE1" <-> "OE2" Residue "b ARG 3": "NH1" <-> "NH2" Residue "b ARG 57": "NH1" <-> "NH2" Residue "b ASP 71": "OD1" <-> "OD2" Residue "b GLU 78": "OE1" <-> "OE2" Residue "c PHE 26": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c ASP 38": "OD1" <-> "OD2" 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 ASP 87": "OD1" <-> "OD2" Residue "d GLU 111": "OE1" <-> "OE2" Residue "d GLU 114": "OE1" <-> "OE2" 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 "f ARG 28": "NH1" <-> "NH2" Residue "f ASP 31": "OD1" <-> "OD2" Residue "f GLU 32": "OE1" <-> "OE2" Residue "f PHE 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "f ARG 46": "NH1" <-> "NH2" Residue "f GLU 52": "OE1" <-> "OE2" Residue "g ARG 25": "NH1" <-> "NH2" Residue "g GLU 28": "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 PHE 76": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "g GLU 94": "OE1" <-> "OE2" Residue "g TYR 99": "CD1" <-> "CD2" "CE1" <-> "CE2" 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 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 "h ASP 129": "OD1" <-> "OD2" Residue "i GLU 6": "OE1" <-> "OE2" Residue "i GLU 16": "OE1" <-> "OE2" Residue "i ARG 18": "NH1" <-> "NH2" Residue "i TYR 64": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "i GLU 111": "OE1" <-> "OE2" Residue "i GLU 121": "OE1" <-> "OE2" Residue "j PHE 14": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "j ASP 43": "OD1" <-> "OD2" Residue "j ASP 45": "OD1" <-> "OD2" Residue "j ASP 69": "OD1" <-> "OD2" Residue "j ASP 70": "OD1" <-> "OD2" Residue "j GLU 71": "OE1" <-> "OE2" Residue "k GLU 14": "OE1" <-> "OE2" Residue "k GLU 29": "OE1" <-> "OE2" Residue "k ARG 38": "NH1" <-> "NH2" Residue "k ARG 41": "NH1" <-> "NH2" Residue "k ASP 42": "OD1" <-> "OD2" Residue "k TYR 52": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "k GLU 84": "OE1" <-> "OE2" Residue "k GLU 88": "OE1" <-> "OE2" Residue "l TYR 13": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "l ARG 30": "NH1" <-> "NH2" Residue "l GLU 32": "OE1" <-> "OE2" Residue "l GLU 35": "OE1" <-> "OE2" Residue "l GLU 57": "OE1" <-> "OE2" Residue "l GLU 75": "OE1" <-> "OE2" Residue "l GLU 141": "OE1" <-> "OE2" Residue "l ARG 142": "NH1" <-> "NH2" Residue "l GLU 157": "OE1" <-> "OE2" Residue "m TYR 5": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "m GLU 6": "OE1" <-> "OE2" Residue "m ASP 18": "OD1" <-> "OD2" Residue "m GLU 21": "OE1" <-> "OE2" Residue "m TYR 22": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "m ASP 23": "OD1" <-> "OD2" Residue "m ARG 39": "NH1" <-> "NH2" Residue "m ARG 55": "NH1" <-> "NH2" Residue "m ARG 71": "NH1" <-> "NH2" Residue "n TYR 8": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "n ARG 21": "NH1" <-> "NH2" Residue "n GLU 27": "OE1" <-> "OE2" Residue "n ARG 37": "NH1" <-> "NH2" Residue "n ASP 48": "OD1" <-> "OD2" Residue "n GLU 49": "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 TYR 114": "CD1" <-> "CD2" "CE1" <-> "CE2" 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 GLU 32": "OE1" <-> "OE2" Residue "o ARG 36": "NH1" <-> "NH2" Residue "o GLU 44": "OE1" <-> "OE2" Residue "o ASP 47": "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 115": "OE1" <-> "OE2" Residue "p PHE 36": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "p GLU 52": "OE1" <-> "OE2" Residue "p TYR 61": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "p ASP 72": "OD1" <-> "OD2" Residue "p GLU 78": "OE1" <-> "OE2" 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 "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 TYR 49": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "q GLU 50": "OE1" <-> "OE2" Residue "q GLU 67": "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 "r ASP 18": "OD1" <-> "OD2" Residue "r TYR 27": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "r GLU 29": "OE1" <-> "OE2" Residue "r ARG 59": "NH1" <-> "NH2" Residue "r GLU 61": "OE1" <-> "OE2" Residue "r ASP 108": "OD1" <-> "OD2" Residue "r GLU 109": "OE1" <-> "OE2" Residue "s ASP 53": "OD1" <-> "OD2" Time to flip residues: 0.16s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 68195 Number of models: 1 Model: "" Number of chains: 115 Chain: "A" Number of atoms: 814 Number of conformers: 1 Conformer: "" Number of residues, atoms: 101, 814 Classifications: {'peptide': 101} Link IDs: {'PTRANS': 4, 'TRANS': 96} 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: 1230 Number of conformers: 1 Conformer: "" Number of residues, atoms: 154, 1230 Classifications: {'peptide': 154} Link IDs: {'PCIS': 2, 'PTRANS': 8, 'TRANS': 143} 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: 3363 Number of conformers: 1 Conformer: "" Number of residues, atoms: 417, 3363 Classifications: {'peptide': 417} Link IDs: {'PTRANS': 27, 'TRANS': 389} Chain breaks: 2 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'2MR:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "E" Number of atoms: 1655 Number of conformers: 1 Conformer: "" Number of residues, atoms: 213, 1655 Classifications: {'peptide': 213} Link IDs: {'PCIS': 1, 'PTRANS': 20, 'TRANS': 191} Chain: "F" Number of atoms: 3310 Number of conformers: 1 Conformer: "" Number of residues, atoms: 430, 3310 Classifications: {'peptide': 430} Link IDs: {'PCIS': 2, 'PTRANS': 19, 'TRANS': 408} Chain: "G" Number of atoms: 5279 Number of conformers: 1 Conformer: "" Number of residues, atoms: 688, 5279 Classifications: {'peptide': 688} Link IDs: {'PTRANS': 32, 'TRANS': 655} Chain: "H" Number of atoms: 2425 Number of conformers: 1 Conformer: "" Number of residues, atoms: 307, 2425 Classifications: {'peptide': 307} Link IDs: {'PCIS': 2, 'PTRANS': 20, 'TRANS': 284} 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: 739 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 739 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 1, 'TRANS': 95} 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: 2342 Number of conformers: 1 Conformer: "" Number of residues, atoms: 294, 2342 Classifications: {'peptide': 294} Link IDs: {'PTRANS': 16, 'TRANS': 277} 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: 911 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 911 Classifications: {'peptide': 112} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 103} Chain: "W" Number of atoms: 971 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 971 Classifications: {'peptide': 114} Link IDs: {'PTRANS': 6, 'TRANS': 107} Chain: "X" Number of atoms: 1402 Number of conformers: 1 Conformer: "" Number of residues, atoms: 171, 1402 Classifications: {'peptide': 171} Link IDs: {'PTRANS': 12, 'TRANS': 158} Chain: "Y" Number of atoms: 1030 Number of conformers: 1 Conformer: "" Number of residues, atoms: 140, 1030 Classifications: {'peptide': 140} Link IDs: {'PTRANS': 5, 'TRANS': 134} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'AYA:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "Z" Number of atoms: 1146 Number of conformers: 1 Conformer: "" Number of residues, atoms: 140, 1146 Classifications: {'peptide': 140} Link IDs: {'PTRANS': 7, 'TRANS': 132} Chain: "a" Number of atoms: 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: 646 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 646 Classifications: {'peptide': 82} Link IDs: {'PTRANS': 11, 'TRANS': 70} Chain: "c" Number of atoms: 405 Number of conformers: 1 Conformer: "" Number of residues, atoms: 48, 405 Classifications: {'peptide': 48} Link IDs: {'PTRANS': 3, 'TRANS': 44} Chain: "d" Number of atoms: 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: 884 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 884 Classifications: {'peptide': 103} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 90} 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: 1043 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 1043 Classifications: {'peptide': 121} Link IDs: {'PCIS': 2, 'PTRANS': 5, 'TRANS': 113} 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: 1201 Number of conformers: 1 Conformer: "" Number of residues, atoms: 144, 1201 Classifications: {'peptide': 144} Link IDs: {'PTRANS': 11, 'TRANS': 132} 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: 364 Number of conformers: 1 Conformer: "" Number of residues, atoms: 43, 364 Classifications: {'peptide': 43} Link IDs: {'PTRANS': 3, 'TRANS': 39} Chain: "A" Number of atoms: 71 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 71 Unusual residues: {'3PE': 1, 'LMT': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 15 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: 51 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 51 Unusual residues: {'3PE': 1, 'I49': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 16 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: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 72 Unusual residues: {'3PE': 1, 'LMT': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 14 Chain: "K" Number of atoms: 67 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 67 Unusual residues: {'CDL': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 33 Unresolved non-hydrogen angles: 33 Unresolved non-hydrogen dihedrals: 33 Chain: "L" Number of atoms: 298 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 298 Unusual residues: {'3PE': 2, 'CDL': 1, 'LMT': 3} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 9 Chain: "M" Number of atoms: 236 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 236 Unusual residues: {'3PE': 2, 'LMT': 3, 'PC1': 1} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 25 Unresolved non-hydrogen angles: 25 Unresolved non-hydrogen dihedrals: 25 Chain: "N" Number of atoms: 93 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 93 Unusual residues: {'3PE': 1, 'I49': 1, 'LMT': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 10 Chain: "O" Number of atoms: 80 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 80 Unusual residues: {' MG': 1, '3PE': 1, 'GTP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "P" Number of atoms: 48 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 48 Unusual residues: {'NDP': 1} Classifications: {'undetermined': 1} Chain: "R" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "T" Number of atoms: 37 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 37 Unusual residues: {'EHZ': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 3 Chain: "U" Number of atoms: 37 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 37 Unusual residues: {'EHZ': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 3 Chain: "X" Number of atoms: 65 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 65 Unusual residues: {'CDL': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 35 Unresolved non-hydrogen angles: 36 Unresolved non-hydrogen dihedrals: 34 Planarities with less than four sites: {'CDL:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "Y" Number of atoms: 35 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 35 Unusual residues: {'3PE': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 16 Chain: "b" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 39 Unusual residues: {'3PE': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 12 Chain: "d" Number of atoms: 65 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 65 Unusual residues: {'CDL': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 35 Unresolved non-hydrogen angles: 35 Unresolved non-hydrogen dihedrals: 35 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: "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: "l" Number of atoms: 35 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 35 Unusual residues: {'LMT': 1} Classifications: {'undetermined': 1} Chain: "o" Number of atoms: 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: 9 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 9 Classifications: {'water': 9} Link IDs: {None: 8} Chain: "B" Number of atoms: 53 Number of conformers: 1 Conformer: "" Number of residues, atoms: 53, 53 Classifications: {'water': 53} Link IDs: {None: 52} Chain: "C" Number of atoms: 82 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 82 Classifications: {'water': 82} Link IDs: {None: 81} Chain: "D" Number of atoms: 150 Number of conformers: 1 Conformer: "" Number of residues, atoms: 150, 150 Classifications: {'water': 150} Link IDs: {None: 149} Chain: "E" Number of atoms: 7 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 7 Classifications: {'water': 7} Link IDs: {None: 6} Chain: "F" Number of atoms: 55 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 55 Classifications: {'water': 55} Link IDs: {None: 54} Chain: "G" Number of atoms: 180 Number of conformers: 1 Conformer: "" Number of residues, atoms: 180, 180 Classifications: {'water': 180} Link IDs: {None: 179} Chain: "H" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 39, 39 Classifications: {'water': 39} Link IDs: {None: 38} Chain: "I" Number of atoms: 89 Number of conformers: 1 Conformer: "" Number of residues, atoms: 89, 89 Classifications: {'water': 89} Link IDs: {None: 88} Chain: "J" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 8 Classifications: {'water': 8} Link IDs: {None: 7} Chain: "K" Number of atoms: 7 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 7 Classifications: {'water': 7} Link IDs: {None: 6} Chain: "L" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 61, 61 Classifications: {'water': 61} Link IDs: {None: 60} Chain: "M" Number of atoms: 63 Number of conformers: 1 Conformer: "" Number of residues, atoms: 63, 63 Classifications: {'water': 63} Link IDs: {None: 62} Chain: "N" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 39, 39 Classifications: {'water': 39} Link IDs: {None: 38} Chain: "O" Number of atoms: 11 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 11 Classifications: {'water': 11} Link IDs: {None: 10} Chain: "P" Number of atoms: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 44, 44 Classifications: {'water': 44} Link IDs: {None: 43} Chain: "Q" Number of atoms: 62 Number of conformers: 1 Conformer: "" Number of residues, atoms: 62, 62 Classifications: {'water': 62} Link IDs: {None: 61} Chain: "R" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 31, 31 Classifications: {'water': 31} Link IDs: {None: 30} Chain: "S" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "T" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "U" Number of atoms: 7 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 7 Classifications: {'water': 7} Link IDs: {None: 6} Chain: "V" Number of atoms: 10 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 10 Classifications: {'water': 10} Link IDs: {None: 9} Chain: "W" Number of atoms: 12 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 12 Classifications: {'water': 12} Link IDs: {None: 11} Chain: "X" Number of atoms: 23 Number of conformers: 1 Conformer: "" Number of residues, atoms: 23, 23 Classifications: {'water': 23} Link IDs: {None: 22} Chain: "Y" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "Z" Number of atoms: 18 Number of conformers: 1 Conformer: "" Number of residues, atoms: 18, 18 Classifications: {'water': 18} Link IDs: {None: 17} Chain: "a" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 14 Classifications: {'water': 14} Link IDs: {None: 13} Chain: "b" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 5 Classifications: {'water': 5} Link IDs: {None: 4} Chain: "d" Number of atoms: 12 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 12 Classifications: {'water': 12} Link IDs: {None: 11} Chain: "e" Number of atoms: 13 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 13 Classifications: {'water': 13} Link IDs: {None: 12} Chain: "f" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Classifications: {'water': 4} Link IDs: {None: 3} Chain: "g" Number of atoms: 17 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 17 Classifications: {'water': 17} Link IDs: {None: 16} Chain: "h" Number of atoms: 18 Number of conformers: 1 Conformer: "" Number of residues, atoms: 18, 18 Classifications: {'water': 18} Link IDs: {None: 17} Chain: "i" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 5 Classifications: {'water': 5} Link IDs: {None: 4} Chain: "j" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "k" Number of atoms: 6 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 6 Classifications: {'water': 6} Link IDs: {None: 5} Chain: "l" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 28, 28 Classifications: {'water': 28} Link IDs: {None: 27} Chain: "m" Number of atoms: 18 Number of conformers: 1 Conformer: "" Number of residues, atoms: 18, 18 Classifications: {'water': 18} Link IDs: {None: 17} Chain: "n" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 29 Classifications: {'water': 29} Link IDs: {None: 28} Chain: "o" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 14 Classifications: {'water': 14} Link IDs: {None: 13} Chain: "p" Number of atoms: 25 Number of conformers: 1 Conformer: "" Number of residues, atoms: 25, 25 Classifications: {'water': 25} Link IDs: {None: 24} Chain: "q" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 29 Classifications: {'water': 29} Link IDs: {None: 28} Chain: "r" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 27, 27 Classifications: {'water': 27} Link IDs: {None: 26} Chain: "s" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 1550 SG CYS B 119 96.809 93.260 205.539 1.00 27.25 S ATOM 1780 SG CYS B 149 94.554 90.935 210.283 1.00 26.47 S ATOM 1046 SG CYS B 54 91.175 89.931 204.686 1.00 30.02 S ATOM 1052 SG CYS B 55 90.956 95.584 207.610 1.00 29.60 S ATOM 7925 SG CYS E 103 114.431 45.315 261.729 1.00 46.41 S ATOM 7959 SG CYS E 108 112.736 42.697 263.775 1.00 47.04 S ATOM 8239 SG CYS E 144 116.419 41.889 258.360 1.00 44.01 S ATOM 8262 SG CYS E 148 115.142 39.176 259.479 1.00 47.89 S ATOM 11471 SG CYS F 362 119.153 51.339 237.844 1.00 30.90 S ATOM 11491 SG CYS F 365 116.380 50.964 242.808 1.00 32.41 S ATOM 11815 SG CYS F 405 120.757 46.319 241.961 1.00 34.02 S ATOM 11452 SG CYS F 359 122.893 52.227 243.273 1.00 33.95 S ATOM 12912 SG CYS G 114 115.861 69.812 228.312 1.00 28.50 S ATOM 12851 SG CYS G 105 110.060 72.369 230.253 1.00 27.08 S ATOM 12872 SG CYS G 108 115.746 74.769 232.265 1.00 28.00 S ATOM 13244 SG CYS G 156 124.252 63.597 233.191 1.00 30.03 S ATOM 13221 SG CYS G 153 121.587 66.023 238.819 1.00 29.84 S ATOM 13268 SG CYS G 159 127.732 66.847 237.247 1.00 32.41 S ATOM 13598 SG CYS G 203 123.146 69.612 233.418 1.00 30.37 S ATOM 12357 SG CYS G 41 124.424 56.764 231.003 1.00 29.96 S ATOM 12443 SG CYS G 52 120.609 57.312 230.101 1.00 29.59 S ATOM 12468 SG CYS G 55 121.996 52.706 226.803 1.00 31.18 S ATOM 12569 SG CYS G 69 125.186 53.333 227.959 1.00 32.35 S ATOM 20744 SG CYS I 119 97.599 85.104 216.388 1.00 25.07 S ATOM 20718 SG CYS I 116 98.079 91.688 217.106 1.00 25.04 S ATOM 20765 SG CYS I 122 99.244 87.348 221.854 1.00 24.80 S ATOM 20492 SG CYS I 87 103.295 87.798 216.618 1.00 24.54 S ATOM 20794 SG CYS I 126 101.890 84.100 229.378 1.00 26.50 S ATOM 20423 SG CYS I 77 106.917 88.344 230.250 1.00 28.04 S ATOM 20465 SG CYS I 83 105.162 86.559 224.351 1.00 25.59 S ATOM 20442 SG CYS I 80 107.326 81.930 227.914 1.00 26.71 S ATOM 40859 SG CYS R 59 103.751 79.969 244.579 1.00 33.93 S ATOM 41037 SG CYS R 84 106.763 80.458 242.456 1.00 34.00 S ATOM 41059 SG CYS R 87 104.533 83.225 243.201 1.00 32.87 S Time building chain proxies: 26.91, per 1000 atoms: 0.39 Number of scatterers: 68195 At special positions: 0 Unit cell: (184.943, 200.294, 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 465 16.00 P 35 15.00 Mg 1 11.99 O 13382 8.00 N 11036 7.00 C 43242 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=2.03 Simple disulfide: pdb=" SG CYS e 32 " - pdb=" SG CYS e 65 " distance=2.03 Simple disulfide: pdb=" SG CYS e 42 " - pdb=" SG CYS e 55 " distance=2.04 Simple disulfide: pdb=" SG CYS 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=4, symmetry=0 Number of additional bonds: simple=4, symmetry=0 Coordination: Other bonds: Time building additional restraints: 24.71 Conformation dependent library (CDL) restraints added in 9.1 seconds Dynamic metal coordination Iron sulfur cluster coordination pdb=" FES E 301 " pdb="FE1 FES E 301 " - pdb=" SG CYS E 103 " pdb="FE1 FES E 301 " - pdb=" SG CYS E 108 " pdb="FE2 FES E 301 " - pdb=" SG CYS E 144 " pdb="FE2 FES E 301 " - pdb=" SG CYS E 148 " pdb=" FES G 803 " pdb="FE1 FES G 803 " - pdb=" SG CYS G 52 " pdb="FE2 FES G 803 " - pdb=" SG CYS G 55 " pdb="FE2 FES G 803 " - pdb=" SG CYS G 69 " pdb="FE1 FES G 803 " - pdb=" SG CYS G 41 " pdb=" SF4 B 201 " pdb="FE1 SF4 B 201 " - pdb=" SG CYS B 119 " pdb="FE2 SF4 B 201 " - pdb=" SG CYS B 149 " pdb="FE3 SF4 B 201 " - pdb=" SG CYS B 54 " pdb="FE4 SF4 B 201 " - pdb=" SG CYS B 55 " pdb=" SF4 F 502 " pdb="FE2 SF4 F 502 " - pdb=" SG CYS F 365 " pdb="FE4 SF4 F 502 " - pdb=" SG CYS F 359 " pdb="FE3 SF4 F 502 " - pdb=" SG CYS F 405 " pdb="FE1 SF4 F 502 " - pdb=" SG CYS F 362 " pdb=" SF4 G 801 " pdb="FE3 SF4 G 801 " - pdb=" NE2 HIS G 101 " pdb="FE4 SF4 G 801 " - pdb=" SG CYS G 108 " pdb="FE1 SF4 G 801 " - pdb=" SG CYS G 114 " pdb="FE2 SF4 G 801 " - pdb=" SG CYS G 105 " pdb=" SF4 G 802 " pdb="FE4 SF4 G 802 " - pdb=" SG CYS G 203 " pdb="FE3 SF4 G 802 " - pdb=" SG CYS G 159 " pdb="FE2 SF4 G 802 " - pdb=" SG CYS G 153 " pdb="FE1 SF4 G 802 " - pdb=" SG CYS G 156 " pdb=" SF4 I 202 " pdb="FE2 SF4 I 202 " - pdb=" SG CYS I 116 " pdb="FE3 SF4 I 202 " - pdb=" SG CYS I 122 " 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="FE1 SF4 I 203 " - pdb=" SG CYS I 126 " pdb="FE2 SF4 I 203 " - pdb=" SG CYS I 77 " pdb="FE4 SF4 I 203 " - pdb=" SG CYS I 80 " Number of angles added : 81 Zn2+ tetrahedral coordination pdb=" ZN R 201 " pdb="ZN ZN R 201 " - pdb=" NE2 HIS R 68 " pdb="ZN ZN R 201 " - pdb=" SG CYS R 84 " pdb="ZN ZN R 201 " - pdb=" SG CYS R 87 " pdb="ZN ZN R 201 " - pdb=" SG CYS R 59 " Number of angles added : 3 15954 Ramachandran restraints generated. 7977 Oldfield, 0 Emsley, 7977 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 15220 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 356 helices and 28 sheets defined 54.4% alpha, 4.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 9.47 Creating SS restraints... Processing helix chain 'A' and resid 3 through 23 Processing helix chain 'A' and resid 53 through 80 Proline residue: A 74 - end of helix removed outlier: 5.483A pdb=" N TRP A 77 " --> pdb=" O LEU A 73 " (cutoff:3.500A) removed outlier: 4.249A 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 27 through 42 Processing helix chain 'B' and resid 54 through 63 removed outlier: 3.750A pdb=" N GLU B 58 " --> pdb=" O CYS B 54 " (cutoff:3.500A) Processing helix chain 'B' and resid 69 through 72 Processing helix chain 'B' and resid 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 169 Processing helix chain 'B' and resid 172 through 177 Processing helix chain 'C' and resid 16 through 32 Processing helix chain 'C' and resid 54 through 66 removed outlier: 4.740A pdb=" N ILE C 58 " --> pdb=" O ASP C 55 " (cutoff:3.500A) Proline residue: C 59 - end of helix removed outlier: 3.502A pdb=" N THR C 62 " --> pdb=" O PRO C 59 " (cutoff:3.500A) Processing helix chain 'C' and resid 125 through 138 removed outlier: 3.808A pdb=" N TRP C 129 " --> pdb=" O ALA C 126 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N GLU C 131 " --> pdb=" O ASN C 128 " (cutoff:3.500A) removed outlier: 3.930A 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: 3.828A pdb=" N GLN D 13 " --> pdb=" O GLU D 9 " (cutoff:3.500A) removed outlier: 4.594A pdb=" N TYR D 14 " --> pdb=" O TRP D 10 " (cutoff:3.500A) Processing helix chain 'D' and resid 87 through 93 removed outlier: 3.884A pdb=" N GLU D 92 " --> pdb=" O GLU D 88 " (cutoff:3.500A) removed outlier: 4.067A pdb=" N TYR D 93 " --> pdb=" O LYS D 89 " (cutoff:3.500A) Processing helix chain 'D' and resid 96 through 105 removed outlier: 3.543A pdb=" N LEU D 100 " --> pdb=" O TYR D 96 " (cutoff:3.500A) Proline residue: D 101 - end of helix removed outlier: 3.873A pdb=" N ASP D 104 " --> pdb=" O LEU D 100 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N ARG D 105 " --> pdb=" O PRO D 101 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 96 through 105' Processing helix chain 'D' and resid 111 through 126 Processing helix chain 'D' and resid 132 through 161 removed outlier: 3.627A pdb=" N ILE D 161 " --> pdb=" O HIS D 157 " (cutoff:3.500A) Processing helix chain 'D' and resid 165 through 185 removed outlier: 3.552A pdb=" N GLU D 172 " --> pdb=" O PHE D 168 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N GLU D 173 " --> pdb=" O TRP D 169 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N PHE D 180 " --> pdb=" O LYS D 176 " (cutoff:3.500A) Processing helix chain 'D' and resid 207 through 229 removed outlier: 3.895A pdb=" N ASN D 217 " --> pdb=" O GLU D 213 " (cutoff:3.500A) removed outlier: 4.438A pdb=" N SER D 219 " --> pdb=" O SER D 215 " (cutoff:3.500A) removed outlier: 5.747A pdb=" N LEU D 220 " --> pdb=" O LYS D 216 " (cutoff:3.500A) removed outlier: 3.635A 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: 4.649A 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: 3.582A pdb=" N LEU D 402 " --> pdb=" O HIS D 398 " (cutoff:3.500A) removed outlier: 4.777A pdb=" N ASP D 403 " --> pdb=" O LEU D 399 " (cutoff:3.500A) removed outlier: 5.221A pdb=" N LYS D 404 " --> pdb=" O ALA D 400 " (cutoff:3.500A) Processing helix chain 'D' and resid 411 through 421 removed outlier: 3.952A pdb=" N VAL D 415 " --> pdb=" O LEU D 411 " (cutoff:3.500A) removed outlier: 3.663A 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: 3.694A pdb=" N ASN E 37 " --> pdb=" O ALA E 33 " (cutoff:3.500A) Processing helix chain 'E' and resid 43 through 58 removed outlier: 4.418A 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 38 Processing helix chain 'F' and resid 45 through 51 Processing helix chain 'F' and resid 53 through 63 Processing helix chain 'F' and resid 75 through 82 removed outlier: 3.570A pdb=" N PHE F 81 " --> pdb=" O LEU F 77 " (cutoff:3.500A) removed outlier: 4.626A pdb=" N MET F 82 " --> pdb=" O LYS F 78 " (cutoff:3.500A) Processing helix chain 'F' and resid 106 through 113 removed outlier: 3.653A pdb=" N ILE F 110 " --> pdb=" O LYS F 106 " (cutoff:3.500A) Processing helix chain 'F' and resid 115 through 128 Processing helix chain 'F' and resid 143 through 158 Processing helix chain 'F' and resid 166 through 168 No H-bonds generated for 'chain 'F' and resid 166 through 168' Processing helix chain 'F' and resid 184 through 187 Processing helix chain 'F' and resid 189 through 196 Processing helix chain 'F' and resid 215 through 217 No H-bonds generated for 'chain 'F' and resid 215 through 217' Processing helix chain 'F' and resid 225 through 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 282 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: 4.187A pdb=" N ASP F 370 " --> pdb=" O ARG F 366 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N ARG F 381 " --> pdb=" O ALA F 377 " (cutoff:3.500A) Processing helix chain 'F' and resid 386 through 399 removed outlier: 3.649A 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: 3.606A 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 32 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: 3.672A 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: 5.077A pdb=" N TYR G 271 " --> pdb=" O THR G 267 " (cutoff:3.500A) removed outlier: 6.428A pdb=" N ASP G 272 " --> pdb=" O ARG G 268 " (cutoff:3.500A) removed outlier: 5.376A pdb=" N GLY G 273 " --> pdb=" O PHE G 269 " (cutoff:3.500A) removed outlier: 4.242A pdb=" N LEU G 274 " --> pdb=" O ALA G 270 " (cutoff:3.500A) removed outlier: 4.335A pdb=" N LYS G 275 " --> pdb=" O TYR G 271 " (cutoff:3.500A) Processing helix chain 'G' and resid 296 through 309 Processing helix chain 'G' and resid 312 through 314 No H-bonds generated for 'chain 'G' and resid 312 through 314' Processing helix chain 'G' and resid 325 through 338 removed outlier: 3.594A 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 373 Processing helix chain 'G' and resid 384 through 387 No H-bonds generated for 'chain 'G' and resid 384 through 387' Processing helix chain 'G' and resid 389 through 402 Processing helix chain 'G' and resid 426 through 434 Processing helix chain 'G' and resid 438 through 445 removed outlier: 3.727A pdb=" N VAL G 442 " --> pdb=" O PRO G 438 " (cutoff:3.500A) 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 504 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 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 649 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: 3.815A 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: 4.241A pdb=" N TRP H 86 " --> pdb=" O ALA H 82 " (cutoff:3.500A) Processing helix chain 'H' and resid 101 through 123 removed outlier: 3.510A pdb=" N LEU H 111 " --> pdb=" O ALA H 107 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N VAL H 113 " --> pdb=" O SER H 109 " (cutoff:3.500A) removed outlier: 5.104A pdb=" N TYR H 114 " --> pdb=" O SER H 110 " (cutoff:3.500A) removed outlier: 4.445A pdb=" N SER H 115 " --> pdb=" O LEU H 111 " (cutoff:3.500A) removed outlier: 4.131A pdb=" N ILE H 116 " --> pdb=" O ALA H 112 " (cutoff:3.500A) Processing helix chain 'H' and resid 126 through 157 removed outlier: 4.042A pdb=" N THR H 145 " --> pdb=" O SER H 141 " (cutoff:3.500A) removed outlier: 4.067A pdb=" N MET H 156 " --> pdb=" O SER H 152 " (cutoff:3.500A) Processing helix chain 'H' and resid 162 through 168 removed outlier: 3.964A pdb=" N ILE H 166 " --> pdb=" O LEU H 162 " (cutoff:3.500A) removed outlier: 3.575A 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 217 through 242 Processing helix chain 'H' and resid 252 through 274 Processing helix chain 'H' and resid 282 through 291 Processing helix chain 'H' and resid 293 through 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 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: 5.667A pdb=" N ALA I 163 " --> pdb=" O ASP I 159 " (cutoff:3.500A) removed outlier: 6.244A pdb=" N GLU I 164 " --> pdb=" O LYS I 160 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N ALA I 167 " --> pdb=" O ALA I 163 " (cutoff:3.500A) removed outlier: 5.397A pdb=" N LEU I 174 " --> pdb=" O GLN I 170 " (cutoff:3.500A) removed outlier: 5.687A 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: 3.679A 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 147 removed outlier: 4.031A pdb=" N LEU J 146 " --> pdb=" O GLY J 142 " (cutoff:3.500A) removed outlier: 4.879A pdb=" N TYR J 147 " --> pdb=" O ILE J 143 " (cutoff:3.500A) Processing helix chain 'J' and resid 151 through 173 Processing helix chain 'K' and resid 3 through 20 removed outlier: 3.996A 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: 3.685A pdb=" N MET K 58 " --> pdb=" O LEU K 55 " (cutoff:3.500A) Proline residue: K 60 - end of helix removed outlier: 3.620A pdb=" N PHE K 66 " --> pdb=" O LEU K 63 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N ALA K 67 " --> pdb=" O LEU K 64 " (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 'L' and resid 3 through 23 removed outlier: 4.117A pdb=" N LEU L 12 " --> pdb=" O SER L 8 " (cutoff:3.500A) Proline residue: L 18 - end of helix removed outlier: 3.886A pdb=" N SER L 23 " --> pdb=" O ILE L 19 " (cutoff:3.500A) Processing helix chain 'L' and resid 29 through 57 removed outlier: 3.667A pdb=" N TYR L 32 " --> pdb=" O PRO L 29 " (cutoff:3.500A) Proline residue: L 33 - end of helix removed outlier: 3.620A pdb=" N ILE L 49 " --> pdb=" O THR L 46 " (cutoff:3.500A) Proline residue: L 50 - end of helix removed outlier: 3.744A 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: 3.754A 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: 3.649A pdb=" N GLY L 148 " --> pdb=" O TRP L 144 " (cutoff:3.500A) Processing helix chain 'L' and resid 162 through 193 removed outlier: 4.188A 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: 4.128A pdb=" N MET L 237 " --> pdb=" O LEU L 233 " (cutoff:3.500A) removed outlier: 5.163A 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 253 through 262 removed outlier: 3.553A pdb=" N GLY L 256 " --> pdb=" O VAL L 253 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N LEU L 259 " --> pdb=" O GLY L 256 " (cutoff:3.500A) Processing helix chain 'L' and resid 264 through 269 removed outlier: 4.566A pdb=" N ASN L 269 " --> pdb=" O PRO L 265 " (cutoff:3.500A) Processing helix chain 'L' and resid 271 through 293 removed outlier: 3.543A pdb=" N LEU L 293 " --> pdb=" O ALA L 289 " (cutoff:3.500A) Processing helix chain 'L' and resid 298 through 319 Processing helix chain 'L' and resid 322 through 349 removed outlier: 3.889A pdb=" N PHE L 334 " --> pdb=" O CYS L 330 " (cutoff:3.500A) removed outlier: 3.872A 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 380 Processing helix chain 'L' and resid 388 through 401 removed outlier: 3.762A pdb=" N LYS L 392 " --> pdb=" O PHE L 389 " (cutoff:3.500A) removed outlier: 5.392A pdb=" N ASP L 393 " --> pdb=" O TYR L 390 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N ILE L 396 " --> pdb=" O ASP L 393 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N GLU L 397 " --> pdb=" O LEU L 394 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N THR L 401 " --> pdb=" O ALA L 398 " (cutoff:3.500A) Processing helix chain 'L' and resid 406 through 431 removed outlier: 3.748A pdb=" N ALA L 420 " --> pdb=" O THR L 416 " (cutoff:3.500A) Processing helix chain 'L' and resid 448 through 471 removed outlier: 3.584A pdb=" N LEU L 457 " --> pdb=" O SER L 453 " (cutoff:3.500A) removed outlier: 6.265A pdb=" N GLY L 465 " --> pdb=" O SER L 461 " (cutoff:3.500A) removed outlier: 5.291A 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: 4.413A 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: 3.827A pdb=" N MET L 533 " --> pdb=" O PRO L 530 " (cutoff:3.500A) removed outlier: 4.443A pdb=" N HIS L 534 " --> pdb=" O THR L 531 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N LEU L 536 " --> pdb=" O MET L 533 " (cutoff:3.500A) removed outlier: 5.588A pdb=" N ALA L 537 " --> pdb=" O HIS L 534 " (cutoff:3.500A) Proline residue: L 538 - end of helix removed outlier: 3.526A pdb=" N ASN L 541 " --> pdb=" O PRO L 538 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N LEU L 542 " --> pdb=" O TYR L 539 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N SER L 543 " --> pdb=" O MET L 540 " (cutoff:3.500A) removed outlier: 3.834A 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: 4.145A pdb=" N MET M 12 " --> pdb=" O THR M 8 " (cutoff:3.500A) Proline residue: M 13 - end of helix Processing helix chain 'M' and resid 20 through 42 removed outlier: 3.987A pdb=" N ILE M 23 " --> pdb=" O ASN M 20 " (cutoff:3.500A) removed outlier: 5.139A pdb=" N TRP M 24 " --> pdb=" O ASN M 21 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N ASN M 26 " --> pdb=" O ILE M 23 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N SER M 27 " --> pdb=" O TRP M 24 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N THR M 28 " --> pdb=" O VAL M 25 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N HIS M 30 " --> pdb=" O SER M 27 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N ILE M 34 " --> pdb=" O SER M 31 " (cutoff:3.500A) Processing helix chain 'M' and resid 60 through 80 Proline residue: M 64 - end of helix removed outlier: 3.651A 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: 4.709A pdb=" N LEU M 126 " --> pdb=" O PHE M 122 " (cutoff:3.500A) removed outlier: 4.295A 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: 3.580A pdb=" N TYR M 148 " --> pdb=" O ALA M 145 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N PHE M 149 " --> pdb=" O GLY M 146 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N PHE M 151 " --> pdb=" O TYR M 148 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N TYR M 152 " --> pdb=" O PHE M 149 " (cutoff:3.500A) removed outlier: 4.731A pdb=" N LEU M 158 " --> pdb=" O ALA M 155 " (cutoff:3.500A) Proline residue: M 159 - end of helix removed outlier: 3.736A pdb=" N VAL M 171 " --> pdb=" O GLN M 168 " (cutoff:3.500A) Processing helix chain 'M' and resid 176 through 182 removed outlier: 3.818A pdb=" N TYR M 181 " --> pdb=" O LEU M 177 " (cutoff:3.500A) Processing helix chain 'M' and resid 190 through 206 removed outlier: 4.575A pdb=" N ALA M 202 " --> pdb=" O ALA M 198 " (cutoff:3.500A) removed outlier: 5.131A pdb=" N PHE M 203 " --> pdb=" O CYS M 199 " (cutoff:3.500A) Processing helix chain 'M' and resid 214 through 222 removed outlier: 3.827A pdb=" N LYS M 218 " --> pdb=" O LEU M 214 " (cutoff:3.500A) Processing helix chain 'M' and resid 225 through 233 Processing helix chain 'M' and resid 235 through 250 removed outlier: 4.200A pdb=" N GLY M 239 " --> pdb=" O LEU M 235 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N GLY M 240 " --> pdb=" O LEU M 236 " (cutoff:3.500A) removed outlier: 4.801A pdb=" N LEU M 248 " --> pdb=" O LEU M 244 " (cutoff:3.500A) removed outlier: 4.730A pdb=" N ILE M 249 " --> pdb=" O ARG M 245 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N LEU M 250 " --> pdb=" O ILE M 246 " (cutoff:3.500A) Processing helix chain 'M' and resid 253 through 257 removed outlier: 3.725A pdb=" N MET M 257 " --> pdb=" O THR M 254 " (cutoff:3.500A) Processing helix chain 'M' and resid 259 through 278 removed outlier: 3.959A pdb=" N ILE M 270 " --> pdb=" O LEU M 266 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N LEU M 277 " --> pdb=" O SER M 273 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N ARG M 278 " --> pdb=" O SER M 274 " (cutoff:3.500A) Processing helix chain 'M' and resid 282 through 303 removed outlier: 3.782A pdb=" N LEU M 296 " --> pdb=" O SER M 292 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N VAL M 297 " --> pdb=" O HIS M 293 " (cutoff:3.500A) Processing helix chain 'M' and resid 306 through 337 removed outlier: 3.514A pdb=" N ASN M 333 " --> pdb=" O LEU M 329 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N ARG M 336 " --> pdb=" O SER M 332 " (cutoff:3.500A) Processing helix chain 'M' and resid 348 through 350 No H-bonds generated for 'chain 'M' and resid 348 through 350' Processing helix chain 'M' and resid 353 through 366 Processing helix chain 'M' and resid 373 through 388 removed outlier: 3.593A pdb=" N SER M 387 " --> pdb=" O MET M 383 " (cutoff:3.500A) Processing helix chain 'M' and resid 390 through 415 removed outlier: 3.738A pdb=" N MET M 396 " --> pdb=" O ILE M 393 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N GLY M 397 " --> pdb=" O ILE M 394 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N SER M 407 " --> pdb=" O ALA M 404 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N LEU M 408 " --> pdb=" O LEU M 405 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N MET M 413 " --> pdb=" O MET M 410 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N THR M 414 " --> pdb=" O LEU M 411 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N GLN M 415 " --> pdb=" O ILE M 412 " (cutoff:3.500A) Processing helix chain 'M' and resid 431 through 454 removed outlier: 3.528A pdb=" N HIS M 440 " --> pdb=" O LEU M 436 " (cutoff:3.500A) Proline residue: M 443 - end of helix removed outlier: 3.878A pdb=" N THR M 448 " --> pdb=" O LEU M 444 " (cutoff:3.500A) removed outlier: 4.246A pdb=" N LEU M 449 " --> pdb=" O LEU M 445 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N ASN M 450 " --> pdb=" O LEU M 446 " (cutoff:3.500A) Proline residue: M 451 - end of helix removed outlier: 4.998A pdb=" N ILE M 454 " --> pdb=" O ASN M 450 " (cutoff:3.500A) Processing helix chain 'N' and resid 3 through 22 Processing helix chain 'N' and resid 26 through 44 removed outlier: 3.539A 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 121 removed outlier: 4.018A 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: 4.409A pdb=" N ALA N 137 " --> pdb=" O TRP N 133 " (cutoff:3.500A) Proline residue: N 138 - end of helix removed outlier: 3.667A pdb=" N GLN N 144 " --> pdb=" O SER N 140 " (cutoff:3.500A) Proline residue: N 147 - end of helix Processing helix chain 'N' and resid 151 through 171 removed outlier: 3.813A pdb=" N LEU N 170 " --> pdb=" O GLY N 166 " (cutoff:3.500A) removed outlier: 4.316A pdb=" N ASN N 171 " --> pdb=" O TRP N 167 " (cutoff:3.500A) Processing helix chain 'N' and resid 175 through 192 Processing helix chain 'N' and resid 198 through 222 removed outlier: 3.872A pdb=" N ASN N 222 " --> pdb=" O MET N 218 " (cutoff:3.500A) Processing helix chain 'N' and resid 227 through 235 removed outlier: 3.745A pdb=" N HIS N 232 " --> pdb=" O LEU N 228 " (cutoff:3.500A) removed outlier: 4.367A pdb=" N THR N 233 " --> pdb=" O SER N 229 " (cutoff:3.500A) removed outlier: 4.970A pdb=" N TRP N 234 " --> pdb=" O LEU N 230 " (cutoff:3.500A) removed outlier: 5.563A pdb=" N ASN N 235 " --> pdb=" O SER N 231 " (cutoff:3.500A) Processing helix chain 'N' and resid 238 through 251 removed outlier: 3.512A pdb=" N VAL N 242 " --> pdb=" O PRO N 238 " (cutoff:3.500A) Processing helix chain 'N' and resid 258 through 273 Proline residue: N 262 - end of helix removed outlier: 3.546A pdb=" N ILE N 266 " --> pdb=" O LYS N 263 " (cutoff:3.500A) Processing helix chain 'N' and resid 277 through 300 removed outlier: 3.715A pdb=" N LEU N 287 " --> pdb=" O ALA N 283 " (cutoff:3.500A) removed outlier: 4.296A pdb=" N LEU N 288 " --> pdb=" O ILE N 284 " (cutoff:3.500A) removed outlier: 4.245A pdb=" N ASN N 289 " --> pdb=" O THR N 285 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N LEU N 296 " --> pdb=" O PHE N 292 " (cutoff:3.500A) Processing helix chain 'N' and resid 309 through 316 Processing helix chain 'N' and resid 326 through 334 Processing helix chain 'N' and resid 337 through 346 Proline residue: N 341 - end of helix Processing helix chain 'O' and resid 5 through 9 Processing helix chain 'O' and resid 14 through 17 No H-bonds generated for 'chain 'O' and resid 14 through 17' Processing helix chain 'O' and resid 35 through 46 Processing helix chain 'O' and resid 58 through 62 Processing helix chain 'O' and resid 71 through 74 Processing helix chain 'O' and resid 79 through 84 Processing helix chain 'O' and resid 92 through 118 Processing helix chain 'O' and resid 131 through 140 removed outlier: 3.695A pdb=" N GLU O 136 " --> pdb=" O VAL O 133 " (cutoff:3.500A) Processing helix chain 'O' and resid 146 through 162 removed outlier: 3.544A pdb=" N VAL O 158 " --> pdb=" O GLN O 154 " (cutoff:3.500A) removed outlier: 4.094A pdb=" N CYS O 161 " --> pdb=" O LYS O 157 " (cutoff:3.500A) removed outlier: 5.432A pdb=" N GLU O 162 " --> pdb=" O VAL O 158 " (cutoff:3.500A) Processing helix chain 'O' and resid 176 through 186 removed outlier: 3.556A pdb=" N GLN O 184 " --> pdb=" O GLN O 180 " (cutoff:3.500A) 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 215 Processing helix chain 'O' and resid 231 through 239 Processing helix chain 'O' and resid 247 through 250 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 272 through 274 No H-bonds generated for 'chain 'O' and resid 272 through 274' Processing helix chain 'O' and resid 286 through 298 removed outlier: 3.530A 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: 4.008A pdb=" N TYR P 33 " --> pdb=" O PHE P 29 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N MET P 41 " --> pdb=" O HIS P 37 " (cutoff:3.500A) Processing helix chain 'P' and resid 53 through 62 removed outlier: 5.140A 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 123 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 249 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 312 No H-bonds generated for 'chain 'P' and resid 310 through 312' Processing helix chain 'P' and resid 314 through 321 removed outlier: 5.245A pdb=" N ARG P 320 " --> pdb=" O GLU P 316 " (cutoff:3.500A) removed outlier: 5.201A 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: 4.114A pdb=" N LYS Q 31 " --> pdb=" O GLU Q 28 " (cutoff:3.500A) Processing helix chain 'Q' and resid 89 through 98 Processing helix chain 'Q' and resid 118 through 122 Processing helix chain 'R' and resid 23 through 28 Processing helix chain 'R' and resid 40 through 46 removed outlier: 3.624A 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: 4.868A pdb=" N GLY S 31 " --> pdb=" O GLY S 28 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N ARG S 39 " --> pdb=" O ILE S 36 " (cutoff:3.500A) removed outlier: 5.748A pdb=" N TYR S 40 " --> pdb=" O GLU S 37 " (cutoff:3.500A) removed outlier: 5.287A 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 95 Processing helix chain 'T' and resid 8 through 21 Processing helix chain 'T' and resid 27 through 29 No H-bonds generated for 'chain 'T' and resid 27 through 29' Processing helix chain 'T' and resid 44A through 58 Processing helix chain 'T' and resid 64 through 69 removed outlier: 4.105A pdb=" N LYS T 69 " --> pdb=" O ILE T 65 " (cutoff:3.500A) Processing helix chain 'T' and resid 73 through 81 Processing helix chain 'U' and resid 8 through 21 Processing helix chain 'U' and resid 44A through 58 Processing helix chain 'U' and resid 64 through 69 removed outlier: 4.538A 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: 4.009A pdb=" N HIS V 36 " --> pdb=" O ASP V 32 " (cutoff:3.500A) Processing helix chain 'V' and resid 42 through 60 Processing helix chain 'V' and resid 64 through 71 Processing helix chain 'V' and resid 76 through 96 removed outlier: 3.824A pdb=" N GLN V 95 " --> pdb=" O ARG V 91 " (cutoff:3.500A) Processing helix chain 'W' and resid 25 through 49 Proline residue: W 44 - end of helix Processing helix chain 'W' and resid 56 through 70 removed outlier: 4.250A pdb=" N ASN W 70 " --> pdb=" O MET W 66 " (cutoff:3.500A) Processing helix chain 'W' and resid 76 through 94 Processing helix chain 'W' and resid 100 through 107 removed outlier: 4.568A pdb=" N PHE W 106 " --> pdb=" O HIS W 102 " (cutoff:3.500A) removed outlier: 5.200A pdb=" N PHE W 107 " --> pdb=" O VAL W 103 " (cutoff:3.500A) Processing helix chain 'W' and resid 118 through 124 Processing helix chain 'X' and resid 9 through 12 Processing helix chain 'X' and resid 21 through 34 removed outlier: 4.771A pdb=" N HIS X 29 " --> pdb=" O LYS X 25 " (cutoff:3.500A) removed outlier: 5.739A pdb=" N HIS X 30 " --> pdb=" O ALA X 26 " (cutoff:3.500A) Processing helix chain 'X' and resid 36 through 49 Processing helix chain 'X' and resid 52 through 76 removed outlier: 4.182A pdb=" N LEU X 56 " --> pdb=" O ARG X 53 " (cutoff:3.500A) removed outlier: 5.805A pdb=" N GLU X 57 " --> pdb=" O ARG X 54 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N VAL X 62 " --> pdb=" O GLY X 59 " (cutoff:3.500A) Processing helix chain 'X' and resid 78 through 90 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 113 Processing helix chain 'Y' and resid 3 through 10 Processing helix chain 'Y' and resid 17 through 42 Processing helix chain 'Y' and resid 48 through 80 Processing helix chain 'Y' and resid 86 through 104 Processing helix chain 'Y' and resid 107 through 130 Processing helix chain 'Z' and resid 32 through 97 Proline residue: Z 73 - end of helix 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: 5.847A pdb=" N PHE Z 140 " --> pdb=" O ALA Z 136 " (cutoff:3.500A) removed outlier: 5.364A pdb=" N ILE Z 141 " --> pdb=" O THR Z 137 " (cutoff:3.500A) Processing helix chain 'a' and resid 2 through 4 No H-bonds generated for 'chain 'a' and resid 2 through 4' Processing helix chain 'a' and resid 6 through 31 Proline residue: a 19 - end of helix Processing helix chain 'a' and resid 42 through 55 Processing helix chain 'a' and resid 66 through 68 No H-bonds generated for 'chain 'a' and resid 66 through 68' Processing helix chain 'b' and resid 3 through 14 Processing helix chain 'b' and resid 16 through 34 Proline residue: b 32 - end of helix Processing helix chain 'b' and resid 38 through 47 removed outlier: 3.832A 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: 3.606A pdb=" N TYR d 74 " --> pdb=" O PHE d 70 " (cutoff:3.500A) Processing helix chain 'd' and resid 98 through 101 Processing helix chain 'e' and resid 5 through 9 Processing helix chain 'e' and resid 15 through 17 No H-bonds generated for 'chain 'e' and resid 15 through 17' Processing helix chain 'e' and resid 25 through 27 No H-bonds generated for 'chain 'e' and resid 25 through 27' Processing helix chain 'e' and resid 33 through 43 Processing helix chain 'e' and resid 48 through 54 removed outlier: 3.982A 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: 5.260A pdb=" N VAL f 16 " --> pdb=" O HIS f 13 " (cutoff:3.500A) Proline residue: f 17 - end of helix Processing helix chain 'g' and resid 37 through 40 No H-bonds generated for 'chain 'g' and resid 37 through 40' Processing helix chain 'g' and resid 51 through 65 Processing helix chain 'g' and resid 69 through 78 Processing helix chain 'g' and resid 83 through 102 removed outlier: 3.670A pdb=" N GLN g 86 " --> pdb=" O TYR g 83 " (cutoff:3.500A) removed outlier: 5.741A pdb=" N GLU g 87 " --> pdb=" O ARG g 84 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N GLU g 94 " --> pdb=" O ARG g 91 " (cutoff:3.500A) removed outlier: 3.584A 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: 3.963A 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: 3.933A 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 Processing helix chain 'i' and resid 75 through 87 Processing helix chain 'j' and resid 19 through 48 removed outlier: 7.270A pdb=" N ASP j 45 " --> pdb=" O TRP j 41 " (cutoff:3.500A) removed outlier: 6.748A pdb=" N ALA j 46 " --> pdb=" O HIS j 42 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N VAL j 47 " --> pdb=" O ASP j 43 " (cutoff:3.500A) Processing helix chain 'j' and resid 56 through 58 No H-bonds generated for 'chain 'j' and resid 56 through 58' Processing helix chain 'k' and resid 18 through 20 No H-bonds generated for 'chain 'k' and resid 18 through 20' Processing helix chain 'k' and resid 27 through 38 removed outlier: 4.031A pdb=" N ARG k 38 " --> pdb=" O LYS k 34 " (cutoff:3.500A) Processing helix chain 'k' and resid 45 through 52 removed outlier: 5.081A 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 22 No H-bonds generated for 'chain 'm' and resid 19 through 22' Processing helix chain 'm' and resid 26 through 50 removed outlier: 3.876A pdb=" N GLN m 49 " --> pdb=" O GLU m 45 " (cutoff:3.500A) Processing helix chain 'm' and resid 62 through 70 Processing helix chain 'm' and resid 76 through 78 No H-bonds generated for 'chain 'm' and resid 76 through 78' Processing helix chain 'm' and resid 83 through 91 Processing helix chain 'm' and resid 95 through 116 Processing helix chain 'n' and resid 11 through 30 Processing helix chain 'n' and resid 33 through 50 removed outlier: 4.226A 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: 3.861A pdb=" N MET n 113 " --> pdb=" O SER n 109 " (cutoff:3.500A) removed outlier: 4.201A pdb=" N TYR n 114 " --> pdb=" O GLU n 110 " (cutoff:3.500A) Proline residue: n 115 - end of helix removed outlier: 4.757A pdb=" N GLU n 133 " --> pdb=" O ARG n 129 " (cutoff:3.500A) removed outlier: 5.220A pdb=" N ARG n 134 " --> pdb=" O GLU n 130 " (cutoff:3.500A) Processing helix chain 'n' and resid 167 through 170 No H-bonds generated for 'chain 'n' and resid 167 through 170' Processing helix chain 'o' and resid 2 through 9 Processing helix chain 'o' and resid 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 72 Processing helix chain 'o' and resid 80 through 120 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: 3.677A pdb=" N GLU p 86 " --> pdb=" O LEU p 82 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N GLY p 117 " --> pdb=" O GLN p 113 " (cutoff:3.500A) removed outlier: 6.479A pdb=" N GLU p 118 " --> pdb=" O GLN p 114 " (cutoff:3.500A) removed outlier: 7.145A pdb=" N SER p 119 " --> pdb=" O ARG p 115 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N HIS p 120 " --> pdb=" O GLU p 116 " (cutoff:3.500A) removed outlier: 5.582A pdb=" N ARG p 121 " --> pdb=" O GLY p 117 " (cutoff:3.500A) removed outlier: 6.294A 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 170 Processing helix chain 'q' and resid 3 through 16 removed outlier: 3.771A pdb=" N VAL q 14 " --> pdb=" O GLY q 10 " (cutoff:3.500A) Processing helix chain 'q' and resid 20 through 30 Processing helix chain 'q' and resid 79 through 81 No H-bonds generated for 'chain 'q' and resid 79 through 81' Processing helix chain 'q' and resid 84 through 90 removed outlier: 4.304A 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 57 Processing helix chain 's' and resid 59 through 61 No H-bonds generated for 'chain 's' and resid 59 through 61' Processing sheet with id= A, first strand: chain 'B' and resid 47 through 51 removed outlier: 6.472A pdb=" N VAL B 85 " --> pdb=" O MET B 48 " (cutoff:3.500A) removed outlier: 7.329A pdb=" N PHE B 50 " --> pdb=" O VAL B 85 " (cutoff:3.500A) removed outlier: 6.666A pdb=" N ILE B 87 " --> pdb=" O PHE B 50 " (cutoff:3.500A) removed outlier: 6.447A pdb=" N TYR B 112 " --> pdb=" O MET B 86 " (cutoff:3.500A) removed outlier: 7.680A pdb=" N VAL B 88 " --> pdb=" O TYR B 112 " (cutoff:3.500A) removed outlier: 6.953A pdb=" N VAL B 114 " --> pdb=" O VAL B 88 " (cutoff:3.500A) removed outlier: 6.252A 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: 6.786A pdb=" N ASN C 95 " --> pdb=" O ALA C 76 " (cutoff:3.500A) removed outlier: 4.307A pdb=" N LEU C 78 " --> pdb=" O VAL C 93 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N VAL C 93 " --> pdb=" O LEU C 78 " (cutoff:3.500A) removed outlier: 4.256A pdb=" N ALA C 80 " --> pdb=" O GLU C 91 " (cutoff:3.500A) removed outlier: 6.336A pdb=" N GLU C 91 " --> pdb=" O ALA C 80 " (cutoff:3.500A) removed outlier: 4.912A pdb=" N LEU C 48 " --> pdb=" O ARG C 104 " (cutoff:3.500A) removed outlier: 4.859A pdb=" N TYR C 110 " --> pdb=" O ILE C 52 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'C' and resid 172 through 177 Processing sheet with id= D, first strand: chain 'D' and resid 47 through 51 removed outlier: 6.263A pdb=" N SER D 69 " --> pdb=" O VAL D 73 " (cutoff:3.500A) removed outlier: 5.493A 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: 6.397A pdb=" N TYR E 98 " --> pdb=" O THR E 138 " (cutoff:3.500A) removed outlier: 7.707A pdb=" N ILE E 140 " --> pdb=" O TYR E 98 " (cutoff:3.500A) removed outlier: 6.282A pdb=" N ILE E 100 " --> pdb=" O ILE E 140 " (cutoff:3.500A) removed outlier: 7.002A pdb=" N VAL E 142 " --> pdb=" O ILE E 100 " (cutoff:3.500A) removed outlier: 5.998A pdb=" N VAL E 102 " --> pdb=" O VAL E 142 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'F' and resid 220 through 224 removed outlier: 6.948A pdb=" N TYR F 92 " --> pdb=" O THR F 221 " (cutoff:3.500A) removed outlier: 8.064A pdb=" N ALA F 223 " --> pdb=" O TYR F 92 " (cutoff:3.500A) removed outlier: 6.384A pdb=" N VAL F 94 " --> pdb=" O ALA F 223 " (cutoff:3.500A) removed outlier: 6.388A pdb=" N ALA F 133 " --> pdb=" O LEU F 93 " (cutoff:3.500A) removed outlier: 7.672A pdb=" N VAL F 95 " --> pdb=" O ALA F 133 " (cutoff:3.500A) removed outlier: 6.529A pdb=" N TYR F 135 " --> pdb=" O VAL F 95 " (cutoff:3.500A) removed outlier: 6.884A pdb=" N ALA F 97 " --> pdb=" O TYR F 135 " (cutoff:3.500A) removed outlier: 6.512A pdb=" N TYR F 137 " --> pdb=" O ALA F 97 " (cutoff:3.500A) removed outlier: 6.402A pdb=" N ASP F 174 " --> pdb=" O ALA F 134 " (cutoff:3.500A) removed outlier: 7.456A pdb=" N ILE F 136 " --> pdb=" O ASP F 174 " (cutoff:3.500A) removed outlier: 6.517A pdb=" N PHE F 176 " --> pdb=" O ILE F 136 " (cutoff:3.500A) removed outlier: 7.292A pdb=" N ILE F 138 " --> pdb=" O PHE F 176 " (cutoff:3.500A) removed outlier: 6.233A pdb=" N VAL F 178 " --> pdb=" O ILE F 138 " (cutoff:3.500A) No H-bonds generated for sheet with id= G Processing sheet with id= H, first strand: chain 'F' and resid 266 through 271 Processing sheet with id= I, first strand: chain 'G' and resid 9 through 13 Processing sheet with id= J, first strand: chain 'G' and resid 146 through 148 Processing sheet with id= K, first strand: chain 'G' and resid 173 through 175 Processing sheet with id= L, first strand: chain 'G' and resid 223 through 228 removed outlier: 6.330A pdb=" N ARG G 243 " --> pdb=" O VAL G 247 " (cutoff:3.500A) removed outlier: 5.466A 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 343 through 345 removed outlier: 8.539A pdb=" N CYS G 344 " --> pdb=" O VAL G 315 " (cutoff:3.500A) removed outlier: 6.290A pdb=" N ALA G 317 " --> pdb=" O CYS G 344 " (cutoff:3.500A) removed outlier: 6.473A pdb=" N MET G 521 " --> pdb=" O ALA G 316 " (cutoff:3.500A) removed outlier: 8.134A pdb=" N ILE G 318 " --> pdb=" O MET G 521 " (cutoff:3.500A) removed outlier: 6.510A pdb=" N PHE G 523 " --> pdb=" O ILE G 318 " (cutoff:3.500A) removed outlier: 6.361A pdb=" N PHE G 542 " --> pdb=" O LEU G 522 " (cutoff:3.500A) removed outlier: 7.308A pdb=" N LEU G 524 " --> pdb=" O PHE G 542 " (cutoff:3.500A) removed outlier: 6.447A pdb=" N VAL G 544 " --> pdb=" O LEU G 524 " (cutoff:3.500A) removed outlier: 6.314A pdb=" N VAL G 559 " --> pdb=" O TYR G 545 " (cutoff:3.500A) removed outlier: 7.878A pdb=" N GLY G 547 " --> pdb=" O VAL G 559 " (cutoff:3.500A) removed outlier: 6.129A pdb=" N LEU G 561 " --> pdb=" O GLY G 547 " (cutoff:3.500A) No H-bonds generated for sheet with id= N Processing sheet with id= O, first strand: chain 'G' and resid 490 through 493 removed outlier: 7.990A pdb=" N ASN G 491 " --> pdb=" O PRO G 449 " (cutoff:3.500A) removed outlier: 6.383A pdb=" N VAL G 451 " --> pdb=" O ASN G 491 " (cutoff:3.500A) removed outlier: 7.109A pdb=" N LEU G 493 " --> pdb=" O VAL G 451 " (cutoff:3.500A) removed outlier: 6.674A pdb=" N LEU G 453 " --> pdb=" O LEU G 493 " (cutoff:3.500A) removed outlier: 6.408A pdb=" N VAL G 376 " --> pdb=" O MET G 450 " (cutoff:3.500A) removed outlier: 7.691A pdb=" N ILE G 452 " --> pdb=" O VAL G 376 " (cutoff:3.500A) removed outlier: 6.315A pdb=" N LEU G 378 " --> pdb=" O ILE G 452 " (cutoff:3.500A) removed outlier: 7.524A pdb=" N GLY G 454 " --> pdb=" O LEU G 378 " (cutoff:3.500A) removed outlier: 7.563A pdb=" N VAL G 380 " --> pdb=" O GLY G 454 " (cutoff:3.500A) removed outlier: 6.498A pdb=" N LYS G 405 " --> pdb=" O VAL G 377 " (cutoff:3.500A) removed outlier: 7.739A pdb=" N LEU G 379 " --> pdb=" O LYS G 405 " (cutoff:3.500A) removed outlier: 6.573A pdb=" N ALA G 407 " --> pdb=" O LEU G 379 " (cutoff:3.500A) removed outlier: 6.504A 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: 6.025A pdb=" N GLU I 97 " --> pdb=" O THR I 106 " (cutoff:3.500A) removed outlier: 5.321A pdb=" N THR I 106 " --> pdb=" O GLU I 97 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'L' and resid 69 through 71 Processing sheet with id= T, first strand: chain 'L' and resid 61 through 67 removed outlier: 6.741A pdb=" N LEU L 78 " --> pdb=" O ASN L 65 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'O' and resid 219 through 224 removed outlier: 6.190A pdb=" N VAL O 122 " --> pdb=" O ILE O 25 " (cutoff:3.500A) removed outlier: 7.764A pdb=" N VAL O 27 " --> pdb=" O VAL O 122 " (cutoff:3.500A) removed outlier: 6.590A pdb=" N LEU O 124 " --> pdb=" O VAL O 27 " (cutoff:3.500A) removed outlier: 8.614A pdb=" N GLY O 29 " --> pdb=" O LEU O 124 " (cutoff:3.500A) removed outlier: 6.504A pdb=" N LYS O 49 " --> pdb=" O VAL O 123 " (cutoff:3.500A) removed outlier: 8.282A pdb=" N GLU O 125 " --> pdb=" O LYS O 49 " (cutoff:3.500A) removed outlier: 8.286A pdb=" N PHE O 51 " --> pdb=" O GLU O 125 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'P' and resid 227 through 230 removed outlier: 6.540A pdb=" N ILE P 165 " --> pdb=" O PHE P 228 " (cutoff:3.500A) removed outlier: 7.609A pdb=" N PHE P 230 " --> pdb=" O ILE P 165 " (cutoff:3.500A) removed outlier: 6.427A pdb=" N LYS P 167 " --> pdb=" O PHE P 230 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ILE P 132 " --> pdb=" O ASN P 93 " (cutoff:3.500A) removed outlier: 6.423A pdb=" N GLN P 44 " --> pdb=" O ALA P 21 " (cutoff:3.500A) removed outlier: 7.428A pdb=" N VAL P 23 " --> pdb=" O GLN P 44 " (cutoff:3.500A) removed outlier: 6.672A pdb=" N ILE P 46 " --> pdb=" O VAL P 23 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'Q' and resid 102 through 105 Processing sheet with id= X, first strand: chain 'Q' and resid 64 through 66 Processing sheet with id= Y, first strand: chain 'R' and resid 50 through 52 Processing sheet with id= Z, first strand: chain 'R' and resid 56 through 59 Processing sheet with id= AA, first strand: chain 'S' and resid 51 through 56 removed outlier: 3.547A pdb=" N LEU S 22 " --> pdb=" O ARG S 55 " (cutoff:3.500A) removed outlier: 6.614A pdb=" N ARG S 67 " --> pdb=" O ARG S 16 " (cutoff:3.500A) removed outlier: 4.350A pdb=" N ILE S 18 " --> pdb=" O TRP S 65 " (cutoff:3.500A) removed outlier: 6.607A pdb=" N TRP S 65 " --> pdb=" O ILE S 18 " (cutoff:3.500A) removed outlier: 4.526A pdb=" N ILE S 20 " --> pdb=" O LYS S 63 " (cutoff:3.500A) removed outlier: 6.518A pdb=" N LYS S 63 " --> pdb=" O ILE S 20 " (cutoff:3.500A) Processing sheet with id= AB, first strand: chain 'q' and resid 60 through 63 removed outlier: 6.509A pdb=" N GLU q 50 " --> pdb=" O LEU q 38 " (cutoff:3.500A) removed outlier: 5.520A pdb=" N LEU q 38 " --> pdb=" O GLU q 50 " (cutoff:3.500A) 2916 hydrogen bonds defined for protein. 7872 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: 21.49 Time building geometry restraints manager: 26.73 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: 27507 1.40 - 1.63: 40114 1.63 - 1.85: 825 1.85 - 2.08: 0 2.08 - 2.30: 82 Bond restraints: 68528 Sorted by residual: bond pdb=" C5 GTP O1202 " pdb=" N7 GTP O1202 " ideal model delta sigma weight residual 1.350 1.520 -0.170 2.00e-02 2.50e+03 7.26e+01 bond pdb=" C6 GTP O1202 " pdb=" O6 GTP O1202 " ideal model delta sigma weight residual 1.230 1.395 -0.165 2.00e-02 2.50e+03 6.77e+01 bond pdb=" C SAC i 1 " pdb=" O SAC i 1 " ideal model delta sigma weight residual 1.231 1.359 -0.128 2.00e-02 2.50e+03 4.10e+01 bond pdb=" CB7 CDL K 401 " pdb=" OB8 CDL K 401 " ideal model delta sigma weight residual 1.334 1.402 -0.068 1.10e-02 8.26e+03 3.79e+01 bond pdb=" CA7 CDL L 704 " pdb=" OA8 CDL L 704 " ideal model delta sigma weight residual 1.334 1.401 -0.067 1.10e-02 8.26e+03 3.69e+01 ... (remaining 68523 not shown) Histogram of bond angle deviations from ideal: 72.57 - 84.88: 77 84.88 - 97.19: 1 97.19 - 109.50: 7472 109.50 - 121.82: 72088 121.82 - 134.13: 13068 Bond angle restraints: 92706 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 74.19 48.81 1.60e+00 3.91e-01 9.31e+02 angle pdb=" O 2MR D 85 " pdb=" C 2MR D 85 " pdb=" N GLY D 86 " ideal model delta sigma weight residual 123.00 101.12 21.88 1.60e+00 3.91e-01 1.87e+02 angle pdb=" C11 CDL L 704 " pdb=" CA5 CDL L 704 " pdb=" OA6 CDL L 704 " ideal model delta sigma weight residual 111.33 121.21 -9.88 1.32e+00 5.72e-01 5.58e+01 angle pdb=" C51 CDL h1001 " pdb=" CB5 CDL h1001 " pdb=" OB6 CDL h1001 " ideal model delta sigma weight residual 111.33 121.10 -9.77 1.32e+00 5.72e-01 5.46e+01 angle pdb=" C51 CDL d 201 " pdb=" CB5 CDL d 201 " pdb=" OB6 CDL d 201 " ideal model delta sigma weight residual 111.33 120.49 -9.16 1.32e+00 5.72e-01 4.80e+01 ... (remaining 92701 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.79: 40157 35.79 - 71.59: 1514 71.59 - 107.38: 197 107.38 - 143.17: 44 143.17 - 178.97: 4 Dihedral angle restraints: 41916 sinusoidal: 18314 harmonic: 23602 Sorted by residual: dihedral pdb=" O3B GTP O1202 " pdb=" O3A GTP O1202 " pdb=" PB GTP O1202 " pdb=" PA GTP O1202 " ideal model delta sinusoidal sigma weight residual 291.08 112.11 178.97 1 2.00e+01 2.50e-03 4.80e+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 82.82 174.77 1 2.00e+01 2.50e-03 4.79e+01 dihedral pdb=" O5' GTP O1202 " pdb=" O3A GTP O1202 " pdb=" PA GTP O1202 " pdb=" PB GTP O1202 " ideal model delta sinusoidal sigma weight residual 274.12 106.82 167.30 1 2.00e+01 2.50e-03 4.74e+01 ... (remaining 41913 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 4.277: 10124 4.277 - 8.555: 0 8.555 - 12.832: 0 12.832 - 17.110: 0 17.110 - 21.387: 16 Chirality restraints: 10140 Sorted by residual: chirality pdb="FE1 SF4 I 202 " pdb=" S2 SF4 I 202 " pdb=" S3 SF4 I 202 " pdb=" S4 SF4 I 202 " both_signs ideal model delta sigma weight residual False -10.55 10.83 -21.39 2.00e-01 2.50e+01 1.14e+04 chirality pdb="FE2 SF4 I 202 " pdb=" S1 SF4 I 202 " pdb=" S3 SF4 I 202 " pdb=" S4 SF4 I 202 " both_signs ideal model delta sigma weight residual False 10.55 -10.79 21.35 2.00e-01 2.50e+01 1.14e+04 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 -10.76 21.32 2.00e-01 2.50e+01 1.14e+04 ... (remaining 10137 not shown) Planarity restraints: 11534 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C08 I49 H 602 " -0.513 2.00e-02 2.50e+03 5.61e-01 6.30e+03 pdb=" C14 I49 H 602 " 0.335 2.00e-02 2.50e+03 pdb=" C15 I49 H 602 " 0.060 2.00e-02 2.50e+03 pdb=" N01 I49 H 602 " 0.114 2.00e-02 2.50e+03 pdb=" N02 I49 H 602 " 0.921 2.00e-02 2.50e+03 pdb=" N03 I49 H 602 " 0.034 2.00e-02 2.50e+03 pdb=" N04 I49 H 602 " -1.119 2.00e-02 2.50e+03 pdb=" N05 I49 H 602 " 0.167 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C08 I49 N 503 " 0.561 2.00e-02 2.50e+03 5.54e-01 6.14e+03 pdb=" C14 I49 N 503 " -0.354 2.00e-02 2.50e+03 pdb=" C15 I49 N 503 " 0.025 2.00e-02 2.50e+03 pdb=" N01 I49 N 503 " 0.108 2.00e-02 2.50e+03 pdb=" N02 I49 N 503 " -0.741 2.00e-02 2.50e+03 pdb=" N03 I49 N 503 " -0.502 2.00e-02 2.50e+03 pdb=" N04 I49 N 503 " -0.179 2.00e-02 2.50e+03 pdb=" N05 I49 N 503 " 1.081 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SAC i 1 " 0.177 2.00e-02 2.50e+03 2.61e-01 6.81e+02 pdb=" C SAC i 1 " -0.450 2.00e-02 2.50e+03 pdb=" O SAC i 1 " 0.118 2.00e-02 2.50e+03 pdb=" N GLY i 2 " 0.155 2.00e-02 2.50e+03 ... (remaining 11531 not shown) Histogram of nonbonded interaction distances: 1.80 - 2.47: 389 2.47 - 3.14: 55609 3.14 - 3.80: 140239 3.80 - 4.47: 216649 4.47 - 5.14: 327940 Nonbonded interactions: 740826 Sorted by model distance: nonbonded pdb=" O2B GTP O1202 " pdb="MG MG O1203 " model vdw 1.801 2.170 nonbonded pdb=" OD1 ASP l 40 " pdb=" OG1 THR l 42 " model vdw 1.913 2.440 nonbonded pdb=" O HOH L 830 " pdb=" O HOH L 833 " model vdw 1.930 2.440 nonbonded pdb=" OH TYR O 83 " pdb=" O3' GTP O1202 " model vdw 1.949 2.440 nonbonded pdb=" O2B LMT L 706 " pdb=" O3' LMT L 706 " model vdw 1.958 2.440 ... (remaining 740821 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: 11.850 Set stop_for_unknowns flag: 0.010 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.060 Extract box with map and model: 56.810 Check model and map are aligned: 0.740 Set scattering table: 0.470 Process input model: 164.230 Find NCS groups from input model: 2.010 Set up NCS constraints: 0.230 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:11.860 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 248.280 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8755 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.170 68528 Z= 0.492 Angle : 0.836 48.813 92706 Z= 0.389 Chirality : 0.847 21.387 10140 Planarity : 0.009 0.561 11534 Dihedral : 18.690 178.968 26678 Min Nonbonded Distance : 1.801 Molprobity Statistics. All-atom Clashscore : 2.78 Ramachandran Plot: Outliers : 0.01 % Allowed : 2.29 % Favored : 97.69 % Rotamer: Outliers : 1.20 % Allowed : 11.86 % Favored : 86.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.54 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.76 (0.09), residues: 7977 helix: 0.81 (0.08), residues: 4317 sheet: 0.34 (0.25), residues: 384 loop : 0.32 (0.11), residues: 3276 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP g 88 HIS 0.008 0.001 HIS C 160 PHE 0.021 0.002 PHE N 292 TYR 0.021 0.002 TYR I 118 ARG 0.020 0.000 ARG q 21 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15954 Ramachandran restraints generated. 7977 Oldfield, 0 Emsley, 7977 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15954 Ramachandran restraints generated. 7977 Oldfield, 0 Emsley, 7977 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1061 residues out of total 7064 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 85 poor density : 976 time to evaluate : 6.025 Fit side-chains REVERT: G 486 ASP cc_start: 0.7205 (t70) cc_final: 0.7004 (t0) REVERT: O 298 GLU cc_start: 0.7923 (OUTLIER) cc_final: 0.7711 (mt-10) REVERT: R 3 ARG cc_start: 0.7184 (ttp80) cc_final: 0.6897 (ptt-90) REVERT: T 29 LYS cc_start: 0.7425 (tttm) cc_final: 0.7053 (tmtp) REVERT: V 109 SER cc_start: 0.8181 (m) cc_final: 0.7718 (p) REVERT: c 41 GLU cc_start: 0.8319 (tp30) cc_final: 0.8102 (tp30) REVERT: e 52 GLU cc_start: 0.7530 (mt-10) cc_final: 0.7132 (pt0) REVERT: j 40 PHE cc_start: 0.8455 (t80) cc_final: 0.7989 (t80) REVERT: m 4 LYS cc_start: 0.8488 (mtpt) cc_final: 0.8249 (mptt) outliers start: 85 outliers final: 72 residues processed: 1049 average time/residue: 1.7619 time to fit residues: 2329.0333 Evaluate side-chains 1021 residues out of total 7064 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 948 time to evaluate : 6.046 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 ILE Chi-restraints excluded: chain A residue 24 LEU Chi-restraints excluded: chain B residue 54 CYS Chi-restraints excluded: chain D residue 76 CYS Chi-restraints excluded: chain D residue 341 SER Chi-restraints excluded: chain D residue 376 VAL Chi-restraints excluded: chain D residue 420 THR Chi-restraints excluded: chain E residue 136 LEU Chi-restraints excluded: chain E residue 203 THR Chi-restraints excluded: chain F residue 339 ARG Chi-restraints excluded: chain G residue 431 ASP Chi-restraints excluded: chain G residue 613 TYR Chi-restraints excluded: chain H residue 54 LYS Chi-restraints excluded: chain H residue 62 ARG Chi-restraints excluded: chain H residue 66 SER Chi-restraints excluded: chain H residue 69 SER Chi-restraints excluded: chain H residue 222 LEU Chi-restraints excluded: chain H residue 259 PHE Chi-restraints excluded: chain I residue 11 SER Chi-restraints excluded: chain J residue 82 ILE Chi-restraints excluded: chain J residue 107 VAL Chi-restraints excluded: chain J residue 133 SER Chi-restraints excluded: chain J residue 148 SER Chi-restraints excluded: chain L residue 10 VAL Chi-restraints excluded: chain L residue 30 SER Chi-restraints excluded: chain L residue 290 MET Chi-restraints excluded: chain L residue 393 ASP Chi-restraints excluded: chain L residue 441 VAL Chi-restraints excluded: chain M residue 80 SER Chi-restraints excluded: chain M residue 116 ILE Chi-restraints excluded: chain M residue 144 ASN Chi-restraints excluded: chain M residue 315 LEU Chi-restraints excluded: chain O residue 19 THR Chi-restraints excluded: chain O residue 60 ASP Chi-restraints excluded: chain O residue 181 SER Chi-restraints excluded: chain O residue 279 LEU Chi-restraints excluded: chain O residue 298 GLU Chi-restraints excluded: chain P residue 140 LYS Chi-restraints excluded: chain Q residue 110 VAL Chi-restraints excluded: chain R residue 4 THR Chi-restraints excluded: chain T residue 34 SER Chi-restraints excluded: chain T residue 44 SER Chi-restraints excluded: chain U residue 83 LYS Chi-restraints excluded: chain V residue 94 ILE Chi-restraints excluded: chain X residue 77 CYS Chi-restraints excluded: chain X residue 82 THR Chi-restraints excluded: chain X residue 99 CYS Chi-restraints excluded: chain X residue 143 SER Chi-restraints excluded: chain Y residue 17 CYS Chi-restraints excluded: chain Y residue 46 THR Chi-restraints excluded: chain Y residue 47 SER Chi-restraints excluded: chain Y residue 73 SER Chi-restraints excluded: chain a residue 30 SER Chi-restraints excluded: chain b residue 4 VAL Chi-restraints excluded: chain d residue 20 SER Chi-restraints excluded: chain e residue 92 THR Chi-restraints excluded: chain i residue 63 THR Chi-restraints excluded: chain i residue 78 VAL Chi-restraints excluded: chain k residue 78 VAL Chi-restraints excluded: chain l residue 6 LYS Chi-restraints excluded: chain l residue 81 LEU Chi-restraints excluded: chain m residue 15 THR Chi-restraints excluded: chain m residue 40 SER Chi-restraints excluded: chain m residue 79 PHE Chi-restraints excluded: chain m residue 85 THR Chi-restraints excluded: chain n residue 140 GLN Chi-restraints excluded: chain o residue 27 ASP Chi-restraints excluded: chain o residue 30 PHE Chi-restraints excluded: chain p residue 134 VAL Chi-restraints excluded: chain p residue 171 GLU Chi-restraints excluded: chain q residue 15 SER Chi-restraints excluded: chain r residue 68 VAL Chi-restraints excluded: chain s residue 59 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 790 random chunks: chunk 667 optimal weight: 3.9990 chunk 598 optimal weight: 0.8980 chunk 332 optimal weight: 2.9990 chunk 204 optimal weight: 7.9990 chunk 403 optimal weight: 5.9990 chunk 319 optimal weight: 0.9990 chunk 619 optimal weight: 0.9990 chunk 239 optimal weight: 0.7980 chunk 376 optimal weight: 1.9990 chunk 460 optimal weight: 3.9990 chunk 717 optimal weight: 7.9990 overall best weight: 1.1386 ------------------------------------------------------------------------------- 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 F 83 ASN F 431 GLN F 435 GLN G 535 GLN H 124 ASN H 194 ASN ** H 317 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 23 GLN N 316 GLN O 190 HIS O 294 GLN P 87 HIS Y 7 GLN Y 88 ASN g 119 GLN i 12 GLN m 125 ASN n 140 GLN o 43 GLN q 112 ASN r 24 GLN Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8660 moved from start: 0.0894 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.273 68528 Z= 0.433 Angle : 1.312 50.667 92706 Z= 0.841 Chirality : 0.257 6.506 10140 Planarity : 0.004 0.059 11534 Dihedral : 14.440 179.541 10804 Min Nonbonded Distance : 2.005 Molprobity Statistics. All-atom Clashscore : 3.25 Ramachandran Plot: Outliers : 0.01 % Allowed : 1.44 % Favored : 98.55 % Rotamer: Outliers : 1.90 % Allowed : 11.84 % Favored : 86.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.54 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.45 (0.09), residues: 7977 helix: 1.57 (0.08), residues: 4292 sheet: 0.24 (0.26), residues: 377 loop : 0.39 (0.11), residues: 3308 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP L 144 HIS 0.005 0.001 HIS N 112 PHE 0.028 0.001 PHE N 292 TYR 0.025 0.001 TYR I 118 ARG 0.004 0.000 ARG W 114 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15954 Ramachandran restraints generated. 7977 Oldfield, 0 Emsley, 7977 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15954 Ramachandran restraints generated. 7977 Oldfield, 0 Emsley, 7977 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1119 residues out of total 7064 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 134 poor density : 985 time to evaluate : 6.124 Fit side-chains REVERT: E 134 ASP cc_start: 0.8097 (OUTLIER) cc_final: 0.7710 (p0) REVERT: E 180 LYS cc_start: 0.8183 (OUTLIER) cc_final: 0.7911 (mtpt) REVERT: F 339 ARG cc_start: 0.8083 (OUTLIER) cc_final: 0.7650 (mtp-110) REVERT: G 180 ASP cc_start: 0.8184 (OUTLIER) cc_final: 0.7851 (t0) REVERT: G 188 GLU cc_start: 0.7904 (OUTLIER) cc_final: 0.7386 (mm-30) REVERT: H 70 MET cc_start: 0.7630 (mtm) cc_final: 0.7381 (mtm) REVERT: N 21 MET cc_start: 0.8929 (mtm) cc_final: 0.8720 (mtm) REVERT: N 100 MET cc_start: 0.8446 (mtt) cc_final: 0.8162 (mtt) REVERT: O 279 LEU cc_start: 0.8644 (OUTLIER) cc_final: 0.8197 (mp) REVERT: R 3 ARG cc_start: 0.7191 (OUTLIER) cc_final: 0.6799 (ptt-90) REVERT: S 25 ARG cc_start: 0.7747 (OUTLIER) cc_final: 0.7314 (mmt180) REVERT: S 90 LEU cc_start: 0.9009 (OUTLIER) cc_final: 0.8540 (mm) REVERT: T 8 LEU cc_start: 0.7375 (OUTLIER) cc_final: 0.6840 (tt) REVERT: T 37 MET cc_start: 0.7664 (OUTLIER) cc_final: 0.7041 (mmt) REVERT: T 57 GLU cc_start: 0.7462 (tp30) cc_final: 0.7004 (tp30) REVERT: U 12 LYS cc_start: 0.8979 (ttpp) cc_final: 0.8776 (tttm) REVERT: V 39 LYS cc_start: 0.8345 (OUTLIER) cc_final: 0.7884 (tmtp) REVERT: X 3 ILE cc_start: 0.8646 (OUTLIER) cc_final: 0.8379 (mp) REVERT: Y 57 ARG cc_start: 0.7773 (ttp80) cc_final: 0.7530 (mtm110) REVERT: Y 85 ASP cc_start: 0.8705 (OUTLIER) cc_final: 0.8494 (t70) REVERT: Z 27 ARG cc_start: 0.7276 (tpt170) cc_final: 0.6723 (tpm170) REVERT: c 41 GLU cc_start: 0.8258 (tp30) cc_final: 0.8027 (tp30) REVERT: e 52 GLU cc_start: 0.7549 (mt-10) cc_final: 0.7157 (pt0) REVERT: i 121 GLU cc_start: 0.6927 (OUTLIER) cc_final: 0.6707 (tt0) REVERT: j 40 PHE cc_start: 0.8367 (t80) cc_final: 0.8013 (t80) REVERT: m 24 ILE cc_start: 0.7683 (mp) cc_final: 0.7440 (mp) REVERT: m 29 ARG cc_start: 0.7778 (OUTLIER) cc_final: 0.7411 (ttm-80) REVERT: p 14 ARG cc_start: 0.7234 (OUTLIER) cc_final: 0.6659 (ttt180) REVERT: r 72 GLN cc_start: 0.7545 (OUTLIER) cc_final: 0.7034 (pp30) outliers start: 134 outliers final: 45 residues processed: 1061 average time/residue: 1.7817 time to fit residues: 2379.0648 Evaluate side-chains 1020 residues out of total 7064 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 957 time to evaluate : 5.972 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 54 CYS Chi-restraints excluded: chain D residue 76 CYS Chi-restraints excluded: chain D residue 420 THR Chi-restraints excluded: chain E residue 134 ASP Chi-restraints excluded: chain E residue 180 LYS Chi-restraints excluded: chain F residue 339 ARG Chi-restraints excluded: chain G residue 180 ASP Chi-restraints excluded: chain G residue 188 GLU Chi-restraints excluded: chain G residue 431 ASP Chi-restraints excluded: chain G residue 613 TYR Chi-restraints excluded: chain H residue 54 LYS Chi-restraints excluded: chain H residue 72 ILE Chi-restraints excluded: chain H residue 121 TRP Chi-restraints excluded: chain H residue 222 LEU Chi-restraints excluded: chain H residue 259 PHE Chi-restraints excluded: chain J residue 130 THR Chi-restraints excluded: chain J residue 133 SER Chi-restraints excluded: chain L residue 30 SER Chi-restraints excluded: chain L residue 252 MET Chi-restraints excluded: chain L residue 507 MET Chi-restraints excluded: chain M residue 116 ILE Chi-restraints excluded: chain M residue 130 LEU Chi-restraints excluded: chain M residue 144 ASN Chi-restraints excluded: chain M residue 315 LEU Chi-restraints excluded: chain O residue 1 LEU Chi-restraints excluded: chain O residue 19 THR Chi-restraints excluded: chain O residue 60 ASP Chi-restraints excluded: chain O residue 279 LEU Chi-restraints excluded: chain R residue 3 ARG Chi-restraints excluded: chain S residue 25 ARG Chi-restraints excluded: chain S residue 90 LEU Chi-restraints excluded: chain T residue 8 LEU Chi-restraints excluded: chain T residue 13 ASP Chi-restraints excluded: chain T residue 25 ILE Chi-restraints excluded: chain T residue 37 MET Chi-restraints excluded: chain T residue 44 SER Chi-restraints excluded: chain V residue 39 LYS Chi-restraints excluded: chain W residue 111 GLU Chi-restraints excluded: chain X residue 3 ILE Chi-restraints excluded: chain X residue 99 CYS Chi-restraints excluded: chain X residue 130 VAL Chi-restraints excluded: chain Y residue 85 ASP Chi-restraints excluded: chain Z residue 144 THR Chi-restraints excluded: chain b residue 15 GLU Chi-restraints excluded: chain b residue 42 LEU Chi-restraints excluded: chain d residue 111 GLU Chi-restraints excluded: chain e residue 92 THR Chi-restraints excluded: chain f residue 9 ASP Chi-restraints excluded: chain i residue 59 VAL Chi-restraints excluded: chain i residue 63 THR Chi-restraints excluded: chain i residue 78 VAL Chi-restraints excluded: chain i residue 121 GLU Chi-restraints excluded: chain j residue 45 ASP Chi-restraints excluded: chain m residue 29 ARG Chi-restraints excluded: chain m residue 85 THR Chi-restraints excluded: chain m residue 88 LEU Chi-restraints excluded: chain o residue 30 PHE Chi-restraints excluded: chain p residue 14 ARG Chi-restraints excluded: chain p residue 134 VAL Chi-restraints excluded: chain r residue 68 VAL Chi-restraints excluded: chain r residue 72 GLN Chi-restraints excluded: chain s residue 36 THR Chi-restraints excluded: chain s residue 59 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 790 random chunks: chunk 398 optimal weight: 5.9990 chunk 222 optimal weight: 3.9990 chunk 597 optimal weight: 7.9990 chunk 488 optimal weight: 4.9990 chunk 197 optimal weight: 0.5980 chunk 718 optimal weight: 6.9990 chunk 776 optimal weight: 6.9990 chunk 640 optimal weight: 1.9990 chunk 712 optimal weight: 2.9990 chunk 245 optimal weight: 4.9990 chunk 576 optimal weight: 7.9990 overall best weight: 2.9188 ------------------------------------------------------------------------------- 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 E 121 GLN G 535 GLN H 47 GLN H 194 ASN ** H 317 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 23 GLN K 97 GLN O 76 ASN O 154 GLN W 45 ASN Y 7 GLN b 73 GLN c 46 ASN g 119 GLN i 12 GLN q 112 ASN r 24 GLN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8682 moved from start: 0.0911 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.241 68528 Z= 0.486 Angle : 1.323 50.577 92706 Z= 0.845 Chirality : 0.259 6.609 10140 Planarity : 0.004 0.054 11534 Dihedral : 12.742 179.841 10729 Min Nonbonded Distance : 1.867 Molprobity Statistics. All-atom Clashscore : 3.48 Ramachandran Plot: Outliers : 0.01 % Allowed : 1.87 % Favored : 98.12 % Rotamer: Outliers : 2.10 % Allowed : 12.21 % Favored : 85.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.54 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.45 (0.09), residues: 7977 helix: 1.58 (0.08), residues: 4304 sheet: 0.13 (0.25), residues: 397 loop : 0.37 (0.11), residues: 3276 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP X 85 HIS 0.007 0.001 HIS C 160 PHE 0.025 0.002 PHE N 292 TYR 0.026 0.002 TYR O 94 ARG 0.006 0.000 ARG q 21 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15954 Ramachandran restraints generated. 7977 Oldfield, 0 Emsley, 7977 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15954 Ramachandran restraints generated. 7977 Oldfield, 0 Emsley, 7977 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1108 residues out of total 7064 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 148 poor density : 960 time to evaluate : 6.108 Fit side-chains REVERT: E 36 LYS cc_start: 0.8509 (OUTLIER) cc_final: 0.8304 (ttmm) REVERT: E 134 ASP cc_start: 0.8062 (OUTLIER) cc_final: 0.7650 (p0) REVERT: E 180 LYS cc_start: 0.8200 (OUTLIER) cc_final: 0.7934 (mtpt) REVERT: F 339 ARG cc_start: 0.8089 (OUTLIER) cc_final: 0.7662 (mtp-110) REVERT: G 16 GLN cc_start: 0.8044 (OUTLIER) cc_final: 0.7243 (tm130) REVERT: G 159 CYS cc_start: 0.8100 (OUTLIER) cc_final: 0.7871 (p) REVERT: G 180 ASP cc_start: 0.8180 (OUTLIER) cc_final: 0.7848 (t0) REVERT: G 188 GLU cc_start: 0.7892 (OUTLIER) cc_final: 0.7336 (mm-30) REVERT: G 337 ARG cc_start: 0.8226 (mtt90) cc_final: 0.7876 (mmm-85) REVERT: H 227 GLU cc_start: 0.7454 (OUTLIER) cc_final: 0.6921 (tm-30) REVERT: N 100 MET cc_start: 0.8431 (mtt) cc_final: 0.8166 (mtt) REVERT: O 279 LEU cc_start: 0.8652 (OUTLIER) cc_final: 0.8205 (mp) REVERT: R 3 ARG cc_start: 0.7184 (ttp80) cc_final: 0.6969 (ptt-90) REVERT: S 25 ARG cc_start: 0.7757 (OUTLIER) cc_final: 0.7439 (mmt180) REVERT: S 90 LEU cc_start: 0.9047 (OUTLIER) cc_final: 0.8594 (mm) REVERT: T 8 LEU cc_start: 0.7406 (OUTLIER) cc_final: 0.6912 (tt) REVERT: T 21 LEU cc_start: 0.8173 (OUTLIER) cc_final: 0.7943 (mp) REVERT: T 29 LYS cc_start: 0.7361 (tmtp) cc_final: 0.7075 (tmtp) REVERT: T 37 MET cc_start: 0.7656 (OUTLIER) cc_final: 0.7066 (mmt) REVERT: T 57 GLU cc_start: 0.7304 (tp30) cc_final: 0.6942 (tp30) REVERT: U 29 LYS cc_start: 0.8106 (OUTLIER) cc_final: 0.7801 (mmmm) REVERT: V 39 LYS cc_start: 0.8321 (OUTLIER) cc_final: 0.7831 (tmtp) REVERT: X 3 ILE cc_start: 0.8632 (OUTLIER) cc_final: 0.8369 (mp) REVERT: Y 57 ARG cc_start: 0.7801 (ttp80) cc_final: 0.7484 (mtp-110) REVERT: Y 85 ASP cc_start: 0.8713 (OUTLIER) cc_final: 0.8417 (t70) REVERT: c 34 GLN cc_start: 0.8473 (OUTLIER) cc_final: 0.6918 (tm-30) REVERT: c 41 GLU cc_start: 0.8316 (tp30) cc_final: 0.8079 (tp30) REVERT: e 7 LYS cc_start: 0.8758 (OUTLIER) cc_final: 0.8379 (tptp) REVERT: e 52 GLU cc_start: 0.7569 (mt-10) cc_final: 0.7166 (pt0) REVERT: g 122 GLU cc_start: 0.6774 (OUTLIER) cc_final: 0.6037 (tm-30) REVERT: i 114 GLU cc_start: 0.8064 (OUTLIER) cc_final: 0.7849 (pt0) REVERT: i 121 GLU cc_start: 0.6934 (OUTLIER) cc_final: 0.6711 (tt0) REVERT: j 40 PHE cc_start: 0.8397 (t80) cc_final: 0.8033 (t80) REVERT: m 21 GLU cc_start: 0.7211 (OUTLIER) cc_final: 0.6651 (mm-30) REVERT: m 24 ILE cc_start: 0.7702 (mp) cc_final: 0.7471 (mp) REVERT: m 29 ARG cc_start: 0.7794 (OUTLIER) cc_final: 0.7425 (ttm-80) REVERT: m 32 GLN cc_start: 0.8676 (OUTLIER) cc_final: 0.8289 (mt0) REVERT: p 14 ARG cc_start: 0.7258 (OUTLIER) cc_final: 0.6673 (ttt180) REVERT: r 72 GLN cc_start: 0.7598 (OUTLIER) cc_final: 0.7113 (pp30) outliers start: 148 outliers final: 59 residues processed: 1045 average time/residue: 1.7567 time to fit residues: 2316.2814 Evaluate side-chains 1033 residues out of total 7064 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 88 poor density : 945 time to evaluate : 5.961 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 LEU Chi-restraints excluded: chain B residue 54 CYS Chi-restraints excluded: chain B residue 161 LEU Chi-restraints excluded: chain D residue 109 VAL Chi-restraints excluded: chain D residue 376 VAL Chi-restraints excluded: chain D residue 420 THR Chi-restraints excluded: chain E residue 36 LYS Chi-restraints excluded: chain E residue 134 ASP Chi-restraints excluded: chain E residue 180 LYS Chi-restraints excluded: chain F residue 339 ARG Chi-restraints excluded: chain G residue 16 GLN Chi-restraints excluded: chain G residue 159 CYS Chi-restraints excluded: chain G residue 180 ASP Chi-restraints excluded: chain G residue 188 GLU Chi-restraints excluded: chain G residue 431 ASP Chi-restraints excluded: chain G residue 613 TYR Chi-restraints excluded: chain H residue 54 LYS Chi-restraints excluded: chain H residue 121 TRP Chi-restraints excluded: chain H residue 222 LEU Chi-restraints excluded: chain H residue 227 GLU Chi-restraints excluded: chain H residue 259 PHE Chi-restraints excluded: chain J residue 130 THR Chi-restraints excluded: chain K residue 15 SER Chi-restraints excluded: chain L residue 104 SER Chi-restraints excluded: chain L residue 252 MET Chi-restraints excluded: chain L residue 596 LEU Chi-restraints excluded: chain M residue 116 ILE Chi-restraints excluded: chain M residue 130 LEU Chi-restraints excluded: chain M residue 144 ASN Chi-restraints excluded: chain M residue 315 LEU Chi-restraints excluded: chain N residue 88 LYS Chi-restraints excluded: chain O residue 1 LEU Chi-restraints excluded: chain O residue 19 THR Chi-restraints excluded: chain O residue 60 ASP Chi-restraints excluded: chain O residue 279 LEU Chi-restraints excluded: chain P residue 109 VAL Chi-restraints excluded: chain P residue 290 THR Chi-restraints excluded: chain R residue 4 THR Chi-restraints excluded: chain R residue 92 ARG Chi-restraints excluded: chain S residue 25 ARG Chi-restraints excluded: chain S residue 90 LEU Chi-restraints excluded: chain T residue 8 LEU Chi-restraints excluded: chain T residue 13 ASP Chi-restraints excluded: chain T residue 21 LEU Chi-restraints excluded: chain T residue 25 ILE Chi-restraints excluded: chain T residue 34 SER Chi-restraints excluded: chain T residue 37 MET Chi-restraints excluded: chain T residue 44 SER Chi-restraints excluded: chain U residue 29 LYS Chi-restraints excluded: chain U residue 88 GLU Chi-restraints excluded: chain V residue 39 LYS Chi-restraints excluded: chain W residue 111 GLU Chi-restraints excluded: chain X residue 3 ILE Chi-restraints excluded: chain X residue 130 VAL Chi-restraints excluded: chain Y residue 73 SER Chi-restraints excluded: chain Y residue 85 ASP Chi-restraints excluded: chain Z residue 144 THR Chi-restraints excluded: chain b residue 15 GLU Chi-restraints excluded: chain b residue 42 LEU Chi-restraints excluded: chain c residue 34 GLN Chi-restraints excluded: chain c residue 40 LEU Chi-restraints excluded: chain d residue 111 GLU Chi-restraints excluded: chain e residue 7 LYS Chi-restraints excluded: chain e residue 92 THR Chi-restraints excluded: chain f residue 9 ASP Chi-restraints excluded: chain g residue 85 MET Chi-restraints excluded: chain g residue 122 GLU Chi-restraints excluded: chain i residue 59 VAL Chi-restraints excluded: chain i residue 78 VAL Chi-restraints excluded: chain i residue 114 GLU Chi-restraints excluded: chain i residue 121 GLU Chi-restraints excluded: chain j residue 45 ASP Chi-restraints excluded: chain l residue 6 LYS Chi-restraints excluded: chain m residue 15 THR Chi-restraints excluded: chain m residue 21 GLU Chi-restraints excluded: chain m residue 29 ARG Chi-restraints excluded: chain m residue 32 GLN Chi-restraints excluded: chain m residue 85 THR Chi-restraints excluded: chain o residue 27 ASP Chi-restraints excluded: chain o residue 30 PHE Chi-restraints excluded: chain p residue 14 ARG Chi-restraints excluded: chain p residue 22 GLN Chi-restraints excluded: chain p residue 134 VAL Chi-restraints excluded: chain p residue 171 GLU Chi-restraints excluded: chain r residue 68 VAL Chi-restraints excluded: chain r residue 72 GLN Chi-restraints excluded: chain s residue 36 THR Chi-restraints excluded: chain s residue 59 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 790 random chunks: chunk 710 optimal weight: 7.9990 chunk 540 optimal weight: 7.9990 chunk 372 optimal weight: 5.9990 chunk 79 optimal weight: 3.9990 chunk 342 optimal weight: 10.0000 chunk 482 optimal weight: 1.9990 chunk 721 optimal weight: 5.9990 chunk 763 optimal weight: 0.9990 chunk 376 optimal weight: 5.9990 chunk 683 optimal weight: 9.9990 chunk 205 optimal weight: 0.9980 overall best weight: 2.7988 ------------------------------------------------------------------------------- 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 E 121 GLN G 535 GLN H 317 GLN S 72 GLN W 45 ASN Y 7 GLN b 61 ASN b 73 GLN g 119 GLN i 12 GLN q 112 ASN r 24 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8680 moved from start: 0.0978 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.239 68528 Z= 0.477 Angle : 1.314 50.587 92706 Z= 0.842 Chirality : 0.259 6.594 10140 Planarity : 0.004 0.051 11534 Dihedral : 12.025 179.746 10724 Min Nonbonded Distance : 1.924 Molprobity Statistics. All-atom Clashscore : 3.71 Ramachandran Plot: Outliers : 0.01 % Allowed : 1.69 % Favored : 98.30 % Rotamer: Outliers : 2.21 % Allowed : 12.25 % Favored : 85.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.54 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.45 (0.09), residues: 7977 helix: 1.59 (0.08), residues: 4309 sheet: 0.12 (0.25), residues: 397 loop : 0.36 (0.11), residues: 3271 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP X 85 HIS 0.006 0.001 HIS C 160 PHE 0.027 0.002 PHE N 292 TYR 0.025 0.002 TYR O 94 ARG 0.008 0.000 ARG q 21 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15954 Ramachandran restraints generated. 7977 Oldfield, 0 Emsley, 7977 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15954 Ramachandran restraints generated. 7977 Oldfield, 0 Emsley, 7977 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1117 residues out of total 7064 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 156 poor density : 961 time to evaluate : 6.142 Fit side-chains REVERT: A 85 ASN cc_start: 0.7774 (OUTLIER) cc_final: 0.7458 (m-40) REVERT: E 36 LYS cc_start: 0.8503 (OUTLIER) cc_final: 0.8303 (ttmm) REVERT: E 134 ASP cc_start: 0.8058 (OUTLIER) cc_final: 0.7646 (p0) REVERT: E 180 LYS cc_start: 0.8194 (OUTLIER) cc_final: 0.7929 (mtpt) REVERT: F 339 ARG cc_start: 0.8082 (OUTLIER) cc_final: 0.7663 (mtp-110) REVERT: G 16 GLN cc_start: 0.8048 (OUTLIER) cc_final: 0.7248 (tm130) REVERT: G 159 CYS cc_start: 0.8419 (OUTLIER) cc_final: 0.8171 (p) REVERT: G 180 ASP cc_start: 0.8183 (OUTLIER) cc_final: 0.7851 (t0) REVERT: G 188 GLU cc_start: 0.7893 (OUTLIER) cc_final: 0.7340 (mm-30) REVERT: G 337 ARG cc_start: 0.8237 (mtt90) cc_final: 0.7880 (mmm-85) REVERT: H 227 GLU cc_start: 0.7445 (OUTLIER) cc_final: 0.6914 (tm-30) REVERT: N 47 ASN cc_start: 0.8635 (OUTLIER) cc_final: 0.8407 (m110) REVERT: N 100 MET cc_start: 0.8424 (mtt) cc_final: 0.8170 (mtt) REVERT: O 279 LEU cc_start: 0.8672 (OUTLIER) cc_final: 0.8239 (mp) REVERT: S 25 ARG cc_start: 0.7770 (OUTLIER) cc_final: 0.7450 (mmt180) REVERT: S 90 LEU cc_start: 0.9040 (OUTLIER) cc_final: 0.8591 (mm) REVERT: T 8 LEU cc_start: 0.7440 (OUTLIER) cc_final: 0.6911 (tt) REVERT: T 21 LEU cc_start: 0.8171 (OUTLIER) cc_final: 0.7950 (mp) REVERT: T 29 LYS cc_start: 0.7369 (tmtp) cc_final: 0.7082 (tmtp) REVERT: T 37 MET cc_start: 0.7666 (OUTLIER) cc_final: 0.7067 (mmt) REVERT: T 57 GLU cc_start: 0.7242 (tp30) cc_final: 0.6914 (tp30) REVERT: U 29 LYS cc_start: 0.8066 (OUTLIER) cc_final: 0.7756 (mmmm) REVERT: V 39 LYS cc_start: 0.8322 (OUTLIER) cc_final: 0.7838 (tmtp) REVERT: V 75 GLN cc_start: 0.8550 (OUTLIER) cc_final: 0.7397 (mt0) REVERT: X 3 ILE cc_start: 0.8625 (OUTLIER) cc_final: 0.8377 (mp) REVERT: Y 57 ARG cc_start: 0.7750 (ttp80) cc_final: 0.7466 (mtp180) REVERT: Y 85 ASP cc_start: 0.8694 (OUTLIER) cc_final: 0.8447 (t70) REVERT: Z 85 GLN cc_start: 0.8058 (OUTLIER) cc_final: 0.7409 (tt0) REVERT: c 34 GLN cc_start: 0.8465 (OUTLIER) cc_final: 0.6915 (tm-30) REVERT: c 41 GLU cc_start: 0.8311 (tp30) cc_final: 0.8068 (tp30) REVERT: e 7 LYS cc_start: 0.8768 (OUTLIER) cc_final: 0.8401 (tptp) REVERT: e 52 GLU cc_start: 0.7566 (mt-10) cc_final: 0.7168 (pt0) REVERT: g 122 GLU cc_start: 0.6783 (OUTLIER) cc_final: 0.6045 (tm-30) REVERT: i 6 GLU cc_start: 0.7713 (mt-10) cc_final: 0.7509 (mt-10) REVERT: i 114 GLU cc_start: 0.8064 (OUTLIER) cc_final: 0.7852 (pt0) REVERT: i 121 GLU cc_start: 0.6916 (OUTLIER) cc_final: 0.6694 (tt0) REVERT: j 40 PHE cc_start: 0.8402 (t80) cc_final: 0.8054 (t80) REVERT: k 89 SER cc_start: 0.7476 (t) cc_final: 0.6941 (p) REVERT: l 149 GLU cc_start: 0.7478 (OUTLIER) cc_final: 0.7235 (mm-30) REVERT: m 4 LYS cc_start: 0.8530 (OUTLIER) cc_final: 0.8247 (mptt) REVERT: m 21 GLU cc_start: 0.7208 (OUTLIER) cc_final: 0.6661 (mm-30) REVERT: m 24 ILE cc_start: 0.7713 (mp) cc_final: 0.7474 (mp) REVERT: m 29 ARG cc_start: 0.7776 (OUTLIER) cc_final: 0.7409 (ttm-80) REVERT: m 32 GLN cc_start: 0.8664 (OUTLIER) cc_final: 0.8277 (mt0) REVERT: o 117 ARG cc_start: 0.7391 (OUTLIER) cc_final: 0.6759 (tmm160) REVERT: p 14 ARG cc_start: 0.7258 (OUTLIER) cc_final: 0.6664 (ttt180) REVERT: r 72 GLN cc_start: 0.7549 (OUTLIER) cc_final: 0.7088 (pp30) outliers start: 156 outliers final: 69 residues processed: 1050 average time/residue: 1.7598 time to fit residues: 2329.8562 Evaluate side-chains 1057 residues out of total 7064 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 105 poor density : 952 time to evaluate : 6.072 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 ILE Chi-restraints excluded: chain A residue 24 LEU Chi-restraints excluded: chain A residue 85 ASN Chi-restraints excluded: chain B residue 54 CYS Chi-restraints excluded: chain B residue 161 LEU Chi-restraints excluded: chain D residue 109 VAL Chi-restraints excluded: chain D residue 376 VAL Chi-restraints excluded: chain D residue 420 THR Chi-restraints excluded: chain E residue 36 LYS Chi-restraints excluded: chain E residue 134 ASP Chi-restraints excluded: chain E residue 180 LYS Chi-restraints excluded: chain F residue 339 ARG Chi-restraints excluded: chain G residue 16 GLN Chi-restraints excluded: chain G residue 159 CYS Chi-restraints excluded: chain G residue 180 ASP Chi-restraints excluded: chain G residue 188 GLU Chi-restraints excluded: chain G residue 288 LYS Chi-restraints excluded: chain G residue 431 ASP Chi-restraints excluded: chain G residue 613 TYR Chi-restraints excluded: chain H residue 54 LYS Chi-restraints excluded: chain H residue 121 TRP Chi-restraints excluded: chain H residue 222 LEU Chi-restraints excluded: chain H residue 227 GLU Chi-restraints excluded: chain H residue 259 PHE Chi-restraints excluded: chain J residue 130 THR Chi-restraints excluded: chain K residue 15 SER Chi-restraints excluded: chain L residue 104 SER Chi-restraints excluded: chain L residue 251 THR Chi-restraints excluded: chain L residue 252 MET Chi-restraints excluded: chain L residue 441 VAL Chi-restraints excluded: chain L residue 507 MET Chi-restraints excluded: chain L residue 596 LEU Chi-restraints excluded: chain M residue 116 ILE Chi-restraints excluded: chain M residue 130 LEU Chi-restraints excluded: chain M residue 144 ASN Chi-restraints excluded: chain M residue 247 THR Chi-restraints excluded: chain M residue 315 LEU Chi-restraints excluded: chain N residue 47 ASN Chi-restraints excluded: chain N residue 88 LYS Chi-restraints excluded: chain O residue 1 LEU Chi-restraints excluded: chain O residue 19 THR Chi-restraints excluded: chain O residue 60 ASP Chi-restraints excluded: chain O residue 279 LEU Chi-restraints excluded: chain P residue 140 LYS Chi-restraints excluded: chain P residue 185 ILE Chi-restraints excluded: chain P residue 290 THR Chi-restraints excluded: chain R residue 92 ARG Chi-restraints excluded: chain S residue 25 ARG Chi-restraints excluded: chain S residue 90 LEU Chi-restraints excluded: chain T residue 8 LEU Chi-restraints excluded: chain T residue 13 ASP Chi-restraints excluded: chain T residue 21 LEU Chi-restraints excluded: chain T residue 25 ILE Chi-restraints excluded: chain T residue 34 SER Chi-restraints excluded: chain T residue 37 MET Chi-restraints excluded: chain T residue 44 SER Chi-restraints excluded: chain U residue 29 LYS Chi-restraints excluded: chain U residue 88 GLU Chi-restraints excluded: chain V residue 39 LYS Chi-restraints excluded: chain V residue 47 THR Chi-restraints excluded: chain V residue 75 GLN Chi-restraints excluded: chain W residue 111 GLU Chi-restraints excluded: chain X residue 3 ILE Chi-restraints excluded: chain X residue 99 CYS Chi-restraints excluded: chain X residue 130 VAL Chi-restraints excluded: chain Y residue 73 SER Chi-restraints excluded: chain Y residue 85 ASP Chi-restraints excluded: chain Z residue 85 GLN Chi-restraints excluded: chain Z residue 144 THR Chi-restraints excluded: chain a residue 48 MET Chi-restraints excluded: chain b residue 42 LEU Chi-restraints excluded: chain c residue 34 GLN Chi-restraints excluded: chain c residue 40 LEU Chi-restraints excluded: chain d residue 85 VAL Chi-restraints excluded: chain d residue 111 GLU Chi-restraints excluded: chain e residue 7 LYS Chi-restraints excluded: chain e residue 92 THR Chi-restraints excluded: chain f residue 9 ASP Chi-restraints excluded: chain g residue 85 MET Chi-restraints excluded: chain g residue 122 GLU Chi-restraints excluded: chain i residue 59 VAL Chi-restraints excluded: chain i residue 63 THR Chi-restraints excluded: chain i residue 78 VAL Chi-restraints excluded: chain i residue 114 GLU Chi-restraints excluded: chain i residue 121 GLU Chi-restraints excluded: chain j residue 45 ASP Chi-restraints excluded: chain l residue 6 LYS Chi-restraints excluded: chain l residue 149 GLU Chi-restraints excluded: chain m residue 4 LYS Chi-restraints excluded: chain m residue 21 GLU Chi-restraints excluded: chain m residue 29 ARG Chi-restraints excluded: chain m residue 32 GLN Chi-restraints excluded: chain m residue 85 THR Chi-restraints excluded: chain o residue 27 ASP Chi-restraints excluded: chain o residue 30 PHE Chi-restraints excluded: chain o residue 117 ARG Chi-restraints excluded: chain p residue 14 ARG Chi-restraints excluded: chain p residue 22 GLN Chi-restraints excluded: chain p residue 134 VAL Chi-restraints excluded: chain p residue 171 GLU Chi-restraints excluded: chain r residue 68 VAL Chi-restraints excluded: chain r residue 72 GLN Chi-restraints excluded: chain s residue 36 THR Chi-restraints excluded: chain s residue 47 SER Chi-restraints excluded: chain s residue 59 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 790 random chunks: chunk 635 optimal weight: 5.9990 chunk 433 optimal weight: 8.9990 chunk 11 optimal weight: 7.9990 chunk 568 optimal weight: 0.9990 chunk 315 optimal weight: 0.6980 chunk 651 optimal weight: 0.6980 chunk 527 optimal weight: 0.3980 chunk 0 optimal weight: 10.0000 chunk 389 optimal weight: 4.9990 chunk 685 optimal weight: 0.8980 chunk 192 optimal weight: 3.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 211 GLN D 157 HIS E 121 GLN ** F 431 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 535 GLN H 124 ASN H 194 ASN H 317 GLN ** N 316 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 72 GLN V 49 GLN W 45 ASN b 73 GLN g 119 GLN i 12 GLN q 112 ASN r 24 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8636 moved from start: 0.1299 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.246 68528 Z= 0.420 Angle : 1.285 50.562 92706 Z= 0.832 Chirality : 0.254 6.425 10140 Planarity : 0.004 0.049 11534 Dihedral : 11.232 177.462 10724 Min Nonbonded Distance : 1.993 Molprobity Statistics. All-atom Clashscore : 3.83 Ramachandran Plot: Outliers : 0.01 % Allowed : 1.60 % Favored : 98.38 % Rotamer: Outliers : 1.63 % Allowed : 13.05 % Favored : 85.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.54 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.70 (0.09), residues: 7977 helix: 1.82 (0.08), residues: 4284 sheet: 0.20 (0.25), residues: 396 loop : 0.46 (0.11), residues: 3297 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP X 85 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 0.007 0.000 ARG q 21 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15954 Ramachandran restraints generated. 7977 Oldfield, 0 Emsley, 7977 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15954 Ramachandran restraints generated. 7977 Oldfield, 0 Emsley, 7977 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1104 residues out of total 7064 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 115 poor density : 989 time to evaluate : 6.159 Fit side-chains REVERT: E 134 ASP cc_start: 0.8048 (OUTLIER) cc_final: 0.7636 (p0) REVERT: E 180 LYS cc_start: 0.8141 (OUTLIER) cc_final: 0.7833 (mtpt) REVERT: F 339 ARG cc_start: 0.8067 (OUTLIER) cc_final: 0.7709 (mtp-110) REVERT: G 16 GLN cc_start: 0.8003 (OUTLIER) cc_final: 0.7249 (tm130) REVERT: G 188 GLU cc_start: 0.7916 (OUTLIER) cc_final: 0.7403 (mm-30) REVERT: G 337 ARG cc_start: 0.8191 (mtt90) cc_final: 0.7944 (mmm-85) REVERT: G 640 ASN cc_start: 0.7582 (t0) cc_final: 0.7240 (m-40) REVERT: M 335 GLU cc_start: 0.8397 (mt-10) cc_final: 0.8133 (mt-10) REVERT: N 100 MET cc_start: 0.8392 (mtt) cc_final: 0.8115 (mtt) REVERT: P 119 GLN cc_start: 0.8450 (tt0) cc_final: 0.8217 (tt0) REVERT: S 25 ARG cc_start: 0.7725 (OUTLIER) cc_final: 0.7441 (mmt90) REVERT: S 90 LEU cc_start: 0.8993 (OUTLIER) cc_final: 0.8522 (mm) REVERT: S 92 ASN cc_start: 0.8253 (OUTLIER) cc_final: 0.7869 (m110) REVERT: T 29 LYS cc_start: 0.7338 (tmtp) cc_final: 0.7060 (tmtp) REVERT: T 37 MET cc_start: 0.7637 (OUTLIER) cc_final: 0.7045 (mmt) REVERT: T 57 GLU cc_start: 0.7162 (tp30) cc_final: 0.6903 (tp30) REVERT: U 12 LYS cc_start: 0.8923 (ttpp) cc_final: 0.8708 (tttm) REVERT: U 29 LYS cc_start: 0.8037 (OUTLIER) cc_final: 0.7745 (mmmm) REVERT: V 39 LYS cc_start: 0.8273 (OUTLIER) cc_final: 0.7835 (tmtp) REVERT: X 3 ILE cc_start: 0.8625 (OUTLIER) cc_final: 0.8398 (mp) REVERT: Y 57 ARG cc_start: 0.7663 (ttp80) cc_final: 0.7421 (mtp180) REVERT: Y 85 ASP cc_start: 0.8701 (t70) cc_final: 0.8470 (t70) REVERT: c 34 GLN cc_start: 0.8445 (OUTLIER) cc_final: 0.6905 (tm-30) REVERT: c 41 GLU cc_start: 0.8291 (tp30) cc_final: 0.8057 (tp30) REVERT: e 52 GLU cc_start: 0.7574 (mt-10) cc_final: 0.7170 (pt0) REVERT: g 122 GLU cc_start: 0.6715 (OUTLIER) cc_final: 0.6005 (tm-30) REVERT: i 6 GLU cc_start: 0.7646 (mt-10) cc_final: 0.7434 (mt-10) REVERT: j 40 PHE cc_start: 0.8403 (t80) cc_final: 0.8069 (t80) REVERT: k 89 SER cc_start: 0.7316 (t) cc_final: 0.6828 (p) REVERT: l 6 LYS cc_start: 0.8114 (OUTLIER) cc_final: 0.7777 (mtpp) REVERT: l 149 GLU cc_start: 0.7437 (OUTLIER) cc_final: 0.7197 (mm-30) REVERT: m 21 GLU cc_start: 0.7194 (OUTLIER) cc_final: 0.6553 (mm-30) REVERT: m 29 ARG cc_start: 0.7727 (OUTLIER) cc_final: 0.7376 (ttm-80) REVERT: p 14 ARG cc_start: 0.7239 (OUTLIER) cc_final: 0.6654 (ttt180) REVERT: r 72 GLN cc_start: 0.7578 (OUTLIER) cc_final: 0.7100 (pp30) REVERT: r 108 ASP cc_start: 0.8696 (t70) cc_final: 0.8464 (t0) outliers start: 115 outliers final: 39 residues processed: 1059 average time/residue: 1.7518 time to fit residues: 2341.5726 Evaluate side-chains 1025 residues out of total 7064 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 966 time to evaluate : 6.015 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 LEU Chi-restraints excluded: chain A residue 51 PHE Chi-restraints excluded: chain B residue 54 CYS Chi-restraints excluded: chain D residue 109 VAL Chi-restraints excluded: chain D residue 420 THR Chi-restraints excluded: chain E residue 134 ASP Chi-restraints excluded: chain E residue 180 LYS Chi-restraints excluded: chain F residue 339 ARG Chi-restraints excluded: chain G residue 16 GLN Chi-restraints excluded: chain G residue 188 GLU Chi-restraints excluded: chain G residue 431 ASP Chi-restraints excluded: chain G residue 613 TYR Chi-restraints excluded: chain H residue 54 LYS Chi-restraints excluded: chain H residue 72 ILE Chi-restraints excluded: chain H residue 121 TRP Chi-restraints excluded: chain H residue 194 ASN Chi-restraints excluded: chain H residue 222 LEU Chi-restraints excluded: chain H residue 259 PHE Chi-restraints excluded: chain J residue 130 THR Chi-restraints excluded: chain L residue 251 THR Chi-restraints excluded: chain L residue 599 MET Chi-restraints excluded: chain M residue 116 ILE Chi-restraints excluded: chain M residue 130 LEU Chi-restraints excluded: chain M residue 247 THR Chi-restraints excluded: chain M residue 296 LEU Chi-restraints excluded: chain M residue 315 LEU Chi-restraints excluded: chain N residue 40 ILE Chi-restraints excluded: chain O residue 19 THR Chi-restraints excluded: chain P residue 109 VAL Chi-restraints excluded: chain P residue 140 LYS Chi-restraints excluded: chain S residue 25 ARG Chi-restraints excluded: chain S residue 90 LEU Chi-restraints excluded: chain S residue 92 ASN Chi-restraints excluded: chain T residue 13 ASP Chi-restraints excluded: chain T residue 25 ILE Chi-restraints excluded: chain T residue 37 MET Chi-restraints excluded: chain U residue 29 LYS Chi-restraints excluded: chain V residue 39 LYS Chi-restraints excluded: chain V residue 94 ILE Chi-restraints excluded: chain W residue 111 GLU Chi-restraints excluded: chain X residue 3 ILE Chi-restraints excluded: chain a residue 48 MET Chi-restraints excluded: chain b residue 42 LEU Chi-restraints excluded: chain c residue 34 GLN Chi-restraints excluded: chain d residue 85 VAL Chi-restraints excluded: chain d residue 92 SER Chi-restraints excluded: chain d residue 111 GLU Chi-restraints excluded: chain e residue 92 THR Chi-restraints excluded: chain g residue 122 GLU Chi-restraints excluded: chain l residue 6 LYS Chi-restraints excluded: chain l residue 149 GLU Chi-restraints excluded: chain m residue 21 GLU Chi-restraints excluded: chain m residue 29 ARG Chi-restraints excluded: chain o residue 30 PHE Chi-restraints excluded: chain p residue 14 ARG Chi-restraints excluded: chain r residue 68 VAL Chi-restraints excluded: chain r residue 72 GLN Chi-restraints excluded: chain s residue 36 THR Chi-restraints excluded: chain s residue 59 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 790 random chunks: chunk 256 optimal weight: 0.7980 chunk 687 optimal weight: 6.9990 chunk 150 optimal weight: 7.9990 chunk 448 optimal weight: 2.9990 chunk 188 optimal weight: 3.9990 chunk 764 optimal weight: 10.0000 chunk 634 optimal weight: 6.9990 chunk 353 optimal weight: 5.9990 chunk 63 optimal weight: 0.8980 chunk 252 optimal weight: 9.9990 chunk 401 optimal weight: 8.9990 overall best weight: 2.9386 ------------------------------------------------------------------------------- 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 157 HIS E 121 GLN ** F 431 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 444 GLN ** G 475 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 535 GLN ** G 643 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 194 ASN H 317 GLN M 144 ASN ** N 316 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 89 ASN P 36 ASN S 72 GLN W 45 ASN Y 7 GLN b 73 GLN c 46 ASN g 119 GLN i 12 GLN o 43 GLN ** o 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** q 112 ASN r 24 GLN Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8677 moved from start: 0.1110 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.246 68528 Z= 0.484 Angle : 1.313 50.618 92706 Z= 0.842 Chirality : 0.259 6.609 10140 Planarity : 0.004 0.049 11534 Dihedral : 11.338 178.649 10714 Min Nonbonded Distance : 1.931 Molprobity Statistics. All-atom Clashscore : 3.85 Ramachandran Plot: Outliers : 0.03 % Allowed : 1.73 % Favored : 98.24 % Rotamer: Outliers : 2.03 % Allowed : 12.88 % Favored : 85.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.54 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.57 (0.09), residues: 7977 helix: 1.69 (0.08), residues: 4317 sheet: 0.20 (0.25), residues: 396 loop : 0.41 (0.11), residues: 3264 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP X 85 HIS 0.007 0.001 HIS C 160 PHE 0.025 0.002 PHE N 292 TYR 0.025 0.002 TYR O 94 ARG 0.007 0.000 ARG a 28 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15954 Ramachandran restraints generated. 7977 Oldfield, 0 Emsley, 7977 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15954 Ramachandran restraints generated. 7977 Oldfield, 0 Emsley, 7977 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1109 residues out of total 7064 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 143 poor density : 966 time to evaluate : 6.110 Fit side-chains REVERT: E 134 ASP cc_start: 0.8059 (OUTLIER) cc_final: 0.7643 (p0) REVERT: E 180 LYS cc_start: 0.8141 (OUTLIER) cc_final: 0.7876 (mtpt) REVERT: F 339 ARG cc_start: 0.8088 (OUTLIER) cc_final: 0.7695 (mtp-110) REVERT: G 16 GLN cc_start: 0.8051 (OUTLIER) cc_final: 0.7258 (tm130) REVERT: G 180 ASP cc_start: 0.8179 (OUTLIER) cc_final: 0.7847 (t0) REVERT: G 188 GLU cc_start: 0.7889 (OUTLIER) cc_final: 0.7342 (mm-30) REVERT: G 337 ARG cc_start: 0.8226 (mtt90) cc_final: 0.7930 (mmm-85) REVERT: G 475 GLN cc_start: 0.7958 (OUTLIER) cc_final: 0.7742 (tp40) REVERT: G 640 ASN cc_start: 0.7622 (t0) cc_final: 0.7271 (m-40) REVERT: H 227 GLU cc_start: 0.7427 (OUTLIER) cc_final: 0.6894 (tm-30) REVERT: N 47 ASN cc_start: 0.8628 (OUTLIER) cc_final: 0.8413 (m110) REVERT: N 100 MET cc_start: 0.8407 (mtt) cc_final: 0.8157 (mtt) REVERT: O 279 LEU cc_start: 0.8671 (OUTLIER) cc_final: 0.8249 (mp) REVERT: Q 112 LYS cc_start: 0.8551 (OUTLIER) cc_final: 0.8038 (ptpp) REVERT: S 25 ARG cc_start: 0.7761 (OUTLIER) cc_final: 0.7443 (mmt180) REVERT: S 90 LEU cc_start: 0.9045 (OUTLIER) cc_final: 0.8577 (mm) REVERT: T 8 LEU cc_start: 0.7445 (OUTLIER) cc_final: 0.6958 (tt) REVERT: T 29 LYS cc_start: 0.7394 (OUTLIER) cc_final: 0.7143 (tmtp) REVERT: T 37 MET cc_start: 0.7668 (OUTLIER) cc_final: 0.7056 (mmt) REVERT: T 57 GLU cc_start: 0.7195 (tp30) cc_final: 0.6899 (tp30) REVERT: U 29 LYS cc_start: 0.8063 (OUTLIER) cc_final: 0.7757 (mmmm) REVERT: V 39 LYS cc_start: 0.8298 (OUTLIER) cc_final: 0.7832 (tmtp) REVERT: V 75 GLN cc_start: 0.8578 (OUTLIER) cc_final: 0.7342 (mt0) REVERT: X 3 ILE cc_start: 0.8660 (OUTLIER) cc_final: 0.8426 (mp) REVERT: Y 57 ARG cc_start: 0.7699 (ttp80) cc_final: 0.7439 (mtp180) REVERT: Y 85 ASP cc_start: 0.8720 (OUTLIER) cc_final: 0.8471 (t70) REVERT: a 4 GLU cc_start: 0.8397 (OUTLIER) cc_final: 0.7975 (mt-10) REVERT: c 34 GLN cc_start: 0.8466 (OUTLIER) cc_final: 0.6922 (tm-30) REVERT: c 41 GLU cc_start: 0.8304 (tp30) cc_final: 0.8077 (tp30) REVERT: d 26 LEU cc_start: 0.8881 (OUTLIER) cc_final: 0.8516 (mp) REVERT: e 7 LYS cc_start: 0.8773 (OUTLIER) cc_final: 0.8403 (tptp) REVERT: e 52 GLU cc_start: 0.7575 (mt-10) cc_final: 0.7134 (pt0) REVERT: i 6 GLU cc_start: 0.7698 (mt-10) cc_final: 0.7491 (mt-10) REVERT: i 121 GLU cc_start: 0.6921 (OUTLIER) cc_final: 0.6695 (tt0) REVERT: j 40 PHE cc_start: 0.8419 (t80) cc_final: 0.8049 (t80) REVERT: k 89 SER cc_start: 0.7249 (t) cc_final: 0.6814 (p) REVERT: l 149 GLU cc_start: 0.7466 (OUTLIER) cc_final: 0.7195 (mm-30) REVERT: m 21 GLU cc_start: 0.7264 (OUTLIER) cc_final: 0.6847 (mm-30) REVERT: m 29 ARG cc_start: 0.7806 (OUTLIER) cc_final: 0.7453 (ttm-80) REVERT: m 32 GLN cc_start: 0.8668 (OUTLIER) cc_final: 0.8286 (mt0) REVERT: o 117 ARG cc_start: 0.7405 (OUTLIER) cc_final: 0.6970 (tmm160) REVERT: p 14 ARG cc_start: 0.7266 (OUTLIER) cc_final: 0.6666 (ttt180) REVERT: p 38 LEU cc_start: 0.8947 (OUTLIER) cc_final: 0.8693 (tm) REVERT: r 72 GLN cc_start: 0.7627 (OUTLIER) cc_final: 0.7157 (pp30) outliers start: 143 outliers final: 64 residues processed: 1044 average time/residue: 1.7673 time to fit residues: 2327.4986 Evaluate side-chains 1057 residues out of total 7064 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 98 poor density : 959 time to evaluate : 5.958 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 ILE Chi-restraints excluded: chain A residue 24 LEU Chi-restraints excluded: chain B residue 54 CYS Chi-restraints excluded: chain B residue 161 LEU Chi-restraints excluded: chain D residue 109 VAL Chi-restraints excluded: chain D residue 376 VAL Chi-restraints excluded: chain D residue 420 THR Chi-restraints excluded: chain E residue 134 ASP Chi-restraints excluded: chain E residue 180 LYS Chi-restraints excluded: chain F residue 339 ARG Chi-restraints excluded: chain G residue 16 GLN Chi-restraints excluded: chain G residue 180 ASP Chi-restraints excluded: chain G residue 188 GLU Chi-restraints excluded: chain G residue 431 ASP Chi-restraints excluded: chain G residue 475 GLN Chi-restraints excluded: chain G residue 613 TYR Chi-restraints excluded: chain G residue 651 LEU Chi-restraints excluded: chain H residue 54 LYS Chi-restraints excluded: chain H residue 72 ILE Chi-restraints excluded: chain H residue 121 TRP Chi-restraints excluded: chain H residue 222 LEU Chi-restraints excluded: chain H residue 227 GLU Chi-restraints excluded: chain H residue 259 PHE Chi-restraints excluded: chain J residue 130 THR Chi-restraints excluded: chain K residue 15 SER Chi-restraints excluded: chain L residue 104 SER Chi-restraints excluded: chain L residue 251 THR Chi-restraints excluded: chain L residue 441 VAL Chi-restraints excluded: chain L residue 596 LEU Chi-restraints excluded: chain M residue 116 ILE Chi-restraints excluded: chain M residue 130 LEU Chi-restraints excluded: chain M residue 144 ASN Chi-restraints excluded: chain M residue 247 THR Chi-restraints excluded: chain M residue 296 LEU Chi-restraints excluded: chain M residue 315 LEU Chi-restraints excluded: chain N residue 40 ILE Chi-restraints excluded: chain N residue 47 ASN Chi-restraints excluded: chain O residue 181 SER Chi-restraints excluded: chain O residue 279 LEU Chi-restraints excluded: chain P residue 109 VAL Chi-restraints excluded: chain P residue 140 LYS Chi-restraints excluded: chain Q residue 112 LYS Chi-restraints excluded: chain R residue 4 THR Chi-restraints excluded: chain S residue 25 ARG Chi-restraints excluded: chain S residue 90 LEU Chi-restraints excluded: chain T residue 8 LEU Chi-restraints excluded: chain T residue 13 ASP Chi-restraints excluded: chain T residue 25 ILE Chi-restraints excluded: chain T residue 29 LYS Chi-restraints excluded: chain T residue 37 MET Chi-restraints excluded: chain T residue 44 SER Chi-restraints excluded: chain U residue 29 LYS Chi-restraints excluded: chain U residue 88 GLU Chi-restraints excluded: chain V residue 39 LYS Chi-restraints excluded: chain V residue 47 THR Chi-restraints excluded: chain V residue 75 GLN Chi-restraints excluded: chain V residue 94 ILE Chi-restraints excluded: chain W residue 111 GLU Chi-restraints excluded: chain X residue 3 ILE Chi-restraints excluded: chain X residue 99 CYS Chi-restraints excluded: chain X residue 130 VAL Chi-restraints excluded: chain Y residue 16 GLU Chi-restraints excluded: chain Y residue 73 SER Chi-restraints excluded: chain Y residue 85 ASP Chi-restraints excluded: chain Y residue 99 ILE Chi-restraints excluded: chain Z residue 144 THR Chi-restraints excluded: chain a residue 4 GLU Chi-restraints excluded: chain a residue 48 MET Chi-restraints excluded: chain c residue 34 GLN Chi-restraints excluded: chain d residue 26 LEU Chi-restraints excluded: chain d residue 85 VAL Chi-restraints excluded: chain d residue 92 SER Chi-restraints excluded: chain d residue 111 GLU Chi-restraints excluded: chain e residue 7 LYS Chi-restraints excluded: chain e residue 92 THR Chi-restraints excluded: chain f residue 9 ASP Chi-restraints excluded: chain g residue 85 MET Chi-restraints excluded: chain i residue 63 THR Chi-restraints excluded: chain i residue 78 VAL Chi-restraints excluded: chain i residue 121 GLU Chi-restraints excluded: chain l residue 6 LYS Chi-restraints excluded: chain l residue 149 GLU Chi-restraints excluded: chain m residue 15 THR Chi-restraints excluded: chain m residue 21 GLU Chi-restraints excluded: chain m residue 29 ARG Chi-restraints excluded: chain m residue 32 GLN Chi-restraints excluded: chain o residue 27 ASP Chi-restraints excluded: chain o residue 30 PHE Chi-restraints excluded: chain o residue 117 ARG Chi-restraints excluded: chain p residue 14 ARG Chi-restraints excluded: chain p residue 22 GLN Chi-restraints excluded: chain p residue 38 LEU Chi-restraints excluded: chain p residue 171 GLU Chi-restraints excluded: chain r residue 68 VAL Chi-restraints excluded: chain r residue 72 GLN Chi-restraints excluded: chain s residue 36 THR Chi-restraints excluded: chain s residue 47 SER Chi-restraints excluded: chain s residue 59 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 790 random chunks: chunk 736 optimal weight: 0.0270 chunk 86 optimal weight: 10.0000 chunk 435 optimal weight: 8.9990 chunk 558 optimal weight: 0.2980 chunk 432 optimal weight: 2.9990 chunk 643 optimal weight: 5.9990 chunk 426 optimal weight: 5.9990 chunk 761 optimal weight: 0.9990 chunk 476 optimal weight: 5.9990 chunk 464 optimal weight: 6.9990 chunk 351 optimal weight: 1.9990 overall best weight: 1.2644 ------------------------------------------------------------------------------- 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 157 HIS E 121 GLN ** F 431 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 444 GLN G 535 GLN H 317 GLN M 144 ASN ** N 316 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 89 ASN P 36 ASN S 72 GLN W 45 ASN b 73 GLN g 119 GLN i 12 GLN q 112 ASN r 24 GLN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8649 moved from start: 0.1292 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.245 68528 Z= 0.428 Angle : 1.290 50.571 92706 Z= 0.834 Chirality : 0.256 6.469 10140 Planarity : 0.004 0.047 11534 Dihedral : 10.961 176.988 10713 Min Nonbonded Distance : 1.975 Molprobity Statistics. All-atom Clashscore : 4.13 Ramachandran Plot: Outliers : 0.01 % Allowed : 1.57 % Favored : 98.42 % Rotamer: Outliers : 1.73 % Allowed : 13.31 % Favored : 84.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.54 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.68 (0.09), residues: 7977 helix: 1.80 (0.08), residues: 4296 sheet: 0.17 (0.25), residues: 396 loop : 0.45 (0.11), residues: 3285 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP X 85 HIS 0.005 0.001 HIS N 112 PHE 0.028 0.001 PHE N 292 TYR 0.021 0.001 TYR L 422 ARG 0.008 0.000 ARG q 21 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15954 Ramachandran restraints generated. 7977 Oldfield, 0 Emsley, 7977 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15954 Ramachandran restraints generated. 7977 Oldfield, 0 Emsley, 7977 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1095 residues out of total 7064 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 122 poor density : 973 time to evaluate : 6.165 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 134 ASP cc_start: 0.8033 (OUTLIER) cc_final: 0.7611 (p0) REVERT: E 180 LYS cc_start: 0.8129 (OUTLIER) cc_final: 0.7824 (mtpt) REVERT: F 339 ARG cc_start: 0.8079 (OUTLIER) cc_final: 0.7710 (mtp-110) REVERT: G 16 GLN cc_start: 0.8016 (OUTLIER) cc_final: 0.7284 (tm130) REVERT: G 188 GLU cc_start: 0.7899 (OUTLIER) cc_final: 0.7387 (mm-30) REVERT: G 337 ARG cc_start: 0.8199 (mtt90) cc_final: 0.7931 (mmm-85) REVERT: G 640 ASN cc_start: 0.7582 (t0) cc_final: 0.7246 (m-40) REVERT: M 335 GLU cc_start: 0.8450 (mt-10) cc_final: 0.8080 (mt-10) REVERT: N 47 ASN cc_start: 0.8599 (OUTLIER) cc_final: 0.8392 (m110) REVERT: N 100 MET cc_start: 0.8390 (mtt) cc_final: 0.8135 (mtt) REVERT: P 119 GLN cc_start: 0.8458 (tt0) cc_final: 0.8229 (tt0) REVERT: S 25 ARG cc_start: 0.7727 (OUTLIER) cc_final: 0.7448 (mmt90) REVERT: S 90 LEU cc_start: 0.9016 (OUTLIER) cc_final: 0.8542 (mm) REVERT: T 8 LEU cc_start: 0.7369 (OUTLIER) cc_final: 0.6880 (tt) REVERT: T 29 LYS cc_start: 0.7342 (OUTLIER) cc_final: 0.7056 (tmtp) REVERT: T 37 MET cc_start: 0.7645 (OUTLIER) cc_final: 0.7043 (mmt) REVERT: T 57 GLU cc_start: 0.7206 (tp30) cc_final: 0.6939 (tp30) REVERT: U 9 GLU cc_start: 0.7647 (OUTLIER) cc_final: 0.7408 (tt0) REVERT: U 29 LYS cc_start: 0.8032 (OUTLIER) cc_final: 0.7733 (mmmm) REVERT: V 39 LYS cc_start: 0.8275 (OUTLIER) cc_final: 0.7823 (tmtp) REVERT: X 3 ILE cc_start: 0.8641 (OUTLIER) cc_final: 0.8410 (mp) REVERT: Y 57 ARG cc_start: 0.7637 (ttp80) cc_final: 0.7422 (mtp180) REVERT: Y 85 ASP cc_start: 0.8705 (OUTLIER) cc_final: 0.8470 (t70) REVERT: c 34 GLN cc_start: 0.8451 (OUTLIER) cc_final: 0.6932 (tm-30) REVERT: c 41 GLU cc_start: 0.8303 (tp30) cc_final: 0.8082 (tp30) REVERT: d 26 LEU cc_start: 0.8844 (OUTLIER) cc_final: 0.8522 (mp) REVERT: e 52 GLU cc_start: 0.7566 (mt-10) cc_final: 0.7135 (pt0) REVERT: g 122 GLU cc_start: 0.6721 (OUTLIER) cc_final: 0.5988 (tm-30) REVERT: i 6 GLU cc_start: 0.7650 (mt-10) cc_final: 0.7443 (mt-10) REVERT: j 40 PHE cc_start: 0.8414 (t80) cc_final: 0.8065 (t80) REVERT: k 89 SER cc_start: 0.7183 (t) cc_final: 0.6764 (p) REVERT: l 149 GLU cc_start: 0.7449 (OUTLIER) cc_final: 0.7183 (mm-30) REVERT: m 21 GLU cc_start: 0.7252 (OUTLIER) cc_final: 0.6831 (mm-30) REVERT: m 29 ARG cc_start: 0.7760 (OUTLIER) cc_final: 0.7431 (ttm-80) REVERT: o 117 ARG cc_start: 0.7430 (OUTLIER) cc_final: 0.7028 (ttm170) REVERT: p 14 ARG cc_start: 0.7254 (OUTLIER) cc_final: 0.6670 (ttt180) REVERT: p 22 GLN cc_start: 0.7828 (OUTLIER) cc_final: 0.7620 (mt0) REVERT: p 38 LEU cc_start: 0.8942 (OUTLIER) cc_final: 0.8717 (tm) REVERT: r 72 GLN cc_start: 0.7585 (OUTLIER) cc_final: 0.7122 (pp30) REVERT: r 108 ASP cc_start: 0.8698 (t70) cc_final: 0.8446 (t0) outliers start: 122 outliers final: 52 residues processed: 1035 average time/residue: 1.7583 time to fit residues: 2293.8627 Evaluate side-chains 1044 residues out of total 7064 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 79 poor density : 965 time to evaluate : 6.116 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 ILE Chi-restraints excluded: chain A residue 24 LEU Chi-restraints excluded: chain B residue 54 CYS Chi-restraints excluded: chain B residue 161 LEU Chi-restraints excluded: chain D residue 109 VAL Chi-restraints excluded: chain D residue 420 THR Chi-restraints excluded: chain E residue 134 ASP Chi-restraints excluded: chain E residue 180 LYS Chi-restraints excluded: chain E residue 203 THR Chi-restraints excluded: chain F residue 105 CYS Chi-restraints excluded: chain F residue 339 ARG Chi-restraints excluded: chain G residue 16 GLN Chi-restraints excluded: chain G residue 188 GLU Chi-restraints excluded: chain G residue 431 ASP Chi-restraints excluded: chain G residue 613 TYR Chi-restraints excluded: chain G residue 651 LEU Chi-restraints excluded: chain H residue 54 LYS Chi-restraints excluded: chain H residue 121 TRP Chi-restraints excluded: chain H residue 222 LEU Chi-restraints excluded: chain H residue 259 PHE Chi-restraints excluded: chain J residue 130 THR Chi-restraints excluded: chain K residue 15 SER Chi-restraints excluded: chain L residue 104 SER Chi-restraints excluded: chain L residue 251 THR Chi-restraints excluded: chain M residue 116 ILE Chi-restraints excluded: chain M residue 130 LEU Chi-restraints excluded: chain M residue 247 THR Chi-restraints excluded: chain M residue 296 LEU Chi-restraints excluded: chain M residue 315 LEU Chi-restraints excluded: chain N residue 40 ILE Chi-restraints excluded: chain N residue 47 ASN Chi-restraints excluded: chain P residue 109 VAL Chi-restraints excluded: chain P residue 140 LYS Chi-restraints excluded: chain P residue 281 ARG Chi-restraints excluded: chain S residue 25 ARG Chi-restraints excluded: chain S residue 90 LEU Chi-restraints excluded: chain T residue 8 LEU Chi-restraints excluded: chain T residue 13 ASP Chi-restraints excluded: chain T residue 25 ILE Chi-restraints excluded: chain T residue 29 LYS Chi-restraints excluded: chain T residue 37 MET Chi-restraints excluded: chain U residue 9 GLU Chi-restraints excluded: chain U residue 29 LYS Chi-restraints excluded: chain U residue 88 GLU Chi-restraints excluded: chain V residue 39 LYS Chi-restraints excluded: chain V residue 75 GLN Chi-restraints excluded: chain V residue 94 ILE Chi-restraints excluded: chain W residue 111 GLU Chi-restraints excluded: chain X residue 3 ILE Chi-restraints excluded: chain X residue 63 ASN Chi-restraints excluded: chain X residue 99 CYS Chi-restraints excluded: chain X residue 130 VAL Chi-restraints excluded: chain Y residue 16 GLU Chi-restraints excluded: chain Y residue 73 SER Chi-restraints excluded: chain Y residue 85 ASP Chi-restraints excluded: chain a residue 48 MET Chi-restraints excluded: chain c residue 34 GLN Chi-restraints excluded: chain d residue 26 LEU Chi-restraints excluded: chain d residue 85 VAL Chi-restraints excluded: chain d residue 92 SER Chi-restraints excluded: chain d residue 111 GLU Chi-restraints excluded: chain e residue 92 THR Chi-restraints excluded: chain f residue 9 ASP Chi-restraints excluded: chain g residue 122 GLU Chi-restraints excluded: chain l residue 149 GLU Chi-restraints excluded: chain m residue 15 THR Chi-restraints excluded: chain m residue 21 GLU Chi-restraints excluded: chain m residue 29 ARG Chi-restraints excluded: chain m residue 88 LEU Chi-restraints excluded: chain o residue 30 PHE Chi-restraints excluded: chain o residue 117 ARG Chi-restraints excluded: chain p residue 14 ARG Chi-restraints excluded: chain p residue 22 GLN Chi-restraints excluded: chain p residue 38 LEU Chi-restraints excluded: chain r residue 68 VAL Chi-restraints excluded: chain r residue 72 GLN Chi-restraints excluded: chain s residue 36 THR Chi-restraints excluded: chain s residue 47 SER Chi-restraints excluded: chain s residue 59 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 790 random chunks: chunk 471 optimal weight: 4.9990 chunk 304 optimal weight: 8.9990 chunk 454 optimal weight: 6.9990 chunk 229 optimal weight: 8.9990 chunk 149 optimal weight: 9.9990 chunk 147 optimal weight: 1.9990 chunk 484 optimal weight: 9.9990 chunk 518 optimal weight: 6.9990 chunk 376 optimal weight: 0.6980 chunk 70 optimal weight: 8.9990 chunk 598 optimal weight: 5.9990 overall best weight: 4.1388 ------------------------------------------------------------------------------- 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 157 HIS E 121 GLN ** F 431 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 444 GLN G 535 GLN H 317 GLN K 97 GLN M 144 ASN ** N 316 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 89 ASN P 36 ASN S 72 GLN Y 7 GLN b 73 GLN c 46 ASN g 119 GLN i 12 GLN ** o 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** q 112 ASN r 24 GLN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8691 moved from start: 0.1043 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.241 68528 Z= 0.538 Angle : 1.333 50.601 92706 Z= 0.850 Chirality : 0.261 6.680 10140 Planarity : 0.005 0.052 11534 Dihedral : 11.437 179.941 10713 Min Nonbonded Distance : 1.964 Molprobity Statistics. All-atom Clashscore : 4.15 Ramachandran Plot: Outliers : 0.01 % Allowed : 1.81 % Favored : 98.18 % Rotamer: Outliers : 2.00 % Allowed : 13.07 % Favored : 84.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.54 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.46 (0.09), residues: 7977 helix: 1.58 (0.08), residues: 4307 sheet: 0.13 (0.25), residues: 395 loop : 0.39 (0.11), residues: 3275 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP g 56 HIS 0.009 0.001 HIS C 160 PHE 0.026 0.002 PHE q 55 TYR 0.027 0.002 TYR O 94 ARG 0.007 0.001 ARG c 44 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15954 Ramachandran restraints generated. 7977 Oldfield, 0 Emsley, 7977 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15954 Ramachandran restraints generated. 7977 Oldfield, 0 Emsley, 7977 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1098 residues out of total 7064 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 141 poor density : 957 time to evaluate : 6.194 Fit side-chains revert: symmetry clash REVERT: A 85 ASN cc_start: 0.7791 (OUTLIER) cc_final: 0.7489 (m-40) REVERT: E 134 ASP cc_start: 0.8066 (OUTLIER) cc_final: 0.7657 (p0) REVERT: E 180 LYS cc_start: 0.8189 (OUTLIER) cc_final: 0.7931 (mtpt) REVERT: F 339 ARG cc_start: 0.8084 (OUTLIER) cc_final: 0.7667 (mtp-110) REVERT: G 16 GLN cc_start: 0.8049 (OUTLIER) cc_final: 0.7242 (tm130) REVERT: G 180 ASP cc_start: 0.8192 (OUTLIER) cc_final: 0.7878 (t0) REVERT: G 188 GLU cc_start: 0.7890 (OUTLIER) cc_final: 0.7257 (mm-30) REVERT: G 288 LYS cc_start: 0.8431 (tppp) cc_final: 0.8048 (tptm) REVERT: G 337 ARG cc_start: 0.8234 (mtt90) cc_final: 0.7858 (mmm-85) REVERT: G 640 ASN cc_start: 0.7606 (t0) cc_final: 0.7272 (m-40) REVERT: H 227 GLU cc_start: 0.7470 (OUTLIER) cc_final: 0.6935 (tm-30) REVERT: J 81 GLU cc_start: 0.6891 (OUTLIER) cc_final: 0.6488 (mm-30) REVERT: N 47 ASN cc_start: 0.8648 (OUTLIER) cc_final: 0.8418 (m110) REVERT: N 100 MET cc_start: 0.8421 (mtt) cc_final: 0.8186 (mtt) REVERT: O 182 ARG cc_start: 0.8748 (OUTLIER) cc_final: 0.7957 (mtp85) REVERT: Q 112 LYS cc_start: 0.8561 (OUTLIER) cc_final: 0.8033 (ptpp) REVERT: S 25 ARG cc_start: 0.7765 (OUTLIER) cc_final: 0.7472 (mmt90) REVERT: S 90 LEU cc_start: 0.9052 (OUTLIER) cc_final: 0.8596 (mm) REVERT: T 8 LEU cc_start: 0.7486 (OUTLIER) cc_final: 0.7001 (tt) REVERT: T 29 LYS cc_start: 0.7355 (OUTLIER) cc_final: 0.7144 (tmtp) REVERT: T 37 MET cc_start: 0.7684 (OUTLIER) cc_final: 0.7060 (mmt) REVERT: T 57 GLU cc_start: 0.7244 (tp30) cc_final: 0.6968 (tp30) REVERT: U 9 GLU cc_start: 0.7746 (OUTLIER) cc_final: 0.7511 (tt0) REVERT: U 29 LYS cc_start: 0.8129 (OUTLIER) cc_final: 0.7804 (mmmm) REVERT: V 39 LYS cc_start: 0.8331 (OUTLIER) cc_final: 0.7885 (tmtp) REVERT: X 3 ILE cc_start: 0.8638 (OUTLIER) cc_final: 0.8410 (mp) REVERT: Y 57 ARG cc_start: 0.7703 (ttp80) cc_final: 0.7438 (mtp-110) REVERT: Z 85 GLN cc_start: 0.8031 (OUTLIER) cc_final: 0.7400 (tt0) REVERT: a 4 GLU cc_start: 0.8412 (OUTLIER) cc_final: 0.7852 (mt-10) REVERT: c 41 GLU cc_start: 0.8317 (tp30) cc_final: 0.8102 (tp30) REVERT: d 26 LEU cc_start: 0.8910 (OUTLIER) cc_final: 0.8566 (mp) REVERT: e 7 LYS cc_start: 0.8778 (OUTLIER) cc_final: 0.8412 (tptp) REVERT: e 52 GLU cc_start: 0.7577 (mt-10) cc_final: 0.7135 (pt0) REVERT: i 6 GLU cc_start: 0.7754 (mt-10) cc_final: 0.7539 (mt-10) REVERT: i 121 GLU cc_start: 0.6948 (OUTLIER) cc_final: 0.6723 (tt0) REVERT: j 40 PHE cc_start: 0.8448 (t80) cc_final: 0.8085 (t80) REVERT: k 89 SER cc_start: 0.7218 (t) cc_final: 0.6779 (p) REVERT: l 149 GLU cc_start: 0.7508 (OUTLIER) cc_final: 0.7216 (mm-30) REVERT: m 29 ARG cc_start: 0.7823 (OUTLIER) cc_final: 0.7493 (ttm-80) REVERT: m 32 GLN cc_start: 0.8673 (OUTLIER) cc_final: 0.8274 (mt0) REVERT: o 117 ARG cc_start: 0.7415 (OUTLIER) cc_final: 0.6932 (tmm160) REVERT: p 14 ARG cc_start: 0.7278 (OUTLIER) cc_final: 0.6678 (ttt180) REVERT: p 38 LEU cc_start: 0.8957 (OUTLIER) cc_final: 0.8731 (tm) REVERT: r 72 GLN cc_start: 0.7571 (OUTLIER) cc_final: 0.7130 (pp30) outliers start: 141 outliers final: 66 residues processed: 1033 average time/residue: 1.7713 time to fit residues: 2301.9948 Evaluate side-chains 1041 residues out of total 7064 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 99 poor density : 942 time to evaluate : 6.051 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 ILE Chi-restraints excluded: chain A residue 24 LEU Chi-restraints excluded: chain A residue 85 ASN Chi-restraints excluded: chain B residue 54 CYS Chi-restraints excluded: chain B residue 161 LEU Chi-restraints excluded: chain D residue 109 VAL Chi-restraints excluded: chain D residue 341 SER Chi-restraints excluded: chain D residue 376 VAL Chi-restraints excluded: chain D residue 420 THR Chi-restraints excluded: chain E residue 134 ASP Chi-restraints excluded: chain E residue 180 LYS Chi-restraints excluded: chain E residue 203 THR Chi-restraints excluded: chain F residue 105 CYS Chi-restraints excluded: chain F residue 339 ARG Chi-restraints excluded: chain G residue 16 GLN Chi-restraints excluded: chain G residue 180 ASP Chi-restraints excluded: chain G residue 188 GLU Chi-restraints excluded: chain G residue 431 ASP Chi-restraints excluded: chain G residue 613 TYR Chi-restraints excluded: chain G residue 651 LEU Chi-restraints excluded: chain H residue 54 LYS Chi-restraints excluded: chain H residue 72 ILE Chi-restraints excluded: chain H residue 121 TRP Chi-restraints excluded: chain H residue 222 LEU Chi-restraints excluded: chain H residue 227 GLU Chi-restraints excluded: chain H residue 259 PHE Chi-restraints excluded: chain J residue 81 GLU Chi-restraints excluded: chain J residue 130 THR Chi-restraints excluded: chain K residue 15 SER Chi-restraints excluded: chain L residue 104 SER Chi-restraints excluded: chain L residue 251 THR Chi-restraints excluded: chain L residue 441 VAL Chi-restraints excluded: chain L residue 507 MET Chi-restraints excluded: chain L residue 596 LEU Chi-restraints excluded: chain M residue 116 ILE Chi-restraints excluded: chain M residue 130 LEU Chi-restraints excluded: chain M residue 247 THR Chi-restraints excluded: chain M residue 296 LEU Chi-restraints excluded: chain M residue 315 LEU Chi-restraints excluded: chain N residue 47 ASN Chi-restraints excluded: chain O residue 181 SER Chi-restraints excluded: chain O residue 182 ARG Chi-restraints excluded: chain P residue 109 VAL Chi-restraints excluded: chain P residue 140 LYS Chi-restraints excluded: chain Q residue 74 SER Chi-restraints excluded: chain Q residue 112 LYS Chi-restraints excluded: chain R residue 4 THR Chi-restraints excluded: chain S residue 25 ARG Chi-restraints excluded: chain S residue 90 LEU Chi-restraints excluded: chain T residue 8 LEU Chi-restraints excluded: chain T residue 13 ASP Chi-restraints excluded: chain T residue 25 ILE Chi-restraints excluded: chain T residue 29 LYS Chi-restraints excluded: chain T residue 34 SER Chi-restraints excluded: chain T residue 37 MET Chi-restraints excluded: chain T residue 44 SER Chi-restraints excluded: chain U residue 9 GLU Chi-restraints excluded: chain U residue 29 LYS Chi-restraints excluded: chain V residue 39 LYS Chi-restraints excluded: chain V residue 75 GLN Chi-restraints excluded: chain W residue 111 GLU Chi-restraints excluded: chain X residue 3 ILE Chi-restraints excluded: chain X residue 99 CYS Chi-restraints excluded: chain X residue 130 VAL Chi-restraints excluded: chain X residue 143 SER Chi-restraints excluded: chain Y residue 73 SER Chi-restraints excluded: chain Y residue 99 ILE Chi-restraints excluded: chain Z residue 85 GLN Chi-restraints excluded: chain Z residue 144 THR Chi-restraints excluded: chain a residue 4 GLU Chi-restraints excluded: chain a residue 48 MET Chi-restraints excluded: chain d residue 26 LEU Chi-restraints excluded: chain d residue 92 SER Chi-restraints excluded: chain d residue 111 GLU Chi-restraints excluded: chain e residue 7 LYS Chi-restraints excluded: chain e residue 92 THR Chi-restraints excluded: chain g residue 85 MET Chi-restraints excluded: chain i residue 63 THR Chi-restraints excluded: chain i residue 78 VAL Chi-restraints excluded: chain i residue 121 GLU Chi-restraints excluded: chain j residue 70 ASP Chi-restraints excluded: chain l residue 149 GLU Chi-restraints excluded: chain m residue 15 THR Chi-restraints excluded: chain m residue 29 ARG Chi-restraints excluded: chain m residue 32 GLN Chi-restraints excluded: chain m residue 85 THR Chi-restraints excluded: chain m residue 88 LEU Chi-restraints excluded: chain o residue 27 ASP Chi-restraints excluded: chain o residue 30 PHE Chi-restraints excluded: chain o residue 117 ARG Chi-restraints excluded: chain p residue 14 ARG Chi-restraints excluded: chain p residue 22 GLN Chi-restraints excluded: chain p residue 38 LEU Chi-restraints excluded: chain q residue 4 LEU Chi-restraints excluded: chain r residue 68 VAL Chi-restraints excluded: chain r residue 72 GLN Chi-restraints excluded: chain s residue 36 THR Chi-restraints excluded: chain s residue 47 SER Chi-restraints excluded: chain s residue 59 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 790 random chunks: chunk 692 optimal weight: 5.9990 chunk 729 optimal weight: 0.9980 chunk 665 optimal weight: 4.9990 chunk 709 optimal weight: 3.9990 chunk 427 optimal weight: 20.0000 chunk 309 optimal weight: 0.9990 chunk 557 optimal weight: 1.9990 chunk 217 optimal weight: 1.9990 chunk 641 optimal weight: 2.9990 chunk 671 optimal weight: 3.9990 chunk 707 optimal weight: 0.0970 overall best weight: 1.2184 ------------------------------------------------------------------------------- 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 157 HIS E 121 GLN ** F 431 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 444 GLN G 535 GLN H 124 ASN M 144 ASN ** N 316 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 72 GLN Y 7 GLN b 73 GLN c 46 ASN g 119 GLN i 12 GLN ** o 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** q 112 ASN r 24 GLN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8650 moved from start: 0.1294 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.245 68528 Z= 0.428 Angle : 1.292 50.540 92706 Z= 0.834 Chirality : 0.256 6.466 10140 Planarity : 0.004 0.047 11534 Dihedral : 10.947 177.944 10713 Min Nonbonded Distance : 1.974 Molprobity Statistics. All-atom Clashscore : 4.11 Ramachandran Plot: Outliers : 0.01 % Allowed : 1.49 % Favored : 98.50 % Rotamer: Outliers : 1.46 % Allowed : 13.68 % Favored : 84.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.54 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.64 (0.09), residues: 7977 helix: 1.76 (0.08), residues: 4300 sheet: 0.16 (0.25), residues: 396 loop : 0.44 (0.11), residues: 3281 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP X 85 HIS 0.005 0.001 HIS N 112 PHE 0.028 0.001 PHE N 292 TYR 0.022 0.001 TYR L 422 ARG 0.009 0.000 ARG q 21 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15954 Ramachandran restraints generated. 7977 Oldfield, 0 Emsley, 7977 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15954 Ramachandran restraints generated. 7977 Oldfield, 0 Emsley, 7977 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1065 residues out of total 7064 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 103 poor density : 962 time to evaluate : 6.466 Fit side-chains revert: symmetry clash REVERT: A 85 ASN cc_start: 0.7548 (OUTLIER) cc_final: 0.7190 (m-40) REVERT: E 134 ASP cc_start: 0.8037 (OUTLIER) cc_final: 0.7631 (p0) REVERT: E 180 LYS cc_start: 0.8134 (OUTLIER) cc_final: 0.7853 (mtpt) REVERT: F 339 ARG cc_start: 0.8085 (OUTLIER) cc_final: 0.7686 (mtp-110) REVERT: G 16 GLN cc_start: 0.8021 (OUTLIER) cc_final: 0.7261 (tm130) REVERT: G 188 GLU cc_start: 0.7899 (OUTLIER) cc_final: 0.7396 (mm-30) REVERT: G 288 LYS cc_start: 0.8417 (tppp) cc_final: 0.8034 (tptm) REVERT: G 337 ARG cc_start: 0.8209 (mtt90) cc_final: 0.7928 (mmm-85) REVERT: G 640 ASN cc_start: 0.7570 (t0) cc_final: 0.7246 (m-40) REVERT: G 682 GLN cc_start: 0.8406 (OUTLIER) cc_final: 0.7969 (mt0) REVERT: M 335 GLU cc_start: 0.8458 (mt-10) cc_final: 0.8104 (mt-10) REVERT: N 47 ASN cc_start: 0.8597 (OUTLIER) cc_final: 0.8397 (m110) REVERT: N 100 MET cc_start: 0.8396 (mtt) cc_final: 0.8152 (mtt) REVERT: O 182 ARG cc_start: 0.8739 (OUTLIER) cc_final: 0.7925 (mtp85) REVERT: P 119 GLN cc_start: 0.8465 (tt0) cc_final: 0.8237 (tt0) REVERT: Q 112 LYS cc_start: 0.8561 (OUTLIER) cc_final: 0.8052 (ptpp) REVERT: S 25 ARG cc_start: 0.7723 (OUTLIER) cc_final: 0.7442 (mmt90) REVERT: S 90 LEU cc_start: 0.9010 (OUTLIER) cc_final: 0.8553 (mm) REVERT: T 8 LEU cc_start: 0.7366 (OUTLIER) cc_final: 0.6880 (tt) REVERT: T 29 LYS cc_start: 0.7339 (OUTLIER) cc_final: 0.7061 (tmtp) REVERT: T 37 MET cc_start: 0.7638 (OUTLIER) cc_final: 0.7033 (mmt) REVERT: T 57 GLU cc_start: 0.7226 (tp30) cc_final: 0.6955 (tp30) REVERT: U 29 LYS cc_start: 0.8046 (OUTLIER) cc_final: 0.7740 (mmmm) REVERT: V 39 LYS cc_start: 0.8264 (OUTLIER) cc_final: 0.7809 (tmtp) REVERT: X 3 ILE cc_start: 0.8622 (OUTLIER) cc_final: 0.8383 (mp) REVERT: Y 57 ARG cc_start: 0.7664 (ttp80) cc_final: 0.7436 (mtp180) REVERT: Z 85 GLN cc_start: 0.8015 (OUTLIER) cc_final: 0.7402 (tt0) REVERT: c 41 GLU cc_start: 0.8303 (tp30) cc_final: 0.8086 (tp30) REVERT: d 26 LEU cc_start: 0.8839 (OUTLIER) cc_final: 0.8517 (mp) REVERT: e 52 GLU cc_start: 0.7575 (mt-10) cc_final: 0.7135 (pt0) REVERT: i 6 GLU cc_start: 0.7653 (mt-10) cc_final: 0.7440 (mt-10) REVERT: i 121 GLU cc_start: 0.6912 (OUTLIER) cc_final: 0.6683 (tt0) REVERT: j 40 PHE cc_start: 0.8411 (t80) cc_final: 0.8051 (t80) REVERT: k 89 SER cc_start: 0.7141 (t) cc_final: 0.6666 (p) REVERT: l 149 GLU cc_start: 0.7403 (OUTLIER) cc_final: 0.7126 (mm-30) REVERT: m 29 ARG cc_start: 0.7756 (OUTLIER) cc_final: 0.7451 (ttm-80) REVERT: o 112 LYS cc_start: 0.8330 (tptp) cc_final: 0.8120 (tptt) REVERT: p 14 ARG cc_start: 0.7261 (OUTLIER) cc_final: 0.6682 (ttt180) REVERT: r 72 GLN cc_start: 0.7599 (OUTLIER) cc_final: 0.7151 (pp30) REVERT: r 108 ASP cc_start: 0.8703 (t70) cc_final: 0.8463 (t0) outliers start: 103 outliers final: 55 residues processed: 1023 average time/residue: 1.7717 time to fit residues: 2281.1813 Evaluate side-chains 1036 residues out of total 7064 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 80 poor density : 956 time to evaluate : 6.013 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 ILE Chi-restraints excluded: chain A residue 24 LEU Chi-restraints excluded: chain A residue 85 ASN Chi-restraints excluded: chain B residue 54 CYS Chi-restraints excluded: chain D residue 109 VAL Chi-restraints excluded: chain D residue 376 VAL Chi-restraints excluded: chain D residue 420 THR Chi-restraints excluded: chain E residue 134 ASP Chi-restraints excluded: chain E residue 180 LYS Chi-restraints excluded: chain E residue 203 THR Chi-restraints excluded: chain F residue 105 CYS Chi-restraints excluded: chain F residue 339 ARG Chi-restraints excluded: chain G residue 16 GLN Chi-restraints excluded: chain G residue 188 GLU Chi-restraints excluded: chain G residue 431 ASP Chi-restraints excluded: chain G residue 613 TYR Chi-restraints excluded: chain G residue 651 LEU Chi-restraints excluded: chain G residue 682 GLN Chi-restraints excluded: chain H residue 54 LYS Chi-restraints excluded: chain H residue 121 TRP Chi-restraints excluded: chain H residue 259 PHE Chi-restraints excluded: chain J residue 130 THR Chi-restraints excluded: chain L residue 104 SER Chi-restraints excluded: chain L residue 251 THR Chi-restraints excluded: chain L residue 507 MET Chi-restraints excluded: chain M residue 116 ILE Chi-restraints excluded: chain M residue 130 LEU Chi-restraints excluded: chain M residue 138 ASN Chi-restraints excluded: chain M residue 247 THR Chi-restraints excluded: chain M residue 296 LEU Chi-restraints excluded: chain M residue 315 LEU Chi-restraints excluded: chain N residue 47 ASN Chi-restraints excluded: chain O residue 182 ARG Chi-restraints excluded: chain P residue 109 VAL Chi-restraints excluded: chain P residue 140 LYS Chi-restraints excluded: chain P residue 281 ARG Chi-restraints excluded: chain Q residue 112 LYS Chi-restraints excluded: chain R residue 4 THR Chi-restraints excluded: chain S residue 25 ARG Chi-restraints excluded: chain S residue 90 LEU Chi-restraints excluded: chain T residue 8 LEU Chi-restraints excluded: chain T residue 13 ASP Chi-restraints excluded: chain T residue 25 ILE Chi-restraints excluded: chain T residue 29 LYS Chi-restraints excluded: chain T residue 37 MET Chi-restraints excluded: chain T residue 44 SER Chi-restraints excluded: chain U residue 29 LYS Chi-restraints excluded: chain V residue 39 LYS Chi-restraints excluded: chain V residue 75 GLN Chi-restraints excluded: chain V residue 94 ILE Chi-restraints excluded: chain W residue 111 GLU Chi-restraints excluded: chain X residue 3 ILE Chi-restraints excluded: chain X residue 99 CYS Chi-restraints excluded: chain X residue 130 VAL Chi-restraints excluded: chain X residue 143 SER Chi-restraints excluded: chain Y residue 16 GLU Chi-restraints excluded: chain Y residue 73 SER Chi-restraints excluded: chain Z residue 85 GLN Chi-restraints excluded: chain a residue 48 MET Chi-restraints excluded: chain b residue 42 LEU Chi-restraints excluded: chain d residue 26 LEU Chi-restraints excluded: chain d residue 92 SER Chi-restraints excluded: chain d residue 111 GLU Chi-restraints excluded: chain e residue 86 ILE Chi-restraints excluded: chain e residue 92 THR Chi-restraints excluded: chain f residue 9 ASP Chi-restraints excluded: chain i residue 63 THR Chi-restraints excluded: chain i residue 78 VAL Chi-restraints excluded: chain i residue 121 GLU Chi-restraints excluded: chain j residue 70 ASP Chi-restraints excluded: chain l residue 149 GLU Chi-restraints excluded: chain m residue 15 THR Chi-restraints excluded: chain m residue 29 ARG Chi-restraints excluded: chain m residue 88 LEU Chi-restraints excluded: chain o residue 30 PHE Chi-restraints excluded: chain p residue 14 ARG Chi-restraints excluded: chain r residue 68 VAL Chi-restraints excluded: chain r residue 72 GLN Chi-restraints excluded: chain s residue 36 THR Chi-restraints excluded: chain s residue 47 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 790 random chunks: chunk 465 optimal weight: 0.8980 chunk 750 optimal weight: 0.0980 chunk 457 optimal weight: 7.9990 chunk 355 optimal weight: 3.9990 chunk 521 optimal weight: 4.9990 chunk 787 optimal weight: 6.9990 chunk 724 optimal weight: 0.0470 chunk 626 optimal weight: 10.0000 chunk 65 optimal weight: 0.9980 chunk 484 optimal weight: 7.9990 chunk 384 optimal weight: 8.9990 overall best weight: 1.2080 ------------------------------------------------------------------------------- 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 157 HIS E 121 GLN ** F 431 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 444 GLN G 535 GLN H 124 ASN ** H 317 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 144 ASN ** N 316 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 89 ASN P 36 ASN R 51 GLN S 72 GLN Y 7 GLN b 61 ASN b 73 GLN e 81 GLN g 119 GLN i 12 GLN q 112 ASN r 24 GLN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8648 moved from start: 0.1341 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.245 68528 Z= 0.428 Angle : 1.293 50.567 92706 Z= 0.834 Chirality : 0.255 6.467 10140 Planarity : 0.004 0.047 11534 Dihedral : 10.734 177.441 10710 Min Nonbonded Distance : 1.978 Molprobity Statistics. All-atom Clashscore : 4.18 Ramachandran Plot: Outliers : 0.01 % Allowed : 1.67 % Favored : 98.32 % Rotamer: Outliers : 1.37 % Allowed : 13.91 % Favored : 84.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.54 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.70 (0.09), residues: 7977 helix: 1.80 (0.08), residues: 4304 sheet: 0.17 (0.25), residues: 396 loop : 0.48 (0.11), residues: 3277 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP X 85 HIS 0.006 0.001 HIS N 112 PHE 0.028 0.001 PHE N 292 TYR 0.030 0.001 TYR T 17 ARG 0.007 0.000 ARG c 44 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15954 Ramachandran restraints generated. 7977 Oldfield, 0 Emsley, 7977 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15954 Ramachandran restraints generated. 7977 Oldfield, 0 Emsley, 7977 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1062 residues out of total 7064 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 97 poor density : 965 time to evaluate : 6.107 Fit side-chains revert: symmetry clash REVERT: E 134 ASP cc_start: 0.8039 (OUTLIER) cc_final: 0.7631 (p0) REVERT: E 180 LYS cc_start: 0.8103 (OUTLIER) cc_final: 0.7797 (mtpt) REVERT: F 339 ARG cc_start: 0.8079 (OUTLIER) cc_final: 0.7680 (mtp-110) REVERT: G 16 GLN cc_start: 0.8002 (OUTLIER) cc_final: 0.7277 (tm130) REVERT: G 188 GLU cc_start: 0.7907 (OUTLIER) cc_final: 0.7369 (mm-30) REVERT: G 288 LYS cc_start: 0.8413 (tppp) cc_final: 0.8031 (tptm) REVERT: G 337 ARG cc_start: 0.8190 (mtt90) cc_final: 0.7989 (mmm-85) REVERT: G 640 ASN cc_start: 0.7608 (t0) cc_final: 0.7284 (m-40) REVERT: G 643 GLN cc_start: 0.7268 (tm-30) cc_final: 0.7001 (tm-30) REVERT: G 647 GLU cc_start: 0.7586 (mt-10) cc_final: 0.7327 (mt-10) REVERT: G 682 GLN cc_start: 0.8402 (OUTLIER) cc_final: 0.7968 (mt0) REVERT: M 335 GLU cc_start: 0.8429 (mt-10) cc_final: 0.8075 (mt-10) REVERT: N 100 MET cc_start: 0.8380 (mtt) cc_final: 0.8139 (mtt) REVERT: O 182 ARG cc_start: 0.8737 (OUTLIER) cc_final: 0.7927 (mtp85) REVERT: P 119 GLN cc_start: 0.8461 (tt0) cc_final: 0.8232 (tt0) REVERT: Q 112 LYS cc_start: 0.8556 (OUTLIER) cc_final: 0.8060 (ptpp) REVERT: R 51 GLN cc_start: 0.8453 (OUTLIER) cc_final: 0.7917 (mp-120) REVERT: R 92 ARG cc_start: 0.8024 (ttm-80) cc_final: 0.7759 (ptm160) REVERT: S 25 ARG cc_start: 0.7713 (OUTLIER) cc_final: 0.7435 (mmt90) REVERT: S 90 LEU cc_start: 0.9015 (OUTLIER) cc_final: 0.8542 (mm) REVERT: T 29 LYS cc_start: 0.7321 (OUTLIER) cc_final: 0.7052 (tmtp) REVERT: T 37 MET cc_start: 0.7644 (OUTLIER) cc_final: 0.7041 (mmt) REVERT: T 57 GLU cc_start: 0.7216 (tp30) cc_final: 0.6992 (tp30) REVERT: U 9 GLU cc_start: 0.7646 (OUTLIER) cc_final: 0.7417 (tt0) REVERT: U 29 LYS cc_start: 0.8033 (OUTLIER) cc_final: 0.7729 (mmmm) REVERT: V 39 LYS cc_start: 0.8296 (OUTLIER) cc_final: 0.7833 (tmtp) REVERT: X 3 ILE cc_start: 0.8643 (OUTLIER) cc_final: 0.8428 (mp) REVERT: Z 85 GLN cc_start: 0.8018 (OUTLIER) cc_final: 0.7405 (tt0) REVERT: c 41 GLU cc_start: 0.8301 (tp30) cc_final: 0.8081 (tp30) REVERT: d 26 LEU cc_start: 0.8822 (OUTLIER) cc_final: 0.8487 (mp) REVERT: e 52 GLU cc_start: 0.7568 (mt-10) cc_final: 0.7135 (pt0) REVERT: i 6 GLU cc_start: 0.7643 (mt-10) cc_final: 0.7430 (mt-10) REVERT: i 121 GLU cc_start: 0.6907 (OUTLIER) cc_final: 0.6670 (tt0) REVERT: j 40 PHE cc_start: 0.8411 (t80) cc_final: 0.8059 (t80) REVERT: j 45 ASP cc_start: 0.7864 (OUTLIER) cc_final: 0.7661 (p0) REVERT: k 89 SER cc_start: 0.7204 (t) cc_final: 0.6739 (p) REVERT: l 149 GLU cc_start: 0.7373 (OUTLIER) cc_final: 0.7093 (mm-30) REVERT: m 29 ARG cc_start: 0.7748 (OUTLIER) cc_final: 0.7446 (ttm-80) REVERT: o 112 LYS cc_start: 0.8311 (tptp) cc_final: 0.8107 (tptt) REVERT: p 14 ARG cc_start: 0.7255 (OUTLIER) cc_final: 0.6678 (ttt180) REVERT: r 72 GLN cc_start: 0.7579 (OUTLIER) cc_final: 0.7127 (pp30) REVERT: r 108 ASP cc_start: 0.8696 (t70) cc_final: 0.8450 (t0) outliers start: 97 outliers final: 50 residues processed: 1022 average time/residue: 1.7910 time to fit residues: 2309.9617 Evaluate side-chains 1035 residues out of total 7064 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 960 time to evaluate : 5.943 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 ILE Chi-restraints excluded: chain A residue 24 LEU Chi-restraints excluded: chain A residue 90 MET Chi-restraints excluded: chain B residue 54 CYS Chi-restraints excluded: chain B residue 161 LEU Chi-restraints excluded: chain D residue 109 VAL Chi-restraints excluded: chain D residue 376 VAL Chi-restraints excluded: chain D residue 420 THR Chi-restraints excluded: chain E residue 134 ASP Chi-restraints excluded: chain E residue 180 LYS Chi-restraints excluded: chain E residue 203 THR Chi-restraints excluded: chain F residue 105 CYS Chi-restraints excluded: chain F residue 339 ARG Chi-restraints excluded: chain G residue 16 GLN Chi-restraints excluded: chain G residue 188 GLU Chi-restraints excluded: chain G residue 431 ASP Chi-restraints excluded: chain G residue 613 TYR Chi-restraints excluded: chain G residue 651 LEU Chi-restraints excluded: chain G residue 682 GLN Chi-restraints excluded: chain H residue 121 TRP Chi-restraints excluded: chain H residue 259 PHE Chi-restraints excluded: chain J residue 130 THR Chi-restraints excluded: chain L residue 104 SER Chi-restraints excluded: chain L residue 251 THR Chi-restraints excluded: chain M residue 130 LEU Chi-restraints excluded: chain M residue 247 THR Chi-restraints excluded: chain M residue 296 LEU Chi-restraints excluded: chain M residue 315 LEU Chi-restraints excluded: chain O residue 182 ARG Chi-restraints excluded: chain P residue 109 VAL Chi-restraints excluded: chain P residue 140 LYS Chi-restraints excluded: chain P residue 281 ARG Chi-restraints excluded: chain Q residue 112 LYS Chi-restraints excluded: chain R residue 51 GLN Chi-restraints excluded: chain S residue 25 ARG Chi-restraints excluded: chain S residue 90 LEU Chi-restraints excluded: chain T residue 25 ILE Chi-restraints excluded: chain T residue 29 LYS Chi-restraints excluded: chain T residue 37 MET Chi-restraints excluded: chain T residue 44 SER Chi-restraints excluded: chain U residue 9 GLU Chi-restraints excluded: chain U residue 29 LYS Chi-restraints excluded: chain V residue 32 ASP Chi-restraints excluded: chain V residue 39 LYS Chi-restraints excluded: chain V residue 75 GLN Chi-restraints excluded: chain W residue 111 GLU Chi-restraints excluded: chain X residue 3 ILE Chi-restraints excluded: chain X residue 99 CYS Chi-restraints excluded: chain X residue 130 VAL Chi-restraints excluded: chain X residue 143 SER Chi-restraints excluded: chain Y residue 16 GLU Chi-restraints excluded: chain Y residue 73 SER Chi-restraints excluded: chain Z residue 85 GLN Chi-restraints excluded: chain a residue 48 MET Chi-restraints excluded: chain d residue 26 LEU Chi-restraints excluded: chain d residue 85 VAL Chi-restraints excluded: chain d residue 92 SER Chi-restraints excluded: chain d residue 111 GLU Chi-restraints excluded: chain e residue 86 ILE Chi-restraints excluded: chain e residue 92 THR Chi-restraints excluded: chain f residue 9 ASP Chi-restraints excluded: chain i residue 63 THR Chi-restraints excluded: chain i residue 78 VAL Chi-restraints excluded: chain i residue 121 GLU Chi-restraints excluded: chain j residue 45 ASP Chi-restraints excluded: chain j residue 70 ASP Chi-restraints excluded: chain l residue 149 GLU Chi-restraints excluded: chain m residue 15 THR Chi-restraints excluded: chain m residue 29 ARG Chi-restraints excluded: chain m residue 88 LEU Chi-restraints excluded: chain o residue 30 PHE Chi-restraints excluded: chain p residue 14 ARG Chi-restraints excluded: chain r residue 68 VAL Chi-restraints excluded: chain r residue 72 GLN Chi-restraints excluded: chain s residue 36 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 790 random chunks: chunk 497 optimal weight: 2.9990 chunk 667 optimal weight: 0.0270 chunk 191 optimal weight: 10.0000 chunk 577 optimal weight: 20.0000 chunk 92 optimal weight: 2.9990 chunk 174 optimal weight: 4.9990 chunk 627 optimal weight: 10.0000 chunk 262 optimal weight: 0.9990 chunk 644 optimal weight: 6.9990 chunk 79 optimal weight: 0.8980 chunk 115 optimal weight: 0.7980 overall best weight: 1.1442 ------------------------------------------------------------------------------- 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 157 HIS E 121 GLN ** F 431 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 444 GLN G 535 GLN H 124 ASN H 317 GLN M 144 ASN ** N 316 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 89 ASN P 36 ASN R 51 GLN S 72 GLN Y 7 GLN b 61 ASN b 73 GLN g 119 GLN i 12 GLN ** o 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** q 112 ASN r 24 GLN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3227 r_free = 0.3227 target = 0.095788 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2913 r_free = 0.2913 target = 0.077502 restraints weight = 67239.711| |-----------------------------------------------------------------------------| r_work (start): 0.2909 rms_B_bonded: 1.09 r_work: 0.2814 rms_B_bonded: 1.52 restraints_weight: 0.5000 r_work: 0.2712 rms_B_bonded: 2.52 restraints_weight: 0.2500 r_work (final): 0.2712 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8906 moved from start: 0.1388 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.245 68528 Z= 0.426 Angle : 1.292 50.571 92706 Z= 0.834 Chirality : 0.255 6.461 10140 Planarity : 0.004 0.046 11534 Dihedral : 10.581 177.418 10704 Min Nonbonded Distance : 1.977 Molprobity Statistics. All-atom Clashscore : 4.31 Ramachandran Plot: Outliers : 0.01 % Allowed : 1.52 % Favored : 98.47 % Rotamer: Outliers : 1.32 % Allowed : 14.01 % Favored : 84.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.54 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.74 (0.09), residues: 7977 helix: 1.83 (0.08), residues: 4299 sheet: 0.18 (0.25), residues: 396 loop : 0.50 (0.11), residues: 3282 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP X 85 HIS 0.006 0.001 HIS N 112 PHE 0.029 0.001 PHE N 292 TYR 0.022 0.001 TYR L 422 ARG 0.009 0.000 ARG q 21 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 31722.66 seconds wall clock time: 549 minutes 36.89 seconds (32976.89 seconds total)