Starting phenix.real_space_refine on Sat Dec 9 21:17:43 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ak6_11811/12_2023/7ak6_11811_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ak6_11811/12_2023/7ak6_11811.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ak6_11811/12_2023/7ak6_11811_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.82 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ak6_11811/12_2023/7ak6_11811_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ak6_11811/12_2023/7ak6_11811_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ak6_11811/12_2023/7ak6_11811.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ak6_11811/12_2023/7ak6_11811.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ak6_11811/12_2023/7ak6_11811_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ak6_11811/12_2023/7ak6_11811_updated.pdb" } resolution = 3.82 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.003 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: 7 Type Number sf(0) Gaussians Fe 28 7.16 5 Zn 1 6.06 5 P 18 5.49 5 S 489 5.16 5 C 42120 2.51 5 N 10948 2.21 5 O 11719 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 38": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 52": "NH1" <-> "NH2" Residue "B ARG 87": "NH1" <-> "NH2" Residue "B ARG 91": "NH1" <-> "NH2" Residue "B TYR 136": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 144": "NH1" <-> "NH2" Residue "B ARG 148": "NH1" <-> "NH2" Residue "B ASP 153": "OD1" <-> "OD2" Residue "B TYR 155": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 168": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 175": "NH1" <-> "NH2" Residue "B ARG 179": "NH1" <-> "NH2" Residue "B ARG 189": "NH1" <-> "NH2" Residue "C ARG 8": "NH1" <-> "NH2" Residue "C PHE 63": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 72": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 77": "OD1" <-> "OD2" Residue "C TYR 94": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 113": "OE1" <-> "OE2" Residue "C PHE 138": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 142": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 143": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 157": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 176": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 182": "NH1" <-> "NH2" Residue "C TYR 209": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 2": "NH1" <-> "NH2" Residue "D GLU 24": "OE1" <-> "OE2" Residue "D ASP 37": "OD1" <-> "OD2" Residue "D ARG 105": "NH1" <-> "NH2" Residue "D TYR 108": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 118": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 133": "NH1" <-> "NH2" Residue "D PHE 167": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 174": "NH1" <-> "NH2" Residue "D ASP 202": "OD1" <-> "OD2" Residue "D ARG 221": "NH1" <-> "NH2" Residue "D ASP 223": "OD1" <-> "OD2" Residue "D TYR 253": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 275": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 290": "NH1" <-> "NH2" Residue "D GLU 343": "OE1" <-> "OE2" Residue "D PHE 349": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 356": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 374": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 425": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 7": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 10": "NH1" <-> "NH2" Residue "E ASP 18": "OD1" <-> "OD2" Residue "E TYR 28": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 38": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 191": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 211": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 12": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 17": "OD1" <-> "OD2" Residue "F TYR 26": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 28": "NH1" <-> "NH2" Residue "F TYR 43": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 92": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 107": "OD1" <-> "OD2" Residue "F TYR 135": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 139": "NH1" <-> "NH2" Residue "F PHE 173": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 176": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 204": "NH1" <-> "NH2" Residue "F PHE 209": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 242": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 256": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 318": "OD1" <-> "OD2" Residue "F ASP 338": "OD1" <-> "OD2" Residue "F ARG 339": "NH1" <-> "NH2" Residue "F ARG 349": "NH1" <-> "NH2" Residue "F ARG 378": "NH1" <-> "NH2" Residue "F ASP 383": "OD1" <-> "OD2" Residue "G PHE 130": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ARG 135": "NH1" <-> "NH2" Residue "G PHE 162": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 170": "OD1" <-> "OD2" Residue "G ARG 218": "NH1" <-> "NH2" Residue "G ASP 232": "OD1" <-> "OD2" Residue "G ARG 243": "NH1" <-> "NH2" Residue "G ARG 249": "NH1" <-> "NH2" Residue "G ARG 253": "NH1" <-> "NH2" Residue "G GLU 261": "OE1" <-> "OE2" Residue "G ARG 268": "NH1" <-> "NH2" Residue "G ARG 285": "NH1" <-> "NH2" Residue "G PHE 310": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 339": "OD1" <-> "OD2" Residue "G GLU 346": "OE1" <-> "OE2" Residue "G ARG 359": "NH1" <-> "NH2" Residue "G TYR 417": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 419": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 504": "OD1" <-> "OD2" Residue "G ARG 515": "NH1" <-> "NH2" Residue "G TYR 545": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 635": "OD1" <-> "OD2" Residue "H PHE 71": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 160": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 202": "OE1" <-> "OE2" Residue "H PHE 220": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 224": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 248": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 259": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 280": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 282": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ARG 25": "NH1" <-> "NH2" Residue "I PHE 54": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ARG 62": "NH1" <-> "NH2" Residue "I GLU 86": "OE1" <-> "OE2" Residue "I ASP 112": "OD1" <-> "OD2" Residue "I PHE 139": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I GLU 154": "OE1" <-> "OE2" Residue "J PHE 6": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 12": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 50": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J GLU 77": "OE1" <-> "OE2" Residue "J ASP 118": "OD1" <-> "OD2" Residue "J ASP 129": "OD1" <-> "OD2" Residue "J TYR 145": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 164": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 5": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 6": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ARG 23": "NH1" <-> "NH2" Residue "K PHE 41": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 85": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 35": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 107": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ARG 116": "NH1" <-> "NH2" Residue "L PHE 152": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ARG 161": "NH1" <-> "NH2" Residue "L PHE 182": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ASP 208": "OD1" <-> "OD2" Residue "L PHE 326": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 385": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 389": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ASP 393": "OD1" <-> "OD2" Residue "L TYR 422": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 429": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ARG 436": "NH1" <-> "NH2" Residue "L PHE 437": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 466": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 485": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 519": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 522": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 528": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ARG 535": "NH1" <-> "NH2" Residue "M PHE 118": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M PHE 149": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M TYR 152": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M TYR 256": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M ASP 281": "OD1" <-> "OD2" Residue "M PHE 391": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M TYR 406": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N PHE 11": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N PHE 60": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N TYR 78": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N PHE 111": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N PHE 291": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N PHE 292": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O ASP 28": "OD1" <-> "OD2" Residue "O TYR 51": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O TYR 58": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O ASP 65": "OD1" <-> "OD2" Residue "O TYR 101": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O ASP 131": "OD1" <-> "OD2" Residue "O PHE 132": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O PHE 134": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O ARG 145": "NH1" <-> "NH2" Residue "O ASP 150": "OD1" <-> "OD2" Residue "O ASP 173": "OD1" <-> "OD2" Residue "O ASP 224": "OD1" <-> "OD2" Residue "O TYR 293": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P TYR 49": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P ARG 50": "NH1" <-> "NH2" Residue "P ARG 76": "NH1" <-> "NH2" Residue "P ARG 102": "NH1" <-> "NH2" Residue "P PHE 129": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P PHE 160": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P PHE 172": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P PHE 178": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P PHE 228": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P ARG 235": "NH1" <-> "NH2" Residue "P TYR 236": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P PHE 246": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P ARG 320": "NH1" <-> "NH2" Residue "P ARG 322": "NH1" <-> "NH2" Residue "Q ASP 18": "OD1" <-> "OD2" Residue "Q PHE 95": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R TYR 23": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R ARG 31": "NH1" <-> "NH2" Residue "R TYR 86": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R PHE 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S ARG 55": "NH1" <-> "NH2" Residue "T TYR 22": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T ASP 23": "OD1" <-> "OD2" Residue "T ASP 39": "OD1" <-> "OD2" Residue "T ASP 56": "OD1" <-> "OD2" Residue "T GLU 61": "OE1" <-> "OE2" Residue "T TYR 79": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U TYR 17": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U ASP 39": "OD1" <-> "OD2" Residue "U ASP 43": "OD1" <-> "OD2" Residue "U ASP 46": "OD1" <-> "OD2" Residue "U PHE 60": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U TYR 79": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V ASP 17": "OD1" <-> "OD2" Residue "V PHE 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V ARG 44": "NH1" <-> "NH2" Residue "V GLU 61": "OE1" <-> "OE2" Residue "W ARG 32": "NH1" <-> "NH2" Residue "W ARG 33": "NH1" <-> "NH2" Residue "W TYR 38": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W ASP 55": "OD1" <-> "OD2" Residue "W ARG 79": "NH1" <-> "NH2" Residue "W ARG 107": "NH1" <-> "NH2" Residue "W PHE 109": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W PHE 120": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W PHE 124": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X ARG 54": "NH1" <-> "NH2" Residue "X TYR 90": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X PHE 106": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X ASP 112": "OD1" <-> "OD2" Residue "X ARG 118": "NH1" <-> "NH2" Residue "X ASP 120": "OD1" <-> "OD2" Residue "X TYR 141": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X ARG 144": "NH1" <-> "NH2" Residue "X ARG 146": "NH1" <-> "NH2" Residue "Y ARG 5": "NH1" <-> "NH2" Residue "Y TYR 40": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y GLU 83": "OE1" <-> "OE2" Residue "Y TYR 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y PHE 92": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y TYR 118": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z ARG 22": "NH1" <-> "NH2" Residue "Z ARG 26": "NH1" <-> "NH2" Residue "Z ARG 27": "NH1" <-> "NH2" Residue "Z PHE 44": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z ARG 48": "NH1" <-> "NH2" Residue "Z GLU 55": "OE1" <-> "OE2" Residue "Z ARG 67": "NH1" <-> "NH2" Residue "Z ASP 79": "OD1" <-> "OD2" Residue "Z ARG 81": "NH1" <-> "NH2" Residue "Z GLU 107": "OE1" <-> "OE2" Residue "a PHE 3": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a ARG 40": "NH1" <-> "NH2" Residue "a ARG 52": "NH1" <-> "NH2" Residue "a ARG 53": "NH1" <-> "NH2" Residue "b TYR 40": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b TYR 52": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c ARG 5": "NH1" <-> "NH2" Residue "c GLU 6": "OE1" <-> "OE2" Residue "c ARG 45": "NH1" <-> "NH2" Residue "d GLU 103": "OE1" <-> "OE2" Residue "d TYR 109": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "e PHE 2": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "e PHE 17": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "e PHE 19": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "e ARG 50": "NH1" <-> "NH2" Residue "e PHE 62": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "e ARG 68": "NH1" <-> "NH2" Residue "e ARG 100": "NH1" <-> "NH2" Residue "e ARG 104": "NH1" <-> "NH2" Residue "f PHE 21": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "g TYR 36": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "g ARG 57": "NH1" <-> "NH2" Residue "g PHE 62": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "g PHE 70": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "g PHE 74": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "g ARG 89": "NH1" <-> "NH2" Residue "g ARG 93": "NH1" <-> "NH2" Residue "g TYR 110": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "g ASP 112": "OD1" <-> "OD2" Residue "h ARG 20": "NH1" <-> "NH2" Residue "h GLU 57": "OE1" <-> "OE2" Residue "h TYR 87": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "h ARG 115": "NH1" <-> "NH2" Residue "i ARG 10": "NH1" <-> "NH2" Residue "i ARG 65": "NH1" <-> "NH2" Residue "i PHE 80": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "i TYR 83": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "i TYR 84": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "i TYR 87": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "i ARG 120": "NH1" <-> "NH2" Residue "i PHE 122": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "j TYR 11": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "j PHE 27": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "j PHE 34": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "j PHE 40": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "j ASP 43": "OD1" <-> "OD2" Residue "j ASP 61": "OD1" <-> "OD2" Residue "k ARG 44": "NH1" <-> "NH2" Residue "k ARG 52": "NH1" <-> "NH2" Residue "k PHE 62": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "l TYR 26": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "l TYR 46": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "l ASP 58": "OD1" <-> "OD2" Residue "l ARG 85": "NH1" <-> "NH2" Residue "l PHE 107": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "l TYR 132": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "m TYR 5": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "m ASP 18": "OD1" <-> "OD2" Residue "m ASP 23": "OD1" <-> "OD2" Residue "m ARG 29": "NH1" <-> "NH2" Residue "m ARG 30": "NH1" <-> "NH2" Residue "m TYR 50": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "m TYR 69": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "m TYR 76": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "m ARG 80": "NH1" <-> "NH2" Residue "n TYR 8": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "n ARG 33": "NH1" <-> "NH2" Residue "n TYR 38": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "n PHE 47": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "n GLU 53": "OE1" <-> "OE2" Residue "n PHE 70": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "n ARG 92": "NH1" <-> "NH2" Residue "n TYR 93": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "n TYR 114": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "n ASP 146": "OD1" <-> "OD2" Residue "n ARG 157": "NH1" <-> "NH2" Residue "n ARG 158": "NH1" <-> "NH2" Residue "n GLU 159": "OE1" <-> "OE2" Residue "o ARG 6": "NH1" <-> "NH2" Residue "o ARG 7": "NH1" <-> "NH2" Residue "o ASP 27": "OD1" <-> "OD2" Residue "o PHE 30": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "o GLU 32": "OE1" <-> "OE2" Residue "o ARG 33": "NH1" <-> "NH2" Residue "o ASP 47": "OD1" <-> "OD2" Residue "o ARG 97": "NH1" <-> "NH2" Residue "o PHE 101": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "o GLU 102": "OE1" <-> "OE2" Residue "o ARG 105": "NH1" <-> "NH2" Residue "o ARG 106": "NH1" <-> "NH2" Residue "o ARG 110": "NH1" <-> "NH2" Residue "p ARG 48": "NH1" <-> "NH2" Residue "p TYR 61": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "p TYR 62": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "p TYR 63": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "p ARG 65": "NH1" <-> "NH2" Residue "p ARG 68": "NH1" <-> "NH2" Residue "p ARG 92": "NH1" <-> "NH2" Residue "p TYR 120": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "p TYR 149": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "q PHE 28": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "q ASP 32": "OD1" <-> "OD2" Residue "q TYR 49": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "q ARG 60": "NH1" <-> "NH2" Residue "q PHE 74": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "q PHE 108": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "q ARG 131": "NH1" <-> "NH2" Residue "q TYR 144": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "r ARG 5": "NH1" <-> "NH2" Residue "r ARG 26": "NH1" <-> "NH2" Residue "r TYR 27": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.16s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/chem_data/mon_lib" Total number of atoms: 65323 Number of models: 1 Model: "" Number of chains: 60 Chain: "A" Number of atoms: 761 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 761 Classifications: {'peptide': 93} Link IDs: {'PTRANS': 4, 'TRANS': 88} 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: 1241 Number of conformers: 1 Conformer: "" Number of residues, atoms: 155, 1241 Classifications: {'peptide': 155} Link IDs: {'PCIS': 2, 'PTRANS': 8, 'TRANS': 144} Chain: "C" Number of atoms: 1721 Number of conformers: 1 Conformer: "" Number of residues, atoms: 207, 1721 Classifications: {'peptide': 207} Link IDs: {'PTRANS': 15, 'TRANS': 191} Chain: "D" Number of atoms: 3369 Number of conformers: 1 Conformer: "" Number of residues, atoms: 417, 3369 Classifications: {'peptide': 417} Link IDs: {'PTRANS': 25, 'TRANS': 391} 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: 1639 Number of conformers: 1 Conformer: "" Number of residues, atoms: 210, 1639 Classifications: {'peptide': 210} Link IDs: {'PTRANS': 21, 'TRANS': 188} Chain: "F" Number of atoms: 3301 Number of conformers: 1 Conformer: "" Number of residues, atoms: 428, 3301 Classifications: {'peptide': 428} Link IDs: {'PCIS': 2, 'PTRANS': 19, 'TRANS': 406} Chain: "G" Number of atoms: 5281 Number of conformers: 1 Conformer: "" Number of residues, atoms: 686, 5281 Classifications: {'peptide': 686} Link IDs: {'PTRANS': 31, 'TRANS': 654} Chain: "H" Number of atoms: 2441 Number of conformers: 1 Conformer: "" Number of residues, atoms: 305, 2441 Classifications: {'peptide': 305} Link IDs: {'PCIS': 2, 'PTRANS': 19, 'TRANS': 283} Chain breaks: 2 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'FME:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "I" Number of atoms: 1408 Number of conformers: 1 Conformer: "" Number of residues, atoms: 178, 1408 Classifications: {'peptide': 178} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 9, 'TRANS': 168} Unresolved non-hydrogen bonds: 23 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 3} Unresolved non-hydrogen planarities: 16 Chain: "J" Number of atoms: 1278 Number of conformers: 1 Conformer: "" Number of residues, atoms: 171, 1278 Classifications: {'peptide': 171} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 2, 'TRANS': 168} Unresolved non-hydrogen bonds: 26 Unresolved non-hydrogen angles: 36 Unresolved non-hydrogen dihedrals: 22 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'FME:plan-2': 1, 'TYR:plan': 2, 'GLU:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 22 Chain: "K" Number of atoms: 737 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 737 Classifications: {'peptide': 98} Link IDs: {'PTRANS': 3, 'TRANS': 94} 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: 4800 Number of conformers: 1 Conformer: "" Number of residues, atoms: 606, 4800 Classifications: {'peptide': 606} Link IDs: {'PTRANS': 26, 'TRANS': 579} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'FME:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "M" Number of atoms: 3632 Number of conformers: 1 Conformer: "" Number of residues, atoms: 459, 3632 Classifications: {'peptide': 459} Link IDs: {'PCIS': 2, 'PTRANS': 18, '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: 2696 Number of conformers: 1 Conformer: "" Number of residues, atoms: 344, 2696 Classifications: {'peptide': 344} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 323} 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: 2599 Number of conformers: 1 Conformer: "" Number of residues, atoms: 319, 2599 Classifications: {'peptide': 319} Link IDs: {'PTRANS': 16, 'TRANS': 302} Chain: "P" Number of atoms: 2281 Number of conformers: 1 Conformer: "" Number of residues, atoms: 288, 2281 Classifications: {'peptide': 288} Link IDs: {'PTRANS': 13, 'TRANS': 274} Chain breaks: 3 Chain: "Q" Number of atoms: 1015 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 1015 Classifications: {'peptide': 125} Link IDs: {'PTRANS': 6, 'TRANS': 118} Chain: "R" Number of atoms: 738 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 738 Classifications: {'peptide': 94} Link IDs: {'PTRANS': 3, 'TRANS': 90} Chain: "S" Number of atoms: 659 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 659 Classifications: {'peptide': 82} Link IDs: {'PTRANS': 4, 'TRANS': 77} Chain: "T" Number of atoms: 584 Number of conformers: 1 Conformer: "" Number of residues, atoms: 72, 584 Classifications: {'peptide': 72} Link IDs: {'PTRANS': 3, 'TRANS': 68} Chain: "U" Number of atoms: 706 Number of conformers: 1 Conformer: "" Number of residues, atoms: 88, 706 Classifications: {'peptide': 88} Link IDs: {'PTRANS': 5, 'TRANS': 82} Chain: "V" Number of atoms: 915 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 915 Classifications: {'peptide': 112} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 103} Chain: "W" Number of atoms: 970 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 970 Classifications: {'peptide': 114} Link IDs: {'PTRANS': 6, 'TRANS': 107} Chain: "X" Number of atoms: 1396 Number of conformers: 1 Conformer: "" Number of residues, atoms: 171, 1396 Classifications: {'peptide': 171} Link IDs: {'PTRANS': 11, 'TRANS': 159} Chain: "Y" Number of atoms: 1037 Number of conformers: 1 Conformer: "" Number of residues, atoms: 140, 1037 Classifications: {'peptide': 140} Link IDs: {'PTRANS': 6, 'TRANS': 133} Chain: "Z" Number of atoms: 1152 Number of conformers: 1 Conformer: "" Number of residues, atoms: 139, 1152 Classifications: {'peptide': 139} Link IDs: {'PTRANS': 9, 'TRANS': 129} Chain: "a" Number of atoms: 556 Number of conformers: 1 Conformer: "" Number of residues, atoms: 68, 556 Classifications: {'peptide': 68} Link IDs: {'PTRANS': 2, 'TRANS': 65} Chain: "b" Number of atoms: 643 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 643 Classifications: {'peptide': 82} Link IDs: {'PTRANS': 11, 'TRANS': 70} Chain: "c" Number of atoms: 381 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 381 Classifications: {'peptide': 46} Link IDs: {'PTRANS': 2, 'TRANS': 43} Chain: "d" Number of atoms: 985 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 985 Classifications: {'peptide': 119} Link IDs: {'PTRANS': 12, 'TRANS': 106} Chain: "e" Number of atoms: 870 Number of conformers: 1 Conformer: "" Number of residues, atoms: 104, 870 Classifications: {'peptide': 104} Link IDs: {'PTRANS': 5, 'TRANS': 98} Chain: "f" Number of atoms: 433 Number of conformers: 1 Conformer: "" Number of residues, atoms: 51, 433 Classifications: {'peptide': 51} Link IDs: {'PTRANS': 2, 'TRANS': 48} Chain: "g" Number of atoms: 858 Number of conformers: 1 Conformer: "" Number of residues, atoms: 102, 858 Classifications: {'peptide': 102} Link IDs: {'PTRANS': 9, 'TRANS': 92} Chain: "h" Number of atoms: 1153 Number of conformers: 1 Conformer: "" Number of residues, atoms: 137, 1153 Classifications: {'peptide': 137} Link IDs: {'PTRANS': 11, 'TRANS': 125} Chain: "i" Number of atoms: 802 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 802 Classifications: {'peptide': 95} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 83} Chain breaks: 1 Chain: "j" Number of atoms: 537 Number of conformers: 1 Conformer: "" Number of residues, atoms: 62, 537 Classifications: {'peptide': 62} Link IDs: {'PTRANS': 6, 'TRANS': 55} Chain: "k" Number of atoms: 626 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 626 Classifications: {'peptide': 77} Link IDs: {'PTRANS': 4, 'TRANS': 72} Chain: "l" Number of atoms: 1312 Number of conformers: 1 Conformer: "" Number of residues, atoms: 156, 1312 Classifications: {'peptide': 156} Link IDs: {'PTRANS': 18, 'TRANS': 137} Chain: "m" Number of atoms: 1044 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 1044 Classifications: {'peptide': 125} Link IDs: {'PTRANS': 11, 'TRANS': 113} Chain: "n" Number of atoms: 1527 Number of conformers: 1 Conformer: "" Number of residues, atoms: 176, 1527 Classifications: {'peptide': 176} Link IDs: {'PTRANS': 15, 'TRANS': 160} Chain: "o" Number of atoms: 984 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 984 Classifications: {'peptide': 114} Link IDs: {'PTRANS': 7, 'TRANS': 106} Chain: "p" Number of atoms: 1424 Number of conformers: 1 Conformer: "" Number of residues, atoms: 168, 1424 Classifications: {'peptide': 168} Link IDs: {'PTRANS': 10, 'TRANS': 157} Chain: "q" Number of atoms: 1192 Number of conformers: 1 Conformer: "" Number of residues, atoms: 143, 1192 Classifications: {'peptide': 143} Link IDs: {'PTRANS': 11, 'TRANS': 131} Chain: "r" Number of atoms: 776 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 776 Classifications: {'peptide': 96} Link IDs: {'PTRANS': 11, 'TRANS': 84} 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: 329 Number of conformers: 1 Conformer: "" Number of residues, atoms: 39, 329 Classifications: {'peptide': 39} Link IDs: {'PTRANS': 3, 'TRANS': 35} Chain: "B" Number of atoms: 34 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 34 Unusual residues: {'PC1': 1, 'SF4': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 28 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen dihedrals: 28 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: 20 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 20 Unusual residues: {'FES': 1, 'SF4': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "H" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 42 Unusual residues: {'3PE': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 9 Chain: "I" Number of atoms: 16 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 16 Unusual residues: {'SF4': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "J" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 38 Unusual residues: {'3PE': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 13 Chain: "L" Number of atoms: 99 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 99 Unusual residues: {'3PE': 1, 'CDL': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 52 Unresolved non-hydrogen angles: 52 Unresolved non-hydrogen dihedrals: 52 Chain: "M" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 38 Unusual residues: {'3PE': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 13 Chain: "O" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Chain: "P" Number of atoms: 48 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 48 Unusual residues: {'NDP': 1} Classifications: {'undetermined': 1} Chain: "R" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "T" Number of atoms: 37 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 37 Unusual residues: {'EHZ': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 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 Unresolved non-hydrogen dihedrals: 1 Chain: "d" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 50 Unusual residues: {'CDL': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 50 Unresolved non-hydrogen angles: 50 Unresolved non-hydrogen dihedrals: 50 List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 1510 SG CYS B 129 97.839 92.118 203.299 1.00 35.88 S ATOM 1013 SG CYS B 65 92.272 94.690 205.581 1.00 36.30 S ATOM 1007 SG CYS B 64 92.376 89.140 202.310 1.00 37.38 S ATOM 1740 SG CYS B 159 95.436 89.369 207.984 1.00 35.63 S ATOM 7894 SG CYS E 103 114.083 43.466 259.945 1.00 61.59 S ATOM 7928 SG CYS E 108 113.029 41.107 262.048 1.00 64.93 S ATOM 8212 SG CYS E 144 115.424 41.244 256.238 1.00 58.68 S ATOM 8235 SG CYS E 148 116.235 37.926 257.375 1.00 67.90 S ATOM 11427 SG CYS F 362 121.572 49.631 236.136 1.00 38.75 S ATOM 11447 SG CYS F 365 117.406 49.581 240.666 1.00 39.67 S ATOM 11769 SG CYS F 405 121.157 44.619 240.443 1.00 43.52 S ATOM 11408 SG CYS F 359 123.696 50.842 241.514 1.00 42.15 S ATOM 12851 SG CYS G 114 116.558 68.152 226.234 1.00 34.51 S ATOM 12790 SG CYS G 105 111.301 70.873 228.751 1.00 34.35 S ATOM 12811 SG CYS G 108 117.264 73.344 229.701 1.00 35.01 S ATOM 13183 SG CYS G 156 125.764 62.238 231.446 1.00 35.60 S ATOM 13160 SG CYS G 153 123.087 64.228 236.976 1.00 35.83 S ATOM 13207 SG CYS G 159 129.082 65.347 235.750 1.00 37.14 S ATOM 13536 SG CYS G 203 124.420 68.249 231.934 1.00 35.83 S ATOM 12297 SG CYS G 41 125.890 55.201 229.012 1.00 35.05 S ATOM 12383 SG CYS G 52 121.764 55.476 228.121 1.00 34.97 S ATOM 12408 SG CYS G 55 123.193 51.220 225.064 1.00 35.08 S ATOM 12509 SG CYS G 69 126.413 51.586 226.543 1.00 37.59 S ATOM 20702 SG CYS I 121 98.460 83.987 215.140 1.00 34.97 S ATOM 20676 SG CYS I 118 99.090 90.578 215.625 1.00 35.11 S ATOM 20723 SG CYS I 124 100.267 86.278 220.300 1.00 35.87 S ATOM 20450 SG CYS I 89 104.232 87.065 214.885 1.00 39.36 S ATOM 20752 SG CYS I 128 102.935 83.539 227.420 1.00 34.52 S ATOM 20422 SG CYS I 85 106.737 85.670 222.203 1.00 36.62 S ATOM 20380 SG CYS I 79 108.271 87.324 228.090 1.00 33.74 S ATOM 20399 SG CYS I 82 107.878 80.946 225.917 1.00 34.74 S ATOM 40680 SG CYS R 59 105.034 78.401 243.250 1.00 37.71 S ATOM 40856 SG CYS R 84 107.998 79.024 240.902 1.00 38.24 S ATOM 40878 SG CYS R 87 106.229 81.730 241.877 1.00 36.35 S Time building chain proxies: 25.72, per 1000 atoms: 0.39 Number of scatterers: 65323 At special positions: 0 Unit cell: (189.72, 190.774, 293.012, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 1 29.99 Fe 28 26.01 S 489 16.00 P 18 15.00 O 11719 8.00 N 10948 7.00 C 42120 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=5, symmetry=0 Simple disulfide: pdb=" SG CYS Y 19 " - pdb=" SG CYS Y 76 " distance=2.03 Simple disulfide: pdb=" SG CYS Y 96 " - pdb=" SG CYS Y 116 " distance=2.03 Simple disulfide: pdb=" SG CYS e 32 " - pdb=" SG CYS e 65 " distance=2.03 Simple disulfide: pdb=" SG CYS e 42 " - pdb=" SG CYS e 55 " distance=2.04 Simple disulfide: pdb=" SG CYS p 76 " - pdb=" SG CYS p 83 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=4, symmetry=0 Number of additional bonds: simple=4, symmetry=0 Coordination: Other bonds: Time building additional restraints: 21.57 Conformation dependent library (CDL) restraints added in 8.9 seconds Dynamic metal coordination Iron sulfur cluster coordination pdb=" FES E 301 " pdb="FE1 FES E 301 " - pdb=" SG CYS E 108 " pdb="FE1 FES E 301 " - pdb=" SG CYS E 103 " 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="FE2 FES G 803 " - pdb=" SG CYS G 69 " pdb="FE1 FES G 803 " - pdb=" SG CYS G 52 " pdb="FE2 FES G 803 " - pdb=" SG CYS G 55 " pdb="FE1 FES G 803 " - pdb=" SG CYS G 41 " pdb=" SF4 B 201 " pdb="FE1 SF4 B 201 " - pdb=" SG CYS B 129 " pdb="FE4 SF4 B 201 " - pdb=" SG CYS B 159 " pdb="FE3 SF4 B 201 " - pdb=" SG CYS B 64 " pdb="FE2 SF4 B 201 " - pdb=" SG CYS B 65 " pdb=" SF4 F 502 " pdb="FE1 SF4 F 502 " - pdb=" SG CYS F 362 " 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=" SF4 G 801 " pdb="FE3 SF4 G 801 " - pdb=" NE2 HIS G 101 " pdb="FE1 SF4 G 801 " - pdb=" SG CYS G 114 " pdb="FE4 SF4 G 801 " - pdb=" SG CYS G 108 " pdb="FE2 SF4 G 801 " - pdb=" SG CYS G 105 " pdb=" SF4 G 802 " pdb="FE2 SF4 G 802 " - pdb=" SG CYS G 153 " pdb="FE1 SF4 G 802 " - pdb=" SG CYS G 156 " pdb="FE4 SF4 G 802 " - pdb=" SG CYS G 203 " pdb="FE3 SF4 G 802 " - pdb=" SG CYS G 159 " pdb=" SF4 I 201 " pdb="FE2 SF4 I 201 " - pdb=" SG CYS I 118 " pdb="FE3 SF4 I 201 " - pdb=" SG CYS I 124 " pdb="FE4 SF4 I 201 " - pdb=" SG CYS I 89 " pdb="FE1 SF4 I 201 " - pdb=" SG CYS I 121 " pdb=" SF4 I 202 " pdb="FE4 SF4 I 202 " - pdb=" SG CYS I 82 " pdb="FE1 SF4 I 202 " - pdb=" SG CYS I 128 " pdb="FE3 SF4 I 202 " - pdb=" SG CYS I 79 " pdb="FE2 SF4 I 202 " - pdb=" SG CYS I 85 " 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 87 " pdb="ZN ZN R 201 " - pdb=" SG CYS R 84 " pdb="ZN ZN R 201 " - pdb=" SG CYS R 59 " Number of angles added : 3 15880 Ramachandran restraints generated. 7940 Oldfield, 0 Emsley, 7940 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 15182 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 317 helices and 26 sheets defined 50.6% alpha, 3.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 8.61 Creating SS restraints... Processing helix chain 'A' and resid 3 through 23 Processing helix chain 'A' and resid 53 through 78 removed outlier: 3.969A pdb=" N GLU A 68 " --> pdb=" O LEU A 64 " (cutoff:3.500A) Proline residue: A 74 - end of helix removed outlier: 5.774A pdb=" N TRP A 77 " --> pdb=" O LEU A 73 " (cutoff:3.500A) Processing helix chain 'A' and resid 84 through 107 removed outlier: 4.092A pdb=" N ILE A 89 " --> pdb=" O SER A 85 " (cutoff:3.500A) Processing helix chain 'B' and resid 37 through 53 Processing helix chain 'B' and resid 67 through 73 Processing helix chain 'B' and resid 79 through 82 Processing helix chain 'B' and resid 90 through 92 No H-bonds generated for 'chain 'B' and resid 90 through 92' Processing helix chain 'B' and resid 107 through 116 Processing helix chain 'B' and resid 128 through 131 No H-bonds generated for 'chain 'B' and resid 128 through 131' Processing helix chain 'B' and resid 134 through 136 No H-bonds generated for 'chain 'B' and resid 134 through 136' Processing helix chain 'B' and resid 146 through 149 No H-bonds generated for 'chain 'B' and resid 146 through 149' Processing helix chain 'B' and resid 163 through 178 Processing helix chain 'B' and resid 182 through 187 Processing helix chain 'C' and resid 17 through 32 removed outlier: 3.883A pdb=" N SER C 23 " --> pdb=" O HIS C 19 " (cutoff:3.500A) Processing helix chain 'C' and resid 54 through 66 removed outlier: 3.859A pdb=" N VAL C 57 " --> pdb=" O PRO C 54 " (cutoff:3.500A) removed outlier: 6.348A pdb=" N ILE C 58 " --> pdb=" O ASP C 55 " (cutoff:3.500A) Proline residue: C 59 - end of helix Processing helix chain 'C' and resid 125 through 137 removed outlier: 4.646A pdb=" N GLU C 131 " --> pdb=" O ASN C 128 " (cutoff:3.500A) Processing helix chain 'D' and resid 8 through 13 removed outlier: 4.385A pdb=" N GLN D 13 " --> pdb=" O GLU D 9 " (cutoff:3.500A) Processing helix chain 'D' and resid 87 through 93 removed outlier: 4.740A pdb=" N GLU D 92 " --> pdb=" O GLU D 88 " (cutoff:3.500A) removed outlier: 4.825A pdb=" N TYR D 93 " --> pdb=" O LYS D 89 " (cutoff:3.500A) Processing helix chain 'D' and resid 100 through 105 Processing helix chain 'D' and resid 112 through 126 removed outlier: 3.930A pdb=" N ALA D 117 " --> pdb=" O CYS D 113 " (cutoff:3.500A) Processing helix chain 'D' and resid 132 through 161 Processing helix chain 'D' and resid 165 through 184 removed outlier: 4.167A pdb=" N GLU D 172 " --> pdb=" O PHE D 168 " (cutoff:3.500A) removed outlier: 4.339A pdb=" N GLU D 173 " --> pdb=" O TRP D 169 " (cutoff:3.500A) Processing helix chain 'D' and resid 208 through 229 removed outlier: 4.243A pdb=" N ASN D 217 " --> pdb=" O GLU D 213 " (cutoff:3.500A) removed outlier: 4.313A pdb=" N SER D 219 " --> pdb=" O SER D 215 " (cutoff:3.500A) removed outlier: 5.467A pdb=" N LEU D 220 " --> pdb=" O LYS D 216 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N MET D 228 " --> pdb=" O GLU D 224 " (cutoff:3.500A) Processing helix chain 'D' and resid 233 through 239 Processing helix chain 'D' and resid 247 through 253 Processing helix chain 'D' and resid 257 through 261 Processing helix chain 'D' and resid 277 through 279 No H-bonds generated for 'chain 'D' and resid 277 through 279' Processing helix chain 'D' and resid 293 through 317 removed outlier: 3.660A pdb=" N LEU D 308 " --> pdb=" O MET D 304 " (cutoff:3.500A) removed outlier: 4.180A pdb=" N GLN D 313 " --> pdb=" O ARG D 309 " (cutoff:3.500A) Processing helix chain 'D' and resid 335 through 340 Processing helix chain 'D' and resid 343 through 353 Processing helix chain 'D' and resid 394 through 405 removed outlier: 4.585A pdb=" N ASP D 403 " --> pdb=" O ALA D 400 " (cutoff:3.500A) Processing helix chain 'D' and resid 411 through 421 removed outlier: 3.721A pdb=" N VAL D 414 " --> pdb=" O LEU D 411 " (cutoff:3.500A) removed outlier: 4.778A pdb=" N VAL D 415 " --> pdb=" O ALA D 412 " (cutoff:3.500A) Processing helix chain 'D' and resid 426 through 429 No H-bonds generated for 'chain 'D' and resid 426 through 429' Processing helix chain 'E' and resid 25 through 37 removed outlier: 3.779A pdb=" N ASN E 37 " --> pdb=" O ALA E 33 " (cutoff:3.500A) Processing helix chain 'E' and resid 45 through 57 removed outlier: 3.759A pdb=" N LEU E 48 " --> pdb=" O ALA E 45 " (cutoff:3.500A) Proline residue: E 49 - end of helix Processing helix chain 'E' and resid 63 through 73 Processing helix chain 'E' and resid 77 through 86 removed outlier: 4.742A pdb=" N GLU E 82 " --> pdb=" O ARG E 79 " (cutoff:3.500A) Processing helix chain 'E' and resid 106 through 110 Processing helix chain 'E' and resid 113 through 124 Processing helix chain 'E' and resid 166 through 177 Processing helix chain 'F' and resid 33 through 39 Processing helix chain 'F' and resid 45 through 51 Processing helix chain 'F' and resid 53 through 63 Processing helix chain 'F' and resid 75 through 80 Processing helix chain 'F' and resid 107 through 113 Processing helix chain 'F' and resid 115 through 128 Processing helix chain 'F' and resid 143 through 159 Processing helix chain 'F' and resid 185 through 187 No H-bonds generated for 'chain 'F' and resid 185 through 187' Processing helix chain 'F' and resid 191 through 197 Processing helix chain 'F' and resid 215 through 217 No H-bonds generated for 'chain 'F' and resid 215 through 217' Processing helix chain 'F' and resid 225 through 237 Proline residue: F 232 - end of helix Processing helix chain 'F' and resid 240 through 245 removed outlier: 3.688A pdb=" N PHE F 245 " --> pdb=" O TRP F 241 " (cutoff:3.500A) 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 301 through 303 No H-bonds generated for 'chain 'F' and resid 301 through 303' Processing helix chain 'F' and resid 309 through 312 No H-bonds generated for 'chain 'F' and resid 309 through 312' Processing helix chain 'F' and resid 319 through 322 No H-bonds generated for 'chain 'F' and resid 319 through 322' Processing helix chain 'F' and resid 343 through 356 removed outlier: 3.753A pdb=" N TYR F 354 " --> pdb=" O LEU F 350 " (cutoff:3.500A) Processing helix chain 'F' and resid 363 through 381 removed outlier: 4.736A pdb=" N ASP F 370 " --> pdb=" O ARG F 366 " (cutoff:3.500A) removed outlier: 4.275A pdb=" N TRP F 371 " --> pdb=" O GLU F 367 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N LYS F 381 " --> pdb=" O ALA F 377 " (cutoff:3.500A) Processing helix chain 'F' and resid 386 through 399 Processing helix chain 'F' and resid 407 through 421 Proline residue: F 414 - end of helix Processing helix chain 'F' and resid 423 through 436 Processing helix chain 'G' and resid 13 through 15 No H-bonds generated for 'chain 'G' and resid 13 through 15' Processing helix chain 'G' and resid 26 through 33 Processing helix chain 'G' and resid 84 through 99 Processing helix chain 'G' and resid 115 through 122 Processing helix chain 'G' and resid 158 through 165 Processing helix chain 'G' and resid 199 through 202 No H-bonds generated for 'chain 'G' and resid 199 through 202' Processing helix chain 'G' and resid 265 through 269 Processing helix chain 'G' and resid 296 through 307 Processing helix chain 'G' and resid 325 through 337 Processing helix chain 'G' and resid 368 through 372 Processing helix chain 'G' and resid 389 through 401 Processing helix chain 'G' and resid 426 through 434 Processing helix chain 'G' and resid 438 through 445 Processing helix chain 'G' and resid 455 through 458 No H-bonds generated for 'chain 'G' and resid 455 through 458' Processing helix chain 'G' and resid 463 through 480 Processing helix chain 'G' and resid 498 through 505 Processing helix chain 'G' and resid 512 through 516 Processing helix chain 'G' and resid 596 through 607 Processing helix chain 'G' and resid 616 through 626 Processing helix chain 'G' and resid 628 through 630 No H-bonds generated for 'chain 'G' and resid 628 through 630' Processing helix chain 'G' and resid 642 through 651 removed outlier: 3.712A pdb=" N LEU G 651 " --> pdb=" O GLU G 647 " (cutoff:3.500A) Processing helix chain 'G' and resid 668 through 671 Processing helix chain 'G' and resid 676 through 680 Processing helix chain 'G' and resid 684 through 691 Processing helix chain 'H' and resid 3 through 31 Proline residue: H 12 - end of helix Processing helix chain 'H' and resid 42 through 44 No H-bonds generated for 'chain 'H' and resid 42 through 44' Processing helix chain 'H' and resid 47 through 57 Processing helix chain 'H' and resid 68 through 86 Proline residue: H 75 - end of helix removed outlier: 4.229A pdb=" N TRP H 86 " --> pdb=" O ALA H 82 " (cutoff:3.500A) Processing helix chain 'H' and resid 101 through 122 removed outlier: 4.746A pdb=" N SER H 112 " --> pdb=" O THR H 108 " (cutoff:3.500A) removed outlier: 5.234A pdb=" N VAL H 113 " --> pdb=" O SER H 109 " (cutoff:3.500A) removed outlier: 4.885A pdb=" N TYR H 114 " --> pdb=" O SER H 110 " (cutoff:3.500A) removed outlier: 4.318A pdb=" N SER H 115 " --> pdb=" O LEU H 111 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N GLY H 120 " --> pdb=" O ILE H 116 " (cutoff:3.500A) Processing helix chain 'H' and resid 126 through 156 removed outlier: 3.653A pdb=" N GLY H 131 " --> pdb=" O TYR H 127 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N THR H 145 " --> pdb=" O SER H 141 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N LEU H 150 " --> pdb=" O MET H 146 " (cutoff:3.500A) removed outlier: 4.704A pdb=" N LEU H 155 " --> pdb=" O LEU H 151 " (cutoff:3.500A) removed outlier: 5.464A pdb=" N MET H 156 " --> pdb=" O SER H 152 " (cutoff:3.500A) Processing helix chain 'H' and resid 164 through 169 Processing helix chain 'H' and resid 179 through 192 removed outlier: 4.408A pdb=" N MET H 184 " --> pdb=" O PRO H 180 " (cutoff:3.500A) removed outlier: 4.610A pdb=" N ILE H 187 " --> pdb=" O MET H 183 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N THR H 189 " --> pdb=" O TRP H 185 " (cutoff:3.500A) removed outlier: 5.066A pdb=" N LEU H 190 " --> pdb=" O PHE H 186 " (cutoff:3.500A) Processing helix chain 'H' and resid 199 through 202 Processing helix chain 'H' and resid 217 through 241 Processing helix chain 'H' and resid 249 through 276 Proline residue: H 252 - end of helix removed outlier: 4.021A pdb=" N PHE H 270 " --> pdb=" O SER H 267 " (cutoff:3.500A) Processing helix chain 'H' and resid 282 through 307 removed outlier: 4.885A pdb=" N LEU H 294 " --> pdb=" O TRP H 290 " (cutoff:3.500A) Proline residue: H 295 - end of helix Processing helix chain 'I' and resid 16 through 27 Processing helix chain 'I' and resid 30 through 44 Processing helix chain 'I' and resid 84 through 88 Processing helix chain 'I' and resid 123 through 127 Processing helix chain 'I' and resid 153 through 177 removed outlier: 6.097A pdb=" N ALA I 165 " --> pdb=" O ASP I 161 " (cutoff:3.500A) removed outlier: 5.987A pdb=" N GLU I 166 " --> pdb=" O LYS I 162 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N ALA I 168 " --> pdb=" O GLU I 164 " (cutoff:3.500A) removed outlier: 5.244A pdb=" N ALA I 169 " --> pdb=" O ALA I 165 " (cutoff:3.500A) removed outlier: 5.603A pdb=" N LEU I 176 " --> pdb=" O GLN I 172 " (cutoff:3.500A) removed outlier: 5.201A pdb=" N TYR I 177 " --> pdb=" O ALA I 173 " (cutoff:3.500A) Processing helix chain 'J' and resid 4 through 20 Processing helix chain 'J' and resid 25 through 46 removed outlier: 4.064A pdb=" N LEU J 30 " --> pdb=" O ILE J 26 " (cutoff:3.500A) removed outlier: 4.422A pdb=" N GLY J 31 " --> pdb=" O TYR J 27 " (cutoff:3.500A) Processing helix chain 'J' and resid 49 through 74 removed outlier: 4.225A pdb=" N LEU J 60 " --> pdb=" O PHE J 56 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N GLY J 61 " --> pdb=" O LEU J 57 " (cutoff:3.500A) removed outlier: 4.815A pdb=" N VAL J 65 " --> pdb=" O GLY J 61 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N VAL J 66 " --> pdb=" O GLY J 62 " (cutoff:3.500A) Processing helix chain 'J' and resid 84 through 109 removed outlier: 3.798A pdb=" N GLY J 90 " --> pdb=" O TRP J 86 " (cutoff:3.500A) removed outlier: 4.470A pdb=" N TYR J 108 " --> pdb=" O CYS J 104 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N TYR J 109 " --> pdb=" O VAL J 105 " (cutoff:3.500A) Processing helix chain 'J' and resid 137 through 145 removed outlier: 4.564A pdb=" N MET J 144 " --> pdb=" O GLY J 140 " (cutoff:3.500A) removed outlier: 5.459A pdb=" N TYR J 145 " --> pdb=" O VAL J 141 " (cutoff:3.500A) Processing helix chain 'J' and resid 149 through 170 removed outlier: 4.325A pdb=" N PHE J 164 " --> pdb=" O PHE J 160 " (cutoff:3.500A) Processing helix chain 'K' and resid 3 through 20 Processing helix chain 'K' and resid 27 through 51 Processing helix chain 'K' and resid 57 through 85 Proline residue: K 60 - end of helix removed outlier: 3.662A pdb=" N TYR K 85 " --> pdb=" O SER K 82 " (cutoff:3.500A) Processing helix chain 'L' and resid 3 through 23 removed outlier: 4.215A pdb=" N PHE L 12 " --> pdb=" O ILE L 8 " (cutoff:3.500A) Proline residue: L 18 - end of helix Processing helix chain 'L' and resid 27 through 29 No H-bonds generated for 'chain 'L' and resid 27 through 29' Processing helix chain 'L' and resid 32 through 57 removed outlier: 4.050A pdb=" N LEU L 49 " --> pdb=" O ILE L 45 " (cutoff:3.500A) Proline residue: L 50 - end of helix Processing helix chain 'L' and resid 84 through 107 removed outlier: 4.177A pdb=" N SER L 91 " --> pdb=" O ILE L 87 " (cutoff:3.500A) removed outlier: 4.140A pdb=" N SER L 99 " --> pdb=" O PHE L 95 " (cutoff:3.500A) Processing helix chain 'L' and resid 114 through 133 Processing helix chain 'L' and resid 137 through 154 Processing helix chain 'L' and resid 162 through 192 removed outlier: 3.579A pdb=" N THR L 166 " --> pdb=" O THR L 162 " (cutoff:3.500A) removed outlier: 4.261A pdb=" N GLY L 181 " --> pdb=" O ILE L 177 " (cutoff:3.500A) Processing helix chain 'L' and resid 198 through 204 removed outlier: 4.428A pdb=" N PHE L 203 " --> pdb=" O GLN L 199 " (cutoff:3.500A) removed outlier: 5.362A pdb=" N SER L 204 " --> pdb=" O GLN L 200 " (cutoff:3.500A) Processing helix chain 'L' and resid 211 through 223 Processing helix chain 'L' and resid 232 through 238 removed outlier: 3.704A pdb=" N ALA L 236 " --> pdb=" O TRP L 232 " (cutoff:3.500A) removed outlier: 4.134A pdb=" N MET L 237 " --> pdb=" O LEU L 233 " (cutoff:3.500A) removed outlier: 4.709A pdb=" N GLU L 238 " --> pdb=" O PRO L 234 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 232 through 238' Processing helix chain 'L' and resid 241 through 249 removed outlier: 3.885A pdb=" N HIS L 248 " --> pdb=" O SER L 244 " (cutoff:3.500A) Processing helix chain 'L' and resid 254 through 262 Processing helix chain 'L' and resid 264 through 266 No H-bonds generated for 'chain 'L' and resid 264 through 266' Processing helix chain 'L' and resid 273 through 276 No H-bonds generated for 'chain 'L' and resid 273 through 276' Processing helix chain 'L' and resid 281 through 287 removed outlier: 3.726A pdb=" N LEU L 286 " --> pdb=" O ALA L 282 " (cutoff:3.500A) Processing helix chain 'L' and resid 290 through 292 No H-bonds generated for 'chain 'L' and resid 290 through 292' Processing helix chain 'L' and resid 298 through 318 Processing helix chain 'L' and resid 322 through 349 removed outlier: 3.827A pdb=" N PHE L 334 " --> pdb=" O CYS L 330 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N PHE L 335 " --> pdb=" O THR L 331 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N PHE L 340 " --> pdb=" O LYS L 336 " (cutoff:3.500A) Processing helix chain 'L' and resid 356 through 358 No H-bonds generated for 'chain 'L' and resid 356 through 358' Processing helix chain 'L' and resid 362 through 365 No H-bonds generated for 'chain 'L' and resid 362 through 365' Processing helix chain 'L' and resid 367 through 381 Processing helix chain 'L' and resid 389 through 401 removed outlier: 5.375A pdb=" N LEU L 394 " --> pdb=" O TYR L 390 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N ASN L 400 " --> pdb=" O ILE L 396 " (cutoff:3.500A) Processing helix chain 'L' and resid 406 through 431 removed outlier: 4.073A pdb=" N ALA L 420 " --> pdb=" O THR L 416 " (cutoff:3.500A) Processing helix chain 'L' and resid 448 through 471 Proline residue: L 453 - end of helix removed outlier: 5.374A pdb=" N GLY L 465 " --> pdb=" O SER L 461 " (cutoff:3.500A) removed outlier: 5.060A pdb=" N PHE L 466 " --> pdb=" O ILE 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 507 Processing helix chain 'L' and resid 518 through 524 Processing helix chain 'L' and resid 529 through 547 removed outlier: 4.322A pdb=" N ARG L 535 " --> pdb=" O SER L 531 " (cutoff:3.500A) Proline residue: L 538 - end of helix 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 577 Processing helix chain 'L' and resid 584 through 605 removed outlier: 4.003A pdb=" N MET L 589 " --> pdb=" O LYS L 585 " (cutoff:3.500A) Processing helix chain 'M' and resid 5 through 17 removed outlier: 4.547A pdb=" N LEU M 12 " --> pdb=" O SER M 8 " (cutoff:3.500A) Proline residue: M 13 - end of helix Processing helix chain 'M' and resid 20 through 42 removed outlier: 4.635A pdb=" N TRP M 24 " --> pdb=" O PRO M 20 " (cutoff:3.500A) removed outlier: 5.849A pdb=" N THR M 25 " --> pdb=" O LYS M 21 " (cutoff:3.500A) removed outlier: 4.130A pdb=" N LEU M 39 " --> pdb=" O SER M 35 " (cutoff:3.500A) removed outlier: 4.925A pdb=" N THR M 40 " --> pdb=" O LEU M 36 " (cutoff:3.500A) removed outlier: 5.463A pdb=" N LEU M 41 " --> pdb=" O THR M 37 " (cutoff:3.500A) removed outlier: 5.604A pdb=" N LEU M 42 " --> pdb=" O SER M 38 " (cutoff:3.500A) Processing helix chain 'M' and resid 60 through 80 Proline residue: M 64 - end of helix Proline residue: M 74 - end of helix Processing helix chain 'M' and resid 89 through 111 Processing helix chain 'M' and resid 115 through 135 removed outlier: 4.877A pdb=" N LEU M 126 " --> pdb=" O PHE M 122 " (cutoff:3.500A) removed outlier: 4.861A pdb=" N ILE M 127 " --> pdb=" O GLU M 123 " (cutoff:3.500A) Proline residue: M 128 - end of helix Processing helix chain 'M' and resid 142 through 170 Proline residue: M 159 - end of helix Processing helix chain 'M' and resid 178 through 181 No H-bonds generated for 'chain 'M' and resid 178 through 181' Processing helix chain 'M' and resid 190 through 206 removed outlier: 5.267A pdb=" N ALA M 202 " --> pdb=" O ALA M 198 " (cutoff:3.500A) removed outlier: 4.913A pdb=" N PHE M 203 " --> pdb=" O CYS M 199 " (cutoff:3.500A) Processing helix chain 'M' and resid 213 through 222 removed outlier: 3.501A pdb=" N LEU M 216 " --> pdb=" O HIS M 213 " (cutoff:3.500A) Proline residue: M 217 - end of helix Processing helix chain 'M' and resid 225 through 233 Processing helix chain 'M' and resid 237 through 246 Processing helix chain 'M' and resid 253 through 255 No H-bonds generated for 'chain 'M' and resid 253 through 255' Processing helix chain 'M' and resid 259 through 278 removed outlier: 3.796A pdb=" N LEU M 277 " --> pdb=" O SER M 273 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N ARG M 278 " --> pdb=" O SER M 274 " (cutoff:3.500A) Processing helix chain 'M' and resid 282 through 302 removed outlier: 3.739A pdb=" N LEU M 296 " --> pdb=" O SER M 292 " (cutoff:3.500A) Processing helix chain 'M' and resid 306 through 335 Processing helix chain 'M' and resid 355 through 366 removed outlier: 3.726A pdb=" N MET M 361 " --> pdb=" O THR M 357 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N ALA M 362 " --> pdb=" O TRP M 358 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N ALA M 365 " --> pdb=" O MET M 361 " (cutoff:3.500A) Processing helix chain 'M' and resid 373 through 388 Processing helix chain 'M' and resid 393 through 412 removed outlier: 4.063A pdb=" N MET M 408 " --> pdb=" O GLY M 404 " (cutoff:3.500A) Processing helix chain 'M' and resid 431 through 449 Proline residue: M 443 - end of helix Processing helix chain 'M' and resid 452 through 454 No H-bonds generated for 'chain 'M' and resid 452 through 454' Processing helix chain 'N' and resid 3 through 22 Proline residue: N 17 - end of helix Processing helix chain 'N' and resid 26 through 45 Proline residue: N 42 - end of helix Processing helix chain 'N' and resid 50 through 80 Processing helix chain 'N' and resid 92 through 106 Processing helix chain 'N' and resid 115 through 121 Processing helix chain 'N' and resid 124 through 132 removed outlier: 4.593A pdb=" N ILE N 129 " --> pdb=" O HIS N 125 " (cutoff:3.500A) Processing helix chain 'N' and resid 137 through 144 removed outlier: 3.776A pdb=" N LEU N 142 " --> pdb=" O PRO N 138 " (cutoff:3.500A) Processing helix chain 'N' and resid 151 through 169 Processing helix chain 'N' and resid 175 through 194 Processing helix chain 'N' and resid 198 through 222 Proline residue: N 214 - end of helix removed outlier: 4.141A pdb=" N ASN N 222 " --> pdb=" O ALA N 218 " (cutoff:3.500A) Processing helix chain 'N' and resid 227 through 236 removed outlier: 4.820A pdb=" N LEU N 232 " --> pdb=" O ASN N 228 " (cutoff:3.500A) removed outlier: 5.193A pdb=" N LEU N 233 " --> pdb=" O SER N 229 " (cutoff:3.500A) removed outlier: 5.058A pdb=" N TRP N 234 " --> pdb=" O ILE N 230 " (cutoff:3.500A) removed outlier: 5.401A pdb=" N ASN N 235 " --> pdb=" O SER N 231 " (cutoff:3.500A) Processing helix chain 'N' and resid 240 through 252 removed outlier: 5.072A pdb=" N SER N 245 " --> pdb=" O THR N 242 " (cutoff:3.500A) Processing helix chain 'N' and resid 259 through 272 removed outlier: 4.457A pdb=" N LYS N 263 " --> pdb=" O GLY N 259 " (cutoff:3.500A) Processing helix chain 'N' and resid 276 through 285 Processing helix chain 'N' and resid 287 through 300 removed outlier: 4.212A pdb=" N LEU N 296 " --> pdb=" O PHE N 292 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N SER N 299 " --> pdb=" O ARG N 295 " (cutoff:3.500A) Processing helix chain 'N' and resid 309 through 315 Processing helix chain 'N' and resid 324 through 334 Processing helix chain 'N' and resid 337 through 339 No H-bonds generated for 'chain 'N' and resid 337 through 339' Processing helix chain 'O' and resid 5 through 10 Processing helix chain 'O' and resid 35 through 46 Processing helix chain 'O' and resid 58 through 62 Processing helix chain 'O' and resid 79 through 84 Processing helix chain 'O' and resid 92 through 117 removed outlier: 4.419A pdb=" N TRP O 99 " --> pdb=" O ARG O 95 " (cutoff:3.500A) Processing helix chain 'O' and resid 133 through 141 Processing helix chain 'O' and resid 146 through 162 Proline residue: O 161 - end of helix Processing helix chain 'O' and resid 176 through 186 Processing helix chain 'O' and resid 191 through 193 No H-bonds generated for 'chain 'O' and resid 191 through 193' Processing helix chain 'O' and resid 196 through 215 removed outlier: 5.249A pdb=" N LEU O 211 " --> pdb=" O LYS O 207 " (cutoff:3.500A) Proline residue: O 212 - end of helix Processing helix chain 'O' and resid 225 through 229 Processing helix chain 'O' and resid 231 through 240 Processing helix chain 'O' and resid 247 through 249 No H-bonds generated for 'chain 'O' and resid 247 through 249' Processing helix chain 'O' and resid 253 through 264 Processing helix chain 'O' and resid 286 through 298 Processing helix chain 'O' and resid 306 through 308 No H-bonds generated for 'chain 'O' and resid 306 through 308' Processing helix chain 'P' and resid 31 through 41 removed outlier: 4.199A pdb=" N ASN P 36 " --> pdb=" O ARG P 32 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N MET P 41 " --> pdb=" O HIS P 37 " (cutoff:3.500A) Processing helix chain 'P' and resid 53 through 59 removed outlier: 5.037A pdb=" N HIS P 58 " --> pdb=" O TYR P 54 " (cutoff:3.500A) removed outlier: 6.285A pdb=" N LEU P 59 " --> pdb=" O ASP P 55 " (cutoff:3.500A) Processing helix chain 'P' and resid 82 through 85 No H-bonds generated for 'chain 'P' and resid 82 through 85' Processing helix chain 'P' and resid 106 through 124 removed outlier: 3.912A pdb=" N ILE P 113 " --> pdb=" O VAL P 109 " (cutoff:3.500A) Proline residue: P 114 - end of helix Processing helix chain 'P' and resid 145 through 159 Processing helix chain 'P' and resid 179 through 182 No H-bonds generated for 'chain 'P' and resid 179 through 182' Processing helix chain 'P' and resid 207 through 219 Processing helix chain 'P' and resid 238 through 248 Processing helix chain 'P' and resid 281 through 287 Processing helix chain 'P' and resid 301 through 303 No H-bonds generated for 'chain 'P' and resid 301 through 303' Processing helix chain 'P' and resid 314 through 321 removed outlier: 5.527A pdb=" N ARG P 320 " --> pdb=" O GLU P 316 " (cutoff:3.500A) removed outlier: 5.802A pdb=" N HIS P 321 " --> pdb=" O VAL P 317 " (cutoff:3.500A) Processing helix chain 'Q' and resid 20 through 23 No H-bonds generated for 'chain 'Q' and resid 20 through 23' Processing helix chain 'Q' and resid 27 through 31 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 89 through 99 Processing helix chain 'Q' and resid 118 through 122 Processing helix chain 'R' and resid 23 through 25 No H-bonds generated for 'chain 'R' and resid 23 through 25' Processing helix chain 'R' and resid 40 through 45 Processing helix chain 'S' and resid 27 through 38 removed outlier: 4.964A pdb=" N GLY S 31 " --> pdb=" O GLY S 28 " (cutoff:3.500A) Processing helix chain 'S' and resid 40 through 46 Processing helix chain 'S' and resid 83 through 94 Processing helix chain 'T' and resid 12 through 21 Processing helix chain 'T' and resid 36 through 39 No H-bonds generated for 'chain 'T' and resid 36 through 39' Processing helix chain 'T' and resid 44 through 58 Processing helix chain 'T' and resid 64 through 69 Processing helix chain 'T' and resid 73 through 81 Processing helix chain 'U' and resid 8 through 21 Processing helix chain 'U' and resid 44 through 57 Processing helix chain 'U' and resid 64 through 67 No H-bonds generated for 'chain 'U' and resid 64 through 67' Processing helix chain 'U' and resid 73 through 84 Processing helix chain 'V' and resid 21 through 36 removed outlier: 4.485A pdb=" N HIS V 36 " --> pdb=" O ASP V 32 " (cutoff:3.500A) Processing helix chain 'V' and resid 42 through 60 removed outlier: 4.813A pdb=" N GLN V 49 " --> pdb=" O LYS V 45 " (cutoff:3.500A) Processing helix chain 'V' and resid 64 through 71 removed outlier: 4.855A pdb=" N ALA V 69 " --> pdb=" O LYS V 65 " (cutoff:3.500A) Processing helix chain 'V' and resid 76 through 95 removed outlier: 3.810A pdb=" N LYS V 95 " --> pdb=" O ARG V 91 " (cutoff:3.500A) Processing helix chain 'W' and resid 27 through 51 Proline residue: W 46 - end of helix Processing helix chain 'W' and resid 58 through 72 removed outlier: 4.435A pdb=" N ASN W 72 " --> pdb=" O MET W 68 " (cutoff:3.500A) Processing helix chain 'W' and resid 78 through 96 Processing helix chain 'W' and resid 102 through 108 removed outlier: 5.264A pdb=" N PHE W 108 " --> pdb=" O HIS W 104 " (cutoff:3.500A) Processing helix chain 'W' and resid 120 through 126 Processing helix chain 'X' and resid 21 through 33 removed outlier: 5.114A pdb=" N HIS X 29 " --> pdb=" O LYS X 25 " (cutoff:3.500A) removed outlier: 5.825A pdb=" N HIS X 30 " --> pdb=" O ALA X 26 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N ALA X 33 " --> pdb=" O HIS X 29 " (cutoff:3.500A) Processing helix chain 'X' and resid 37 through 48 Processing helix chain 'X' and resid 57 through 75 removed outlier: 4.164A pdb=" N LEU X 61 " --> pdb=" O LYS X 57 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N VAL X 62 " --> pdb=" O GLU X 58 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N GLN X 72 " --> pdb=" O ASN X 68 " (cutoff:3.500A) Processing helix chain 'X' and resid 79 through 88 Processing helix chain 'X' and resid 100 through 102 No H-bonds generated for 'chain 'X' and resid 100 through 102' Processing helix chain 'X' and resid 104 through 113 Processing helix chain 'Y' and resid 5 through 11 removed outlier: 5.566A pdb=" N TYR Y 10 " --> pdb=" O PHE Y 6 " (cutoff:3.500A) removed outlier: 5.602A pdb=" N HIS Y 11 " --> pdb=" O PHE Y 7 " (cutoff:3.500A) Processing helix chain 'Y' and resid 19 through 43 removed outlier: 3.851A pdb=" N TYR Y 24 " --> pdb=" O HIS Y 20 " (cutoff:3.500A) Processing helix chain 'Y' and resid 50 through 81 removed outlier: 3.559A pdb=" N ALA Y 79 " --> pdb=" O THR Y 75 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N GLN Y 80 " --> pdb=" O CYS Y 76 " (cutoff:3.500A) Processing helix chain 'Y' and resid 89 through 106 Processing helix chain 'Y' and resid 109 through 132 Processing helix chain 'Z' and resid 31 through 96 removed outlier: 3.814A pdb=" N GLU Z 55 " --> pdb=" O ARG Z 51 " (cutoff:3.500A) Proline residue: Z 72 - end of helix removed outlier: 4.311A pdb=" N ILE Z 95 " --> pdb=" O GLU Z 91 " (cutoff:3.500A) Processing helix chain 'Z' and resid 120 through 125 Processing helix chain 'Z' and resid 129 through 136 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 removed outlier: 4.764A pdb=" N ILE a 11 " --> pdb=" O PRO a 7 " (cutoff:3.500A) Proline residue: a 19 - end of helix Processing helix chain 'a' and resid 42 through 54 Processing helix chain 'b' and resid 3 through 14 removed outlier: 4.344A pdb=" N ALA b 13 " --> pdb=" O LYS b 9 " (cutoff:3.500A) Processing helix chain 'b' and resid 16 through 33 Proline residue: b 32 - end of helix Processing helix chain 'b' and resid 39 through 47 Processing helix chain 'b' and resid 78 through 80 No H-bonds generated for 'chain 'b' and resid 78 through 80' Processing helix chain 'c' and resid 8 through 10 No H-bonds generated for 'chain 'c' and resid 8 through 10' Processing helix chain 'c' and resid 14 through 45 Processing helix chain 'd' and resid 16 through 19 Processing helix chain 'd' and resid 29 through 48 Processing helix chain 'd' and resid 58 through 96 removed outlier: 4.318A pdb=" N PHE d 74 " --> pdb=" O PHE d 70 " (cutoff:3.500A) Processing helix chain 'd' and resid 99 through 101 No H-bonds generated for 'chain 'd' and resid 99 through 101' Processing helix chain 'e' and resid 5 through 9 Processing helix chain 'e' and resid 33 through 42 removed outlier: 3.572A pdb=" N GLU e 41 " --> pdb=" O LYS e 37 " (cutoff:3.500A) Processing helix chain 'e' and resid 48 through 54 removed outlier: 3.559A pdb=" N LYS e 52 " --> pdb=" O THR e 49 " (cutoff:3.500A) Processing helix chain 'e' and resid 56 through 67 removed outlier: 4.612A pdb=" N ASP e 61 " --> pdb=" O ILE e 57 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N PHE e 62 " --> pdb=" O GLU e 58 " (cutoff:3.500A) Processing helix chain 'e' and resid 69 through 88 Processing helix chain 'e' and resid 95 through 98 No H-bonds generated for 'chain 'e' and resid 95 through 98' Processing helix chain 'f' and resid 6 through 9 No H-bonds generated for 'chain 'f' and resid 6 through 9' Processing helix chain 'f' and resid 11 through 31 removed outlier: 4.940A pdb=" N VAL f 15 " --> pdb=" O HIS f 12 " (cutoff:3.500A) Proline residue: f 16 - end of helix Processing helix chain 'g' and resid 49 through 64 Processing helix chain 'g' and resid 67 through 76 Processing helix chain 'g' and resid 81 through 83 No H-bonds generated for 'chain 'g' and resid 81 through 83' Processing helix chain 'g' and resid 86 through 101 Processing helix chain 'h' and resid 16 through 46 removed outlier: 4.357A pdb=" N PHE h 21 " --> pdb=" O TYR h 17 " (cutoff:3.500A) removed outlier: 5.123A 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 70 through 78 Processing helix chain 'h' and resid 83 through 117 removed outlier: 4.102A pdb=" N GLU h 109 " --> pdb=" O LEU h 105 " (cutoff:3.500A) Processing helix chain 'i' and resid 5 through 25 removed outlier: 3.809A pdb=" N ARG i 20 " --> pdb=" O GLU i 16 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N LYS i 23 " --> pdb=" O ARG i 19 " (cutoff:3.500A) Processing helix chain 'i' and resid 65 through 88 removed outlier: 5.569A pdb=" N ILE i 76 " --> pdb=" O SER i 72 " (cutoff:3.500A) Proline residue: i 77 - end of helix Processing helix chain 'j' and resid 19 through 42 Processing helix chain 'j' and resid 44 through 46 No H-bonds generated for 'chain 'j' and resid 44 through 46' Processing helix chain 'k' and resid 33 through 44 Processing helix chain 'k' and resid 49 through 56 removed outlier: 3.645A pdb=" N ARG k 52 " --> pdb=" O PRO k 49 " (cutoff:3.500A) Processing helix chain 'k' and resid 68 through 72 Processing helix chain 'k' and resid 76 through 92 Processing helix chain 'l' and resid 5 through 7 No H-bonds generated for 'chain 'l' and resid 5 through 7' Processing helix chain 'l' and resid 16 through 26 removed outlier: 3.726A pdb=" N ALA l 21 " --> pdb=" O GLU l 17 " (cutoff:3.500A) Processing helix chain 'l' and resid 30 through 32 No H-bonds generated for 'chain 'l' and resid 30 through 32' Processing helix chain 'l' and resid 80 through 82 No H-bonds generated for 'chain 'l' and resid 80 through 82' Processing helix chain 'l' and resid 97 through 120 Processing helix chain 'm' and resid 26 through 50 removed outlier: 3.926A pdb=" N GLN m 49 " --> pdb=" O GLU m 45 " (cutoff:3.500A) Processing helix chain 'm' and resid 62 through 72 Processing helix chain 'm' and resid 75 through 78 No H-bonds generated for 'chain 'm' and resid 75 through 78' Processing helix chain 'm' and resid 85 through 117 Proline residue: m 96 - end of helix Processing helix chain 'n' and resid 11 through 29 Processing helix chain 'n' and resid 33 through 51 removed outlier: 3.969A pdb=" N HIS n 50 " --> pdb=" O ARG n 46 " (cutoff:3.500A) Processing helix chain 'n' and resid 56 through 72 Processing helix chain 'n' and resid 101 through 103 No H-bonds generated for 'chain 'n' and resid 101 through 103' Processing helix chain 'n' and resid 108 through 111 No H-bonds generated for 'chain 'n' and resid 108 through 111' Processing helix chain 'n' and resid 115 through 131 removed outlier: 4.343A pdb=" N GLU n 122 " --> pdb=" O PHE n 118 " (cutoff:3.500A) removed outlier: 4.796A pdb=" N GLN n 123 " --> pdb=" O SER n 119 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N LEU n 127 " --> pdb=" O GLN n 123 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N GLU n 130 " --> pdb=" O LYS n 126 " (cutoff:3.500A) removed outlier: 4.893A pdb=" N SER n 131 " --> pdb=" O LEU n 127 " (cutoff:3.500A) Processing helix chain 'n' and resid 133 through 140 removed outlier: 3.511A pdb=" N LYS n 137 " --> pdb=" O ASP n 133 " (cutoff:3.500A) removed outlier: 4.273A pdb=" N LEU n 139 " --> pdb=" O GLU n 135 " (cutoff:3.500A) Processing helix chain 'o' and resid 3 through 8 Processing helix chain 'o' and resid 18 through 23 removed outlier: 4.229A pdb=" N ILE o 21 " --> pdb=" O PRO o 18 " (cutoff:3.500A) Proline residue: o 22 - end of helix No H-bonds generated for 'chain 'o' and resid 18 through 23' Processing helix chain 'o' and resid 42 through 47 Processing helix chain 'o' and resid 59 through 70 Processing helix chain 'o' and resid 81 through 113 removed outlier: 3.526A pdb=" N ASP o 85 " --> pdb=" O HIS o 81 " (cutoff:3.500A) Processing helix chain 'p' and resid 28 through 58 removed outlier: 3.849A pdb=" N ASP p 41 " --> pdb=" O ASP p 37 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N TRP p 42 " --> pdb=" O LEU p 38 " (cutoff:3.500A) Proline residue: p 43 - end of helix Processing helix chain 'p' and resid 82 through 121 removed outlier: 4.089A pdb=" N GLN p 90 " --> pdb=" O GLU p 86 " (cutoff:3.500A) removed outlier: 5.776A pdb=" N GLU p 118 " --> pdb=" O GLN p 114 " (cutoff:3.500A) removed outlier: 7.638A pdb=" N ASN p 119 " --> pdb=" O ARG p 115 " (cutoff:3.500A) removed outlier: 4.558A pdb=" N TYR p 120 " --> pdb=" O GLU p 116 " (cutoff:3.500A) removed outlier: 5.860A pdb=" N GLN p 121 " --> pdb=" O GLY p 117 " (cutoff:3.500A) Processing helix chain 'p' and resid 126 through 142 Processing helix chain 'p' and resid 151 through 170 Processing helix chain 'q' and resid 4 through 16 Processing helix chain 'q' and resid 19 through 29 Processing helix chain 'q' and resid 84 through 90 removed outlier: 4.999A pdb=" N TRP q 89 " --> pdb=" O GLU q 85 " (cutoff:3.500A) Processing helix chain 'r' and resid 5 through 15 Processing helix chain 'r' and resid 53 through 55 No H-bonds generated for 'chain 'r' and resid 53 through 55' Processing helix chain 's' and resid 44 through 54 removed outlier: 4.360A pdb=" N LYS s 54 " --> pdb=" O LEU s 50 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'B' and resid 57 through 61 removed outlier: 7.011A pdb=" N VAL B 95 " --> pdb=" O MET B 58 " (cutoff:3.500A) removed outlier: 7.355A pdb=" N PHE B 60 " --> pdb=" O VAL B 95 " (cutoff:3.500A) removed outlier: 6.064A pdb=" N ILE B 97 " --> pdb=" O PHE B 60 " (cutoff:3.500A) removed outlier: 6.818A pdb=" N TYR B 122 " --> pdb=" O MET B 96 " (cutoff:3.500A) removed outlier: 7.725A pdb=" N VAL B 98 " --> pdb=" O TYR B 122 " (cutoff:3.500A) removed outlier: 6.452A pdb=" N VAL B 124 " --> pdb=" O VAL B 98 " (cutoff:3.500A) No H-bonds generated for sheet with id= A Processing sheet with id= B, first strand: chain 'C' and resid 77 through 82 removed outlier: 5.292A pdb=" N LEU C 48 " --> pdb=" O ARG C 104 " (cutoff:3.500A) removed outlier: 4.218A pdb=" N TYR C 110 " --> pdb=" O ILE C 52 " (cutoff:3.500A) removed outlier: 4.642A pdb=" N GLN C 39 " --> pdb=" O CYS C 51 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'C' and resid 172 through 176 Processing sheet with id= D, first strand: chain 'C' and resid 72 through 75 removed outlier: 5.936A pdb=" N LEU C 97 " --> pdb=" O LYS C 73 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'D' and resid 49 through 51 removed outlier: 5.461A pdb=" N SER D 69 " --> pdb=" O VAL D 73 " (cutoff:3.500A) removed outlier: 5.094A pdb=" N VAL D 73 " --> pdb=" O SER D 69 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'D' and resid 361 through 364 removed outlier: 3.515A pdb=" N SER D 380 " --> pdb=" O GLY D 361 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N THR D 363 " --> pdb=" O LEU D 378 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N LEU D 378 " --> pdb=" O THR D 363 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N ARG D 388 " --> pdb=" O VAL D 379 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'E' and resid 98 through 103 Processing sheet with id= H, first strand: chain 'F' and resid 219 through 223 removed outlier: 6.422A pdb=" N ALA F 133 " --> pdb=" O LEU F 93 " (cutoff:3.500A) removed outlier: 8.061A pdb=" N VAL F 95 " --> pdb=" O ALA F 133 " (cutoff:3.500A) removed outlier: 6.871A pdb=" N TYR F 135 " --> pdb=" O VAL F 95 " (cutoff:3.500A) removed outlier: 6.879A pdb=" N ASP F 174 " --> pdb=" O ALA F 134 " (cutoff:3.500A) removed outlier: 7.931A pdb=" N ILE F 136 " --> pdb=" O ASP F 174 " (cutoff:3.500A) removed outlier: 6.930A pdb=" N PHE F 176 " --> pdb=" O ILE F 136 " (cutoff:3.500A) removed outlier: 7.969A pdb=" N ILE F 138 " --> pdb=" O PHE F 176 " (cutoff:3.500A) removed outlier: 6.344A pdb=" N VAL F 178 " --> pdb=" O ILE F 138 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'F' and resid 266 through 271 Processing sheet with id= J, first strand: chain 'G' and resid 9 through 13 Processing sheet with id= K, first strand: chain 'G' and resid 146 through 148 Processing sheet with id= L, first strand: chain 'G' and resid 225 through 227 removed outlier: 3.763A pdb=" N ARG G 249 " --> pdb=" O SER G 241 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'G' and resid 282 through 285 Processing sheet with id= N, first strand: chain 'G' and resid 343 through 345 removed outlier: 8.505A pdb=" N CYS G 344 " --> pdb=" O VAL G 315 " (cutoff:3.500A) removed outlier: 6.368A pdb=" N ALA G 317 " --> pdb=" O CYS G 344 " (cutoff:3.500A) removed outlier: 6.497A pdb=" N MET G 521 " --> pdb=" O ALA G 316 " (cutoff:3.500A) removed outlier: 7.764A pdb=" N ILE G 318 " --> pdb=" O MET G 521 " (cutoff:3.500A) removed outlier: 6.616A pdb=" N PHE G 523 " --> pdb=" O ILE G 318 " (cutoff:3.500A) removed outlier: 6.750A pdb=" N PHE G 542 " --> pdb=" O LEU G 522 " (cutoff:3.500A) removed outlier: 7.733A pdb=" N LEU G 524 " --> pdb=" O PHE G 542 " (cutoff:3.500A) removed outlier: 6.040A pdb=" N VAL G 544 " --> pdb=" O LEU G 524 " (cutoff:3.500A) removed outlier: 6.851A pdb=" N VAL G 559 " --> pdb=" O TYR G 545 " (cutoff:3.500A) removed outlier: 7.774A pdb=" N GLY G 547 " --> pdb=" O VAL G 559 " (cutoff:3.500A) removed outlier: 6.127A 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 406 through 409 removed outlier: 6.310A pdb=" N VAL G 377 " --> pdb=" O ALA G 407 " (cutoff:3.500A) removed outlier: 8.186A pdb=" N ILE G 409 " --> pdb=" O VAL G 377 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N LEU G 379 " --> pdb=" O ILE G 409 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N GLY G 454 " --> pdb=" O VAL G 380 " (cutoff:3.500A) 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 95 through 100 removed outlier: 5.289A pdb=" N GLU I 99 " --> pdb=" O THR I 108 " (cutoff:3.500A) removed outlier: 4.812A pdb=" N THR I 108 " --> pdb=" O GLU I 99 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'L' and resid 61 through 64 Processing sheet with id= S, first strand: chain 'L' and resid 67 through 70 removed outlier: 6.965A pdb=" N LEU L 76 " --> pdb=" O TRP L 68 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'O' and resid 219 through 223 removed outlier: 6.963A pdb=" N VAL O 122 " --> pdb=" O ILE O 25 " (cutoff:3.500A) removed outlier: 8.405A pdb=" N VAL O 27 " --> pdb=" O VAL O 122 " (cutoff:3.500A) removed outlier: 8.101A pdb=" N LEU O 124 " --> pdb=" O VAL O 27 " (cutoff:3.500A) removed outlier: 6.661A pdb=" N LYS O 49 " --> pdb=" O VAL O 123 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'P' and resid 164 through 168 removed outlier: 6.514A pdb=" N GLN P 44 " --> pdb=" O ALA P 21 " (cutoff:3.500A) removed outlier: 7.525A pdb=" N VAL P 23 " --> pdb=" O GLN P 44 " (cutoff:3.500A) removed outlier: 6.814A pdb=" N ILE P 46 " --> pdb=" O VAL P 23 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'Q' and resid 102 through 105 Processing sheet with id= W, first strand: chain 'R' and resid 50 through 52 Processing sheet with id= X, first strand: chain 'R' and resid 57 through 59 Processing sheet with id= Y, first strand: chain 'S' and resid 51 through 57 removed outlier: 6.669A pdb=" N ARG S 67 " --> pdb=" O ARG S 16 " (cutoff:3.500A) removed outlier: 4.857A pdb=" N ILE S 18 " --> pdb=" O TRP S 65 " (cutoff:3.500A) removed outlier: 7.084A pdb=" N TRP S 65 " --> pdb=" O ILE S 18 " (cutoff:3.500A) removed outlier: 4.971A pdb=" N VAL S 20 " --> pdb=" O LYS S 63 " (cutoff:3.500A) removed outlier: 6.920A pdb=" N LYS S 63 " --> pdb=" O VAL S 20 " (cutoff:3.500A) Processing sheet with id= Z, first strand: chain 'q' and resid 47 through 50 2735 hydrogen bonds defined for protein. 7674 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: 17.75 Time building geometry restraints manager: 23.52 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: 27159 1.40 - 1.63: 38918 1.63 - 1.85: 822 1.85 - 2.07: 0 2.07 - 2.30: 80 Bond restraints: 66979 Sorted by residual: bond pdb=" C4 ATP O 401 " pdb=" C5 ATP O 401 " ideal model delta sigma weight residual 1.388 1.466 -0.078 1.00e-02 1.00e+04 6.07e+01 bond pdb=" C5 ATP O 401 " pdb=" C6 ATP O 401 " ideal model delta sigma weight residual 1.409 1.475 -0.066 1.00e-02 1.00e+04 4.32e+01 bond pdb=" CB7 CDL L 702 " pdb=" OB8 CDL L 702 " ideal model delta sigma weight residual 1.334 1.402 -0.068 1.10e-02 8.26e+03 3.87e+01 bond pdb=" CA7 CDL d 201 " pdb=" OA8 CDL d 201 " ideal model delta sigma weight residual 1.334 1.402 -0.068 1.10e-02 8.26e+03 3.80e+01 bond pdb=" CB7 CDL d 201 " pdb=" OB8 CDL d 201 " ideal model delta sigma weight residual 1.334 1.402 -0.068 1.10e-02 8.26e+03 3.78e+01 ... (remaining 66974 not shown) Histogram of bond angle deviations from ideal: 73.01 - 85.61: 76 85.61 - 98.21: 2 98.21 - 110.82: 24636 110.82 - 123.42: 63733 123.42 - 136.02: 2368 Bond angle restraints: 90815 Sorted by residual: angle pdb=" PB ATP O 401 " pdb=" O3B ATP O 401 " pdb=" PG ATP O 401 " ideal model delta sigma weight residual 139.87 119.10 20.77 1.00e+00 1.00e+00 4.31e+02 angle pdb=" PA ATP O 401 " pdb=" O3A ATP O 401 " pdb=" PB ATP O 401 " ideal model delta sigma weight residual 136.83 117.21 19.62 1.00e+00 1.00e+00 3.85e+02 angle pdb=" C5 ATP O 401 " pdb=" C4 ATP O 401 " pdb=" N3 ATP O 401 " ideal model delta sigma weight residual 126.80 118.56 8.24 1.00e+00 1.00e+00 6.79e+01 angle pdb=" N3 ATP O 401 " pdb=" C4 ATP O 401 " pdb=" N9 ATP O 401 " ideal model delta sigma weight residual 127.04 135.36 -8.32 1.15e+00 7.59e-01 5.25e+01 angle pdb=" C51 CDL d 201 " pdb=" CB5 CDL d 201 " pdb=" OB6 CDL d 201 " ideal model delta sigma weight residual 111.33 120.78 -9.45 1.32e+00 5.72e-01 5.11e+01 ... (remaining 90810 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 28.52: 38568 28.52 - 57.04: 1602 57.04 - 85.56: 127 85.56 - 114.08: 11 114.08 - 142.60: 4 Dihedral angle restraints: 40312 sinusoidal: 16795 harmonic: 23517 Sorted by residual: dihedral pdb=" CB CYS p 76 " pdb=" SG CYS p 76 " pdb=" SG CYS p 83 " pdb=" CB CYS p 83 " ideal model delta sinusoidal sigma weight residual -86.00 -152.17 66.17 1 1.00e+01 1.00e-02 5.72e+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 257.59 114.99 142.60 1 2.00e+01 2.50e-03 4.31e+01 dihedral pdb=" CB CYS e 42 " pdb=" SG CYS e 42 " pdb=" SG CYS e 55 " pdb=" CB CYS e 55 " ideal model delta sinusoidal sigma weight residual 93.00 144.29 -51.29 1 1.00e+01 1.00e-02 3.60e+01 ... (remaining 40309 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 4.242: 9961 4.242 - 8.484: 0 8.484 - 12.727: 0 12.727 - 16.969: 0 16.969 - 21.211: 24 Chirality restraints: 9985 Sorted by residual: chirality pdb="FE3 SF4 F 502 " pdb=" S1 SF4 F 502 " pdb=" S2 SF4 F 502 " pdb=" S4 SF4 F 502 " both_signs ideal model delta sigma weight residual False -10.55 10.66 -21.21 2.00e-01 2.50e+01 1.12e+04 chirality pdb="FE1 SF4 G 802 " pdb=" S2 SF4 G 802 " pdb=" S3 SF4 G 802 " pdb=" S4 SF4 G 802 " both_signs ideal model delta sigma weight residual False -10.55 10.61 -21.16 2.00e-01 2.50e+01 1.12e+04 chirality pdb="FE1 SF4 I 201 " pdb=" S2 SF4 I 201 " pdb=" S3 SF4 I 201 " pdb=" S4 SF4 I 201 " both_signs ideal model delta sigma weight residual False -10.55 10.61 -21.16 2.00e-01 2.50e+01 1.12e+04 ... (remaining 9982 not shown) Planarity restraints: 11430 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LYS m 84 " -0.021 2.00e-02 2.50e+03 4.19e-02 1.76e+01 pdb=" C LYS m 84 " 0.073 2.00e-02 2.50e+03 pdb=" O LYS m 84 " -0.027 2.00e-02 2.50e+03 pdb=" N ASN m 85 " -0.024 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA HIS V 20 " 0.018 2.00e-02 2.50e+03 3.57e-02 1.27e+01 pdb=" C HIS V 20 " -0.062 2.00e-02 2.50e+03 pdb=" O HIS V 20 " 0.023 2.00e-02 2.50e+03 pdb=" N GLU V 21 " 0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA MET M 177 " 0.016 2.00e-02 2.50e+03 3.22e-02 1.03e+01 pdb=" C MET M 177 " -0.056 2.00e-02 2.50e+03 pdb=" O MET M 177 " 0.021 2.00e-02 2.50e+03 pdb=" N ILE M 178 " 0.019 2.00e-02 2.50e+03 ... (remaining 11427 not shown) Histogram of nonbonded interaction distances: 1.89 - 2.49: 592 2.49 - 3.09: 53797 3.09 - 3.70: 96955 3.70 - 4.30: 141517 4.30 - 4.90: 235154 Nonbonded interactions: 528015 Sorted by model distance: nonbonded pdb=" OD2 ASP M 46 " pdb=" OH TYR p 67 " model vdw 1.892 2.440 nonbonded pdb=" OE1 GLU H 24 " pdb=" OH TYR H 228 " model vdw 1.901 2.440 nonbonded pdb=" OH TYR O 83 " pdb=" O2' ATP O 401 " model vdw 1.934 2.440 nonbonded pdb=" O ILE M 244 " pdb=" OH TYR p 148 " model vdw 1.937 2.440 nonbonded pdb=" OH TYR Z 20 " pdb=" OD2 ASP r 108 " model vdw 1.939 2.440 ... (remaining 528010 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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 group one per residue 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: 4.010 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.050 Extract box with map and model: 20.280 Check model and map are aligned: 0.750 Set scattering table: 0.470 Process input model: 147.620 Find NCS groups from input model: 2.160 Set up NCS constraints: 0.210 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.250 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 177.810 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7525 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 : 0.006 0.086 66979 Z= 0.396 Angle : 0.706 20.765 90815 Z= 0.382 Chirality : 1.037 21.211 9985 Planarity : 0.005 0.056 11430 Dihedral : 15.034 142.604 25115 Min Nonbonded Distance : 1.892 Molprobity Statistics. All-atom Clashscore : 11.06 Ramachandran Plot: Outliers : 0.01 % Allowed : 10.08 % Favored : 89.91 % Rotamer: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.30 % 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: -4.80 (0.07), residues: 7940 helix: -2.06 (0.07), residues: 4261 sheet: -3.41 (0.21), residues: 347 loop : -4.76 (0.08), residues: 3332 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP I 29 HIS 0.008 0.001 HIS q 59 PHE 0.025 0.001 PHE D 167 TYR 0.018 0.001 TYR m 102 ARG 0.008 0.000 ARG D 221 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15880 Ramachandran restraints generated. 7940 Oldfield, 0 Emsley, 7940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15880 Ramachandran restraints generated. 7940 Oldfield, 0 Emsley, 7940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1607 residues out of total 7072 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 1607 time to evaluate : 7.223 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 1607 average time/residue: 0.6970 time to fit residues: 1842.3080 Evaluate side-chains 948 residues out of total 7072 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 948 time to evaluate : 5.859 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 7.7799 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 783 random chunks: chunk 661 optimal weight: 4.9990 chunk 593 optimal weight: 0.0270 chunk 329 optimal weight: 20.0000 chunk 202 optimal weight: 1.9990 chunk 400 optimal weight: 2.9990 chunk 317 optimal weight: 0.9990 chunk 613 optimal weight: 0.9990 chunk 237 optimal weight: 1.9990 chunk 373 optimal weight: 0.9980 chunk 456 optimal weight: 5.9990 chunk 711 optimal weight: 2.9990 overall best weight: 1.0044 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 26 GLN ** B 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 41 GLN C 69 ASN C 88 ASN C 144 ASN D 98 GLN D 114 ASN D 135 GLN ** D 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 347 HIS E 27 ASN ** E 99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 214 GLN F 29 HIS F 96 ASN F 144 ASN F 437 HIS G 36 GLN G 430 GLN G 472 ASN G 475 GLN ** G 499 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 682 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 5 ASN ** H 169 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 230 ASN H 235 ASN H 258 ASN ** J 3 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 320 ASN L 572 ASN L 594 ASN M 26 ASN M 374 ASN N 87 GLN N 134 GLN N 150 ASN N 172 GLN ** N 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 222 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 317 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 50 HIS O 120 GLN ** O 271 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 2 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 8 HIS P 103 ASN P 134 HIS ** P 216 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 74 GLN V 52 ASN X 108 GLN X 142 HIS Z 7 GLN Z 23 ASN Z 75 GLN Z 89 ASN a 31 ASN b 51 ASN d 61 GLN e 81 GLN f 9 HIS f 38 ASN ** h 44 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 50 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** l 65 HIS l 71 ASN l 77 HIS l 86 ASN l 103 HIS ** m 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** m 125 ASN n 74 GLN ** n 168 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 84 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** o 91 HIS p 64 HIS p 90 GLN ** p 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** q 12 GLN q 123 GLN r 72 GLN r 109 GLN ** s 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** s 59 GLN Total number of N/Q/H flips: 66 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7597 moved from start: 0.2338 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.266 66979 Z= 0.518 Angle : 1.615 51.048 90815 Z= 1.039 Chirality : 0.309 6.707 9985 Planarity : 0.005 0.082 11430 Dihedral : 9.104 145.936 9190 Min Nonbonded Distance : 2.063 Molprobity Statistics. All-atom Clashscore : 9.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.20 % Favored : 93.80 % Rotamer: Outliers : 1.53 % Allowed : 10.18 % Favored : 88.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.30 % 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: -2.17 (0.09), residues: 7940 helix: -0.03 (0.08), residues: 4247 sheet: -2.30 (0.24), residues: 374 loop : -3.32 (0.10), residues: 3319 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP N 264 HIS 0.014 0.001 HIS f 9 PHE 0.021 0.002 PHE H 104 TYR 0.026 0.002 TYR p 62 ARG 0.007 0.000 ARG o 110 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15880 Ramachandran restraints generated. 7940 Oldfield, 0 Emsley, 7940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15880 Ramachandran restraints generated. 7940 Oldfield, 0 Emsley, 7940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1270 residues out of total 7072 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 108 poor density : 1162 time to evaluate : 6.025 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 108 outliers final: 58 residues processed: 1224 average time/residue: 0.6140 time to fit residues: 1283.0726 Evaluate side-chains 1012 residues out of total 7072 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 954 time to evaluate : 5.851 Switching outliers to nearest non-outliers outliers start: 58 outliers final: 0 residues processed: 58 average time/residue: 0.4864 time to fit residues: 60.6179 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 783 random chunks: chunk 395 optimal weight: 0.0980 chunk 220 optimal weight: 3.9990 chunk 591 optimal weight: 0.9990 chunk 484 optimal weight: 0.4980 chunk 196 optimal weight: 4.9990 chunk 712 optimal weight: 0.0770 chunk 769 optimal weight: 3.9990 chunk 634 optimal weight: 2.9990 chunk 706 optimal weight: 6.9990 chunk 242 optimal weight: 0.9990 chunk 571 optimal weight: 0.0370 overall best weight: 0.3418 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 71 HIS ** B 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 144 ASN ** D 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 431 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 499 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 546 GLN H 32 GLN H 163 GLN ** H 169 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 3 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 320 ASN L 506 ASN L 570 HIS L 579 ASN M 44 GLN ** M 192 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 430 HIS N 134 GLN N 150 ASN ** N 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 222 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 317 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 57 GLN ** O 271 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 2 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 216 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 240 HIS R 3 GLN U 47 GLN V 49 GLN a 31 ASN f 9 HIS g 55 ASN ** g 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** j 24 GLN l 154 HIS ** m 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 11 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 168 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** o 91 HIS ** p 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** p 158 GLN r 109 GLN s 34 ASN Total number of N/Q/H flips: 27 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7577 moved from start: 0.2929 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.250 66979 Z= 0.504 Angle : 1.585 50.651 90815 Z= 1.026 Chirality : 0.312 6.392 9985 Planarity : 0.004 0.054 11430 Dihedral : 8.588 146.439 9190 Min Nonbonded Distance : 2.111 Molprobity Statistics. All-atom Clashscore : 8.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.84 % Favored : 95.16 % Rotamer: Outliers : 1.35 % Allowed : 12.56 % Favored : 86.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.30 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.12 (0.10), residues: 7940 helix: 0.72 (0.08), residues: 4236 sheet: -1.73 (0.25), residues: 378 loop : -2.66 (0.10), residues: 3326 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP j 59 HIS 0.008 0.001 HIS P 288 PHE 0.023 0.001 PHE N 292 TYR 0.023 0.001 TYR k 24 ARG 0.007 0.000 ARG b 57 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15880 Ramachandran restraints generated. 7940 Oldfield, 0 Emsley, 7940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15880 Ramachandran restraints generated. 7940 Oldfield, 0 Emsley, 7940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1210 residues out of total 7072 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 95 poor density : 1115 time to evaluate : 5.827 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 95 outliers final: 31 residues processed: 1170 average time/residue: 0.6180 time to fit residues: 1243.0846 Evaluate side-chains 977 residues out of total 7072 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 946 time to evaluate : 5.798 Switching outliers to nearest non-outliers outliers start: 31 outliers final: 0 residues processed: 31 average time/residue: 0.4890 time to fit residues: 35.9054 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 783 random chunks: chunk 703 optimal weight: 7.9990 chunk 535 optimal weight: 1.9990 chunk 369 optimal weight: 7.9990 chunk 78 optimal weight: 2.9990 chunk 339 optimal weight: 6.9990 chunk 478 optimal weight: 4.9990 chunk 714 optimal weight: 6.9990 chunk 756 optimal weight: 0.8980 chunk 373 optimal weight: 0.5980 chunk 677 optimal weight: 8.9990 chunk 203 optimal weight: 4.9990 overall best weight: 2.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 398 HIS E 37 ASN ** E 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 257 ASN ** F 431 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 51 ASN G 179 ASN G 308 GLN ** G 499 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 32 GLN ** H 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 163 GLN H 304 HIS ** J 3 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 320 ASN L 323 HIS L 579 ASN M 44 GLN M 192 ASN ** M 399 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 440 HIS N 144 GLN ** N 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 222 ASN N 316 HIS ** N 317 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 271 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 2 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 216 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 35 HIS X 63 ASN X 98 HIS Y 107 HIS Z 23 ASN a 31 ASN d 59 HIS f 9 HIS f 12 HIS g 39 ASN l 86 ASN ** m 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** m 78 ASN o 53 GLN o 84 HIS o 91 HIS ** p 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** q 101 ASN s 38 HIS Total number of N/Q/H flips: 35 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7704 moved from start: 0.3453 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.243 66979 Z= 0.528 Angle : 1.601 50.810 90815 Z= 1.033 Chirality : 0.311 6.411 9985 Planarity : 0.005 0.052 11430 Dihedral : 8.297 148.972 9190 Min Nonbonded Distance : 2.081 Molprobity Statistics. All-atom Clashscore : 9.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.68 % Favored : 94.32 % Rotamer: Outliers : 1.94 % Allowed : 14.63 % Favored : 83.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.30 % 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: -0.85 (0.10), residues: 7940 helix: 0.81 (0.08), residues: 4250 sheet: -1.55 (0.25), residues: 403 loop : -2.36 (0.11), residues: 3287 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP M 267 HIS 0.011 0.001 HIS f 9 PHE 0.024 0.002 PHE I 141 TYR 0.028 0.002 TYR e 26 ARG 0.004 0.000 ARG B 175 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15880 Ramachandran restraints generated. 7940 Oldfield, 0 Emsley, 7940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15880 Ramachandran restraints generated. 7940 Oldfield, 0 Emsley, 7940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1177 residues out of total 7072 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 137 poor density : 1040 time to evaluate : 5.929 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 137 outliers final: 68 residues processed: 1119 average time/residue: 0.6170 time to fit residues: 1191.4931 Evaluate side-chains 1002 residues out of total 7072 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 934 time to evaluate : 5.855 Switching outliers to nearest non-outliers outliers start: 68 outliers final: 0 residues processed: 68 average time/residue: 0.4801 time to fit residues: 69.1606 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 783 random chunks: chunk 630 optimal weight: 6.9990 chunk 429 optimal weight: 10.0000 chunk 10 optimal weight: 5.9990 chunk 563 optimal weight: 2.9990 chunk 312 optimal weight: 0.9980 chunk 645 optimal weight: 4.9990 chunk 523 optimal weight: 0.9990 chunk 0 optimal weight: 10.0000 chunk 386 optimal weight: 0.9980 chunk 679 optimal weight: 10.0000 chunk 190 optimal weight: 5.9990 overall best weight: 2.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 96 ASN ** F 431 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 499 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 546 GLN G 654 GLN H 32 GLN H 163 GLN ** J 2 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 3 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 2 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 139 GLN M 304 GLN ** M 399 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 112 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 317 GLN O 271 ASN ** P 2 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 216 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 93 GLN f 9 HIS ** m 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** n 72 GLN n 74 GLN o 53 GLN o 91 HIS ** p 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** q 12 GLN q 101 ASN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7733 moved from start: 0.3908 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.241 66979 Z= 0.520 Angle : 1.595 50.795 90815 Z= 1.030 Chirality : 0.311 6.472 9985 Planarity : 0.004 0.055 11430 Dihedral : 8.062 148.907 9190 Min Nonbonded Distance : 2.074 Molprobity Statistics. All-atom Clashscore : 9.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.95 % Favored : 95.05 % Rotamer: Outliers : 1.69 % Allowed : 15.79 % Favored : 82.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.30 % 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: -0.61 (0.10), residues: 7940 helix: 0.92 (0.08), residues: 4235 sheet: -1.19 (0.25), residues: 407 loop : -2.12 (0.11), residues: 3298 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP M 307 HIS 0.008 0.001 HIS f 9 PHE 0.022 0.001 PHE I 141 TYR 0.026 0.001 TYR I 120 ARG 0.004 0.000 ARG c 44 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15880 Ramachandran restraints generated. 7940 Oldfield, 0 Emsley, 7940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15880 Ramachandran restraints generated. 7940 Oldfield, 0 Emsley, 7940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1146 residues out of total 7072 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 119 poor density : 1027 time to evaluate : 5.925 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 119 outliers final: 55 residues processed: 1096 average time/residue: 0.6107 time to fit residues: 1156.0843 Evaluate side-chains 983 residues out of total 7072 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 928 time to evaluate : 6.246 Switching outliers to nearest non-outliers outliers start: 55 outliers final: 0 residues processed: 55 average time/residue: 0.4847 time to fit residues: 58.5546 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 783 random chunks: chunk 254 optimal weight: 1.9990 chunk 681 optimal weight: 0.6980 chunk 149 optimal weight: 5.9990 chunk 444 optimal weight: 9.9990 chunk 186 optimal weight: 0.9990 chunk 757 optimal weight: 2.9990 chunk 628 optimal weight: 7.9990 chunk 350 optimal weight: 0.9990 chunk 62 optimal weight: 0.0170 chunk 250 optimal weight: 1.9990 chunk 397 optimal weight: 0.9990 overall best weight: 0.7424 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 37 ASN E 74 GLN ** E 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 431 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 499 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 3 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 2 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 399 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 422 HIS ** N 112 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 2 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 216 ASN ** S 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 93 GLN f 9 HIS l 86 ASN o 91 HIS ** p 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** q 12 GLN q 101 ASN r 109 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7690 moved from start: 0.4152 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.245 66979 Z= 0.499 Angle : 1.583 50.663 90815 Z= 1.024 Chirality : 0.311 6.517 9985 Planarity : 0.004 0.055 11430 Dihedral : 7.771 150.523 9190 Min Nonbonded Distance : 2.115 Molprobity Statistics. All-atom Clashscore : 9.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.76 % Favored : 95.24 % Rotamer: Outliers : 1.16 % Allowed : 16.91 % Favored : 81.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.30 % 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: -0.30 (0.10), residues: 7940 helix: 1.12 (0.08), residues: 4219 sheet: -0.93 (0.26), residues: 401 loop : -1.90 (0.11), residues: 3320 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.057 0.001 TRP M 307 HIS 0.007 0.001 HIS M 319 PHE 0.025 0.001 PHE H 104 TYR 0.037 0.001 TYR C 28 ARG 0.006 0.000 ARG f 45 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15880 Ramachandran restraints generated. 7940 Oldfield, 0 Emsley, 7940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15880 Ramachandran restraints generated. 7940 Oldfield, 0 Emsley, 7940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1146 residues out of total 7072 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 82 poor density : 1064 time to evaluate : 5.919 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 82 outliers final: 40 residues processed: 1112 average time/residue: 0.6137 time to fit residues: 1179.7487 Evaluate side-chains 987 residues out of total 7072 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 947 time to evaluate : 5.947 Switching outliers to nearest non-outliers outliers start: 40 outliers final: 0 residues processed: 40 average time/residue: 0.4795 time to fit residues: 44.0553 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 783 random chunks: chunk 730 optimal weight: 9.9990 chunk 85 optimal weight: 0.6980 chunk 431 optimal weight: 0.2980 chunk 553 optimal weight: 5.9990 chunk 428 optimal weight: 6.9990 chunk 637 optimal weight: 7.9990 chunk 423 optimal weight: 1.9990 chunk 754 optimal weight: 6.9990 chunk 472 optimal weight: 9.9990 chunk 460 optimal weight: 10.0000 chunk 348 optimal weight: 9.9990 overall best weight: 3.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 88 ASN ** C 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 157 HIS E 37 ASN ** E 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 96 ASN F 324 GLN ** F 431 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 365 ASN ** G 499 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 32 GLN ** J 3 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 50 ASN L 320 ASN ** L 328 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 505 ASN L 534 HIS L 579 ASN ** M 399 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 112 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 2 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 47 GLN ** S 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 136 ASN f 9 HIS ** g 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 44 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** h 135 HIS ** m 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** q 12 GLN ** q 91 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** q 101 ASN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7794 moved from start: 0.4441 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.239 66979 Z= 0.553 Angle : 1.617 50.824 90815 Z= 1.039 Chirality : 0.312 6.372 9985 Planarity : 0.005 0.054 11430 Dihedral : 7.897 151.150 9190 Min Nonbonded Distance : 2.049 Molprobity Statistics. All-atom Clashscore : 10.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.59 % Favored : 94.41 % Rotamer: Outliers : 1.47 % Allowed : 18.14 % Favored : 80.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.30 % 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: -0.46 (0.10), residues: 7940 helix: 0.91 (0.08), residues: 4241 sheet: -0.88 (0.26), residues: 391 loop : -1.90 (0.11), residues: 3308 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.069 0.002 TRP M 307 HIS 0.010 0.001 HIS o 91 PHE 0.023 0.002 PHE H 104 TYR 0.033 0.002 TYR C 28 ARG 0.012 0.001 ARG g 57 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15880 Ramachandran restraints generated. 7940 Oldfield, 0 Emsley, 7940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15880 Ramachandran restraints generated. 7940 Oldfield, 0 Emsley, 7940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1117 residues out of total 7072 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 104 poor density : 1013 time to evaluate : 5.997 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 104 outliers final: 53 residues processed: 1080 average time/residue: 0.6162 time to fit residues: 1144.8908 Evaluate side-chains 996 residues out of total 7072 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 943 time to evaluate : 5.856 Switching outliers to nearest non-outliers outliers start: 53 outliers final: 0 residues processed: 53 average time/residue: 0.4807 time to fit residues: 56.2733 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 783 random chunks: chunk 466 optimal weight: 5.9990 chunk 301 optimal weight: 6.9990 chunk 450 optimal weight: 7.9990 chunk 227 optimal weight: 3.9990 chunk 148 optimal weight: 5.9990 chunk 146 optimal weight: 1.9990 chunk 479 optimal weight: 1.9990 chunk 514 optimal weight: 4.9990 chunk 373 optimal weight: 0.9980 chunk 70 optimal weight: 0.6980 chunk 593 optimal weight: 7.9990 overall best weight: 1.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 37 ASN ** E 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 431 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 499 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 32 GLN ** J 3 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 50 ASN ** L 328 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 534 HIS ** M 399 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 112 HIS ** N 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 150 ASN ** P 2 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** f 9 HIS ** h 44 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** l 86 ASN ** m 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** n 74 GLN o 91 HIS ** p 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** p 130 GLN q 12 GLN ** q 91 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** q 101 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7771 moved from start: 0.4614 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.242 66979 Z= 0.517 Angle : 1.598 50.701 90815 Z= 1.031 Chirality : 0.311 6.406 9985 Planarity : 0.004 0.054 11430 Dihedral : 7.748 152.815 9190 Min Nonbonded Distance : 2.075 Molprobity Statistics. All-atom Clashscore : 10.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.85 % Favored : 95.15 % Rotamer: Outliers : 0.85 % Allowed : 18.97 % Favored : 80.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.30 % 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: -0.35 (0.10), residues: 7940 helix: 0.99 (0.08), residues: 4233 sheet: -0.78 (0.27), residues: 394 loop : -1.82 (0.11), residues: 3313 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.072 0.001 TRP M 307 HIS 0.008 0.001 HIS o 91 PHE 0.023 0.001 PHE N 292 TYR 0.033 0.001 TYR C 28 ARG 0.006 0.000 ARG B 111 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15880 Ramachandran restraints generated. 7940 Oldfield, 0 Emsley, 7940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15880 Ramachandran restraints generated. 7940 Oldfield, 0 Emsley, 7940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1076 residues out of total 7072 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 1016 time to evaluate : 6.122 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 60 outliers final: 23 residues processed: 1043 average time/residue: 0.6436 time to fit residues: 1161.7019 Evaluate side-chains 976 residues out of total 7072 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 953 time to evaluate : 5.941 Switching outliers to nearest non-outliers outliers start: 23 outliers final: 0 residues processed: 23 average time/residue: 0.5106 time to fit residues: 29.8261 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 783 random chunks: chunk 686 optimal weight: 5.9990 chunk 723 optimal weight: 6.9990 chunk 659 optimal weight: 6.9990 chunk 703 optimal weight: 7.9990 chunk 722 optimal weight: 1.9990 chunk 423 optimal weight: 0.8980 chunk 306 optimal weight: 4.9990 chunk 552 optimal weight: 4.9990 chunk 215 optimal weight: 9.9990 chunk 635 optimal weight: 0.3980 chunk 665 optimal weight: 8.9990 overall best weight: 2.6586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 157 HIS ** E 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 324 GLN ** F 431 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 499 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 194 ASN ** J 2 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 3 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 194 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 328 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 534 HIS ** M 399 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 2 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** f 9 HIS ** g 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 44 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** o 91 HIS ** p 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 91 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** q 101 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7800 moved from start: 0.4803 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.239 66979 Z= 0.537 Angle : 1.612 50.706 90815 Z= 1.036 Chirality : 0.312 6.406 9985 Planarity : 0.005 0.066 11430 Dihedral : 7.748 160.410 9190 Min Nonbonded Distance : 2.059 Molprobity Statistics. All-atom Clashscore : 10.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.57 % Favored : 94.43 % Rotamer: Outliers : 0.52 % Allowed : 19.70 % Favored : 79.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.30 % 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: -0.40 (0.10), residues: 7940 helix: 0.92 (0.08), residues: 4232 sheet: -0.81 (0.27), residues: 391 loop : -1.81 (0.11), residues: 3317 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.051 0.001 TRP M 307 HIS 0.009 0.001 HIS o 91 PHE 0.056 0.002 PHE J 67 TYR 0.035 0.002 TYR C 28 ARG 0.006 0.000 ARG B 175 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15880 Ramachandran restraints generated. 7940 Oldfield, 0 Emsley, 7940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15880 Ramachandran restraints generated. 7940 Oldfield, 0 Emsley, 7940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1038 residues out of total 7072 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 1001 time to evaluate : 6.019 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 37 outliers final: 16 residues processed: 1023 average time/residue: 0.6449 time to fit residues: 1137.0420 Evaluate side-chains 974 residues out of total 7072 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 958 time to evaluate : 5.980 Switching outliers to nearest non-outliers outliers start: 16 outliers final: 0 residues processed: 16 average time/residue: 0.5017 time to fit residues: 23.0269 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 783 random chunks: chunk 700 optimal weight: 2.9990 chunk 461 optimal weight: 2.9990 chunk 743 optimal weight: 9.9990 chunk 453 optimal weight: 0.0020 chunk 352 optimal weight: 0.4980 chunk 516 optimal weight: 6.9990 chunk 780 optimal weight: 6.9990 chunk 717 optimal weight: 0.0980 chunk 621 optimal weight: 0.8980 chunk 64 optimal weight: 3.9990 chunk 479 optimal weight: 0.9980 overall best weight: 0.4988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 157 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 37 ASN ** E 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 324 GLN ** F 431 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 499 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 107 ASN ** L 2 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 136 ASN ** L 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 328 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 354 GLN ** L 534 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 399 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 2 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** f 9 HIS g 109 ASN ** h 44 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** l 86 ASN ** m 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** o 53 GLN o 91 HIS ** p 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** q 101 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7722 moved from start: 0.4931 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.244 66979 Z= 0.502 Angle : 1.594 50.566 90815 Z= 1.028 Chirality : 0.311 6.329 9985 Planarity : 0.004 0.060 11430 Dihedral : 7.467 163.078 9190 Min Nonbonded Distance : 2.111 Molprobity Statistics. All-atom Clashscore : 10.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.19 % Favored : 95.81 % Rotamer: Outliers : 0.16 % Allowed : 20.08 % Favored : 79.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.30 % 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: -0.10 (0.10), residues: 7940 helix: 1.15 (0.08), residues: 4206 sheet: -0.79 (0.26), residues: 411 loop : -1.60 (0.11), residues: 3323 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.053 0.001 TRP M 307 HIS 0.008 0.001 HIS o 91 PHE 0.033 0.001 PHE S 70 TYR 0.033 0.001 TYR C 28 ARG 0.008 0.000 ARG S 16 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15880 Ramachandran restraints generated. 7940 Oldfield, 0 Emsley, 7940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15880 Ramachandran restraints generated. 7940 Oldfield, 0 Emsley, 7940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1076 residues out of total 7072 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 1065 time to evaluate : 5.981 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 11 outliers final: 7 residues processed: 1070 average time/residue: 0.6273 time to fit residues: 1156.9290 Evaluate side-chains 985 residues out of total 7072 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 978 time to evaluate : 5.972 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.5061 time to fit residues: 14.5073 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 783 random chunks: chunk 380 optimal weight: 3.9990 chunk 493 optimal weight: 0.6980 chunk 661 optimal weight: 4.9990 chunk 190 optimal weight: 6.9990 chunk 572 optimal weight: 7.9990 chunk 91 optimal weight: 0.9990 chunk 172 optimal weight: 5.9990 chunk 622 optimal weight: 0.9990 chunk 260 optimal weight: 8.9990 chunk 638 optimal weight: 4.9990 chunk 78 optimal weight: 0.9990 overall best weight: 1.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 144 ASN ** D 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 157 HIS ** E 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 324 GLN ** F 431 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 499 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 2 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 194 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 328 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 534 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 399 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 2 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** f 9 HIS g 109 ASN ** m 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** n 50 HIS ** n 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** o 53 GLN o 91 HIS ** p 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 91 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** q 101 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.099594 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3223 r_free = 0.3223 target = 0.088079 restraints weight = 150277.126| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3236 r_free = 0.3236 target = 0.088945 restraints weight = 111131.939| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3245 r_free = 0.3245 target = 0.089494 restraints weight = 83100.791| |-----------------------------------------------------------------------------| r_work (final): 0.3244 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7847 moved from start: 0.5023 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.242 66979 Z= 0.511 Angle : 1.598 50.619 90815 Z= 1.030 Chirality : 0.311 6.354 9985 Planarity : 0.004 0.056 11430 Dihedral : 7.427 165.714 9190 Min Nonbonded Distance : 2.081 Molprobity Statistics. All-atom Clashscore : 10.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.75 % Favored : 95.25 % Rotamer: Outliers : 0.33 % Allowed : 20.51 % Favored : 79.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.30 % 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: -0.07 (0.10), residues: 7940 helix: 1.15 (0.08), residues: 4215 sheet: -0.74 (0.26), residues: 412 loop : -1.56 (0.11), residues: 3313 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.067 0.001 TRP M 307 HIS 0.011 0.001 HIS o 91 PHE 0.040 0.001 PHE J 67 TYR 0.036 0.001 TYR C 28 ARG 0.008 0.000 ARG c 44 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 17722.77 seconds wall clock time: 311 minutes 8.39 seconds (18668.39 seconds total)