Starting phenix.real_space_refine (version: 1.21rc1) on Mon Apr 24 22:33:20 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7b93_12095/04_2023/7b93_12095_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7b93_12095/04_2023/7b93_12095.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7b93_12095/04_2023/7b93_12095_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.04 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7b93_12095/04_2023/7b93_12095_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7b93_12095/04_2023/7b93_12095_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7b93_12095/04_2023/7b93_12095.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7b93_12095/04_2023/7b93_12095.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7b93_12095/04_2023/7b93_12095_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7b93_12095/04_2023/7b93_12095_updated.pdb" } resolution = 3.04 write_initial_geo_file = False refinement { macro_cycles = 10 } 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 ------------------------------------------------------------------------------- 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= 0.008 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: 8 Type Number sf(0) Gaussians Fe 28 7.16 5 Zn 1 6.06 5 P 36 5.49 5 S 494 5.16 5 C 43600 2.51 5 N 11189 2.21 5 O 12141 1.98 5 F 3 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 48": "NH1" <-> "NH2" Residue "A PHE 56": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 52": "NH1" <-> "NH2" Residue "B PHE 86": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 111": "NH1" <-> "NH2" Residue "B ARG 121": "NH1" <-> "NH2" Residue "B TYR 136": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 140": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 155": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 168": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 189": "NH1" <-> "NH2" Residue "C ARG 14": "NH1" <-> "NH2" Residue "C ASP 16": "OD1" <-> "OD2" Residue "C ASP 77": "OD1" <-> "OD2" Residue "C TYR 94": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 110": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 133": "OE1" <-> "OE2" Residue "C PHE 138": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 142": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 147": "OD1" <-> "OD2" Residue "C PHE 166": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 173": "OE1" <-> "OE2" Residue "C ARG 182": "NH1" <-> "NH2" Residue "C TYR 209": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 210": "NH1" <-> "NH2" Residue "D ARG 2": "NH1" <-> "NH2" Residue "D PHE 14": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 24": "OE1" <-> "OE2" Residue "D ASP 35": "OD1" <-> "OD2" Residue "D ARG 63": "NH1" <-> "NH2" Residue "D TYR 93": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 108": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 133": "NH1" <-> "NH2" Residue "D ARG 146": "NH1" <-> "NH2" Residue "D ASP 160": "OD1" <-> "OD2" Residue "D PHE 167": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 168": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 174": "NH1" <-> "NH2" Residue "D ARG 221": "NH1" <-> "NH2" Residue "D GLU 248": "OE1" <-> "OE2" Residue "D TYR 253": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 275": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 349": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 356": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 387": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 10": "NH1" <-> "NH2" Residue "E ASP 11": "OD1" <-> "OD2" Residue "E GLU 40": "OE1" <-> "OE2" Residue "E ASP 112": "OD1" <-> "OD2" Residue "E GLU 170": "OE1" <-> "OE2" Residue "E GLU 171": "OE1" <-> "OE2" Residue "E ARG 187": "NH1" <-> "NH2" Residue "F ASP 17": "OD1" <-> "OD2" Residue "F GLU 18": "OE1" <-> "OE2" Residue "F ARG 28": "NH1" <-> "NH2" Residue "F ARG 32": "NH1" <-> "NH2" Residue "F TYR 43": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 73": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 107": "OD1" <-> "OD2" Residue "F GLU 120": "OE1" <-> "OE2" Residue "F ARG 127": "NH1" <-> "NH2" Residue "F TYR 137": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 139": "NH1" <-> "NH2" Residue "F ASP 212": "OD1" <-> "OD2" Residue "F PHE 245": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 349": "NH1" <-> "NH2" Residue "F ARG 378": "NH1" <-> "NH2" Residue "F GLU 427": "OE1" <-> "OE2" Residue "F PHE 433": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 14": "OD1" <-> "OD2" Residue "G ARG 135": "NH1" <-> "NH2" Residue "G PHE 162": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ARG 218": "NH1" <-> "NH2" Residue "G ARG 243": "NH1" <-> "NH2" Residue "G GLU 246": "OE1" <-> "OE2" Residue "G ARG 249": "NH1" <-> "NH2" Residue "G ARG 253": "NH1" <-> "NH2" Residue "G ARG 268": "NH1" <-> "NH2" Residue "G ASP 272": "OD1" <-> "OD2" Residue "G GLU 346": "OE1" <-> "OE2" Residue "G ASP 357": "OD1" <-> "OD2" Residue "G ARG 359": "NH1" <-> "NH2" Residue "G TYR 362": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 417": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 461": "OD1" <-> "OD2" Residue "G ARG 534": "NH1" <-> "NH2" Residue "G TYR 545": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 551": "OD1" <-> "OD2" Residue "G TYR 573": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 613": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 617": "OD1" <-> "OD2" Residue "G ARG 620": "NH1" <-> "NH2" Residue "G GLU 637": "OE1" <-> "OE2" Residue "G GLU 693": "OE1" <-> "OE2" Residue "H ARG 62": "NH1" <-> "NH2" Residue "H TYR 142": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 202": "OE1" <-> "OE2" Residue "H GLU 204": "OE1" <-> "OE2" Residue "H PHE 224": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 228": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 255": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 259": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 280": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 310": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I GLU 11": "OE1" <-> "OE2" Residue "I ARG 34": "NH1" <-> "NH2" Residue "I ARG 62": "NH1" <-> "NH2" Residue "I TYR 111": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 120": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 139": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I GLU 144": "OE1" <-> "OE2" Residue "I GLU 148": "OE1" <-> "OE2" Residue "J PHE 12": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 59": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 67": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 108": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 109": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 126": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J GLU 127": "OE1" <-> "OE2" Residue "J ASP 130": "OD1" <-> "OD2" Residue "J TYR 145": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 164": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 12": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K GLU 34": "OE1" <-> "OE2" Residue "K PHE 41": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 66": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 4": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 61": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 89": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ASP 111": "OD1" <-> "OD2" Residue "L ARG 116": "NH1" <-> "NH2" Residue "L TYR 159": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ARG 161": "NH1" <-> "NH2" Residue "L PHE 182": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L GLU 197": "OE1" <-> "OE2" Residue "L PHE 258": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ARG 262": "NH1" <-> "NH2" Residue "L PHE 263": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 272": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 335": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 422": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ARG 436": "NH1" <-> "NH2" Residue "L PHE 437": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L GLU 503": "OE1" <-> "OE2" Residue "L PHE 522": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 529": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ARG 535": "NH1" <-> "NH2" Residue "M GLU 47": "OE1" <-> "OE2" Residue "M ASP 87": "OD1" <-> "OD2" Residue "M TYR 119": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M PHE 122": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M GLU 222": "OE1" <-> "OE2" Residue "M TYR 256": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M TYR 259": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M PHE 380": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M TYR 406": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N TYR 146": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N GLU 269": "OE1" <-> "OE2" Residue "N PHE 291": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N PHE 292": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N ARG 295": "NH1" <-> "NH2" Residue "N PHE 326": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O ARG 2": "NH1" <-> "NH2" Residue "O ARG 67": "NH1" <-> "NH2" Residue "O TYR 129": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O PHE 132": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O PHE 134": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O ARG 145": "NH1" <-> "NH2" Residue "O TYR 152": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O ASP 188": "OD1" <-> "OD2" Residue "O GLU 227": "OE1" <-> "OE2" Residue "O GLU 236": "OE1" <-> "OE2" Residue "O ASP 253": "OD1" <-> "OD2" Residue "P ARG 13": "NH1" <-> "NH2" Residue "P TYR 33": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P ARG 40": "NH1" <-> "NH2" Residue "P ARG 50": "NH1" <-> "NH2" Residue "P ARG 102": "NH1" <-> "NH2" Residue "P PHE 160": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P PHE 172": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P ARG 186": "NH1" <-> "NH2" Residue "P ASP 209": "OD1" <-> "OD2" Residue "P ASP 222": "OD1" <-> "OD2" Residue "P ARG 251": "NH1" <-> "NH2" Residue "P TYR 256": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P PHE 261": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P ARG 320": "NH1" <-> "NH2" Residue "P ARG 322": "NH1" <-> "NH2" Residue "Q PHE 59": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q PHE 86": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q GLU 106": "OE1" <-> "OE2" Residue "R GLU 20": "OE1" <-> "OE2" Residue "R TYR 23": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R ARG 31": "NH1" <-> "NH2" Residue "R PHE 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S ARG 25": "NH1" <-> "NH2" Residue "S ARG 55": "NH1" <-> "NH2" Residue "S GLU 59": "OE1" <-> "OE2" Residue "T ASP 26": "OD1" <-> "OD2" Residue "T GLU 55": "OE1" <-> "OE2" Residue "T GLU 57": "OE1" <-> "OE2" Residue "U GLU 28": "OE1" <-> "OE2" Residue "U ASP 39": "OD1" <-> "OD2" Residue "U ASP 56": "OD1" <-> "OD2" Residue "U PHE 60": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U TYR 87": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V PHE 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V ASP 63": "OD1" <-> "OD2" Residue "V GLU 78": "OE1" <-> "OE2" Residue "V GLU 104": "OE1" <-> "OE2" Residue "W ARG 32": "NH1" <-> "NH2" Residue "W ARG 33": "NH1" <-> "NH2" Residue "W TYR 42": "CD1" <-> "CD2" "CE1" <-> "CE2" 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 "X GLU 15": "OE1" <-> "OE2" Residue "X ASP 107": "OD1" <-> "OD2" Residue "X ARG 118": "NH1" <-> "NH2" Residue "X ARG 144": "NH1" <-> "NH2" Residue "X ARG 146": "NH1" <-> "NH2" Residue "X ASP 156": "OD1" <-> "OD2" Residue "X PHE 167": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X PHE 168": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y PHE 5": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y TYR 8": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y ASP 13": "OD1" <-> "OD2" Residue "Y PHE 90": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y ARG 103": "NH1" <-> "NH2" Residue "Y TYR 107": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y TYR 116": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y PHE 124": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z TYR 20": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z ARG 22": "NH1" <-> "NH2" Residue "Z ARG 26": "NH1" <-> "NH2" Residue "Z ARG 57": "NH1" <-> "NH2" Residue "Z ASP 63": "OD1" <-> "OD2" Residue "Z ARG 67": "NH1" <-> "NH2" Residue "Z ARG 81": "NH1" <-> "NH2" Residue "Z ARG 114": "NH1" <-> "NH2" Residue "Z TYR 142": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a ARG 37": "NH1" <-> "NH2" Residue "a ARG 40": "NH1" <-> "NH2" Residue "a TYR 46": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a ARG 52": "NH1" <-> "NH2" Residue "a ARG 53": "NH1" <-> "NH2" Residue "a TYR 60": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a TYR 61": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b PHE 7": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b TYR 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c PHE 2": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c TYR 30": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c GLU 41": "OE1" <-> "OE2" Residue "c ARG 45": "NH1" <-> "NH2" Residue "d ASP 16": "OD1" <-> "OD2" Residue "d ARG 55": "NH1" <-> "NH2" Residue "d PHE 70": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d PHE 116": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d ARG 120": "NH1" <-> "NH2" Residue "e ASP 4": "OD1" <-> "OD2" Residue "e ARG 15": "NH1" <-> "NH2" Residue "e PHE 17": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "e PHE 19": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "e GLU 38": "OE1" <-> "OE2" Residue "e ARG 50": "NH1" <-> "NH2" Residue "e ARG 68": "NH1" <-> "NH2" Residue "e TYR 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "e ARG 104": "NH1" <-> "NH2" Residue "f PHE 3": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "f PHE 36": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "f GLU 52": "OE1" <-> "OE2" Residue "g ARG 57": "NH1" <-> "NH2" Residue "g PHE 64": "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 97": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "g TYR 110": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "h ARG 20": "NH1" <-> "NH2" Residue "h GLU 49": "OE1" <-> "OE2" Residue "h GLU 57": "OE1" <-> "OE2" Residue "h ARG 77": "NH1" <-> "NH2" Residue "h TYR 80": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "h ARG 115": "NH1" <-> "NH2" Residue "i ARG 10": "NH1" <-> "NH2" Residue "i ARG 30": "NH1" <-> "NH2" Residue "i PHE 69": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "i PHE 80": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "i ASP 121": "OD1" <-> "OD2" Residue "j PHE 14": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "j PHE 40": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "j ASP 70": "OD1" <-> "OD2" Residue "k TYR 24": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "k GLU 30": "OE1" <-> "OE2" Residue "k ARG 44": "NH1" <-> "NH2" Residue "k ARG 52": "NH1" <-> "NH2" Residue "k TYR 58": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "k PHE 80": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "k TYR 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "k PHE 92": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "l ASP 58": "OD1" <-> "OD2" Residue "l ARG 85": "NH1" <-> "NH2" Residue "l PHE 110": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "l TYR 138": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "l ASP 144": "OD1" <-> "OD2" Residue "m ARG 29": "NH1" <-> "NH2" Residue "m ARG 30": "NH1" <-> "NH2" Residue "m ARG 44": "NH1" <-> "NH2" Residue "m TYR 69": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "m TYR 76": "CD1" <-> "CD2" "CE1" <-> "CE2" 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 ASP 55": "OD1" <-> "OD2" Residue "n TYR 114": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "n ARG 158": "NH1" <-> "NH2" Residue "o ARG 6": "NH1" <-> "NH2" Residue "o ARG 7": "NH1" <-> "NH2" Residue "o ASP 17": "OD1" <-> "OD2" Residue "o GLU 19": "OE1" <-> "OE2" Residue "o ASP 27": "OD1" <-> "OD2" Residue "o ARG 33": "NH1" <-> "NH2" Residue "o GLU 44": "OE1" <-> "OE2" Residue "o ARG 64": "NH1" <-> "NH2" Residue "o ASP 71": "OD1" <-> "OD2" Residue "o ARG 97": "NH1" <-> "NH2" Residue "o PHE 101": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "o ARG 106": "NH1" <-> "NH2" Residue "o ARG 110": "NH1" <-> "NH2" Residue "o ARG 114": "NH1" <-> "NH2" Residue "p TYR 36": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "p ARG 48": "NH1" <-> "NH2" Residue "p TYR 61": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "p ARG 68": "NH1" <-> "NH2" Residue "p GLU 86": "OE1" <-> "OE2" Residue "p GLU 107": "OE1" <-> "OE2" Residue "p TYR 138": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "p TYR 149": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "q ARG 21": "NH1" <-> "NH2" Residue "q TYR 48": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "q PHE 55": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "q ARG 60": "NH1" <-> "NH2" Residue "q GLU 67": "OE1" <-> "OE2" Residue "q PHE 108": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "q PHE 115": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "r ARG 5": "NH1" <-> "NH2" Residue "r ARG 26": "NH1" <-> "NH2" Residue "r ASP 57": "OD1" <-> "OD2" Residue "r GLU 90": "OE1" <-> "OE2" Residue "r ARG 102": "NH1" <-> "NH2" Residue "r ASP 108": "OD1" <-> "OD2" Residue "s PHE 45": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "s ASP 51": "OD1" <-> "OD2" Time to flip residues: 0.17s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4938/modules/chem_data/mon_lib" Total number of atoms: 67492 Number of models: 1 Model: "" Number of chains: 67 Chain: "A" Number of atoms: 933 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 933 Classifications: {'peptide': 115} Link IDs: {'PTRANS': 6, 'TRANS': 108} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'FME:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "B" Number of atoms: 1247 Number of conformers: 1 Conformer: "" Number of residues, atoms: 156, 1247 Classifications: {'peptide': 156} Link IDs: {'PCIS': 2, 'PTRANS': 8, 'TRANS': 145} Chain: "C" Number of atoms: 1721 Number of conformers: 1 Conformer: "" Number of residues, atoms: 207, 1721 Classifications: {'peptide': 207} Link IDs: {'PTRANS': 15, 'TRANS': 191} Chain: "D" Number of atoms: 3464 Number of conformers: 1 Conformer: "" Number of residues, atoms: 430, 3464 Classifications: {'peptide': 430} Link IDs: {'PCIS': 1, 'PTRANS': 25, 'TRANS': 403} 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: 1664 Number of conformers: 1 Conformer: "" Number of residues, atoms: 215, 1664 Classifications: {'peptide': 215} Link IDs: {'PCIS': 1, 'PTRANS': 20, 'TRANS': 193} Chain: "F" Number of atoms: 3310 Number of conformers: 1 Conformer: "" Number of residues, atoms: 429, 3310 Classifications: {'peptide': 429} Link IDs: {'PCIS': 2, 'PTRANS': 19, 'TRANS': 407} Chain: "G" Number of atoms: 5305 Number of conformers: 1 Conformer: "" Number of residues, atoms: 690, 5305 Classifications: {'peptide': 690} Link IDs: {'PTRANS': 31, 'TRANS': 658} Chain: "H" Number of atoms: 2540 Number of conformers: 1 Conformer: "" Number of residues, atoms: 318, 2540 Classifications: {'peptide': 318} Link IDs: {'PCIS': 2, 'PTRANS': 20, 'TRANS': 295} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'FME:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "I" Number of atoms: 1431 Number of conformers: 1 Conformer: "" Number of residues, atoms: 178, 1431 Classifications: {'peptide': 178} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 168} Chain: "J" Number of atoms: 1308 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 1308 Classifications: {'peptide': 172} Link IDs: {'PTRANS': 3, 'TRANS': 168} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'FME:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "K" Number of atoms: 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: 4809 Number of conformers: 1 Conformer: "" Number of residues, atoms: 607, 4809 Classifications: {'peptide': 607} Link IDs: {'PTRANS': 26, 'TRANS': 580} 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': 3, 'PTRANS': 17, 'TRANS': 438} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'FME:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "N" Number of atoms: 2703 Number of conformers: 1 Conformer: "" Number of residues, atoms: 345, 2703 Classifications: {'peptide': 345} Link IDs: {'PCIS': 3, 'PTRANS': 17, 'TRANS': 324} 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: 2607 Number of conformers: 1 Conformer: "" Number of residues, atoms: 320, 2607 Classifications: {'peptide': 320} Link IDs: {'PTRANS': 16, 'TRANS': 303} Chain: "P" Number of atoms: 2748 Number of conformers: 1 Conformer: "" Number of residues, atoms: 342, 2748 Classifications: {'peptide': 342} Link IDs: {'PTRANS': 19, 'TRANS': 322} Chain: "Q" Number of atoms: 1022 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 1022 Classifications: {'peptide': 126} Link IDs: {'PTRANS': 6, 'TRANS': 119} Chain: "R" Number of atoms: 758 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 758 Classifications: {'peptide': 96} Link IDs: {'PTRANS': 3, 'TRANS': 92} Chain: "S" Number of atoms: 671 Number of conformers: 1 Conformer: "" Number of residues, atoms: 84, 671 Classifications: {'peptide': 84} Link IDs: {'PTRANS': 4, 'TRANS': 79} Chain: "T" Number of atoms: 637 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 637 Classifications: {'peptide': 79} Link IDs: {'PTRANS': 3, 'TRANS': 75} 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: 932 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 932 Classifications: {'peptide': 115} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 106} 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: 1177 Number of conformers: 1 Conformer: "" Number of residues, atoms: 143, 1177 Classifications: {'peptide': 143} Link IDs: {'PTRANS': 9, 'TRANS': 133} Chain: "a" Number of atoms: 572 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 572 Classifications: {'peptide': 70} Link IDs: {'PTRANS': 2, 'TRANS': 67} Chain: "b" Number of atoms: 628 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 628 Classifications: {'peptide': 80} Link IDs: {'PTRANS': 11, 'TRANS': 68} Chain: "c" Number of atoms: 407 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 407 Classifications: {'peptide': 49} Link IDs: {'PTRANS': 2, 'TRANS': 46} Chain: "d" Number of atoms: 996 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 996 Classifications: {'peptide': 120} Link IDs: {'PTRANS': 12, 'TRANS': 107} Chain: "e" Number of atoms: 877 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 877 Classifications: {'peptide': 105} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 98} Chain: "f" Number of atoms: 482 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 482 Classifications: {'peptide': 56} Link IDs: {'PTRANS': 2, 'TRANS': 53} Chain: "g" Number of atoms: 858 Number of conformers: 1 Conformer: "" Number of residues, atoms: 102, 858 Classifications: {'peptide': 102} Link IDs: {'PTRANS': 8, 'TRANS': 93} Chain: "h" Number of atoms: 1162 Number of conformers: 1 Conformer: "" Number of residues, atoms: 138, 1162 Classifications: {'peptide': 138} Link IDs: {'PCIS': 2, 'PTRANS': 9, 'TRANS': 126} Chain: "i" Number of atoms: 814 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 814 Classifications: {'peptide': 97} Link IDs: {'PCIS': 2, 'PTRANS': 10, 'TRANS': 84} Chain breaks: 1 Chain: "j" Number of atoms: 580 Number of conformers: 1 Conformer: "" Number of residues, atoms: 67, 580 Classifications: {'peptide': 67} Link IDs: {'PTRANS': 6, 'TRANS': 60} 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: 1323 Number of conformers: 1 Conformer: "" Number of residues, atoms: 157, 1323 Classifications: {'peptide': 157} Link IDs: {'PTRANS': 18, 'TRANS': 138} Chain: "m" Number of atoms: 1050 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 1050 Classifications: {'peptide': 126} Link IDs: {'PTRANS': 11, 'TRANS': 114} Chain: "n" Number of atoms: 1541 Number of conformers: 1 Conformer: "" Number of residues, atoms: 178, 1541 Classifications: {'peptide': 178} Link IDs: {'PTRANS': 16, 'TRANS': 161} Chain: "o" Number of atoms: 988 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 988 Classifications: {'peptide': 115} Link IDs: {'PCIS': 2, 'PTRANS': 5, 'TRANS': 107} Chain: "p" Number of atoms: 1444 Number of conformers: 1 Conformer: "" Number of residues, atoms: 171, 1444 Classifications: {'peptide': 171} Link IDs: {'PTRANS': 10, 'TRANS': 160} Chain: "q" Number of atoms: 1213 Number of conformers: 1 Conformer: "" Number of residues, atoms: 145, 1213 Classifications: {'peptide': 145} Link IDs: {'PTRANS': 11, 'TRANS': 133} Chain: "r" Number of atoms: 809 Number of conformers: 1 Conformer: "" Number of residues, atoms: 101, 809 Classifications: {'peptide': 101} Link IDs: {'PTRANS': 11, 'TRANS': 89} 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: 368 Number of conformers: 1 Conformer: "" Number of residues, atoms: 44, 368 Classifications: {'peptide': 44} Link IDs: {'PTRANS': 3, 'TRANS': 40} Chain: "B" Number of atoms: 86 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 86 Unusual residues: {'PC1': 2, 'SF4': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 30 Unresolved non-hydrogen angles: 30 Unresolved non-hydrogen dihedrals: 30 Chain: "D" Number of atoms: 49 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 49 Unusual residues: {'3PE': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 2 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: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 126 Unusual residues: {'3PE': 1, 'PC1': 1, 'T2Q': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 19 Unresolved non-hydrogen angles: 19 Unresolved non-hydrogen dihedrals: 19 Chain: "I" Number of atoms: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 112 Unusual residues: {'3PE': 1, 'PC1': 1, 'SF4': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 9 Chain: "K" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 33 Unusual residues: {'3PE': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 18 Chain: "L" Number of atoms: 123 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 123 Unusual residues: {'3PE': 1, 'CDL': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 28 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen dihedrals: 28 Chain: "M" 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: "N" Number of atoms: 65 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 65 Unusual residues: {'CDL': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 35 Unresolved non-hydrogen angles: 35 Unresolved non-hydrogen dihedrals: 35 Chain: "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: "X" Number of atoms: 67 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 67 Unusual residues: {'CDL': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 33 Unresolved non-hydrogen angles: 33 Unresolved non-hydrogen dihedrals: 33 Chain: "Y" Number of atoms: 41 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 41 Unusual residues: {'3PE': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 10 Chain: "d" Number of atoms: 122 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 122 Unusual residues: {'CDL': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 78 Unresolved non-hydrogen angles: 79 Unresolved non-hydrogen dihedrals: 76 Planarities with less than four sites: {'CDL:plan-1': 1} Unresolved non-hydrogen planarities: 3 Chain: "h" Number of atoms: 107 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 107 Unusual residues: {'3PE': 1, 'CDL': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 44 Unresolved non-hydrogen angles: 44 Unresolved non-hydrogen dihedrals: 44 Chain: "i" 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: "q" Number of atoms: 57 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 57 Unusual residues: {'CDL': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 43 Unresolved non-hydrogen angles: 43 Unresolved non-hydrogen dihedrals: 43 List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 1688 SG CYS B 129 97.014 94.682 201.965 1.00 35.05 S ATOM 1191 SG CYS B 65 91.150 96.785 204.216 1.00 37.49 S ATOM 1185 SG CYS B 64 91.291 91.262 201.148 1.00 38.20 S ATOM 1918 SG CYS B 159 94.630 91.683 206.695 1.00 34.54 S ATOM 8175 SG CYS E 103 116.854 44.650 255.548 1.00 62.24 S ATOM 8209 SG CYS E 108 115.177 41.634 257.447 1.00 64.35 S ATOM 8493 SG CYS E 144 118.946 41.250 252.015 1.00 62.00 S ATOM 8516 SG CYS E 148 117.835 38.776 252.999 1.00 64.89 S ATOM 11734 SG CYS F 362 120.867 51.885 231.988 1.00 44.54 S ATOM 11754 SG CYS F 365 118.263 51.545 237.166 1.00 46.50 S ATOM 12076 SG CYS F 405 122.205 46.826 235.735 1.00 48.89 S ATOM 11715 SG CYS F 359 124.730 52.704 237.136 1.00 49.15 S ATOM 13169 SG CYS G 114 117.121 70.578 223.242 1.00 37.23 S ATOM 13108 SG CYS G 105 111.463 73.071 225.515 1.00 35.54 S ATOM 13129 SG CYS G 108 117.260 75.366 227.389 1.00 36.80 S ATOM 13501 SG CYS G 156 126.094 64.614 227.606 1.00 41.38 S ATOM 13478 SG CYS G 153 123.239 66.347 233.350 1.00 39.69 S ATOM 13525 SG CYS G 159 129.378 67.498 232.058 1.00 43.74 S ATOM 13854 SG CYS G 203 124.665 70.614 228.595 1.00 40.77 S ATOM 12615 SG CYS G 41 126.277 58.204 224.783 1.00 41.33 S ATOM 12701 SG CYS G 52 122.107 58.175 224.202 1.00 40.82 S ATOM 12726 SG CYS G 55 123.727 53.790 221.230 1.00 40.91 S ATOM 12827 SG CYS G 69 126.841 54.274 222.305 1.00 42.86 S ATOM 21155 SG CYS I 121 98.312 85.897 212.655 1.00 33.36 S ATOM 21129 SG CYS I 118 98.376 92.484 213.579 1.00 32.53 S ATOM 21176 SG CYS I 124 100.062 88.122 218.197 1.00 32.76 S ATOM 20903 SG CYS I 89 103.770 89.208 212.791 1.00 32.73 S ATOM 21205 SG CYS I 128 103.008 85.007 225.268 1.00 33.46 S ATOM 20875 SG CYS I 85 106.479 87.471 220.154 1.00 33.83 S ATOM 20833 SG CYS I 79 108.145 88.920 226.081 1.00 36.07 S ATOM 20852 SG CYS I 82 108.260 82.585 223.413 1.00 34.98 S ATOM 41661 SG CYS R 59 105.311 79.864 240.230 1.00 40.17 S ATOM 41837 SG CYS R 84 108.147 80.505 237.713 1.00 41.24 S ATOM 41859 SG CYS R 87 106.349 83.078 239.159 1.00 40.09 S Time building chain proxies: 26.45, per 1000 atoms: 0.39 Number of scatterers: 67492 At special positions: 0 Unit cell: (188.845, 195.175, 286.96, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 8 Type Number sf(0) Zn 1 29.99 Fe 28 26.01 S 494 16.00 P 36 15.00 F 3 9.00 O 12141 8.00 N 11189 7.00 C 43600 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=10, symmetry=0 Simple disulfide: pdb=" SG CYS X 45 " - pdb=" SG CYS X 55 " distance=2.03 Simple disulfide: pdb=" SG CYS X 77 " - pdb=" SG CYS X 109 " distance=2.03 Simple disulfide: pdb=" SG CYS X 87 " - pdb=" SG CYS X 99 " distance=2.03 Simple disulfide: pdb=" SG CYS Y 17 " - pdb=" SG CYS Y 74 " distance=2.03 Simple disulfide: pdb=" SG CYS Y 94 " - pdb=" SG CYS Y 114 " distance=2.03 Simple disulfide: pdb=" SG CYS e 32 " - pdb=" SG CYS e 65 " distance=2.03 Simple disulfide: pdb=" SG CYS e 42 " - pdb=" SG CYS e 55 " distance=2.03 Simple disulfide: pdb=" SG CYS o 68 " - pdb=" SG CYS o 79 " distance=2.03 Simple disulfide: pdb=" SG CYS p 76 " - pdb=" SG CYS p 83 " distance=2.03 Simple disulfide: pdb=" SG CYS p 112 " - pdb=" SG CYS p 124 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=3, symmetry=0 Number of additional bonds: simple=3, symmetry=0 Coordination: Other bonds: Time building additional restraints: 22.48 Conformation dependent library (CDL) restraints added in 7.6 seconds Dynamic metal coordination Iron sulfur cluster coordination pdb=" FES E 301 " pdb="FE2 FES E 301 " - pdb=" SG CYS E 148 " pdb="FE2 FES E 301 " - pdb=" SG CYS E 144 " pdb="FE1 FES E 301 " - pdb=" SG CYS E 103 " pdb="FE1 FES E 301 " - pdb=" SG CYS E 108 " pdb=" FES G 803 " pdb="FE2 FES G 803 " - pdb=" SG CYS G 55 " pdb="FE2 FES G 803 " - pdb=" SG CYS G 69 " pdb="FE1 FES G 803 " - pdb=" SG CYS G 52 " 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="FE2 SF4 B 201 " - pdb=" SG CYS B 65 " pdb="FE3 SF4 B 201 " - pdb=" SG CYS B 64 " pdb=" SF4 F 502 " pdb="FE4 SF4 F 502 " - pdb=" SG CYS F 359 " pdb="FE2 SF4 F 502 " - pdb=" SG CYS F 365 " pdb="FE1 SF4 F 502 " - pdb=" SG CYS F 362 " pdb="FE3 SF4 F 502 " - pdb=" SG CYS F 405 " pdb=" SF4 G 801 " pdb="FE3 SF4 G 801 " - pdb=" NE2 HIS G 101 " pdb="FE2 SF4 G 801 " - pdb=" SG CYS G 105 " pdb="FE4 SF4 G 801 " - pdb=" SG CYS G 108 " pdb="FE1 SF4 G 801 " - pdb=" SG CYS G 114 " pdb=" SF4 G 802 " pdb="FE1 SF4 G 802 " - pdb=" SG CYS G 156 " pdb="FE2 SF4 G 802 " - pdb=" SG CYS G 153 " pdb="FE3 SF4 G 802 " - pdb=" SG CYS G 159 " pdb="FE4 SF4 G 802 " - pdb=" SG CYS G 203 " pdb=" SF4 I 203 " pdb="FE4 SF4 I 203 " - pdb=" SG CYS I 89 " pdb="FE2 SF4 I 203 " - pdb=" SG CYS I 118 " pdb="FE1 SF4 I 203 " - pdb=" SG CYS I 121 " pdb="FE3 SF4 I 203 " - pdb=" SG CYS I 124 " pdb=" SF4 I 204 " pdb="FE2 SF4 I 204 " - pdb=" SG CYS I 85 " pdb="FE1 SF4 I 204 " - pdb=" SG CYS I 128 " pdb="FE4 SF4 I 204 " - pdb=" SG CYS I 82 " pdb="FE3 SF4 I 204 " - pdb=" SG CYS I 79 " 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 16258 Ramachandran restraints generated. 8129 Oldfield, 0 Emsley, 8129 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 15504 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 341 helices and 30 sheets defined 51.3% alpha, 4.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.57 Creating SS restraints... Processing helix chain 'A' and resid 3 through 23 Processing helix chain 'A' and resid 31 through 34 No H-bonds generated for 'chain 'A' and resid 31 through 34' Processing helix chain 'A' and resid 56 through 80 removed outlier: 3.517A pdb=" N LEU A 64 " --> pdb=" O ILE A 60 " (cutoff:3.500A) Proline residue: A 74 - end of helix removed outlier: 5.569A pdb=" N TRP A 77 " --> pdb=" O LEU A 73 " (cutoff:3.500A) removed outlier: 4.552A pdb=" N GLN A 80 " --> pdb=" O PRO A 76 " (cutoff:3.500A) Processing helix chain 'A' and resid 84 through 107 Processing helix chain 'B' and resid 36 through 53 Processing helix chain 'B' and resid 64 through 73 Processing helix chain 'B' and resid 75 through 77 No H-bonds generated for 'chain 'B' and resid 75 through 77' Processing helix chain 'B' and resid 80 through 82 No H-bonds generated for 'chain 'B' and resid 80 through 82' Processing helix chain 'B' and resid 90 through 92 No H-bonds generated for 'chain 'B' and resid 90 through 92' Processing helix chain 'B' and resid 104 through 116 Proline residue: B 108 - end of helix Processing helix chain 'B' and resid 128 through 132 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 148 No H-bonds generated for 'chain 'B' and resid 146 through 148' Processing helix chain 'B' and resid 163 through 179 Processing helix chain 'B' and resid 182 through 188 Processing helix chain 'C' and resid 16 through 32 Processing helix chain 'C' and resid 54 through 66 removed outlier: 5.142A 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 138 removed outlier: 4.310A pdb=" N TRP C 129 " --> pdb=" O ALA C 126 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N PHE C 138 " --> pdb=" O TRP C 135 " (cutoff:3.500A) Processing helix chain 'C' and resid 207 through 209 No H-bonds generated for 'chain 'C' and resid 207 through 209' Processing helix chain 'D' and resid 8 through 14 removed outlier: 4.050A pdb=" N GLN D 13 " --> pdb=" O GLU D 9 " (cutoff:3.500A) removed outlier: 4.275A pdb=" N PHE D 14 " --> pdb=" O TRP D 10 " (cutoff:3.500A) Processing helix chain 'D' and resid 87 through 93 removed outlier: 3.968A pdb=" N GLU D 92 " --> pdb=" O GLU D 88 " (cutoff:3.500A) Processing helix chain 'D' and resid 97 through 106 Proline residue: D 101 - end of helix removed outlier: 3.661A pdb=" N LEU D 106 " --> pdb=" O PHE D 103 " (cutoff:3.500A) Processing helix chain 'D' and resid 111 through 126 Processing helix chain 'D' and resid 132 through 161 Processing helix chain 'D' and resid 165 through 185 removed outlier: 3.812A pdb=" N GLU D 172 " --> pdb=" O PHE D 168 " (cutoff:3.500A) removed outlier: 4.288A pdb=" N GLU D 173 " --> pdb=" O TRP D 169 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N LYS D 176 " --> pdb=" O GLU D 172 " (cutoff:3.500A) Processing helix chain 'D' and resid 207 through 229 removed outlier: 4.102A pdb=" N ASN D 217 " --> pdb=" O GLU D 213 " (cutoff:3.500A) removed outlier: 4.427A pdb=" N SER D 219 " --> pdb=" O SER D 215 " (cutoff:3.500A) removed outlier: 5.883A pdb=" N LEU D 220 " --> pdb=" O LYS D 216 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N ARG D 221 " --> pdb=" O ASN D 217 " (cutoff:3.500A) Processing helix chain 'D' and resid 233 through 239 Processing helix chain 'D' and resid 247 through 253 Processing helix chain 'D' and resid 257 through 261 Processing helix chain 'D' and resid 293 through 316 removed outlier: 3.618A pdb=" N GLN D 313 " --> pdb=" O ARG D 309 " (cutoff:3.500A) Processing helix chain 'D' and resid 335 through 338 No H-bonds generated for 'chain 'D' and resid 335 through 338' Processing helix chain 'D' and resid 342 through 353 Processing helix chain 'D' and resid 396 through 400 Processing helix chain 'D' and resid 402 through 405 No H-bonds generated for 'chain 'D' and resid 402 through 405' Processing helix chain 'D' and resid 411 through 420 Processing helix chain 'D' and resid 425 through 428 No H-bonds generated for 'chain 'D' and resid 425 through 428' Processing helix chain 'E' and resid 25 through 37 removed outlier: 3.618A pdb=" N LYS E 29 " --> pdb=" O PRO E 25 " (cutoff:3.500A) Processing helix chain 'E' and resid 47 through 58 Processing helix chain 'E' and resid 63 through 73 Processing helix chain 'E' and resid 77 through 86 removed outlier: 4.370A pdb=" N GLU E 82 " --> pdb=" O ARG E 79 " (cutoff:3.500A) Processing helix chain 'E' and resid 106 through 111 removed outlier: 4.329A pdb=" N ARG E 111 " --> pdb=" O PRO E 107 " (cutoff:3.500A) Processing helix chain 'E' and resid 114 through 124 Processing helix chain 'E' and resid 166 through 178 removed outlier: 3.552A pdb=" N ALA E 178 " --> pdb=" O ASP E 174 " (cutoff:3.500A) Processing helix chain 'F' and resid 17 through 19 No H-bonds generated for 'chain 'F' and resid 17 through 19' Processing helix chain 'F' and resid 33 through 39 Processing helix chain 'F' and resid 45 through 50 Processing helix chain 'F' and resid 53 through 62 Processing helix chain 'F' and resid 75 through 80 Processing helix chain 'F' and resid 106 through 113 Processing helix chain 'F' and resid 115 through 129 Processing helix chain 'F' and resid 143 through 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 189 through 197 removed outlier: 3.559A pdb=" N ILE F 193 " --> pdb=" O GLU F 189 " (cutoff:3.500A) 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 239 through 244 Processing helix chain 'F' and resid 276 through 283 removed outlier: 3.818A pdb=" N HIS F 283 " --> pdb=" O LEU F 279 " (cutoff:3.500A) Processing helix chain 'F' and resid 291 through 293 No H-bonds generated for 'chain 'F' and resid 291 through 293' Processing helix chain 'F' and resid 309 through 312 No H-bonds generated for 'chain 'F' and resid 309 through 312' Processing helix chain 'F' and resid 319 through 324 Processing helix chain 'F' and resid 343 through 357 Processing helix chain 'F' and resid 363 through 381 removed outlier: 4.252A pdb=" N ASP F 370 " --> pdb=" O ARG F 366 " (cutoff:3.500A) Processing helix chain 'F' and resid 386 through 400 removed outlier: 3.777A pdb=" N ILE F 389 " --> pdb=" O PRO F 386 " (cutoff:3.500A) removed outlier: 4.201A pdb=" N ASP F 390 " --> pdb=" O ALA F 387 " (cutoff:3.500A) 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 26 through 32 Processing helix chain 'G' and resid 84 through 99 Processing helix chain 'G' and resid 105 through 107 No H-bonds generated for 'chain 'G' and resid 105 through 107' Processing helix chain 'G' and resid 115 through 123 Processing helix chain 'G' and resid 150 through 152 No H-bonds generated for 'chain 'G' and resid 150 through 152' Processing helix chain 'G' and resid 158 through 165 Processing helix chain 'G' and resid 178 through 180 No H-bonds generated for 'chain 'G' and resid 178 through 180' Processing helix chain 'G' and resid 197 through 202 removed outlier: 3.838A pdb=" N ASP G 201 " --> pdb=" O GLY G 197 " (cutoff:3.500A) Processing helix chain 'G' and resid 265 through 275 removed outlier: 4.928A pdb=" N TYR G 271 " --> pdb=" O THR G 267 " (cutoff:3.500A) removed outlier: 6.596A pdb=" N ASP G 272 " --> pdb=" O ARG G 268 " (cutoff:3.500A) removed outlier: 5.655A pdb=" N GLY G 273 " --> pdb=" O PHE G 269 " (cutoff:3.500A) removed outlier: 4.648A pdb=" N LEU G 274 " --> pdb=" O ALA G 270 " (cutoff:3.500A) removed outlier: 4.377A pdb=" N LYS G 275 " --> pdb=" O TYR G 271 " (cutoff:3.500A) Processing helix chain 'G' and resid 296 through 308 Processing helix chain 'G' and resid 325 through 337 Processing helix chain 'G' and resid 355 through 357 No H-bonds generated for 'chain 'G' and resid 355 through 357' Processing helix chain 'G' and resid 359 through 361 No H-bonds generated for 'chain 'G' and resid 359 through 361' Processing helix chain 'G' and resid 368 through 372 Processing helix chain 'G' and resid 384 through 387 No H-bonds generated for 'chain 'G' and resid 384 through 387' Processing helix chain 'G' and resid 389 through 401 Processing helix chain 'G' and resid 426 through 433 removed outlier: 3.505A pdb=" N GLN G 430 " --> pdb=" O LYS G 427 " (cutoff:3.500A) Processing helix chain 'G' and resid 438 through 445 Processing helix chain 'G' and resid 455 through 459 Processing helix chain 'G' and resid 461 through 481 removed outlier: 4.640A pdb=" N ALA G 464 " --> pdb=" O ASP G 461 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N THR G 481 " --> pdb=" O ARG G 478 " (cutoff:3.500A) Processing helix chain 'G' and resid 497 through 505 removed outlier: 3.817A pdb=" N VAL G 500 " --> pdb=" O ALA G 497 " (cutoff:3.500A) Processing helix chain 'G' and resid 512 through 516 Processing helix chain 'G' and resid 534 through 536 No H-bonds generated for 'chain 'G' and resid 534 through 536' Processing helix chain 'G' and resid 566 through 568 No H-bonds generated for 'chain 'G' and resid 566 through 568' Processing helix chain 'G' and resid 596 through 606 Processing helix chain 'G' and resid 616 through 626 Processing helix chain 'G' and resid 628 through 630 No H-bonds generated for 'chain 'G' and resid 628 through 630' Processing helix chain 'G' and resid 642 through 651 removed outlier: 4.946A pdb=" N LEU G 651 " --> pdb=" O GLU G 647 " (cutoff:3.500A) Processing helix chain 'G' and resid 668 through 670 No H-bonds generated for 'chain 'G' and resid 668 through 670' Processing helix chain 'G' and resid 676 through 679 No H-bonds generated for 'chain 'G' and resid 676 through 679' Processing helix chain 'G' and resid 682 through 693 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: 4.477A pdb=" N TRP H 86 " --> pdb=" O ALA H 82 " (cutoff:3.500A) Processing helix chain 'H' and resid 101 through 123 removed outlier: 3.723A pdb=" N VAL H 113 " --> pdb=" O SER H 109 " (cutoff:3.500A) removed outlier: 4.722A pdb=" N TYR H 114 " --> pdb=" O SER H 110 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N SER H 115 " --> pdb=" O LEU H 111 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N ILE H 116 " --> pdb=" O SER H 112 " (cutoff:3.500A) Processing helix chain 'H' and resid 126 through 156 removed outlier: 4.796A pdb=" N VAL H 144 " --> pdb=" O ILE H 140 " (cutoff:3.500A) removed outlier: 4.715A pdb=" N THR H 145 " --> pdb=" O SER H 141 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N ALA H 147 " --> pdb=" O GLU H 143 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N ILE H 148 " --> pdb=" O VAL H 144 " (cutoff:3.500A) removed outlier: 4.531A pdb=" N MET H 156 " --> pdb=" O SER H 152 " (cutoff:3.500A) Processing helix chain 'H' and resid 164 through 168 Processing helix chain 'H' and resid 179 through 192 Processing helix chain 'H' and resid 210 through 212 No H-bonds generated for 'chain 'H' and resid 210 through 212' Processing helix chain 'H' and resid 217 through 241 removed outlier: 3.920A pdb=" N ILE H 232 " --> pdb=" O TYR H 228 " (cutoff:3.500A) Processing helix chain 'H' and resid 252 through 276 Processing helix chain 'H' and resid 282 through 291 removed outlier: 3.865A pdb=" N MET H 286 " --> pdb=" O TYR H 282 " (cutoff:3.500A) Processing helix chain 'H' and resid 294 through 310 Proline residue: H 308 - end of helix Processing helix chain 'I' and resid 16 through 28 Processing helix chain 'I' and resid 30 through 44 removed outlier: 3.683A pdb=" N GLY I 35 " --> pdb=" O GLU I 31 " (cutoff:3.500A) Processing helix chain 'I' and resid 84 through 88 Processing helix chain 'I' and resid 123 through 127 Processing helix chain 'I' and resid 147 through 149 No H-bonds generated for 'chain 'I' and resid 147 through 149' Processing helix chain 'I' and resid 153 through 174 removed outlier: 6.632A pdb=" N ALA I 165 " --> pdb=" O ASP I 161 " (cutoff:3.500A) removed outlier: 6.205A pdb=" N GLU I 166 " --> pdb=" O LYS I 162 " (cutoff:3.500A) removed outlier: 4.104A pdb=" N ALA I 169 " --> pdb=" O ALA I 165 " (cutoff:3.500A) Processing helix chain 'J' and resid 4 through 20 Processing helix chain 'J' and resid 25 through 46 Processing helix chain 'J' and resid 50 through 70 Processing helix chain 'J' and resid 86 through 109 removed outlier: 3.929A pdb=" N TYR J 108 " --> pdb=" O CYS J 104 " (cutoff:3.500A) Processing helix chain 'J' and resid 137 through 146 removed outlier: 3.633A pdb=" N MET J 144 " --> pdb=" O VAL J 141 " (cutoff:3.500A) Processing helix chain 'J' and resid 149 through 170 Processing helix chain 'K' and resid 3 through 20 Processing helix chain 'K' and resid 27 through 50 Processing helix chain 'K' and resid 57 through 85 removed outlier: 3.962A pdb=" N ILE K 61 " --> pdb=" O MET K 57 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N THR K 62 " --> pdb=" O PRO K 58 " (cutoff:3.500A) Processing helix chain 'L' and resid 3 through 22 removed outlier: 4.164A 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 25 through 28 Processing helix chain 'L' and resid 32 through 57 removed outlier: 4.112A 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: 3.615A pdb=" N GLN L 102 " --> pdb=" O TRP L 98 " (cutoff:3.500A) Processing helix chain 'L' and resid 114 through 132 Processing helix chain 'L' and resid 137 through 157 Processing helix chain 'L' and resid 164 through 192 removed outlier: 3.933A pdb=" N GLY L 181 " --> pdb=" O ILE L 177 " (cutoff:3.500A) Processing helix chain 'L' and resid 198 through 204 removed outlier: 4.718A pdb=" N PHE L 203 " --> pdb=" O GLN L 199 " (cutoff:3.500A) removed outlier: 4.615A pdb=" N SER L 204 " --> pdb=" O GLN L 200 " (cutoff:3.500A) Processing helix chain 'L' and resid 210 through 223 Processing helix chain 'L' and resid 227 through 229 No H-bonds generated for 'chain 'L' and resid 227 through 229' Processing helix chain 'L' and resid 232 through 238 removed outlier: 4.004A pdb=" N MET L 237 " --> pdb=" O LEU L 233 " (cutoff:3.500A) removed outlier: 4.836A pdb=" N GLU L 238 " --> pdb=" O PRO L 234 " (cutoff:3.500A) Processing helix chain 'L' and resid 241 through 246 Processing helix chain 'L' and resid 253 through 262 removed outlier: 3.983A pdb=" N GLY L 256 " --> pdb=" O VAL L 253 " (cutoff:3.500A) Processing helix chain 'L' and resid 264 through 267 No H-bonds generated for 'chain 'L' and resid 264 through 267' Processing helix chain 'L' and resid 271 through 294 removed outlier: 3.689A pdb=" N LEU L 293 " --> pdb=" O ALA L 289 " (cutoff:3.500A) removed outlier: 4.263A pdb=" N THR L 294 " --> pdb=" O ILE L 290 " (cutoff:3.500A) Processing helix chain 'L' and resid 298 through 319 Processing helix chain 'L' and resid 322 through 349 removed outlier: 3.725A pdb=" N ALA L 333 " --> pdb=" O ILE L 329 " (cutoff:3.500A) removed outlier: 4.548A pdb=" N PHE L 334 " --> pdb=" O CYS L 330 " (cutoff:3.500A) removed outlier: 4.462A pdb=" N PHE L 335 " --> pdb=" O THR L 331 " (cutoff:3.500A) Processing helix chain 'L' and resid 356 through 358 No H-bonds generated for 'chain 'L' and resid 356 through 358' Processing helix chain 'L' and resid 367 through 380 Processing helix chain 'L' and resid 389 through 401 removed outlier: 5.167A pdb=" N LEU L 394 " --> pdb=" O TYR L 390 " (cutoff:3.500A) Processing helix chain 'L' and resid 406 through 431 Processing helix chain 'L' and resid 448 through 471 Proline residue: L 453 - end of helix removed outlier: 5.822A pdb=" N GLY L 465 " --> pdb=" O SER L 461 " (cutoff:3.500A) removed outlier: 5.336A 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 508 Processing helix chain 'L' and resid 518 through 524 removed outlier: 3.628A pdb=" N PHE L 522 " --> pdb=" O PRO L 518 " (cutoff:3.500A) removed outlier: 4.197A pdb=" N SER L 523 " --> pdb=" O TYR L 519 " (cutoff:3.500A) Processing helix chain 'L' and resid 526 through 547 Proline residue: L 530 - end of helix removed outlier: 5.283A pdb=" N HIS L 534 " --> pdb=" O SER L 531 " (cutoff:3.500A) removed outlier: 5.626A pdb=" N THR L 537 " --> pdb=" O HIS L 534 " (cutoff:3.500A) Proline residue: L 538 - end of helix removed outlier: 4.018A pdb=" N SER L 545 " --> pdb=" O LEU L 542 " (cutoff:3.500A) Processing helix chain 'L' and resid 551 through 554 No H-bonds generated for 'chain 'L' and resid 551 through 554' Processing helix chain 'L' and resid 557 through 561 Processing helix chain 'L' and resid 563 through 578 removed outlier: 4.066A pdb=" N THR L 568 " --> pdb=" O LYS L 564 " (cutoff:3.500A) Processing helix chain 'L' and resid 584 through 605 Processing helix chain 'M' and resid 5 through 16 removed outlier: 4.255A 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 23 through 42 removed outlier: 3.828A pdb=" N LEU M 39 " --> pdb=" O SER M 35 " (cutoff:3.500A) removed outlier: 4.566A pdb=" N THR M 40 " --> pdb=" O LEU M 36 " (cutoff:3.500A) removed outlier: 5.187A pdb=" N LEU M 41 " --> pdb=" O THR M 37 " (cutoff:3.500A) removed outlier: 4.976A pdb=" N LEU M 42 " --> pdb=" O SER M 38 " (cutoff:3.500A) Processing helix chain 'M' and resid 60 through 79 Proline residue: M 64 - end of helix removed outlier: 3.830A pdb=" N LEU M 73 " --> pdb=" O THR M 69 " (cutoff:3.500A) Proline residue: M 74 - end of helix Processing helix chain 'M' and resid 89 through 111 Processing helix chain 'M' and resid 115 through 136 removed outlier: 4.641A pdb=" N LEU M 126 " --> pdb=" O PHE M 122 " (cutoff:3.500A) removed outlier: 4.468A 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 140 through 171 removed outlier: 3.573A pdb=" N LEU M 143 " --> pdb=" O THR M 140 " (cutoff:3.500A) removed outlier: 4.388A pdb=" N TYR M 152 " --> pdb=" O PHE M 149 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ILE M 155 " --> pdb=" O TYR M 152 " (cutoff:3.500A) removed outlier: 4.325A pdb=" N ILE M 158 " --> pdb=" O ILE M 155 " (cutoff:3.500A) 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: 4.480A pdb=" N ALA M 202 " --> pdb=" O ALA M 198 " (cutoff:3.500A) removed outlier: 5.123A pdb=" N PHE M 203 " --> pdb=" O CYS M 199 " (cutoff:3.500A) Processing helix chain 'M' and resid 214 through 222 removed outlier: 3.732A pdb=" N LYS M 218 " --> pdb=" O LEU M 214 " (cutoff:3.500A) Processing helix chain 'M' and resid 225 through 234 Processing helix chain 'M' and resid 237 through 248 removed outlier: 4.774A pdb=" N ILE M 248 " --> pdb=" O ILE M 244 " (cutoff:3.500A) 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 275 removed outlier: 3.801A pdb=" N ILE M 270 " --> pdb=" O LEU M 266 " (cutoff:3.500A) Processing helix chain 'M' and resid 282 through 303 removed outlier: 3.962A pdb=" N LEU M 296 " --> pdb=" O SER M 292 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N VAL M 297 " --> pdb=" O HIS M 293 " (cutoff:3.500A) Processing helix chain 'M' and resid 306 through 337 removed outlier: 3.536A pdb=" N ASN M 333 " --> pdb=" O LEU M 329 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N ARG M 336 " --> pdb=" O SER M 332 " (cutoff:3.500A) Processing helix chain 'M' and resid 353 through 366 removed outlier: 3.767A pdb=" N THR M 357 " --> pdb=" O PRO M 353 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N TRP M 358 " --> pdb=" O LEU M 354 " (cutoff:3.500A) Processing helix chain 'M' and resid 373 through 388 removed outlier: 3.788A pdb=" N GLU M 378 " --> pdb=" O ASN M 374 " (cutoff:3.500A) Processing helix chain 'M' and resid 392 through 415 Processing helix chain 'M' and resid 431 through 449 Proline residue: M 443 - end of helix Processing helix chain 'M' and resid 451 through 454 Processing helix chain 'N' and resid 3 through 21 Proline residue: N 17 - end of helix Processing helix chain 'N' and resid 26 through 47 removed outlier: 4.146A pdb=" N ILE N 41 " --> pdb=" O LEU N 37 " (cutoff:3.500A) Proline residue: N 42 - end of helix removed outlier: 5.448A pdb=" N LYS N 47 " --> pdb=" O MET N 43 " (cutoff:3.500A) Processing helix chain 'N' and resid 50 through 79 removed outlier: 3.544A pdb=" N THR N 62 " --> pdb=" O LYS N 58 " (cutoff:3.500A) Processing helix chain 'N' and resid 92 through 106 Processing helix chain 'N' and resid 115 through 120 Processing helix chain 'N' and resid 124 through 132 Processing helix chain 'N' and resid 136 through 144 Processing helix chain 'N' and resid 146 through 148 No H-bonds generated for 'chain 'N' and resid 146 through 148' Processing helix chain 'N' and resid 151 through 171 removed outlier: 4.329A pdb=" N ASN N 171 " --> pdb=" O TRP N 167 " (cutoff:3.500A) Processing helix chain 'N' and resid 175 through 192 Processing helix chain 'N' and resid 198 through 221 removed outlier: 3.547A pdb=" N LEU N 202 " --> pdb=" O PRO N 198 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N LEU N 203 " --> pdb=" O SER N 199 " (cutoff:3.500A) Proline residue: N 214 - end of helix Processing helix chain 'N' and resid 227 through 236 removed outlier: 3.877A pdb=" N LEU N 232 " --> pdb=" O ASN N 228 " (cutoff:3.500A) removed outlier: 4.189A pdb=" N LEU N 233 " --> pdb=" O SER N 229 " (cutoff:3.500A) removed outlier: 4.980A pdb=" N TRP N 234 " --> pdb=" O ILE N 230 " (cutoff:3.500A) removed outlier: 5.737A pdb=" N ASN N 235 " --> pdb=" O SER N 231 " (cutoff:3.500A) Processing helix chain 'N' and resid 238 through 252 removed outlier: 4.894A pdb=" N THR N 242 " --> pdb=" O ALA N 239 " (cutoff:3.500A) Processing helix chain 'N' and resid 259 through 273 removed outlier: 4.432A pdb=" N LYS N 263 " --> pdb=" O GLY N 259 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N ASN N 273 " --> pdb=" O GLU N 269 " (cutoff:3.500A) Processing helix chain 'N' and resid 276 through 300 removed outlier: 3.900A pdb=" N LEU N 288 " --> pdb=" O MET N 284 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N PHE N 292 " --> pdb=" O LEU N 288 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N TYR N 293 " --> pdb=" O ASN N 289 " (cutoff:3.500A) Processing helix chain 'N' and resid 311 through 316 Processing helix chain 'N' and resid 324 through 331 Processing helix chain 'N' and resid 337 through 344 Proline residue: N 341 - end of helix removed outlier: 3.542A pdb=" N ILE N 344 " --> pdb=" O PRO N 341 " (cutoff:3.500A) 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 61 No H-bonds generated for 'chain 'O' and resid 58 through 61' Processing helix chain 'O' and resid 79 through 84 Processing helix chain 'O' and resid 92 through 118 Processing helix chain 'O' and resid 128 through 130 No H-bonds generated for 'chain 'O' and resid 128 through 130' Processing helix chain 'O' and resid 132 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 removed outlier: 4.012A pdb=" N GLN O 184 " --> pdb=" O GLN O 180 " (cutoff:3.500A) Processing helix chain 'O' and resid 191 through 193 No H-bonds generated for 'chain 'O' and resid 191 through 193' Processing helix chain 'O' and resid 196 through 216 removed outlier: 4.748A pdb=" N LEU O 211 " --> pdb=" O LYS O 207 " (cutoff:3.500A) Proline residue: O 212 - end of helix removed outlier: 4.586A pdb=" N GLU O 216 " --> pdb=" O PRO O 212 " (cutoff:3.500A) Processing helix chain 'O' and resid 225 through 228 No H-bonds generated for 'chain 'O' and resid 225 through 228' Processing helix chain 'O' and resid 232 through 239 Processing helix chain 'O' and resid 253 through 263 Processing helix chain 'O' and resid 266 through 273 removed outlier: 5.169A pdb=" N TYR O 272 " --> pdb=" O GLU O 268 " (cutoff:3.500A) removed outlier: 5.252A pdb=" N THR O 273 " --> pdb=" O VAL O 269 " (cutoff:3.500A) Processing helix chain 'O' and resid 286 through 297 Processing helix chain 'O' and resid 300 through 302 No H-bonds generated for 'chain 'O' and resid 300 through 302' Processing helix chain 'O' and resid 310 through 312 No H-bonds generated for 'chain 'O' and resid 310 through 312' Processing helix chain 'O' and resid 316 through 319 Processing helix chain 'P' and resid 29 through 40 removed outlier: 4.388A pdb=" N TYR P 33 " --> pdb=" O PHE P 29 " (cutoff:3.500A) Processing helix chain 'P' and resid 53 through 55 No H-bonds generated for 'chain 'P' and resid 53 through 55' Processing helix chain 'P' and resid 57 through 60 No H-bonds generated for 'chain 'P' and resid 57 through 60' Processing helix chain 'P' and resid 79 through 85 removed outlier: 4.048A pdb=" N ALA P 84 " --> pdb=" O SER P 80 " (cutoff:3.500A) Processing helix chain 'P' and resid 106 through 110 Processing helix chain 'P' and resid 112 through 124 Processing helix chain 'P' and resid 144 through 159 Processing helix chain 'P' and resid 179 through 188 removed outlier: 5.317A pdb=" N ARG P 186 " --> pdb=" O PHE P 182 " (cutoff:3.500A) removed outlier: 5.190A pdb=" N TRP P 187 " --> pdb=" O ALA P 183 " (cutoff:3.500A) removed outlier: 4.711A pdb=" N PHE P 188 " --> pdb=" O ASN P 184 " (cutoff:3.500A) Processing helix chain 'P' and resid 194 through 197 Processing helix chain 'P' and resid 207 through 219 removed outlier: 4.230A pdb=" N LYS P 219 " --> pdb=" O VAL P 215 " (cutoff:3.500A) Processing helix chain 'P' and resid 238 through 248 Processing helix chain 'P' and resid 260 through 272 removed outlier: 4.238A pdb=" N TRP P 265 " --> pdb=" O PHE P 261 " (cutoff:3.500A) Processing helix chain 'P' and resid 281 through 286 Processing helix chain 'P' and resid 300 through 303 No H-bonds generated for 'chain 'P' and resid 300 through 303' Processing helix chain 'P' and resid 310 through 313 No H-bonds generated for 'chain 'P' and resid 310 through 313' Processing helix chain 'P' and resid 315 through 318 No H-bonds generated for 'chain 'P' and resid 315 through 318' Processing helix chain 'Q' and resid 20 through 22 No H-bonds generated for 'chain 'Q' and resid 20 through 22' Processing helix chain 'Q' and resid 27 through 31 Processing helix chain 'Q' and resid 78 through 81 removed outlier: 4.386A pdb=" N ASN Q 81 " --> pdb=" O PRO Q 78 " (cutoff:3.500A) No H-bonds generated for 'chain 'Q' and resid 78 through 81' Processing helix chain 'Q' and resid 89 through 99 Processing helix chain 'R' and resid 23 through 28 removed outlier: 3.968A pdb=" N ARG R 27 " --> pdb=" O ARG R 24 " (cutoff:3.500A) Processing helix chain 'R' and resid 40 through 46 Processing helix chain 'S' and resid 28 through 46 removed outlier: 4.135A pdb=" N GLY S 31 " --> pdb=" O GLY S 28 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N ARG S 33 " --> pdb=" O GLN S 30 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N ASP S 34 " --> pdb=" O GLY S 31 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N PHE S 35 " --> pdb=" O VAL S 32 " (cutoff:3.500A) removed outlier: 5.412A pdb=" N TYR S 40 " --> pdb=" O VAL S 37 " (cutoff:3.500A) removed outlier: 5.446A pdb=" N VAL S 41 " --> pdb=" O GLN S 38 " (cutoff:3.500A) Processing helix chain 'S' and resid 83 through 95 Processing helix chain 'T' and resid 10 through 22 Processing helix chain 'T' and resid 27 through 29 No H-bonds generated for 'chain 'T' and resid 27 through 29' Processing helix chain 'T' and resid 45 through 58 removed outlier: 3.754A pdb=" N ILE T 50 " --> pdb=" O ASP T 46 " (cutoff:3.500A) Processing helix chain 'T' and resid 64 through 67 No H-bonds generated for 'chain 'T' and resid 64 through 67' Processing helix chain 'T' and resid 73 through 83 Processing helix chain 'U' and resid 8 through 20 Processing helix chain 'U' and resid 27 through 29 No H-bonds generated for 'chain 'U' and resid 27 through 29' Processing helix chain 'U' and resid 44 through 58 removed outlier: 3.792A pdb=" N GLU U 49 " --> pdb=" O LEU U 45 " (cutoff:3.500A) Processing helix chain 'U' and resid 64 through 69 removed outlier: 4.497A pdb=" N LYS U 69 " --> pdb=" O ILE U 65 " (cutoff:3.500A) Processing helix chain 'U' and resid 73 through 84 Processing helix chain 'V' and resid 19 through 34 Processing helix chain 'V' and resid 42 through 60 Processing helix chain 'V' and resid 64 through 71 Processing helix chain 'V' and resid 76 through 96 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: 4.159A 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 109 removed outlier: 4.178A pdb=" N PHE W 108 " --> pdb=" O HIS W 104 " (cutoff:3.500A) removed outlier: 4.483A pdb=" N PHE W 109 " --> pdb=" O VAL W 105 " (cutoff:3.500A) Processing helix chain 'W' and resid 120 through 125 Processing helix chain 'X' and resid 21 through 33 removed outlier: 4.910A pdb=" N HIS X 29 " --> pdb=" O LYS X 25 " (cutoff:3.500A) removed outlier: 5.560A pdb=" N HIS X 30 " --> pdb=" O ALA X 26 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N ALA X 33 " --> pdb=" O HIS X 29 " (cutoff:3.500A) Processing helix chain 'X' and resid 36 through 49 Processing helix chain 'X' and resid 57 through 76 removed outlier: 3.518A pdb=" N HIS X 76 " --> pdb=" O GLN X 72 " (cutoff:3.500A) Processing helix chain 'X' and resid 78 through 88 Processing helix chain 'X' and resid 96 through 98 No H-bonds generated for 'chain 'X' and resid 96 through 98' Processing helix chain 'X' and resid 100 through 113 removed outlier: 3.694A pdb=" N LYS X 105 " --> pdb=" O GLN X 101 " (cutoff:3.500A) Processing helix chain 'Y' and resid 2 through 9 removed outlier: 4.029A pdb=" N TYR Y 8 " --> pdb=" O PHE Y 4 " (cutoff:3.500A) removed outlier: 5.240A pdb=" N HIS Y 9 " --> pdb=" O PHE Y 5 " (cutoff:3.500A) Processing helix chain 'Y' and resid 17 through 41 Processing helix chain 'Y' and resid 48 through 79 Processing helix chain 'Y' and resid 86 through 104 Processing helix chain 'Y' and resid 107 through 129 removed outlier: 4.000A pdb=" N THR Y 119 " --> pdb=" O VAL Y 115 " (cutoff:3.500A) Processing helix chain 'Z' and resid 32 through 95 Proline residue: Z 72 - end of helix Processing helix chain 'Z' and resid 120 through 123 No H-bonds generated for 'chain 'Z' and resid 120 through 123' Processing helix chain 'Z' and resid 130 through 137 removed outlier: 3.951A pdb=" N ALA Z 135 " --> pdb=" O GLU Z 131 " (cutoff:3.500A) Processing helix chain 'a' and resid 2 through 4 No H-bonds generated for 'chain 'a' and resid 2 through 4' Processing helix chain 'a' and resid 6 through 30 Proline residue: a 19 - end of helix Processing helix chain 'a' and resid 42 through 54 Processing helix chain 'a' and resid 66 through 68 No H-bonds generated for 'chain 'a' and resid 66 through 68' Processing helix chain 'b' and resid 5 through 14 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 removed outlier: 3.714A pdb=" N MET b 43 " --> pdb=" O LYS b 39 " (cutoff:3.500A) Processing helix chain 'b' and resid 78 through 81 No H-bonds generated for 'chain 'b' and resid 78 through 81' Processing helix chain 'c' and resid 14 through 45 Processing helix chain 'd' and resid 2 through 4 No H-bonds generated for 'chain 'd' and resid 2 through 4' Processing helix chain 'd' and resid 18 through 20 No H-bonds generated for 'chain 'd' and resid 18 through 20' Processing helix chain 'd' and resid 29 through 48 removed outlier: 3.716A pdb=" N LEU d 36 " --> pdb=" O VAL d 32 " (cutoff:3.500A) Processing helix chain 'd' and resid 58 through 96 Processing helix chain 'e' and resid 5 through 9 Processing helix chain 'e' and resid 25 through 27 No H-bonds generated for 'chain 'e' and resid 25 through 27' Processing helix chain 'e' and resid 33 through 42 Processing helix chain 'e' and resid 48 through 54 removed outlier: 4.219A pdb=" N LYS e 53 " --> pdb=" O THR e 49 " (cutoff:3.500A) Processing helix chain 'e' and resid 56 through 67 Processing helix chain 'e' and resid 69 through 87 Processing helix chain 'e' and resid 95 through 97 No H-bonds generated for 'chain 'e' and resid 95 through 97' Processing helix chain 'f' and resid 3 through 6 No H-bonds generated for 'chain 'f' and resid 3 through 6' Processing helix chain 'f' and resid 11 through 32 removed outlier: 3.531A pdb=" N LEU f 14 " --> pdb=" O VAL f 11 " (cutoff:3.500A) removed outlier: 5.521A 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 35 through 38 No H-bonds generated for 'chain 'g' and resid 35 through 38' Processing helix chain 'g' and resid 49 through 64 Processing helix chain 'g' and resid 67 through 76 removed outlier: 4.257A pdb=" N THR g 72 " --> pdb=" O LEU g 68 " (cutoff:3.500A) Processing helix chain 'g' and resid 84 through 100 Processing helix chain 'g' and resid 113 through 115 No H-bonds generated for 'chain 'g' and resid 113 through 115' Processing helix chain 'h' and resid 16 through 45 removed outlier: 3.703A pdb=" N PHE h 21 " --> pdb=" O TYR h 17 " (cutoff:3.500A) removed outlier: 4.312A pdb=" N THR h 32 " --> pdb=" O TYR h 28 " (cutoff:3.500A) Proline residue: h 35 - end of helix Processing helix chain 'h' and resid 63 through 66 removed outlier: 3.672A pdb=" N TYR h 66 " --> pdb=" O HIS h 63 " (cutoff:3.500A) No H-bonds generated for 'chain 'h' and resid 63 through 66' Processing helix chain 'h' and resid 70 through 79 Processing helix chain 'h' and resid 84 through 117 removed outlier: 3.898A pdb=" N ARG h 112 " --> pdb=" O GLN h 108 " (cutoff:3.500A) Processing helix chain 'i' and resid 5 through 24 removed outlier: 3.615A pdb=" N LYS i 23 " --> pdb=" O ARG i 19 " (cutoff:3.500A) Processing helix chain 'i' and resid 69 through 88 removed outlier: 5.096A 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 61 through 64 No H-bonds generated for 'chain 'j' and resid 61 through 64' Processing helix chain 'k' and resid 24 through 26 No H-bonds generated for 'chain 'k' and resid 24 through 26' Processing helix chain 'k' and resid 33 through 44 removed outlier: 4.306A pdb=" N ARG k 44 " --> pdb=" O LYS k 40 " (cutoff:3.500A) Processing helix chain 'k' and resid 49 through 58 removed outlier: 3.955A pdb=" N ARG k 52 " --> pdb=" O PRO k 49 " (cutoff:3.500A) removed outlier: 5.304A pdb=" N TRP k 56 " --> pdb=" O ASN k 53 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N ARG k 57 " --> pdb=" O GLU k 54 " (cutoff:3.500A) Processing helix chain 'k' and resid 68 through 72 Processing helix chain 'k' and resid 76 through 93 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 25 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 97 through 120 Processing helix chain 'l' and resid 133 through 137 Processing helix chain 'm' and resid 26 through 50 removed outlier: 4.025A 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 83 through 117 removed outlier: 3.530A pdb=" N LEU m 87 " --> pdb=" O PRO m 83 " (cutoff:3.500A) Proline residue: m 96 - end of helix Processing helix chain 'n' and resid 11 through 29 Processing helix chain 'n' and resid 33 through 50 removed outlier: 4.324A pdb=" N HIS n 50 " --> pdb=" O ARG n 46 " (cutoff:3.500A) Processing helix chain 'n' and resid 57 through 71 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 112 Processing helix chain 'n' and resid 115 through 140 removed outlier: 4.962A pdb=" N ASP n 133 " --> pdb=" O MET n 129 " (cutoff:3.500A) removed outlier: 4.717A pdb=" N ARG n 134 " --> pdb=" O GLU n 130 " (cutoff:3.500A) Processing helix chain 'o' and resid 12 through 14 No H-bonds generated for 'chain 'o' and resid 12 through 14' Processing helix chain 'o' and resid 42 through 47 Processing helix chain 'o' and resid 52 through 54 No H-bonds generated for 'chain 'o' and resid 52 through 54' Processing helix chain 'o' and resid 59 through 71 Processing helix chain 'o' and resid 80 through 114 Processing helix chain 'p' and resid 28 through 56 removed outlier: 4.509A 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 73 through 75 No H-bonds generated for 'chain 'p' and resid 73 through 75' Processing helix chain 'p' and resid 81 through 116 Processing helix chain 'p' and resid 125 through 142 Processing helix chain 'p' and resid 151 through 170 Processing helix chain 'q' and resid 3 through 15 Processing helix chain 'q' and resid 20 through 29 Processing helix chain 'q' and resid 56 through 58 No H-bonds generated for 'chain 'q' and resid 56 through 58' Processing helix chain 'q' and resid 79 through 81 No H-bonds generated for 'chain 'q' and resid 79 through 81' Processing helix chain 'q' and resid 84 through 90 removed outlier: 4.247A pdb=" N TRP q 89 " --> pdb=" O GLU q 85 " (cutoff:3.500A) Processing helix chain 'r' and resid 7 through 15 Processing helix chain 'r' and resid 19 through 21 No H-bonds generated for 'chain 'r' and resid 19 through 21' Processing helix chain 's' and resid 37 through 39 No H-bonds generated for 'chain 's' and resid 37 through 39' Processing helix chain 's' and resid 44 through 55 removed outlier: 4.176A pdb=" N LYS s 54 " --> pdb=" O LEU s 50 " (cutoff:3.500A) removed outlier: 5.048A pdb=" N PHE s 55 " --> pdb=" O ASP s 51 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'B' and resid 95 through 99 removed outlier: 7.061A pdb=" N TYR B 122 " --> pdb=" O MET B 96 " (cutoff:3.500A) removed outlier: 8.099A pdb=" N VAL B 98 " --> pdb=" O TYR B 122 " (cutoff:3.500A) removed outlier: 7.251A pdb=" N VAL B 124 " --> pdb=" O VAL B 98 " (cutoff:3.500A) removed outlier: 6.617A pdb=" N ILE B 154 " --> pdb=" O SER B 125 " (cutoff:3.500A) No H-bonds generated for sheet with id= A Processing sheet with id= B, first strand: chain 'C' and resid 49 through 51 removed outlier: 8.889A pdb=" N ILE C 50 " --> pdb=" O ARG C 104 " (cutoff:3.500A) removed outlier: 6.506A pdb=" N ARG C 106 " --> pdb=" O ILE C 50 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N ASP C 77 " --> pdb=" O ASN C 95 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'C' and resid 172 through 177 Processing sheet with id= D, first strand: chain 'C' and resid 72 through 75 removed outlier: 7.086A pdb=" N LEU C 97 " --> pdb=" O LYS C 73 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'D' and resid 47 through 50 removed outlier: 3.739A pdb=" N LYS D 75 " --> pdb=" O GLU D 67 " (cutoff:3.500A) removed outlier: 6.312A pdb=" N SER D 69 " --> pdb=" O VAL D 73 " (cutoff:3.500A) removed outlier: 5.673A 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 369 Processing sheet with id= G, first strand: chain 'E' and resid 137 through 142 removed outlier: 6.722A pdb=" N TYR E 98 " --> pdb=" O THR E 138 " (cutoff:3.500A) removed outlier: 8.039A pdb=" N ILE E 140 " --> pdb=" O TYR E 98 " (cutoff:3.500A) removed outlier: 6.504A pdb=" N ILE E 100 " --> pdb=" O ILE E 140 " (cutoff:3.500A) removed outlier: 7.084A pdb=" N VAL E 142 " --> pdb=" O ILE E 100 " (cutoff:3.500A) removed outlier: 5.967A pdb=" N VAL E 102 " --> pdb=" O VAL E 142 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N CYS E 103 " --> pdb=" O MET E 153 " (cutoff:3.500A) removed outlier: 5.624A pdb=" N MET E 153 " --> pdb=" O CYS E 103 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'F' and resid 222 through 224 removed outlier: 8.469A pdb=" N ALA F 223 " --> pdb=" O TYR F 92 " (cutoff:3.500A) removed outlier: 6.365A pdb=" N VAL F 94 " --> pdb=" O ALA F 223 " (cutoff:3.500A) removed outlier: 6.415A pdb=" N ALA F 133 " --> pdb=" O LEU F 93 " (cutoff:3.500A) removed outlier: 7.791A pdb=" N VAL F 95 " --> pdb=" O ALA F 133 " (cutoff:3.500A) removed outlier: 6.729A pdb=" N TYR F 135 " --> pdb=" O VAL F 95 " (cutoff:3.500A) removed outlier: 7.326A pdb=" N ALA F 97 " --> pdb=" O TYR F 135 " (cutoff:3.500A) removed outlier: 7.438A pdb=" N TYR F 137 " --> pdb=" O ALA F 97 " (cutoff:3.500A) removed outlier: 6.778A pdb=" N ASP F 174 " --> pdb=" O ALA F 134 " (cutoff:3.500A) removed outlier: 7.809A pdb=" N ILE F 136 " --> pdb=" O ASP F 174 " (cutoff:3.500A) removed outlier: 6.867A pdb=" N PHE F 176 " --> pdb=" O ILE F 136 " (cutoff:3.500A) removed outlier: 7.267A pdb=" N ILE F 138 " --> pdb=" O PHE F 176 " (cutoff:3.500A) removed outlier: 5.844A pdb=" N VAL F 178 " --> pdb=" O ILE F 138 " (cutoff:3.500A) No H-bonds generated for sheet with id= H 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 56 through 58 Processing sheet with id= L, first strand: chain 'G' and resid 146 through 148 Processing sheet with id= M, first strand: chain 'G' and resid 173 through 175 Processing sheet with id= N, first strand: chain 'G' and resid 223 through 228 removed outlier: 3.672A pdb=" N ARG G 249 " --> pdb=" O SER G 241 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'G' and resid 283 through 285 Processing sheet with id= P, first strand: chain 'G' and resid 315 through 319 removed outlier: 6.400A pdb=" N MET G 521 " --> pdb=" O ALA G 316 " (cutoff:3.500A) removed outlier: 8.275A pdb=" N ILE G 318 " --> pdb=" O MET G 521 " (cutoff:3.500A) removed outlier: 6.762A pdb=" N PHE G 523 " --> pdb=" O ILE G 318 " (cutoff:3.500A) removed outlier: 6.422A pdb=" N PHE G 542 " --> pdb=" O LEU G 522 " (cutoff:3.500A) removed outlier: 7.592A pdb=" N LEU G 524 " --> pdb=" O PHE G 542 " (cutoff:3.500A) removed outlier: 6.533A pdb=" N VAL G 544 " --> pdb=" O LEU G 524 " (cutoff:3.500A) removed outlier: 6.590A pdb=" N VAL G 559 " --> pdb=" O TYR G 545 " (cutoff:3.500A) removed outlier: 8.247A pdb=" N GLY G 547 " --> pdb=" O VAL G 559 " (cutoff:3.500A) removed outlier: 6.354A pdb=" N LEU G 561 " --> pdb=" O GLY G 547 " (cutoff:3.500A) No H-bonds generated for sheet with id= P Processing sheet with id= Q, first strand: chain 'G' and resid 490 through 493 removed outlier: 8.295A pdb=" N ASN G 491 " --> pdb=" O PRO G 449 " (cutoff:3.500A) removed outlier: 6.445A pdb=" N VAL G 451 " --> pdb=" O ASN G 491 " (cutoff:3.500A) removed outlier: 7.422A pdb=" N LEU G 493 " --> pdb=" O VAL G 451 " (cutoff:3.500A) removed outlier: 6.427A pdb=" N LEU G 453 " --> pdb=" O LEU G 493 " (cutoff:3.500A) removed outlier: 6.621A pdb=" N VAL G 376 " --> pdb=" O MET G 450 " (cutoff:3.500A) removed outlier: 7.899A pdb=" N VAL G 452 " --> pdb=" O VAL G 376 " (cutoff:3.500A) removed outlier: 6.270A pdb=" N LEU G 378 " --> pdb=" O VAL G 452 " (cutoff:3.500A) removed outlier: 7.753A pdb=" N GLY G 454 " --> pdb=" O LEU G 378 " (cutoff:3.500A) removed outlier: 7.691A pdb=" N VAL G 380 " --> pdb=" O GLY G 454 " (cutoff:3.500A) removed outlier: 6.602A pdb=" N LYS G 405 " --> pdb=" O VAL G 377 " (cutoff:3.500A) removed outlier: 8.109A pdb=" N LEU G 379 " --> pdb=" O LYS G 405 " (cutoff:3.500A) removed outlier: 6.778A pdb=" N ALA G 407 " --> pdb=" O LEU G 379 " (cutoff:3.500A) removed outlier: 6.619A pdb=" N ASP G 420 " --> pdb=" O LEU G 408 " (cutoff:3.500A) No H-bonds generated for sheet with id= Q Processing sheet with id= R, first strand: chain 'G' and resid 571 through 574 removed outlier: 3.649A pdb=" N ALA G 571 " --> pdb=" O THR G 583 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'I' and resid 67 through 69 Processing sheet with id= T, first strand: chain 'I' and resid 94 through 100 removed outlier: 5.751A pdb=" N GLU I 99 " --> pdb=" O THR I 108 " (cutoff:3.500A) removed outlier: 5.040A pdb=" N THR I 108 " --> pdb=" O GLU I 99 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'L' and resid 61 through 64 Processing sheet with id= V, first strand: chain 'L' and resid 67 through 71 removed outlier: 7.115A pdb=" N LEU L 76 " --> pdb=" O TRP L 68 " (cutoff:3.500A) removed outlier: 5.069A pdb=" N THR L 70 " --> pdb=" O MET L 74 " (cutoff:3.500A) removed outlier: 6.487A pdb=" N MET L 74 " --> pdb=" O THR L 70 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'O' and resid 219 through 224 removed outlier: 6.598A pdb=" N VAL O 122 " --> pdb=" O ILE O 25 " (cutoff:3.500A) removed outlier: 7.818A pdb=" N VAL O 27 " --> pdb=" O VAL O 122 " (cutoff:3.500A) removed outlier: 6.668A pdb=" N LEU O 124 " --> pdb=" O VAL O 27 " (cutoff:3.500A) removed outlier: 8.385A pdb=" N GLY O 29 " --> pdb=" O LEU O 124 " (cutoff:3.500A) removed outlier: 6.555A pdb=" N LYS O 49 " --> pdb=" O VAL O 123 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain 'P' and resid 227 through 230 removed outlier: 6.939A pdb=" N ILE P 165 " --> pdb=" O PHE P 228 " (cutoff:3.500A) removed outlier: 7.662A pdb=" N PHE P 230 " --> pdb=" O ILE P 165 " (cutoff:3.500A) removed outlier: 6.577A pdb=" N ARG P 167 " --> pdb=" O PHE P 230 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N VAL P 132 " --> pdb=" O ASN P 93 " (cutoff:3.500A) removed outlier: 6.505A pdb=" N GLN P 44 " --> pdb=" O ALA P 21 " (cutoff:3.500A) removed outlier: 7.413A pdb=" N VAL P 23 " --> pdb=" O GLN P 44 " (cutoff:3.500A) removed outlier: 6.685A pdb=" N ILE P 46 " --> pdb=" O VAL P 23 " (cutoff:3.500A) Processing sheet with id= Y, first strand: chain 'P' and resid 191 through 193 Processing sheet with id= Z, first strand: chain 'Q' and resid 102 through 105 removed outlier: 3.637A pdb=" N ILE Q 37 " --> pdb=" O ASP Q 104 " (cutoff:3.500A) Processing sheet with id= AA, first strand: chain 'R' and resid 50 through 52 Processing sheet with id= AB, first strand: chain 'R' and resid 56 through 59 Processing sheet with id= AC, first strand: chain 'S' and resid 51 through 57 removed outlier: 4.150A pdb=" N LEU S 22 " --> pdb=" O ARG S 55 " (cutoff:3.500A) removed outlier: 7.174A pdb=" N ARG S 67 " --> pdb=" O ARG S 16 " (cutoff:3.500A) removed outlier: 4.545A pdb=" N ILE S 18 " --> pdb=" O TRP S 65 " (cutoff:3.500A) removed outlier: 6.921A pdb=" N TRP S 65 " --> pdb=" O ILE S 18 " (cutoff:3.500A) removed outlier: 4.877A pdb=" N VAL S 20 " --> pdb=" O LYS S 63 " (cutoff:3.500A) removed outlier: 6.703A pdb=" N LYS S 63 " --> pdb=" O VAL S 20 " (cutoff:3.500A) Processing sheet with id= AD, first strand: chain 'q' and resid 60 through 63 removed outlier: 3.727A pdb=" N GLY q 40 " --> pdb=" O TYR q 48 " (cutoff:3.500A) removed outlier: 6.350A pdb=" N GLU q 50 " --> pdb=" O LEU q 38 " (cutoff:3.500A) removed outlier: 5.339A pdb=" N LEU q 38 " --> pdb=" O GLU q 50 " (cutoff:3.500A) 2814 hydrogen bonds defined for protein. 7878 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 22.57 Time building geometry restraints manager: 24.47 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.41: 28044 1.41 - 1.63: 40203 1.63 - 1.86: 867 1.86 - 2.08: 0 2.08 - 2.31: 80 Bond restraints: 69194 Sorted by residual: bond pdb=" C8 T2Q H 403 " pdb=" O4 T2Q H 403 " ideal model delta sigma weight residual 1.219 1.397 -0.178 2.00e-02 2.50e+03 7.93e+01 bond pdb=" C4 ATP O 401 " pdb=" C5 ATP O 401 " ideal model delta sigma weight residual 1.388 1.463 -0.075 1.00e-02 1.00e+04 5.67e+01 bond pdb=" C5 ATP O 401 " pdb=" C6 ATP O 401 " ideal model delta sigma weight residual 1.409 1.477 -0.068 1.00e-02 1.00e+04 4.57e+01 bond pdb=" CA7 CDL L 702 " pdb=" OA8 CDL L 702 " ideal model delta sigma weight residual 1.334 1.403 -0.069 1.10e-02 8.26e+03 3.95e+01 bond pdb=" CA7 CDL X 201 " pdb=" OA8 CDL X 201 " ideal model delta sigma weight residual 1.334 1.403 -0.069 1.10e-02 8.26e+03 3.91e+01 ... (remaining 69189 not shown) Histogram of bond angle deviations from ideal: 73.05 - 90.54: 78 90.54 - 108.03: 3726 108.03 - 125.52: 88476 125.52 - 143.01: 1418 143.01 - 160.49: 1 Bond angle restraints: 93699 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 139.87 121.59 18.28 1.00e+00 1.00e+00 3.34e+02 angle pdb=" PA ATP O 401 " pdb=" O3A ATP O 401 " pdb=" PB ATP O 401 " ideal model delta sigma weight residual 136.83 119.91 16.92 1.00e+00 1.00e+00 2.86e+02 angle pdb=" C8 EHZ U 201 " pdb=" C9 EHZ U 201 " pdb=" S1 EHZ U 201 " ideal model delta sigma weight residual 119.98 160.49 -40.51 3.00e+00 1.11e-01 1.82e+02 angle pdb=" O2 EHZ U 201 " pdb=" C9 EHZ U 201 " pdb=" S1 EHZ U 201 " ideal model delta sigma weight residual 119.97 79.47 40.50 3.00e+00 1.11e-01 1.82e+02 angle pdb=" C8 EHZ U 201 " pdb=" C9 EHZ U 201 " pdb=" O2 EHZ U 201 " ideal model delta sigma weight residual 119.98 81.03 38.95 3.00e+00 1.11e-01 1.69e+02 ... (remaining 93694 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.97: 40513 33.97 - 67.94: 968 67.94 - 101.91: 69 101.91 - 135.88: 2 135.88 - 169.86: 4 Dihedral angle restraints: 41556 sinusoidal: 17529 harmonic: 24027 Sorted by residual: dihedral pdb=" CB CYS p 112 " pdb=" SG CYS p 112 " pdb=" SG CYS p 124 " pdb=" CB CYS p 124 " ideal model delta sinusoidal sigma weight residual 93.00 171.78 -78.78 1 1.00e+01 1.00e-02 7.73e+01 dihedral pdb=" CB CYS X 45 " pdb=" SG CYS X 45 " pdb=" SG CYS X 55 " pdb=" CB CYS X 55 " ideal model delta sinusoidal sigma weight residual 93.00 157.97 -64.97 1 1.00e+01 1.00e-02 5.54e+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 87.74 169.86 1 2.00e+01 2.50e-03 4.76e+01 ... (remaining 41553 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 4.295: 10187 4.295 - 8.590: 0 8.590 - 12.885: 0 12.885 - 17.180: 0 17.180 - 21.475: 24 Chirality restraints: 10211 Sorted by residual: chirality pdb="FE3 SF4 B 201 " pdb=" S1 SF4 B 201 " pdb=" S2 SF4 B 201 " pdb=" S4 SF4 B 201 " both_signs ideal model delta sigma weight residual False -10.55 10.92 -21.47 2.00e-01 2.50e+01 1.15e+04 chirality pdb="FE2 SF4 B 201 " pdb=" S1 SF4 B 201 " pdb=" S3 SF4 B 201 " pdb=" S4 SF4 B 201 " both_signs ideal model delta sigma weight residual False 10.55 -10.76 21.31 2.00e-01 2.50e+01 1.14e+04 chirality pdb="FE3 SF4 I 203 " pdb=" S1 SF4 I 203 " pdb=" S2 SF4 I 203 " pdb=" S4 SF4 I 203 " both_signs ideal model delta sigma weight residual False -10.55 10.73 -21.29 2.00e-01 2.50e+01 1.13e+04 ... (remaining 10208 not shown) Planarity restraints: 11730 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA AME q 1 " -0.082 2.00e-02 2.50e+03 1.47e-01 2.17e+02 pdb=" C AME q 1 " 0.255 2.00e-02 2.50e+03 pdb=" O AME q 1 " -0.091 2.00e-02 2.50e+03 pdb=" N GLU q 2 " -0.082 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' FMN F 501 " -0.028 2.00e-02 2.50e+03 1.72e-02 1.41e+01 pdb=" C10 FMN F 501 " -0.010 2.00e-02 2.50e+03 pdb=" C2 FMN F 501 " 0.022 2.00e-02 2.50e+03 pdb=" C4 FMN F 501 " -0.003 2.00e-02 2.50e+03 pdb=" C4A FMN F 501 " -0.010 2.00e-02 2.50e+03 pdb=" C5A FMN F 501 " -0.011 2.00e-02 2.50e+03 pdb=" C6 FMN F 501 " -0.006 2.00e-02 2.50e+03 pdb=" C7 FMN F 501 " 0.009 2.00e-02 2.50e+03 pdb=" C7M FMN F 501 " 0.021 2.00e-02 2.50e+03 pdb=" C8 FMN F 501 " 0.011 2.00e-02 2.50e+03 pdb=" C8M FMN F 501 " 0.026 2.00e-02 2.50e+03 pdb=" C9 FMN F 501 " -0.009 2.00e-02 2.50e+03 pdb=" C9A FMN F 501 " -0.012 2.00e-02 2.50e+03 pdb=" N1 FMN F 501 " -0.004 2.00e-02 2.50e+03 pdb=" N10 FMN F 501 " -0.016 2.00e-02 2.50e+03 pdb=" N3 FMN F 501 " 0.017 2.00e-02 2.50e+03 pdb=" N5 FMN F 501 " -0.019 2.00e-02 2.50e+03 pdb=" O2 FMN F 501 " 0.037 2.00e-02 2.50e+03 pdb=" O4 FMN F 501 " -0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA AME q 1 " 0.013 2.00e-02 2.50e+03 2.57e-02 6.61e+00 pdb=" C AME q 1 " -0.044 2.00e-02 2.50e+03 pdb=" O AME q 1 " 0.016 2.00e-02 2.50e+03 pdb=" OXT AME q 1 " 0.016 2.00e-02 2.50e+03 ... (remaining 11727 not shown) Histogram of nonbonded interaction distances: 1.90 - 2.50: 519 2.50 - 3.10: 52618 3.10 - 3.70: 104299 3.70 - 4.30: 161549 4.30 - 4.90: 265304 Nonbonded interactions: 584289 Sorted by model distance: nonbonded pdb=" OXT AME q 1 " pdb=" CA GLU q 2 " model vdw 1.904 2.776 nonbonded pdb=" O LEU M 329 " pdb=" OG SER M 332 " model vdw 1.919 2.440 nonbonded pdb=" O LEU A 73 " pdb=" OH TYR H 160 " model vdw 1.934 2.440 nonbonded pdb=" OD1 ASN L 594 " pdb=" OH TYR Y 38 " model vdw 1.953 2.440 nonbonded pdb=" O VAL P 215 " pdb=" OG1 THR P 218 " model vdw 1.954 2.440 ... (remaining 584284 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'T' selection = (chain 'U' and (resid 6 through 84 or resid 201)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.200 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: 0.060 Extract box with map and model: 22.690 Check model and map are aligned: 0.940 Set scattering table: 0.490 Process input model: 154.780 Find NCS groups from input model: 2.130 Set up NCS constraints: 0.290 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.020 Load rotamer database and sin/cos tables:2.740 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 188.340 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8243 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 0.178 69194 Z= 0.397 Angle : 0.814 40.514 93699 Z= 0.413 Chirality : 1.030 21.475 10211 Planarity : 0.004 0.147 11730 Dihedral : 14.701 169.855 26022 Min Nonbonded Distance : 1.904 Molprobity Statistics. All-atom Clashscore : 7.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.11 % Favored : 95.89 % Rotamer Outliers : 0.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.67 % 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: -3.26 (0.08), residues: 8129 helix: -1.61 (0.07), residues: 4325 sheet: -2.40 (0.24), residues: 372 loop : -2.80 (0.09), residues: 3432 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16258 Ramachandran restraints generated. 8129 Oldfield, 0 Emsley, 8129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16258 Ramachandran restraints generated. 8129 Oldfield, 0 Emsley, 8129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1008 residues out of total 7219 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 1006 time to evaluate : 6.324 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 2 outliers final: 1 residues processed: 1007 average time/residue: 0.6965 time to fit residues: 1173.4690 Evaluate side-chains 727 residues out of total 7219 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 726 time to evaluate : 6.329 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.4789 time to fit residues: 9.1836 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 802 random chunks: chunk 677 optimal weight: 5.9990 chunk 607 optimal weight: 0.6980 chunk 337 optimal weight: 6.9990 chunk 207 optimal weight: 0.6980 chunk 410 optimal weight: 0.7980 chunk 324 optimal weight: 8.9990 chunk 628 optimal weight: 0.8980 chunk 243 optimal weight: 0.9990 chunk 382 optimal weight: 0.9980 chunk 467 optimal weight: 0.4980 chunk 728 optimal weight: 2.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 172 GLN D 5 GLN D 114 ASN E 91 ASN ** F 257 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 421 HIS F 431 GLN ** G 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 361 ASN G 629 ASN G 654 GLN H 5 ASN ** H 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 157 ASN ** H 169 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 67 HIS L 209 ASN M 26 ASN ** M 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 134 GLN N 144 GLN O 45 GLN ** O 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 200 GLN P 131 HIS P 288 HIS R 95 HIS W 28 ASN Y 78 GLN Z 136 ASN d 3 ASN e 96 HIS g 43 HIS l 135 ASN o 53 GLN o 54 GLN p 90 GLN s 34 ASN Total number of N/Q/H flips: 32 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8266 moved from start: 0.1422 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.008 0.272 69194 Z= 0.516 Angle : 1.574 50.915 93699 Z= 1.011 Chirality : 0.312 6.633 10211 Planarity : 0.005 0.052 11730 Dihedral : 10.464 169.091 9748 Min Nonbonded Distance : 1.949 Molprobity Statistics. All-atom Clashscore : 7.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer Outliers : 0.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.67 % 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: -0.98 (0.09), residues: 8129 helix: 0.28 (0.08), residues: 4326 sheet: -1.73 (0.24), residues: 399 loop : -1.71 (0.10), residues: 3404 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16258 Ramachandran restraints generated. 8129 Oldfield, 0 Emsley, 8129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16258 Ramachandran restraints generated. 8129 Oldfield, 0 Emsley, 8129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 838 residues out of total 7219 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 778 time to evaluate : 6.362 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 60 outliers final: 32 residues processed: 812 average time/residue: 0.6748 time to fit residues: 941.2055 Evaluate side-chains 728 residues out of total 7219 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 696 time to evaluate : 6.446 Switching outliers to nearest non-outliers outliers start: 32 outliers final: 0 residues processed: 32 average time/residue: 0.5385 time to fit residues: 40.8069 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 802 random chunks: chunk 404 optimal weight: 2.9990 chunk 226 optimal weight: 5.9990 chunk 606 optimal weight: 9.9990 chunk 495 optimal weight: 8.9990 chunk 200 optimal weight: 7.9990 chunk 729 optimal weight: 0.0010 chunk 788 optimal weight: 0.4980 chunk 649 optimal weight: 4.9990 chunk 723 optimal weight: 4.9990 chunk 248 optimal weight: 6.9990 chunk 585 optimal weight: 10.0000 overall best weight: 2.6992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 95 ASN D 149 ASN ** E 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 55 GLN E 150 ASN ** F 257 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 36 GLN I 10 GLN K 7 ASN L 72 ASN ** L 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 194 ASN ** L 199 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 97 GLN O 294 ASN Q 44 ASN ** S 21 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 38 GLN V 109 ASN X 63 ASN Y 78 GLN Z 136 ASN d 3 ASN d 61 GLN f 50 ASN l 77 HIS n 77 GLN p 106 GLN p 171 GLN q 123 GLN r 20 GLN s 34 ASN s 69 HIS Total number of N/Q/H flips: 28 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8390 moved from start: 0.2117 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.009 0.247 69194 Z= 0.567 Angle : 1.587 50.789 93699 Z= 1.018 Chirality : 0.310 6.442 10211 Planarity : 0.005 0.062 11730 Dihedral : 10.067 171.541 9748 Min Nonbonded Distance : 1.933 Molprobity Statistics. All-atom Clashscore : 7.23 Ramachandran Plot: Outliers : 0.01 % Allowed : 3.48 % Favored : 96.51 % Rotamer Outliers : 1.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.01 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.25 (0.09), residues: 8129 helix: 0.76 (0.08), residues: 4357 sheet: -0.88 (0.25), residues: 395 loop : -1.28 (0.10), residues: 3377 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16258 Ramachandran restraints generated. 8129 Oldfield, 0 Emsley, 8129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16258 Ramachandran restraints generated. 8129 Oldfield, 0 Emsley, 8129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 821 residues out of total 7219 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 80 poor density : 741 time to evaluate : 6.436 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 80 outliers final: 37 residues processed: 799 average time/residue: 0.6758 time to fit residues: 932.3655 Evaluate side-chains 737 residues out of total 7219 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 700 time to evaluate : 6.295 Switching outliers to nearest non-outliers outliers start: 37 outliers final: 0 residues processed: 37 average time/residue: 0.5588 time to fit residues: 46.5125 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 802 random chunks: chunk 720 optimal weight: 7.9990 chunk 548 optimal weight: 5.9990 chunk 378 optimal weight: 2.9990 chunk 80 optimal weight: 1.9990 chunk 348 optimal weight: 0.3980 chunk 489 optimal weight: 7.9990 chunk 732 optimal weight: 1.9990 chunk 775 optimal weight: 9.9990 chunk 382 optimal weight: 5.9990 chunk 693 optimal weight: 3.9990 chunk 208 optimal weight: 7.9990 overall best weight: 2.2788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 257 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 157 ASN L 135 ASN L 199 GLN P 112 ASN ** S 21 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 61 GLN d 3 ASN p 171 GLN q 12 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8399 moved from start: 0.2486 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.008 0.245 69194 Z= 0.542 Angle : 1.575 50.774 93699 Z= 1.013 Chirality : 0.308 6.420 10211 Planarity : 0.004 0.055 11730 Dihedral : 9.790 170.973 9748 Min Nonbonded Distance : 1.941 Molprobity Statistics. All-atom Clashscore : 7.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.40 % Favored : 96.60 % Rotamer Outliers : 1.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.67 % 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: 0.17 (0.09), residues: 8129 helix: 1.02 (0.08), residues: 4356 sheet: -0.61 (0.26), residues: 386 loop : -0.96 (0.11), residues: 3387 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16258 Ramachandran restraints generated. 8129 Oldfield, 0 Emsley, 8129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16258 Ramachandran restraints generated. 8129 Oldfield, 0 Emsley, 8129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 802 residues out of total 7219 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 727 time to evaluate : 6.400 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 75 outliers final: 34 residues processed: 786 average time/residue: 0.6684 time to fit residues: 908.6211 Evaluate side-chains 727 residues out of total 7219 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 693 time to evaluate : 7.356 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 34 outliers final: 1 residues processed: 34 average time/residue: 0.5226 time to fit residues: 42.0944 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 802 random chunks: chunk 645 optimal weight: 5.9990 chunk 440 optimal weight: 20.0000 chunk 11 optimal weight: 9.9990 chunk 577 optimal weight: 4.9990 chunk 319 optimal weight: 0.9980 chunk 661 optimal weight: 0.8980 chunk 535 optimal weight: 8.9990 chunk 0 optimal weight: 8.9990 chunk 395 optimal weight: 0.7980 chunk 695 optimal weight: 10.0000 chunk 195 optimal weight: 4.9990 overall best weight: 2.5384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 149 ASN ** E 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 257 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 283 HIS G 336 ASN H 157 ASN L 194 ASN O 153 ASN ** S 21 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 61 GLN V 82 GLN d 117 HIS f 50 ASN l 55 HIS p 90 GLN p 106 GLN p 171 GLN ** s 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8421 moved from start: 0.2741 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.009 0.243 69194 Z= 0.554 Angle : 1.579 50.730 93699 Z= 1.014 Chirality : 0.309 6.425 10211 Planarity : 0.004 0.056 11730 Dihedral : 9.649 171.300 9748 Min Nonbonded Distance : 1.941 Molprobity Statistics. All-atom Clashscore : 7.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.40 % Favored : 96.60 % Rotamer Outliers : 0.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.67 % 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: 0.34 (0.09), residues: 8129 helix: 1.10 (0.08), residues: 4368 sheet: -0.34 (0.26), residues: 390 loop : -0.82 (0.11), residues: 3371 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16258 Ramachandran restraints generated. 8129 Oldfield, 0 Emsley, 8129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16258 Ramachandran restraints generated. 8129 Oldfield, 0 Emsley, 8129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 786 residues out of total 7219 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 729 time to evaluate : 6.466 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 57 outliers final: 25 residues processed: 769 average time/residue: 0.6850 time to fit residues: 911.3299 Evaluate side-chains 724 residues out of total 7219 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 699 time to evaluate : 6.421 Switching outliers to nearest non-outliers outliers start: 25 outliers final: 0 residues processed: 25 average time/residue: 0.5222 time to fit residues: 33.8876 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 802 random chunks: chunk 260 optimal weight: 2.9990 chunk 698 optimal weight: 6.9990 chunk 153 optimal weight: 9.9990 chunk 455 optimal weight: 6.9990 chunk 191 optimal weight: 6.9990 chunk 775 optimal weight: 9.9990 chunk 644 optimal weight: 10.0000 chunk 359 optimal weight: 5.9990 chunk 64 optimal weight: 3.9990 chunk 256 optimal weight: 0.6980 chunk 407 optimal weight: 2.9990 overall best weight: 3.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 149 ASN ** E 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 37 ASN ** F 257 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 157 ASN L 194 ASN Q 44 ASN Q 46 GLN ** S 21 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** X 108 GLN Z 84 GLN f 50 ASN p 106 GLN p 171 GLN s 49 ASN ** s 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8448 moved from start: 0.2955 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.009 0.242 69194 Z= 0.585 Angle : 1.590 50.721 93699 Z= 1.018 Chirality : 0.310 6.445 10211 Planarity : 0.005 0.067 11730 Dihedral : 9.697 172.266 9748 Min Nonbonded Distance : 1.938 Molprobity Statistics. All-atom Clashscore : 7.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.68 % Favored : 96.32 % Rotamer Outliers : 0.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.67 % 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: 0.39 (0.09), residues: 8129 helix: 1.09 (0.08), residues: 4358 sheet: -0.30 (0.26), residues: 404 loop : -0.72 (0.11), residues: 3367 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16258 Ramachandran restraints generated. 8129 Oldfield, 0 Emsley, 8129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16258 Ramachandran restraints generated. 8129 Oldfield, 0 Emsley, 8129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 777 residues out of total 7219 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 711 time to evaluate : 6.509 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 66 outliers final: 33 residues processed: 760 average time/residue: 0.6868 time to fit residues: 898.8205 Evaluate side-chains 725 residues out of total 7219 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 692 time to evaluate : 6.375 Switching outliers to nearest non-outliers outliers start: 33 outliers final: 0 residues processed: 33 average time/residue: 0.5287 time to fit residues: 41.5540 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 802 random chunks: chunk 748 optimal weight: 6.9990 chunk 87 optimal weight: 0.5980 chunk 442 optimal weight: 6.9990 chunk 566 optimal weight: 0.9980 chunk 439 optimal weight: 1.9990 chunk 653 optimal weight: 0.7980 chunk 433 optimal weight: 4.9990 chunk 772 optimal weight: 6.9990 chunk 483 optimal weight: 4.9990 chunk 471 optimal weight: 1.9990 chunk 356 optimal weight: 2.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 149 ASN ** E 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 257 ASN G 51 ASN L 194 ASN ** S 21 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Z 84 GLN f 50 ASN p 106 GLN p 171 GLN ** q 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8406 moved from start: 0.3040 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.008 0.244 69194 Z= 0.516 Angle : 1.566 50.796 93699 Z= 1.009 Chirality : 0.309 6.514 10211 Planarity : 0.004 0.054 11730 Dihedral : 9.358 170.138 9748 Min Nonbonded Distance : 1.946 Molprobity Statistics. All-atom Clashscore : 7.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer Outliers : 0.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.67 % 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: 0.67 (0.09), residues: 8129 helix: 1.32 (0.08), residues: 4333 sheet: -0.17 (0.26), residues: 390 loop : -0.58 (0.11), residues: 3406 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16258 Ramachandran restraints generated. 8129 Oldfield, 0 Emsley, 8129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16258 Ramachandran restraints generated. 8129 Oldfield, 0 Emsley, 8129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 770 residues out of total 7219 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 736 time to evaluate : 6.538 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 34 outliers final: 14 residues processed: 759 average time/residue: 0.7357 time to fit residues: 974.5574 Evaluate side-chains 707 residues out of total 7219 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 693 time to evaluate : 6.487 Switching outliers to nearest non-outliers outliers start: 14 outliers final: 0 residues processed: 14 average time/residue: 0.6153 time to fit residues: 24.2955 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 802 random chunks: chunk 478 optimal weight: 8.9990 chunk 308 optimal weight: 9.9990 chunk 461 optimal weight: 4.9990 chunk 232 optimal weight: 5.9990 chunk 151 optimal weight: 4.9990 chunk 149 optimal weight: 0.9990 chunk 491 optimal weight: 4.9990 chunk 526 optimal weight: 2.9990 chunk 382 optimal weight: 1.9990 chunk 72 optimal weight: 8.9990 chunk 607 optimal weight: 0.8980 overall best weight: 2.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 149 ASN ** E 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 157 ASN ** S 21 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** f 50 ASN ** s 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8429 moved from start: 0.3104 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.009 0.243 69194 Z= 0.547 Angle : 1.577 50.771 93699 Z= 1.012 Chirality : 0.310 6.444 10211 Planarity : 0.004 0.053 11730 Dihedral : 9.356 171.033 9748 Min Nonbonded Distance : 1.942 Molprobity Statistics. All-atom Clashscore : 7.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.46 % Favored : 96.54 % Rotamer Outliers : 0.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.67 % 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: 0.69 (0.09), residues: 8129 helix: 1.32 (0.08), residues: 4335 sheet: -0.09 (0.27), residues: 382 loop : -0.55 (0.11), residues: 3412 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16258 Ramachandran restraints generated. 8129 Oldfield, 0 Emsley, 8129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16258 Ramachandran restraints generated. 8129 Oldfield, 0 Emsley, 8129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 734 residues out of total 7219 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 702 time to evaluate : 6.395 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 32 outliers final: 15 residues processed: 724 average time/residue: 0.6891 time to fit residues: 862.2338 Evaluate side-chains 705 residues out of total 7219 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 690 time to evaluate : 6.488 Switching outliers to nearest non-outliers outliers start: 15 outliers final: 0 residues processed: 15 average time/residue: 0.5727 time to fit residues: 24.1242 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 802 random chunks: chunk 703 optimal weight: 5.9990 chunk 740 optimal weight: 4.9990 chunk 675 optimal weight: 4.9990 chunk 720 optimal weight: 1.9990 chunk 433 optimal weight: 4.9990 chunk 313 optimal weight: 0.9990 chunk 565 optimal weight: 0.5980 chunk 221 optimal weight: 3.9990 chunk 650 optimal weight: 3.9990 chunk 681 optimal weight: 7.9990 chunk 717 optimal weight: 0.0270 overall best weight: 1.5244 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 157 ASN ** S 21 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Y 43 ASN f 50 ASN ** q 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8409 moved from start: 0.3173 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.008 0.243 69194 Z= 0.522 Angle : 1.567 50.737 93699 Z= 1.009 Chirality : 0.309 6.415 10211 Planarity : 0.004 0.052 11730 Dihedral : 9.159 170.159 9748 Min Nonbonded Distance : 1.944 Molprobity Statistics. All-atom Clashscore : 7.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Rotamer Outliers : 0.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.67 % 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: 0.79 (0.09), residues: 8129 helix: 1.41 (0.08), residues: 4328 sheet: -0.13 (0.26), residues: 392 loop : -0.49 (0.11), residues: 3409 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16258 Ramachandran restraints generated. 8129 Oldfield, 0 Emsley, 8129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16258 Ramachandran restraints generated. 8129 Oldfield, 0 Emsley, 8129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 738 residues out of total 7219 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 724 time to evaluate : 6.542 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 14 outliers final: 8 residues processed: 734 average time/residue: 0.6911 time to fit residues: 878.2570 Evaluate side-chains 705 residues out of total 7219 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 697 time to evaluate : 6.401 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.5386 time to fit residues: 16.5792 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 802 random chunks: chunk 473 optimal weight: 6.9990 chunk 761 optimal weight: 4.9990 chunk 464 optimal weight: 0.8980 chunk 361 optimal weight: 2.9990 chunk 529 optimal weight: 4.9990 chunk 798 optimal weight: 5.9990 chunk 735 optimal weight: 0.7980 chunk 636 optimal weight: 0.9990 chunk 66 optimal weight: 0.9990 chunk 491 optimal weight: 1.9990 chunk 390 optimal weight: 0.0870 overall best weight: 0.7562 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 240 HIS S 21 HIS X 108 GLN b 82 ASN ** q 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8379 moved from start: 0.3265 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.008 0.245 69194 Z= 0.510 Angle : 1.562 50.710 93699 Z= 1.006 Chirality : 0.308 6.402 10211 Planarity : 0.004 0.054 11730 Dihedral : 8.850 169.537 9748 Min Nonbonded Distance : 1.949 Molprobity Statistics. All-atom Clashscore : 8.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % Rotamer Outliers : 0.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.67 % 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: 0.96 (0.10), residues: 8129 helix: 1.53 (0.08), residues: 4323 sheet: -0.05 (0.26), residues: 392 loop : -0.40 (0.11), residues: 3414 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16258 Ramachandran restraints generated. 8129 Oldfield, 0 Emsley, 8129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16258 Ramachandran restraints generated. 8129 Oldfield, 0 Emsley, 8129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 737 residues out of total 7219 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 731 time to evaluate : 6.424 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 6 outliers final: 3 residues processed: 735 average time/residue: 0.6917 time to fit residues: 882.1521 Evaluate side-chains 704 residues out of total 7219 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 701 time to evaluate : 6.500 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.5182 time to fit residues: 11.3625 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 802 random chunks: chunk 505 optimal weight: 5.9990 chunk 677 optimal weight: 2.9990 chunk 194 optimal weight: 0.9980 chunk 586 optimal weight: 10.0000 chunk 93 optimal weight: 0.9980 chunk 176 optimal weight: 1.9990 chunk 637 optimal weight: 0.8980 chunk 266 optimal weight: 6.9990 chunk 654 optimal weight: 2.9990 chunk 80 optimal weight: 6.9990 chunk 117 optimal weight: 0.0870 overall best weight: 0.9960 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** f 50 ASN ** q 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3212 r_free = 0.3212 target = 0.068577 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2974 r_free = 0.2974 target = 0.058023 restraints weight = 154879.119| |-----------------------------------------------------------------------------| r_work (start): 0.2972 rms_B_bonded: 1.77 r_work: 0.2876 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.2762 rms_B_bonded: 3.90 restraints_weight: 0.2500 r_work (final): 0.2762 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8615 moved from start: 0.3296 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.008 0.244 69194 Z= 0.513 Angle : 1.566 50.715 93699 Z= 1.007 Chirality : 0.308 6.399 10211 Planarity : 0.004 0.056 11730 Dihedral : 8.739 169.709 9748 Min Nonbonded Distance : 1.949 Molprobity Statistics. All-atom Clashscore : 8.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer Outliers : 0.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.67 % 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: 0.99 (0.10), residues: 8129 helix: 1.55 (0.08), residues: 4331 sheet: -0.02 (0.26), residues: 398 loop : -0.36 (0.11), residues: 3400 =============================================================================== Job complete usr+sys time: 16123.35 seconds wall clock time: 285 minutes 1.04 seconds (17101.04 seconds total)