Starting phenix.real_space_refine (version: dev) on Thu Dec 22 10:37:52 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6u8y_20692/12_2022/6u8y_20692_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6u8y_20692/12_2022/6u8y_20692.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6u8y_20692/12_2022/6u8y_20692.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6u8y_20692/12_2022/6u8y_20692.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6u8y_20692/12_2022/6u8y_20692_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6u8y_20692/12_2022/6u8y_20692_updated.pdb" } resolution = 4.0 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= 0.001 sd= 0.003 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Convert atoms to be neutral Process input model Symmetric amino acids flipped Residue "A PHE 39": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 54": "NH1" <-> "NH2" Residue "A ARG 63": "NH1" <-> "NH2" Residue "A TYR 66": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 73": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 94": "NH1" <-> "NH2" Residue "A PHE 167": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 24": "NH1" <-> "NH2" Residue "B ASP 30": "OD1" <-> "OD2" Residue "B TYR 52": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 54": "NH1" <-> "NH2" Residue "B ARG 55": "NH1" <-> "NH2" Residue "B ARG 78": "NH1" <-> "NH2" Residue "C ARG 28": "NH1" <-> "NH2" Residue "C TYR 33": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 91": "NH1" <-> "NH2" Residue "C TYR 94": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 114": "OE1" <-> "OE2" Residue "D TYR 9": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 26": "NH1" <-> "NH2" Residue "D ARG 76": "NH1" <-> "NH2" Residue "D ARG 79": "NH1" <-> "NH2" Residue "E ARG 7": "NH1" <-> "NH2" Residue "E TYR 40": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 41": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 62": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 63": "NH1" <-> "NH2" Residue "E ASP 66": "OD1" <-> "OD2" Residue "E ARG 90": "NH1" <-> "NH2" Residue "E PHE 121": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 157": "NH1" <-> "NH2" Residue "E PHE 159": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 170": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 183": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 187": "OD1" <-> "OD2" Residue "E ARG 202": "NH1" <-> "NH2" Residue "E GLU 223": "OE1" <-> "OE2" Residue "G GLU 37": "OE1" <-> "OE2" Residue "G GLU 60": "OE1" <-> "OE2" Residue "G ASP 69": "OD1" <-> "OD2" Residue "G ARG 110": "NH1" <-> "NH2" Residue "H PHE 18": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 79": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 105": "OE1" <-> "OE2" Residue "H PHE 131": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 138": "OE1" <-> "OE2" Residue "H ASP 199": "OD1" <-> "OD2" Residue "H PHE 214": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ASP 231": "OD1" <-> "OD2" Residue "H PHE 247": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 288": "OE1" <-> "OE2" Residue "H GLU 358": "OE1" <-> "OE2" Residue "H PHE 360": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ARG 366": "NH1" <-> "NH2" Residue "H ARG 395": "NH1" <-> "NH2" Residue "H TYR 422": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 424": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ARG 425": "NH1" <-> "NH2" Residue "H ARG 439": "NH1" <-> "NH2" Residue "X ARG 22": "NH1" <-> "NH2" Residue "X ARG 27": "NH1" <-> "NH2" Residue "X GLU 50": "OE1" <-> "OE2" Residue "X ARG 55": "NH1" <-> "NH2" Residue "X GLU 100": "OE1" <-> "OE2" Residue "X ASP 119": "OD1" <-> "OD2" Residue "X PHE 123": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X PHE 124": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X GLU 128": "OE1" <-> "OE2" Residue "X ARG 143": "NH1" <-> "NH2" Residue "X ARG 184": "NH1" <-> "NH2" Residue "X ASP 229": "OD1" <-> "OD2" Residue "X ASP 302": "OD1" <-> "OD2" Residue "X PHE 307": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X PHE 343": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X ARG 357": "NH1" <-> "NH2" Residue "X GLU 362": "OE1" <-> "OE2" Residue "X TYR 366": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X ARG 409": "NH1" <-> "NH2" Residue "X PHE 426": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X TYR 428": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X ARG 431": "NH1" <-> "NH2" Residue "X ARG 441": "NH1" <-> "NH2" Residue "X ARG 478": "NH1" <-> "NH2" Residue "X PHE 484": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X PHE 500": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X ARG 502": "NH1" <-> "NH2" Residue "X TYR 523": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X ASP 536": "OD1" <-> "OD2" Residue "X ARG 553": "NH1" <-> "NH2" Residue "X ARG 554": "NH1" <-> "NH2" Residue "X GLU 562": "OE1" <-> "OE2" Residue "X ASP 573": "OD1" <-> "OD2" Residue "X ARG 574": "NH1" <-> "NH2" Residue "X GLU 585": "OE1" <-> "OE2" Residue "X ARG 591": "NH1" <-> "NH2" Residue "X TYR 605": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ARG 15": "NH1" <-> "NH2" Residue "J PHE 24": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ARG 45": "NH1" <-> "NH2" Residue "J ASP 58": "OD1" <-> "OD2" Residue "J ARG 73": "NH1" <-> "NH2" Residue "J ASP 83": "OD1" <-> "OD2" Residue "J TYR 86": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ASP 102": "OD1" <-> "OD2" Residue "J GLU 128": "OE1" <-> "OE2" Residue "J ASP 132": "OD1" <-> "OD2" Residue "J GLU 145": "OE1" <-> "OE2" Residue "J ARG 160": "NH1" <-> "NH2" Residue "J ASP 164": "OD1" <-> "OD2" Residue "K TYR 19": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ARG 25": "NH1" <-> "NH2" Residue "K ARG 26": "NH1" <-> "NH2" Residue "K ARG 28": "NH1" <-> "NH2" Residue "K ARG 29": "NH1" <-> "NH2" Residue "K PHE 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ARG 33": "NH1" <-> "NH2" Residue "K ARG 40": "NH1" <-> "NH2" Residue "K ARG 44": "NH1" <-> "NH2" Residue "K GLU 69": "OE1" <-> "OE2" Residue "K ARG 88": "NH1" <-> "NH2" Residue "K ARG 91": "NH1" <-> "NH2" Residue "K ASP 92": "OD1" <-> "OD2" Residue "K ARG 97": "NH1" <-> "NH2" Residue "K GLU 109": "OE1" <-> "OE2" Residue "K ASP 136": "OD1" <-> "OD2" Residue "K ASP 168": "OD1" <-> "OD2" Residue "K ASP 170": "OD1" <-> "OD2" Residue "L GLU 38": "OE1" <-> "OE2" Residue "L ASP 47": "OD1" <-> "OD2" Residue "L ARG 83": "NH1" <-> "NH2" Residue "L ASP 90": "OD1" <-> "OD2" Residue "L GLU 121": "OE1" <-> "OE2" Residue "L TYR 142": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ARG 152": "NH1" <-> "NH2" Residue "L ARG 154": "NH1" <-> "NH2" Residue "L ARG 178": "NH1" <-> "NH2" Residue "L ARG 188": "NH1" <-> "NH2" Residue "L ARG 191": "NH1" <-> "NH2" Residue "L GLU 210": "OE1" <-> "OE2" Residue "L TYR 215": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 257": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 262": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ARG 279": "NH1" <-> "NH2" Residue "L ASP 295": "OD1" <-> "OD2" Residue "L ARG 315": "NH1" <-> "NH2" Residue "L ASP 333": "OD1" <-> "OD2" Residue "L GLU 364": "OE1" <-> "OE2" Residue "L ARG 371": "NH1" <-> "NH2" Residue "L ARG 391": "NH1" <-> "NH2" Residue "M ARG 7": "NH1" <-> "NH2" Residue "M ARG 91": "NH1" <-> "NH2" Residue "M TYR 121": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M GLU 149": "OE1" <-> "OE2" Residue "M GLU 158": "OE1" <-> "OE2" Residue "M TYR 182": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M ASP 183": "OD1" <-> "OD2" Residue "M ASP 196": "OD1" <-> "OD2" Residue "M GLU 211": "OE1" <-> "OE2" Residue "M PHE 234": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M ARG 282": "NH1" <-> "NH2" Residue "M ASP 286": "OD1" <-> "OD2" Residue "N GLU 11": "OE1" <-> "OE2" Residue "N PHE 20": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N PHE 25": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N TYR 29": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N GLU 42": "OE1" <-> "OE2" Residue "N ARG 49": "NH1" <-> "NH2" Residue "N ARG 51": "NH1" <-> "NH2" Residue "N ARG 74": "NH1" <-> "NH2" Residue "N GLU 77": "OE1" <-> "OE2" Residue "N ASP 92": "OD1" <-> "OD2" Residue "N ARG 95": "NH1" <-> "NH2" Residue "N TYR 117": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N ARG 124": "NH1" <-> "NH2" Residue "N TYR 151": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N GLU 159": "OE1" <-> "OE2" Residue "N ARG 172": "NH1" <-> "NH2" Residue "N ASP 173": "OD1" <-> "OD2" Residue "N PHE 179": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a PHE 39": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a ARG 54": "NH1" <-> "NH2" Residue "a ARG 63": "NH1" <-> "NH2" Residue "a TYR 66": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a TYR 73": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a ARG 94": "NH1" <-> "NH2" Residue "a PHE 167": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b ARG 24": "NH1" <-> "NH2" Residue "b ASP 30": "OD1" <-> "OD2" Residue "b TYR 52": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b ARG 54": "NH1" <-> "NH2" Residue "b ARG 55": "NH1" <-> "NH2" Residue "b ARG 78": "NH1" <-> "NH2" Residue "c ARG 28": "NH1" <-> "NH2" Residue "c TYR 33": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c ARG 91": "NH1" <-> "NH2" Residue "c TYR 94": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c GLU 114": "OE1" <-> "OE2" Residue "d TYR 9": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d ARG 26": "NH1" <-> "NH2" Residue "d ARG 76": "NH1" <-> "NH2" Residue "d ARG 79": "NH1" <-> "NH2" Residue "e ARG 7": "NH1" <-> "NH2" Residue "e TYR 40": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "e TYR 41": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "e TYR 62": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "e ARG 63": "NH1" <-> "NH2" Residue "e ASP 66": "OD1" <-> "OD2" Residue "e ARG 90": "NH1" <-> "NH2" Residue "e PHE 121": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "e ARG 157": "NH1" <-> "NH2" Residue "e PHE 159": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "e TYR 170": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "e TYR 183": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "e ASP 187": "OD1" <-> "OD2" Residue "e GLU 223": "OE1" <-> "OE2" Residue "g GLU 37": "OE1" <-> "OE2" Residue "g GLU 60": "OE1" <-> "OE2" Residue "g ASP 69": "OD1" <-> "OD2" Residue "g ARG 110": "NH1" <-> "NH2" Residue "h PHE 18": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "h PHE 79": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "h GLU 105": "OE1" <-> "OE2" Residue "h PHE 131": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "h GLU 138": "OE1" <-> "OE2" Residue "h ASP 199": "OD1" <-> "OD2" Residue "h PHE 214": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "h ASP 231": "OD1" <-> "OD2" Residue "h PHE 247": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "h GLU 288": "OE1" <-> "OE2" Residue "h GLU 358": "OE1" <-> "OE2" Residue "h PHE 360": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "h ARG 366": "NH1" <-> "NH2" Residue "h ARG 395": "NH1" <-> "NH2" Residue "h TYR 422": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "h PHE 424": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "h ARG 425": "NH1" <-> "NH2" Residue "h ARG 439": "NH1" <-> "NH2" Residue "x ARG 22": "NH1" <-> "NH2" Residue "x ARG 27": "NH1" <-> "NH2" Residue "x GLU 50": "OE1" <-> "OE2" Residue "x ARG 55": "NH1" <-> "NH2" Residue "x GLU 100": "OE1" <-> "OE2" Residue "x ASP 119": "OD1" <-> "OD2" Residue "x PHE 123": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "x PHE 124": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "x GLU 128": "OE1" <-> "OE2" Residue "x ARG 143": "NH1" <-> "NH2" Residue "x ARG 184": "NH1" <-> "NH2" Residue "x ASP 229": "OD1" <-> "OD2" Residue "x ASP 302": "OD1" <-> "OD2" Residue "x PHE 307": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "x PHE 343": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "x ARG 357": "NH1" <-> "NH2" Residue "x GLU 362": "OE1" <-> "OE2" Residue "x TYR 366": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "x ARG 409": "NH1" <-> "NH2" Residue "x PHE 426": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "x TYR 428": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "x ARG 431": "NH1" <-> "NH2" Residue "x ARG 441": "NH1" <-> "NH2" Residue "x ARG 478": "NH1" <-> "NH2" Residue "x PHE 484": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "x PHE 500": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "x ARG 502": "NH1" <-> "NH2" Residue "x TYR 523": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "x ASP 536": "OD1" <-> "OD2" Residue "x ARG 553": "NH1" <-> "NH2" Residue "x ARG 554": "NH1" <-> "NH2" Residue "x GLU 562": "OE1" <-> "OE2" Residue "x ASP 573": "OD1" <-> "OD2" Residue "x ARG 574": "NH1" <-> "NH2" Residue "x GLU 585": "OE1" <-> "OE2" Residue "x ARG 591": "NH1" <-> "NH2" Residue "x TYR 605": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "j ARG 15": "NH1" <-> "NH2" Residue "j PHE 24": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "j ARG 45": "NH1" <-> "NH2" Residue "j ASP 58": "OD1" <-> "OD2" Residue "j ARG 73": "NH1" <-> "NH2" Residue "j ASP 83": "OD1" <-> "OD2" Residue "j TYR 86": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "j ASP 102": "OD1" <-> "OD2" Residue "j GLU 128": "OE1" <-> "OE2" Residue "j ASP 132": "OD1" <-> "OD2" Residue "j GLU 145": "OE1" <-> "OE2" Residue "j ARG 160": "NH1" <-> "NH2" Residue "j ASP 164": "OD1" <-> "OD2" Residue "k TYR 19": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "k ARG 25": "NH1" <-> "NH2" Residue "k ARG 26": "NH1" <-> "NH2" Residue "k ARG 28": "NH1" <-> "NH2" Residue "k ARG 29": "NH1" <-> "NH2" Residue "k PHE 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "k ARG 33": "NH1" <-> "NH2" Residue "k ARG 40": "NH1" <-> "NH2" Residue "k ARG 44": "NH1" <-> "NH2" Residue "k GLU 69": "OE1" <-> "OE2" Residue "k ARG 88": "NH1" <-> "NH2" Residue "k ARG 91": "NH1" <-> "NH2" Residue "k ASP 92": "OD1" <-> "OD2" Residue "k ARG 97": "NH1" <-> "NH2" Residue "k GLU 109": "OE1" <-> "OE2" Residue "k ASP 136": "OD1" <-> "OD2" Residue "k ASP 168": "OD1" <-> "OD2" Residue "k ASP 170": "OD1" <-> "OD2" Residue "l GLU 38": "OE1" <-> "OE2" Residue "l ASP 47": "OD1" <-> "OD2" Residue "l ARG 83": "NH1" <-> "NH2" Residue "l ASP 90": "OD1" <-> "OD2" Residue "l GLU 121": "OE1" <-> "OE2" Residue "l TYR 142": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "l ARG 152": "NH1" <-> "NH2" Residue "l ARG 154": "NH1" <-> "NH2" Residue "l ARG 178": "NH1" <-> "NH2" Residue "l ARG 188": "NH1" <-> "NH2" Residue "l ARG 191": "NH1" <-> "NH2" Residue "l GLU 210": "OE1" <-> "OE2" Residue "l TYR 215": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "l TYR 257": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "l PHE 262": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "l ARG 279": "NH1" <-> "NH2" Residue "l ASP 295": "OD1" <-> "OD2" Residue "l ARG 315": "NH1" <-> "NH2" Residue "l ASP 333": "OD1" <-> "OD2" Residue "l GLU 364": "OE1" <-> "OE2" Residue "l ARG 371": "NH1" <-> "NH2" Residue "l ARG 391": "NH1" <-> "NH2" Residue "m ARG 7": "NH1" <-> "NH2" Residue "m ARG 91": "NH1" <-> "NH2" Residue "m TYR 121": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "m GLU 149": "OE1" <-> "OE2" Residue "m GLU 158": "OE1" <-> "OE2" Residue "m TYR 182": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "m ASP 183": "OD1" <-> "OD2" Residue "m ASP 196": "OD1" <-> "OD2" Residue "m GLU 211": "OE1" <-> "OE2" Residue "m PHE 234": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "m ARG 282": "NH1" <-> "NH2" Residue "m ASP 286": "OD1" <-> "OD2" Residue "n GLU 11": "OE1" <-> "OE2" Residue "n PHE 20": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "n PHE 25": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "n TYR 29": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "n GLU 42": "OE1" <-> "OE2" Residue "n ARG 49": "NH1" <-> "NH2" Residue "n ARG 51": "NH1" <-> "NH2" Residue "n ARG 74": "NH1" <-> "NH2" Residue "n GLU 77": "OE1" <-> "OE2" Residue "n ASP 92": "OD1" <-> "OD2" Residue "n ARG 95": "NH1" <-> "NH2" Residue "n TYR 117": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "n ARG 124": "NH1" <-> "NH2" Residue "n TYR 151": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "n GLU 159": "OE1" <-> "OE2" Residue "n ARG 172": "NH1" <-> "NH2" Residue "n ASP 173": "OD1" <-> "OD2" Residue "n PHE 179": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.14s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/chem_data/mon_lib" Total number of atoms: 48364 Number of models: 1 Model: "" Number of chains: 30 Chain: "A" Number of atoms: 1300 Number of conformers: 1 Conformer: "" Number of residues, atoms: 161, 1300 Classifications: {'peptide': 161} Link IDs: {'PTRANS': 8, 'TRANS': 152} Chain: "B" Number of atoms: 624 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 624 Classifications: {'peptide': 79} Link IDs: {'PTRANS': 1, 'TRANS': 77} Chain: "C" Number of atoms: 858 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 858 Classifications: {'peptide': 112} Link IDs: {'PTRANS': 3, 'TRANS': 108} Chain: "D" Number of atoms: 685 Number of conformers: 1 Conformer: "" Number of residues, atoms: 89, 685 Classifications: {'peptide': 89} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 1, 'TRANS': 87} Chain breaks: 1 Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 10 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 3} Unresolved non-hydrogen planarities: 12 Chain: "E" Number of atoms: 1792 Number of conformers: 1 Conformer: "" Number of residues, atoms: 232, 1792 Classifications: {'peptide': 232} Link IDs: {'PTRANS': 6, 'TRANS': 225} Chain: "G" Number of atoms: 816 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 816 Classifications: {'peptide': 110} Link IDs: {'PTRANS': 3, 'TRANS': 106} Chain: "H" Number of atoms: 3696 Number of conformers: 1 Conformer: "" Number of residues, atoms: 487, 3696 Classifications: {'peptide': 487} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 468} Chain: "X" Number of atoms: 4677 Number of conformers: 1 Conformer: "" Number of residues, atoms: 603, 4677 Classifications: {'peptide': 603} Link IDs: {'CIS': 1, 'PTRANS': 23, 'TRANS': 578} Chain breaks: 1 Chain: "J" Number of atoms: 1461 Number of conformers: 1 Conformer: "" Number of residues, atoms: 177, 1461 Classifications: {'peptide': 177} Link IDs: {'CIS': 1, 'PTRANS': 14, 'TRANS': 161} Chain: "K" Number of atoms: 1437 Number of conformers: 1 Conformer: "" Number of residues, atoms: 170, 1437 Classifications: {'peptide': 170} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 159} Chain: "L" Number of atoms: 3010 Number of conformers: 1 Conformer: "" Number of residues, atoms: 373, 3010 Classifications: {'peptide': 373} Link IDs: {'PTRANS': 26, 'TRANS': 346} Chain: "M" Number of atoms: 2319 Number of conformers: 1 Conformer: "" Number of residues, atoms: 301, 2319 Classifications: {'peptide': 301} Link IDs: {'PTRANS': 15, 'TRANS': 285} Chain breaks: 1 Chain: "N" Number of atoms: 1483 Number of conformers: 1 Conformer: "" Number of residues, atoms: 176, 1483 Classifications: {'peptide': 176} Link IDs: {'CIS': 1, 'PTRANS': 14, 'TRANS': 160} Chain breaks: 1 Chain: "a" Number of atoms: 1300 Number of conformers: 1 Conformer: "" Number of residues, atoms: 161, 1300 Classifications: {'peptide': 161} Link IDs: {'PTRANS': 8, 'TRANS': 152} Chain: "b" Number of atoms: 624 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 624 Classifications: {'peptide': 79} Link IDs: {'PTRANS': 1, 'TRANS': 77} Chain: "c" Number of atoms: 858 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 858 Classifications: {'peptide': 112} Link IDs: {'PTRANS': 3, 'TRANS': 108} Chain: "d" Number of atoms: 685 Number of conformers: 1 Conformer: "" Number of residues, atoms: 89, 685 Classifications: {'peptide': 89} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 1, 'TRANS': 87} Chain breaks: 1 Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 10 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 3} Unresolved non-hydrogen planarities: 12 Chain: "e" Number of atoms: 1792 Number of conformers: 1 Conformer: "" Number of residues, atoms: 232, 1792 Classifications: {'peptide': 232} Link IDs: {'PTRANS': 6, 'TRANS': 225} Chain: "g" Number of atoms: 816 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 816 Classifications: {'peptide': 110} Link IDs: {'PTRANS': 3, 'TRANS': 106} Chain: "h" Number of atoms: 3696 Number of conformers: 1 Conformer: "" Number of residues, atoms: 487, 3696 Classifications: {'peptide': 487} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 468} Chain: "x" Number of atoms: 4677 Number of conformers: 1 Conformer: "" Number of residues, atoms: 603, 4677 Classifications: {'peptide': 603} Link IDs: {'CIS': 1, 'PTRANS': 23, 'TRANS': 578} Chain breaks: 1 Chain: "j" Number of atoms: 1461 Number of conformers: 1 Conformer: "" Number of residues, atoms: 177, 1461 Classifications: {'peptide': 177} Link IDs: {'CIS': 1, 'PTRANS': 14, 'TRANS': 161} Chain: "k" Number of atoms: 1437 Number of conformers: 1 Conformer: "" Number of residues, atoms: 170, 1437 Classifications: {'peptide': 170} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 159} Chain: "l" Number of atoms: 3010 Number of conformers: 1 Conformer: "" Number of residues, atoms: 373, 3010 Classifications: {'peptide': 373} Link IDs: {'PTRANS': 26, 'TRANS': 346} Chain: "m" Number of atoms: 2319 Number of conformers: 1 Conformer: "" Number of residues, atoms: 301, 2319 Classifications: {'peptide': 301} Link IDs: {'PTRANS': 15, 'TRANS': 285} Chain breaks: 1 Chain: "n" Number of atoms: 1483 Number of conformers: 1 Conformer: "" Number of residues, atoms: 176, 1483 Classifications: {'peptide': 176} Link IDs: {'CIS': 1, 'PTRANS': 14, 'TRANS': 160} Chain breaks: 1 Chain: "J" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 8 Unusual residues: {'SF4': 1} Classifications: {'undetermined': 1} Chain: "N" Number of atoms: 16 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 16 Unusual residues: {'SF4': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "j" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 8 Unusual residues: {'SF4': 1} Classifications: {'undetermined': 1} Chain: "n" Number of atoms: 16 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 16 Unusual residues: {'SF4': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 15149 SG CYS J 93 104.344 149.602 40.032 1.00 28.91 S ATOM 15387 SG CYS J 123 111.604 149.957 39.313 1.00 18.86 S ATOM 23443 SG CYS N 102 116.187 156.410 27.846 1.00 48.79 S ATOM 39307 SG CYS j 93 97.452 58.254 39.938 1.00 28.82 S ATOM 39545 SG CYS j 123 89.981 57.823 39.317 1.00 21.53 S ATOM 47601 SG CYS n 102 85.582 51.570 28.419 1.00 48.79 S ATOM 47387 SG CYS n 71 89.949 52.838 28.959 1.00 31.06 S ATOM 47551 SG CYS n 96 88.453 51.410 34.789 1.00 48.79 S ATOM 47320 SG CYS n 61 82.620 41.855 23.688 1.00 30.43 S Time building chain proxies: 25.26, per 1000 atoms: 0.52 Number of scatterers: 48364 At special positions: 0 Unit cell: (202.713, 209.916, 131.712, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Fe 24 26.01 S 258 16.00 O 8256 8.00 N 7704 7.00 C 32122 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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=0, symmetry=0 Time building additional restraints: 18.40 Conformation dependent library (CDL) restraints added in 6.9 seconds Dynamic metal coordination Iron sulfur cluster coordination pdb=" SF4 J 201 " pdb=" FE1 SF4 J 201 " - pdb=" SG CYS J 93 " pdb=" FE2 SF4 J 201 " - pdb=" SG CYS J 123 " pdb=" FE3 SF4 J 201 " - pdb=" SG CYS J 28 " pdb=" SF4 N 301 " pdb=" FE1 SF4 N 301 " - pdb=" SG CYS N 102 " pdb=" FE4 SF4 N 301 " - pdb=" SG CYS N 96 " pdb=" FE2 SF4 N 301 " - pdb=" SG CYS N 99 " pdb=" FE3 SF4 N 301 " - pdb=" SG CYS N 71 " pdb=" SF4 N 302 " pdb=" FE4 SF4 N 302 " - pdb=" SG CYS N 67 " pdb=" FE2 SF4 N 302 " - pdb=" SG CYS N 106 " pdb=" FE3 SF4 N 302 " - pdb=" SG CYS N 64 " pdb=" FE1 SF4 N 302 " - pdb=" SG CYS N 61 " pdb=" SF4 j 201 " pdb=" FE2 SF4 j 201 " - pdb=" SG CYS j 123 " pdb=" FE1 SF4 j 201 " - pdb=" SG CYS j 93 " pdb=" FE3 SF4 j 201 " - pdb=" SG CYS j 28 " pdb=" SF4 n 301 " pdb=" FE1 SF4 n 301 " - pdb=" SG CYS n 102 " pdb=" FE4 SF4 n 301 " - pdb=" SG CYS n 96 " pdb=" FE3 SF4 n 301 " - pdb=" SG CYS n 71 " pdb=" FE2 SF4 n 301 " - pdb=" SG CYS n 99 " pdb=" SF4 n 302 " pdb=" FE1 SF4 n 302 " - pdb=" SG CYS n 61 " pdb=" FE4 SF4 n 302 " - pdb=" SG CYS n 67 " pdb=" FE2 SF4 n 302 " - pdb=" SG CYS n 106 " pdb=" FE3 SF4 n 302 " - pdb=" SG CYS n 64 " Number of angles added : 66 12144 Ramachandran restraints generated. 6072 Oldfield, 0 Emsley, 6072 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 11280 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 257 helices and 18 sheets defined 51.8% alpha, 2.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.94 Creating SS restraints... Processing helix chain 'A' and resid 8 through 24 Processing helix chain 'A' and resid 33 through 46 Processing helix chain 'A' and resid 61 through 87 removed outlier: 3.731A pdb=" N LEU A 65 " --> pdb=" O PRO A 61 " (cutoff:3.500A) Proline residue: A 72 - end of helix Processing helix chain 'A' and resid 111 through 121 Processing helix chain 'A' and resid 160 through 165 removed outlier: 4.005A pdb=" N VAL A 165 " --> pdb=" O LYS A 161 " (cutoff:3.500A) Processing helix chain 'B' and resid 6 through 23 removed outlier: 4.361A pdb=" N TYR B 20 " --> pdb=" O LEU B 16 " (cutoff:3.500A) removed outlier: 5.257A pdb=" N ARG B 21 " --> pdb=" O LEU B 17 " (cutoff:3.500A) removed outlier: 4.299A pdb=" N VAL B 22 " --> pdb=" O SER B 18 " (cutoff:3.500A) Processing helix chain 'B' and resid 30 through 53 removed outlier: 3.631A pdb=" N ILE B 37 " --> pdb=" O VAL B 33 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N THR B 40 " --> pdb=" O ASP B 36 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N LEU B 48 " --> pdb=" O GLY B 44 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N ALA B 50 " --> pdb=" O MET B 46 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N LEU B 51 " --> pdb=" O VAL B 47 " (cutoff:3.500A) Processing helix chain 'B' and resid 62 through 76 removed outlier: 4.485A pdb=" N PHE B 70 " --> pdb=" O ALA B 66 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N GLY B 72 " --> pdb=" O LEU B 68 " (cutoff:3.500A) Processing helix chain 'C' and resid 6 through 27 removed outlier: 3.978A pdb=" N LEU C 13 " --> pdb=" O GLU C 9 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N ILE C 27 " --> pdb=" O THR C 23 " (cutoff:3.500A) Processing helix chain 'C' and resid 32 through 42 removed outlier: 3.502A pdb=" N ALA C 39 " --> pdb=" O ARG C 35 " (cutoff:3.500A) Processing helix chain 'C' and resid 45 through 57 Processing helix chain 'C' and resid 66 through 94 removed outlier: 3.540A pdb=" N LYS C 70 " --> pdb=" O ALA C 66 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N LEU C 80 " --> pdb=" O ALA C 76 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N ASN C 82 " --> pdb=" O LEU C 78 " (cutoff:3.500A) Proline residue: C 83 - end of helix removed outlier: 3.597A pdb=" N ALA C 92 " --> pdb=" O ALA C 88 " (cutoff:3.500A) Processing helix chain 'C' and resid 107 through 113 Processing helix chain 'D' and resid 6 through 22 removed outlier: 3.589A pdb=" N ALA D 22 " --> pdb=" O SER D 18 " (cutoff:3.500A) Processing helix chain 'D' and resid 28 through 48 Processing helix chain 'D' and resid 52 through 62 Processing helix chain 'D' and resid 71 through 74 No H-bonds generated for 'chain 'D' and resid 71 through 74' Processing helix chain 'E' and resid 5 through 24 Processing helix chain 'E' and resid 38 through 43 removed outlier: 3.513A pdb=" N LEU E 42 " --> pdb=" O GLY E 38 " (cutoff:3.500A) Processing helix chain 'E' and resid 55 through 60 removed outlier: 3.835A pdb=" N VAL E 60 " --> pdb=" O THR E 56 " (cutoff:3.500A) Processing helix chain 'E' and resid 67 through 84 Processing helix chain 'E' and resid 103 through 108 Processing helix chain 'E' and resid 110 through 122 removed outlier: 3.730A pdb=" N PHE E 116 " --> pdb=" O PHE E 112 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N MET E 118 " --> pdb=" O ALA E 114 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N PHE E 121 " --> pdb=" O GLY E 117 " (cutoff:3.500A) Processing helix chain 'E' and resid 131 through 146 Processing helix chain 'E' and resid 160 through 175 removed outlier: 3.629A pdb=" N THR E 173 " --> pdb=" O GLY E 169 " (cutoff:3.500A) Processing helix chain 'E' and resid 177 through 179 No H-bonds generated for 'chain 'E' and resid 177 through 179' Processing helix chain 'E' and resid 209 through 231 removed outlier: 4.055A pdb=" N LEU E 224 " --> pdb=" O VAL E 220 " (cutoff:3.500A) removed outlier: 4.330A pdb=" N SER E 225 " --> pdb=" O GLY E 221 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N GLY E 226 " --> pdb=" O THR E 222 " (cutoff:3.500A) Processing helix chain 'G' and resid 4 through 21 removed outlier: 3.810A pdb=" N VAL G 20 " --> pdb=" O GLY G 16 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N LEU G 21 " --> pdb=" O LEU G 17 " (cutoff:3.500A) Processing helix chain 'G' and resid 26 through 45 Processing helix chain 'G' and resid 72 through 79 removed outlier: 3.563A pdb=" N LEU G 77 " --> pdb=" O GLN G 73 " (cutoff:3.500A) removed outlier: 4.271A pdb=" N THR G 78 " --> pdb=" O ALA G 74 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N ALA G 79 " --> pdb=" O LEU G 75 " (cutoff:3.500A) Processing helix chain 'G' and resid 81 through 100 removed outlier: 3.687A pdb=" N SER G 92 " --> pdb=" O ALA G 88 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N VAL G 93 " --> pdb=" O MET G 89 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N TYR G 98 " --> pdb=" O ALA G 94 " (cutoff:3.500A) Processing helix chain 'H' and resid 3 through 5 No H-bonds generated for 'chain 'H' and resid 3 through 5' Processing helix chain 'H' and resid 7 through 18 Proline residue: H 12 - end of helix Processing helix chain 'H' and resid 31 through 52 removed outlier: 3.870A pdb=" N VAL H 35 " --> pdb=" O PRO H 32 " (cutoff:3.500A) removed outlier: 4.185A pdb=" N ILE H 36 " --> pdb=" O PHE H 33 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N ILE H 37 " --> pdb=" O LEU H 34 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N THR H 38 " --> pdb=" O VAL H 35 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N TRP H 47 " --> pdb=" O ILE H 44 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N VAL H 50 " --> pdb=" O TRP H 47 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N VAL H 52 " --> pdb=" O PHE H 49 " (cutoff:3.500A) Processing helix chain 'H' and resid 78 through 95 removed outlier: 3.894A pdb=" N LEU H 82 " --> pdb=" O HIS H 78 " (cutoff:3.500A) Processing helix chain 'H' and resid 98 through 100 No H-bonds generated for 'chain 'H' and resid 98 through 100' Processing helix chain 'H' and resid 110 through 126 removed outlier: 3.876A pdb=" N ALA H 126 " --> pdb=" O THR H 122 " (cutoff:3.500A) Processing helix chain 'H' and resid 130 through 148 Processing helix chain 'H' and resid 157 through 184 removed outlier: 3.712A pdb=" N MET H 161 " --> pdb=" O ALA H 157 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N LYS H 162 " --> pdb=" O GLU H 158 " (cutoff:3.500A) removed outlier: 4.486A pdb=" N TYR H 163 " --> pdb=" O ALA H 159 " (cutoff:3.500A) Processing helix chain 'H' and resid 190 through 194 Processing helix chain 'H' and resid 205 through 219 removed outlier: 4.525A pdb=" N GLU H 219 " --> pdb=" O GLY H 215 " (cutoff:3.500A) Processing helix chain 'H' and resid 229 through 232 No H-bonds generated for 'chain 'H' and resid 229 through 232' Processing helix chain 'H' and resid 238 through 246 removed outlier: 3.828A pdb=" N VAL H 242 " --> pdb=" O HIS H 238 " (cutoff:3.500A) Processing helix chain 'H' and resid 248 through 262 removed outlier: 3.760A pdb=" N TYR H 261 " --> pdb=" O ALA H 257 " (cutoff:3.500A) Processing helix chain 'H' and resid 269 through 290 removed outlier: 3.599A pdb=" N ALA H 278 " --> pdb=" O LYS H 274 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N PHE H 286 " --> pdb=" O LEU H 282 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ALA H 287 " --> pdb=" O THR H 283 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N GLU H 288 " --> pdb=" O VAL H 284 " (cutoff:3.500A) Processing helix chain 'H' and resid 297 through 316 removed outlier: 4.091A pdb=" N SER H 304 " --> pdb=" O MET H 300 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ILE H 306 " --> pdb=" O ALA H 302 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N VAL H 309 " --> pdb=" O SER H 305 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N LEU H 311 " --> pdb=" O GLY H 307 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N ALA H 315 " --> pdb=" O LEU H 311 " (cutoff:3.500A) Processing helix chain 'H' and resid 328 through 351 removed outlier: 3.941A pdb=" N ASN H 333 " --> pdb=" O PHE H 329 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N ALA H 335 " --> pdb=" O MET H 331 " (cutoff:3.500A) removed outlier: 4.677A pdb=" N ILE H 336 " --> pdb=" O LEU H 332 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N PHE H 342 " --> pdb=" O LYS H 338 " (cutoff:3.500A) Processing helix chain 'H' and resid 370 through 382 removed outlier: 3.800A pdb=" N ALA H 380 " --> pdb=" O ILE H 376 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N THR H 381 " --> pdb=" O GLY H 377 " (cutoff:3.500A) removed outlier: 4.581A pdb=" N VAL H 382 " --> pdb=" O GLY H 378 " (cutoff:3.500A) Processing helix chain 'H' and resid 388 through 399 Processing helix chain 'H' and resid 412 through 424 removed outlier: 3.906A pdb=" N VAL H 417 " --> pdb=" O LEU H 413 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N VAL H 421 " --> pdb=" O VAL H 417 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N TYR H 423 " --> pdb=" O GLU H 419 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N PHE H 424 " --> pdb=" O ALA H 420 " (cutoff:3.500A) Processing helix chain 'H' and resid 428 through 431 No H-bonds generated for 'chain 'H' and resid 428 through 431' Processing helix chain 'H' and resid 448 through 453 Processing helix chain 'H' and resid 464 through 472 removed outlier: 3.748A pdb=" N ASN H 468 " --> pdb=" O THR H 464 " (cutoff:3.500A) removed outlier: 4.955A pdb=" N LEU H 469 " --> pdb=" O PRO H 465 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N VAL H 470 " --> pdb=" O PHE H 466 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N THR H 471 " --> pdb=" O TRP H 467 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N LYS H 472 " --> pdb=" O ASN H 468 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 464 through 472' Processing helix chain 'H' and resid 481 through 485 Processing helix chain 'X' and resid 6 through 20 Proline residue: X 11 - end of helix removed outlier: 4.550A pdb=" N TRP X 19 " --> pdb=" O GLY X 15 " (cutoff:3.500A) removed outlier: 4.540A pdb=" N LEU X 20 " --> pdb=" O ALA X 16 " (cutoff:3.500A) Processing helix chain 'X' and resid 29 through 32 No H-bonds generated for 'chain 'X' and resid 29 through 32' Processing helix chain 'X' and resid 37 through 44 Processing helix chain 'X' and resid 47 through 49 No H-bonds generated for 'chain 'X' and resid 47 through 49' Processing helix chain 'X' and resid 73 through 88 Processing helix chain 'X' and resid 101 through 104 No H-bonds generated for 'chain 'X' and resid 101 through 104' Processing helix chain 'X' and resid 106 through 115 Processing helix chain 'X' and resid 123 through 138 Processing helix chain 'X' and resid 143 through 169 removed outlier: 3.590A pdb=" N LYS X 148 " --> pdb=" O HIS X 144 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N TYR X 149 " --> pdb=" O ALA X 145 " (cutoff:3.500A) Processing helix chain 'X' and resid 176 through 185 removed outlier: 3.976A pdb=" N SER X 180 " --> pdb=" O PHE X 176 " (cutoff:3.500A) removed outlier: 4.310A pdb=" N ALA X 181 " --> pdb=" O PRO X 177 " (cutoff:3.500A) Processing helix chain 'X' and resid 204 through 215 removed outlier: 3.603A pdb=" N ALA X 208 " --> pdb=" O LEU X 204 " (cutoff:3.500A) Processing helix chain 'X' and resid 227 through 230 No H-bonds generated for 'chain 'X' and resid 227 through 230' Processing helix chain 'X' and resid 236 through 242 removed outlier: 4.028A pdb=" N ALA X 240 " --> pdb=" O GLN X 236 " (cutoff:3.500A) removed outlier: 5.210A pdb=" N MET X 241 " --> pdb=" O SER X 237 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N PHE X 242 " --> pdb=" O TYR X 238 " (cutoff:3.500A) No H-bonds generated for 'chain 'X' and resid 236 through 242' Processing helix chain 'X' and resid 248 through 260 Processing helix chain 'X' and resid 264 through 267 No H-bonds generated for 'chain 'X' and resid 264 through 267' Processing helix chain 'X' and resid 277 through 296 Processing helix chain 'X' and resid 305 through 311 removed outlier: 3.889A pdb=" N TYR X 309 " --> pdb=" O LYS X 305 " (cutoff:3.500A) Processing helix chain 'X' and resid 315 through 321 Processing helix chain 'X' and resid 329 through 356 removed outlier: 4.298A pdb=" N TYR X 335 " --> pdb=" O ALA X 331 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N LEU X 346 " --> pdb=" O LEU X 342 " (cutoff:3.500A) Processing helix chain 'X' and resid 374 through 385 Processing helix chain 'X' and resid 394 through 407 removed outlier: 3.849A pdb=" N ILE X 407 " --> pdb=" O PHE X 403 " (cutoff:3.500A) Processing helix chain 'X' and resid 412 through 435 removed outlier: 3.644A pdb=" N ALA X 416 " --> pdb=" O PRO X 412 " (cutoff:3.500A) removed outlier: 4.317A pdb=" N MET X 417 " --> pdb=" O ILE X 413 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N VAL X 418 " --> pdb=" O LEU X 414 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N TYR X 428 " --> pdb=" O ILE X 424 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N LEU X 429 " --> pdb=" O GLY X 425 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N ILE X 430 " --> pdb=" O PHE X 426 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N ALA X 435 " --> pdb=" O ARG X 431 " (cutoff:3.500A) Processing helix chain 'X' and resid 453 through 470 removed outlier: 3.767A pdb=" N GLY X 458 " --> pdb=" O PRO X 454 " (cutoff:3.500A) Processing helix chain 'X' and resid 475 through 481 Processing helix chain 'X' and resid 506 through 521 removed outlier: 4.827A pdb=" N TRP X 511 " --> pdb=" O LEU X 507 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N LEU X 512 " --> pdb=" O LEU X 508 " (cutoff:3.500A) Processing helix chain 'X' and resid 558 through 563 Processing helix chain 'X' and resid 567 through 569 No H-bonds generated for 'chain 'X' and resid 567 through 569' Processing helix chain 'X' and resid 573 through 593 removed outlier: 3.717A pdb=" N SER X 592 " --> pdb=" O ASP X 588 " (cutoff:3.500A) Processing helix chain 'X' and resid 599 through 615 Processing helix chain 'J' and resid 9 through 17 removed outlier: 3.510A pdb=" N TRP J 13 " --> pdb=" O PRO J 9 " (cutoff:3.500A) removed outlier: 4.279A pdb=" N ALA J 14 " --> pdb=" O LEU J 10 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N LYS J 16 " --> pdb=" O ASN J 12 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N LYS J 17 " --> pdb=" O TRP J 13 " (cutoff:3.500A) Processing helix chain 'J' and resid 35 through 37 No H-bonds generated for 'chain 'J' and resid 35 through 37' Processing helix chain 'J' and resid 68 through 78 removed outlier: 3.799A pdb=" N LYS J 72 " --> pdb=" O PRO J 68 " (cutoff:3.500A) removed outlier: 4.870A pdb=" N ARG J 73 " --> pdb=" O LYS J 69 " (cutoff:3.500A) Processing helix chain 'J' and resid 100 through 102 No H-bonds generated for 'chain 'J' and resid 100 through 102' Processing helix chain 'J' and resid 110 through 112 No H-bonds generated for 'chain 'J' and resid 110 through 112' Processing helix chain 'J' and resid 127 through 143 removed outlier: 4.406A pdb=" N ASN J 143 " --> pdb=" O GLU J 139 " (cutoff:3.500A) Processing helix chain 'J' and resid 151 through 154 No H-bonds generated for 'chain 'J' and resid 151 through 154' Processing helix chain 'J' and resid 156 through 166 removed outlier: 3.618A pdb=" N LYS J 161 " --> pdb=" O GLU J 157 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N LEU J 166 " --> pdb=" O ASN J 162 " (cutoff:3.500A) Processing helix chain 'J' and resid 171 through 174 No H-bonds generated for 'chain 'J' and resid 171 through 174' Processing helix chain 'J' and resid 177 through 180 No H-bonds generated for 'chain 'J' and resid 177 through 180' Processing helix chain 'K' and resid 5 through 15 Processing helix chain 'K' and resid 36 through 38 No H-bonds generated for 'chain 'K' and resid 36 through 38' Processing helix chain 'K' and resid 43 through 49 Processing helix chain 'K' and resid 107 through 109 No H-bonds generated for 'chain 'K' and resid 107 through 109' Processing helix chain 'K' and resid 111 through 118 Processing helix chain 'K' and resid 155 through 158 No H-bonds generated for 'chain 'K' and resid 155 through 158' Processing helix chain 'L' and resid 82 through 84 No H-bonds generated for 'chain 'L' and resid 82 through 84' Processing helix chain 'L' and resid 91 through 104 removed outlier: 3.647A pdb=" N TYR L 96 " --> pdb=" O PRO L 92 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N MET L 98 " --> pdb=" O ALA L 94 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ASP L 101 " --> pdb=" O SER L 97 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N GLU L 102 " --> pdb=" O MET L 98 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ILE L 104 " --> pdb=" O VAL L 100 " (cutoff:3.500A) Processing helix chain 'L' and resid 110 through 136 removed outlier: 3.711A pdb=" N ARG L 124 " --> pdb=" O LEU L 120 " (cutoff:3.500A) Processing helix chain 'L' and resid 143 through 162 removed outlier: 3.547A pdb=" N ALA L 148 " --> pdb=" O ALA L 144 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N ARG L 154 " --> pdb=" O ALA L 150 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N PHE L 155 " --> pdb=" O TYR L 151 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N GLN L 161 " --> pdb=" O ALA L 157 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N LEU L 162 " --> pdb=" O LEU L 158 " (cutoff:3.500A) Processing helix chain 'L' and resid 184 through 203 removed outlier: 3.957A pdb=" N GLN L 189 " --> pdb=" O LYS L 185 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N ARG L 191 " --> pdb=" O LEU L 187 " (cutoff:3.500A) removed outlier: 4.829A pdb=" N LYS L 202 " --> pdb=" O LYS L 198 " (cutoff:3.500A) removed outlier: 5.193A pdb=" N ASP L 203 " --> pdb=" O ASP L 199 " (cutoff:3.500A) Processing helix chain 'L' and resid 205 through 208 No H-bonds generated for 'chain 'L' and resid 205 through 208' Processing helix chain 'L' and resid 214 through 217 No H-bonds generated for 'chain 'L' and resid 214 through 217' Processing helix chain 'L' and resid 248 through 251 No H-bonds generated for 'chain 'L' and resid 248 through 251' Processing helix chain 'L' and resid 272 through 296 removed outlier: 3.841A pdb=" N LEU L 277 " --> pdb=" O ALA L 274 " (cutoff:3.500A) removed outlier: 5.006A pdb=" N VAL L 278 " --> pdb=" O ARG L 275 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N GLN L 285 " --> pdb=" O GLU L 282 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N GLU L 291 " --> pdb=" O TYR L 288 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N LEU L 293 " --> pdb=" O ILE L 290 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N LEU L 294 " --> pdb=" O GLU L 291 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N ASP L 295 " --> pdb=" O GLN L 292 " (cutoff:3.500A) Processing helix chain 'L' and resid 308 through 310 No H-bonds generated for 'chain 'L' and resid 308 through 310' Processing helix chain 'L' and resid 372 through 381 Proline residue: L 376 - end of helix Processing helix chain 'L' and resid 386 through 388 No H-bonds generated for 'chain 'L' and resid 386 through 388' Processing helix chain 'M' and resid 3 through 34 removed outlier: 4.815A pdb=" N ILE M 21 " --> pdb=" O PHE M 17 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N HIS M 34 " --> pdb=" O THR M 30 " (cutoff:3.500A) Processing helix chain 'M' and resid 43 through 51 Processing helix chain 'M' and resid 62 through 79 removed outlier: 4.149A pdb=" N PHE M 66 " --> pdb=" O LEU M 62 " (cutoff:3.500A) removed outlier: 4.734A pdb=" N ILE M 68 " --> pdb=" O TYR M 64 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N LEU M 79 " --> pdb=" O THR M 75 " (cutoff:3.500A) Processing helix chain 'M' and resid 96 through 112 removed outlier: 3.928A pdb=" N GLU M 104 " --> pdb=" O THR M 100 " (cutoff:3.500A) Proline residue: M 106 - end of helix removed outlier: 4.258A pdb=" N MET M 111 " --> pdb=" O MET M 107 " (cutoff:3.500A) Processing helix chain 'M' and resid 120 through 151 removed outlier: 3.852A pdb=" N LEU M 131 " --> pdb=" O GLN M 127 " (cutoff:3.500A) removed outlier: 4.468A pdb=" N THR M 132 " --> pdb=" O ARG M 128 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N LEU M 133 " --> pdb=" O ALA M 129 " (cutoff:3.500A) removed outlier: 4.253A pdb=" N GLN M 137 " --> pdb=" O LEU M 133 " (cutoff:3.500A) removed outlier: 4.514A pdb=" N VAL M 138 " --> pdb=" O LEU M 134 " (cutoff:3.500A) Proline residue: M 139 - end of helix removed outlier: 3.908A pdb=" N LEU M 142 " --> pdb=" O VAL M 138 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N TYR M 150 " --> pdb=" O ALA M 146 " (cutoff:3.500A) Processing helix chain 'M' and resid 156 through 165 removed outlier: 4.116A pdb=" N VAL M 160 " --> pdb=" O TYR M 157 " (cutoff:3.500A) removed outlier: 5.216A pdb=" N MET M 161 " --> pdb=" O GLU M 158 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N GLN M 164 " --> pdb=" O MET M 161 " (cutoff:3.500A) removed outlier: 4.493A pdb=" N LYS M 165 " --> pdb=" O ALA M 162 " (cutoff:3.500A) Processing helix chain 'M' and resid 173 through 190 removed outlier: 4.404A pdb=" N ALA M 178 " --> pdb=" O PRO M 174 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N ALA M 181 " --> pdb=" O LEU M 177 " (cutoff:3.500A) removed outlier: 4.393A pdb=" N GLN M 187 " --> pdb=" O ASP M 183 " (cutoff:3.500A) removed outlier: 4.149A pdb=" N ALA M 188 " --> pdb=" O ILE M 184 " (cutoff:3.500A) Processing helix chain 'M' and resid 193 through 198 removed outlier: 3.557A pdb=" N ASP M 196 " --> pdb=" O GLU M 193 " (cutoff:3.500A) removed outlier: 5.618A pdb=" N ILE M 197 " --> pdb=" O PRO M 194 " (cutoff:3.500A) removed outlier: 4.677A pdb=" N MET M 198 " --> pdb=" O PHE M 195 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 193 through 198' Processing helix chain 'M' and resid 207 through 209 No H-bonds generated for 'chain 'M' and resid 207 through 209' Processing helix chain 'M' and resid 214 through 239 removed outlier: 3.511A pdb=" N ILE M 238 " --> pdb=" O PHE M 234 " (cutoff:3.500A) Processing helix chain 'M' and resid 252 through 276 removed outlier: 3.975A pdb=" N ALA M 257 " --> pdb=" O LEU M 253 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N VAL M 269 " --> pdb=" O LYS M 265 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N PHE M 275 " --> pdb=" O LEU M 271 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N VAL M 276 " --> pdb=" O ILE M 272 " (cutoff:3.500A) Processing helix chain 'M' and resid 285 through 306 removed outlier: 3.692A pdb=" N TYR M 292 " --> pdb=" O ALA M 288 " (cutoff:3.500A) removed outlier: 4.169A pdb=" N TRP M 293 " --> pdb=" O ALA M 289 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N LYS M 294 " --> pdb=" O LYS M 290 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N TRP M 295 " --> pdb=" O PHE M 291 " (cutoff:3.500A) Proline residue: M 296 - end of helix Processing helix chain 'N' and resid 22 through 26 Processing helix chain 'N' and resid 28 through 30 No H-bonds generated for 'chain 'N' and resid 28 through 30' Processing helix chain 'N' and resid 67 through 69 No H-bonds generated for 'chain 'N' and resid 67 through 69' Processing helix chain 'N' and resid 129 through 131 No H-bonds generated for 'chain 'N' and resid 129 through 131' Processing helix chain 'N' and resid 138 through 142 Processing helix chain 'a' and resid 8 through 24 Processing helix chain 'a' and resid 33 through 46 Processing helix chain 'a' and resid 61 through 87 removed outlier: 3.731A pdb=" N LEU a 65 " --> pdb=" O PRO a 61 " (cutoff:3.500A) Proline residue: a 72 - end of helix Processing helix chain 'a' and resid 111 through 121 Processing helix chain 'a' and resid 160 through 165 removed outlier: 4.005A pdb=" N VAL a 165 " --> pdb=" O LYS a 161 " (cutoff:3.500A) Processing helix chain 'b' and resid 6 through 23 removed outlier: 4.361A pdb=" N TYR b 20 " --> pdb=" O LEU b 16 " (cutoff:3.500A) removed outlier: 5.256A pdb=" N ARG b 21 " --> pdb=" O LEU b 17 " (cutoff:3.500A) removed outlier: 4.298A pdb=" N VAL b 22 " --> pdb=" O SER b 18 " (cutoff:3.500A) Processing helix chain 'b' and resid 30 through 53 removed outlier: 3.630A pdb=" N ILE b 37 " --> pdb=" O VAL b 33 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N THR b 40 " --> pdb=" O ASP b 36 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N LEU b 48 " --> pdb=" O GLY b 44 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N ALA b 50 " --> pdb=" O MET b 46 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N LEU b 51 " --> pdb=" O VAL b 47 " (cutoff:3.500A) Processing helix chain 'b' and resid 62 through 76 removed outlier: 4.485A pdb=" N PHE b 70 " --> pdb=" O ALA b 66 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N GLY b 72 " --> pdb=" O LEU b 68 " (cutoff:3.500A) Processing helix chain 'c' and resid 6 through 27 removed outlier: 3.979A pdb=" N LEU c 13 " --> pdb=" O GLU c 9 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N ILE c 27 " --> pdb=" O THR c 23 " (cutoff:3.500A) Processing helix chain 'c' and resid 32 through 42 removed outlier: 3.502A pdb=" N ALA c 39 " --> pdb=" O ARG c 35 " (cutoff:3.500A) Processing helix chain 'c' and resid 45 through 57 Processing helix chain 'c' and resid 66 through 94 removed outlier: 3.540A pdb=" N LYS c 70 " --> pdb=" O ALA c 66 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N LEU c 80 " --> pdb=" O ALA c 76 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N ASN c 82 " --> pdb=" O LEU c 78 " (cutoff:3.500A) Proline residue: c 83 - end of helix removed outlier: 3.597A pdb=" N ALA c 92 " --> pdb=" O ALA c 88 " (cutoff:3.500A) Processing helix chain 'c' and resid 107 through 113 Processing helix chain 'd' and resid 6 through 22 removed outlier: 3.589A pdb=" N ALA d 22 " --> pdb=" O SER d 18 " (cutoff:3.500A) Processing helix chain 'd' and resid 28 through 48 Processing helix chain 'd' and resid 52 through 62 Processing helix chain 'd' and resid 71 through 74 No H-bonds generated for 'chain 'd' and resid 71 through 74' Processing helix chain 'e' and resid 5 through 24 Processing helix chain 'e' and resid 38 through 43 removed outlier: 3.513A pdb=" N LEU e 42 " --> pdb=" O GLY e 38 " (cutoff:3.500A) Processing helix chain 'e' and resid 55 through 60 removed outlier: 3.834A pdb=" N VAL e 60 " --> pdb=" O THR e 56 " (cutoff:3.500A) Processing helix chain 'e' and resid 67 through 84 Processing helix chain 'e' and resid 103 through 108 Processing helix chain 'e' and resid 110 through 122 removed outlier: 3.729A pdb=" N PHE e 116 " --> pdb=" O PHE e 112 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N MET e 118 " --> pdb=" O ALA e 114 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N PHE e 121 " --> pdb=" O GLY e 117 " (cutoff:3.500A) Processing helix chain 'e' and resid 131 through 146 Processing helix chain 'e' and resid 160 through 175 removed outlier: 3.629A pdb=" N THR e 173 " --> pdb=" O GLY e 169 " (cutoff:3.500A) Processing helix chain 'e' and resid 177 through 179 No H-bonds generated for 'chain 'e' and resid 177 through 179' Processing helix chain 'e' and resid 209 through 231 removed outlier: 4.055A pdb=" N LEU e 224 " --> pdb=" O VAL e 220 " (cutoff:3.500A) removed outlier: 4.330A pdb=" N SER e 225 " --> pdb=" O GLY e 221 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N GLY e 226 " --> pdb=" O THR e 222 " (cutoff:3.500A) Processing helix chain 'g' and resid 4 through 21 removed outlier: 3.810A pdb=" N VAL g 20 " --> pdb=" O GLY g 16 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N LEU g 21 " --> pdb=" O LEU g 17 " (cutoff:3.500A) Processing helix chain 'g' and resid 26 through 45 Processing helix chain 'g' and resid 72 through 79 removed outlier: 3.563A pdb=" N LEU g 77 " --> pdb=" O GLN g 73 " (cutoff:3.500A) removed outlier: 4.271A pdb=" N THR g 78 " --> pdb=" O ALA g 74 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ALA g 79 " --> pdb=" O LEU g 75 " (cutoff:3.500A) Processing helix chain 'g' and resid 81 through 100 removed outlier: 3.687A pdb=" N SER g 92 " --> pdb=" O ALA g 88 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N VAL g 93 " --> pdb=" O MET g 89 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N TYR g 98 " --> pdb=" O ALA g 94 " (cutoff:3.500A) Processing helix chain 'h' and resid 3 through 5 No H-bonds generated for 'chain 'h' and resid 3 through 5' Processing helix chain 'h' and resid 7 through 18 Proline residue: h 12 - end of helix Processing helix chain 'h' and resid 31 through 52 removed outlier: 3.871A pdb=" N VAL h 35 " --> pdb=" O PRO h 32 " (cutoff:3.500A) removed outlier: 4.185A pdb=" N ILE h 36 " --> pdb=" O PHE h 33 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N ILE h 37 " --> pdb=" O LEU h 34 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N THR h 38 " --> pdb=" O VAL h 35 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N TRP h 47 " --> pdb=" O ILE h 44 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N VAL h 50 " --> pdb=" O TRP h 47 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N VAL h 52 " --> pdb=" O PHE h 49 " (cutoff:3.500A) Processing helix chain 'h' and resid 78 through 95 removed outlier: 3.895A pdb=" N LEU h 82 " --> pdb=" O HIS h 78 " (cutoff:3.500A) Processing helix chain 'h' and resid 98 through 100 No H-bonds generated for 'chain 'h' and resid 98 through 100' Processing helix chain 'h' and resid 110 through 126 removed outlier: 3.876A pdb=" N ALA h 126 " --> pdb=" O THR h 122 " (cutoff:3.500A) Processing helix chain 'h' and resid 130 through 148 Processing helix chain 'h' and resid 157 through 184 removed outlier: 3.712A pdb=" N MET h 161 " --> pdb=" O ALA h 157 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N LYS h 162 " --> pdb=" O GLU h 158 " (cutoff:3.500A) removed outlier: 4.485A pdb=" N TYR h 163 " --> pdb=" O ALA h 159 " (cutoff:3.500A) Processing helix chain 'h' and resid 190 through 194 Processing helix chain 'h' and resid 205 through 219 removed outlier: 4.524A pdb=" N GLU h 219 " --> pdb=" O GLY h 215 " (cutoff:3.500A) Processing helix chain 'h' and resid 229 through 232 No H-bonds generated for 'chain 'h' and resid 229 through 232' Processing helix chain 'h' and resid 238 through 246 removed outlier: 3.828A pdb=" N VAL h 242 " --> pdb=" O HIS h 238 " (cutoff:3.500A) Processing helix chain 'h' and resid 248 through 262 removed outlier: 3.760A pdb=" N TYR h 261 " --> pdb=" O ALA h 257 " (cutoff:3.500A) Processing helix chain 'h' and resid 269 through 290 removed outlier: 3.600A pdb=" N ALA h 278 " --> pdb=" O LYS h 274 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N PHE h 286 " --> pdb=" O LEU h 282 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ALA h 287 " --> pdb=" O THR h 283 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N GLU h 288 " --> pdb=" O VAL h 284 " (cutoff:3.500A) Processing helix chain 'h' and resid 297 through 316 removed outlier: 4.091A pdb=" N SER h 304 " --> pdb=" O MET h 300 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ILE h 306 " --> pdb=" O ALA h 302 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N VAL h 309 " --> pdb=" O SER h 305 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N LEU h 311 " --> pdb=" O GLY h 307 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N ALA h 315 " --> pdb=" O LEU h 311 " (cutoff:3.500A) Processing helix chain 'h' and resid 328 through 351 removed outlier: 3.941A pdb=" N ASN h 333 " --> pdb=" O PHE h 329 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N ALA h 335 " --> pdb=" O MET h 331 " (cutoff:3.500A) removed outlier: 4.678A pdb=" N ILE h 336 " --> pdb=" O LEU h 332 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N PHE h 342 " --> pdb=" O LYS h 338 " (cutoff:3.500A) Processing helix chain 'h' and resid 370 through 382 removed outlier: 3.800A pdb=" N ALA h 380 " --> pdb=" O ILE h 376 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N THR h 381 " --> pdb=" O GLY h 377 " (cutoff:3.500A) removed outlier: 4.582A pdb=" N VAL h 382 " --> pdb=" O GLY h 378 " (cutoff:3.500A) Processing helix chain 'h' and resid 388 through 399 Processing helix chain 'h' and resid 412 through 424 removed outlier: 3.905A pdb=" N VAL h 417 " --> pdb=" O LEU h 413 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N VAL h 421 " --> pdb=" O VAL h 417 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N TYR h 423 " --> pdb=" O GLU h 419 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N PHE h 424 " --> pdb=" O ALA h 420 " (cutoff:3.500A) Processing helix chain 'h' and resid 428 through 431 No H-bonds generated for 'chain 'h' and resid 428 through 431' Processing helix chain 'h' and resid 448 through 453 Processing helix chain 'h' and resid 464 through 472 removed outlier: 3.747A pdb=" N ASN h 468 " --> pdb=" O THR h 464 " (cutoff:3.500A) removed outlier: 4.954A pdb=" N LEU h 469 " --> pdb=" O PRO h 465 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N VAL h 470 " --> pdb=" O PHE h 466 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N THR h 471 " --> pdb=" O TRP h 467 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N LYS h 472 " --> pdb=" O ASN h 468 " (cutoff:3.500A) No H-bonds generated for 'chain 'h' and resid 464 through 472' Processing helix chain 'h' and resid 481 through 485 Processing helix chain 'x' and resid 6 through 20 Proline residue: x 11 - end of helix removed outlier: 4.549A pdb=" N TRP x 19 " --> pdb=" O GLY x 15 " (cutoff:3.500A) removed outlier: 4.540A pdb=" N LEU x 20 " --> pdb=" O ALA x 16 " (cutoff:3.500A) Processing helix chain 'x' and resid 29 through 32 No H-bonds generated for 'chain 'x' and resid 29 through 32' Processing helix chain 'x' and resid 37 through 44 Processing helix chain 'x' and resid 47 through 49 No H-bonds generated for 'chain 'x' and resid 47 through 49' Processing helix chain 'x' and resid 73 through 88 Processing helix chain 'x' and resid 101 through 104 No H-bonds generated for 'chain 'x' and resid 101 through 104' Processing helix chain 'x' and resid 106 through 115 Processing helix chain 'x' and resid 123 through 138 Processing helix chain 'x' and resid 143 through 169 removed outlier: 3.589A pdb=" N LYS x 148 " --> pdb=" O HIS x 144 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N TYR x 149 " --> pdb=" O ALA x 145 " (cutoff:3.500A) Processing helix chain 'x' and resid 176 through 185 removed outlier: 3.976A pdb=" N SER x 180 " --> pdb=" O PHE x 176 " (cutoff:3.500A) removed outlier: 4.310A pdb=" N ALA x 181 " --> pdb=" O PRO x 177 " (cutoff:3.500A) Processing helix chain 'x' and resid 204 through 215 removed outlier: 3.603A pdb=" N ALA x 208 " --> pdb=" O LEU x 204 " (cutoff:3.500A) Processing helix chain 'x' and resid 227 through 230 No H-bonds generated for 'chain 'x' and resid 227 through 230' Processing helix chain 'x' and resid 236 through 242 removed outlier: 4.028A pdb=" N ALA x 240 " --> pdb=" O GLN x 236 " (cutoff:3.500A) removed outlier: 5.210A pdb=" N MET x 241 " --> pdb=" O SER x 237 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N PHE x 242 " --> pdb=" O TYR x 238 " (cutoff:3.500A) No H-bonds generated for 'chain 'x' and resid 236 through 242' Processing helix chain 'x' and resid 248 through 260 Processing helix chain 'x' and resid 264 through 267 No H-bonds generated for 'chain 'x' and resid 264 through 267' Processing helix chain 'x' and resid 277 through 296 Processing helix chain 'x' and resid 305 through 311 removed outlier: 3.890A pdb=" N TYR x 309 " --> pdb=" O LYS x 305 " (cutoff:3.500A) Processing helix chain 'x' and resid 315 through 321 Processing helix chain 'x' and resid 329 through 356 removed outlier: 4.298A pdb=" N TYR x 335 " --> pdb=" O ALA x 331 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N LEU x 346 " --> pdb=" O LEU x 342 " (cutoff:3.500A) Processing helix chain 'x' and resid 374 through 385 Processing helix chain 'x' and resid 394 through 407 removed outlier: 3.848A pdb=" N ILE x 407 " --> pdb=" O PHE x 403 " (cutoff:3.500A) Processing helix chain 'x' and resid 412 through 435 removed outlier: 3.644A pdb=" N ALA x 416 " --> pdb=" O PRO x 412 " (cutoff:3.500A) removed outlier: 4.318A pdb=" N MET x 417 " --> pdb=" O ILE x 413 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N VAL x 418 " --> pdb=" O LEU x 414 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N TYR x 428 " --> pdb=" O ILE x 424 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N LEU x 429 " --> pdb=" O GLY x 425 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N ILE x 430 " --> pdb=" O PHE x 426 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N ALA x 435 " --> pdb=" O ARG x 431 " (cutoff:3.500A) Processing helix chain 'x' and resid 453 through 470 removed outlier: 3.767A pdb=" N GLY x 458 " --> pdb=" O PRO x 454 " (cutoff:3.500A) Processing helix chain 'x' and resid 475 through 481 Processing helix chain 'x' and resid 506 through 521 removed outlier: 4.828A pdb=" N TRP x 511 " --> pdb=" O LEU x 507 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N LEU x 512 " --> pdb=" O LEU x 508 " (cutoff:3.500A) Processing helix chain 'x' and resid 558 through 563 Processing helix chain 'x' and resid 567 through 569 No H-bonds generated for 'chain 'x' and resid 567 through 569' Processing helix chain 'x' and resid 573 through 593 removed outlier: 3.716A pdb=" N SER x 592 " --> pdb=" O ASP x 588 " (cutoff:3.500A) Processing helix chain 'x' and resid 599 through 615 Processing helix chain 'j' and resid 9 through 17 removed outlier: 3.510A pdb=" N TRP j 13 " --> pdb=" O PRO j 9 " (cutoff:3.500A) removed outlier: 4.279A pdb=" N ALA j 14 " --> pdb=" O LEU j 10 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N LYS j 16 " --> pdb=" O ASN j 12 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N LYS j 17 " --> pdb=" O TRP j 13 " (cutoff:3.500A) Processing helix chain 'j' and resid 35 through 37 No H-bonds generated for 'chain 'j' and resid 35 through 37' Processing helix chain 'j' and resid 68 through 78 removed outlier: 3.800A pdb=" N LYS j 72 " --> pdb=" O PRO j 68 " (cutoff:3.500A) removed outlier: 4.870A pdb=" N ARG j 73 " --> pdb=" O LYS j 69 " (cutoff:3.500A) Processing helix chain 'j' and resid 100 through 102 No H-bonds generated for 'chain 'j' and resid 100 through 102' Processing helix chain 'j' and resid 110 through 112 No H-bonds generated for 'chain 'j' and resid 110 through 112' Processing helix chain 'j' and resid 127 through 143 removed outlier: 4.406A pdb=" N ASN j 143 " --> pdb=" O GLU j 139 " (cutoff:3.500A) Processing helix chain 'j' and resid 151 through 154 No H-bonds generated for 'chain 'j' and resid 151 through 154' Processing helix chain 'j' and resid 156 through 166 removed outlier: 3.617A pdb=" N LYS j 161 " --> pdb=" O GLU j 157 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N LEU j 166 " --> pdb=" O ASN j 162 " (cutoff:3.500A) Processing helix chain 'j' and resid 171 through 174 No H-bonds generated for 'chain 'j' and resid 171 through 174' Processing helix chain 'j' and resid 177 through 180 No H-bonds generated for 'chain 'j' and resid 177 through 180' Processing helix chain 'k' and resid 5 through 15 Processing helix chain 'k' and resid 36 through 38 No H-bonds generated for 'chain 'k' and resid 36 through 38' Processing helix chain 'k' and resid 43 through 49 Processing helix chain 'k' and resid 107 through 109 No H-bonds generated for 'chain 'k' and resid 107 through 109' Processing helix chain 'k' and resid 111 through 118 Processing helix chain 'k' and resid 155 through 158 No H-bonds generated for 'chain 'k' and resid 155 through 158' Processing helix chain 'l' and resid 82 through 84 No H-bonds generated for 'chain 'l' and resid 82 through 84' Processing helix chain 'l' and resid 91 through 104 removed outlier: 3.646A pdb=" N TYR l 96 " --> pdb=" O PRO l 92 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N MET l 98 " --> pdb=" O ALA l 94 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ASP l 101 " --> pdb=" O SER l 97 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N GLU l 102 " --> pdb=" O MET l 98 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ILE l 104 " --> pdb=" O VAL l 100 " (cutoff:3.500A) Processing helix chain 'l' and resid 110 through 136 removed outlier: 3.711A pdb=" N ARG l 124 " --> pdb=" O LEU l 120 " (cutoff:3.500A) Processing helix chain 'l' and resid 143 through 162 removed outlier: 3.547A pdb=" N ALA l 148 " --> pdb=" O ALA l 144 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N ARG l 154 " --> pdb=" O ALA l 150 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N PHE l 155 " --> pdb=" O TYR l 151 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N GLN l 161 " --> pdb=" O ALA l 157 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N LEU l 162 " --> pdb=" O LEU l 158 " (cutoff:3.500A) Processing helix chain 'l' and resid 184 through 203 removed outlier: 3.957A pdb=" N GLN l 189 " --> pdb=" O LYS l 185 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N ARG l 191 " --> pdb=" O LEU l 187 " (cutoff:3.500A) removed outlier: 4.828A pdb=" N LYS l 202 " --> pdb=" O LYS l 198 " (cutoff:3.500A) removed outlier: 5.192A pdb=" N ASP l 203 " --> pdb=" O ASP l 199 " (cutoff:3.500A) Processing helix chain 'l' and resid 205 through 208 No H-bonds generated for 'chain 'l' and resid 205 through 208' Processing helix chain 'l' and resid 214 through 217 No H-bonds generated for 'chain 'l' and resid 214 through 217' Processing helix chain 'l' and resid 248 through 251 No H-bonds generated for 'chain 'l' and resid 248 through 251' Processing helix chain 'l' and resid 272 through 296 removed outlier: 3.841A pdb=" N LEU l 277 " --> pdb=" O ALA l 274 " (cutoff:3.500A) removed outlier: 5.007A pdb=" N VAL l 278 " --> pdb=" O ARG l 275 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N GLN l 285 " --> pdb=" O GLU l 282 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N GLU l 291 " --> pdb=" O TYR l 288 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N LEU l 293 " --> pdb=" O ILE l 290 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N LEU l 294 " --> pdb=" O GLU l 291 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N ASP l 295 " --> pdb=" O GLN l 292 " (cutoff:3.500A) Processing helix chain 'l' and resid 308 through 310 No H-bonds generated for 'chain 'l' and resid 308 through 310' Processing helix chain 'l' and resid 372 through 381 Proline residue: l 376 - end of helix Processing helix chain 'l' and resid 386 through 388 No H-bonds generated for 'chain 'l' and resid 386 through 388' Processing helix chain 'm' and resid 3 through 34 removed outlier: 4.816A pdb=" N ILE m 21 " --> pdb=" O PHE m 17 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N HIS m 34 " --> pdb=" O THR m 30 " (cutoff:3.500A) Processing helix chain 'm' and resid 43 through 51 Processing helix chain 'm' and resid 62 through 79 removed outlier: 4.150A pdb=" N PHE m 66 " --> pdb=" O LEU m 62 " (cutoff:3.500A) removed outlier: 4.734A pdb=" N ILE m 68 " --> pdb=" O TYR m 64 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N LEU m 79 " --> pdb=" O THR m 75 " (cutoff:3.500A) Processing helix chain 'm' and resid 96 through 112 removed outlier: 3.927A pdb=" N GLU m 104 " --> pdb=" O THR m 100 " (cutoff:3.500A) Proline residue: m 106 - end of helix removed outlier: 4.259A pdb=" N MET m 111 " --> pdb=" O MET m 107 " (cutoff:3.500A) Processing helix chain 'm' and resid 120 through 151 removed outlier: 3.852A pdb=" N LEU m 131 " --> pdb=" O GLN m 127 " (cutoff:3.500A) removed outlier: 4.469A pdb=" N THR m 132 " --> pdb=" O ARG m 128 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N LEU m 133 " --> pdb=" O ALA m 129 " (cutoff:3.500A) removed outlier: 4.253A pdb=" N GLN m 137 " --> pdb=" O LEU m 133 " (cutoff:3.500A) removed outlier: 4.514A pdb=" N VAL m 138 " --> pdb=" O LEU m 134 " (cutoff:3.500A) Proline residue: m 139 - end of helix removed outlier: 3.908A pdb=" N LEU m 142 " --> pdb=" O VAL m 138 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N TYR m 150 " --> pdb=" O ALA m 146 " (cutoff:3.500A) Processing helix chain 'm' and resid 156 through 165 removed outlier: 4.114A pdb=" N VAL m 160 " --> pdb=" O TYR m 157 " (cutoff:3.500A) removed outlier: 5.214A pdb=" N MET m 161 " --> pdb=" O GLU m 158 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N GLN m 164 " --> pdb=" O MET m 161 " (cutoff:3.500A) removed outlier: 4.493A pdb=" N LYS m 165 " --> pdb=" O ALA m 162 " (cutoff:3.500A) Processing helix chain 'm' and resid 173 through 190 removed outlier: 4.404A pdb=" N ALA m 178 " --> pdb=" O PRO m 174 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N ALA m 181 " --> pdb=" O LEU m 177 " (cutoff:3.500A) removed outlier: 4.392A pdb=" N GLN m 187 " --> pdb=" O ASP m 183 " (cutoff:3.500A) removed outlier: 4.148A pdb=" N ALA m 188 " --> pdb=" O ILE m 184 " (cutoff:3.500A) Processing helix chain 'm' and resid 193 through 198 removed outlier: 3.557A pdb=" N ASP m 196 " --> pdb=" O GLU m 193 " (cutoff:3.500A) removed outlier: 5.618A pdb=" N ILE m 197 " --> pdb=" O PRO m 194 " (cutoff:3.500A) removed outlier: 4.677A pdb=" N MET m 198 " --> pdb=" O PHE m 195 " (cutoff:3.500A) No H-bonds generated for 'chain 'm' and resid 193 through 198' Processing helix chain 'm' and resid 207 through 209 No H-bonds generated for 'chain 'm' and resid 207 through 209' Processing helix chain 'm' and resid 214 through 239 removed outlier: 3.511A pdb=" N ILE m 238 " --> pdb=" O PHE m 234 " (cutoff:3.500A) Processing helix chain 'm' and resid 252 through 276 removed outlier: 3.974A pdb=" N ALA m 257 " --> pdb=" O LEU m 253 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N VAL m 269 " --> pdb=" O LYS m 265 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N PHE m 275 " --> pdb=" O LEU m 271 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N VAL m 276 " --> pdb=" O ILE m 272 " (cutoff:3.500A) Processing helix chain 'm' and resid 285 through 306 removed outlier: 3.692A pdb=" N TYR m 292 " --> pdb=" O ALA m 288 " (cutoff:3.500A) removed outlier: 4.170A pdb=" N TRP m 293 " --> pdb=" O ALA m 289 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N LYS m 294 " --> pdb=" O LYS m 290 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N TRP m 295 " --> pdb=" O PHE m 291 " (cutoff:3.500A) Proline residue: m 296 - end of helix Processing helix chain 'n' and resid 22 through 26 Processing helix chain 'n' and resid 28 through 30 No H-bonds generated for 'chain 'n' and resid 28 through 30' Processing helix chain 'n' and resid 67 through 69 No H-bonds generated for 'chain 'n' and resid 67 through 69' Processing helix chain 'n' and resid 93 through 95 No H-bonds generated for 'chain 'n' and resid 93 through 95' Processing helix chain 'n' and resid 129 through 131 No H-bonds generated for 'chain 'n' and resid 129 through 131' Processing helix chain 'n' and resid 138 through 142 Processing sheet with id= A, first strand: chain 'A' and resid 102 through 104 Processing sheet with id= B, first strand: chain 'H' and resid 59 through 62 removed outlier: 3.626A pdb=" N ILE H 59 " --> pdb=" O ILE H 76 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'X' and resid 54 through 56 removed outlier: 4.697A pdb=" N ILE X 54 " --> pdb=" O LEU X 69 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'J' and resid 60 through 62 Processing sheet with id= E, first strand: chain 'K' and resid 21 through 25 removed outlier: 3.952A pdb=" N GLU K 21 " --> pdb=" O ARG K 33 " (cutoff:3.500A) removed outlier: 4.193A pdb=" N ARG K 33 " --> pdb=" O GLU K 21 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N ARG K 25 " --> pdb=" O ARG K 29 " (cutoff:3.500A) removed outlier: 4.091A pdb=" N ARG K 29 " --> pdb=" O ARG K 25 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'K' and resid 57 through 60 removed outlier: 3.544A pdb=" N VAL K 60 " --> pdb=" O GLU K 69 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'L' and resid 321 through 327 removed outlier: 3.624A pdb=" N GLY L 321 " --> pdb=" O SER L 340 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N ALA L 325 " --> pdb=" O ALA L 336 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N VAL L 327 " --> pdb=" O PHE L 334 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N ARG L 348 " --> pdb=" O VAL L 339 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'L' and resid 41 through 47 removed outlier: 3.886A pdb=" N LYS L 53 " --> pdb=" O LYS L 45 " (cutoff:3.500A) removed outlier: 6.099A pdb=" N ASP L 47 " --> pdb=" O VAL L 51 " (cutoff:3.500A) removed outlier: 5.299A pdb=" N VAL L 51 " --> pdb=" O ASP L 47 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'N' and resid 166 through 168 removed outlier: 3.672A pdb=" N PHE N 179 " --> pdb=" O VAL N 167 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'a' and resid 102 through 104 Processing sheet with id= K, first strand: chain 'h' and resid 59 through 62 removed outlier: 3.627A pdb=" N ILE h 59 " --> pdb=" O ILE h 76 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'x' and resid 54 through 56 removed outlier: 4.697A pdb=" N ILE x 54 " --> pdb=" O LEU x 69 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'j' and resid 60 through 62 Processing sheet with id= N, first strand: chain 'k' and resid 21 through 25 removed outlier: 3.951A pdb=" N GLU k 21 " --> pdb=" O ARG k 33 " (cutoff:3.500A) removed outlier: 4.194A pdb=" N ARG k 33 " --> pdb=" O GLU k 21 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N ARG k 25 " --> pdb=" O ARG k 29 " (cutoff:3.500A) removed outlier: 4.092A pdb=" N ARG k 29 " --> pdb=" O ARG k 25 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'k' and resid 57 through 60 removed outlier: 3.544A pdb=" N VAL k 60 " --> pdb=" O GLU k 69 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'l' and resid 321 through 327 removed outlier: 3.624A pdb=" N GLY l 321 " --> pdb=" O SER l 340 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N ALA l 325 " --> pdb=" O ALA l 336 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N VAL l 327 " --> pdb=" O PHE l 334 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N ARG l 348 " --> pdb=" O VAL l 339 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'l' and resid 41 through 47 removed outlier: 3.885A pdb=" N LYS l 53 " --> pdb=" O LYS l 45 " (cutoff:3.500A) removed outlier: 6.099A pdb=" N ASP l 47 " --> pdb=" O VAL l 51 " (cutoff:3.500A) removed outlier: 5.299A pdb=" N VAL l 51 " --> pdb=" O ASP l 47 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'n' and resid 166 through 168 removed outlier: 3.672A pdb=" N PHE n 179 " --> pdb=" O VAL n 167 " (cutoff:3.500A) 1884 hydrogen bonds defined for protein. 5400 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: 14.58 Time building geometry restraints manager: 19.92 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.43: 20555 1.43 - 1.64: 28563 1.64 - 1.85: 434 1.85 - 2.06: 0 2.06 - 2.27: 72 Bond restraints: 49624 Sorted by residual: bond pdb=" C PRO j 34 " pdb=" N PRO j 35 " ideal model delta sigma weight residual 1.337 1.395 -0.058 1.11e-02 8.12e+03 2.76e+01 bond pdb=" C PRO J 34 " pdb=" N PRO J 35 " ideal model delta sigma weight residual 1.337 1.394 -0.058 1.11e-02 8.12e+03 2.69e+01 bond pdb=" CA CYS N 102 " pdb=" C CYS N 102 " ideal model delta sigma weight residual 1.522 1.459 0.063 1.37e-02 5.33e+03 2.14e+01 bond pdb=" C ILE e 209 " pdb=" N PRO e 210 " ideal model delta sigma weight residual 1.336 1.390 -0.054 1.20e-02 6.94e+03 2.04e+01 bond pdb=" C ILE E 209 " pdb=" N PRO E 210 " ideal model delta sigma weight residual 1.336 1.390 -0.054 1.20e-02 6.94e+03 2.00e+01 ... (remaining 49619 not shown) Histogram of bond angle deviations from ideal: 73.37 - 85.70: 72 85.70 - 98.04: 5 98.04 - 110.37: 12422 110.37 - 122.71: 51048 122.71 - 135.04: 3911 Bond angle restraints: 67458 Sorted by residual: angle pdb=" C LEU e 203 " pdb=" CA LEU e 203 " pdb=" CB LEU e 203 " ideal model delta sigma weight residual 109.37 91.50 17.87 1.83e+00 2.99e-01 9.54e+01 angle pdb=" N GLY E 201 " pdb=" CA GLY E 201 " pdb=" C GLY E 201 " ideal model delta sigma weight residual 112.55 99.48 13.07 1.44e+00 4.82e-01 8.23e+01 angle pdb=" N VAL h 104 " pdb=" CA VAL h 104 " pdb=" C VAL h 104 " ideal model delta sigma weight residual 113.71 105.91 7.80 9.50e-01 1.11e+00 6.74e+01 angle pdb=" N VAL H 104 " pdb=" CA VAL H 104 " pdb=" C VAL H 104 " ideal model delta sigma weight residual 113.71 105.94 7.77 9.50e-01 1.11e+00 6.69e+01 angle pdb=" C LYS M 192 " pdb=" N GLU M 193 " pdb=" CA GLU M 193 " ideal model delta sigma weight residual 120.09 128.89 -8.80 1.25e+00 6.40e-01 4.96e+01 ... (remaining 67453 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.83: 25323 17.83 - 35.67: 2907 35.67 - 53.50: 594 53.50 - 71.34: 84 71.34 - 89.17: 40 Dihedral angle restraints: 28948 sinusoidal: 11268 harmonic: 17680 Sorted by residual: dihedral pdb=" CA ASN X 486 " pdb=" C ASN X 486 " pdb=" N PRO X 487 " pdb=" CA PRO X 487 " ideal model delta harmonic sigma weight residual -180.00 -132.58 -47.42 0 5.00e+00 4.00e-02 8.99e+01 dihedral pdb=" CA ASN x 486 " pdb=" C ASN x 486 " pdb=" N PRO x 487 " pdb=" CA PRO x 487 " ideal model delta harmonic sigma weight residual 180.00 -132.59 -47.41 0 5.00e+00 4.00e-02 8.99e+01 dihedral pdb=" CA THR A 123 " pdb=" C THR A 123 " pdb=" N PRO A 124 " pdb=" CA PRO A 124 " ideal model delta harmonic sigma weight residual -180.00 -133.25 -46.75 0 5.00e+00 4.00e-02 8.74e+01 ... (remaining 28945 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.106: 7047 0.106 - 0.212: 664 0.212 - 0.319: 42 0.319 - 0.425: 11 0.425 - 0.531: 4 Chirality restraints: 7768 Sorted by residual: chirality pdb=" CB ILE n 76 " pdb=" CA ILE n 76 " pdb=" CG1 ILE n 76 " pdb=" CG2 ILE n 76 " both_signs ideal model delta sigma weight residual False 2.64 2.11 0.53 2.00e-01 2.50e+01 7.05e+00 chirality pdb=" CB ILE N 76 " pdb=" CA ILE N 76 " pdb=" CG1 ILE N 76 " pdb=" CG2 ILE N 76 " both_signs ideal model delta sigma weight residual False 2.64 2.12 0.53 2.00e-01 2.50e+01 7.00e+00 chirality pdb=" CB ILE A 42 " pdb=" CA ILE A 42 " pdb=" CG1 ILE A 42 " pdb=" CG2 ILE A 42 " both_signs ideal model delta sigma weight residual False 2.64 2.22 0.43 2.00e-01 2.50e+01 4.61e+00 ... (remaining 7765 not shown) Planarity restraints: 8248 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLY j 144 " -0.032 2.00e-02 2.50e+03 6.19e-02 3.83e+01 pdb=" C GLY j 144 " 0.107 2.00e-02 2.50e+03 pdb=" O GLY j 144 " -0.040 2.00e-02 2.50e+03 pdb=" N GLU j 145 " -0.035 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLY J 144 " 0.032 2.00e-02 2.50e+03 6.18e-02 3.82e+01 pdb=" C GLY J 144 " -0.107 2.00e-02 2.50e+03 pdb=" O GLY J 144 " 0.040 2.00e-02 2.50e+03 pdb=" N GLU J 145 " 0.035 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA TYR d 80 " -0.031 2.00e-02 2.50e+03 6.07e-02 3.69e+01 pdb=" C TYR d 80 " 0.105 2.00e-02 2.50e+03 pdb=" O TYR d 80 " -0.040 2.00e-02 2.50e+03 pdb=" N GLU d 81 " -0.034 2.00e-02 2.50e+03 ... (remaining 8245 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 6844 2.75 - 3.29: 47609 3.29 - 3.82: 83807 3.82 - 4.36: 97767 4.36 - 4.90: 164097 Nonbonded interactions: 400124 Sorted by model distance: nonbonded pdb=" OG1 THR X 537 " pdb=" OE2 GLU M 211 " model vdw 2.209 2.440 nonbonded pdb=" O TYR e 170 " pdb=" OG1 THR e 173 " model vdw 2.248 2.440 nonbonded pdb=" O TYR E 170 " pdb=" OG1 THR E 173 " model vdw 2.248 2.440 nonbonded pdb=" O ILE a 120 " pdb=" OG1 THR a 126 " model vdw 2.259 2.440 nonbonded pdb=" O ILE A 120 " pdb=" OG1 THR A 126 " model vdw 2.259 2.440 ... (remaining 400119 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 'A' selection = chain 'a' } ncs_group { reference = chain 'B' selection = chain 'b' } ncs_group { reference = chain 'C' selection = chain 'c' } ncs_group { reference = chain 'D' selection = chain 'd' } ncs_group { reference = chain 'E' selection = chain 'e' } ncs_group { reference = chain 'G' selection = chain 'g' } ncs_group { reference = chain 'H' selection = chain 'h' } ncs_group { reference = chain 'J' selection = chain 'j' } ncs_group { reference = chain 'K' selection = chain 'k' } ncs_group { reference = chain 'L' selection = chain 'l' } ncs_group { reference = chain 'M' selection = chain 'm' } ncs_group { reference = chain 'N' selection = chain 'n' } ncs_group { reference = chain 'X' selection = chain 'x' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians Fe 24 7.16 5 S 258 5.16 5 C 32122 2.51 5 N 7704 2.21 5 O 8256 1.98 5 sf(0) = scattering factor at diffraction angle 0. Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.010 Normalize map: mean=0, sd=1: 2.000 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: 0.030 Extract box with map and model: 12.120 Check model and map are aligned: 0.630 Convert atoms to be neutral: 0.360 Process input model: 116.770 Find NCS groups from input model: 2.660 Set up NCS constraints: 0.420 Set refine NCS operators: 0.000 Set scattering table: 0.010 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.880 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 137.890 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7755 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.008 0.102 49624 Z= 0.503 Angle : 1.208 17.871 67458 Z= 0.664 Chirality : 0.065 0.531 7768 Planarity : 0.009 0.090 8248 Dihedral : 15.795 89.169 17668 Min Nonbonded Distance : 2.209 Molprobity Statistics. All-atom Clashscore : 9.26 Ramachandran Plot: Outliers : 0.33 % Allowed : 12.14 % Favored : 87.53 % Rotamer Outliers : 2.01 % Cbeta Deviations : 0.02 % Peptide Plane: Cis-proline : 1.43 % Cis-general : 0.10 % Twisted Proline : 2.14 % Twisted General : 0.31 % 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: -5.88 (0.07), residues: 6072 helix: -3.56 (0.05), residues: 3432 sheet: -3.48 (0.28), residues: 186 loop : -4.34 (0.10), residues: 2454 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12144 Ramachandran restraints generated. 6072 Oldfield, 0 Emsley, 6072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12144 Ramachandran restraints generated. 6072 Oldfield, 0 Emsley, 6072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1483 residues out of total 5044 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 101 poor density : 1382 time to evaluate : 5.545 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 101 outliers final: 35 residues processed: 1455 average time/residue: 0.5963 time to fit residues: 1421.1853 Evaluate side-chains 1021 residues out of total 5044 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 986 time to evaluate : 5.511 Switching outliers to nearest non-outliers outliers start: 35 outliers final: 0 residues processed: 35 average time/residue: 0.4289 time to fit residues: 35.6647 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 604 random chunks: chunk 510 optimal weight: 0.5980 chunk 457 optimal weight: 8.9990 chunk 254 optimal weight: 5.9990 chunk 156 optimal weight: 0.9980 chunk 308 optimal weight: 5.9990 chunk 244 optimal weight: 0.7980 chunk 473 optimal weight: 30.0000 chunk 183 optimal weight: 0.9980 chunk 287 optimal weight: 5.9990 chunk 352 optimal weight: 8.9990 chunk 548 optimal weight: 8.9990 overall best weight: 1.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 58 ASN A 91 HIS ** A 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 123 HIS ** H 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 308 GLN ** X 340 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** X 466 ASN J 109 GLN K 73 HIS ** K 126 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 33 GLN L 62 HIS L 292 GLN M 43 GLN M 57 ASN M 163 GLN ** M 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 187 GLN ** M 223 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 54 HIS N 100 GLN N 145 GLN a 58 ASN ** g 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** h 41 GLN ** h 308 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** x 340 HIS x 466 ASN k 73 HIS ** k 126 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** l 33 GLN ** l 62 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** l 292 GLN l 326 HIS ** m 34 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** m 43 GLN m 57 ASN m 163 GLN m 187 GLN ** n 54 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 29 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7798 moved from start: 0.2154 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.053 49624 Z= 0.266 Angle : 0.789 13.236 67458 Z= 0.400 Chirality : 0.045 0.273 7768 Planarity : 0.006 0.075 8248 Dihedral : 6.206 46.057 6638 Min Nonbonded Distance : 1.995 Molprobity Statistics. All-atom Clashscore : 17.80 Ramachandran Plot: Outliers : 0.18 % Allowed : 11.51 % Favored : 88.31 % Rotamer Outliers : 4.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.43 % Cis-general : 0.10 % Twisted Proline : 1.43 % Twisted General : 0.12 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.30 (0.09), residues: 6072 helix: -2.00 (0.08), residues: 3450 sheet: -3.52 (0.29), residues: 200 loop : -4.06 (0.10), residues: 2422 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12144 Ramachandran restraints generated. 6072 Oldfield, 0 Emsley, 6072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12144 Ramachandran restraints generated. 6072 Oldfield, 0 Emsley, 6072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1297 residues out of total 5044 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 212 poor density : 1085 time to evaluate : 6.071 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 212 outliers final: 116 residues processed: 1201 average time/residue: 0.5608 time to fit residues: 1141.6453 Evaluate side-chains 1068 residues out of total 5044 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 116 poor density : 952 time to evaluate : 5.664 Switching outliers to nearest non-outliers outliers start: 116 outliers final: 0 residues processed: 116 average time/residue: 0.4578 time to fit residues: 105.2276 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 604 random chunks: chunk 304 optimal weight: 0.0970 chunk 170 optimal weight: 5.9990 chunk 456 optimal weight: 6.9990 chunk 373 optimal weight: 0.0770 chunk 151 optimal weight: 4.9990 chunk 549 optimal weight: 0.8980 chunk 593 optimal weight: 2.9990 chunk 489 optimal weight: 0.9990 chunk 544 optimal weight: 0.5980 chunk 187 optimal weight: 0.7980 chunk 440 optimal weight: 2.9990 overall best weight: 0.4936 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 91 HIS ** A 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 118 ASN G 41 ASN ** H 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 334 HIS ** X 340 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** X 596 ASN J 109 GLN K 73 HIS ** K 126 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 33 GLN M 172 HIS M 224 HIS N 145 GLN e 123 HIS h 189 ASN h 308 GLN h 334 HIS ** j 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 126 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** l 33 GLN m 172 HIS m 224 HIS n 54 HIS Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7738 moved from start: 0.2618 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.054 49624 Z= 0.204 Angle : 0.743 13.672 67458 Z= 0.367 Chirality : 0.043 0.332 7768 Planarity : 0.005 0.062 8248 Dihedral : 5.792 42.495 6638 Min Nonbonded Distance : 2.114 Molprobity Statistics. All-atom Clashscore : 17.54 Ramachandran Plot: Outliers : 0.08 % Allowed : 10.82 % Favored : 89.10 % Rotamer Outliers : 3.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.43 % Cis-general : 0.10 % Twisted Proline : 1.43 % Twisted General : 0.12 % 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: -3.57 (0.10), residues: 6072 helix: -1.31 (0.08), residues: 3444 sheet: -3.21 (0.30), residues: 198 loop : -3.89 (0.11), residues: 2430 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12144 Ramachandran restraints generated. 6072 Oldfield, 0 Emsley, 6072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12144 Ramachandran restraints generated. 6072 Oldfield, 0 Emsley, 6072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1250 residues out of total 5044 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 162 poor density : 1088 time to evaluate : 5.672 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 162 outliers final: 72 residues processed: 1187 average time/residue: 0.5612 time to fit residues: 1140.9879 Evaluate side-chains 1044 residues out of total 5044 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 972 time to evaluate : 5.477 Switching outliers to nearest non-outliers outliers start: 72 outliers final: 0 residues processed: 72 average time/residue: 0.4644 time to fit residues: 68.6140 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 604 random chunks: chunk 542 optimal weight: 1.9990 chunk 413 optimal weight: 6.9990 chunk 285 optimal weight: 10.0000 chunk 60 optimal weight: 8.9990 chunk 262 optimal weight: 10.0000 chunk 368 optimal weight: 2.9990 chunk 551 optimal weight: 6.9990 chunk 583 optimal weight: 5.9990 chunk 288 optimal weight: 4.9990 chunk 522 optimal weight: 5.9990 chunk 157 optimal weight: 4.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 118 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 156 HIS G 41 ASN ** G 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 41 GLN H 189 ASN ** X 340 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 163 GLN ** K 126 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 34 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 34 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 118 ASN e 156 HIS g 41 ASN g 73 GLN x 300 GLN ** j 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 126 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** l 33 GLN l 62 HIS l 113 GLN ** m 34 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** m 60 HIS ** m 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7888 moved from start: 0.2943 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.078 49624 Z= 0.408 Angle : 0.815 12.012 67458 Z= 0.407 Chirality : 0.048 0.252 7768 Planarity : 0.006 0.064 8248 Dihedral : 5.781 42.787 6638 Min Nonbonded Distance : 1.976 Molprobity Statistics. All-atom Clashscore : 20.67 Ramachandran Plot: Outliers : 0.10 % Allowed : 12.78 % Favored : 87.12 % Rotamer Outliers : 4.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.43 % Cis-general : 0.10 % Twisted Proline : 1.43 % Twisted General : 0.10 % 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: -3.35 (0.10), residues: 6072 helix: -1.09 (0.08), residues: 3460 sheet: -3.43 (0.33), residues: 202 loop : -3.86 (0.11), residues: 2410 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12144 Ramachandran restraints generated. 6072 Oldfield, 0 Emsley, 6072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12144 Ramachandran restraints generated. 6072 Oldfield, 0 Emsley, 6072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1235 residues out of total 5044 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 241 poor density : 994 time to evaluate : 5.455 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 241 outliers final: 144 residues processed: 1148 average time/residue: 0.5649 time to fit residues: 1119.2215 Evaluate side-chains 1059 residues out of total 5044 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 144 poor density : 915 time to evaluate : 5.947 Switching outliers to nearest non-outliers outliers start: 144 outliers final: 0 residues processed: 144 average time/residue: 0.4494 time to fit residues: 128.6438 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 604 random chunks: chunk 486 optimal weight: 1.9990 chunk 331 optimal weight: 5.9990 chunk 8 optimal weight: 5.9990 chunk 434 optimal weight: 0.9990 chunk 240 optimal weight: 6.9990 chunk 498 optimal weight: 0.9980 chunk 403 optimal weight: 2.9990 chunk 0 optimal weight: 10.0000 chunk 298 optimal weight: 1.9990 chunk 524 optimal weight: 1.9990 chunk 147 optimal weight: 9.9990 overall best weight: 1.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 91 HIS A 118 ASN G 41 ASN H 132 ASN ** J 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 126 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 33 GLN g 73 GLN ** x 300 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 126 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** l 33 GLN n 100 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7818 moved from start: 0.3134 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.053 49624 Z= 0.235 Angle : 0.749 15.426 67458 Z= 0.368 Chirality : 0.045 0.359 7768 Planarity : 0.005 0.058 8248 Dihedral : 5.580 41.743 6638 Min Nonbonded Distance : 2.065 Molprobity Statistics. All-atom Clashscore : 19.11 Ramachandran Plot: Outliers : 0.05 % Allowed : 11.20 % Favored : 88.75 % Rotamer Outliers : 2.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.43 % Cis-general : 0.10 % Twisted Proline : 1.43 % Twisted General : 0.09 % 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: -3.08 (0.10), residues: 6072 helix: -0.83 (0.09), residues: 3448 sheet: -3.37 (0.30), residues: 222 loop : -3.78 (0.11), residues: 2402 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12144 Ramachandran restraints generated. 6072 Oldfield, 0 Emsley, 6072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12144 Ramachandran restraints generated. 6072 Oldfield, 0 Emsley, 6072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1172 residues out of total 5044 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 140 poor density : 1032 time to evaluate : 5.918 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 140 outliers final: 63 residues processed: 1127 average time/residue: 0.5481 time to fit residues: 1061.1780 Evaluate side-chains 1007 residues out of total 5044 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 944 time to evaluate : 5.884 Switching outliers to nearest non-outliers outliers start: 63 outliers final: 0 residues processed: 63 average time/residue: 0.4232 time to fit residues: 58.0220 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 604 random chunks: chunk 196 optimal weight: 0.5980 chunk 525 optimal weight: 3.9990 chunk 115 optimal weight: 8.9990 chunk 342 optimal weight: 6.9990 chunk 144 optimal weight: 4.9990 chunk 584 optimal weight: 1.9990 chunk 485 optimal weight: 1.9990 chunk 270 optimal weight: 8.9990 chunk 48 optimal weight: 7.9990 chunk 193 optimal weight: 1.9990 chunk 306 optimal weight: 8.9990 overall best weight: 2.1188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 91 HIS A 118 ASN G 41 ASN ** K 126 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 113 GLN ** M 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 91 HIS ** x 300 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** j 109 GLN ** k 126 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** l 33 GLN ** m 34 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** m 127 GLN ** m 266 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7835 moved from start: 0.3301 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.055 49624 Z= 0.266 Angle : 0.761 14.635 67458 Z= 0.373 Chirality : 0.045 0.239 7768 Planarity : 0.005 0.059 8248 Dihedral : 5.500 40.908 6638 Min Nonbonded Distance : 2.081 Molprobity Statistics. All-atom Clashscore : 19.86 Ramachandran Plot: Outliers : 0.07 % Allowed : 11.84 % Favored : 88.09 % Rotamer Outliers : 2.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.43 % Cis-general : 0.10 % Twisted Proline : 1.43 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.92 (0.10), residues: 6072 helix: -0.72 (0.09), residues: 3456 sheet: -3.34 (0.31), residues: 212 loop : -3.70 (0.11), residues: 2404 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12144 Ramachandran restraints generated. 6072 Oldfield, 0 Emsley, 6072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12144 Ramachandran restraints generated. 6072 Oldfield, 0 Emsley, 6072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1122 residues out of total 5044 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 130 poor density : 992 time to evaluate : 5.404 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 130 outliers final: 76 residues processed: 1072 average time/residue: 0.5527 time to fit residues: 1013.7709 Evaluate side-chains 1004 residues out of total 5044 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 928 time to evaluate : 5.338 Switching outliers to nearest non-outliers outliers start: 76 outliers final: 0 residues processed: 76 average time/residue: 0.4394 time to fit residues: 69.6071 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 604 random chunks: chunk 563 optimal weight: 0.7980 chunk 65 optimal weight: 0.1980 chunk 332 optimal weight: 5.9990 chunk 426 optimal weight: 5.9990 chunk 330 optimal weight: 10.0000 chunk 491 optimal weight: 1.9990 chunk 326 optimal weight: 9.9990 chunk 582 optimal weight: 1.9990 chunk 364 optimal weight: 0.7980 chunk 354 optimal weight: 10.0000 chunk 268 optimal weight: 3.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 118 ASN ** X 300 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 126 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 33 GLN L 39 ASN M 127 GLN ** a 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 91 HIS h 132 ASN ** x 300 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 126 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** l 33 GLN ** l 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 223 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 266 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7795 moved from start: 0.3448 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.056 49624 Z= 0.218 Angle : 0.754 15.907 67458 Z= 0.367 Chirality : 0.044 0.413 7768 Planarity : 0.005 0.058 8248 Dihedral : 5.399 39.809 6638 Min Nonbonded Distance : 2.079 Molprobity Statistics. All-atom Clashscore : 18.98 Ramachandran Plot: Outliers : 0.10 % Allowed : 11.05 % Favored : 88.85 % Rotamer Outliers : 1.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.43 % Cis-general : 0.10 % Twisted Proline : 1.43 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.75 (0.11), residues: 6072 helix: -0.58 (0.09), residues: 3446 sheet: -3.27 (0.30), residues: 222 loop : -3.61 (0.12), residues: 2404 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12144 Ramachandran restraints generated. 6072 Oldfield, 0 Emsley, 6072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12144 Ramachandran restraints generated. 6072 Oldfield, 0 Emsley, 6072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1096 residues out of total 5044 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 90 poor density : 1006 time to evaluate : 5.429 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 90 outliers final: 55 residues processed: 1060 average time/residue: 0.5694 time to fit residues: 1035.4234 Evaluate side-chains 980 residues out of total 5044 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 925 time to evaluate : 5.462 Switching outliers to nearest non-outliers outliers start: 55 outliers final: 0 residues processed: 55 average time/residue: 0.4757 time to fit residues: 55.2717 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 604 random chunks: chunk 360 optimal weight: 6.9990 chunk 232 optimal weight: 3.9990 chunk 347 optimal weight: 0.8980 chunk 175 optimal weight: 0.9990 chunk 114 optimal weight: 1.9990 chunk 112 optimal weight: 10.0000 chunk 370 optimal weight: 5.9990 chunk 396 optimal weight: 10.0000 chunk 287 optimal weight: 6.9990 chunk 54 optimal weight: 0.0270 chunk 457 optimal weight: 7.9990 overall best weight: 1.5844 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 91 HIS A 118 ASN ** H 226 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 118 ASN ** X 300 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 126 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 33 GLN L 113 GLN ** a 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 91 HIS a 118 ASN d 50 GLN ** k 126 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** l 169 HIS m 137 GLN ** m 266 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7802 moved from start: 0.3605 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.057 49624 Z= 0.241 Angle : 0.770 16.382 67458 Z= 0.375 Chirality : 0.044 0.320 7768 Planarity : 0.005 0.059 8248 Dihedral : 5.353 40.233 6638 Min Nonbonded Distance : 1.996 Molprobity Statistics. All-atom Clashscore : 19.53 Ramachandran Plot: Outliers : 0.10 % Allowed : 11.28 % Favored : 88.62 % Rotamer Outliers : 1.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.43 % Cis-general : 0.10 % Twisted Proline : 1.43 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.64 (0.11), residues: 6072 helix: -0.48 (0.09), residues: 3438 sheet: -3.23 (0.30), residues: 222 loop : -3.56 (0.12), residues: 2412 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12144 Ramachandran restraints generated. 6072 Oldfield, 0 Emsley, 6072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12144 Ramachandran restraints generated. 6072 Oldfield, 0 Emsley, 6072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1044 residues out of total 5044 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 974 time to evaluate : 5.109 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 70 outliers final: 38 residues processed: 1014 average time/residue: 0.5691 time to fit residues: 985.8371 Evaluate side-chains 958 residues out of total 5044 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 920 time to evaluate : 5.418 Switching outliers to nearest non-outliers outliers start: 38 outliers final: 0 residues processed: 38 average time/residue: 0.4646 time to fit residues: 40.1276 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 604 random chunks: chunk 529 optimal weight: 6.9990 chunk 557 optimal weight: 6.9990 chunk 508 optimal weight: 1.9990 chunk 542 optimal weight: 9.9990 chunk 326 optimal weight: 7.9990 chunk 236 optimal weight: 10.0000 chunk 425 optimal weight: 0.2980 chunk 166 optimal weight: 0.9990 chunk 490 optimal weight: 0.9980 chunk 513 optimal weight: 8.9990 chunk 540 optimal weight: 4.9990 overall best weight: 1.8586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 66 ASN ** X 300 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 126 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 39 ASN M 57 ASN ** M 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 223 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 91 HIS a 118 ASN g 66 ASN ** k 126 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 34 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 266 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7808 moved from start: 0.3701 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.059 49624 Z= 0.256 Angle : 0.782 16.111 67458 Z= 0.379 Chirality : 0.045 0.397 7768 Planarity : 0.005 0.059 8248 Dihedral : 5.329 40.289 6638 Min Nonbonded Distance : 2.025 Molprobity Statistics. All-atom Clashscore : 20.54 Ramachandran Plot: Outliers : 0.10 % Allowed : 11.51 % Favored : 88.39 % Rotamer Outliers : 0.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.43 % Cis-general : 0.10 % Twisted Proline : 1.43 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.56 (0.11), residues: 6072 helix: -0.43 (0.09), residues: 3432 sheet: -3.18 (0.31), residues: 222 loop : -3.51 (0.12), residues: 2418 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12144 Ramachandran restraints generated. 6072 Oldfield, 0 Emsley, 6072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12144 Ramachandran restraints generated. 6072 Oldfield, 0 Emsley, 6072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1013 residues out of total 5044 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 963 time to evaluate : 5.298 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 50 outliers final: 29 residues processed: 994 average time/residue: 0.5642 time to fit residues: 961.5400 Evaluate side-chains 952 residues out of total 5044 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 923 time to evaluate : 5.395 Switching outliers to nearest non-outliers outliers start: 29 outliers final: 0 residues processed: 29 average time/residue: 0.4830 time to fit residues: 32.5544 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 604 random chunks: chunk 356 optimal weight: 0.0270 chunk 573 optimal weight: 0.4980 chunk 350 optimal weight: 0.8980 chunk 272 optimal weight: 1.9990 chunk 398 optimal weight: 6.9990 chunk 601 optimal weight: 3.9990 chunk 553 optimal weight: 2.9990 chunk 479 optimal weight: 10.0000 chunk 49 optimal weight: 5.9990 chunk 370 optimal weight: 1.9990 chunk 293 optimal weight: 0.7980 overall best weight: 0.8440 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 66 ASN ** H 189 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 300 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 126 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 39 ASN L 189 GLN ** M 223 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 91 HIS a 118 ASN h 189 ASN ** h 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 126 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** l 33 GLN l 39 ASN l 113 GLN l 292 GLN ** m 266 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7760 moved from start: 0.3876 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.094 49624 Z= 0.216 Angle : 0.784 19.090 67458 Z= 0.378 Chirality : 0.044 0.356 7768 Planarity : 0.005 0.062 8248 Dihedral : 5.271 41.078 6638 Min Nonbonded Distance : 2.066 Molprobity Statistics. All-atom Clashscore : 19.70 Ramachandran Plot: Outliers : 0.12 % Allowed : 10.92 % Favored : 88.97 % Rotamer Outliers : 0.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.43 % Cis-general : 0.10 % Twisted Proline : 1.43 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.45 (0.11), residues: 6072 helix: -0.35 (0.09), residues: 3422 sheet: -3.01 (0.32), residues: 220 loop : -3.43 (0.12), residues: 2430 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12144 Ramachandran restraints generated. 6072 Oldfield, 0 Emsley, 6072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12144 Ramachandran restraints generated. 6072 Oldfield, 0 Emsley, 6072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1018 residues out of total 5044 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 992 time to evaluate : 5.650 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 26 outliers final: 10 residues processed: 1007 average time/residue: 0.5939 time to fit residues: 1030.8430 Evaluate side-chains 928 residues out of total 5044 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 918 time to evaluate : 5.167 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 0 residues processed: 10 average time/residue: 0.4747 time to fit residues: 15.5591 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 604 random chunks: chunk 380 optimal weight: 4.9990 chunk 510 optimal weight: 5.9990 chunk 146 optimal weight: 10.0000 chunk 441 optimal weight: 1.9990 chunk 70 optimal weight: 0.3980 chunk 133 optimal weight: 4.9990 chunk 479 optimal weight: 1.9990 chunk 200 optimal weight: 4.9990 chunk 492 optimal weight: 0.4980 chunk 60 optimal weight: 2.9990 chunk 88 optimal weight: 10.0000 overall best weight: 1.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 66 ASN ** H 189 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 226 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 126 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 39 ASN L 189 GLN ** M 34 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 223 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 91 HIS a 118 ASN ** h 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** x 300 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 126 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** l 33 GLN l 39 ASN m 137 GLN ** m 266 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3644 r_free = 0.3644 target = 0.114083 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.099443 restraints weight = 101294.517| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.102466 restraints weight = 137793.444| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.102926 restraints weight = 64111.519| |-----------------------------------------------------------------------------| r_work (final): 0.3461 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7786 moved from start: 0.3962 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.060 49624 Z= 0.246 Angle : 0.798 18.984 67458 Z= 0.383 Chirality : 0.045 0.270 7768 Planarity : 0.005 0.059 8248 Dihedral : 5.260 38.789 6638 Min Nonbonded Distance : 2.028 Molprobity Statistics. All-atom Clashscore : 20.34 Ramachandran Plot: Outliers : 0.07 % Allowed : 11.22 % Favored : 88.72 % Rotamer Outliers : 0.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.43 % Cis-general : 0.10 % Twisted Proline : 0.36 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.39 (0.11), residues: 6072 helix: -0.30 (0.09), residues: 3422 sheet: -2.81 (0.34), residues: 198 loop : -3.42 (0.12), residues: 2452 =============================================================================== Job complete usr+sys time: 15118.36 seconds wall clock time: 269 minutes 7.26 seconds (16147.26 seconds total)