Starting phenix.real_space_refine on Mon Mar 25 11:10:46 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6u8y_20692/03_2024/6u8y_20692_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6u8y_20692/03_2024/6u8y_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_20692/03_2024/6u8y_20692.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6u8y_20692/03_2024/6u8y_20692.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6u8y_20692/03_2024/6u8y_20692_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6u8y_20692/03_2024/6u8y_20692_updated.pdb" } resolution = 4.0 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 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 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. 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: 0.17s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/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: 22.04, per 1000 atoms: 0.46 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: 17.27 Conformation dependent library (CDL) restraints added in 8.7 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: 8.15 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: 15.08 Time building geometry restraints manager: 19.00 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 Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.220 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.080 Extract box with map and model: 9.870 Check model and map are aligned: 0.760 Set scattering table: 0.440 Process input model: 119.970 Find NCS groups from input model: 2.700 Set up NCS constraints: 0.430 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.780 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 139.270 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7742 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 : 1.209 17.871 67458 Z= 0.665 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 : 8.36 Ramachandran Plot: Outliers : 0.33 % Allowed : 12.14 % Favored : 87.53 % Rotamer: Outliers : 2.01 % Allowed : 12.55 % Favored : 85.44 % 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 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP J 149 HIS 0.008 0.002 HIS h 330 PHE 0.046 0.003 PHE H 247 TYR 0.023 0.003 TYR J 113 ARG 0.012 0.001 ARG K 44 *********************** 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 : 5.301 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 130 ASP cc_start: 0.7715 (t0) cc_final: 0.7124 (t0) REVERT: A 131 VAL cc_start: 0.8176 (t) cc_final: 0.7972 (t) REVERT: C 10 LEU cc_start: 0.7810 (OUTLIER) cc_final: 0.7516 (mp) REVERT: C 18 PHE cc_start: 0.7411 (t80) cc_final: 0.6885 (t80) REVERT: C 89 LEU cc_start: 0.8148 (tp) cc_final: 0.7930 (tp) REVERT: D 21 LEU cc_start: 0.8956 (mm) cc_final: 0.8226 (mm) REVERT: D 46 PHE cc_start: 0.8681 (m-10) cc_final: 0.8366 (m-80) REVERT: E 147 LEU cc_start: 0.9099 (tp) cc_final: 0.8727 (tp) REVERT: E 219 LYS cc_start: 0.9035 (tttp) cc_final: 0.8618 (tmmt) REVERT: E 225 SER cc_start: 0.8524 (OUTLIER) cc_final: 0.8246 (p) REVERT: G 100 LYS cc_start: 0.8990 (mmtm) cc_final: 0.8714 (mmtt) REVERT: H 112 MET cc_start: 0.7202 (ptp) cc_final: 0.6570 (ptp) REVERT: H 254 TYR cc_start: 0.7901 (t80) cc_final: 0.7417 (t80) REVERT: H 300 MET cc_start: 0.7709 (ttt) cc_final: 0.7289 (ttt) REVERT: H 422 TYR cc_start: 0.8443 (p90) cc_final: 0.7555 (p90) REVERT: H 450 LEU cc_start: 0.8221 (mm) cc_final: 0.7991 (mm) REVERT: H 454 MET cc_start: 0.7198 (mmp) cc_final: 0.6697 (ttp) REVERT: X 216 VAL cc_start: 0.8798 (m) cc_final: 0.8160 (t) REVERT: X 318 ILE cc_start: 0.8982 (mt) cc_final: 0.8714 (mt) REVERT: X 379 MET cc_start: 0.7319 (mmt) cc_final: 0.6857 (mmt) REVERT: X 434 TYR cc_start: 0.7745 (t80) cc_final: 0.7309 (t80) REVERT: X 507 LEU cc_start: 0.7166 (tp) cc_final: 0.6593 (tp) REVERT: X 552 ILE cc_start: 0.9271 (pt) cc_final: 0.8996 (pt) REVERT: J 57 TYR cc_start: 0.8847 (p90) cc_final: 0.8618 (p90) REVERT: J 93 CYS cc_start: 0.7565 (OUTLIER) cc_final: 0.7241 (m) REVERT: J 102 ASP cc_start: 0.7361 (t0) cc_final: 0.7128 (t0) REVERT: K 110 THR cc_start: 0.9239 (OUTLIER) cc_final: 0.9038 (t) REVERT: K 145 HIS cc_start: 0.7947 (m-70) cc_final: 0.7516 (m170) REVERT: L 33 GLN cc_start: 0.9024 (tm-30) cc_final: 0.8792 (tm-30) REVERT: L 82 LEU cc_start: 0.9378 (OUTLIER) cc_final: 0.9139 (mm) REVERT: L 96 TYR cc_start: 0.8959 (t80) cc_final: 0.8707 (t80) REVERT: L 133 MET cc_start: 0.8110 (tmm) cc_final: 0.7900 (tmm) REVERT: L 189 GLN cc_start: 0.7960 (tp40) cc_final: 0.7739 (tp40) REVERT: L 280 ARG cc_start: 0.8026 (ttt-90) cc_final: 0.7751 (ttt90) REVERT: L 333 ASP cc_start: 0.7838 (t0) cc_final: 0.7005 (p0) REVERT: M 35 ARG cc_start: 0.8584 (mtt-85) cc_final: 0.8257 (mtp85) REVERT: M 104 GLU cc_start: 0.7518 (mt-10) cc_final: 0.7180 (mt-10) REVERT: M 169 SER cc_start: 0.7872 (t) cc_final: 0.7609 (t) REVERT: M 198 MET cc_start: 0.6927 (pmm) cc_final: 0.6663 (pmm) REVERT: M 290 LYS cc_start: 0.8757 (ttmt) cc_final: 0.8140 (tptt) REVERT: N 30 LEU cc_start: 0.9023 (mt) cc_final: 0.8763 (mt) REVERT: N 92 ASP cc_start: 0.8545 (p0) cc_final: 0.8269 (p0) REVERT: a 126 THR cc_start: 0.6852 (p) cc_final: 0.5763 (p) REVERT: a 130 ASP cc_start: 0.7817 (t0) cc_final: 0.7496 (t0) REVERT: d 14 LEU cc_start: 0.8957 (tp) cc_final: 0.8724 (tp) REVERT: d 21 LEU cc_start: 0.9052 (mm) cc_final: 0.8817 (mm) REVERT: d 70 PHE cc_start: 0.8011 (t80) cc_final: 0.7485 (t80) REVERT: e 147 LEU cc_start: 0.9282 (tp) cc_final: 0.9059 (tp) REVERT: e 219 LYS cc_start: 0.9223 (tttp) cc_final: 0.8680 (tmmt) REVERT: g 24 LYS cc_start: 0.8086 (mttt) cc_final: 0.7853 (mttp) REVERT: g 36 MET cc_start: 0.7773 (ttt) cc_final: 0.7537 (ttt) REVERT: g 37 GLU cc_start: 0.7820 (mm-30) cc_final: 0.7499 (mm-30) REVERT: g 69 ASP cc_start: 0.6505 (p0) cc_final: 0.6238 (p0) REVERT: g 77 LEU cc_start: 0.8615 (tp) cc_final: 0.8355 (tp) REVERT: g 100 LYS cc_start: 0.9003 (mmtm) cc_final: 0.8620 (mmtt) REVERT: h 104 VAL cc_start: 0.6776 (OUTLIER) cc_final: 0.6520 (p) REVERT: h 112 MET cc_start: 0.7105 (ptp) cc_final: 0.6537 (ptp) REVERT: h 119 LEU cc_start: 0.8245 (tt) cc_final: 0.8045 (tp) REVERT: h 158 GLU cc_start: 0.8467 (tm-30) cc_final: 0.8263 (tm-30) REVERT: h 254 TYR cc_start: 0.7994 (t80) cc_final: 0.7472 (t80) REVERT: h 422 TYR cc_start: 0.8488 (p90) cc_final: 0.7698 (p90) REVERT: h 454 MET cc_start: 0.7038 (mmp) cc_final: 0.6607 (ttp) REVERT: x 216 VAL cc_start: 0.8774 (m) cc_final: 0.8181 (t) REVERT: x 300 GLN cc_start: 0.8617 (tp-100) cc_final: 0.8141 (tp-100) REVERT: x 318 ILE cc_start: 0.8953 (mt) cc_final: 0.8739 (mt) REVERT: x 369 LEU cc_start: 0.8711 (tp) cc_final: 0.8475 (tt) REVERT: x 373 MET cc_start: 0.7783 (ptp) cc_final: 0.7533 (ptp) REVERT: x 379 MET cc_start: 0.7318 (mmt) cc_final: 0.6862 (mmt) REVERT: x 434 TYR cc_start: 0.7722 (t80) cc_final: 0.7210 (t80) REVERT: x 507 LEU cc_start: 0.7275 (tp) cc_final: 0.6703 (tp) REVERT: j 93 CYS cc_start: 0.7882 (OUTLIER) cc_final: 0.7652 (m) REVERT: k 145 HIS cc_start: 0.7894 (m-70) cc_final: 0.7409 (m-70) REVERT: l 33 GLN cc_start: 0.9018 (tm-30) cc_final: 0.8749 (tm-30) REVERT: l 82 LEU cc_start: 0.9362 (OUTLIER) cc_final: 0.8960 (mm) REVERT: l 93 GLU cc_start: 0.8003 (pt0) cc_final: 0.7715 (pt0) REVERT: l 96 TYR cc_start: 0.8855 (t80) cc_final: 0.8602 (t80) REVERT: l 133 MET cc_start: 0.8248 (tmm) cc_final: 0.8021 (tmm) REVERT: l 215 TYR cc_start: 0.7532 (t80) cc_final: 0.7293 (t80) REVERT: l 280 ARG cc_start: 0.7935 (ttt-90) cc_final: 0.7533 (ttt90) REVERT: l 333 ASP cc_start: 0.7913 (t0) cc_final: 0.6547 (p0) REVERT: m 35 ARG cc_start: 0.8601 (mtt-85) cc_final: 0.8318 (mtp85) REVERT: m 49 LEU cc_start: 0.9139 (tp) cc_final: 0.8883 (tp) REVERT: m 169 SER cc_start: 0.7820 (t) cc_final: 0.7571 (t) REVERT: m 193 GLU cc_start: 0.8370 (tp30) cc_final: 0.8150 (tp30) REVERT: m 290 LYS cc_start: 0.8779 (ttmt) cc_final: 0.8173 (tptt) REVERT: n 66 MET cc_start: 0.8356 (tpt) cc_final: 0.8129 (tpt) REVERT: n 92 ASP cc_start: 0.8555 (p0) cc_final: 0.8280 (p0) outliers start: 101 outliers final: 35 residues processed: 1455 average time/residue: 0.6528 time to fit residues: 1562.6948 Evaluate side-chains 1052 residues out of total 5044 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 1009 time to evaluate : 5.310 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 THR Chi-restraints excluded: chain A residue 27 SER Chi-restraints excluded: chain A residue 28 LEU Chi-restraints excluded: chain B residue 73 VAL Chi-restraints excluded: chain C residue 10 LEU Chi-restraints excluded: chain C residue 34 ASN Chi-restraints excluded: chain D residue 31 SER Chi-restraints excluded: chain D residue 39 SER Chi-restraints excluded: chain E residue 200 ILE Chi-restraints excluded: chain E residue 225 SER Chi-restraints excluded: chain H residue 61 ILE Chi-restraints excluded: chain H residue 143 SER Chi-restraints excluded: chain H residue 207 VAL Chi-restraints excluded: chain H residue 225 LEU Chi-restraints excluded: chain H residue 384 VAL Chi-restraints excluded: chain X residue 299 LEU Chi-restraints excluded: chain X residue 351 VAL Chi-restraints excluded: chain J residue 25 CYS Chi-restraints excluded: chain J residue 93 CYS Chi-restraints excluded: chain K residue 85 VAL Chi-restraints excluded: chain K residue 110 THR Chi-restraints excluded: chain L residue 82 LEU Chi-restraints excluded: chain L residue 235 THR Chi-restraints excluded: chain L residue 349 VAL Chi-restraints excluded: chain N residue 74 ARG Chi-restraints excluded: chain N residue 96 CYS Chi-restraints excluded: chain a residue 25 THR Chi-restraints excluded: chain a residue 28 LEU Chi-restraints excluded: chain b residue 73 VAL Chi-restraints excluded: chain c residue 34 ASN Chi-restraints excluded: chain d residue 31 SER Chi-restraints excluded: chain d residue 39 SER Chi-restraints excluded: chain e residue 200 ILE Chi-restraints excluded: chain h residue 61 ILE Chi-restraints excluded: chain h residue 104 VAL Chi-restraints excluded: chain h residue 207 VAL Chi-restraints excluded: chain h residue 225 LEU Chi-restraints excluded: chain x residue 299 LEU Chi-restraints excluded: chain x residue 351 VAL Chi-restraints excluded: chain j residue 93 CYS Chi-restraints excluded: chain k residue 85 VAL Chi-restraints excluded: chain l residue 82 LEU Chi-restraints excluded: chain l residue 349 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 604 random chunks: chunk 510 optimal weight: 0.9990 chunk 457 optimal weight: 8.9990 chunk 254 optimal weight: 0.9990 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: 0.6980 chunk 287 optimal weight: 0.5980 chunk 352 optimal weight: 8.9990 chunk 548 optimal weight: 0.6980 overall best weight: 0.7580 ------------------------------------------------------------------------------- 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 300 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 34 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 292 GLN L 326 HIS 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 x 340 HIS x 466 ASN k 73 HIS ** k 126 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 34 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 Total number of N/Q/H flips: 29 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7731 moved from start: 0.2086 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 49624 Z= 0.216 Angle : 0.762 13.242 67458 Z= 0.384 Chirality : 0.044 0.272 7768 Planarity : 0.006 0.071 8248 Dihedral : 6.884 59.854 6699 Min Nonbonded Distance : 2.094 Molprobity Statistics. All-atom Clashscore : 15.51 Ramachandran Plot: Outliers : 0.13 % Allowed : 11.03 % Favored : 88.83 % Rotamer: Outliers : 4.15 % Allowed : 20.08 % Favored : 75.77 % 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: -4.27 (0.09), residues: 6072 helix: -1.97 (0.08), residues: 3440 sheet: -3.60 (0.29), residues: 180 loop : -4.03 (0.10), residues: 2452 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP J 149 HIS 0.008 0.001 HIS c 87 PHE 0.027 0.002 PHE x 343 TYR 0.028 0.002 TYR L 26 ARG 0.009 0.001 ARG x 502 *********************** 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 1344 residues out of total 5044 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 209 poor density : 1135 time to evaluate : 5.556 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: A 21 TRP cc_start: 0.7680 (t-100) cc_final: 0.7476 (t60) REVERT: A 130 ASP cc_start: 0.7575 (t0) cc_final: 0.7233 (t0) REVERT: B 76 PHE cc_start: 0.7285 (m-80) cc_final: 0.6938 (m-80) REVERT: C 10 LEU cc_start: 0.7838 (OUTLIER) cc_final: 0.7497 (mp) REVERT: C 18 PHE cc_start: 0.7217 (t80) cc_final: 0.6947 (t80) REVERT: C 35 ARG cc_start: 0.8558 (ttm110) cc_final: 0.8337 (ttm110) REVERT: E 120 ILE cc_start: 0.8433 (mm) cc_final: 0.8168 (mt) REVERT: E 145 MET cc_start: 0.8012 (tpt) cc_final: 0.7438 (tpp) REVERT: E 147 LEU cc_start: 0.8995 (tp) cc_final: 0.8716 (tp) REVERT: E 225 SER cc_start: 0.8625 (OUTLIER) cc_final: 0.8229 (p) REVERT: G 21 LEU cc_start: 0.9305 (mp) cc_final: 0.9100 (mt) REVERT: H 79 PHE cc_start: 0.8467 (t80) cc_final: 0.8046 (t80) REVERT: H 112 MET cc_start: 0.7303 (ptp) cc_final: 0.6356 (ptp) REVERT: H 254 TYR cc_start: 0.8205 (t80) cc_final: 0.7705 (t80) REVERT: H 300 MET cc_start: 0.7673 (ttt) cc_final: 0.7363 (ttt) REVERT: H 422 TYR cc_start: 0.8432 (p90) cc_final: 0.8002 (p90) REVERT: H 450 LEU cc_start: 0.8249 (mm) cc_final: 0.7933 (mm) REVERT: H 454 MET cc_start: 0.7018 (mmp) cc_final: 0.6554 (tmm) REVERT: X 13 ILE cc_start: 0.7758 (OUTLIER) cc_final: 0.7328 (pt) REVERT: X 78 MET cc_start: 0.7818 (tpt) cc_final: 0.7534 (tpt) REVERT: X 137 MET cc_start: 0.7520 (tpt) cc_final: 0.7044 (tpt) REVERT: X 216 VAL cc_start: 0.8575 (m) cc_final: 0.7995 (t) REVERT: X 379 MET cc_start: 0.7199 (mmt) cc_final: 0.6763 (mmt) REVERT: X 434 TYR cc_start: 0.7651 (t80) cc_final: 0.7420 (t80) REVERT: X 459 MET cc_start: 0.8428 (mtm) cc_final: 0.7806 (mtm) REVERT: X 552 ILE cc_start: 0.9152 (OUTLIER) cc_final: 0.8611 (pt) REVERT: K 145 HIS cc_start: 0.7810 (m-70) cc_final: 0.7296 (m-70) REVERT: L 26 TYR cc_start: 0.8774 (p90) cc_final: 0.8454 (p90) REVERT: L 33 GLN cc_start: 0.9045 (tm-30) cc_final: 0.8838 (tm-30) REVERT: L 66 GLU cc_start: 0.7175 (tt0) cc_final: 0.5609 (tt0) REVERT: L 82 LEU cc_start: 0.9442 (OUTLIER) cc_final: 0.9093 (mm) REVERT: L 96 TYR cc_start: 0.8791 (t80) cc_final: 0.8446 (t80) REVERT: L 133 MET cc_start: 0.8211 (tmm) cc_final: 0.7921 (tmm) REVERT: L 160 GLU cc_start: 0.7783 (tm-30) cc_final: 0.7370 (tm-30) REVERT: L 168 TYR cc_start: 0.7841 (m-10) cc_final: 0.7617 (m-80) REVERT: M 35 ARG cc_start: 0.8483 (mtt-85) cc_final: 0.8258 (mtp85) REVERT: M 158 GLU cc_start: 0.8117 (mp0) cc_final: 0.7808 (mm-30) REVERT: M 209 MET cc_start: 0.8333 (pmm) cc_final: 0.7857 (pmm) REVERT: M 290 LYS cc_start: 0.8576 (ttmt) cc_final: 0.8039 (tptt) REVERT: M 295 TRP cc_start: 0.8290 (m100) cc_final: 0.7949 (m100) REVERT: N 81 ILE cc_start: 0.7986 (OUTLIER) cc_final: 0.7697 (mm) REVERT: a 91 HIS cc_start: 0.4337 (OUTLIER) cc_final: 0.4044 (t-170) REVERT: b 57 ILE cc_start: 0.8516 (pt) cc_final: 0.8158 (pt) REVERT: d 70 PHE cc_start: 0.7888 (t80) cc_final: 0.7422 (t80) REVERT: e 145 MET cc_start: 0.7976 (tpt) cc_final: 0.7418 (tpp) REVERT: e 147 LEU cc_start: 0.9194 (tp) cc_final: 0.8976 (tp) REVERT: e 219 LYS cc_start: 0.9101 (tttp) cc_final: 0.8401 (tmmt) REVERT: e 233 LYS cc_start: 0.8818 (mmtp) cc_final: 0.8512 (mmmm) REVERT: g 100 LYS cc_start: 0.8930 (mmtm) cc_final: 0.8658 (mmtt) REVERT: h 79 PHE cc_start: 0.8443 (t80) cc_final: 0.8133 (t80) REVERT: h 112 MET cc_start: 0.7042 (ptp) cc_final: 0.6198 (ptp) REVERT: h 158 GLU cc_start: 0.8502 (tm-30) cc_final: 0.8227 (tm-30) REVERT: h 254 TYR cc_start: 0.8220 (t80) cc_final: 0.7837 (t80) REVERT: h 422 TYR cc_start: 0.8454 (p90) cc_final: 0.8023 (p90) REVERT: x 13 ILE cc_start: 0.7772 (OUTLIER) cc_final: 0.7252 (pt) REVERT: x 216 VAL cc_start: 0.8585 (m) cc_final: 0.8044 (t) REVERT: x 305 LYS cc_start: 0.8793 (OUTLIER) cc_final: 0.8389 (ttpp) REVERT: x 373 MET cc_start: 0.7737 (ptp) cc_final: 0.7531 (ptp) REVERT: x 379 MET cc_start: 0.7254 (mmt) cc_final: 0.6659 (mmt) REVERT: x 404 GLU cc_start: 0.8287 (mm-30) cc_final: 0.7848 (mm-30) REVERT: x 434 TYR cc_start: 0.7443 (t80) cc_final: 0.7235 (t80) REVERT: x 459 MET cc_start: 0.8401 (mtm) cc_final: 0.7778 (mtm) REVERT: x 524 PHE cc_start: 0.7302 (OUTLIER) cc_final: 0.7034 (m-80) REVERT: k 145 HIS cc_start: 0.7791 (m-70) cc_final: 0.7234 (m-70) REVERT: l 26 TYR cc_start: 0.8839 (p90) cc_final: 0.8473 (p90) REVERT: l 33 GLN cc_start: 0.9029 (tm-30) cc_final: 0.8791 (tm-30) REVERT: l 82 LEU cc_start: 0.9368 (OUTLIER) cc_final: 0.9008 (mm) REVERT: l 96 TYR cc_start: 0.8733 (t80) cc_final: 0.8390 (t80) REVERT: l 133 MET cc_start: 0.8300 (tmm) cc_final: 0.8056 (tmm) REVERT: l 163 THR cc_start: 0.9117 (OUTLIER) cc_final: 0.8910 (t) REVERT: m 69 ILE cc_start: 0.8652 (mm) cc_final: 0.8392 (tp) REVERT: m 157 TYR cc_start: 0.7333 (t80) cc_final: 0.6786 (t80) REVERT: m 158 GLU cc_start: 0.8022 (mp0) cc_final: 0.7767 (mm-30) REVERT: m 186 LEU cc_start: 0.9073 (mt) cc_final: 0.8773 (tt) REVERT: m 209 MET cc_start: 0.8386 (pmm) cc_final: 0.7871 (pmm) REVERT: m 290 LYS cc_start: 0.8738 (ttmt) cc_final: 0.8104 (tptt) REVERT: n 30 LEU cc_start: 0.9171 (mt) cc_final: 0.8844 (mt) REVERT: n 81 ILE cc_start: 0.7912 (OUTLIER) cc_final: 0.7144 (tp) outliers start: 209 outliers final: 114 residues processed: 1253 average time/residue: 0.5602 time to fit residues: 1188.9538 Evaluate side-chains 1124 residues out of total 5044 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 127 poor density : 997 time to evaluate : 5.883 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 THR Chi-restraints excluded: chain A residue 28 LEU Chi-restraints excluded: chain A residue 75 LEU Chi-restraints excluded: chain A residue 110 ASN Chi-restraints excluded: chain A residue 156 THR Chi-restraints excluded: chain B residue 6 ILE Chi-restraints excluded: chain B residue 31 ARG Chi-restraints excluded: chain B residue 70 PHE Chi-restraints excluded: chain B residue 73 VAL Chi-restraints excluded: chain C residue 10 LEU Chi-restraints excluded: chain C residue 63 PHE Chi-restraints excluded: chain C residue 80 LEU Chi-restraints excluded: chain D residue 31 SER Chi-restraints excluded: chain D residue 33 VAL Chi-restraints excluded: chain D residue 39 SER Chi-restraints excluded: chain D residue 53 ASP Chi-restraints excluded: chain D residue 54 VAL Chi-restraints excluded: chain D residue 77 THR Chi-restraints excluded: chain E residue 11 ILE Chi-restraints excluded: chain E residue 45 VAL Chi-restraints excluded: chain E residue 73 VAL Chi-restraints excluded: chain E residue 123 HIS Chi-restraints excluded: chain E residue 200 ILE Chi-restraints excluded: chain E residue 225 SER Chi-restraints excluded: chain G residue 40 VAL Chi-restraints excluded: chain H residue 139 ILE Chi-restraints excluded: chain H residue 207 VAL Chi-restraints excluded: chain H residue 221 GLU Chi-restraints excluded: chain H residue 225 LEU Chi-restraints excluded: chain H residue 334 HIS Chi-restraints excluded: chain H residue 384 VAL Chi-restraints excluded: chain H residue 412 VAL Chi-restraints excluded: chain H residue 417 VAL Chi-restraints excluded: chain H residue 448 VAL Chi-restraints excluded: chain H residue 477 ILE Chi-restraints excluded: chain X residue 8 LEU Chi-restraints excluded: chain X residue 13 ILE Chi-restraints excluded: chain X residue 105 LEU Chi-restraints excluded: chain X residue 141 TYR Chi-restraints excluded: chain X residue 205 LEU Chi-restraints excluded: chain X residue 289 THR Chi-restraints excluded: chain X residue 299 LEU Chi-restraints excluded: chain X residue 351 VAL Chi-restraints excluded: chain X residue 382 VAL Chi-restraints excluded: chain X residue 419 PHE Chi-restraints excluded: chain X residue 506 LEU Chi-restraints excluded: chain X residue 529 VAL Chi-restraints excluded: chain X residue 532 VAL Chi-restraints excluded: chain X residue 544 VAL Chi-restraints excluded: chain X residue 552 ILE Chi-restraints excluded: chain X residue 610 LEU Chi-restraints excluded: chain J residue 143 ASN Chi-restraints excluded: chain J residue 154 GLU Chi-restraints excluded: chain K residue 81 THR Chi-restraints excluded: chain K residue 85 VAL Chi-restraints excluded: chain K residue 87 THR Chi-restraints excluded: chain K residue 117 ASP Chi-restraints excluded: chain K residue 137 ASP Chi-restraints excluded: chain L residue 81 LEU Chi-restraints excluded: chain L residue 82 LEU Chi-restraints excluded: chain L residue 221 ILE Chi-restraints excluded: chain L residue 235 THR Chi-restraints excluded: chain M residue 95 ASP Chi-restraints excluded: chain M residue 110 ILE Chi-restraints excluded: chain M residue 133 LEU Chi-restraints excluded: chain M residue 155 SER Chi-restraints excluded: chain N residue 55 THR Chi-restraints excluded: chain N residue 81 ILE Chi-restraints excluded: chain a residue 25 THR Chi-restraints excluded: chain a residue 28 LEU Chi-restraints excluded: chain a residue 73 TYR Chi-restraints excluded: chain a residue 91 HIS Chi-restraints excluded: chain a residue 110 ASN Chi-restraints excluded: chain a residue 156 THR Chi-restraints excluded: chain b residue 73 VAL Chi-restraints excluded: chain c residue 80 LEU Chi-restraints excluded: chain c residue 115 ARG Chi-restraints excluded: chain d residue 31 SER Chi-restraints excluded: chain d residue 39 SER Chi-restraints excluded: chain d residue 45 LEU Chi-restraints excluded: chain d residue 77 THR Chi-restraints excluded: chain e residue 73 VAL Chi-restraints excluded: chain e residue 193 TRP Chi-restraints excluded: chain e residue 213 TYR Chi-restraints excluded: chain e residue 214 THR Chi-restraints excluded: chain g residue 40 VAL Chi-restraints excluded: chain h residue 207 VAL Chi-restraints excluded: chain h residue 225 LEU Chi-restraints excluded: chain h residue 334 HIS Chi-restraints excluded: chain h residue 412 VAL Chi-restraints excluded: chain h residue 417 VAL Chi-restraints excluded: chain h residue 477 ILE Chi-restraints excluded: chain x residue 13 ILE Chi-restraints excluded: chain x residue 105 LEU Chi-restraints excluded: chain x residue 141 TYR Chi-restraints excluded: chain x residue 205 LEU Chi-restraints excluded: chain x residue 289 THR Chi-restraints excluded: chain x residue 299 LEU Chi-restraints excluded: chain x residue 305 LYS Chi-restraints excluded: chain x residue 351 VAL Chi-restraints excluded: chain x residue 382 VAL Chi-restraints excluded: chain x residue 419 PHE Chi-restraints excluded: chain x residue 506 LEU Chi-restraints excluded: chain x residue 524 PHE Chi-restraints excluded: chain x residue 529 VAL Chi-restraints excluded: chain x residue 532 VAL Chi-restraints excluded: chain x residue 544 VAL Chi-restraints excluded: chain j residue 41 TYR Chi-restraints excluded: chain j residue 143 ASN Chi-restraints excluded: chain j residue 154 GLU Chi-restraints excluded: chain k residue 58 THR Chi-restraints excluded: chain k residue 71 VAL Chi-restraints excluded: chain k residue 81 THR Chi-restraints excluded: chain k residue 85 VAL Chi-restraints excluded: chain k residue 87 THR Chi-restraints excluded: chain k residue 117 ASP Chi-restraints excluded: chain k residue 137 ASP Chi-restraints excluded: chain l residue 82 LEU Chi-restraints excluded: chain l residue 126 THR Chi-restraints excluded: chain l residue 163 THR Chi-restraints excluded: chain l residue 349 VAL Chi-restraints excluded: chain l residue 356 ILE Chi-restraints excluded: chain m residue 95 ASP Chi-restraints excluded: chain m residue 155 SER Chi-restraints excluded: chain n residue 55 THR Chi-restraints excluded: chain n residue 74 ARG Chi-restraints excluded: chain n residue 81 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 604 random chunks: chunk 304 optimal weight: 0.0370 chunk 170 optimal weight: 4.9990 chunk 456 optimal weight: 7.9990 chunk 373 optimal weight: 20.0000 chunk 151 optimal weight: 2.9990 chunk 549 optimal weight: 2.9990 chunk 593 optimal weight: 0.0870 chunk 489 optimal weight: 2.9990 chunk 544 optimal weight: 8.9990 chunk 187 optimal weight: 1.9990 chunk 440 optimal weight: 3.9990 overall best weight: 1.6242 ------------------------------------------------------------------------------- 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 H 189 ASN ** X 340 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** X 596 ASN ** K 73 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 126 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 34 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 62 HIS M 172 HIS ** M 223 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 224 HIS e 123 HIS h 189 ASN ** j 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 126 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 34 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** l 62 HIS m 172 HIS m 224 HIS ** 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: 0.7767 moved from start: 0.2533 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= 0.240 Angle : 0.731 11.467 67458 Z= 0.365 Chirality : 0.043 0.223 7768 Planarity : 0.005 0.120 8248 Dihedral : 6.385 59.072 6676 Min Nonbonded Distance : 2.097 Molprobity Statistics. All-atom Clashscore : 16.88 Ramachandran Plot: Outliers : 0.08 % Allowed : 11.35 % Favored : 88.57 % Rotamer: Outliers : 5.42 % Allowed : 21.15 % Favored : 73.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.43 % Cis-general : 0.10 % Twisted Proline : 1.43 % Twisted General : 0.14 % 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: -3.59 (0.10), residues: 6072 helix: -1.31 (0.08), residues: 3464 sheet: -3.31 (0.31), residues: 212 loop : -3.93 (0.11), residues: 2396 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP a 21 HIS 0.019 0.001 HIS E 123 PHE 0.036 0.002 PHE x 221 TYR 0.032 0.002 TYR E 152 ARG 0.021 0.000 ARG x 554 *********************** 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 1324 residues out of total 5044 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 273 poor density : 1051 time to evaluate : 4.898 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: A 21 TRP cc_start: 0.7605 (t-100) cc_final: 0.7388 (t60) REVERT: A 114 MET cc_start: 0.7502 (mtt) cc_final: 0.7096 (ttm) REVERT: B 49 PHE cc_start: 0.7338 (OUTLIER) cc_final: 0.6981 (m-80) REVERT: B 67 ILE cc_start: 0.7690 (mp) cc_final: 0.7430 (tp) REVERT: B 76 PHE cc_start: 0.7243 (m-80) cc_final: 0.6944 (m-80) REVERT: C 10 LEU cc_start: 0.7914 (OUTLIER) cc_final: 0.7705 (mp) REVERT: C 18 PHE cc_start: 0.7261 (t80) cc_final: 0.6935 (t80) REVERT: C 45 LEU cc_start: 0.7881 (OUTLIER) cc_final: 0.7618 (mm) REVERT: C 90 ILE cc_start: 0.9063 (OUTLIER) cc_final: 0.8859 (mm) REVERT: D 21 LEU cc_start: 0.8818 (mm) cc_final: 0.8307 (mm) REVERT: E 120 ILE cc_start: 0.8559 (mm) cc_final: 0.8275 (mt) REVERT: E 145 MET cc_start: 0.7744 (tpt) cc_final: 0.7509 (tpp) REVERT: E 147 LEU cc_start: 0.9109 (tp) cc_final: 0.8880 (tp) REVERT: G 99 GLU cc_start: 0.7459 (tp30) cc_final: 0.7208 (tp30) REVERT: H 79 PHE cc_start: 0.8478 (t80) cc_final: 0.8120 (t80) REVERT: H 112 MET cc_start: 0.7281 (ptp) cc_final: 0.6356 (ptp) REVERT: H 190 MET cc_start: 0.8875 (mtt) cc_final: 0.8642 (mtm) REVERT: H 254 TYR cc_start: 0.8081 (t80) cc_final: 0.7650 (t80) REVERT: H 279 MET cc_start: 0.7188 (OUTLIER) cc_final: 0.6871 (mmm) REVERT: H 300 MET cc_start: 0.7680 (ttt) cc_final: 0.7353 (ttt) REVERT: H 422 TYR cc_start: 0.8420 (p90) cc_final: 0.8059 (p90) REVERT: H 454 MET cc_start: 0.6965 (mmp) cc_final: 0.6542 (tmm) REVERT: X 13 ILE cc_start: 0.7722 (OUTLIER) cc_final: 0.7299 (pt) REVERT: X 216 VAL cc_start: 0.8497 (m) cc_final: 0.7887 (t) REVERT: X 379 MET cc_start: 0.7158 (mmt) cc_final: 0.6945 (mmt) REVERT: X 434 TYR cc_start: 0.7477 (t80) cc_final: 0.7246 (t80) REVERT: X 546 MET cc_start: 0.6791 (ppp) cc_final: 0.6583 (ppp) REVERT: X 552 ILE cc_start: 0.9232 (pt) cc_final: 0.8437 (pt) REVERT: J 57 TYR cc_start: 0.8953 (p90) cc_final: 0.8730 (p90) REVERT: K 145 HIS cc_start: 0.7638 (m-70) cc_final: 0.7339 (m-70) REVERT: L 66 GLU cc_start: 0.7179 (tt0) cc_final: 0.5677 (tt0) REVERT: L 93 GLU cc_start: 0.8215 (pt0) cc_final: 0.7236 (pt0) REVERT: L 96 TYR cc_start: 0.8833 (t80) cc_final: 0.8513 (t80) REVERT: L 133 MET cc_start: 0.8231 (tmm) cc_final: 0.7867 (tmm) REVERT: L 160 GLU cc_start: 0.7826 (tm-30) cc_final: 0.7583 (tm-30) REVERT: L 333 ASP cc_start: 0.7872 (OUTLIER) cc_final: 0.7668 (p0) REVERT: M 35 ARG cc_start: 0.8560 (mtt-85) cc_final: 0.8217 (mtp85) REVERT: M 103 LEU cc_start: 0.8892 (mm) cc_final: 0.8597 (mp) REVERT: M 104 GLU cc_start: 0.7204 (mt-10) cc_final: 0.6888 (mt-10) REVERT: M 158 GLU cc_start: 0.8120 (mp0) cc_final: 0.7762 (mm-30) REVERT: M 209 MET cc_start: 0.8245 (pmm) cc_final: 0.7870 (pmm) REVERT: M 226 MET cc_start: 0.8189 (mmp) cc_final: 0.7820 (mmp) REVERT: M 290 LYS cc_start: 0.8641 (ttmt) cc_final: 0.8091 (tptt) REVERT: M 295 TRP cc_start: 0.8371 (m100) cc_final: 0.7998 (m100) REVERT: N 81 ILE cc_start: 0.8024 (OUTLIER) cc_final: 0.7345 (tp) REVERT: a 91 HIS cc_start: 0.4409 (OUTLIER) cc_final: 0.4089 (t-170) REVERT: a 130 ASP cc_start: 0.8035 (t0) cc_final: 0.7727 (t0) REVERT: b 67 ILE cc_start: 0.7991 (mp) cc_final: 0.7717 (tp) REVERT: c 19 TYR cc_start: 0.7008 (m-80) cc_final: 0.6620 (m-80) REVERT: c 36 MET cc_start: 0.8947 (ppp) cc_final: 0.8462 (ppp) REVERT: d 53 ASP cc_start: 0.7708 (OUTLIER) cc_final: 0.7491 (m-30) REVERT: d 70 PHE cc_start: 0.7949 (t80) cc_final: 0.7436 (t80) REVERT: e 145 MET cc_start: 0.7595 (tpt) cc_final: 0.7049 (tpp) REVERT: e 147 LEU cc_start: 0.9166 (tp) cc_final: 0.8959 (tp) REVERT: e 168 MET cc_start: 0.5430 (mtt) cc_final: 0.4790 (mtp) REVERT: e 219 LYS cc_start: 0.9081 (tttp) cc_final: 0.8826 (ttpp) REVERT: e 223 GLU cc_start: 0.6920 (tp30) cc_final: 0.6589 (tp30) REVERT: g 5 TYR cc_start: 0.7260 (m-80) cc_final: 0.7056 (m-80) REVERT: g 41 ASN cc_start: 0.9187 (p0) cc_final: 0.8917 (p0) REVERT: g 73 GLN cc_start: 0.7960 (OUTLIER) cc_final: 0.7652 (mp10) REVERT: g 100 LYS cc_start: 0.8988 (mmtm) cc_final: 0.8673 (mmtt) REVERT: h 18 PHE cc_start: 0.6832 (t80) cc_final: 0.6522 (t80) REVERT: h 79 PHE cc_start: 0.8476 (t80) cc_final: 0.8245 (t80) REVERT: h 94 MET cc_start: 0.6710 (mmp) cc_final: 0.6494 (mmp) REVERT: h 112 MET cc_start: 0.7082 (ptp) cc_final: 0.6220 (ptp) REVERT: h 158 GLU cc_start: 0.8555 (tm-30) cc_final: 0.8258 (tm-30) REVERT: h 190 MET cc_start: 0.8926 (mtt) cc_final: 0.8701 (mtm) REVERT: h 207 VAL cc_start: 0.9145 (OUTLIER) cc_final: 0.8870 (p) REVERT: h 254 TYR cc_start: 0.8141 (t80) cc_final: 0.7706 (t80) REVERT: h 422 TYR cc_start: 0.8430 (p90) cc_final: 0.8022 (p90) REVERT: x 13 ILE cc_start: 0.7773 (OUTLIER) cc_final: 0.7230 (pt) REVERT: x 216 VAL cc_start: 0.8487 (m) cc_final: 0.7944 (t) REVERT: x 300 GLN cc_start: 0.9003 (tp-100) cc_final: 0.8777 (tp-100) REVERT: x 379 MET cc_start: 0.7283 (mmt) cc_final: 0.7056 (mmt) REVERT: x 404 GLU cc_start: 0.8268 (mm-30) cc_final: 0.7926 (mm-30) REVERT: x 434 TYR cc_start: 0.7586 (t80) cc_final: 0.7203 (t80) REVERT: x 524 PHE cc_start: 0.7330 (OUTLIER) cc_final: 0.7116 (m-80) REVERT: x 554 ARG cc_start: 0.8351 (OUTLIER) cc_final: 0.7969 (tpp-160) REVERT: j 80 MET cc_start: 0.7574 (mtm) cc_final: 0.7239 (mtm) REVERT: k 145 HIS cc_start: 0.7747 (m-70) cc_final: 0.7209 (m-70) REVERT: k 167 GLU cc_start: 0.7363 (pm20) cc_final: 0.7081 (pm20) REVERT: l 33 GLN cc_start: 0.9068 (tm-30) cc_final: 0.8826 (tm-30) REVERT: l 82 LEU cc_start: 0.9358 (OUTLIER) cc_final: 0.9108 (mm) REVERT: l 93 GLU cc_start: 0.7926 (pt0) cc_final: 0.7719 (pt0) REVERT: l 96 TYR cc_start: 0.8817 (t80) cc_final: 0.8567 (t80) REVERT: l 133 MET cc_start: 0.8314 (tmm) cc_final: 0.8036 (tmm) REVERT: l 333 ASP cc_start: 0.7501 (t0) cc_final: 0.7071 (p0) REVERT: m 69 ILE cc_start: 0.8634 (mm) cc_final: 0.8363 (tp) REVERT: m 104 GLU cc_start: 0.6594 (mt-10) cc_final: 0.6391 (mt-10) REVERT: m 133 LEU cc_start: 0.8830 (OUTLIER) cc_final: 0.8442 (tp) REVERT: m 137 GLN cc_start: 0.8791 (mm-40) cc_final: 0.8155 (mm-40) REVERT: m 157 TYR cc_start: 0.7295 (t80) cc_final: 0.6863 (t80) REVERT: m 158 GLU cc_start: 0.8013 (mp0) cc_final: 0.7777 (mm-30) REVERT: m 186 LEU cc_start: 0.8997 (mt) cc_final: 0.8718 (tt) REVERT: m 209 MET cc_start: 0.8430 (pmm) cc_final: 0.8061 (pmm) REVERT: m 290 LYS cc_start: 0.8749 (ttmt) cc_final: 0.8130 (tptt) REVERT: n 74 ARG cc_start: 0.8938 (OUTLIER) cc_final: 0.8382 (tpt90) REVERT: n 132 ASP cc_start: 0.7499 (t0) cc_final: 0.6967 (t70) outliers start: 273 outliers final: 159 residues processed: 1220 average time/residue: 0.5595 time to fit residues: 1161.8807 Evaluate side-chains 1149 residues out of total 5044 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 177 poor density : 972 time to evaluate : 5.323 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 THR Chi-restraints excluded: chain A residue 28 LEU Chi-restraints excluded: chain A residue 66 TYR Chi-restraints excluded: chain A residue 73 TYR Chi-restraints excluded: chain A residue 85 VAL Chi-restraints excluded: chain A residue 110 ASN Chi-restraints excluded: chain A residue 156 THR Chi-restraints excluded: chain B residue 6 ILE Chi-restraints excluded: chain B residue 22 VAL Chi-restraints excluded: chain B residue 29 VAL Chi-restraints excluded: chain B residue 49 PHE Chi-restraints excluded: chain B residue 73 VAL Chi-restraints excluded: chain B residue 74 ILE Chi-restraints excluded: chain C residue 10 LEU Chi-restraints excluded: chain C residue 23 THR Chi-restraints excluded: chain C residue 34 ASN Chi-restraints excluded: chain C residue 45 LEU Chi-restraints excluded: chain C residue 63 PHE Chi-restraints excluded: chain C residue 79 LEU Chi-restraints excluded: chain C residue 90 ILE Chi-restraints excluded: chain D residue 16 ILE Chi-restraints excluded: chain D residue 31 SER Chi-restraints excluded: chain D residue 39 SER Chi-restraints excluded: chain D residue 53 ASP Chi-restraints excluded: chain D residue 54 VAL Chi-restraints excluded: chain D residue 77 THR Chi-restraints excluded: chain E residue 11 ILE Chi-restraints excluded: chain E residue 16 VAL Chi-restraints excluded: chain E residue 45 VAL Chi-restraints excluded: chain E residue 73 VAL Chi-restraints excluded: chain E residue 200 ILE Chi-restraints excluded: chain E residue 213 TYR Chi-restraints excluded: chain G residue 4 SER Chi-restraints excluded: chain G residue 22 VAL Chi-restraints excluded: chain G residue 40 VAL Chi-restraints excluded: chain G residue 73 GLN Chi-restraints excluded: chain G residue 93 VAL Chi-restraints excluded: chain G residue 103 THR Chi-restraints excluded: chain G residue 105 ASN Chi-restraints excluded: chain H residue 139 ILE Chi-restraints excluded: chain H residue 221 GLU Chi-restraints excluded: chain H residue 225 LEU Chi-restraints excluded: chain H residue 279 MET Chi-restraints excluded: chain H residue 311 LEU Chi-restraints excluded: chain H residue 312 ILE Chi-restraints excluded: chain H residue 334 HIS Chi-restraints excluded: chain H residue 384 VAL Chi-restraints excluded: chain H residue 417 VAL Chi-restraints excluded: chain H residue 477 ILE Chi-restraints excluded: chain X residue 13 ILE Chi-restraints excluded: chain X residue 131 THR Chi-restraints excluded: chain X residue 141 TYR Chi-restraints excluded: chain X residue 205 LEU Chi-restraints excluded: chain X residue 258 TYR Chi-restraints excluded: chain X residue 289 THR Chi-restraints excluded: chain X residue 299 LEU Chi-restraints excluded: chain X residue 351 VAL Chi-restraints excluded: chain X residue 382 VAL Chi-restraints excluded: chain X residue 398 SER Chi-restraints excluded: chain X residue 419 PHE Chi-restraints excluded: chain X residue 448 VAL Chi-restraints excluded: chain X residue 467 VAL Chi-restraints excluded: chain X residue 529 VAL Chi-restraints excluded: chain X residue 532 VAL Chi-restraints excluded: chain X residue 544 VAL Chi-restraints excluded: chain X residue 593 TYR Chi-restraints excluded: chain X residue 606 LEU Chi-restraints excluded: chain X residue 610 LEU Chi-restraints excluded: chain J residue 41 TYR Chi-restraints excluded: chain J residue 116 VAL Chi-restraints excluded: chain J residue 143 ASN Chi-restraints excluded: chain J residue 154 GLU Chi-restraints excluded: chain J residue 171 TRP Chi-restraints excluded: chain K residue 71 VAL Chi-restraints excluded: chain K residue 81 THR Chi-restraints excluded: chain K residue 85 VAL Chi-restraints excluded: chain K residue 87 THR Chi-restraints excluded: chain K residue 117 ASP Chi-restraints excluded: chain K residue 137 ASP Chi-restraints excluded: chain L residue 81 LEU Chi-restraints excluded: chain L residue 82 LEU Chi-restraints excluded: chain L residue 126 THR Chi-restraints excluded: chain L residue 244 VAL Chi-restraints excluded: chain L residue 318 VAL Chi-restraints excluded: chain L residue 333 ASP Chi-restraints excluded: chain M residue 79 LEU Chi-restraints excluded: chain M residue 95 ASP Chi-restraints excluded: chain M residue 155 SER Chi-restraints excluded: chain M residue 169 SER Chi-restraints excluded: chain M residue 283 PHE Chi-restraints excluded: chain N residue 20 PHE Chi-restraints excluded: chain N residue 55 THR Chi-restraints excluded: chain N residue 81 ILE Chi-restraints excluded: chain a residue 28 LEU Chi-restraints excluded: chain a residue 39 PHE Chi-restraints excluded: chain a residue 66 TYR Chi-restraints excluded: chain a residue 85 VAL Chi-restraints excluded: chain a residue 91 HIS Chi-restraints excluded: chain a residue 110 ASN Chi-restraints excluded: chain b residue 29 VAL Chi-restraints excluded: chain b residue 70 PHE Chi-restraints excluded: chain b residue 73 VAL Chi-restraints excluded: chain b residue 74 ILE Chi-restraints excluded: chain c residue 34 ASN Chi-restraints excluded: chain c residue 80 LEU Chi-restraints excluded: chain c residue 115 ARG Chi-restraints excluded: chain d residue 31 SER Chi-restraints excluded: chain d residue 45 LEU Chi-restraints excluded: chain d residue 53 ASP Chi-restraints excluded: chain d residue 54 VAL Chi-restraints excluded: chain d residue 72 PHE Chi-restraints excluded: chain d residue 77 THR Chi-restraints excluded: chain e residue 45 VAL Chi-restraints excluded: chain e residue 73 VAL Chi-restraints excluded: chain e residue 123 HIS Chi-restraints excluded: chain e residue 193 TRP Chi-restraints excluded: chain e residue 213 TYR Chi-restraints excluded: chain g residue 2 ILE Chi-restraints excluded: chain g residue 40 VAL Chi-restraints excluded: chain g residue 73 GLN Chi-restraints excluded: chain g residue 93 VAL Chi-restraints excluded: chain h residue 34 LEU Chi-restraints excluded: chain h residue 207 VAL Chi-restraints excluded: chain h residue 221 GLU Chi-restraints excluded: chain h residue 225 LEU Chi-restraints excluded: chain h residue 311 LEU Chi-restraints excluded: chain h residue 312 ILE Chi-restraints excluded: chain h residue 334 HIS Chi-restraints excluded: chain h residue 412 VAL Chi-restraints excluded: chain h residue 417 VAL Chi-restraints excluded: chain h residue 477 ILE Chi-restraints excluded: chain x residue 8 LEU Chi-restraints excluded: chain x residue 13 ILE Chi-restraints excluded: chain x residue 131 THR Chi-restraints excluded: chain x residue 141 TYR Chi-restraints excluded: chain x residue 205 LEU Chi-restraints excluded: chain x residue 258 TYR Chi-restraints excluded: chain x residue 289 THR Chi-restraints excluded: chain x residue 299 LEU Chi-restraints excluded: chain x residue 351 VAL Chi-restraints excluded: chain x residue 382 VAL Chi-restraints excluded: chain x residue 398 SER Chi-restraints excluded: chain x residue 448 VAL Chi-restraints excluded: chain x residue 467 VAL Chi-restraints excluded: chain x residue 524 PHE Chi-restraints excluded: chain x residue 529 VAL Chi-restraints excluded: chain x residue 532 VAL Chi-restraints excluded: chain x residue 544 VAL Chi-restraints excluded: chain x residue 554 ARG Chi-restraints excluded: chain x residue 579 ILE Chi-restraints excluded: chain x residue 606 LEU Chi-restraints excluded: chain x residue 610 LEU Chi-restraints excluded: chain j residue 41 TYR Chi-restraints excluded: chain j residue 56 GLN Chi-restraints excluded: chain j residue 114 ILE Chi-restraints excluded: chain j residue 143 ASN Chi-restraints excluded: chain j residue 154 GLU Chi-restraints excluded: chain k residue 58 THR Chi-restraints excluded: chain k residue 81 THR Chi-restraints excluded: chain k residue 85 VAL Chi-restraints excluded: chain k residue 87 THR Chi-restraints excluded: chain k residue 117 ASP Chi-restraints excluded: chain k residue 137 ASP Chi-restraints excluded: chain l residue 82 LEU Chi-restraints excluded: chain l residue 126 THR Chi-restraints excluded: chain l residue 244 VAL Chi-restraints excluded: chain l residue 318 VAL Chi-restraints excluded: chain l residue 349 VAL Chi-restraints excluded: chain m residue 95 ASP Chi-restraints excluded: chain m residue 133 LEU Chi-restraints excluded: chain m residue 155 SER Chi-restraints excluded: chain m residue 169 SER Chi-restraints excluded: chain m residue 226 MET Chi-restraints excluded: chain m residue 283 PHE Chi-restraints excluded: chain n residue 55 THR Chi-restraints excluded: chain n residue 74 ARG Chi-restraints excluded: chain n residue 81 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 604 random chunks: chunk 542 optimal weight: 5.9990 chunk 413 optimal weight: 6.9990 chunk 285 optimal weight: 8.9990 chunk 60 optimal weight: 9.9990 chunk 262 optimal weight: 8.9990 chunk 368 optimal weight: 1.9990 chunk 551 optimal weight: 7.9990 chunk 583 optimal weight: 0.9990 chunk 288 optimal weight: 5.9990 chunk 522 optimal weight: 2.9990 chunk 157 optimal weight: 5.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 109 ASN D 50 GLN E 123 HIS E 156 HIS G 41 ASN ** H 226 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 340 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 163 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 73 HIS ** K 126 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 33 GLN ** L 34 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 34 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** e 156 HIS ** j 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 126 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** l 34 HIS ** m 34 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** n 100 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7864 moved from start: 0.2876 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= 0.360 Angle : 0.773 12.437 67458 Z= 0.387 Chirality : 0.046 0.222 7768 Planarity : 0.005 0.082 8248 Dihedral : 6.273 58.338 6671 Min Nonbonded Distance : 2.022 Molprobity Statistics. All-atom Clashscore : 18.71 Ramachandran Plot: Outliers : 0.10 % Allowed : 12.57 % Favored : 87.34 % Rotamer: Outliers : 6.99 % Allowed : 22.97 % Favored : 70.04 % 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: -3.28 (0.10), residues: 6072 helix: -0.99 (0.09), residues: 3452 sheet: -3.34 (0.31), residues: 220 loop : -3.90 (0.11), residues: 2400 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP a 21 HIS 0.029 0.002 HIS e 123 PHE 0.032 0.002 PHE H 247 TYR 0.033 0.002 TYR e 152 ARG 0.009 0.001 ARG x 554 *********************** 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 1356 residues out of total 5044 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 352 poor density : 1004 time to evaluate : 5.682 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 21 TRP cc_start: 0.7618 (t-100) cc_final: 0.7396 (t60) REVERT: B 49 PHE cc_start: 0.7443 (OUTLIER) cc_final: 0.7186 (m-10) REVERT: C 18 PHE cc_start: 0.7330 (t80) cc_final: 0.6952 (t80) REVERT: C 77 PHE cc_start: 0.6980 (t80) cc_final: 0.6750 (t80) REVERT: D 70 PHE cc_start: 0.8178 (t80) cc_final: 0.7425 (t80) REVERT: E 120 ILE cc_start: 0.8623 (mm) cc_final: 0.8311 (mt) REVERT: E 145 MET cc_start: 0.7797 (tpt) cc_final: 0.7464 (tpp) REVERT: E 147 LEU cc_start: 0.9062 (tp) cc_final: 0.8845 (tp) REVERT: E 199 ASN cc_start: 0.7320 (p0) cc_final: 0.6906 (p0) REVERT: G 99 GLU cc_start: 0.7532 (tp30) cc_final: 0.7296 (tp30) REVERT: H 79 PHE cc_start: 0.8533 (t80) cc_final: 0.8257 (t80) REVERT: H 112 MET cc_start: 0.7345 (ptp) cc_final: 0.6377 (ptp) REVERT: H 190 MET cc_start: 0.8836 (mtt) cc_final: 0.8607 (mtm) REVERT: H 254 TYR cc_start: 0.8210 (t80) cc_final: 0.7965 (t80) REVERT: H 300 MET cc_start: 0.7643 (ttt) cc_final: 0.7299 (ttt) REVERT: H 422 TYR cc_start: 0.8316 (p90) cc_final: 0.7977 (p90) REVERT: H 454 MET cc_start: 0.7095 (mmp) cc_final: 0.6604 (tmm) REVERT: X 137 MET cc_start: 0.7431 (tpp) cc_final: 0.6716 (tpp) REVERT: X 216 VAL cc_start: 0.8546 (m) cc_final: 0.7987 (t) REVERT: X 379 MET cc_start: 0.7150 (mmt) cc_final: 0.6690 (mmt) REVERT: X 434 TYR cc_start: 0.7744 (t80) cc_final: 0.7389 (t80) REVERT: X 459 MET cc_start: 0.8376 (mtm) cc_final: 0.7817 (mtm) REVERT: X 546 MET cc_start: 0.7035 (ppp) cc_final: 0.6731 (ppp) REVERT: J 42 ASP cc_start: 0.7851 (OUTLIER) cc_final: 0.7459 (p0) REVERT: J 141 ILE cc_start: 0.9138 (tp) cc_final: 0.8894 (tp) REVERT: L 26 TYR cc_start: 0.8980 (p90) cc_final: 0.8456 (p90) REVERT: L 93 GLU cc_start: 0.8280 (pt0) cc_final: 0.7282 (pt0) REVERT: L 96 TYR cc_start: 0.8938 (t80) cc_final: 0.8556 (t80) REVERT: L 133 MET cc_start: 0.8207 (tmm) cc_final: 0.7870 (tmm) REVERT: L 160 GLU cc_start: 0.7887 (tm-30) cc_final: 0.7666 (tm-30) REVERT: L 187 LEU cc_start: 0.9270 (OUTLIER) cc_final: 0.8886 (mm) REVERT: M 35 ARG cc_start: 0.8645 (mtt-85) cc_final: 0.8209 (mtp85) REVERT: M 79 LEU cc_start: 0.8140 (OUTLIER) cc_final: 0.7648 (pp) REVERT: M 104 GLU cc_start: 0.7535 (mt-10) cc_final: 0.7145 (mt-10) REVERT: M 158 GLU cc_start: 0.8316 (mp0) cc_final: 0.8105 (mp0) REVERT: M 209 MET cc_start: 0.8288 (pmm) cc_final: 0.8087 (pmm) REVERT: M 226 MET cc_start: 0.8409 (mmp) cc_final: 0.7798 (mmp) REVERT: M 271 LEU cc_start: 0.8657 (OUTLIER) cc_final: 0.8423 (mp) REVERT: M 290 LYS cc_start: 0.8712 (ttmt) cc_final: 0.8183 (tptt) REVERT: M 295 TRP cc_start: 0.8391 (m100) cc_final: 0.8091 (m100) REVERT: N 27 LEU cc_start: 0.9455 (OUTLIER) cc_final: 0.9146 (tt) REVERT: N 74 ARG cc_start: 0.9152 (OUTLIER) cc_final: 0.8608 (tpt90) REVERT: N 132 ASP cc_start: 0.7680 (OUTLIER) cc_final: 0.7029 (t0) REVERT: a 78 MET cc_start: 0.8146 (mpp) cc_final: 0.7851 (mtm) REVERT: a 83 LEU cc_start: 0.7416 (OUTLIER) cc_final: 0.7150 (mm) REVERT: a 91 HIS cc_start: 0.4358 (t-90) cc_final: 0.4056 (t-170) REVERT: a 130 ASP cc_start: 0.7997 (t0) cc_final: 0.7704 (t0) REVERT: b 49 PHE cc_start: 0.7193 (OUTLIER) cc_final: 0.6926 (m-10) REVERT: b 73 VAL cc_start: 0.8786 (OUTLIER) cc_final: 0.8563 (t) REVERT: c 36 MET cc_start: 0.8935 (ppp) cc_final: 0.8430 (ppp) REVERT: c 56 ILE cc_start: 0.6781 (pt) cc_final: 0.6555 (mp) REVERT: d 53 ASP cc_start: 0.7846 (OUTLIER) cc_final: 0.7623 (m-30) REVERT: d 70 PHE cc_start: 0.8079 (t80) cc_final: 0.7547 (t80) REVERT: e 145 MET cc_start: 0.7579 (tpt) cc_final: 0.7140 (tpt) REVERT: e 146 TYR cc_start: 0.8321 (t80) cc_final: 0.7460 (t80) REVERT: e 147 LEU cc_start: 0.9172 (tp) cc_final: 0.8947 (tp) REVERT: e 168 MET cc_start: 0.5553 (mtt) cc_final: 0.4907 (mtp) REVERT: e 219 LYS cc_start: 0.9068 (tttp) cc_final: 0.8754 (ttpp) REVERT: g 5 TYR cc_start: 0.7581 (m-80) cc_final: 0.7358 (m-80) REVERT: g 73 GLN cc_start: 0.8080 (OUTLIER) cc_final: 0.7695 (mp10) REVERT: g 100 LYS cc_start: 0.9031 (mmtm) cc_final: 0.8703 (mmtt) REVERT: h 18 PHE cc_start: 0.6866 (t80) cc_final: 0.6607 (t80) REVERT: h 79 PHE cc_start: 0.8544 (t80) cc_final: 0.8281 (t80) REVERT: h 112 MET cc_start: 0.7106 (ptp) cc_final: 0.6164 (ptp) REVERT: h 158 GLU cc_start: 0.8669 (tm-30) cc_final: 0.8352 (tm-30) REVERT: h 190 MET cc_start: 0.8904 (mtt) cc_final: 0.8690 (mtm) REVERT: h 207 VAL cc_start: 0.9201 (OUTLIER) cc_final: 0.8932 (p) REVERT: h 262 LEU cc_start: 0.8469 (OUTLIER) cc_final: 0.8046 (mt) REVERT: h 279 MET cc_start: 0.7237 (mmp) cc_final: 0.6695 (mtp) REVERT: h 422 TYR cc_start: 0.8420 (p90) cc_final: 0.8122 (p90) REVERT: h 450 LEU cc_start: 0.7832 (OUTLIER) cc_final: 0.7615 (mm) REVERT: h 454 MET cc_start: 0.6781 (mmp) cc_final: 0.6377 (ppp) REVERT: x 216 VAL cc_start: 0.8484 (m) cc_final: 0.7952 (t) REVERT: x 300 GLN cc_start: 0.9109 (tp-100) cc_final: 0.8594 (tp-100) REVERT: x 305 LYS cc_start: 0.8969 (OUTLIER) cc_final: 0.8308 (ttpp) REVERT: x 379 MET cc_start: 0.7271 (mmt) cc_final: 0.6772 (mmt) REVERT: x 459 MET cc_start: 0.8383 (mtm) cc_final: 0.7773 (mtm) REVERT: k 145 HIS cc_start: 0.7765 (m-70) cc_final: 0.7340 (m170) REVERT: l 33 GLN cc_start: 0.9157 (tm-30) cc_final: 0.8952 (tm-30) REVERT: l 82 LEU cc_start: 0.9495 (OUTLIER) cc_final: 0.9256 (mm) REVERT: l 96 TYR cc_start: 0.8898 (t80) cc_final: 0.8555 (t80) REVERT: l 133 MET cc_start: 0.8290 (tmm) cc_final: 0.8088 (tmm) REVERT: l 187 LEU cc_start: 0.9184 (OUTLIER) cc_final: 0.8908 (mm) REVERT: l 260 LEU cc_start: 0.7820 (OUTLIER) cc_final: 0.7545 (mt) REVERT: m 69 ILE cc_start: 0.8618 (mm) cc_final: 0.8375 (tp) REVERT: m 103 LEU cc_start: 0.8971 (OUTLIER) cc_final: 0.8709 (mp) REVERT: m 133 LEU cc_start: 0.8923 (OUTLIER) cc_final: 0.8467 (tp) REVERT: m 158 GLU cc_start: 0.8087 (mp0) cc_final: 0.7862 (mm-30) REVERT: m 186 LEU cc_start: 0.9016 (mt) cc_final: 0.8782 (tt) REVERT: m 209 MET cc_start: 0.8473 (pmm) cc_final: 0.8197 (pmm) REVERT: m 266 GLN cc_start: 0.8567 (mm-40) cc_final: 0.8327 (mm-40) REVERT: m 271 LEU cc_start: 0.8701 (OUTLIER) cc_final: 0.8439 (mp) REVERT: m 290 LYS cc_start: 0.8850 (ttmt) cc_final: 0.8221 (tptt) REVERT: n 74 ARG cc_start: 0.9138 (OUTLIER) cc_final: 0.8549 (tpt90) REVERT: n 132 ASP cc_start: 0.7915 (t0) cc_final: 0.7161 (t70) outliers start: 352 outliers final: 238 residues processed: 1238 average time/residue: 0.5344 time to fit residues: 1135.5243 Evaluate side-chains 1197 residues out of total 5044 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 262 poor density : 935 time to evaluate : 5.579 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 THR Chi-restraints excluded: chain A residue 28 LEU Chi-restraints excluded: chain A residue 66 TYR Chi-restraints excluded: chain A residue 73 TYR Chi-restraints excluded: chain A residue 83 LEU Chi-restraints excluded: chain A residue 85 VAL Chi-restraints excluded: chain A residue 101 VAL Chi-restraints excluded: chain A residue 110 ASN Chi-restraints excluded: chain A residue 111 VAL Chi-restraints excluded: chain B residue 6 ILE Chi-restraints excluded: chain B residue 22 VAL Chi-restraints excluded: chain B residue 27 THR Chi-restraints excluded: chain B residue 29 VAL Chi-restraints excluded: chain B residue 31 ARG Chi-restraints excluded: chain B residue 35 VAL Chi-restraints excluded: chain B residue 49 PHE Chi-restraints excluded: chain B residue 70 PHE Chi-restraints excluded: chain B residue 73 VAL Chi-restraints excluded: chain B residue 74 ILE Chi-restraints excluded: chain C residue 19 TYR Chi-restraints excluded: chain C residue 23 THR Chi-restraints excluded: chain C residue 34 ASN Chi-restraints excluded: chain C residue 63 PHE Chi-restraints excluded: chain C residue 72 ILE Chi-restraints excluded: chain C residue 79 LEU Chi-restraints excluded: chain C residue 80 LEU Chi-restraints excluded: chain D residue 16 ILE Chi-restraints excluded: chain D residue 31 SER Chi-restraints excluded: chain D residue 33 VAL Chi-restraints excluded: chain D residue 53 ASP Chi-restraints excluded: chain D residue 54 VAL Chi-restraints excluded: chain D residue 65 LEU Chi-restraints excluded: chain D residue 77 THR Chi-restraints excluded: chain E residue 11 ILE Chi-restraints excluded: chain E residue 16 VAL Chi-restraints excluded: chain E residue 45 VAL Chi-restraints excluded: chain E residue 52 VAL Chi-restraints excluded: chain E residue 59 VAL Chi-restraints excluded: chain E residue 72 THR Chi-restraints excluded: chain E residue 73 VAL Chi-restraints excluded: chain E residue 140 THR Chi-restraints excluded: chain E residue 144 LEU Chi-restraints excluded: chain E residue 209 ILE Chi-restraints excluded: chain E residue 213 TYR Chi-restraints excluded: chain G residue 4 SER Chi-restraints excluded: chain G residue 22 VAL Chi-restraints excluded: chain G residue 40 VAL Chi-restraints excluded: chain G residue 62 VAL Chi-restraints excluded: chain G residue 73 GLN Chi-restraints excluded: chain G residue 93 VAL Chi-restraints excluded: chain G residue 105 ASN Chi-restraints excluded: chain H residue 39 LEU Chi-restraints excluded: chain H residue 72 ILE Chi-restraints excluded: chain H residue 93 LEU Chi-restraints excluded: chain H residue 139 ILE Chi-restraints excluded: chain H residue 221 GLU Chi-restraints excluded: chain H residue 225 LEU Chi-restraints excluded: chain H residue 253 LEU Chi-restraints excluded: chain H residue 262 LEU Chi-restraints excluded: chain H residue 311 LEU Chi-restraints excluded: chain H residue 321 GLN Chi-restraints excluded: chain H residue 334 HIS Chi-restraints excluded: chain H residue 384 VAL Chi-restraints excluded: chain H residue 412 VAL Chi-restraints excluded: chain H residue 417 VAL Chi-restraints excluded: chain H residue 430 MET Chi-restraints excluded: chain H residue 448 VAL Chi-restraints excluded: chain H residue 450 LEU Chi-restraints excluded: chain H residue 477 ILE Chi-restraints excluded: chain H residue 480 VAL Chi-restraints excluded: chain X residue 8 LEU Chi-restraints excluded: chain X residue 13 ILE Chi-restraints excluded: chain X residue 131 THR Chi-restraints excluded: chain X residue 141 TYR Chi-restraints excluded: chain X residue 205 LEU Chi-restraints excluded: chain X residue 254 PHE Chi-restraints excluded: chain X residue 258 TYR Chi-restraints excluded: chain X residue 289 THR Chi-restraints excluded: chain X residue 299 LEU Chi-restraints excluded: chain X residue 351 VAL Chi-restraints excluded: chain X residue 382 VAL Chi-restraints excluded: chain X residue 398 SER Chi-restraints excluded: chain X residue 401 LEU Chi-restraints excluded: chain X residue 448 VAL Chi-restraints excluded: chain X residue 467 VAL Chi-restraints excluded: chain X residue 532 VAL Chi-restraints excluded: chain X residue 544 VAL Chi-restraints excluded: chain X residue 593 TYR Chi-restraints excluded: chain X residue 606 LEU Chi-restraints excluded: chain X residue 610 LEU Chi-restraints excluded: chain J residue 28 CYS Chi-restraints excluded: chain J residue 41 TYR Chi-restraints excluded: chain J residue 42 ASP Chi-restraints excluded: chain J residue 56 GLN Chi-restraints excluded: chain J residue 67 THR Chi-restraints excluded: chain J residue 74 ILE Chi-restraints excluded: chain J residue 116 VAL Chi-restraints excluded: chain J residue 143 ASN Chi-restraints excluded: chain J residue 154 GLU Chi-restraints excluded: chain J residue 171 TRP Chi-restraints excluded: chain K residue 72 TYR Chi-restraints excluded: chain K residue 81 THR Chi-restraints excluded: chain K residue 85 VAL Chi-restraints excluded: chain K residue 87 THR Chi-restraints excluded: chain K residue 117 ASP Chi-restraints excluded: chain K residue 137 ASP Chi-restraints excluded: chain L residue 82 LEU Chi-restraints excluded: chain L residue 122 MET Chi-restraints excluded: chain L residue 172 THR Chi-restraints excluded: chain L residue 187 LEU Chi-restraints excluded: chain L residue 199 ASP Chi-restraints excluded: chain L residue 211 ASN Chi-restraints excluded: chain L residue 244 VAL Chi-restraints excluded: chain L residue 273 LEU Chi-restraints excluded: chain L residue 318 VAL Chi-restraints excluded: chain L residue 333 ASP Chi-restraints excluded: chain M residue 79 LEU Chi-restraints excluded: chain M residue 95 ASP Chi-restraints excluded: chain M residue 133 LEU Chi-restraints excluded: chain M residue 155 SER Chi-restraints excluded: chain M residue 169 SER Chi-restraints excluded: chain M residue 210 VAL Chi-restraints excluded: chain M residue 212 PHE Chi-restraints excluded: chain M residue 271 LEU Chi-restraints excluded: chain M residue 283 PHE Chi-restraints excluded: chain N residue 20 PHE Chi-restraints excluded: chain N residue 27 LEU Chi-restraints excluded: chain N residue 55 THR Chi-restraints excluded: chain N residue 74 ARG Chi-restraints excluded: chain N residue 79 THR Chi-restraints excluded: chain N residue 81 ILE Chi-restraints excluded: chain N residue 92 ASP Chi-restraints excluded: chain N residue 129 LEU Chi-restraints excluded: chain N residue 132 ASP Chi-restraints excluded: chain N residue 150 ASP Chi-restraints excluded: chain a residue 28 LEU Chi-restraints excluded: chain a residue 39 PHE Chi-restraints excluded: chain a residue 66 TYR Chi-restraints excluded: chain a residue 83 LEU Chi-restraints excluded: chain a residue 85 VAL Chi-restraints excluded: chain a residue 101 VAL Chi-restraints excluded: chain a residue 110 ASN Chi-restraints excluded: chain a residue 156 THR Chi-restraints excluded: chain b residue 27 THR Chi-restraints excluded: chain b residue 29 VAL Chi-restraints excluded: chain b residue 35 VAL Chi-restraints excluded: chain b residue 49 PHE Chi-restraints excluded: chain b residue 70 PHE Chi-restraints excluded: chain b residue 73 VAL Chi-restraints excluded: chain b residue 74 ILE Chi-restraints excluded: chain c residue 16 THR Chi-restraints excluded: chain c residue 23 THR Chi-restraints excluded: chain c residue 34 ASN Chi-restraints excluded: chain c residue 72 ILE Chi-restraints excluded: chain c residue 80 LEU Chi-restraints excluded: chain c residue 113 LEU Chi-restraints excluded: chain c residue 115 ARG Chi-restraints excluded: chain d residue 31 SER Chi-restraints excluded: chain d residue 33 VAL Chi-restraints excluded: chain d residue 53 ASP Chi-restraints excluded: chain d residue 54 VAL Chi-restraints excluded: chain d residue 65 LEU Chi-restraints excluded: chain d residue 72 PHE Chi-restraints excluded: chain d residue 77 THR Chi-restraints excluded: chain e residue 45 VAL Chi-restraints excluded: chain e residue 73 VAL Chi-restraints excluded: chain e residue 140 THR Chi-restraints excluded: chain e residue 180 ILE Chi-restraints excluded: chain e residue 199 ASN Chi-restraints excluded: chain e residue 209 ILE Chi-restraints excluded: chain e residue 213 TYR Chi-restraints excluded: chain e residue 214 THR Chi-restraints excluded: chain g residue 38 THR Chi-restraints excluded: chain g residue 40 VAL Chi-restraints excluded: chain g residue 73 GLN Chi-restraints excluded: chain g residue 93 VAL Chi-restraints excluded: chain g residue 99 GLU Chi-restraints excluded: chain h residue 34 LEU Chi-restraints excluded: chain h residue 39 LEU Chi-restraints excluded: chain h residue 93 LEU Chi-restraints excluded: chain h residue 207 VAL Chi-restraints excluded: chain h residue 221 GLU Chi-restraints excluded: chain h residue 225 LEU Chi-restraints excluded: chain h residue 253 LEU Chi-restraints excluded: chain h residue 262 LEU Chi-restraints excluded: chain h residue 311 LEU Chi-restraints excluded: chain h residue 321 GLN Chi-restraints excluded: chain h residue 334 HIS Chi-restraints excluded: chain h residue 339 THR Chi-restraints excluded: chain h residue 412 VAL Chi-restraints excluded: chain h residue 417 VAL Chi-restraints excluded: chain h residue 450 LEU Chi-restraints excluded: chain h residue 477 ILE Chi-restraints excluded: chain h residue 480 VAL Chi-restraints excluded: chain x residue 8 LEU Chi-restraints excluded: chain x residue 13 ILE Chi-restraints excluded: chain x residue 131 THR Chi-restraints excluded: chain x residue 141 TYR Chi-restraints excluded: chain x residue 205 LEU Chi-restraints excluded: chain x residue 254 PHE Chi-restraints excluded: chain x residue 258 TYR Chi-restraints excluded: chain x residue 289 THR Chi-restraints excluded: chain x residue 299 LEU Chi-restraints excluded: chain x residue 305 LYS Chi-restraints excluded: chain x residue 351 VAL Chi-restraints excluded: chain x residue 382 VAL Chi-restraints excluded: chain x residue 398 SER Chi-restraints excluded: chain x residue 401 LEU Chi-restraints excluded: chain x residue 448 VAL Chi-restraints excluded: chain x residue 467 VAL Chi-restraints excluded: chain x residue 529 VAL Chi-restraints excluded: chain x residue 532 VAL Chi-restraints excluded: chain x residue 544 VAL Chi-restraints excluded: chain x residue 554 ARG Chi-restraints excluded: chain x residue 579 ILE Chi-restraints excluded: chain x residue 606 LEU Chi-restraints excluded: chain x residue 610 LEU Chi-restraints excluded: chain j residue 25 CYS Chi-restraints excluded: chain j residue 41 TYR Chi-restraints excluded: chain j residue 56 GLN Chi-restraints excluded: chain j residue 67 THR Chi-restraints excluded: chain j residue 74 ILE Chi-restraints excluded: chain j residue 114 ILE Chi-restraints excluded: chain j residue 116 VAL Chi-restraints excluded: chain j residue 143 ASN Chi-restraints excluded: chain j residue 154 GLU Chi-restraints excluded: chain j residue 171 TRP Chi-restraints excluded: chain k residue 58 THR Chi-restraints excluded: chain k residue 72 TYR Chi-restraints excluded: chain k residue 81 THR Chi-restraints excluded: chain k residue 85 VAL Chi-restraints excluded: chain k residue 87 THR Chi-restraints excluded: chain k residue 117 ASP Chi-restraints excluded: chain k residue 137 ASP Chi-restraints excluded: chain l residue 82 LEU Chi-restraints excluded: chain l residue 117 THR Chi-restraints excluded: chain l residue 126 THR Chi-restraints excluded: chain l residue 172 THR Chi-restraints excluded: chain l residue 187 LEU Chi-restraints excluded: chain l residue 199 ASP Chi-restraints excluded: chain l residue 211 ASN Chi-restraints excluded: chain l residue 244 VAL Chi-restraints excluded: chain l residue 260 LEU Chi-restraints excluded: chain l residue 318 VAL Chi-restraints excluded: chain m residue 95 ASP Chi-restraints excluded: chain m residue 103 LEU Chi-restraints excluded: chain m residue 133 LEU Chi-restraints excluded: chain m residue 155 SER Chi-restraints excluded: chain m residue 169 SER Chi-restraints excluded: chain m residue 210 VAL Chi-restraints excluded: chain m residue 212 PHE Chi-restraints excluded: chain m residue 226 MET Chi-restraints excluded: chain m residue 271 LEU Chi-restraints excluded: chain m residue 274 ILE Chi-restraints excluded: chain m residue 283 PHE Chi-restraints excluded: chain m residue 306 MET Chi-restraints excluded: chain n residue 55 THR Chi-restraints excluded: chain n residue 74 ARG Chi-restraints excluded: chain n residue 79 THR Chi-restraints excluded: chain n residue 81 ILE Chi-restraints excluded: chain n residue 129 LEU Chi-restraints excluded: chain n residue 156 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 604 random chunks: chunk 486 optimal weight: 5.9990 chunk 331 optimal weight: 5.9990 chunk 8 optimal weight: 3.9990 chunk 434 optimal weight: 0.9980 chunk 240 optimal weight: 7.9990 chunk 498 optimal weight: 0.9990 chunk 403 optimal weight: 3.9990 chunk 0 optimal weight: 10.0000 chunk 298 optimal weight: 6.9990 chunk 524 optimal weight: 2.9990 chunk 147 optimal weight: 0.9980 overall best weight: 1.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 41 ASN ** H 226 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 163 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 126 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 34 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 223 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** e 123 HIS ** k 126 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7825 moved from start: 0.3043 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 49624 Z= 0.258 Angle : 0.732 14.367 67458 Z= 0.362 Chirality : 0.044 0.229 7768 Planarity : 0.005 0.066 8248 Dihedral : 6.032 58.150 6665 Min Nonbonded Distance : 2.070 Molprobity Statistics. All-atom Clashscore : 17.91 Ramachandran Plot: Outliers : 0.07 % Allowed : 11.43 % Favored : 88.50 % Rotamer: Outliers : 6.45 % Allowed : 25.16 % Favored : 68.39 % 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: -3.06 (0.10), residues: 6072 helix: -0.80 (0.09), residues: 3470 sheet: -3.29 (0.32), residues: 210 loop : -3.84 (0.11), residues: 2392 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP k 62 HIS 0.004 0.001 HIS X 340 PHE 0.036 0.002 PHE H 247 TYR 0.027 0.002 TYR e 152 ARG 0.007 0.000 ARG M 91 *********************** 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 1323 residues out of total 5044 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 325 poor density : 998 time to evaluate : 5.739 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 21 TRP cc_start: 0.7597 (t-100) cc_final: 0.7361 (t60) REVERT: B 67 ILE cc_start: 0.7759 (mp) cc_final: 0.7490 (tp) REVERT: B 76 PHE cc_start: 0.6995 (m-80) cc_final: 0.6579 (m-80) REVERT: C 18 PHE cc_start: 0.7163 (t80) cc_final: 0.6947 (t80) REVERT: D 38 VAL cc_start: 0.8733 (t) cc_final: 0.8481 (p) REVERT: D 70 PHE cc_start: 0.8070 (t80) cc_final: 0.7380 (t80) REVERT: E 120 ILE cc_start: 0.8567 (mm) cc_final: 0.8239 (mt) REVERT: E 145 MET cc_start: 0.7877 (tpt) cc_final: 0.7592 (tpp) REVERT: E 147 LEU cc_start: 0.9061 (tp) cc_final: 0.8845 (tp) REVERT: G 99 GLU cc_start: 0.7589 (tp30) cc_final: 0.7324 (tp30) REVERT: H 79 PHE cc_start: 0.8441 (t80) cc_final: 0.8139 (t80) REVERT: H 112 MET cc_start: 0.7298 (ptp) cc_final: 0.6364 (ptp) REVERT: H 190 MET cc_start: 0.8803 (mtt) cc_final: 0.8550 (mtm) REVERT: H 254 TYR cc_start: 0.8143 (t80) cc_final: 0.7757 (t80) REVERT: H 300 MET cc_start: 0.7580 (ttt) cc_final: 0.7283 (ttt) REVERT: H 388 ASN cc_start: 0.7740 (OUTLIER) cc_final: 0.6765 (p0) REVERT: H 395 ARG cc_start: 0.8554 (mmm-85) cc_final: 0.8285 (mmt180) REVERT: H 422 TYR cc_start: 0.8276 (p90) cc_final: 0.8068 (p90) REVERT: H 454 MET cc_start: 0.6850 (mmp) cc_final: 0.6550 (tmm) REVERT: X 136 MET cc_start: 0.8006 (tpt) cc_final: 0.7758 (tpt) REVERT: X 310 SER cc_start: 0.9354 (OUTLIER) cc_final: 0.9144 (p) REVERT: X 379 MET cc_start: 0.7133 (mmt) cc_final: 0.6701 (mmt) REVERT: X 546 MET cc_start: 0.6965 (ppp) cc_final: 0.6597 (ppp) REVERT: J 42 ASP cc_start: 0.7801 (OUTLIER) cc_final: 0.7532 (p0) REVERT: L 26 TYR cc_start: 0.8881 (p90) cc_final: 0.8478 (p90) REVERT: L 93 GLU cc_start: 0.8195 (pt0) cc_final: 0.7148 (pt0) REVERT: L 96 TYR cc_start: 0.8889 (t80) cc_final: 0.8515 (t80) REVERT: L 133 MET cc_start: 0.8136 (tmm) cc_final: 0.7843 (tmm) REVERT: L 160 GLU cc_start: 0.7824 (tm-30) cc_final: 0.7598 (tm-30) REVERT: L 187 LEU cc_start: 0.9205 (OUTLIER) cc_final: 0.8960 (mm) REVERT: M 35 ARG cc_start: 0.8607 (mtt-85) cc_final: 0.8225 (mtp85) REVERT: M 103 LEU cc_start: 0.8965 (OUTLIER) cc_final: 0.8632 (mp) REVERT: M 104 GLU cc_start: 0.7541 (mt-10) cc_final: 0.6842 (mt-10) REVERT: M 133 LEU cc_start: 0.9007 (OUTLIER) cc_final: 0.8710 (tp) REVERT: M 137 GLN cc_start: 0.8700 (mm-40) cc_final: 0.7829 (mm-40) REVERT: M 158 GLU cc_start: 0.8373 (mp0) cc_final: 0.8125 (mp0) REVERT: M 226 MET cc_start: 0.8323 (mmp) cc_final: 0.7997 (mmp) REVERT: M 290 LYS cc_start: 0.8727 (ttmt) cc_final: 0.8183 (tptt) REVERT: M 295 TRP cc_start: 0.8196 (m100) cc_final: 0.7987 (m100) REVERT: N 27 LEU cc_start: 0.9430 (OUTLIER) cc_final: 0.9226 (tt) REVERT: N 74 ARG cc_start: 0.9130 (OUTLIER) cc_final: 0.8632 (tpt90) REVERT: N 132 ASP cc_start: 0.7539 (OUTLIER) cc_final: 0.6981 (t0) REVERT: a 78 MET cc_start: 0.8171 (mpp) cc_final: 0.7968 (mtm) REVERT: a 91 HIS cc_start: 0.4399 (OUTLIER) cc_final: 0.4115 (t-170) REVERT: a 114 MET cc_start: 0.7120 (mtt) cc_final: 0.6899 (tpp) REVERT: a 130 ASP cc_start: 0.7841 (t0) cc_final: 0.7506 (t0) REVERT: b 67 ILE cc_start: 0.7802 (mp) cc_final: 0.7417 (tp) REVERT: d 53 ASP cc_start: 0.7906 (OUTLIER) cc_final: 0.7653 (m-30) REVERT: d 70 PHE cc_start: 0.7972 (t80) cc_final: 0.7455 (t80) REVERT: e 146 TYR cc_start: 0.8294 (t80) cc_final: 0.7449 (t80) REVERT: e 168 MET cc_start: 0.5530 (mtt) cc_final: 0.4892 (mtp) REVERT: e 219 LYS cc_start: 0.9052 (tttp) cc_final: 0.8756 (ttpp) REVERT: g 73 GLN cc_start: 0.8023 (OUTLIER) cc_final: 0.7647 (mp10) REVERT: g 100 LYS cc_start: 0.9020 (mmtm) cc_final: 0.8784 (mmtt) REVERT: h 18 PHE cc_start: 0.6773 (t80) cc_final: 0.6543 (t80) REVERT: h 96 LEU cc_start: 0.8046 (pp) cc_final: 0.7840 (pp) REVERT: h 112 MET cc_start: 0.7076 (ptp) cc_final: 0.6158 (ptp) REVERT: h 129 ASP cc_start: 0.7770 (OUTLIER) cc_final: 0.7487 (t0) REVERT: h 158 GLU cc_start: 0.8679 (tm-30) cc_final: 0.8362 (tm-30) REVERT: h 207 VAL cc_start: 0.9197 (OUTLIER) cc_final: 0.8953 (p) REVERT: h 262 LEU cc_start: 0.8403 (OUTLIER) cc_final: 0.7958 (mt) REVERT: h 342 PHE cc_start: 0.8246 (m-80) cc_final: 0.8024 (m-80) REVERT: h 422 TYR cc_start: 0.8368 (p90) cc_final: 0.8068 (p90) REVERT: h 450 LEU cc_start: 0.7845 (OUTLIER) cc_final: 0.7633 (mm) REVERT: h 454 MET cc_start: 0.6680 (mmp) cc_final: 0.6412 (ppp) REVERT: x 216 VAL cc_start: 0.8392 (m) cc_final: 0.7850 (t) REVERT: x 300 GLN cc_start: 0.9123 (tp-100) cc_final: 0.8581 (tp-100) REVERT: x 305 LYS cc_start: 0.8894 (OUTLIER) cc_final: 0.8192 (ttpp) REVERT: x 379 MET cc_start: 0.7253 (mmt) cc_final: 0.6751 (mmt) REVERT: x 546 MET cc_start: 0.6834 (OUTLIER) cc_final: 0.6604 (ppp) REVERT: k 145 HIS cc_start: 0.7712 (m-70) cc_final: 0.7121 (m-70) REVERT: l 96 TYR cc_start: 0.8901 (t80) cc_final: 0.8550 (t80) REVERT: l 133 MET cc_start: 0.8240 (tmm) cc_final: 0.7975 (tmm) REVERT: l 187 LEU cc_start: 0.9140 (OUTLIER) cc_final: 0.8872 (mm) REVERT: m 69 ILE cc_start: 0.8641 (mm) cc_final: 0.8339 (tp) REVERT: m 103 LEU cc_start: 0.8989 (OUTLIER) cc_final: 0.8712 (mp) REVERT: m 133 LEU cc_start: 0.8912 (OUTLIER) cc_final: 0.8424 (tp) REVERT: m 137 GLN cc_start: 0.8750 (mm-40) cc_final: 0.8073 (mm-40) REVERT: m 158 GLU cc_start: 0.8051 (mp0) cc_final: 0.7806 (mm-30) REVERT: m 186 LEU cc_start: 0.9024 (mt) cc_final: 0.8773 (tt) REVERT: m 266 GLN cc_start: 0.8538 (mm-40) cc_final: 0.8317 (mm-40) REVERT: m 290 LYS cc_start: 0.8840 (ttmt) cc_final: 0.8212 (tptt) REVERT: n 74 ARG cc_start: 0.9087 (OUTLIER) cc_final: 0.8626 (tpt90) REVERT: n 132 ASP cc_start: 0.7780 (t0) cc_final: 0.7086 (t70) outliers start: 325 outliers final: 228 residues processed: 1216 average time/residue: 0.5376 time to fit residues: 1120.8862 Evaluate side-chains 1191 residues out of total 5044 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 250 poor density : 941 time to evaluate : 4.833 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 THR Chi-restraints excluded: chain A residue 28 LEU Chi-restraints excluded: chain A residue 66 TYR Chi-restraints excluded: chain A residue 73 TYR Chi-restraints excluded: chain A residue 83 LEU Chi-restraints excluded: chain A residue 85 VAL Chi-restraints excluded: chain A residue 101 VAL Chi-restraints excluded: chain A residue 110 ASN Chi-restraints excluded: chain A residue 156 THR Chi-restraints excluded: chain B residue 6 ILE Chi-restraints excluded: chain B residue 22 VAL Chi-restraints excluded: chain B residue 29 VAL Chi-restraints excluded: chain B residue 35 VAL Chi-restraints excluded: chain B residue 74 ILE Chi-restraints excluded: chain C residue 23 THR Chi-restraints excluded: chain C residue 34 ASN Chi-restraints excluded: chain C residue 63 PHE Chi-restraints excluded: chain C residue 79 LEU Chi-restraints excluded: chain C residue 80 LEU Chi-restraints excluded: chain D residue 16 ILE Chi-restraints excluded: chain D residue 53 ASP Chi-restraints excluded: chain D residue 54 VAL Chi-restraints excluded: chain D residue 65 LEU Chi-restraints excluded: chain D residue 77 THR Chi-restraints excluded: chain E residue 11 ILE Chi-restraints excluded: chain E residue 16 VAL Chi-restraints excluded: chain E residue 45 VAL Chi-restraints excluded: chain E residue 72 THR Chi-restraints excluded: chain E residue 73 VAL Chi-restraints excluded: chain E residue 140 THR Chi-restraints excluded: chain E residue 144 LEU Chi-restraints excluded: chain E residue 175 LEU Chi-restraints excluded: chain E residue 180 ILE Chi-restraints excluded: chain E residue 209 ILE Chi-restraints excluded: chain E residue 213 TYR Chi-restraints excluded: chain G residue 22 VAL Chi-restraints excluded: chain G residue 38 THR Chi-restraints excluded: chain G residue 40 VAL Chi-restraints excluded: chain G residue 93 VAL Chi-restraints excluded: chain G residue 105 ASN Chi-restraints excluded: chain H residue 39 LEU Chi-restraints excluded: chain H residue 59 ILE Chi-restraints excluded: chain H residue 72 ILE Chi-restraints excluded: chain H residue 93 LEU Chi-restraints excluded: chain H residue 129 ASP Chi-restraints excluded: chain H residue 139 ILE Chi-restraints excluded: chain H residue 225 LEU Chi-restraints excluded: chain H residue 253 LEU Chi-restraints excluded: chain H residue 279 MET Chi-restraints excluded: chain H residue 311 LEU Chi-restraints excluded: chain H residue 321 GLN Chi-restraints excluded: chain H residue 334 HIS Chi-restraints excluded: chain H residue 384 VAL Chi-restraints excluded: chain H residue 388 ASN Chi-restraints excluded: chain H residue 423 TYR Chi-restraints excluded: chain H residue 430 MET Chi-restraints excluded: chain H residue 450 LEU Chi-restraints excluded: chain H residue 477 ILE Chi-restraints excluded: chain H residue 480 VAL Chi-restraints excluded: chain X residue 13 ILE Chi-restraints excluded: chain X residue 131 THR Chi-restraints excluded: chain X residue 141 TYR Chi-restraints excluded: chain X residue 154 ILE Chi-restraints excluded: chain X residue 205 LEU Chi-restraints excluded: chain X residue 258 TYR Chi-restraints excluded: chain X residue 289 THR Chi-restraints excluded: chain X residue 299 LEU Chi-restraints excluded: chain X residue 310 SER Chi-restraints excluded: chain X residue 351 VAL Chi-restraints excluded: chain X residue 382 VAL Chi-restraints excluded: chain X residue 398 SER Chi-restraints excluded: chain X residue 401 LEU Chi-restraints excluded: chain X residue 448 VAL Chi-restraints excluded: chain X residue 467 VAL Chi-restraints excluded: chain X residue 514 ILE Chi-restraints excluded: chain X residue 529 VAL Chi-restraints excluded: chain X residue 532 VAL Chi-restraints excluded: chain X residue 544 VAL Chi-restraints excluded: chain X residue 593 TYR Chi-restraints excluded: chain X residue 606 LEU Chi-restraints excluded: chain X residue 610 LEU Chi-restraints excluded: chain J residue 41 TYR Chi-restraints excluded: chain J residue 42 ASP Chi-restraints excluded: chain J residue 61 LEU Chi-restraints excluded: chain J residue 67 THR Chi-restraints excluded: chain J residue 74 ILE Chi-restraints excluded: chain J residue 116 VAL Chi-restraints excluded: chain J residue 120 ILE Chi-restraints excluded: chain J residue 143 ASN Chi-restraints excluded: chain J residue 171 TRP Chi-restraints excluded: chain K residue 71 VAL Chi-restraints excluded: chain K residue 81 THR Chi-restraints excluded: chain K residue 85 VAL Chi-restraints excluded: chain K residue 87 THR Chi-restraints excluded: chain K residue 117 ASP Chi-restraints excluded: chain K residue 137 ASP Chi-restraints excluded: chain L residue 81 LEU Chi-restraints excluded: chain L residue 82 LEU Chi-restraints excluded: chain L residue 126 THR Chi-restraints excluded: chain L residue 187 LEU Chi-restraints excluded: chain L residue 199 ASP Chi-restraints excluded: chain L residue 211 ASN Chi-restraints excluded: chain L residue 239 LEU Chi-restraints excluded: chain L residue 244 VAL Chi-restraints excluded: chain L residue 318 VAL Chi-restraints excluded: chain L residue 333 ASP Chi-restraints excluded: chain M residue 49 LEU Chi-restraints excluded: chain M residue 79 LEU Chi-restraints excluded: chain M residue 95 ASP Chi-restraints excluded: chain M residue 103 LEU Chi-restraints excluded: chain M residue 133 LEU Chi-restraints excluded: chain M residue 155 SER Chi-restraints excluded: chain M residue 169 SER Chi-restraints excluded: chain M residue 212 PHE Chi-restraints excluded: chain M residue 283 PHE Chi-restraints excluded: chain N residue 20 PHE Chi-restraints excluded: chain N residue 27 LEU Chi-restraints excluded: chain N residue 44 ILE Chi-restraints excluded: chain N residue 55 THR Chi-restraints excluded: chain N residue 74 ARG Chi-restraints excluded: chain N residue 81 ILE Chi-restraints excluded: chain N residue 92 ASP Chi-restraints excluded: chain N residue 129 LEU Chi-restraints excluded: chain N residue 132 ASP Chi-restraints excluded: chain a residue 28 LEU Chi-restraints excluded: chain a residue 39 PHE Chi-restraints excluded: chain a residue 66 TYR Chi-restraints excluded: chain a residue 85 VAL Chi-restraints excluded: chain a residue 91 HIS Chi-restraints excluded: chain a residue 101 VAL Chi-restraints excluded: chain a residue 110 ASN Chi-restraints excluded: chain a residue 132 ASP Chi-restraints excluded: chain a residue 156 THR Chi-restraints excluded: chain b residue 29 VAL Chi-restraints excluded: chain b residue 35 VAL Chi-restraints excluded: chain b residue 70 PHE Chi-restraints excluded: chain b residue 74 ILE Chi-restraints excluded: chain c residue 19 TYR Chi-restraints excluded: chain c residue 23 THR Chi-restraints excluded: chain c residue 34 ASN Chi-restraints excluded: chain c residue 80 LEU Chi-restraints excluded: chain c residue 113 LEU Chi-restraints excluded: chain c residue 115 ARG Chi-restraints excluded: chain d residue 8 GLU Chi-restraints excluded: chain d residue 53 ASP Chi-restraints excluded: chain d residue 54 VAL Chi-restraints excluded: chain d residue 65 LEU Chi-restraints excluded: chain d residue 72 PHE Chi-restraints excluded: chain d residue 77 THR Chi-restraints excluded: chain e residue 45 VAL Chi-restraints excluded: chain e residue 101 VAL Chi-restraints excluded: chain e residue 140 THR Chi-restraints excluded: chain e residue 144 LEU Chi-restraints excluded: chain e residue 175 LEU Chi-restraints excluded: chain e residue 180 ILE Chi-restraints excluded: chain e residue 209 ILE Chi-restraints excluded: chain e residue 213 TYR Chi-restraints excluded: chain e residue 214 THR Chi-restraints excluded: chain e residue 227 ILE Chi-restraints excluded: chain g residue 40 VAL Chi-restraints excluded: chain g residue 73 GLN Chi-restraints excluded: chain g residue 86 THR Chi-restraints excluded: chain g residue 105 ASN Chi-restraints excluded: chain h residue 34 LEU Chi-restraints excluded: chain h residue 39 LEU Chi-restraints excluded: chain h residue 59 ILE Chi-restraints excluded: chain h residue 72 ILE Chi-restraints excluded: chain h residue 93 LEU Chi-restraints excluded: chain h residue 129 ASP Chi-restraints excluded: chain h residue 207 VAL Chi-restraints excluded: chain h residue 221 GLU Chi-restraints excluded: chain h residue 225 LEU Chi-restraints excluded: chain h residue 253 LEU Chi-restraints excluded: chain h residue 262 LEU Chi-restraints excluded: chain h residue 311 LEU Chi-restraints excluded: chain h residue 321 GLN Chi-restraints excluded: chain h residue 334 HIS Chi-restraints excluded: chain h residue 423 TYR Chi-restraints excluded: chain h residue 450 LEU Chi-restraints excluded: chain h residue 477 ILE Chi-restraints excluded: chain h residue 480 VAL Chi-restraints excluded: chain x residue 8 LEU Chi-restraints excluded: chain x residue 13 ILE Chi-restraints excluded: chain x residue 131 THR Chi-restraints excluded: chain x residue 141 TYR Chi-restraints excluded: chain x residue 154 ILE Chi-restraints excluded: chain x residue 205 LEU Chi-restraints excluded: chain x residue 258 TYR Chi-restraints excluded: chain x residue 299 LEU Chi-restraints excluded: chain x residue 305 LYS Chi-restraints excluded: chain x residue 310 SER Chi-restraints excluded: chain x residue 351 VAL Chi-restraints excluded: chain x residue 382 VAL Chi-restraints excluded: chain x residue 398 SER Chi-restraints excluded: chain x residue 401 LEU Chi-restraints excluded: chain x residue 448 VAL Chi-restraints excluded: chain x residue 467 VAL Chi-restraints excluded: chain x residue 514 ILE Chi-restraints excluded: chain x residue 529 VAL Chi-restraints excluded: chain x residue 532 VAL Chi-restraints excluded: chain x residue 544 VAL Chi-restraints excluded: chain x residue 546 MET Chi-restraints excluded: chain x residue 554 ARG Chi-restraints excluded: chain x residue 579 ILE Chi-restraints excluded: chain x residue 606 LEU Chi-restraints excluded: chain j residue 25 CYS Chi-restraints excluded: chain j residue 41 TYR Chi-restraints excluded: chain j residue 56 GLN Chi-restraints excluded: chain j residue 61 LEU Chi-restraints excluded: chain j residue 67 THR Chi-restraints excluded: chain j residue 74 ILE Chi-restraints excluded: chain j residue 114 ILE Chi-restraints excluded: chain j residue 116 VAL Chi-restraints excluded: chain j residue 120 ILE Chi-restraints excluded: chain j residue 143 ASN Chi-restraints excluded: chain j residue 154 GLU Chi-restraints excluded: chain j residue 171 TRP Chi-restraints excluded: chain k residue 58 THR Chi-restraints excluded: chain k residue 72 TYR Chi-restraints excluded: chain k residue 81 THR Chi-restraints excluded: chain k residue 85 VAL Chi-restraints excluded: chain k residue 87 THR Chi-restraints excluded: chain k residue 100 THR Chi-restraints excluded: chain k residue 117 ASP Chi-restraints excluded: chain k residue 137 ASP Chi-restraints excluded: chain l residue 126 THR Chi-restraints excluded: chain l residue 167 VAL Chi-restraints excluded: chain l residue 187 LEU Chi-restraints excluded: chain l residue 197 LEU Chi-restraints excluded: chain l residue 199 ASP Chi-restraints excluded: chain l residue 211 ASN Chi-restraints excluded: chain l residue 235 THR Chi-restraints excluded: chain l residue 244 VAL Chi-restraints excluded: chain l residue 273 LEU Chi-restraints excluded: chain l residue 318 VAL Chi-restraints excluded: chain m residue 23 MET Chi-restraints excluded: chain m residue 95 ASP Chi-restraints excluded: chain m residue 103 LEU Chi-restraints excluded: chain m residue 133 LEU Chi-restraints excluded: chain m residue 155 SER Chi-restraints excluded: chain m residue 169 SER Chi-restraints excluded: chain m residue 226 MET Chi-restraints excluded: chain m residue 274 ILE Chi-restraints excluded: chain m residue 283 PHE Chi-restraints excluded: chain m residue 306 MET Chi-restraints excluded: chain n residue 55 THR Chi-restraints excluded: chain n residue 74 ARG Chi-restraints excluded: chain n residue 79 THR Chi-restraints excluded: chain n residue 81 ILE Chi-restraints excluded: chain n residue 92 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 604 random chunks: chunk 196 optimal weight: 2.9990 chunk 525 optimal weight: 6.9990 chunk 115 optimal weight: 0.9980 chunk 342 optimal weight: 9.9990 chunk 144 optimal weight: 3.9990 chunk 584 optimal weight: 4.9990 chunk 485 optimal weight: 0.8980 chunk 270 optimal weight: 4.9990 chunk 48 optimal weight: 2.9990 chunk 193 optimal weight: 2.9990 chunk 306 optimal weight: 4.9990 overall best weight: 2.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 91 HIS G 41 ASN ** H 226 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 163 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 126 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 33 GLN ** L 34 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 113 GLN ** M 223 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 118 ASN ** k 126 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** l 33 GLN l 113 GLN m 57 ASN m 127 GLN ** m 223 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7829 moved from start: 0.3211 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= 0.268 Angle : 0.742 13.618 67458 Z= 0.365 Chirality : 0.044 0.187 7768 Planarity : 0.005 0.058 8248 Dihedral : 5.883 59.246 6659 Min Nonbonded Distance : 2.074 Molprobity Statistics. All-atom Clashscore : 18.18 Ramachandran Plot: Outliers : 0.05 % Allowed : 11.78 % Favored : 88.18 % Rotamer: Outliers : 6.79 % Allowed : 26.05 % Favored : 67.16 % 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: -2.90 (0.11), residues: 6072 helix: -0.66 (0.09), residues: 3468 sheet: -3.34 (0.32), residues: 210 loop : -3.77 (0.11), residues: 2394 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP k 62 HIS 0.005 0.001 HIS X 340 PHE 0.037 0.002 PHE H 247 TYR 0.023 0.002 TYR h 422 ARG 0.009 0.000 ARG C 35 *********************** 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 1333 residues out of total 5044 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 342 poor density : 991 time to evaluate : 5.342 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 67 ILE cc_start: 0.7656 (OUTLIER) cc_final: 0.7413 (tp) REVERT: C 19 TYR cc_start: 0.7454 (OUTLIER) cc_final: 0.7037 (m-10) REVERT: D 38 VAL cc_start: 0.8734 (t) cc_final: 0.8482 (p) REVERT: D 70 PHE cc_start: 0.8046 (t80) cc_final: 0.7393 (t80) REVERT: E 120 ILE cc_start: 0.8498 (mm) cc_final: 0.8174 (mt) REVERT: E 145 MET cc_start: 0.7850 (tpt) cc_final: 0.7524 (tpp) REVERT: G 73 GLN cc_start: 0.8067 (mp10) cc_final: 0.7788 (mp10) REVERT: G 99 GLU cc_start: 0.7578 (tp30) cc_final: 0.7345 (tp30) REVERT: H 79 PHE cc_start: 0.8381 (t80) cc_final: 0.7962 (t80) REVERT: H 112 MET cc_start: 0.7306 (ptp) cc_final: 0.6359 (ptp) REVERT: H 129 ASP cc_start: 0.7695 (OUTLIER) cc_final: 0.7456 (t0) REVERT: H 254 TYR cc_start: 0.8137 (t80) cc_final: 0.7760 (t80) REVERT: H 300 MET cc_start: 0.7654 (ttt) cc_final: 0.7357 (ttt) REVERT: H 388 ASN cc_start: 0.7792 (OUTLIER) cc_final: 0.6798 (p0) REVERT: H 395 ARG cc_start: 0.8602 (mmm-85) cc_final: 0.8381 (mmt180) REVERT: H 454 MET cc_start: 0.6848 (mmp) cc_final: 0.6582 (tmm) REVERT: X 136 MET cc_start: 0.7954 (tpt) cc_final: 0.7722 (tpt) REVERT: X 310 SER cc_start: 0.9368 (OUTLIER) cc_final: 0.9130 (p) REVERT: X 379 MET cc_start: 0.7149 (mmt) cc_final: 0.6685 (mmt) REVERT: X 546 MET cc_start: 0.6954 (ppp) cc_final: 0.6586 (ppp) REVERT: J 42 ASP cc_start: 0.7864 (OUTLIER) cc_final: 0.7495 (p0) REVERT: J 141 ILE cc_start: 0.9144 (tp) cc_final: 0.8900 (tp) REVERT: K 50 ASN cc_start: 0.8107 (p0) cc_final: 0.7843 (p0) REVERT: L 26 TYR cc_start: 0.8881 (p90) cc_final: 0.8509 (p90) REVERT: L 93 GLU cc_start: 0.8225 (pt0) cc_final: 0.7150 (pt0) REVERT: L 96 TYR cc_start: 0.8892 (t80) cc_final: 0.8525 (t80) REVERT: L 133 MET cc_start: 0.8159 (tmm) cc_final: 0.7864 (tmm) REVERT: L 160 GLU cc_start: 0.7831 (tm-30) cc_final: 0.7599 (tm-30) REVERT: L 187 LEU cc_start: 0.9208 (OUTLIER) cc_final: 0.8963 (mm) REVERT: M 35 ARG cc_start: 0.8635 (mtt-85) cc_final: 0.8223 (mtp85) REVERT: M 103 LEU cc_start: 0.8915 (OUTLIER) cc_final: 0.8626 (mp) REVERT: M 104 GLU cc_start: 0.7580 (mt-10) cc_final: 0.7082 (mt-10) REVERT: M 112 PHE cc_start: 0.8344 (t80) cc_final: 0.8046 (t80) REVERT: M 115 MET cc_start: 0.7654 (ttm) cc_final: 0.7119 (ttm) REVERT: M 133 LEU cc_start: 0.8971 (OUTLIER) cc_final: 0.8535 (tp) REVERT: M 158 GLU cc_start: 0.8392 (mp0) cc_final: 0.8116 (mp0) REVERT: M 209 MET cc_start: 0.8550 (pmm) cc_final: 0.8272 (pmm) REVERT: M 226 MET cc_start: 0.8326 (mmp) cc_final: 0.8075 (mmp) REVERT: M 265 LYS cc_start: 0.9046 (OUTLIER) cc_final: 0.8706 (mtpp) REVERT: M 290 LYS cc_start: 0.8733 (ttmt) cc_final: 0.8225 (tptt) REVERT: N 74 ARG cc_start: 0.9135 (OUTLIER) cc_final: 0.8758 (tpt90) REVERT: N 95 ARG cc_start: 0.8576 (OUTLIER) cc_final: 0.7390 (ptp90) REVERT: N 132 ASP cc_start: 0.7563 (OUTLIER) cc_final: 0.6984 (t70) REVERT: a 21 TRP cc_start: 0.7487 (t60) cc_final: 0.7285 (t60) REVERT: a 78 MET cc_start: 0.8196 (mpp) cc_final: 0.7879 (mtm) REVERT: a 91 HIS cc_start: 0.4418 (OUTLIER) cc_final: 0.4145 (t-170) REVERT: a 130 ASP cc_start: 0.7863 (t0) cc_final: 0.7480 (t0) REVERT: b 49 PHE cc_start: 0.7151 (OUTLIER) cc_final: 0.6866 (m-10) REVERT: b 67 ILE cc_start: 0.7703 (mp) cc_final: 0.7361 (tp) REVERT: d 14 LEU cc_start: 0.8966 (tp) cc_final: 0.8744 (tp) REVERT: d 53 ASP cc_start: 0.7886 (OUTLIER) cc_final: 0.7626 (m-30) REVERT: d 70 PHE cc_start: 0.7970 (t80) cc_final: 0.7420 (t80) REVERT: e 146 TYR cc_start: 0.8246 (t80) cc_final: 0.7558 (t80) REVERT: e 168 MET cc_start: 0.5535 (mtt) cc_final: 0.4926 (mtp) REVERT: e 219 LYS cc_start: 0.9064 (tttp) cc_final: 0.8350 (tmmt) REVERT: g 24 LYS cc_start: 0.8157 (mttp) cc_final: 0.7904 (mmtp) REVERT: g 73 GLN cc_start: 0.8118 (OUTLIER) cc_final: 0.7877 (mp10) REVERT: g 100 LYS cc_start: 0.8911 (mmtm) cc_final: 0.8697 (mmtt) REVERT: h 18 PHE cc_start: 0.6733 (t80) cc_final: 0.6526 (t80) REVERT: h 112 MET cc_start: 0.7076 (ptp) cc_final: 0.6143 (ptp) REVERT: h 129 ASP cc_start: 0.7733 (OUTLIER) cc_final: 0.7493 (t0) REVERT: h 158 GLU cc_start: 0.8675 (tm-30) cc_final: 0.8359 (tm-30) REVERT: h 207 VAL cc_start: 0.9233 (OUTLIER) cc_final: 0.8995 (p) REVERT: h 258 ARG cc_start: 0.8018 (tpp80) cc_final: 0.7713 (ttt180) REVERT: h 279 MET cc_start: 0.7215 (mmp) cc_final: 0.6688 (mtp) REVERT: h 342 PHE cc_start: 0.8178 (m-80) cc_final: 0.7933 (m-80) REVERT: h 450 LEU cc_start: 0.7837 (OUTLIER) cc_final: 0.7616 (mm) REVERT: h 454 MET cc_start: 0.6620 (mmp) cc_final: 0.6402 (ppp) REVERT: x 300 GLN cc_start: 0.9119 (tp-100) cc_final: 0.8634 (tp-100) REVERT: x 305 LYS cc_start: 0.8896 (OUTLIER) cc_final: 0.8231 (ttpp) REVERT: x 310 SER cc_start: 0.9359 (OUTLIER) cc_final: 0.9091 (p) REVERT: x 434 TYR cc_start: 0.7771 (t80) cc_final: 0.7521 (t80) REVERT: x 546 MET cc_start: 0.6837 (OUTLIER) cc_final: 0.6614 (ppp) REVERT: j 141 ILE cc_start: 0.9159 (tp) cc_final: 0.8860 (tp) REVERT: l 93 GLU cc_start: 0.8192 (pt0) cc_final: 0.7383 (pt0) REVERT: l 96 TYR cc_start: 0.8826 (t80) cc_final: 0.8490 (t80) REVERT: l 166 ARG cc_start: 0.8454 (OUTLIER) cc_final: 0.8123 (mmm-85) REVERT: l 187 LEU cc_start: 0.9153 (OUTLIER) cc_final: 0.8728 (mm) REVERT: m 69 ILE cc_start: 0.8653 (mm) cc_final: 0.8350 (tp) REVERT: m 103 LEU cc_start: 0.8965 (OUTLIER) cc_final: 0.8680 (mp) REVERT: m 133 LEU cc_start: 0.8902 (OUTLIER) cc_final: 0.8365 (tp) REVERT: m 186 LEU cc_start: 0.9027 (mt) cc_final: 0.8804 (tt) REVERT: m 209 MET cc_start: 0.8535 (pmm) cc_final: 0.8101 (pmm) REVERT: m 266 GLN cc_start: 0.8472 (mm-40) cc_final: 0.8217 (mm-40) REVERT: m 290 LYS cc_start: 0.8852 (ttmt) cc_final: 0.8254 (tptt) REVERT: n 8 ILE cc_start: 0.8571 (mm) cc_final: 0.8296 (mt) REVERT: n 74 ARG cc_start: 0.9115 (OUTLIER) cc_final: 0.8718 (tpt90) REVERT: n 132 ASP cc_start: 0.7777 (t0) cc_final: 0.7110 (t70) outliers start: 342 outliers final: 253 residues processed: 1222 average time/residue: 0.5505 time to fit residues: 1149.8317 Evaluate side-chains 1231 residues out of total 5044 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 281 poor density : 950 time to evaluate : 6.019 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 LEU Chi-restraints excluded: chain A residue 75 LEU Chi-restraints excluded: chain A residue 83 LEU Chi-restraints excluded: chain A residue 85 VAL Chi-restraints excluded: chain A residue 101 VAL Chi-restraints excluded: chain A residue 110 ASN Chi-restraints excluded: chain A residue 132 ASP Chi-restraints excluded: chain A residue 156 THR Chi-restraints excluded: chain B residue 6 ILE Chi-restraints excluded: chain B residue 22 VAL Chi-restraints excluded: chain B residue 27 THR Chi-restraints excluded: chain B residue 29 VAL Chi-restraints excluded: chain B residue 35 VAL Chi-restraints excluded: chain B residue 67 ILE Chi-restraints excluded: chain B residue 74 ILE Chi-restraints excluded: chain C residue 19 TYR Chi-restraints excluded: chain C residue 23 THR Chi-restraints excluded: chain C residue 63 PHE Chi-restraints excluded: chain C residue 72 ILE Chi-restraints excluded: chain C residue 79 LEU Chi-restraints excluded: chain C residue 80 LEU Chi-restraints excluded: chain D residue 7 ILE Chi-restraints excluded: chain D residue 16 ILE Chi-restraints excluded: chain D residue 53 ASP Chi-restraints excluded: chain D residue 54 VAL Chi-restraints excluded: chain D residue 65 LEU Chi-restraints excluded: chain D residue 77 THR Chi-restraints excluded: chain E residue 11 ILE Chi-restraints excluded: chain E residue 16 VAL Chi-restraints excluded: chain E residue 45 VAL Chi-restraints excluded: chain E residue 52 VAL Chi-restraints excluded: chain E residue 59 VAL Chi-restraints excluded: chain E residue 73 VAL Chi-restraints excluded: chain E residue 140 THR Chi-restraints excluded: chain E residue 144 LEU Chi-restraints excluded: chain E residue 175 LEU Chi-restraints excluded: chain E residue 180 ILE Chi-restraints excluded: chain E residue 188 TRP Chi-restraints excluded: chain E residue 209 ILE Chi-restraints excluded: chain E residue 213 TYR Chi-restraints excluded: chain E residue 227 ILE Chi-restraints excluded: chain G residue 22 VAL Chi-restraints excluded: chain G residue 40 VAL Chi-restraints excluded: chain G residue 93 VAL Chi-restraints excluded: chain G residue 105 ASN Chi-restraints excluded: chain H residue 39 LEU Chi-restraints excluded: chain H residue 59 ILE Chi-restraints excluded: chain H residue 72 ILE Chi-restraints excluded: chain H residue 93 LEU Chi-restraints excluded: chain H residue 129 ASP Chi-restraints excluded: chain H residue 139 ILE Chi-restraints excluded: chain H residue 200 ILE Chi-restraints excluded: chain H residue 225 LEU Chi-restraints excluded: chain H residue 253 LEU Chi-restraints excluded: chain H residue 279 MET Chi-restraints excluded: chain H residue 311 LEU Chi-restraints excluded: chain H residue 321 GLN Chi-restraints excluded: chain H residue 334 HIS Chi-restraints excluded: chain H residue 384 VAL Chi-restraints excluded: chain H residue 388 ASN Chi-restraints excluded: chain H residue 423 TYR Chi-restraints excluded: chain H residue 430 MET Chi-restraints excluded: chain H residue 448 VAL Chi-restraints excluded: chain H residue 450 LEU Chi-restraints excluded: chain H residue 477 ILE Chi-restraints excluded: chain H residue 480 VAL Chi-restraints excluded: chain X residue 13 ILE Chi-restraints excluded: chain X residue 89 LEU Chi-restraints excluded: chain X residue 131 THR Chi-restraints excluded: chain X residue 141 TYR Chi-restraints excluded: chain X residue 205 LEU Chi-restraints excluded: chain X residue 248 LYS Chi-restraints excluded: chain X residue 258 TYR Chi-restraints excluded: chain X residue 289 THR Chi-restraints excluded: chain X residue 299 LEU Chi-restraints excluded: chain X residue 310 SER Chi-restraints excluded: chain X residue 351 VAL Chi-restraints excluded: chain X residue 382 VAL Chi-restraints excluded: chain X residue 398 SER Chi-restraints excluded: chain X residue 401 LEU Chi-restraints excluded: chain X residue 448 VAL Chi-restraints excluded: chain X residue 467 VAL Chi-restraints excluded: chain X residue 514 ILE Chi-restraints excluded: chain X residue 529 VAL Chi-restraints excluded: chain X residue 532 VAL Chi-restraints excluded: chain X residue 544 VAL Chi-restraints excluded: chain X residue 548 TYR Chi-restraints excluded: chain X residue 593 TYR Chi-restraints excluded: chain X residue 606 LEU Chi-restraints excluded: chain X residue 610 LEU Chi-restraints excluded: chain J residue 41 TYR Chi-restraints excluded: chain J residue 42 ASP Chi-restraints excluded: chain J residue 56 GLN Chi-restraints excluded: chain J residue 61 LEU Chi-restraints excluded: chain J residue 67 THR Chi-restraints excluded: chain J residue 74 ILE Chi-restraints excluded: chain J residue 116 VAL Chi-restraints excluded: chain J residue 120 ILE Chi-restraints excluded: chain J residue 131 MET Chi-restraints excluded: chain J residue 143 ASN Chi-restraints excluded: chain J residue 171 TRP Chi-restraints excluded: chain K residue 71 VAL Chi-restraints excluded: chain K residue 72 TYR Chi-restraints excluded: chain K residue 81 THR Chi-restraints excluded: chain K residue 85 VAL Chi-restraints excluded: chain K residue 87 THR Chi-restraints excluded: chain K residue 100 THR Chi-restraints excluded: chain K residue 117 ASP Chi-restraints excluded: chain K residue 137 ASP Chi-restraints excluded: chain L residue 81 LEU Chi-restraints excluded: chain L residue 82 LEU Chi-restraints excluded: chain L residue 122 MET Chi-restraints excluded: chain L residue 126 THR Chi-restraints excluded: chain L residue 166 ARG Chi-restraints excluded: chain L residue 167 VAL Chi-restraints excluded: chain L residue 187 LEU Chi-restraints excluded: chain L residue 197 LEU Chi-restraints excluded: chain L residue 199 ASP Chi-restraints excluded: chain L residue 211 ASN Chi-restraints excluded: chain L residue 234 VAL Chi-restraints excluded: chain L residue 239 LEU Chi-restraints excluded: chain L residue 244 VAL Chi-restraints excluded: chain L residue 273 LEU Chi-restraints excluded: chain L residue 318 VAL Chi-restraints excluded: chain L residue 333 ASP Chi-restraints excluded: chain M residue 49 LEU Chi-restraints excluded: chain M residue 79 LEU Chi-restraints excluded: chain M residue 95 ASP Chi-restraints excluded: chain M residue 103 LEU Chi-restraints excluded: chain M residue 133 LEU Chi-restraints excluded: chain M residue 155 SER Chi-restraints excluded: chain M residue 169 SER Chi-restraints excluded: chain M residue 256 LEU Chi-restraints excluded: chain M residue 265 LYS Chi-restraints excluded: chain M residue 283 PHE Chi-restraints excluded: chain N residue 20 PHE Chi-restraints excluded: chain N residue 44 ILE Chi-restraints excluded: chain N residue 55 THR Chi-restraints excluded: chain N residue 74 ARG Chi-restraints excluded: chain N residue 79 THR Chi-restraints excluded: chain N residue 81 ILE Chi-restraints excluded: chain N residue 92 ASP Chi-restraints excluded: chain N residue 95 ARG Chi-restraints excluded: chain N residue 129 LEU Chi-restraints excluded: chain N residue 132 ASP Chi-restraints excluded: chain N residue 156 GLU Chi-restraints excluded: chain a residue 28 LEU Chi-restraints excluded: chain a residue 39 PHE Chi-restraints excluded: chain a residue 66 TYR Chi-restraints excluded: chain a residue 85 VAL Chi-restraints excluded: chain a residue 91 HIS Chi-restraints excluded: chain a residue 101 VAL Chi-restraints excluded: chain a residue 110 ASN Chi-restraints excluded: chain a residue 132 ASP Chi-restraints excluded: chain a residue 156 THR Chi-restraints excluded: chain b residue 22 VAL Chi-restraints excluded: chain b residue 27 THR Chi-restraints excluded: chain b residue 29 VAL Chi-restraints excluded: chain b residue 35 VAL Chi-restraints excluded: chain b residue 46 MET Chi-restraints excluded: chain b residue 49 PHE Chi-restraints excluded: chain b residue 70 PHE Chi-restraints excluded: chain b residue 73 VAL Chi-restraints excluded: chain b residue 74 ILE Chi-restraints excluded: chain c residue 16 THR Chi-restraints excluded: chain c residue 19 TYR Chi-restraints excluded: chain c residue 23 THR Chi-restraints excluded: chain c residue 34 ASN Chi-restraints excluded: chain c residue 72 ILE Chi-restraints excluded: chain c residue 80 LEU Chi-restraints excluded: chain c residue 113 LEU Chi-restraints excluded: chain c residue 115 ARG Chi-restraints excluded: chain d residue 53 ASP Chi-restraints excluded: chain d residue 54 VAL Chi-restraints excluded: chain d residue 65 LEU Chi-restraints excluded: chain d residue 69 VAL Chi-restraints excluded: chain d residue 72 PHE Chi-restraints excluded: chain d residue 77 THR Chi-restraints excluded: chain e residue 45 VAL Chi-restraints excluded: chain e residue 52 VAL Chi-restraints excluded: chain e residue 73 VAL Chi-restraints excluded: chain e residue 101 VAL Chi-restraints excluded: chain e residue 140 THR Chi-restraints excluded: chain e residue 144 LEU Chi-restraints excluded: chain e residue 175 LEU Chi-restraints excluded: chain e residue 188 TRP Chi-restraints excluded: chain e residue 199 ASN Chi-restraints excluded: chain e residue 209 ILE Chi-restraints excluded: chain e residue 213 TYR Chi-restraints excluded: chain e residue 214 THR Chi-restraints excluded: chain g residue 40 VAL Chi-restraints excluded: chain g residue 73 GLN Chi-restraints excluded: chain g residue 86 THR Chi-restraints excluded: chain g residue 93 VAL Chi-restraints excluded: chain g residue 103 THR Chi-restraints excluded: chain g residue 105 ASN Chi-restraints excluded: chain h residue 34 LEU Chi-restraints excluded: chain h residue 39 LEU Chi-restraints excluded: chain h residue 59 ILE Chi-restraints excluded: chain h residue 72 ILE Chi-restraints excluded: chain h residue 93 LEU Chi-restraints excluded: chain h residue 129 ASP Chi-restraints excluded: chain h residue 207 VAL Chi-restraints excluded: chain h residue 221 GLU Chi-restraints excluded: chain h residue 225 LEU Chi-restraints excluded: chain h residue 253 LEU Chi-restraints excluded: chain h residue 311 LEU Chi-restraints excluded: chain h residue 321 GLN Chi-restraints excluded: chain h residue 334 HIS Chi-restraints excluded: chain h residue 423 TYR Chi-restraints excluded: chain h residue 450 LEU Chi-restraints excluded: chain h residue 458 VAL Chi-restraints excluded: chain h residue 477 ILE Chi-restraints excluded: chain h residue 480 VAL Chi-restraints excluded: chain x residue 13 ILE Chi-restraints excluded: chain x residue 89 LEU Chi-restraints excluded: chain x residue 131 THR Chi-restraints excluded: chain x residue 141 TYR Chi-restraints excluded: chain x residue 154 ILE Chi-restraints excluded: chain x residue 205 LEU Chi-restraints excluded: chain x residue 258 TYR Chi-restraints excluded: chain x residue 299 LEU Chi-restraints excluded: chain x residue 305 LYS Chi-restraints excluded: chain x residue 310 SER Chi-restraints excluded: chain x residue 351 VAL Chi-restraints excluded: chain x residue 382 VAL Chi-restraints excluded: chain x residue 398 SER Chi-restraints excluded: chain x residue 401 LEU Chi-restraints excluded: chain x residue 448 VAL Chi-restraints excluded: chain x residue 467 VAL Chi-restraints excluded: chain x residue 514 ILE Chi-restraints excluded: chain x residue 529 VAL Chi-restraints excluded: chain x residue 532 VAL Chi-restraints excluded: chain x residue 544 VAL Chi-restraints excluded: chain x residue 546 MET Chi-restraints excluded: chain x residue 593 TYR Chi-restraints excluded: chain x residue 606 LEU Chi-restraints excluded: chain x residue 610 LEU Chi-restraints excluded: chain j residue 25 CYS Chi-restraints excluded: chain j residue 41 TYR Chi-restraints excluded: chain j residue 56 GLN Chi-restraints excluded: chain j residue 61 LEU Chi-restraints excluded: chain j residue 67 THR Chi-restraints excluded: chain j residue 74 ILE Chi-restraints excluded: chain j residue 114 ILE Chi-restraints excluded: chain j residue 120 ILE Chi-restraints excluded: chain j residue 143 ASN Chi-restraints excluded: chain j residue 154 GLU Chi-restraints excluded: chain j residue 171 TRP Chi-restraints excluded: chain k residue 58 THR Chi-restraints excluded: chain k residue 72 TYR Chi-restraints excluded: chain k residue 81 THR Chi-restraints excluded: chain k residue 85 VAL Chi-restraints excluded: chain k residue 87 THR Chi-restraints excluded: chain k residue 117 ASP Chi-restraints excluded: chain k residue 137 ASP Chi-restraints excluded: chain l residue 126 THR Chi-restraints excluded: chain l residue 166 ARG Chi-restraints excluded: chain l residue 167 VAL Chi-restraints excluded: chain l residue 187 LEU Chi-restraints excluded: chain l residue 199 ASP Chi-restraints excluded: chain l residue 211 ASN Chi-restraints excluded: chain l residue 235 THR Chi-restraints excluded: chain l residue 244 VAL Chi-restraints excluded: chain l residue 273 LEU Chi-restraints excluded: chain l residue 318 VAL Chi-restraints excluded: chain m residue 95 ASP Chi-restraints excluded: chain m residue 103 LEU Chi-restraints excluded: chain m residue 133 LEU Chi-restraints excluded: chain m residue 155 SER Chi-restraints excluded: chain m residue 169 SER Chi-restraints excluded: chain m residue 226 MET Chi-restraints excluded: chain m residue 274 ILE Chi-restraints excluded: chain m residue 283 PHE Chi-restraints excluded: chain m residue 306 MET Chi-restraints excluded: chain n residue 44 ILE Chi-restraints excluded: chain n residue 55 THR Chi-restraints excluded: chain n residue 74 ARG Chi-restraints excluded: chain n residue 79 THR Chi-restraints excluded: chain n residue 81 ILE Chi-restraints excluded: chain n residue 129 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 604 random chunks: chunk 563 optimal weight: 0.8980 chunk 65 optimal weight: 1.9990 chunk 332 optimal weight: 6.9990 chunk 426 optimal weight: 0.6980 chunk 330 optimal weight: 0.2980 chunk 491 optimal weight: 2.9990 chunk 326 optimal weight: 9.9990 chunk 582 optimal weight: 10.0000 chunk 364 optimal weight: 2.9990 chunk 354 optimal weight: 8.9990 chunk 268 optimal weight: 0.9980 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 118 ASN G 41 ASN ** H 226 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 163 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** ** a 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 126 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** l 33 GLN l 39 ASN ** m 223 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7774 moved from start: 0.3366 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= 0.208 Angle : 0.734 17.308 67458 Z= 0.357 Chirality : 0.043 0.228 7768 Planarity : 0.005 0.057 8248 Dihedral : 5.745 59.807 6658 Min Nonbonded Distance : 2.060 Molprobity Statistics. All-atom Clashscore : 17.16 Ramachandran Plot: Outliers : 0.07 % Allowed : 10.92 % Favored : 89.02 % Rotamer: Outliers : 6.08 % Allowed : 27.64 % Favored : 66.28 % 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: -2.72 (0.11), residues: 6072 helix: -0.50 (0.09), residues: 3450 sheet: -3.28 (0.31), residues: 212 loop : -3.69 (0.11), residues: 2410 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.001 TRP A 21 HIS 0.003 0.001 HIS x 336 PHE 0.040 0.001 PHE H 247 TYR 0.036 0.001 TYR M 157 ARG 0.015 0.000 ARG c 35 *********************** 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 1344 residues out of total 5044 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 306 poor density : 1038 time to evaluate : 5.317 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 46 MET cc_start: 0.7527 (ttm) cc_final: 0.7313 (ttm) REVERT: D 38 VAL cc_start: 0.8721 (t) cc_final: 0.8462 (p) REVERT: D 70 PHE cc_start: 0.8029 (t80) cc_final: 0.7374 (t80) REVERT: E 70 GLU cc_start: 0.7478 (tm-30) cc_final: 0.7086 (tm-30) REVERT: E 120 ILE cc_start: 0.8454 (mm) cc_final: 0.8124 (mt) REVERT: E 145 MET cc_start: 0.7880 (tpt) cc_final: 0.7580 (tpp) REVERT: E 146 TYR cc_start: 0.8007 (t80) cc_final: 0.7124 (t80) REVERT: G 99 GLU cc_start: 0.7540 (tp30) cc_final: 0.7322 (tp30) REVERT: H 79 PHE cc_start: 0.8343 (t80) cc_final: 0.7966 (t80) REVERT: H 112 MET cc_start: 0.7232 (ptp) cc_final: 0.6289 (ptp) REVERT: H 254 TYR cc_start: 0.7992 (t80) cc_final: 0.7536 (t80) REVERT: H 388 ASN cc_start: 0.7759 (OUTLIER) cc_final: 0.6757 (p0) REVERT: X 13 ILE cc_start: 0.7815 (OUTLIER) cc_final: 0.7588 (tt) REVERT: X 136 MET cc_start: 0.8011 (tpt) cc_final: 0.7801 (tpt) REVERT: X 305 LYS cc_start: 0.8726 (mtpt) cc_final: 0.8480 (mtpp) REVERT: X 310 SER cc_start: 0.9348 (p) cc_final: 0.9107 (p) REVERT: X 379 MET cc_start: 0.7173 (mmt) cc_final: 0.6809 (mmt) REVERT: X 434 TYR cc_start: 0.7659 (t80) cc_final: 0.7379 (t80) REVERT: X 546 MET cc_start: 0.6790 (ppp) cc_final: 0.6358 (ppp) REVERT: X 614 VAL cc_start: 0.8643 (OUTLIER) cc_final: 0.8411 (p) REVERT: J 57 TYR cc_start: 0.8951 (p90) cc_final: 0.8634 (p90) REVERT: J 141 ILE cc_start: 0.9151 (tp) cc_final: 0.8918 (tp) REVERT: K 50 ASN cc_start: 0.8109 (p0) cc_final: 0.7693 (p0) REVERT: K 62 TRP cc_start: 0.8465 (m100) cc_final: 0.8237 (m100) REVERT: L 26 TYR cc_start: 0.8733 (p90) cc_final: 0.8480 (p90) REVERT: L 93 GLU cc_start: 0.8178 (pt0) cc_final: 0.7059 (pt0) REVERT: L 96 TYR cc_start: 0.8852 (t80) cc_final: 0.8490 (t80) REVERT: L 133 MET cc_start: 0.8138 (tmm) cc_final: 0.7830 (tmm) REVERT: L 187 LEU cc_start: 0.9173 (OUTLIER) cc_final: 0.8954 (mm) REVERT: L 189 GLN cc_start: 0.7484 (tp40) cc_final: 0.7283 (tp40) REVERT: M 21 ILE cc_start: 0.9272 (mm) cc_final: 0.8853 (mt) REVERT: M 35 ARG cc_start: 0.8575 (mtt-85) cc_final: 0.8247 (mtp85) REVERT: M 103 LEU cc_start: 0.8929 (OUTLIER) cc_final: 0.8589 (mp) REVERT: M 104 GLU cc_start: 0.7496 (mt-10) cc_final: 0.6998 (mt-10) REVERT: M 115 MET cc_start: 0.7603 (ttm) cc_final: 0.7139 (ttm) REVERT: M 209 MET cc_start: 0.8655 (pmm) cc_final: 0.8080 (pmm) REVERT: M 265 LYS cc_start: 0.8971 (OUTLIER) cc_final: 0.8651 (mtpp) REVERT: M 290 LYS cc_start: 0.8735 (ttmt) cc_final: 0.8236 (tptt) REVERT: N 74 ARG cc_start: 0.9071 (OUTLIER) cc_final: 0.8712 (tpt90) REVERT: N 132 ASP cc_start: 0.7358 (OUTLIER) cc_final: 0.6891 (t0) REVERT: a 21 TRP cc_start: 0.7457 (t60) cc_final: 0.7201 (t60) REVERT: a 66 TYR cc_start: 0.6772 (OUTLIER) cc_final: 0.6513 (m-80) REVERT: a 78 MET cc_start: 0.8130 (mpp) cc_final: 0.7773 (mtm) REVERT: a 91 HIS cc_start: 0.4403 (OUTLIER) cc_final: 0.4117 (t-170) REVERT: a 114 MET cc_start: 0.7078 (tpp) cc_final: 0.6730 (mtp) REVERT: a 130 ASP cc_start: 0.7784 (t0) cc_final: 0.7461 (t0) REVERT: b 67 ILE cc_start: 0.7557 (mp) cc_final: 0.7238 (tp) REVERT: c 36 MET cc_start: 0.8957 (ppp) cc_final: 0.8399 (ppp) REVERT: d 14 LEU cc_start: 0.9058 (tp) cc_final: 0.8801 (tp) REVERT: d 70 PHE cc_start: 0.7920 (t80) cc_final: 0.7373 (t80) REVERT: e 146 TYR cc_start: 0.8259 (t80) cc_final: 0.7980 (t80) REVERT: e 168 MET cc_start: 0.5561 (mtt) cc_final: 0.4944 (mtp) REVERT: e 199 ASN cc_start: 0.7710 (OUTLIER) cc_final: 0.7398 (p0) REVERT: e 219 LYS cc_start: 0.9034 (tttp) cc_final: 0.8308 (tmmt) REVERT: g 24 LYS cc_start: 0.8107 (mttp) cc_final: 0.7862 (mmtp) REVERT: g 73 GLN cc_start: 0.8094 (OUTLIER) cc_final: 0.7867 (mp10) REVERT: h 112 MET cc_start: 0.7069 (ptp) cc_final: 0.6094 (ptp) REVERT: h 158 GLU cc_start: 0.8631 (tm-30) cc_final: 0.8313 (tm-30) REVERT: h 207 VAL cc_start: 0.9219 (OUTLIER) cc_final: 0.8987 (p) REVERT: h 258 ARG cc_start: 0.7994 (tpp80) cc_final: 0.7777 (ttt180) REVERT: h 279 MET cc_start: 0.7171 (mmp) cc_final: 0.6684 (mtp) REVERT: h 342 PHE cc_start: 0.8122 (m-80) cc_final: 0.7920 (m-80) REVERT: h 407 TRP cc_start: 0.8016 (m100) cc_final: 0.7779 (m100) REVERT: h 450 LEU cc_start: 0.7671 (OUTLIER) cc_final: 0.7451 (mm) REVERT: x 13 ILE cc_start: 0.7836 (OUTLIER) cc_final: 0.7616 (tt) REVERT: x 300 GLN cc_start: 0.9076 (tp-100) cc_final: 0.8612 (tp-100) REVERT: x 305 LYS cc_start: 0.8836 (OUTLIER) cc_final: 0.8132 (ttpp) REVERT: x 310 SER cc_start: 0.9352 (p) cc_final: 0.8993 (p) REVERT: x 614 VAL cc_start: 0.8643 (p) cc_final: 0.8430 (p) REVERT: j 57 TYR cc_start: 0.8912 (p90) cc_final: 0.8591 (p90) REVERT: j 141 ILE cc_start: 0.9138 (tp) cc_final: 0.8837 (tp) REVERT: k 131 MET cc_start: 0.7581 (ttm) cc_final: 0.7322 (ttm) REVERT: k 145 HIS cc_start: 0.7592 (m-70) cc_final: 0.7261 (m170) REVERT: l 81 LEU cc_start: 0.8955 (tp) cc_final: 0.8556 (tt) REVERT: l 93 GLU cc_start: 0.8187 (pt0) cc_final: 0.7300 (pt0) REVERT: l 96 TYR cc_start: 0.8767 (t80) cc_final: 0.8446 (t80) REVERT: l 166 ARG cc_start: 0.8423 (OUTLIER) cc_final: 0.8114 (mmm-85) REVERT: l 189 GLN cc_start: 0.7362 (tp40) cc_final: 0.7106 (tp40) REVERT: m 69 ILE cc_start: 0.8643 (mm) cc_final: 0.8269 (tp) REVERT: m 103 LEU cc_start: 0.8945 (OUTLIER) cc_final: 0.8561 (mp) REVERT: m 104 GLU cc_start: 0.6944 (mt-10) cc_final: 0.6687 (mt-10) REVERT: m 133 LEU cc_start: 0.8801 (OUTLIER) cc_final: 0.7911 (tp) REVERT: m 186 LEU cc_start: 0.8992 (mt) cc_final: 0.8754 (tt) REVERT: m 209 MET cc_start: 0.8633 (pmm) cc_final: 0.8088 (pmm) REVERT: m 232 THR cc_start: 0.8879 (OUTLIER) cc_final: 0.8054 (m) REVERT: m 266 GLN cc_start: 0.8423 (mm-40) cc_final: 0.8123 (mm-40) REVERT: m 290 LYS cc_start: 0.8830 (ttmt) cc_final: 0.8242 (tptt) REVERT: n 8 ILE cc_start: 0.8557 (mm) cc_final: 0.8284 (mt) REVERT: n 74 ARG cc_start: 0.9053 (OUTLIER) cc_final: 0.8707 (tpt90) REVERT: n 132 ASP cc_start: 0.7558 (t0) cc_final: 0.6986 (t70) outliers start: 306 outliers final: 214 residues processed: 1242 average time/residue: 0.5567 time to fit residues: 1175.4625 Evaluate side-chains 1203 residues out of total 5044 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 235 poor density : 968 time to evaluate : 5.732 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 PHE Chi-restraints excluded: chain A residue 85 VAL Chi-restraints excluded: chain A residue 110 ASN Chi-restraints excluded: chain A residue 132 ASP Chi-restraints excluded: chain A residue 156 THR Chi-restraints excluded: chain B residue 6 ILE Chi-restraints excluded: chain B residue 29 VAL Chi-restraints excluded: chain B residue 35 VAL Chi-restraints excluded: chain B residue 74 ILE Chi-restraints excluded: chain C residue 19 TYR Chi-restraints excluded: chain C residue 23 THR Chi-restraints excluded: chain C residue 63 PHE Chi-restraints excluded: chain C residue 72 ILE Chi-restraints excluded: chain C residue 79 LEU Chi-restraints excluded: chain C residue 80 LEU Chi-restraints excluded: chain C residue 113 LEU Chi-restraints excluded: chain D residue 7 ILE Chi-restraints excluded: chain D residue 16 ILE Chi-restraints excluded: chain D residue 53 ASP Chi-restraints excluded: chain D residue 54 VAL Chi-restraints excluded: chain D residue 56 MET Chi-restraints excluded: chain D residue 65 LEU Chi-restraints excluded: chain D residue 77 THR Chi-restraints excluded: chain E residue 16 VAL Chi-restraints excluded: chain E residue 45 VAL Chi-restraints excluded: chain E residue 52 VAL Chi-restraints excluded: chain E residue 59 VAL Chi-restraints excluded: chain E residue 140 THR Chi-restraints excluded: chain E residue 144 LEU Chi-restraints excluded: chain E residue 175 LEU Chi-restraints excluded: chain E residue 180 ILE Chi-restraints excluded: chain E residue 188 TRP Chi-restraints excluded: chain E residue 200 ILE Chi-restraints excluded: chain E residue 209 ILE Chi-restraints excluded: chain E residue 213 TYR Chi-restraints excluded: chain G residue 4 SER Chi-restraints excluded: chain G residue 22 VAL Chi-restraints excluded: chain G residue 105 ASN Chi-restraints excluded: chain H residue 39 LEU Chi-restraints excluded: chain H residue 72 ILE Chi-restraints excluded: chain H residue 93 LEU Chi-restraints excluded: chain H residue 129 ASP Chi-restraints excluded: chain H residue 139 ILE Chi-restraints excluded: chain H residue 225 LEU Chi-restraints excluded: chain H residue 262 LEU Chi-restraints excluded: chain H residue 279 MET Chi-restraints excluded: chain H residue 311 LEU Chi-restraints excluded: chain H residue 321 GLN Chi-restraints excluded: chain H residue 334 HIS Chi-restraints excluded: chain H residue 384 VAL Chi-restraints excluded: chain H residue 388 ASN Chi-restraints excluded: chain H residue 423 TYR Chi-restraints excluded: chain H residue 450 LEU Chi-restraints excluded: chain H residue 477 ILE Chi-restraints excluded: chain H residue 480 VAL Chi-restraints excluded: chain X residue 13 ILE Chi-restraints excluded: chain X residue 131 THR Chi-restraints excluded: chain X residue 141 TYR Chi-restraints excluded: chain X residue 154 ILE Chi-restraints excluded: chain X residue 205 LEU Chi-restraints excluded: chain X residue 258 TYR Chi-restraints excluded: chain X residue 289 THR Chi-restraints excluded: chain X residue 299 LEU Chi-restraints excluded: chain X residue 351 VAL Chi-restraints excluded: chain X residue 382 VAL Chi-restraints excluded: chain X residue 398 SER Chi-restraints excluded: chain X residue 448 VAL Chi-restraints excluded: chain X residue 467 VAL Chi-restraints excluded: chain X residue 514 ILE Chi-restraints excluded: chain X residue 529 VAL Chi-restraints excluded: chain X residue 532 VAL Chi-restraints excluded: chain X residue 544 VAL Chi-restraints excluded: chain X residue 548 TYR Chi-restraints excluded: chain X residue 593 TYR Chi-restraints excluded: chain X residue 606 LEU Chi-restraints excluded: chain X residue 610 LEU Chi-restraints excluded: chain X residue 614 VAL Chi-restraints excluded: chain J residue 41 TYR Chi-restraints excluded: chain J residue 56 GLN Chi-restraints excluded: chain J residue 61 LEU Chi-restraints excluded: chain J residue 74 ILE Chi-restraints excluded: chain J residue 120 ILE Chi-restraints excluded: chain J residue 143 ASN Chi-restraints excluded: chain J residue 171 TRP Chi-restraints excluded: chain K residue 30 LEU Chi-restraints excluded: chain K residue 71 VAL Chi-restraints excluded: chain K residue 81 THR Chi-restraints excluded: chain K residue 85 VAL Chi-restraints excluded: chain K residue 87 THR Chi-restraints excluded: chain K residue 100 THR Chi-restraints excluded: chain K residue 117 ASP Chi-restraints excluded: chain K residue 137 ASP Chi-restraints excluded: chain L residue 82 LEU Chi-restraints excluded: chain L residue 126 THR Chi-restraints excluded: chain L residue 166 ARG Chi-restraints excluded: chain L residue 167 VAL Chi-restraints excluded: chain L residue 187 LEU Chi-restraints excluded: chain L residue 197 LEU Chi-restraints excluded: chain L residue 199 ASP Chi-restraints excluded: chain L residue 234 VAL Chi-restraints excluded: chain L residue 244 VAL Chi-restraints excluded: chain L residue 273 LEU Chi-restraints excluded: chain L residue 318 VAL Chi-restraints excluded: chain M residue 49 LEU Chi-restraints excluded: chain M residue 79 LEU Chi-restraints excluded: chain M residue 95 ASP Chi-restraints excluded: chain M residue 103 LEU Chi-restraints excluded: chain M residue 133 LEU Chi-restraints excluded: chain M residue 154 PHE Chi-restraints excluded: chain M residue 212 PHE Chi-restraints excluded: chain M residue 265 LYS Chi-restraints excluded: chain M residue 283 PHE Chi-restraints excluded: chain M residue 306 MET Chi-restraints excluded: chain N residue 20 PHE Chi-restraints excluded: chain N residue 44 ILE Chi-restraints excluded: chain N residue 55 THR Chi-restraints excluded: chain N residue 74 ARG Chi-restraints excluded: chain N residue 81 ILE Chi-restraints excluded: chain N residue 92 ASP Chi-restraints excluded: chain N residue 129 LEU Chi-restraints excluded: chain N residue 132 ASP Chi-restraints excluded: chain a residue 25 THR Chi-restraints excluded: chain a residue 28 LEU Chi-restraints excluded: chain a residue 39 PHE Chi-restraints excluded: chain a residue 66 TYR Chi-restraints excluded: chain a residue 85 VAL Chi-restraints excluded: chain a residue 91 HIS Chi-restraints excluded: chain a residue 110 ASN Chi-restraints excluded: chain a residue 132 ASP Chi-restraints excluded: chain a residue 156 THR Chi-restraints excluded: chain b residue 22 VAL Chi-restraints excluded: chain b residue 27 THR Chi-restraints excluded: chain b residue 29 VAL Chi-restraints excluded: chain b residue 35 VAL Chi-restraints excluded: chain b residue 46 MET Chi-restraints excluded: chain b residue 70 PHE Chi-restraints excluded: chain c residue 19 TYR Chi-restraints excluded: chain c residue 23 THR Chi-restraints excluded: chain c residue 72 ILE Chi-restraints excluded: chain c residue 80 LEU Chi-restraints excluded: chain c residue 113 LEU Chi-restraints excluded: chain c residue 115 ARG Chi-restraints excluded: chain d residue 54 VAL Chi-restraints excluded: chain d residue 65 LEU Chi-restraints excluded: chain d residue 72 PHE Chi-restraints excluded: chain d residue 77 THR Chi-restraints excluded: chain e residue 45 VAL Chi-restraints excluded: chain e residue 101 VAL Chi-restraints excluded: chain e residue 140 THR Chi-restraints excluded: chain e residue 144 LEU Chi-restraints excluded: chain e residue 175 LEU Chi-restraints excluded: chain e residue 180 ILE Chi-restraints excluded: chain e residue 199 ASN Chi-restraints excluded: chain e residue 209 ILE Chi-restraints excluded: chain e residue 213 TYR Chi-restraints excluded: chain g residue 40 VAL Chi-restraints excluded: chain g residue 73 GLN Chi-restraints excluded: chain g residue 103 THR Chi-restraints excluded: chain g residue 105 ASN Chi-restraints excluded: chain h residue 34 LEU Chi-restraints excluded: chain h residue 39 LEU Chi-restraints excluded: chain h residue 72 ILE Chi-restraints excluded: chain h residue 89 VAL Chi-restraints excluded: chain h residue 93 LEU Chi-restraints excluded: chain h residue 200 ILE Chi-restraints excluded: chain h residue 207 VAL Chi-restraints excluded: chain h residue 221 GLU Chi-restraints excluded: chain h residue 225 LEU Chi-restraints excluded: chain h residue 311 LEU Chi-restraints excluded: chain h residue 321 GLN Chi-restraints excluded: chain h residue 334 HIS Chi-restraints excluded: chain h residue 423 TYR Chi-restraints excluded: chain h residue 450 LEU Chi-restraints excluded: chain h residue 458 VAL Chi-restraints excluded: chain h residue 477 ILE Chi-restraints excluded: chain h residue 480 VAL Chi-restraints excluded: chain x residue 13 ILE Chi-restraints excluded: chain x residue 131 THR Chi-restraints excluded: chain x residue 141 TYR Chi-restraints excluded: chain x residue 205 LEU Chi-restraints excluded: chain x residue 248 LYS Chi-restraints excluded: chain x residue 258 TYR Chi-restraints excluded: chain x residue 299 LEU Chi-restraints excluded: chain x residue 305 LYS Chi-restraints excluded: chain x residue 351 VAL Chi-restraints excluded: chain x residue 382 VAL Chi-restraints excluded: chain x residue 398 SER Chi-restraints excluded: chain x residue 401 LEU Chi-restraints excluded: chain x residue 448 VAL Chi-restraints excluded: chain x residue 467 VAL Chi-restraints excluded: chain x residue 529 VAL Chi-restraints excluded: chain x residue 532 VAL Chi-restraints excluded: chain x residue 544 VAL Chi-restraints excluded: chain x residue 593 TYR Chi-restraints excluded: chain x residue 606 LEU Chi-restraints excluded: chain x residue 610 LEU Chi-restraints excluded: chain j residue 25 CYS Chi-restraints excluded: chain j residue 41 TYR Chi-restraints excluded: chain j residue 56 GLN Chi-restraints excluded: chain j residue 61 LEU Chi-restraints excluded: chain j residue 74 ILE Chi-restraints excluded: chain j residue 120 ILE Chi-restraints excluded: chain j residue 143 ASN Chi-restraints excluded: chain j residue 171 TRP Chi-restraints excluded: chain k residue 58 THR Chi-restraints excluded: chain k residue 81 THR Chi-restraints excluded: chain k residue 85 VAL Chi-restraints excluded: chain k residue 87 THR Chi-restraints excluded: chain k residue 100 THR Chi-restraints excluded: chain k residue 117 ASP Chi-restraints excluded: chain k residue 137 ASP Chi-restraints excluded: chain l residue 126 THR Chi-restraints excluded: chain l residue 166 ARG Chi-restraints excluded: chain l residue 167 VAL Chi-restraints excluded: chain l residue 172 THR Chi-restraints excluded: chain l residue 197 LEU Chi-restraints excluded: chain l residue 199 ASP Chi-restraints excluded: chain l residue 235 THR Chi-restraints excluded: chain l residue 244 VAL Chi-restraints excluded: chain l residue 273 LEU Chi-restraints excluded: chain l residue 318 VAL Chi-restraints excluded: chain l residue 356 ILE Chi-restraints excluded: chain m residue 95 ASP Chi-restraints excluded: chain m residue 103 LEU Chi-restraints excluded: chain m residue 133 LEU Chi-restraints excluded: chain m residue 232 THR Chi-restraints excluded: chain m residue 259 LEU Chi-restraints excluded: chain m residue 274 ILE Chi-restraints excluded: chain m residue 283 PHE Chi-restraints excluded: chain m residue 306 MET Chi-restraints excluded: chain n residue 44 ILE Chi-restraints excluded: chain n residue 55 THR Chi-restraints excluded: chain n residue 74 ARG Chi-restraints excluded: chain n residue 81 ILE Chi-restraints excluded: chain n residue 129 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 604 random chunks: chunk 360 optimal weight: 5.9990 chunk 232 optimal weight: 2.9990 chunk 347 optimal weight: 0.0870 chunk 175 optimal weight: 10.0000 chunk 114 optimal weight: 0.8980 chunk 112 optimal weight: 2.9990 chunk 370 optimal weight: 2.9990 chunk 396 optimal weight: 0.9980 chunk 287 optimal weight: 0.0470 chunk 54 optimal weight: 5.9990 chunk 457 optimal weight: 8.9990 overall best weight: 1.0058 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 118 ASN G 41 ASN H 132 ASN ** H 226 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 163 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 126 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 39 ASN ** 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 139 HIS d 50 GLN g 66 ASN h 132 ASN ** k 126 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** l 169 HIS ** m 223 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7766 moved from start: 0.3507 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.079 49624 Z= 0.212 Angle : 0.739 16.864 67458 Z= 0.359 Chirality : 0.043 0.187 7768 Planarity : 0.005 0.076 8248 Dihedral : 5.624 59.145 6656 Min Nonbonded Distance : 2.077 Molprobity Statistics. All-atom Clashscore : 17.57 Ramachandran Plot: Outliers : 0.07 % Allowed : 11.00 % Favored : 88.93 % Rotamer: Outliers : 5.88 % Allowed : 27.84 % Favored : 66.28 % 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: -2.59 (0.11), residues: 6072 helix: -0.41 (0.09), residues: 3444 sheet: -3.12 (0.30), residues: 236 loop : -3.62 (0.12), residues: 2392 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.042 0.001 TRP k 62 HIS 0.003 0.001 HIS x 71 PHE 0.038 0.001 PHE D 47 TYR 0.036 0.001 TYR l 26 ARG 0.010 0.000 ARG J 177 *********************** 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 1301 residues out of total 5044 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 296 poor density : 1005 time to evaluate : 5.185 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 126 THR cc_start: 0.6450 (p) cc_final: 0.6008 (p) REVERT: B 49 PHE cc_start: 0.7173 (OUTLIER) cc_final: 0.6942 (m-10) REVERT: D 38 VAL cc_start: 0.8703 (t) cc_final: 0.8487 (p) REVERT: D 70 PHE cc_start: 0.8009 (t80) cc_final: 0.7380 (t80) REVERT: E 120 ILE cc_start: 0.8450 (mm) cc_final: 0.8208 (mt) REVERT: E 145 MET cc_start: 0.7862 (tpt) cc_final: 0.7585 (tpp) REVERT: E 146 TYR cc_start: 0.7925 (t80) cc_final: 0.7044 (t80) REVERT: G 99 GLU cc_start: 0.7529 (tp30) cc_final: 0.7303 (tp30) REVERT: H 79 PHE cc_start: 0.8282 (t80) cc_final: 0.7828 (t80) REVERT: H 112 MET cc_start: 0.7218 (ptp) cc_final: 0.6299 (ptp) REVERT: H 129 ASP cc_start: 0.7727 (OUTLIER) cc_final: 0.7495 (t0) REVERT: H 254 TYR cc_start: 0.8021 (t80) cc_final: 0.7597 (t80) REVERT: H 388 ASN cc_start: 0.7735 (OUTLIER) cc_final: 0.6693 (p0) REVERT: X 305 LYS cc_start: 0.8775 (mtpt) cc_final: 0.8538 (mtpp) REVERT: X 310 SER cc_start: 0.9367 (p) cc_final: 0.9141 (p) REVERT: X 546 MET cc_start: 0.6733 (ppp) cc_final: 0.6341 (ppp) REVERT: X 614 VAL cc_start: 0.8656 (p) cc_final: 0.8453 (p) REVERT: J 57 TYR cc_start: 0.8959 (p90) cc_final: 0.8646 (p90) REVERT: J 141 ILE cc_start: 0.9155 (tp) cc_final: 0.8919 (tp) REVERT: K 50 ASN cc_start: 0.8153 (p0) cc_final: 0.7701 (p0) REVERT: K 62 TRP cc_start: 0.8466 (m100) cc_final: 0.8234 (m100) REVERT: L 26 TYR cc_start: 0.8732 (p90) cc_final: 0.8512 (p90) REVERT: L 93 GLU cc_start: 0.8188 (pt0) cc_final: 0.7048 (pt0) REVERT: L 96 TYR cc_start: 0.8832 (t80) cc_final: 0.8486 (t80) REVERT: L 133 MET cc_start: 0.8126 (tmm) cc_final: 0.7838 (tmm) REVERT: L 160 GLU cc_start: 0.7745 (tm-30) cc_final: 0.7537 (tm-30) REVERT: L 187 LEU cc_start: 0.9185 (OUTLIER) cc_final: 0.8943 (mm) REVERT: L 189 GLN cc_start: 0.7481 (tp40) cc_final: 0.7239 (tp40) REVERT: M 21 ILE cc_start: 0.9281 (mm) cc_final: 0.8874 (mt) REVERT: M 35 ARG cc_start: 0.8553 (mtt-85) cc_final: 0.8264 (mtp85) REVERT: M 79 LEU cc_start: 0.8010 (OUTLIER) cc_final: 0.7752 (pp) REVERT: M 93 TYR cc_start: 0.8674 (OUTLIER) cc_final: 0.8385 (p90) REVERT: M 103 LEU cc_start: 0.8927 (OUTLIER) cc_final: 0.8577 (mp) REVERT: M 104 GLU cc_start: 0.7533 (mt-10) cc_final: 0.7008 (mt-10) REVERT: M 115 MET cc_start: 0.7553 (ttm) cc_final: 0.7044 (ttm) REVERT: M 226 MET cc_start: 0.8008 (mmp) cc_final: 0.7586 (mmp) REVERT: M 290 LYS cc_start: 0.8726 (ttmt) cc_final: 0.8272 (tptt) REVERT: N 74 ARG cc_start: 0.9063 (OUTLIER) cc_final: 0.8786 (tpt90) REVERT: N 95 ARG cc_start: 0.8467 (OUTLIER) cc_final: 0.7287 (ptp90) REVERT: N 132 ASP cc_start: 0.7295 (OUTLIER) cc_final: 0.6815 (t0) REVERT: a 21 TRP cc_start: 0.7570 (t60) cc_final: 0.7314 (t60) REVERT: a 66 TYR cc_start: 0.6886 (OUTLIER) cc_final: 0.6214 (m-80) REVERT: a 78 MET cc_start: 0.8167 (mpp) cc_final: 0.7825 (mtm) REVERT: a 83 LEU cc_start: 0.7143 (OUTLIER) cc_final: 0.6792 (mm) REVERT: a 91 HIS cc_start: 0.4391 (OUTLIER) cc_final: 0.4120 (t-170) REVERT: a 114 MET cc_start: 0.7114 (tpp) cc_final: 0.6774 (mtp) REVERT: a 130 ASP cc_start: 0.7784 (t0) cc_final: 0.7475 (t0) REVERT: a 156 THR cc_start: 0.0099 (OUTLIER) cc_final: -0.0198 (m) REVERT: b 67 ILE cc_start: 0.7517 (OUTLIER) cc_final: 0.7233 (tp) REVERT: c 36 MET cc_start: 0.8949 (ppp) cc_final: 0.8388 (ppp) REVERT: d 14 LEU cc_start: 0.9026 (tp) cc_final: 0.8799 (tp) REVERT: d 70 PHE cc_start: 0.7936 (t80) cc_final: 0.7409 (t80) REVERT: e 146 TYR cc_start: 0.8125 (t80) cc_final: 0.7904 (t80) REVERT: e 168 MET cc_start: 0.5675 (mtt) cc_final: 0.5082 (mtp) REVERT: e 199 ASN cc_start: 0.7698 (OUTLIER) cc_final: 0.7385 (p0) REVERT: e 219 LYS cc_start: 0.9032 (tttp) cc_final: 0.8308 (tmmt) REVERT: g 5 TYR cc_start: 0.7158 (m-80) cc_final: 0.6923 (m-80) REVERT: g 24 LYS cc_start: 0.8083 (mttp) cc_final: 0.7844 (mmtp) REVERT: h 112 MET cc_start: 0.7056 (ptp) cc_final: 0.6092 (ptp) REVERT: h 158 GLU cc_start: 0.8650 (tm-30) cc_final: 0.8347 (tm-30) REVERT: h 207 VAL cc_start: 0.9209 (OUTLIER) cc_final: 0.8956 (p) REVERT: h 258 ARG cc_start: 0.8060 (tpp80) cc_final: 0.7775 (ttt180) REVERT: h 279 MET cc_start: 0.7110 (mmp) cc_final: 0.6622 (mtp) REVERT: h 342 PHE cc_start: 0.8191 (m-80) cc_final: 0.7983 (m-80) REVERT: h 407 TRP cc_start: 0.7964 (m100) cc_final: 0.7673 (m100) REVERT: x 13 ILE cc_start: 0.7829 (OUTLIER) cc_final: 0.7625 (tt) REVERT: x 300 GLN cc_start: 0.9041 (tp-100) cc_final: 0.8585 (tp-100) REVERT: x 305 LYS cc_start: 0.8833 (OUTLIER) cc_final: 0.8094 (ttpp) REVERT: x 310 SER cc_start: 0.9357 (p) cc_final: 0.9018 (p) REVERT: j 141 ILE cc_start: 0.9148 (tp) cc_final: 0.8857 (tp) REVERT: k 145 HIS cc_start: 0.7586 (m-70) cc_final: 0.7272 (m170) REVERT: l 26 TYR cc_start: 0.8832 (p90) cc_final: 0.8544 (p90) REVERT: l 81 LEU cc_start: 0.8888 (tp) cc_final: 0.8540 (tt) REVERT: l 93 GLU cc_start: 0.8181 (pt0) cc_final: 0.7225 (pt0) REVERT: l 96 TYR cc_start: 0.8765 (t80) cc_final: 0.8443 (t80) REVERT: l 166 ARG cc_start: 0.8424 (OUTLIER) cc_final: 0.8165 (mmm-85) REVERT: l 187 LEU cc_start: 0.9041 (OUTLIER) cc_final: 0.8780 (mm) REVERT: l 189 GLN cc_start: 0.7354 (tp40) cc_final: 0.7065 (tp40) REVERT: m 21 ILE cc_start: 0.9256 (mm) cc_final: 0.8824 (mt) REVERT: m 103 LEU cc_start: 0.8955 (OUTLIER) cc_final: 0.8641 (mp) REVERT: m 186 LEU cc_start: 0.8997 (mt) cc_final: 0.8786 (tt) REVERT: m 209 MET cc_start: 0.8637 (pmm) cc_final: 0.7935 (pmm) REVERT: m 232 THR cc_start: 0.8845 (OUTLIER) cc_final: 0.8631 (m) REVERT: m 274 ILE cc_start: 0.8796 (OUTLIER) cc_final: 0.8504 (tp) REVERT: m 290 LYS cc_start: 0.8804 (ttmt) cc_final: 0.8243 (tptt) REVERT: n 8 ILE cc_start: 0.8532 (mm) cc_final: 0.8262 (mt) REVERT: n 74 ARG cc_start: 0.9046 (OUTLIER) cc_final: 0.8802 (tpt90) REVERT: n 132 ASP cc_start: 0.7555 (t0) cc_final: 0.7013 (t70) outliers start: 296 outliers final: 221 residues processed: 1209 average time/residue: 0.5441 time to fit residues: 1122.3044 Evaluate side-chains 1210 residues out of total 5044 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 246 poor density : 964 time to evaluate : 5.333 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 PHE Chi-restraints excluded: chain A residue 39 PHE Chi-restraints excluded: chain A residue 85 VAL Chi-restraints excluded: chain A residue 101 VAL Chi-restraints excluded: chain A residue 110 ASN Chi-restraints excluded: chain A residue 132 ASP Chi-restraints excluded: chain A residue 156 THR Chi-restraints excluded: chain B residue 6 ILE Chi-restraints excluded: chain B residue 27 THR Chi-restraints excluded: chain B residue 29 VAL Chi-restraints excluded: chain B residue 35 VAL Chi-restraints excluded: chain B residue 49 PHE Chi-restraints excluded: chain B residue 74 ILE Chi-restraints excluded: chain C residue 19 TYR Chi-restraints excluded: chain C residue 23 THR Chi-restraints excluded: chain C residue 34 ASN Chi-restraints excluded: chain C residue 63 PHE Chi-restraints excluded: chain C residue 72 ILE Chi-restraints excluded: chain C residue 78 LEU Chi-restraints excluded: chain C residue 79 LEU Chi-restraints excluded: chain C residue 80 LEU Chi-restraints excluded: chain C residue 101 TRP Chi-restraints excluded: chain C residue 113 LEU Chi-restraints excluded: chain D residue 7 ILE Chi-restraints excluded: chain D residue 8 GLU Chi-restraints excluded: chain D residue 16 ILE Chi-restraints excluded: chain D residue 53 ASP Chi-restraints excluded: chain D residue 54 VAL Chi-restraints excluded: chain D residue 56 MET Chi-restraints excluded: chain D residue 65 LEU Chi-restraints excluded: chain D residue 77 THR Chi-restraints excluded: chain E residue 11 ILE Chi-restraints excluded: chain E residue 16 VAL Chi-restraints excluded: chain E residue 45 VAL Chi-restraints excluded: chain E residue 52 VAL Chi-restraints excluded: chain E residue 59 VAL Chi-restraints excluded: chain E residue 123 HIS Chi-restraints excluded: chain E residue 140 THR Chi-restraints excluded: chain E residue 144 LEU Chi-restraints excluded: chain E residue 175 LEU Chi-restraints excluded: chain E residue 180 ILE Chi-restraints excluded: chain E residue 188 TRP Chi-restraints excluded: chain E residue 209 ILE Chi-restraints excluded: chain E residue 213 TYR Chi-restraints excluded: chain G residue 4 SER Chi-restraints excluded: chain G residue 22 VAL Chi-restraints excluded: chain G residue 41 ASN Chi-restraints excluded: chain G residue 105 ASN Chi-restraints excluded: chain H residue 72 ILE Chi-restraints excluded: chain H residue 115 LEU Chi-restraints excluded: chain H residue 129 ASP Chi-restraints excluded: chain H residue 139 ILE Chi-restraints excluded: chain H residue 262 LEU Chi-restraints excluded: chain H residue 279 MET Chi-restraints excluded: chain H residue 321 GLN Chi-restraints excluded: chain H residue 334 HIS Chi-restraints excluded: chain H residue 384 VAL Chi-restraints excluded: chain H residue 388 ASN Chi-restraints excluded: chain H residue 423 TYR Chi-restraints excluded: chain H residue 450 LEU Chi-restraints excluded: chain H residue 477 ILE Chi-restraints excluded: chain H residue 480 VAL Chi-restraints excluded: chain X residue 131 THR Chi-restraints excluded: chain X residue 141 TYR Chi-restraints excluded: chain X residue 154 ILE Chi-restraints excluded: chain X residue 205 LEU Chi-restraints excluded: chain X residue 248 LYS Chi-restraints excluded: chain X residue 258 TYR Chi-restraints excluded: chain X residue 289 THR Chi-restraints excluded: chain X residue 299 LEU Chi-restraints excluded: chain X residue 351 VAL Chi-restraints excluded: chain X residue 382 VAL Chi-restraints excluded: chain X residue 398 SER Chi-restraints excluded: chain X residue 448 VAL Chi-restraints excluded: chain X residue 467 VAL Chi-restraints excluded: chain X residue 514 ILE Chi-restraints excluded: chain X residue 529 VAL Chi-restraints excluded: chain X residue 532 VAL Chi-restraints excluded: chain X residue 544 VAL Chi-restraints excluded: chain X residue 593 TYR Chi-restraints excluded: chain X residue 606 LEU Chi-restraints excluded: chain J residue 41 TYR Chi-restraints excluded: chain J residue 56 GLN Chi-restraints excluded: chain J residue 61 LEU Chi-restraints excluded: chain J residue 74 ILE Chi-restraints excluded: chain J residue 120 ILE Chi-restraints excluded: chain J residue 143 ASN Chi-restraints excluded: chain J residue 171 TRP Chi-restraints excluded: chain K residue 30 LEU Chi-restraints excluded: chain K residue 71 VAL Chi-restraints excluded: chain K residue 81 THR Chi-restraints excluded: chain K residue 85 VAL Chi-restraints excluded: chain K residue 87 THR Chi-restraints excluded: chain K residue 100 THR Chi-restraints excluded: chain K residue 117 ASP Chi-restraints excluded: chain K residue 137 ASP Chi-restraints excluded: chain K residue 162 LEU Chi-restraints excluded: chain L residue 82 LEU Chi-restraints excluded: chain L residue 126 THR Chi-restraints excluded: chain L residue 166 ARG Chi-restraints excluded: chain L residue 167 VAL Chi-restraints excluded: chain L residue 172 THR Chi-restraints excluded: chain L residue 187 LEU Chi-restraints excluded: chain L residue 197 LEU Chi-restraints excluded: chain L residue 199 ASP Chi-restraints excluded: chain L residue 234 VAL Chi-restraints excluded: chain L residue 244 VAL Chi-restraints excluded: chain L residue 273 LEU Chi-restraints excluded: chain L residue 318 VAL Chi-restraints excluded: chain M residue 49 LEU Chi-restraints excluded: chain M residue 79 LEU Chi-restraints excluded: chain M residue 93 TYR Chi-restraints excluded: chain M residue 95 ASP Chi-restraints excluded: chain M residue 103 LEU Chi-restraints excluded: chain M residue 133 LEU Chi-restraints excluded: chain M residue 154 PHE Chi-restraints excluded: chain M residue 259 LEU Chi-restraints excluded: chain M residue 283 PHE Chi-restraints excluded: chain M residue 306 MET Chi-restraints excluded: chain N residue 20 PHE Chi-restraints excluded: chain N residue 44 ILE Chi-restraints excluded: chain N residue 55 THR Chi-restraints excluded: chain N residue 74 ARG Chi-restraints excluded: chain N residue 81 ILE Chi-restraints excluded: chain N residue 92 ASP Chi-restraints excluded: chain N residue 95 ARG Chi-restraints excluded: chain N residue 129 LEU Chi-restraints excluded: chain N residue 132 ASP Chi-restraints excluded: chain a residue 25 THR Chi-restraints excluded: chain a residue 28 LEU Chi-restraints excluded: chain a residue 39 PHE Chi-restraints excluded: chain a residue 66 TYR Chi-restraints excluded: chain a residue 83 LEU Chi-restraints excluded: chain a residue 85 VAL Chi-restraints excluded: chain a residue 91 HIS Chi-restraints excluded: chain a residue 110 ASN Chi-restraints excluded: chain a residue 132 ASP Chi-restraints excluded: chain a residue 156 THR Chi-restraints excluded: chain b residue 22 VAL Chi-restraints excluded: chain b residue 27 THR Chi-restraints excluded: chain b residue 29 VAL Chi-restraints excluded: chain b residue 35 VAL Chi-restraints excluded: chain b residue 46 MET Chi-restraints excluded: chain b residue 67 ILE Chi-restraints excluded: chain b residue 74 ILE Chi-restraints excluded: chain c residue 19 TYR Chi-restraints excluded: chain c residue 23 THR Chi-restraints excluded: chain c residue 72 ILE Chi-restraints excluded: chain c residue 80 LEU Chi-restraints excluded: chain c residue 113 LEU Chi-restraints excluded: chain c residue 115 ARG Chi-restraints excluded: chain d residue 54 VAL Chi-restraints excluded: chain d residue 65 LEU Chi-restraints excluded: chain d residue 72 PHE Chi-restraints excluded: chain d residue 77 THR Chi-restraints excluded: chain e residue 45 VAL Chi-restraints excluded: chain e residue 101 VAL Chi-restraints excluded: chain e residue 140 THR Chi-restraints excluded: chain e residue 144 LEU Chi-restraints excluded: chain e residue 175 LEU Chi-restraints excluded: chain e residue 180 ILE Chi-restraints excluded: chain e residue 188 TRP Chi-restraints excluded: chain e residue 199 ASN Chi-restraints excluded: chain e residue 209 ILE Chi-restraints excluded: chain e residue 213 TYR Chi-restraints excluded: chain e residue 231 MET Chi-restraints excluded: chain g residue 40 VAL Chi-restraints excluded: chain g residue 103 THR Chi-restraints excluded: chain g residue 105 ASN Chi-restraints excluded: chain h residue 34 LEU Chi-restraints excluded: chain h residue 39 LEU Chi-restraints excluded: chain h residue 89 VAL Chi-restraints excluded: chain h residue 93 LEU Chi-restraints excluded: chain h residue 200 ILE Chi-restraints excluded: chain h residue 207 VAL Chi-restraints excluded: chain h residue 221 GLU Chi-restraints excluded: chain h residue 225 LEU Chi-restraints excluded: chain h residue 321 GLN Chi-restraints excluded: chain h residue 334 HIS Chi-restraints excluded: chain h residue 423 TYR Chi-restraints excluded: chain h residue 458 VAL Chi-restraints excluded: chain h residue 477 ILE Chi-restraints excluded: chain h residue 480 VAL Chi-restraints excluded: chain x residue 13 ILE Chi-restraints excluded: chain x residue 131 THR Chi-restraints excluded: chain x residue 141 TYR Chi-restraints excluded: chain x residue 154 ILE Chi-restraints excluded: chain x residue 205 LEU Chi-restraints excluded: chain x residue 248 LYS Chi-restraints excluded: chain x residue 258 TYR Chi-restraints excluded: chain x residue 299 LEU Chi-restraints excluded: chain x residue 305 LYS Chi-restraints excluded: chain x residue 351 VAL Chi-restraints excluded: chain x residue 382 VAL Chi-restraints excluded: chain x residue 398 SER Chi-restraints excluded: chain x residue 401 LEU Chi-restraints excluded: chain x residue 448 VAL Chi-restraints excluded: chain x residue 529 VAL Chi-restraints excluded: chain x residue 532 VAL Chi-restraints excluded: chain x residue 544 VAL Chi-restraints excluded: chain x residue 548 TYR Chi-restraints excluded: chain x residue 593 TYR Chi-restraints excluded: chain x residue 606 LEU Chi-restraints excluded: chain x residue 610 LEU Chi-restraints excluded: chain j residue 25 CYS Chi-restraints excluded: chain j residue 41 TYR Chi-restraints excluded: chain j residue 61 LEU Chi-restraints excluded: chain j residue 74 ILE Chi-restraints excluded: chain j residue 120 ILE Chi-restraints excluded: chain j residue 143 ASN Chi-restraints excluded: chain j residue 171 TRP Chi-restraints excluded: chain k residue 58 THR Chi-restraints excluded: chain k residue 72 TYR Chi-restraints excluded: chain k residue 81 THR Chi-restraints excluded: chain k residue 85 VAL Chi-restraints excluded: chain k residue 87 THR Chi-restraints excluded: chain k residue 117 ASP Chi-restraints excluded: chain l residue 75 TYR Chi-restraints excluded: chain l residue 126 THR Chi-restraints excluded: chain l residue 166 ARG Chi-restraints excluded: chain l residue 167 VAL Chi-restraints excluded: chain l residue 187 LEU Chi-restraints excluded: chain l residue 197 LEU Chi-restraints excluded: chain l residue 199 ASP Chi-restraints excluded: chain l residue 235 THR Chi-restraints excluded: chain l residue 244 VAL Chi-restraints excluded: chain l residue 271 ASP Chi-restraints excluded: chain l residue 273 LEU Chi-restraints excluded: chain l residue 318 VAL Chi-restraints excluded: chain l residue 356 ILE Chi-restraints excluded: chain m residue 23 MET Chi-restraints excluded: chain m residue 95 ASP Chi-restraints excluded: chain m residue 103 LEU Chi-restraints excluded: chain m residue 133 LEU Chi-restraints excluded: chain m residue 154 PHE Chi-restraints excluded: chain m residue 232 THR Chi-restraints excluded: chain m residue 256 LEU Chi-restraints excluded: chain m residue 259 LEU Chi-restraints excluded: chain m residue 274 ILE Chi-restraints excluded: chain m residue 283 PHE Chi-restraints excluded: chain m residue 306 MET Chi-restraints excluded: chain n residue 44 ILE Chi-restraints excluded: chain n residue 55 THR Chi-restraints excluded: chain n residue 74 ARG Chi-restraints excluded: chain n residue 81 ILE Chi-restraints excluded: chain n residue 129 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 604 random chunks: chunk 529 optimal weight: 0.8980 chunk 557 optimal weight: 5.9990 chunk 508 optimal weight: 8.9990 chunk 542 optimal weight: 4.9990 chunk 326 optimal weight: 10.0000 chunk 236 optimal weight: 10.0000 chunk 425 optimal weight: 0.7980 chunk 166 optimal weight: 4.9990 chunk 490 optimal weight: 5.9990 chunk 513 optimal weight: 4.9990 chunk 540 optimal weight: 4.9990 overall best weight: 3.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 118 ASN ** G 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 163 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 126 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 113 GLN ** M 34 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 118 ASN ** k 126 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** l 33 GLN ** m 34 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7860 moved from start: 0.3616 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.081 49624 Z= 0.348 Angle : 0.803 17.053 67458 Z= 0.394 Chirality : 0.047 0.471 7768 Planarity : 0.005 0.064 8248 Dihedral : 5.738 58.374 6654 Min Nonbonded Distance : 1.955 Molprobity Statistics. All-atom Clashscore : 19.51 Ramachandran Plot: Outliers : 0.08 % Allowed : 12.53 % Favored : 87.38 % Rotamer: Outliers : 5.68 % Allowed : 28.28 % Favored : 66.04 % 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: -2.66 (0.11), residues: 6072 helix: -0.49 (0.09), residues: 3452 sheet: -3.14 (0.30), residues: 240 loop : -3.61 (0.12), residues: 2380 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP k 62 HIS 0.009 0.001 HIS X 340 PHE 0.041 0.002 PHE D 47 TYR 0.035 0.002 TYR l 26 ARG 0.008 0.001 ARG L 371 *********************** 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 1267 residues out of total 5044 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 286 poor density : 981 time to evaluate : 5.262 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: A 126 THR cc_start: 0.6757 (p) cc_final: 0.6415 (p) REVERT: B 46 MET cc_start: 0.7663 (ttm) cc_final: 0.7231 (ttm) REVERT: B 49 PHE cc_start: 0.7341 (OUTLIER) cc_final: 0.7105 (m-10) REVERT: B 67 ILE cc_start: 0.7775 (mp) cc_final: 0.7379 (tp) REVERT: D 38 VAL cc_start: 0.8777 (t) cc_final: 0.8566 (p) REVERT: D 70 PHE cc_start: 0.8012 (t80) cc_final: 0.7454 (t80) REVERT: E 120 ILE cc_start: 0.8480 (mm) cc_final: 0.8176 (mt) REVERT: E 145 MET cc_start: 0.7865 (tpt) cc_final: 0.7573 (tpp) REVERT: E 146 TYR cc_start: 0.8100 (t80) cc_final: 0.7185 (t80) REVERT: G 99 GLU cc_start: 0.7601 (tp30) cc_final: 0.7399 (tp30) REVERT: H 79 PHE cc_start: 0.8445 (t80) cc_final: 0.8126 (t80) REVERT: H 112 MET cc_start: 0.7259 (ptp) cc_final: 0.6353 (ptp) REVERT: H 388 ASN cc_start: 0.7846 (OUTLIER) cc_final: 0.6923 (p0) REVERT: X 136 MET cc_start: 0.8142 (tpt) cc_final: 0.7910 (tpt) REVERT: X 434 TYR cc_start: 0.7719 (t80) cc_final: 0.7359 (t80) REVERT: X 546 MET cc_start: 0.7034 (ppp) cc_final: 0.6604 (ppp) REVERT: J 42 ASP cc_start: 0.7690 (OUTLIER) cc_final: 0.7394 (p0) REVERT: J 141 ILE cc_start: 0.9162 (tp) cc_final: 0.8937 (tp) REVERT: K 50 ASN cc_start: 0.8321 (p0) cc_final: 0.7940 (p0) REVERT: L 93 GLU cc_start: 0.8215 (pt0) cc_final: 0.7117 (pt0) REVERT: L 96 TYR cc_start: 0.8840 (t80) cc_final: 0.8497 (t80) REVERT: L 133 MET cc_start: 0.8202 (tmm) cc_final: 0.7907 (tmm) REVERT: L 189 GLN cc_start: 0.7668 (tp40) cc_final: 0.7437 (tp40) REVERT: M 21 ILE cc_start: 0.9300 (mm) cc_final: 0.8895 (mt) REVERT: M 35 ARG cc_start: 0.8628 (mtt-85) cc_final: 0.8224 (mtp85) REVERT: M 79 LEU cc_start: 0.8129 (OUTLIER) cc_final: 0.7839 (pp) REVERT: M 93 TYR cc_start: 0.8803 (OUTLIER) cc_final: 0.8427 (p90) REVERT: M 103 LEU cc_start: 0.8897 (OUTLIER) cc_final: 0.8437 (mp) REVERT: M 104 GLU cc_start: 0.7545 (mt-10) cc_final: 0.7043 (mt-10) REVERT: M 226 MET cc_start: 0.8178 (mmp) cc_final: 0.7666 (mmp) REVERT: M 290 LYS cc_start: 0.8755 (ttmt) cc_final: 0.8284 (tptt) REVERT: N 43 PHE cc_start: 0.7264 (OUTLIER) cc_final: 0.6741 (t80) REVERT: N 74 ARG cc_start: 0.9233 (OUTLIER) cc_final: 0.8895 (tpt90) REVERT: N 95 ARG cc_start: 0.8628 (OUTLIER) cc_final: 0.7426 (ptp90) REVERT: N 132 ASP cc_start: 0.7766 (t0) cc_final: 0.7050 (t0) REVERT: a 21 TRP cc_start: 0.7617 (t60) cc_final: 0.7300 (t60) REVERT: a 66 TYR cc_start: 0.6885 (OUTLIER) cc_final: 0.6208 (m-80) REVERT: a 78 MET cc_start: 0.8244 (mpp) cc_final: 0.7929 (mtm) REVERT: a 83 LEU cc_start: 0.7455 (OUTLIER) cc_final: 0.7171 (mm) REVERT: a 91 HIS cc_start: 0.4399 (t-90) cc_final: 0.4120 (t-170) REVERT: a 114 MET cc_start: 0.7294 (tpp) cc_final: 0.6905 (mtp) REVERT: a 118 ASN cc_start: 0.7758 (m-40) cc_final: 0.7399 (m110) REVERT: a 130 ASP cc_start: 0.7804 (t0) cc_final: 0.7462 (t0) REVERT: b 67 ILE cc_start: 0.7673 (OUTLIER) cc_final: 0.7369 (tp) REVERT: c 36 MET cc_start: 0.8987 (ppp) cc_final: 0.8423 (ppp) REVERT: d 8 GLU cc_start: 0.8355 (OUTLIER) cc_final: 0.8044 (tt0) REVERT: d 70 PHE cc_start: 0.8037 (t80) cc_final: 0.7486 (t80) REVERT: e 146 TYR cc_start: 0.8168 (t80) cc_final: 0.7954 (t80) REVERT: e 168 MET cc_start: 0.5846 (mtt) cc_final: 0.5310 (mtp) REVERT: e 199 ASN cc_start: 0.7878 (OUTLIER) cc_final: 0.7585 (p0) REVERT: e 219 LYS cc_start: 0.9032 (tttp) cc_final: 0.8284 (tmmt) REVERT: g 5 TYR cc_start: 0.7377 (m-80) cc_final: 0.7027 (m-80) REVERT: h 112 MET cc_start: 0.7122 (ptp) cc_final: 0.6149 (ptp) REVERT: h 158 GLU cc_start: 0.8744 (tm-30) cc_final: 0.8433 (tm-30) REVERT: h 258 ARG cc_start: 0.8110 (tpp80) cc_final: 0.7812 (ttt180) REVERT: h 279 MET cc_start: 0.7244 (mmp) cc_final: 0.6696 (mtp) REVERT: x 216 VAL cc_start: 0.8401 (m) cc_final: 0.7874 (t) REVERT: x 379 MET cc_start: 0.7719 (mmt) cc_final: 0.7080 (mmt) REVERT: x 434 TYR cc_start: 0.7744 (t80) cc_final: 0.7483 (t80) REVERT: x 459 MET cc_start: 0.8511 (mtm) cc_final: 0.8291 (mtm) REVERT: j 141 ILE cc_start: 0.9190 (tp) cc_final: 0.8891 (tp) REVERT: l 26 TYR cc_start: 0.8817 (p90) cc_final: 0.8580 (p90) REVERT: l 81 LEU cc_start: 0.9075 (tp) cc_final: 0.8578 (tt) REVERT: l 93 GLU cc_start: 0.8185 (pt0) cc_final: 0.7279 (pt0) REVERT: l 96 TYR cc_start: 0.8792 (t80) cc_final: 0.8468 (t80) REVERT: l 166 ARG cc_start: 0.8544 (OUTLIER) cc_final: 0.8175 (mmm-85) REVERT: l 187 LEU cc_start: 0.9134 (OUTLIER) cc_final: 0.8853 (mm) REVERT: m 103 LEU cc_start: 0.8897 (OUTLIER) cc_final: 0.8514 (mp) REVERT: m 104 GLU cc_start: 0.7090 (mt-10) cc_final: 0.6883 (mt-10) REVERT: m 133 LEU cc_start: 0.8861 (OUTLIER) cc_final: 0.8306 (tp) REVERT: m 209 MET cc_start: 0.8761 (pmm) cc_final: 0.8186 (pmm) REVERT: m 232 THR cc_start: 0.8947 (OUTLIER) cc_final: 0.8095 (m) REVERT: m 266 GLN cc_start: 0.8448 (mm-40) cc_final: 0.8095 (mm-40) REVERT: m 274 ILE cc_start: 0.8932 (OUTLIER) cc_final: 0.8629 (tp) REVERT: m 290 LYS cc_start: 0.8840 (ttmt) cc_final: 0.8303 (tptt) REVERT: n 8 ILE cc_start: 0.8618 (mm) cc_final: 0.8375 (mt) REVERT: n 74 ARG cc_start: 0.9164 (OUTLIER) cc_final: 0.8900 (tpt90) REVERT: n 132 ASP cc_start: 0.7884 (t0) cc_final: 0.7239 (t70) outliers start: 286 outliers final: 226 residues processed: 1180 average time/residue: 0.5434 time to fit residues: 1096.4147 Evaluate side-chains 1185 residues out of total 5044 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 247 poor density : 938 time to evaluate : 5.316 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 PHE Chi-restraints excluded: chain A residue 39 PHE Chi-restraints excluded: chain A residue 75 LEU Chi-restraints excluded: chain A residue 83 LEU Chi-restraints excluded: chain A residue 85 VAL Chi-restraints excluded: chain A residue 101 VAL Chi-restraints excluded: chain A residue 110 ASN Chi-restraints excluded: chain A residue 132 ASP Chi-restraints excluded: chain A residue 156 THR Chi-restraints excluded: chain B residue 6 ILE Chi-restraints excluded: chain B residue 27 THR Chi-restraints excluded: chain B residue 29 VAL Chi-restraints excluded: chain B residue 35 VAL Chi-restraints excluded: chain B residue 49 PHE Chi-restraints excluded: chain B residue 73 VAL Chi-restraints excluded: chain B residue 74 ILE Chi-restraints excluded: chain C residue 19 TYR Chi-restraints excluded: chain C residue 23 THR Chi-restraints excluded: chain C residue 34 ASN Chi-restraints excluded: chain C residue 63 PHE Chi-restraints excluded: chain C residue 72 ILE Chi-restraints excluded: chain C residue 78 LEU Chi-restraints excluded: chain C residue 79 LEU Chi-restraints excluded: chain C residue 80 LEU Chi-restraints excluded: chain C residue 101 TRP Chi-restraints excluded: chain C residue 113 LEU Chi-restraints excluded: chain D residue 16 ILE Chi-restraints excluded: chain D residue 53 ASP Chi-restraints excluded: chain D residue 54 VAL Chi-restraints excluded: chain D residue 56 MET Chi-restraints excluded: chain D residue 65 LEU Chi-restraints excluded: chain D residue 77 THR Chi-restraints excluded: chain E residue 11 ILE Chi-restraints excluded: chain E residue 16 VAL Chi-restraints excluded: chain E residue 45 VAL Chi-restraints excluded: chain E residue 52 VAL Chi-restraints excluded: chain E residue 59 VAL Chi-restraints excluded: chain E residue 140 THR Chi-restraints excluded: chain E residue 144 LEU Chi-restraints excluded: chain E residue 175 LEU Chi-restraints excluded: chain E residue 180 ILE Chi-restraints excluded: chain E residue 188 TRP Chi-restraints excluded: chain E residue 209 ILE Chi-restraints excluded: chain E residue 213 TYR Chi-restraints excluded: chain G residue 4 SER Chi-restraints excluded: chain G residue 22 VAL Chi-restraints excluded: chain G residue 35 ILE Chi-restraints excluded: chain G residue 105 ASN Chi-restraints excluded: chain H residue 39 LEU Chi-restraints excluded: chain H residue 72 ILE Chi-restraints excluded: chain H residue 93 LEU Chi-restraints excluded: chain H residue 115 LEU Chi-restraints excluded: chain H residue 139 ILE Chi-restraints excluded: chain H residue 262 LEU Chi-restraints excluded: chain H residue 279 MET Chi-restraints excluded: chain H residue 321 GLN Chi-restraints excluded: chain H residue 334 HIS Chi-restraints excluded: chain H residue 384 VAL Chi-restraints excluded: chain H residue 388 ASN Chi-restraints excluded: chain H residue 448 VAL Chi-restraints excluded: chain H residue 450 LEU Chi-restraints excluded: chain H residue 477 ILE Chi-restraints excluded: chain H residue 480 VAL Chi-restraints excluded: chain X residue 13 ILE Chi-restraints excluded: chain X residue 131 THR Chi-restraints excluded: chain X residue 141 TYR Chi-restraints excluded: chain X residue 154 ILE Chi-restraints excluded: chain X residue 205 LEU Chi-restraints excluded: chain X residue 258 TYR Chi-restraints excluded: chain X residue 289 THR Chi-restraints excluded: chain X residue 299 LEU Chi-restraints excluded: chain X residue 310 SER Chi-restraints excluded: chain X residue 382 VAL Chi-restraints excluded: chain X residue 398 SER Chi-restraints excluded: chain X residue 401 LEU Chi-restraints excluded: chain X residue 448 VAL Chi-restraints excluded: chain X residue 467 VAL Chi-restraints excluded: chain X residue 514 ILE Chi-restraints excluded: chain X residue 529 VAL Chi-restraints excluded: chain X residue 532 VAL Chi-restraints excluded: chain X residue 544 VAL Chi-restraints excluded: chain X residue 606 LEU Chi-restraints excluded: chain J residue 41 TYR Chi-restraints excluded: chain J residue 42 ASP Chi-restraints excluded: chain J residue 56 GLN Chi-restraints excluded: chain J residue 61 LEU Chi-restraints excluded: chain J residue 74 ILE Chi-restraints excluded: chain J residue 116 VAL Chi-restraints excluded: chain J residue 120 ILE Chi-restraints excluded: chain J residue 143 ASN Chi-restraints excluded: chain J residue 171 TRP Chi-restraints excluded: chain K residue 81 THR Chi-restraints excluded: chain K residue 85 VAL Chi-restraints excluded: chain K residue 87 THR Chi-restraints excluded: chain K residue 100 THR Chi-restraints excluded: chain K residue 117 ASP Chi-restraints excluded: chain K residue 137 ASP Chi-restraints excluded: chain L residue 81 LEU Chi-restraints excluded: chain L residue 82 LEU Chi-restraints excluded: chain L residue 166 ARG Chi-restraints excluded: chain L residue 167 VAL Chi-restraints excluded: chain L residue 172 THR Chi-restraints excluded: chain L residue 187 LEU Chi-restraints excluded: chain L residue 197 LEU Chi-restraints excluded: chain L residue 199 ASP Chi-restraints excluded: chain L residue 211 ASN Chi-restraints excluded: chain L residue 234 VAL Chi-restraints excluded: chain L residue 244 VAL Chi-restraints excluded: chain L residue 273 LEU Chi-restraints excluded: chain L residue 318 VAL Chi-restraints excluded: chain M residue 49 LEU Chi-restraints excluded: chain M residue 65 ASP Chi-restraints excluded: chain M residue 79 LEU Chi-restraints excluded: chain M residue 93 TYR Chi-restraints excluded: chain M residue 95 ASP Chi-restraints excluded: chain M residue 103 LEU Chi-restraints excluded: chain M residue 133 LEU Chi-restraints excluded: chain M residue 259 LEU Chi-restraints excluded: chain M residue 283 PHE Chi-restraints excluded: chain M residue 306 MET Chi-restraints excluded: chain N residue 20 PHE Chi-restraints excluded: chain N residue 43 PHE Chi-restraints excluded: chain N residue 44 ILE Chi-restraints excluded: chain N residue 55 THR Chi-restraints excluded: chain N residue 74 ARG Chi-restraints excluded: chain N residue 81 ILE Chi-restraints excluded: chain N residue 92 ASP Chi-restraints excluded: chain N residue 95 ARG Chi-restraints excluded: chain N residue 129 LEU Chi-restraints excluded: chain a residue 25 THR Chi-restraints excluded: chain a residue 28 LEU Chi-restraints excluded: chain a residue 66 TYR Chi-restraints excluded: chain a residue 83 LEU Chi-restraints excluded: chain a residue 85 VAL Chi-restraints excluded: chain a residue 110 ASN Chi-restraints excluded: chain a residue 132 ASP Chi-restraints excluded: chain a residue 156 THR Chi-restraints excluded: chain b residue 22 VAL Chi-restraints excluded: chain b residue 27 THR Chi-restraints excluded: chain b residue 29 VAL Chi-restraints excluded: chain b residue 46 MET Chi-restraints excluded: chain b residue 67 ILE Chi-restraints excluded: chain b residue 74 ILE Chi-restraints excluded: chain c residue 16 THR Chi-restraints excluded: chain c residue 19 TYR Chi-restraints excluded: chain c residue 23 THR Chi-restraints excluded: chain c residue 34 ASN Chi-restraints excluded: chain c residue 72 ILE Chi-restraints excluded: chain c residue 80 LEU Chi-restraints excluded: chain c residue 113 LEU Chi-restraints excluded: chain c residue 115 ARG Chi-restraints excluded: chain d residue 8 GLU Chi-restraints excluded: chain d residue 54 VAL Chi-restraints excluded: chain d residue 65 LEU Chi-restraints excluded: chain d residue 72 PHE Chi-restraints excluded: chain d residue 77 THR Chi-restraints excluded: chain e residue 45 VAL Chi-restraints excluded: chain e residue 101 VAL Chi-restraints excluded: chain e residue 140 THR Chi-restraints excluded: chain e residue 144 LEU Chi-restraints excluded: chain e residue 175 LEU Chi-restraints excluded: chain e residue 180 ILE Chi-restraints excluded: chain e residue 188 TRP Chi-restraints excluded: chain e residue 199 ASN Chi-restraints excluded: chain e residue 209 ILE Chi-restraints excluded: chain e residue 213 TYR Chi-restraints excluded: chain e residue 231 MET Chi-restraints excluded: chain g residue 40 VAL Chi-restraints excluded: chain g residue 103 THR Chi-restraints excluded: chain g residue 105 ASN Chi-restraints excluded: chain h residue 34 LEU Chi-restraints excluded: chain h residue 39 LEU Chi-restraints excluded: chain h residue 89 VAL Chi-restraints excluded: chain h residue 93 LEU Chi-restraints excluded: chain h residue 200 ILE Chi-restraints excluded: chain h residue 221 GLU Chi-restraints excluded: chain h residue 225 LEU Chi-restraints excluded: chain h residue 321 GLN Chi-restraints excluded: chain h residue 334 HIS Chi-restraints excluded: chain h residue 430 MET Chi-restraints excluded: chain h residue 458 VAL Chi-restraints excluded: chain h residue 477 ILE Chi-restraints excluded: chain h residue 480 VAL Chi-restraints excluded: chain x residue 13 ILE Chi-restraints excluded: chain x residue 131 THR Chi-restraints excluded: chain x residue 141 TYR Chi-restraints excluded: chain x residue 154 ILE Chi-restraints excluded: chain x residue 205 LEU Chi-restraints excluded: chain x residue 248 LYS Chi-restraints excluded: chain x residue 258 TYR Chi-restraints excluded: chain x residue 299 LEU Chi-restraints excluded: chain x residue 305 LYS Chi-restraints excluded: chain x residue 382 VAL Chi-restraints excluded: chain x residue 398 SER Chi-restraints excluded: chain x residue 401 LEU Chi-restraints excluded: chain x residue 448 VAL Chi-restraints excluded: chain x residue 514 ILE Chi-restraints excluded: chain x residue 529 VAL Chi-restraints excluded: chain x residue 532 VAL Chi-restraints excluded: chain x residue 544 VAL Chi-restraints excluded: chain x residue 593 TYR Chi-restraints excluded: chain x residue 606 LEU Chi-restraints excluded: chain x residue 610 LEU Chi-restraints excluded: chain j residue 25 CYS Chi-restraints excluded: chain j residue 41 TYR Chi-restraints excluded: chain j residue 74 ILE Chi-restraints excluded: chain j residue 116 VAL Chi-restraints excluded: chain j residue 143 ASN Chi-restraints excluded: chain j residue 171 TRP Chi-restraints excluded: chain k residue 58 THR Chi-restraints excluded: chain k residue 72 TYR Chi-restraints excluded: chain k residue 81 THR Chi-restraints excluded: chain k residue 85 VAL Chi-restraints excluded: chain k residue 87 THR Chi-restraints excluded: chain k residue 117 ASP Chi-restraints excluded: chain k residue 137 ASP Chi-restraints excluded: chain l residue 117 THR Chi-restraints excluded: chain l residue 166 ARG Chi-restraints excluded: chain l residue 167 VAL Chi-restraints excluded: chain l residue 172 THR Chi-restraints excluded: chain l residue 187 LEU Chi-restraints excluded: chain l residue 197 LEU Chi-restraints excluded: chain l residue 199 ASP Chi-restraints excluded: chain l residue 235 THR Chi-restraints excluded: chain l residue 244 VAL Chi-restraints excluded: chain l residue 271 ASP Chi-restraints excluded: chain l residue 273 LEU Chi-restraints excluded: chain l residue 318 VAL Chi-restraints excluded: chain l residue 356 ILE Chi-restraints excluded: chain m residue 23 MET Chi-restraints excluded: chain m residue 65 ASP Chi-restraints excluded: chain m residue 95 ASP Chi-restraints excluded: chain m residue 103 LEU Chi-restraints excluded: chain m residue 133 LEU Chi-restraints excluded: chain m residue 154 PHE Chi-restraints excluded: chain m residue 155 SER Chi-restraints excluded: chain m residue 232 THR Chi-restraints excluded: chain m residue 256 LEU Chi-restraints excluded: chain m residue 259 LEU Chi-restraints excluded: chain m residue 274 ILE Chi-restraints excluded: chain m residue 283 PHE Chi-restraints excluded: chain m residue 306 MET Chi-restraints excluded: chain n residue 44 ILE Chi-restraints excluded: chain n residue 55 THR Chi-restraints excluded: chain n residue 74 ARG Chi-restraints excluded: chain n residue 81 ILE Chi-restraints excluded: chain n residue 129 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 604 random chunks: chunk 356 optimal weight: 0.0980 chunk 573 optimal weight: 0.0170 chunk 350 optimal weight: 0.9990 chunk 272 optimal weight: 1.9990 chunk 398 optimal weight: 5.9990 chunk 601 optimal weight: 0.9990 chunk 553 optimal weight: 1.9990 chunk 479 optimal weight: 4.9990 chunk 49 optimal weight: 1.9990 chunk 370 optimal weight: 0.9980 chunk 293 optimal weight: 0.6980 overall best weight: 0.5620 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 41 ASN ** H 189 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 300 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 163 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 126 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 33 GLN L 292 GLN M 57 ASN ** M 223 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 118 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** h 189 ASN ** x 300 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** l 33 GLN ** m 223 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7759 moved from start: 0.3756 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 49624 Z= 0.211 Angle : 0.775 20.227 67458 Z= 0.375 Chirality : 0.044 0.445 7768 Planarity : 0.005 0.060 8248 Dihedral : 5.557 57.651 6651 Min Nonbonded Distance : 2.099 Molprobity Statistics. All-atom Clashscore : 18.18 Ramachandran Plot: Outliers : 0.10 % Allowed : 10.59 % Favored : 89.31 % Rotamer: Outliers : 4.73 % Allowed : 29.57 % Favored : 65.71 % 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: -2.46 (0.11), residues: 6072 helix: -0.33 (0.09), residues: 3434 sheet: -2.95 (0.32), residues: 212 loop : -3.52 (0.12), residues: 2426 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.001 TRP k 62 HIS 0.004 0.001 HIS h 330 PHE 0.051 0.002 PHE D 47 TYR 0.034 0.002 TYR M 157 ARG 0.013 0.000 ARG L 371 ********************** 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 1241 residues out of total 5044 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 238 poor density : 1003 time to evaluate : 5.179 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: A 126 THR cc_start: 0.6371 (p) cc_final: 0.6068 (p) REVERT: B 46 MET cc_start: 0.7552 (ttm) cc_final: 0.7093 (ttm) REVERT: B 67 ILE cc_start: 0.7754 (mp) cc_final: 0.7407 (tp) REVERT: D 38 VAL cc_start: 0.8693 (t) cc_final: 0.8461 (p) REVERT: D 70 PHE cc_start: 0.7952 (t80) cc_final: 0.7404 (t80) REVERT: E 9 LEU cc_start: 0.8377 (tt) cc_final: 0.7424 (mt) REVERT: E 120 ILE cc_start: 0.8466 (mm) cc_final: 0.8194 (mt) REVERT: E 145 MET cc_start: 0.7744 (tpt) cc_final: 0.7238 (tpp) REVERT: E 146 TYR cc_start: 0.7907 (t80) cc_final: 0.7017 (t80) REVERT: E 233 LYS cc_start: 0.8836 (mmtp) cc_final: 0.8506 (mmmm) REVERT: G 37 GLU cc_start: 0.7813 (tm-30) cc_final: 0.7545 (tm-30) REVERT: G 99 GLU cc_start: 0.7461 (tp30) cc_final: 0.7236 (tp30) REVERT: H 112 MET cc_start: 0.6945 (ptp) cc_final: 0.6012 (ptp) REVERT: H 388 ASN cc_start: 0.7822 (OUTLIER) cc_final: 0.6864 (p0) REVERT: X 120 PHE cc_start: 0.7337 (t80) cc_final: 0.6644 (t80) REVERT: X 310 SER cc_start: 0.9370 (OUTLIER) cc_final: 0.9065 (p) REVERT: X 379 MET cc_start: 0.7352 (mmt) cc_final: 0.7003 (mmt) REVERT: X 546 MET cc_start: 0.6738 (ppp) cc_final: 0.6379 (ppp) REVERT: X 614 VAL cc_start: 0.8619 (p) cc_final: 0.8419 (p) REVERT: J 57 TYR cc_start: 0.8934 (p90) cc_final: 0.8637 (p90) REVERT: J 141 ILE cc_start: 0.9163 (tp) cc_final: 0.8919 (tp) REVERT: K 50 ASN cc_start: 0.8168 (p0) cc_final: 0.7687 (p0) REVERT: K 62 TRP cc_start: 0.8449 (m100) cc_final: 0.8208 (m100) REVERT: L 93 GLU cc_start: 0.8184 (pt0) cc_final: 0.7052 (pt0) REVERT: L 96 TYR cc_start: 0.8765 (t80) cc_final: 0.8446 (t80) REVERT: L 133 MET cc_start: 0.8121 (tmm) cc_final: 0.7860 (tmm) REVERT: M 21 ILE cc_start: 0.9300 (mm) cc_final: 0.8914 (mt) REVERT: M 35 ARG cc_start: 0.8532 (mtt-85) cc_final: 0.8277 (mtp85) REVERT: M 79 LEU cc_start: 0.8039 (OUTLIER) cc_final: 0.7763 (pp) REVERT: M 93 TYR cc_start: 0.8698 (OUTLIER) cc_final: 0.8256 (p90) REVERT: M 103 LEU cc_start: 0.8876 (OUTLIER) cc_final: 0.8479 (mp) REVERT: M 104 GLU cc_start: 0.7576 (mt-10) cc_final: 0.7037 (mt-10) REVERT: M 115 MET cc_start: 0.7340 (ttm) cc_final: 0.7065 (ttm) REVERT: M 149 GLU cc_start: 0.7061 (mm-30) cc_final: 0.6844 (mt-10) REVERT: M 226 MET cc_start: 0.7894 (mmp) cc_final: 0.7632 (mmp) REVERT: M 290 LYS cc_start: 0.8741 (ttmt) cc_final: 0.8316 (tptt) REVERT: N 43 PHE cc_start: 0.7123 (OUTLIER) cc_final: 0.6672 (t80) REVERT: N 74 ARG cc_start: 0.9053 (OUTLIER) cc_final: 0.8727 (tpt90) REVERT: N 132 ASP cc_start: 0.7456 (t0) cc_final: 0.6947 (t0) REVERT: a 21 TRP cc_start: 0.7552 (t60) cc_final: 0.7273 (t60) REVERT: a 66 TYR cc_start: 0.6903 (OUTLIER) cc_final: 0.6251 (m-80) REVERT: a 78 MET cc_start: 0.8124 (mpp) cc_final: 0.7762 (mtm) REVERT: a 83 LEU cc_start: 0.7277 (OUTLIER) cc_final: 0.6946 (mm) REVERT: a 114 MET cc_start: 0.6992 (tpp) cc_final: 0.6509 (mtp) REVERT: a 130 ASP cc_start: 0.7824 (t0) cc_final: 0.6898 (t0) REVERT: b 67 ILE cc_start: 0.7597 (OUTLIER) cc_final: 0.7280 (tp) REVERT: c 36 MET cc_start: 0.8971 (ppp) cc_final: 0.8417 (ppp) REVERT: c 109 TYR cc_start: 0.8184 (t80) cc_final: 0.7707 (t80) REVERT: d 8 GLU cc_start: 0.8369 (OUTLIER) cc_final: 0.7946 (tt0) REVERT: d 70 PHE cc_start: 0.7940 (t80) cc_final: 0.7493 (t80) REVERT: e 146 TYR cc_start: 0.7999 (t80) cc_final: 0.7704 (t80) REVERT: e 168 MET cc_start: 0.5816 (mtt) cc_final: 0.5271 (mtp) REVERT: e 219 LYS cc_start: 0.8994 (tttp) cc_final: 0.8298 (tmmt) REVERT: g 5 TYR cc_start: 0.7221 (m-80) cc_final: 0.6966 (m-80) REVERT: g 24 LYS cc_start: 0.8054 (mttp) cc_final: 0.7476 (pttm) REVERT: h 112 MET cc_start: 0.7049 (ptp) cc_final: 0.6245 (ptp) REVERT: h 158 GLU cc_start: 0.8634 (tm-30) cc_final: 0.8343 (tm-30) REVERT: h 258 ARG cc_start: 0.7987 (tpp80) cc_final: 0.7771 (ttm170) REVERT: h 279 MET cc_start: 0.7124 (mmp) cc_final: 0.6622 (mtp) REVERT: h 342 PHE cc_start: 0.8148 (m-80) cc_final: 0.7876 (m-80) REVERT: h 407 TRP cc_start: 0.7843 (m100) cc_final: 0.7524 (m100) REVERT: x 300 GLN cc_start: 0.8984 (tp-100) cc_final: 0.8149 (tp40) REVERT: x 305 LYS cc_start: 0.8695 (OUTLIER) cc_final: 0.7979 (mtpp) REVERT: x 310 SER cc_start: 0.9373 (p) cc_final: 0.9030 (p) REVERT: x 379 MET cc_start: 0.7666 (mmt) cc_final: 0.7027 (mmt) REVERT: x 434 TYR cc_start: 0.7620 (t80) cc_final: 0.7341 (t80) REVERT: x 459 MET cc_start: 0.8477 (mtm) cc_final: 0.8197 (mtm) REVERT: x 614 VAL cc_start: 0.8639 (p) cc_final: 0.8427 (p) REVERT: j 57 TYR cc_start: 0.8876 (p90) cc_final: 0.8535 (p90) REVERT: j 141 ILE cc_start: 0.9185 (tp) cc_final: 0.8896 (tp) REVERT: k 167 GLU cc_start: 0.6855 (pm20) cc_final: 0.6220 (pm20) REVERT: l 81 LEU cc_start: 0.8944 (tp) cc_final: 0.8598 (tt) REVERT: l 93 GLU cc_start: 0.8095 (pt0) cc_final: 0.7143 (pt0) REVERT: l 96 TYR cc_start: 0.8711 (t80) cc_final: 0.8461 (t80) REVERT: l 97 SER cc_start: 0.9020 (t) cc_final: 0.8817 (t) REVERT: l 166 ARG cc_start: 0.8477 (OUTLIER) cc_final: 0.8139 (mmm-85) REVERT: l 187 LEU cc_start: 0.9059 (OUTLIER) cc_final: 0.8808 (mm) REVERT: l 189 GLN cc_start: 0.7404 (tp40) cc_final: 0.7159 (tp40) REVERT: m 103 LEU cc_start: 0.8941 (OUTLIER) cc_final: 0.8593 (mp) REVERT: m 209 MET cc_start: 0.8601 (pmm) cc_final: 0.8000 (pmm) REVERT: m 274 ILE cc_start: 0.8838 (OUTLIER) cc_final: 0.8542 (tp) REVERT: m 290 LYS cc_start: 0.8856 (ttmt) cc_final: 0.8304 (tptt) REVERT: n 8 ILE cc_start: 0.8498 (mm) cc_final: 0.8266 (mt) REVERT: n 66 MET cc_start: 0.8322 (tpt) cc_final: 0.7936 (tpt) REVERT: n 132 ASP cc_start: 0.7725 (t0) cc_final: 0.7005 (t70) outliers start: 238 outliers final: 190 residues processed: 1160 average time/residue: 0.5463 time to fit residues: 1087.2547 Evaluate side-chains 1168 residues out of total 5044 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 206 poor density : 962 time to evaluate : 4.779 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 PHE Chi-restraints excluded: chain A residue 85 VAL Chi-restraints excluded: chain A residue 101 VAL Chi-restraints excluded: chain A residue 132 ASP Chi-restraints excluded: chain A residue 156 THR Chi-restraints excluded: chain B residue 6 ILE Chi-restraints excluded: chain B residue 27 THR Chi-restraints excluded: chain B residue 29 VAL Chi-restraints excluded: chain B residue 35 VAL Chi-restraints excluded: chain B residue 74 ILE Chi-restraints excluded: chain C residue 19 TYR Chi-restraints excluded: chain C residue 23 THR Chi-restraints excluded: chain C residue 34 ASN Chi-restraints excluded: chain C residue 63 PHE Chi-restraints excluded: chain C residue 80 LEU Chi-restraints excluded: chain C residue 113 LEU Chi-restraints excluded: chain D residue 16 ILE Chi-restraints excluded: chain D residue 31 SER Chi-restraints excluded: chain D residue 53 ASP Chi-restraints excluded: chain D residue 54 VAL Chi-restraints excluded: chain D residue 56 MET Chi-restraints excluded: chain D residue 65 LEU Chi-restraints excluded: chain D residue 77 THR Chi-restraints excluded: chain E residue 16 VAL Chi-restraints excluded: chain E residue 59 VAL Chi-restraints excluded: chain E residue 140 THR Chi-restraints excluded: chain E residue 144 LEU Chi-restraints excluded: chain E residue 175 LEU Chi-restraints excluded: chain E residue 180 ILE Chi-restraints excluded: chain E residue 188 TRP Chi-restraints excluded: chain E residue 209 ILE Chi-restraints excluded: chain E residue 213 TYR Chi-restraints excluded: chain G residue 4 SER Chi-restraints excluded: chain G residue 22 VAL Chi-restraints excluded: chain G residue 35 ILE Chi-restraints excluded: chain G residue 41 ASN Chi-restraints excluded: chain G residue 86 THR Chi-restraints excluded: chain G residue 105 ASN Chi-restraints excluded: chain H residue 93 LEU Chi-restraints excluded: chain H residue 115 LEU Chi-restraints excluded: chain H residue 139 ILE Chi-restraints excluded: chain H residue 279 MET Chi-restraints excluded: chain H residue 334 HIS Chi-restraints excluded: chain H residue 384 VAL Chi-restraints excluded: chain H residue 388 ASN Chi-restraints excluded: chain H residue 423 TYR Chi-restraints excluded: chain H residue 430 MET Chi-restraints excluded: chain H residue 450 LEU Chi-restraints excluded: chain H residue 477 ILE Chi-restraints excluded: chain X residue 131 THR Chi-restraints excluded: chain X residue 141 TYR Chi-restraints excluded: chain X residue 154 ILE Chi-restraints excluded: chain X residue 205 LEU Chi-restraints excluded: chain X residue 289 THR Chi-restraints excluded: chain X residue 310 SER Chi-restraints excluded: chain X residue 382 VAL Chi-restraints excluded: chain X residue 398 SER Chi-restraints excluded: chain X residue 414 LEU Chi-restraints excluded: chain X residue 448 VAL Chi-restraints excluded: chain X residue 514 ILE Chi-restraints excluded: chain X residue 529 VAL Chi-restraints excluded: chain X residue 532 VAL Chi-restraints excluded: chain X residue 544 VAL Chi-restraints excluded: chain X residue 548 TYR Chi-restraints excluded: chain X residue 606 LEU Chi-restraints excluded: chain X residue 610 LEU Chi-restraints excluded: chain J residue 41 TYR Chi-restraints excluded: chain J residue 56 GLN Chi-restraints excluded: chain J residue 74 ILE Chi-restraints excluded: chain J residue 120 ILE Chi-restraints excluded: chain J residue 143 ASN Chi-restraints excluded: chain J residue 171 TRP Chi-restraints excluded: chain K residue 58 THR Chi-restraints excluded: chain K residue 81 THR Chi-restraints excluded: chain K residue 85 VAL Chi-restraints excluded: chain K residue 87 THR Chi-restraints excluded: chain K residue 100 THR Chi-restraints excluded: chain K residue 117 ASP Chi-restraints excluded: chain K residue 137 ASP Chi-restraints excluded: chain L residue 33 GLN Chi-restraints excluded: chain L residue 82 LEU Chi-restraints excluded: chain L residue 166 ARG Chi-restraints excluded: chain L residue 167 VAL Chi-restraints excluded: chain L residue 197 LEU Chi-restraints excluded: chain L residue 199 ASP Chi-restraints excluded: chain L residue 234 VAL Chi-restraints excluded: chain L residue 244 VAL Chi-restraints excluded: chain L residue 271 ASP Chi-restraints excluded: chain L residue 273 LEU Chi-restraints excluded: chain L residue 318 VAL Chi-restraints excluded: chain M residue 49 LEU Chi-restraints excluded: chain M residue 79 LEU Chi-restraints excluded: chain M residue 93 TYR Chi-restraints excluded: chain M residue 95 ASP Chi-restraints excluded: chain M residue 103 LEU Chi-restraints excluded: chain M residue 133 LEU Chi-restraints excluded: chain M residue 259 LEU Chi-restraints excluded: chain N residue 20 PHE Chi-restraints excluded: chain N residue 43 PHE Chi-restraints excluded: chain N residue 44 ILE Chi-restraints excluded: chain N residue 55 THR Chi-restraints excluded: chain N residue 74 ARG Chi-restraints excluded: chain N residue 81 ILE Chi-restraints excluded: chain N residue 92 ASP Chi-restraints excluded: chain N residue 129 LEU Chi-restraints excluded: chain a residue 28 LEU Chi-restraints excluded: chain a residue 66 TYR Chi-restraints excluded: chain a residue 83 LEU Chi-restraints excluded: chain a residue 85 VAL Chi-restraints excluded: chain a residue 110 ASN Chi-restraints excluded: chain a residue 132 ASP Chi-restraints excluded: chain a residue 156 THR Chi-restraints excluded: chain b residue 22 VAL Chi-restraints excluded: chain b residue 27 THR Chi-restraints excluded: chain b residue 29 VAL Chi-restraints excluded: chain b residue 46 MET Chi-restraints excluded: chain b residue 67 ILE Chi-restraints excluded: chain b residue 74 ILE Chi-restraints excluded: chain c residue 19 TYR Chi-restraints excluded: chain c residue 23 THR Chi-restraints excluded: chain c residue 34 ASN Chi-restraints excluded: chain c residue 80 LEU Chi-restraints excluded: chain c residue 113 LEU Chi-restraints excluded: chain c residue 115 ARG Chi-restraints excluded: chain d residue 8 GLU Chi-restraints excluded: chain d residue 54 VAL Chi-restraints excluded: chain d residue 56 MET Chi-restraints excluded: chain d residue 65 LEU Chi-restraints excluded: chain d residue 72 PHE Chi-restraints excluded: chain d residue 77 THR Chi-restraints excluded: chain e residue 45 VAL Chi-restraints excluded: chain e residue 101 VAL Chi-restraints excluded: chain e residue 140 THR Chi-restraints excluded: chain e residue 144 LEU Chi-restraints excluded: chain e residue 175 LEU Chi-restraints excluded: chain e residue 180 ILE Chi-restraints excluded: chain e residue 188 TRP Chi-restraints excluded: chain e residue 213 TYR Chi-restraints excluded: chain e residue 231 MET Chi-restraints excluded: chain g residue 40 VAL Chi-restraints excluded: chain g residue 103 THR Chi-restraints excluded: chain g residue 105 ASN Chi-restraints excluded: chain h residue 34 LEU Chi-restraints excluded: chain h residue 39 LEU Chi-restraints excluded: chain h residue 93 LEU Chi-restraints excluded: chain h residue 200 ILE Chi-restraints excluded: chain h residue 221 GLU Chi-restraints excluded: chain h residue 225 LEU Chi-restraints excluded: chain h residue 334 HIS Chi-restraints excluded: chain h residue 458 VAL Chi-restraints excluded: chain h residue 477 ILE Chi-restraints excluded: chain x residue 131 THR Chi-restraints excluded: chain x residue 141 TYR Chi-restraints excluded: chain x residue 154 ILE Chi-restraints excluded: chain x residue 205 LEU Chi-restraints excluded: chain x residue 248 LYS Chi-restraints excluded: chain x residue 299 LEU Chi-restraints excluded: chain x residue 305 LYS Chi-restraints excluded: chain x residue 382 VAL Chi-restraints excluded: chain x residue 398 SER Chi-restraints excluded: chain x residue 401 LEU Chi-restraints excluded: chain x residue 448 VAL Chi-restraints excluded: chain x residue 529 VAL Chi-restraints excluded: chain x residue 532 VAL Chi-restraints excluded: chain x residue 544 VAL Chi-restraints excluded: chain x residue 593 TYR Chi-restraints excluded: chain x residue 606 LEU Chi-restraints excluded: chain j residue 25 CYS Chi-restraints excluded: chain j residue 41 TYR Chi-restraints excluded: chain j residue 143 ASN Chi-restraints excluded: chain j residue 171 TRP Chi-restraints excluded: chain k residue 58 THR Chi-restraints excluded: chain k residue 72 TYR Chi-restraints excluded: chain k residue 81 THR Chi-restraints excluded: chain k residue 85 VAL Chi-restraints excluded: chain k residue 87 THR Chi-restraints excluded: chain k residue 117 ASP Chi-restraints excluded: chain l residue 33 GLN Chi-restraints excluded: chain l residue 166 ARG Chi-restraints excluded: chain l residue 172 THR Chi-restraints excluded: chain l residue 187 LEU Chi-restraints excluded: chain l residue 197 LEU Chi-restraints excluded: chain l residue 199 ASP Chi-restraints excluded: chain l residue 211 ASN Chi-restraints excluded: chain l residue 234 VAL Chi-restraints excluded: chain l residue 235 THR Chi-restraints excluded: chain l residue 244 VAL Chi-restraints excluded: chain l residue 271 ASP Chi-restraints excluded: chain l residue 273 LEU Chi-restraints excluded: chain l residue 318 VAL Chi-restraints excluded: chain l residue 356 ILE Chi-restraints excluded: chain m residue 23 MET Chi-restraints excluded: chain m residue 95 ASP Chi-restraints excluded: chain m residue 103 LEU Chi-restraints excluded: chain m residue 133 LEU Chi-restraints excluded: chain m residue 154 PHE Chi-restraints excluded: chain m residue 212 PHE Chi-restraints excluded: chain m residue 256 LEU Chi-restraints excluded: chain m residue 259 LEU Chi-restraints excluded: chain m residue 274 ILE Chi-restraints excluded: chain m residue 283 PHE Chi-restraints excluded: chain m residue 306 MET Chi-restraints excluded: chain n residue 44 ILE Chi-restraints excluded: chain n residue 55 THR Chi-restraints excluded: chain n residue 81 ILE Chi-restraints excluded: chain n residue 129 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 604 random chunks: chunk 380 optimal weight: 0.0570 chunk 510 optimal weight: 7.9990 chunk 146 optimal weight: 7.9990 chunk 441 optimal weight: 0.9990 chunk 70 optimal weight: 0.9990 chunk 133 optimal weight: 20.0000 chunk 479 optimal weight: 7.9990 chunk 200 optimal weight: 0.6980 chunk 492 optimal weight: 0.9990 chunk 60 optimal weight: 7.9990 chunk 88 optimal weight: 9.9990 overall best weight: 0.7504 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 189 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 321 GLN ** X 300 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 163 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 126 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 33 GLN L 39 ASN ** M 223 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 91 HIS ** a 118 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 189 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** h 321 GLN ** x 300 GLN ** 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** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3647 r_free = 0.3647 target = 0.114261 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.098476 restraints weight = 100930.753| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.102122 restraints weight = 131012.457| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.102434 restraints weight = 61254.959| |-----------------------------------------------------------------------------| r_work (final): 0.3454 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7770 moved from start: 0.3792 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.316 49624 Z= 0.322 Angle : 0.922 59.179 67458 Z= 0.493 Chirality : 0.047 1.139 7768 Planarity : 0.005 0.060 8248 Dihedral : 5.509 57.443 6649 Min Nonbonded Distance : 1.867 Molprobity Statistics. All-atom Clashscore : 20.72 Ramachandran Plot: Outliers : 0.13 % Allowed : 10.69 % Favored : 89.18 % Rotamer: Outliers : 4.41 % Allowed : 30.52 % Favored : 65.07 % Cbeta Deviations : 0.05 % 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: -2.46 (0.11), residues: 6072 helix: -0.33 (0.09), residues: 3434 sheet: -2.94 (0.32), residues: 212 loop : -3.52 (0.12), residues: 2426 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP k 62 HIS 0.003 0.001 HIS x 336 PHE 0.043 0.002 PHE h 247 TYR 0.040 0.002 TYR d 78 ARG 0.016 0.000 ARG J 177 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 15948.39 seconds wall clock time: 283 minutes 56.10 seconds (17036.10 seconds total)