Starting phenix.real_space_refine on Sat Mar 16 08:06:17 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7b0n_11969/03_2024/7b0n_11969_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7b0n_11969/03_2024/7b0n_11969.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7b0n_11969/03_2024/7b0n_11969_trim_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7b0n_11969/03_2024/7b0n_11969_trim_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7b0n_11969/03_2024/7b0n_11969_trim_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7b0n_11969/03_2024/7b0n_11969.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7b0n_11969/03_2024/7b0n_11969.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7b0n_11969/03_2024/7b0n_11969_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7b0n_11969/03_2024/7b0n_11969_trim_updated.pdb" } resolution = 3.7 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.007 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 8 Type Number sf(0) Gaussians Fe 24 7.16 5 Zn 1 6.06 5 P 35 5.49 5 S 308 5.16 5 C 42284 2.51 5 N 10750 2.21 5 O 11950 1.98 5 H 64087 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 4": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 7": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ARG 49": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A PHE 52": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ASP 67": "OD1" <-> "OD2" Residue "A GLU 69": "OE1" <-> "OE2" Residue "B ASP 65": "OD1" <-> "OD2" Residue "B PHE 76": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B ASP 99": "OD1" <-> "OD2" Residue "B ARG 102": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B PHE 107": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B ARG 112": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 165": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ASP 174": "OD1" <-> "OD2" Residue "B TYR 176": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B ARG 199": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 209": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C GLU 37": "OE1" <-> "OE2" Residue "C GLU 52": "OE1" <-> "OE2" Residue "C ASP 62": "OD1" <-> "OD2" Residue "C PHE 89": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C TYR 142": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C TYR 158": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C TYR 172": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C GLU 181": "OE1" <-> "OE2" Residue "C PHE 190": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C ASP 195": "OD1" <-> "OD2" Residue "C ARG 198": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C PHE 214": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C TYR 219": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C GLU 221": "OE1" <-> "OE2" Residue "C ARG 223": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C ARG 230": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C TYR 233": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C GLU 237": "OE1" <-> "OE2" Residue "C ARG 259": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C ASP 260": "OD1" <-> "OD2" Residue "C ASP 264": "OD1" <-> "OD2" Residue "C PHE 266": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D PHE 53": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D ARG 54": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D GLU 63": "OE1" <-> "OE2" Residue "D TYR 129": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D TYR 138": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D ASP 143": "OD1" <-> "OD2" Residue "D ARG 169": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D TYR 172": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D ARG 174": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D PHE 177": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D PHE 203": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D ARG 231": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D ARG 257": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D ASP 259": "OD1" <-> "OD2" Residue "D ASP 304": "OD1" <-> "OD2" Residue "D ARG 306": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D TYR 311": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D GLU 362": "OE1" <-> "OE2" Residue "D ASP 363": "OD1" <-> "OD2" Residue "D PHE 385": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D TYR 392": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D TYR 400": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D ASP 417": "OD1" <-> "OD2" Residue "D TYR 423": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D ASP 439": "OD1" <-> "OD2" Residue "D GLU 463": "OE1" <-> "OE2" Residue "D ASP 465": "OD1" <-> "OD2" Residue "D ARG 466": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "E ARG 34": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "E TYR 84": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E GLU 98": "OE1" <-> "OE2" Residue "E GLU 142": "OE1" <-> "OE2" Residue "E GLU 231": "OE1" <-> "OE2" Residue "E GLU 241": "OE1" <-> "OE2" Residue "F TYR 31": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F ASP 36": "OD1" <-> "OD2" Residue "F ASP 46": "OD1" <-> "OD2" Residue "F ASP 51": "OD1" <-> "OD2" Residue "F ARG 56": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "F ASP 60": "OD1" <-> "OD2" Residue "F GLU 110": "OE1" <-> "OE2" Residue "F ARG 113": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "F ASP 129": "OD1" <-> "OD2" Residue "F ASP 136": "OD1" <-> "OD2" Residue "F GLU 142": "OE1" <-> "OE2" Residue "F TYR 157": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F TYR 159": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F TYR 179": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F ASP 196": "OD1" <-> "OD2" Residue "F PHE 231": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F GLU 270": "OE1" <-> "OE2" Residue "F ARG 299": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "F PHE 341": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F ASP 342": "OD1" <-> "OD2" Residue "F ARG 371": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "F PHE 375": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F GLU 379": "OE1" <-> "OE2" Residue "F ARG 400": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "F TYR 415": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F ASP 457": "OD1" <-> "OD2" Residue "F ARG 472": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "G ARG 89": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "G GLU 112": "OE1" <-> "OE2" Residue "G GLU 141": "OE1" <-> "OE2" Residue "G ARG 150": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "G ARG 155": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "G ARG 165": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "G ASP 169": "OD1" <-> "OD2" Residue "G ASP 231": "OD1" <-> "OD2" Residue "G ARG 248": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "G ARG 283": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "G ASP 287": "OD1" <-> "OD2" Residue "G ARG 298": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "G ARG 315": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "G ASP 326": "OD1" <-> "OD2" Residue "G ASP 344": "OD1" <-> "OD2" Residue "G GLU 355": "OE1" <-> "OE2" Residue "G PHE 391": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "G ARG 392": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "G TYR 395": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "G ARG 434": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "G ASP 447": "OD1" <-> "OD2" Residue "G PHE 450": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "G ASP 451": "OD1" <-> "OD2" Residue "G ASP 493": "OD1" <-> "OD2" Residue "G PHE 497": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "G PHE 504": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "G GLU 506": "OE1" <-> "OE2" Residue "G ARG 528": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "G ASP 540": "OD1" <-> "OD2" Residue "G GLU 541": "OE1" <-> "OE2" Residue "G ASP 577": "OD1" <-> "OD2" Residue "G TYR 599": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "G GLU 631": "OE1" <-> "OE2" Residue "G TYR 639": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "G ASP 641": "OD1" <-> "OD2" Residue "G TYR 698": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "G ARG 705": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "G ASP 720": "OD1" <-> "OD2" Residue "H PHE 17": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "H ARG 27": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "H ARG 35": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "H ARG 36": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "H PHE 41": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "H PHE 108": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "H PHE 118": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "H PHE 154": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "H ARG 174": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "H PHE 189": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "H ARG 199": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "H PHE 202": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "H ASP 203": "OD1" <-> "OD2" Residue "H PHE 228": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "H TYR 244": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "H TYR 250": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "H TYR 255": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "H TYR 268": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "H PHE 291": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "H PHE 293": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "H ARG 297": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "H ASP 306": "OD1" <-> "OD2" Residue "H PHE 321": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "I PHE 252": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "I ARG 253": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "I ARG 256": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "I TYR 274": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "I TYR 299": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "I ARG 310": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "I PHE 311": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "I GLU 324": "OE1" <-> "OE2" Residue "I GLU 347": "OE1" <-> "OE2" Residue "I TYR 359": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "I TYR 368": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "I TYR 371": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "I GLU 383": "OE1" <-> "OE2" Residue "I ASP 409": "OD1" <-> "OD2" Residue "I ASP 422": "OD1" <-> "OD2" Residue "I ARG 426": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "J TYR 3": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "J PHE 71": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "J PHE 73": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "J ASP 79": "OD1" <-> "OD2" Residue "J ARG 92": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "J ASP 137": "OD1" <-> "OD2" Residue "K PHE 15": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "K ASP 48": "OD1" <-> "OD2" Residue "K ASP 49": "OD1" <-> "OD2" Residue "K TYR 77": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "K TYR 87": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "L PHE 723": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "L PHE 735": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "L TYR 754": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "L TYR 756": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "L ASP 776": "OD1" <-> "OD2" Residue "L ASP 779": "OD1" <-> "OD2" Residue "L GLU 785": "OE1" <-> "OE2" Residue "L ASP 787": "OD1" <-> "OD2" Residue "L TYR 811": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "L GLU 813": "OE1" <-> "OE2" Residue "L PHE 822": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "L PHE 885": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "L PHE 886": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "L PHE 897": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "L GLU 946": "OE1" <-> "OE2" Residue "L ARG 970": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "L PHE 1043": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "L GLU 1061": "OE1" <-> "OE2" Residue "L TYR 1074": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "L TYR 1133": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "L TYR 1153": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "L PHE 1173": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "L ASP 1206": "OD1" <-> "OD2" Residue "L PHE 1214": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "L PHE 1236": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "L PHE 1237": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "L TYR 1247": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "L ASP 1262": "OD1" <-> "OD2" Residue "L PHE 1268": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "L ASP 1285": "OD1" <-> "OD2" Residue "L TYR 1290": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "L PHE 1359": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "M PHE 555": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "M PHE 559": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "M ASP 574": "OD1" <-> "OD2" Residue "M PHE 590": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "M TYR 616": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "M PHE 639": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "M ARG 664": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "M PHE 679": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "M PHE 696": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "M ASP 707": "OD1" <-> "OD2" Residue "M GLU 739": "OE1" <-> "OE2" Residue "M TYR 758": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "M GLU 770": "OE1" <-> "OE2" Residue "M TYR 780": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "M ASP 854": "OD1" <-> "OD2" Residue "M ARG 907": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "M TYR 925": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "M ASP 947": "OD1" <-> "OD2" Residue "M PHE 954": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "M TYR 986": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "N ARG 2424": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "N TYR 2433": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "N PHE 2463": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "N PHE 2466": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "N ASP 2471": "OD1" <-> "OD2" Residue "N TYR 2487": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "N TYR 2490": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "N TYR 2495": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "N GLU 2504": "OE1" <-> "OE2" Residue "N ASP 2524": "OD1" <-> "OD2" Residue "N TYR 2550": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "N TYR 2559": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "N TYR 2577": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "N ARG 2685": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "N TYR 2713": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "N PHE 2731": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "N TYR 2748": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "N TYR 2761": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "N PHE 2799": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "N TYR 2814": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "N ASP 2825": "OD1" <-> "OD2" Residue "N PHE 2866": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "N PHE 2870": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "O TYR 417": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "O TYR 420": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "O ASP 426": "OD1" <-> "OD2" Residue "O PHE 429": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "O TYR 435": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "O TYR 441": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "O ASP 462": "OD1" <-> "OD2" Residue "O PHE 484": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "O PHE 499": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "O TYR 509": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "O ASP 512": "OD1" <-> "OD2" Residue "O PHE 552": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "O PHE 554": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "P TYR 68": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "P ARG 85": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "P GLU 86": "OE1" <-> "OE2" Residue "P ASP 98": "OD1" <-> "OD2" Residue "P ARG 110": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "P TYR 133": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "P ASP 142": "OD1" <-> "OD2" Residue "P PHE 179": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "P PHE 206": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "P ASP 251": "OD1" <-> "OD2" Residue "P PHE 259": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "P TYR 262": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "P GLU 278": "OE1" <-> "OE2" Residue "P GLU 288": "OE1" <-> "OE2" Residue "P ARG 316": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "P ASP 324": "OD1" <-> "OD2" Residue "P ASP 334": "OD1" <-> "OD2" Residue "P GLU 339": "OE1" <-> "OE2" Residue "P ASP 342": "OD1" <-> "OD2" Residue "P ARG 352": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "Q ASP 37": "OD1" <-> "OD2" Residue "Q ARG 56": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "Q ARG 59": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "Q ARG 79": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "Q ASP 81": "OD1" <-> "OD2" Residue "Q ASP 83": "OD1" <-> "OD2" Residue "Q GLU 92": "OE1" <-> "OE2" Residue "Q TYR 104": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "R GLU 33": "OE1" <-> "OE2" Residue "R GLU 65": "OE1" <-> "OE2" Residue "R ASP 68": "OD1" <-> "OD2" Residue "R TYR 76": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "R PHE 89": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "R PHE 114": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "R ASP 118": "OD1" <-> "OD2" Residue "R TYR 132": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "S PHE 25": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "S PHE 33": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "S ARG 45": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "S PHE 55": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "S ARG 57": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "S ASP 69": "OD1" <-> "OD2" Residue "S GLU 73": "OE1" <-> "OE2" Residue "T ASP 31": "OD1" <-> "OD2" Residue "T ARG 35": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "T ASP 86": "OD1" <-> "OD2" Residue "T ASP 90": "OD1" <-> "OD2" Residue "T GLU 100": "OE1" <-> "OE2" Residue "T TYR 101": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "U ASP 71": "OD1" <-> "OD2" Residue "U ASP 84": "OD1" <-> "OD2" Residue "U GLU 102": "OE1" <-> "OE2" Residue "U ASP 113": "OD1" <-> "OD2" Residue "V GLU 27": "OE1" <-> "OE2" Residue "V TYR 37": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "V GLU 86": "OE1" <-> "OE2" Residue "V GLU 119": "OE1" <-> "OE2" Residue "V GLU 127": "OE1" <-> "OE2" Residue "W PHE 14": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "W GLU 44": "OE1" <-> "OE2" Residue "W PHE 47": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "W PHE 60": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "W GLU 61": "OE1" <-> "OE2" Residue "W ARG 62": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "W GLU 82": "OE1" <-> "OE2" Residue "X ARG 3": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "X ASP 24": "OD1" <-> "OD2" Residue "X TYR 49": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "X ASP 67": "OD1" <-> "OD2" Residue "X ARG 74": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "X ASP 85": "OD1" <-> "OD2" Residue "X ASP 92": "OD1" <-> "OD2" Residue "X ARG 136": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "X ASP 138": "OD1" <-> "OD2" Residue "X PHE 143": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "X ASP 155": "OD1" <-> "OD2" Residue "X TYR 163": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "Y PHE 1254": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "Y TYR 1261": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "Y ARG 1294": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "Y PHE 1301": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "Y PHE 1322": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "Y ARG 1326": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "Y ARG 1353": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "Y GLU 1364": "OE1" <-> "OE2" Residue "Y GLU 1378": "OE1" <-> "OE2" Residue "Z ASP 7": "OD1" <-> "OD2" Residue "Z ARG 20": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "Z ARG 21": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "Z TYR 33": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "Z ARG 66": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "Z ARG 79": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "Z GLU 90": "OE1" <-> "OE2" Residue "Z ASP 102": "OD1" <-> "OD2" Residue "Z ASP 104": "OD1" <-> "OD2" Residue "Z TYR 108": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "a ARG 32": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "a ARG 37": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "a ASP 43": "OD1" <-> "OD2" Residue "a ASP 46": "OD1" <-> "OD2" Residue "a ARG 52": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "a ARG 55": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "b ARG 14": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "b ARG 23": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "b PHE 27": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "b PHE 28": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "b ARG 47": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "b TYR 52": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "b TYR 62": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "b ARG 67": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "b ARG 69": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "b GLU 78": "OE1" <-> "OE2" Residue "c PHE 10": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "c TYR 13": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "c ARG 25": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "c ARG 45": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "c GLU 54": "OE1" <-> "OE2" Residue "c ASP 60": "OD1" <-> "OD2" Residue "c ASP 78": "OD1" <-> "OD2" Residue "c PHE 89": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "c ASP 90": "OD1" <-> "OD2" Residue "c ASP 110": "OD1" <-> "OD2" Residue "c ASP 138": "OD1" <-> "OD2" Residue "c TYR 141": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "c TYR 176": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "c ARG 179": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "c PHE 181": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "d PHE 4": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "e ARG 12": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "f TYR 6": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "f ARG 7": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "f ARG 10": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "f ARG 34": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "f ASP 49": "OD1" <-> "OD2" Residue "f TYR 60": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "f GLU 62": "OE1" <-> "OE2" Residue "f GLU 65": "OE1" <-> "OE2" Residue "f TYR 68": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "f TYR 83": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "g GLU 53": "OE1" <-> "OE2" Residue "g ARG 62": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "g PHE 73": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "g TYR 119": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "g ASP 138": "OD1" <-> "OD2" Residue "g ARG 156": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "g ASP 163": "OD1" <-> "OD2" Residue "g GLU 189": "OE1" <-> "OE2" Residue "g GLU 198": "OE1" <-> "OE2" Residue "g ASP 212": "OD1" <-> "OD2" Residue "g GLU 217": "OE1" <-> "OE2" Residue "g ASP 219": "OD1" <-> "OD2" Residue "g ASP 230": "OD1" <-> "OD2" Residue "g TYR 231": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "h PHE 46": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "h TYR 50": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "h TYR 65": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "h TYR 127": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "h ARG 149": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "h GLU 150": "OE1" <-> "OE2" Residue "i ARG 5": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "i TYR 6": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "i PHE 8": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "i ARG 53": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "i ARG 55": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "i ARG 75": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "j TYR 56": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "k ARG 11": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "k GLU 13": "OE1" <-> "OE2" Residue "k TYR 17": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "k TYR 44": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "l PHE 29": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "l TYR 57": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "l ASP 59": "OD1" <-> "OD2" Residue "l ARG 64": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "l ASP 83": "OD1" <-> "OD2" Residue "l PHE 104": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "l PHE 114": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "l GLU 117": "OE1" <-> "OE2" Residue "l GLU 133": "OE1" <-> "OE2" Residue "l PHE 143": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "m ARG 12": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "m ASP 21": "OD1" <-> "OD2" Residue "m PHE 41": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "m TYR 42": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "m PHE 80": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "n PHE 7": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "n ARG 33": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "n ARG 44": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "n PHE 47": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "n ARG 67": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "n ASP 77": "OD1" <-> "OD2" Residue "o GLU 3": "OE1" <-> "OE2" Residue "o ASP 12": "OD1" <-> "OD2" Residue "o GLU 35": "OE1" <-> "OE2" Residue "o ARG 37": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "o TYR 42": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "o GLU 50": "OE1" <-> "OE2" Residue "o ASP 61": "OD1" <-> "OD2" Residue "o ARG 65": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "o GLU 78": "OE1" <-> "OE2" Residue "p ASP 14": "OD1" <-> "OD2" Residue "p TYR 17": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "p TYR 30": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "p TYR 52": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "p TYR 82": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "p ASP 89": "OD1" <-> "OD2" 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: 129439 Number of models: 1 Model: "" Number of chains: 62 Chain: "A" Number of atoms: 1583 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 1583 Classifications: {'peptide': 94} Link IDs: {'PTRANS': 4, 'TRANS': 89} Chain breaks: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'FME:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "B" Number of atoms: 2766 Number of conformers: 1 Conformer: "" Number of residues, atoms: 177, 2766 Classifications: {'peptide': 177} Link IDs: {'PCIS': 2, 'PTRANS': 12, 'TRANS': 162} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 2 Chain: "C" Number of atoms: 3924 Number of conformers: 1 Conformer: "" Number of residues, atoms: 242, 3924 Classifications: {'peptide': 242} Link IDs: {'PTRANS': 20, 'TRANS': 221} Chain: "D" Number of atoms: 6788 Number of conformers: 1 Conformer: "" Number of residues, atoms: 437, 6788 Classifications: {'peptide': 437} Link IDs: {'PTRANS': 25, 'TRANS': 411} Unresolved non-hydrogen bonds: 29 Unresolved non-hydrogen angles: 38 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 1, 'HIS:plan': 2} Unresolved non-hydrogen planarities: 21 Chain: "E" Number of atoms: 3348 Number of conformers: 1 Conformer: "" Number of residues, atoms: 216, 3348 Classifications: {'peptide': 216} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 197} Chain: "F" Number of atoms: 7072 Number of conformers: 1 Conformer: "" Number of residues, atoms: 460, 7072 Classifications: {'peptide': 460} Link IDs: {'PCIS': 2, 'PTRANS': 20, 'TRANS': 437} Chain: "G" Number of atoms: 10447 Number of conformers: 1 Conformer: "" Number of residues, atoms: 694, 10447 Classifications: {'peptide': 694} Link IDs: {'PTRANS': 34, 'TRANS': 659} Chain: "H" Number of atoms: 5453 Number of conformers: 1 Conformer: "" Number of residues, atoms: 341, 5453 Classifications: {'peptide': 341} Link IDs: {'PCIS': 2, 'PTRANS': 12, 'TRANS': 326} Unresolved non-hydrogen bonds: 39 Unresolved non-hydrogen angles: 53 Unresolved non-hydrogen dihedrals: 33 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'FME:plan-2': 1, 'GLU:plan': 2, 'PHE:plan': 1, 'TYR:plan': 2} Unresolved non-hydrogen planarities: 29 Chain: "I" Number of atoms: 2997 Number of conformers: 1 Conformer: "" Number of residues, atoms: 191, 2997 Classifications: {'peptide': 191} Link IDs: {'PTRANS': 12, 'TRANS': 178} Chain: "J" Number of atoms: 3034 Number of conformers: 1 Conformer: "" Number of residues, atoms: 185, 3034 Classifications: {'peptide': 185} Link IDs: {'PTRANS': 3, 'TRANS': 181} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'FME:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "K" Number of atoms: 1436 Number of conformers: 1 Conformer: "" Number of residues, atoms: 89, 1436 Classifications: {'peptide': 89} Link IDs: {'TRANS': 88} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'FME:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "L" Number of atoms: 10561 Number of conformers: 1 Conformer: "" Number of residues, atoms: 655, 10561 Classifications: {'peptide': 655} Link IDs: {'PTRANS': 15, 'TRANS': 639} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'FME:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "M" Number of atoms: 7900 Number of conformers: 1 Conformer: "" Number of residues, atoms: 486, 7900 Classifications: {'peptide': 486} Link IDs: {'PCIS': 2, 'PTRANS': 12, 'TRANS': 471} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'FME:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "N" Number of atoms: 7770 Number of conformers: 1 Conformer: "" Number of residues, atoms: 469, 7770 Classifications: {'peptide': 469} Link IDs: {'PCIS': 2, 'PTRANS': 5, 'TRANS': 461} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'FME:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "O" Number of atoms: 2586 Number of conformers: 1 Conformer: "" Number of residues, atoms: 168, 2586 Classifications: {'peptide': 168} Link IDs: {'PTRANS': 11, 'TRANS': 156} Chain: "P" Number of atoms: 5575 Number of conformers: 1 Conformer: "" Number of residues, atoms: 355, 5575 Classifications: {'peptide': 355} Link IDs: {'PTRANS': 15, 'TRANS': 339} Unresolved non-hydrogen bonds: 41 Unresolved non-hydrogen angles: 54 Unresolved non-hydrogen dihedrals: 32 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLN:plan1': 2, 'ASN:plan1': 1, 'ASP:plan': 1, 'PHE:plan': 1, 'GLU:plan': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 29 Chain: "Q" Number of atoms: 2031 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 2031 Classifications: {'peptide': 125} Link IDs: {'PTRANS': 4, 'TRANS': 120} Chain: "R" Number of atoms: 1798 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 1798 Classifications: {'peptide': 118} Link IDs: {'PTRANS': 9, 'TRANS': 108} Chain: "S" Number of atoms: 1351 Number of conformers: 1 Conformer: "" Number of residues, atoms: 86, 1351 Classifications: {'peptide': 86} Link IDs: {'PTRANS': 3, 'TRANS': 82} Chain: "T" Number of atoms: 1234 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 1234 Classifications: {'peptide': 81} Link IDs: {'PTRANS': 5, 'TRANS': 75} Chain: "U" Number of atoms: 1322 Number of conformers: 1 Conformer: "" Number of residues, atoms: 88, 1322 Classifications: {'peptide': 88} Link IDs: {'PTRANS': 2, 'TRANS': 85} Chain: "V" Number of atoms: 2049 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 2049 Classifications: {'peptide': 126} Link IDs: {'PTRANS': 7, 'TRANS': 118} Chain: "W" Number of atoms: 2054 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 2054 Classifications: {'peptide': 123} Link IDs: {'PTRANS': 4, 'TRANS': 118} Chain: "X" Number of atoms: 2678 Number of conformers: 1 Conformer: "" Number of residues, atoms: 171, 2678 Classifications: {'peptide': 171} Link IDs: {'PTRANS': 10, 'TRANS': 160} Chain: "Y" Number of atoms: 2638 Number of conformers: 1 Conformer: "" Number of residues, atoms: 179, 2638 Classifications: {'peptide': 179} Link IDs: {'PTRANS': 7, 'TRANS': 171} Chain: "Z" Number of atoms: 1983 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 1983 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 9, 'TRANS': 112} Chain: "a" Number of atoms: 1353 Number of conformers: 1 Conformer: "" Number of residues, atoms: 86, 1353 Classifications: {'peptide': 86} Link IDs: {'PTRANS': 4, 'TRANS': 81} Chain: "b" Number of atoms: 1257 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 1257 Classifications: {'peptide': 78} Modifications used: {'NH1NOTPRO': 1} Link IDs: {'PTRANS': 10, 'TRANS': 67} Chain: "c" Number of atoms: 2804 Number of conformers: 1 Conformer: "" Number of residues, atoms: 182, 2804 Classifications: {'peptide': 182} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 2, 'PTRANS': 18, 'TRANS': 161} Chain: "d" Number of atoms: 1042 Number of conformers: 1 Conformer: "" Number of residues, atoms: 67, 1042 Classifications: {'peptide': 67} Link IDs: {'PTRANS': 2, 'TRANS': 64} Chain: "e" Number of atoms: 1082 Number of conformers: 1 Conformer: "" Number of residues, atoms: 68, 1082 Classifications: {'peptide': 68} Link IDs: {'PTRANS': 1, 'TRANS': 66} Chain: "f" Number of atoms: 2225 Number of conformers: 1 Conformer: "" Number of residues, atoms: 137, 2225 Classifications: {'peptide': 137} Link IDs: {'PTRANS': 10, 'TRANS': 126} Chain: "g" Number of atoms: 3188 Number of conformers: 1 Conformer: "" Number of residues, atoms: 198, 3188 Classifications: {'peptide': 198} Link IDs: {'PTRANS': 10, 'TRANS': 187} Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 30 Unresolved non-hydrogen angles: 37 Unresolved non-hydrogen dihedrals: 25 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 3, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 17 Chain: "h" Number of atoms: 1786 Number of conformers: 1 Conformer: "" Number of residues, atoms: 113, 1786 Classifications: {'peptide': 113} Link IDs: {'PTRANS': 8, 'TRANS': 104} Chain: "i" Number of atoms: 1300 Number of conformers: 1 Conformer: "" Number of residues, atoms: 86, 1300 Classifications: {'peptide': 86} Link IDs: {'PTRANS': 4, 'TRANS': 81} Chain: "j" Number of atoms: 884 Number of conformers: 1 Conformer: "" Number of residues, atoms: 53, 884 Classifications: {'peptide': 53} Link IDs: {'PTRANS': 6, 'TRANS': 46} Chain: "k" Number of atoms: 734 Number of conformers: 1 Conformer: "" Number of residues, atoms: 47, 734 Classifications: {'peptide': 47} Link IDs: {'PTRANS': 3, 'TRANS': 43} Chain: "l" Number of atoms: 2012 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 2012 Classifications: {'peptide': 125} Link IDs: {'PTRANS': 10, 'TRANS': 114} Chain: "m" Number of atoms: 1453 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 1453 Classifications: {'peptide': 92} Link IDs: {'PTRANS': 4, 'TRANS': 87} Chain: "n" Number of atoms: 1804 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 1804 Classifications: {'peptide': 108} Link IDs: {'PTRANS': 11, 'TRANS': 96} Chain: "o" Number of atoms: 1366 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 1366 Classifications: {'peptide': 83} Link IDs: {'PTRANS': 4, 'TRANS': 78} Chain: "p" Number of atoms: 1492 Number of conformers: 1 Conformer: "" Number of residues, atoms: 91, 1492 Classifications: {'peptide': 91} Link IDs: {'PTRANS': 4, 'TRANS': 86} Chain: "D" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'PLC': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 15 Chain: "E" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 4 Unusual residues: {'FES': 1} Classifications: {'undetermined': 1} Chain: "F" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 39 Unusual residues: {'FMN': 1, 'SF4': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "G" Number of atoms: 20 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 20 Unusual residues: {'FES': 1, 'SF4': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "H" Number of atoms: 96 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 96 Unusual residues: {'3PE': 2, 'PLC': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 49 Unresolved non-hydrogen angles: 51 Unresolved non-hydrogen dihedrals: 48 Chain: "I" Number of atoms: 48 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 48 Unusual residues: {'3PE': 1, 'SF4': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 19 Unresolved non-hydrogen angles: 19 Unresolved non-hydrogen dihedrals: 19 Chain: "L" Number of atoms: 229 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 229 Unusual residues: {'3PE': 3, 'PLC': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 8 Chain: "M" Number of atoms: 113 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 113 Unusual residues: {'3PE': 1, 'CDL': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 38 Unresolved non-hydrogen angles: 38 Unresolved non-hydrogen dihedrals: 38 Chain: "N" Number of atoms: 93 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 93 Unusual residues: {'3PE': 1, 'PLC': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "O" Number of atoms: 63 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 63 Unusual residues: {'CDL': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 37 Unresolved non-hydrogen angles: 37 Unresolved non-hydrogen dihedrals: 37 Chain: "P" Number of atoms: 48 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 48 Unusual residues: {'NDP': 1} Classifications: {'undetermined': 1} Chain: "R" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "T" Number of atoms: 35 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 35 Unusual residues: {'EHZ': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 Chain: "U" Number of atoms: 36 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 36 Unusual residues: {'EHZ': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 2 Chain: "Y" Number of atoms: 103 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 103 Unusual residues: {'3PE': 1, 'LMT': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 18 Chain: "Z" Number of atoms: 100 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 100 Unusual residues: {'3PE': 1, 'CDL': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 51 Unresolved non-hydrogen angles: 51 Unresolved non-hydrogen dihedrals: 51 Chain: "a" Number of atoms: 52 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 52 Unusual residues: {'CDL': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 48 Unresolved non-hydrogen angles: 48 Unresolved non-hydrogen dihedrals: 48 Chain: "b" Number of atoms: 91 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 91 Unusual residues: {'3PE': 1, 'CDL': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 60 Unresolved non-hydrogen angles: 60 Unresolved non-hydrogen dihedrals: 60 Chain: "d" Number of atoms: 51 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 51 Unusual residues: {'3PE': 1, 'PLC': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 42 Unresolved non-hydrogen angles: 42 Unresolved non-hydrogen dihedrals: 42 Chain: "g" Number of atoms: 30 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 30 Unusual residues: {'3PE': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 21 Unresolved non-hydrogen angles: 21 Unresolved non-hydrogen dihedrals: 21 List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 16689 SG CYS E 127 106.374 49.472 259.203 1.00 43.21 S ATOM 16755 SG CYS E 132 104.575 46.975 261.450 1.00 44.36 S ATOM 17286 SG CYS E 168 108.957 45.828 256.593 1.00 39.93 S ATOM 17332 SG CYS E 172 107.487 43.413 257.556 1.00 49.12 S ATOM 23808 SG CYS F 381 116.825 54.945 240.581 1.00 20.18 S ATOM 23842 SG CYS F 384 113.404 54.146 235.539 1.00 16.47 S ATOM 24540 SG CYS F 427 114.127 49.222 239.493 1.00 20.88 S ATOM 23880 SG CYS F 387 110.273 54.103 240.204 1.00 17.69 S ATOM 26976 SG CYS G 133 106.704 75.501 226.347 1.00 15.67 S ATOM 27084 SG CYS G 142 112.278 71.990 224.868 1.00 17.86 S ATOM 27016 SG CYS G 136 112.560 77.206 227.976 1.00 17.82 S ATOM 28473 SG CYS G 233 119.047 71.452 230.296 1.00 18.70 S ATOM 27742 SG CYS G 183 116.904 68.291 235.365 1.00 18.17 S ATOM 27836 SG CYS G 189 123.214 68.312 234.343 1.00 20.05 S ATOM 27788 SG CYS G 186 119.795 66.112 230.538 1.00 18.29 S ATOM 25989 SG CYS G 69 119.730 58.540 227.608 1.00 16.38 S ATOM 26150 SG CYS G 80 116.102 59.162 226.907 1.00 16.31 S ATOM 26201 SG CYS G 83 116.916 54.493 223.984 1.00 16.56 S ATOM 26410 SG CYS G 97 119.950 54.624 226.037 1.00 15.86 S ATOM 42873 SG CYS I 330 104.294 85.600 223.628 1.00 18.35 S ATOM 42924 SG CYS I 333 103.269 89.993 219.915 1.00 15.58 S ATOM 42834 SG CYS I 327 104.534 91.842 225.649 1.00 18.52 S ATOM 43574 SG CYS I 376 99.367 88.019 224.961 1.00 17.43 S ATOM 43521 SG CYS I 372 96.963 91.208 217.241 1.00 15.94 S ATOM 43483 SG CYS I 369 95.798 89.210 211.707 1.00 16.81 S ATOM 42978 SG CYS I 337 100.844 91.039 212.388 1.00 16.18 S ATOM 43433 SG CYS I 366 96.564 95.401 212.274 1.00 15.78 S ATOM 86514 SG CYS R 97 100.234 84.041 240.208 1.00 21.52 S ATOM 86882 SG CYS R 125 103.546 84.120 237.676 1.00 18.75 S ATOM 86930 SG CYS R 128 101.174 86.843 238.389 1.00 18.83 S Time building chain proxies: 39.73, per 1000 atoms: 0.31 Number of scatterers: 129439 At special positions: 0 Unit cell: (185.85, 191.1, 290.85, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 8 Type Number sf(0) Zn 1 29.99 Fe 24 26.01 S 308 16.00 P 35 15.00 O 11950 8.00 N 10750 7.00 C 42284 6.00 H 64087 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=5, symmetry=0 Simple disulfide: pdb=" SG CYS F 127 " - pdb=" SG CYS F 279 " distance=2.05 Simple disulfide: pdb=" SG CYS X 46 " - pdb=" SG CYS X 78 " distance=2.05 Simple disulfide: pdb=" SG CYS e 15 " - pdb=" SG CYS e 47 " distance=2.05 Simple disulfide: pdb=" SG CYS o 36 " - pdb=" SG CYS o 47 " distance=2.05 Simple disulfide: pdb=" SG CYS p 51 " - pdb=" SG CYS p 63 " distance=2.05 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: 72.50 Conformation dependent library (CDL) restraints added in 9.7 seconds Dynamic metal coordination Iron sulfur cluster coordination pdb=" FES E 301 " pdb="FE2 FES E 301 " - pdb=" SG CYS E 172 " pdb="FE2 FES E 301 " - pdb=" SG CYS E 168 " pdb="FE1 FES E 301 " - pdb=" SG CYS E 132 " pdb="FE1 FES E 301 " - pdb=" SG CYS E 127 " pdb=" FES G 803 " pdb="FE1 FES G 803 " - pdb=" SG CYS G 80 " pdb="FE2 FES G 803 " - pdb=" SG CYS G 83 " pdb="FE1 FES G 803 " - pdb=" SG CYS G 69 " pdb="FE2 FES G 803 " - pdb=" SG CYS G 97 " pdb=" SF4 F 502 " pdb="FE2 SF4 F 502 " - pdb=" SG CYS F 384 " pdb="FE1 SF4 F 502 " - pdb=" SG CYS F 381 " pdb="FE3 SF4 F 502 " - pdb=" SG CYS F 427 " pdb="FE4 SF4 F 502 " - pdb=" SG CYS F 387 " pdb=" SF4 G 801 " pdb="FE3 SF4 G 801 " - pdb=" NE2 HIS G 129 " pdb="FE1 SF4 G 801 " - pdb=" SG CYS G 133 " pdb="FE4 SF4 G 801 " - pdb=" SG CYS G 136 " pdb="FE2 SF4 G 801 " - pdb=" SG CYS G 142 " pdb=" SF4 G 802 " pdb="FE4 SF4 G 802 " - pdb=" SG CYS G 186 " pdb="FE2 SF4 G 802 " - pdb=" SG CYS G 183 " pdb="FE3 SF4 G 802 " - pdb=" SG CYS G 189 " pdb="FE1 SF4 G 802 " - pdb=" SG CYS G 233 " pdb=" SF4 I 502 " pdb="FE1 SF4 I 502 " - pdb=" SG CYS I 330 " pdb="FE3 SF4 I 502 " - pdb=" SG CYS I 327 " pdb="FE4 SF4 I 502 " - pdb=" SG CYS I 376 " pdb="FE2 SF4 I 502 " - pdb=" SG CYS I 333 " pdb=" SF4 I 503 " pdb="FE2 SF4 I 503 " - pdb=" SG CYS I 369 " pdb="FE3 SF4 I 503 " - pdb=" SG CYS I 337 " pdb="FE4 SF4 I 503 " - pdb=" SG CYS I 366 " pdb="FE1 SF4 I 503 " - pdb=" SG CYS I 372 " pdb="FE4 SF4 I 503 " - pdb=" NE2 HIS I 315 " Number of angles added : 69 Zn2+ tetrahedral coordination pdb=" ZN R 201 " pdb="ZN ZN R 201 " - pdb=" NE2 HIS R 110 " pdb="ZN ZN R 201 " - pdb=" SG CYS R 128 " pdb="ZN ZN R 201 " - pdb=" SG CYS R 97 " pdb="ZN ZN R 201 " - pdb=" SG CYS R 125 " Number of angles added : 3 15998 Ramachandran restraints generated. 7999 Oldfield, 0 Emsley, 7999 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 15134 Finding SS restraints... Warning!!! ksdssp method is not applicable for structures that cannot fit in PDB format. Switching to from_ca. running find_ss_from_ca liberal... Secondary structure from input PDB file: 335 helices and 29 sheets defined 62.1% alpha, 4.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 49.03 Creating SS restraints... Processing helix chain 'A' and resid 2 through 14 removed outlier: 3.931A pdb=" N ILE A 9 " --> pdb=" O ILE A 5 " (cutoff:3.500A) Proline residue: A 12 - end of helix Processing helix chain 'A' and resid 53 through 84 removed outlier: 3.908A pdb=" N ILE A 57 " --> pdb=" O ASN A 53 " (cutoff:3.500A) removed outlier: 4.376A pdb=" N ALA A 60 " --> pdb=" O PHE A 56 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N LEU A 64 " --> pdb=" O ALA A 60 " (cutoff:3.500A) Proline residue: A 65 - end of helix removed outlier: 3.998A pdb=" N LEU A 74 " --> pdb=" O ILE A 70 " (cutoff:3.500A) Proline residue: A 75 - end of helix removed outlier: 6.104A pdb=" N TYR A 81 " --> pdb=" O VAL A 77 " (cutoff:3.500A) removed outlier: 6.652A pdb=" N LEU A 82 " --> pdb=" O MET A 78 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N SER A 84 " --> pdb=" O ILE A 80 " (cutoff:3.500A) Processing helix chain 'A' and resid 85 through 109 removed outlier: 4.076A pdb=" N THR A 89 " --> pdb=" O ASN A 85 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N GLY A 101 " --> pdb=" O ILE A 97 " (cutoff:3.500A) Processing helix chain 'B' and resid 55 through 76 removed outlier: 4.422A pdb=" N PHE B 76 " --> pdb=" O ARG B 72 " (cutoff:3.500A) Processing helix chain 'B' and resid 86 through 96 removed outlier: 4.078A pdb=" N MET B 90 " --> pdb=" O CYS B 86 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N VAL B 93 " --> pdb=" O GLU B 89 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N SER B 94 " --> pdb=" O MET B 90 " (cutoff:3.500A) Proline residue: B 96 - end of helix Processing helix chain 'B' and resid 99 through 104 removed outlier: 4.677A pdb=" N LEU B 103 " --> pdb=" O ASP B 99 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N GLY B 104 " --> pdb=" O GLN B 100 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 99 through 104' Processing helix chain 'B' and resid 110 through 115 removed outlier: 3.840A pdb=" N SER B 114 " --> pdb=" O SER B 110 " (cutoff:3.500A) removed outlier: 4.853A pdb=" N ASP B 115 " --> pdb=" O PRO B 111 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 110 through 115' Processing helix chain 'B' and resid 124 through 139 Proline residue: B 129 - end of helix Proline residue: B 139 - end of helix Processing helix chain 'B' and resid 148 through 153 Processing helix chain 'B' and resid 166 through 171 removed outlier: 4.796A pdb=" N ILE B 170 " --> pdb=" O GLY B 166 " (cutoff:3.500A) Processing helix chain 'B' and resid 183 through 201 Processing helix chain 'B' and resid 203 through 210 removed outlier: 4.067A pdb=" N TRP B 207 " --> pdb=" O ILE B 203 " (cutoff:3.500A) Processing helix chain 'C' and resid 41 through 46 removed outlier: 4.139A pdb=" N ASP C 45 " --> pdb=" O ASP C 41 " (cutoff:3.500A) Proline residue: C 46 - end of helix No H-bonds generated for 'chain 'C' and resid 41 through 46' Processing helix chain 'C' and resid 59 through 83 removed outlier: 4.707A pdb=" N ARG C 63 " --> pdb=" O ASN C 59 " (cutoff:3.500A) removed outlier: 4.998A pdb=" N TYR C 64 " --> pdb=" O PRO C 60 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N LEU C 65 " --> pdb=" O ALA C 61 " (cutoff:3.500A) removed outlier: 5.659A pdb=" N GLN C 66 " --> pdb=" O ASP C 62 " (cutoff:3.500A) removed outlier: 5.751A pdb=" N HIS C 67 " --> pdb=" O ARG C 63 " (cutoff:3.500A) Proline residue: C 83 - end of helix Processing helix chain 'C' and resid 101 through 115 removed outlier: 3.865A pdb=" N VAL C 105 " --> pdb=" O ALA C 101 " (cutoff:3.500A) removed outlier: 5.340A pdb=" N ILE C 106 " --> pdb=" O PRO C 102 " (cutoff:3.500A) Proline residue: C 107 - end of helix Processing helix chain 'C' and resid 174 through 186 removed outlier: 4.088A pdb=" N PHE C 178 " --> pdb=" O GLY C 174 " (cutoff:3.500A) Processing helix chain 'C' and resid 263 through 268 removed outlier: 3.598A pdb=" N LYS C 267 " --> pdb=" O PRO C 263 " (cutoff:3.500A) removed outlier: 5.851A pdb=" N LEU C 268 " --> pdb=" O ASP C 264 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 263 through 268' Processing helix chain 'C' and resid 244 through 249 removed outlier: 5.716A pdb=" N ALA C 247 " --> pdb=" O ASN C 244 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N GLY C 248 " --> pdb=" O PHE C 245 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N SER C 249 " --> pdb=" O SER C 246 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 244 through 249' Processing helix chain 'D' and resid 45 through 50 removed outlier: 4.851A pdb=" N GLN D 49 " --> pdb=" O ASP D 45 " (cutoff:3.500A) removed outlier: 4.901A pdb=" N ASP D 50 " --> pdb=" O GLU D 46 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 45 through 50' Processing helix chain 'D' and resid 69 through 74 removed outlier: 4.429A pdb=" N SER D 74 " --> pdb=" O PRO D 70 " (cutoff:3.500A) Processing helix chain 'D' and resid 122 through 131 removed outlier: 3.510A pdb=" N LEU D 126 " --> pdb=" O GLY D 122 " (cutoff:3.500A) removed outlier: 4.297A pdb=" N GLU D 128 " --> pdb=" O GLU D 124 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N TYR D 129 " --> pdb=" O LYS D 125 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N LYS D 130 " --> pdb=" O LEU D 126 " (cutoff:3.500A) removed outlier: 5.197A pdb=" N THR D 131 " --> pdb=" O ILE D 127 " (cutoff:3.500A) Processing helix chain 'D' and resid 132 through 144 removed outlier: 3.901A pdb=" N LEU D 136 " --> pdb=" O TYR D 132 " (cutoff:3.500A) Proline residue: D 137 - end of helix removed outlier: 3.732A pdb=" N ASP D 140 " --> pdb=" O LEU D 136 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N ARG D 141 " --> pdb=" O PRO D 137 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N LEU D 142 " --> pdb=" O TYR D 138 " (cutoff:3.500A) removed outlier: 4.972A pdb=" N ASP D 143 " --> pdb=" O PHE D 139 " (cutoff:3.500A) removed outlier: 5.385A pdb=" N TYR D 144 " --> pdb=" O ASP D 140 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 132 through 144' Processing helix chain 'D' and resid 146 through 163 removed outlier: 3.635A pdb=" N ASN D 150 " --> pdb=" O SER D 146 " (cutoff:3.500A) removed outlier: 4.098A pdb=" N PHE D 154 " --> pdb=" O ASN D 150 " (cutoff:3.500A) Processing helix chain 'D' and resid 167 through 198 removed outlier: 3.718A pdb=" N MET D 188 " --> pdb=" O LEU D 184 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N MET D 195 " --> pdb=" O CYS D 191 " (cutoff:3.500A) Processing helix chain 'D' and resid 199 through 221 removed outlier: 4.628A pdb=" N PHE D 203 " --> pdb=" O ALA D 199 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N LEU D 204 " --> pdb=" O LEU D 200 " (cutoff:3.500A) removed outlier: 4.149A pdb=" N GLU D 208 " --> pdb=" O LEU D 204 " (cutoff:3.500A) removed outlier: 4.556A pdb=" N GLU D 209 " --> pdb=" O TRP D 205 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N GLU D 215 " --> pdb=" O GLU D 211 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N PHE D 216 " --> pdb=" O LYS D 212 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N TYR D 217 " --> pdb=" O LEU D 213 " (cutoff:3.500A) Processing helix chain 'D' and resid 242 through 266 removed outlier: 4.415A pdb=" N ASP D 246 " --> pdb=" O GLY D 242 " (cutoff:3.500A) removed outlier: 4.289A pdb=" N GLY D 255 " --> pdb=" O ALA D 251 " (cutoff:3.500A) removed outlier: 5.409A pdb=" N ASP D 256 " --> pdb=" O THR D 252 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N ARG D 257 " --> pdb=" O GLN D 253 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N LEU D 264 " --> pdb=" O GLU D 260 " (cutoff:3.500A) Processing helix chain 'D' and resid 268 through 276 removed outlier: 3.586A pdb=" N LYS D 272 " --> pdb=" O ASN D 268 " (cutoff:3.500A) Processing helix chain 'D' and resid 282 through 290 removed outlier: 3.654A pdb=" N GLY D 290 " --> pdb=" O ALA D 286 " (cutoff:3.500A) Processing helix chain 'D' and resid 293 through 300 removed outlier: 4.296A pdb=" N SER D 299 " --> pdb=" O MET D 295 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N GLY D 300 " --> pdb=" O LEU D 296 " (cutoff:3.500A) Processing helix chain 'D' and resid 304 through 309 Processing helix chain 'D' and resid 313 through 318 removed outlier: 3.519A pdb=" N VAL D 317 " --> pdb=" O ALA D 313 " (cutoff:3.500A) removed outlier: 5.531A pdb=" N ASP D 318 " --> pdb=" O TYR D 314 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 313 through 318' Processing helix chain 'D' and resid 328 through 354 removed outlier: 3.653A pdb=" N ARG D 332 " --> pdb=" O ASP D 328 " (cutoff:3.500A) Processing helix chain 'D' and resid 370 through 377 removed outlier: 4.102A pdb=" N GLU D 376 " --> pdb=" O ASN D 372 " (cutoff:3.500A) Processing helix chain 'D' and resid 378 through 390 Processing helix chain 'D' and resid 429 through 443 removed outlier: 3.789A pdb=" N ALA D 433 " --> pdb=" O ALA D 429 " (cutoff:3.500A) removed outlier: 4.321A pdb=" N ASP D 439 " --> pdb=" O LEU D 435 " (cutoff:3.500A) removed outlier: 4.764A pdb=" N HIS D 440 " --> pdb=" O GLY D 436 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N ARG D 443 " --> pdb=" O ASP D 439 " (cutoff:3.500A) Processing helix chain 'D' and resid 446 through 458 Processing helix chain 'D' and resid 460 through 466 Processing helix chain 'E' and resid 48 through 63 removed outlier: 3.667A pdb=" N LYS E 61 " --> pdb=" O GLU E 57 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N TYR E 62 " --> pdb=" O VAL E 58 " (cutoff:3.500A) Proline residue: E 63 - end of helix Processing helix chain 'E' and resid 66 through 83 removed outlier: 4.654A pdb=" N ALA E 70 " --> pdb=" O TYR E 66 " (cutoff:3.500A) removed outlier: 4.508A pdb=" N VAL E 71 " --> pdb=" O LYS E 67 " (cutoff:3.500A) removed outlier: 5.147A pdb=" N MET E 72 " --> pdb=" O LYS E 68 " (cutoff:3.500A) Proline residue: E 73 - end of helix removed outlier: 4.067A pdb=" N GLY E 83 " --> pdb=" O GLN E 79 " (cutoff:3.500A) Processing helix chain 'E' and resid 86 through 98 Processing helix chain 'E' and resid 100 through 112 removed outlier: 3.811A pdb=" N VAL E 104 " --> pdb=" O PRO E 100 " (cutoff:3.500A) removed outlier: 4.234A pdb=" N VAL E 107 " --> pdb=" O ARG E 103 " (cutoff:3.500A) removed outlier: 5.389A pdb=" N THR E 112 " --> pdb=" O ALA E 108 " (cutoff:3.500A) Processing helix chain 'E' and resid 129 through 136 Processing helix chain 'E' and resid 137 through 149 Processing helix chain 'E' and resid 189 through 203 removed outlier: 3.648A pdb=" N ALA E 202 " --> pdb=" O GLU E 198 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N GLY E 203 " --> pdb=" O ASP E 199 " (cutoff:3.500A) Processing helix chain 'E' and resid 234 through 239 removed outlier: 4.356A pdb=" N PHE E 238 " --> pdb=" O ASN E 234 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N LEU E 239 " --> pdb=" O VAL E 235 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 234 through 239' Processing helix chain 'F' and resid 35 through 40 removed outlier: 5.609A pdb=" N ILE F 40 " --> pdb=" O ASP F 36 " (cutoff:3.500A) Processing helix chain 'F' and resid 51 through 59 removed outlier: 3.510A pdb=" N ARG F 56 " --> pdb=" O LEU F 52 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N LYS F 57 " --> pdb=" O ALA F 53 " (cutoff:3.500A) Processing helix chain 'F' and resid 63 through 71 removed outlier: 4.387A pdb=" N GLY F 71 " --> pdb=" O LEU F 67 " (cutoff:3.500A) Processing helix chain 'F' and resid 72 through 83 Processing helix chain 'F' and resid 93 through 103 removed outlier: 3.641A pdb=" N LYS F 97 " --> pdb=" O PRO F 93 " (cutoff:3.500A) removed outlier: 6.151A pdb=" N TRP F 98 " --> pdb=" O SER F 94 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N MET F 101 " --> pdb=" O LYS F 97 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N ASN F 102 " --> pdb=" O TRP F 98 " (cutoff:3.500A) Proline residue: F 103 - end of helix Processing helix chain 'F' and resid 105 through 110 removed outlier: 4.910A pdb=" N ASN F 109 " --> pdb=" O GLY F 105 " (cutoff:3.500A) removed outlier: 4.605A pdb=" N GLU F 110 " --> pdb=" O TRP F 106 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 105 through 110' Processing helix chain 'F' and resid 127 through 135 removed outlier: 3.614A pdb=" N GLU F 131 " --> pdb=" O CYS F 127 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N MET F 133 " --> pdb=" O ASP F 129 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N LYS F 135 " --> pdb=" O GLU F 131 " (cutoff:3.500A) Processing helix chain 'F' and resid 136 through 152 removed outlier: 4.079A pdb=" N LEU F 140 " --> pdb=" O ASP F 136 " (cutoff:3.500A) Processing helix chain 'F' and resid 164 through 182 removed outlier: 3.722A pdb=" N ALA F 168 " --> pdb=" O PHE F 164 " (cutoff:3.500A) Processing helix chain 'F' and resid 205 through 210 removed outlier: 4.143A pdb=" N GLY F 209 " --> pdb=" O ALA F 205 " (cutoff:3.500A) removed outlier: 4.291A pdb=" N GLU F 210 " --> pdb=" O TYR F 206 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 205 through 210' Processing helix chain 'F' and resid 211 through 220 removed outlier: 3.646A pdb=" N ILE F 215 " --> pdb=" O GLU F 211 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N GLY F 220 " --> pdb=" O GLU F 216 " (cutoff:3.500A) Processing helix chain 'F' and resid 246 through 260 removed outlier: 4.087A pdb=" N ALA F 253 " --> pdb=" O THR F 249 " (cutoff:3.500A) Proline residue: F 254 - end of helix Processing helix chain 'F' and resid 261 through 268 removed outlier: 5.283A pdb=" N GLY F 268 " --> pdb=" O PHE F 264 " (cutoff:3.500A) Processing helix chain 'F' and resid 297 through 304 Processing helix chain 'F' and resid 330 through 337 removed outlier: 3.712A pdb=" N GLU F 335 " --> pdb=" O LYS F 331 " (cutoff:3.500A) removed outlier: 4.924A pdb=" N ASP F 336 " --> pdb=" O ASN F 332 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N VAL F 337 " --> pdb=" O ILE F 333 " (cutoff:3.500A) Processing helix chain 'F' and resid 340 through 348 removed outlier: 3.505A pdb=" N LEU F 344 " --> pdb=" O ASP F 340 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N GLN F 348 " --> pdb=" O LEU F 344 " (cutoff:3.500A) Processing helix chain 'F' and resid 364 through 380 Processing helix chain 'F' and resid 384 through 404 removed outlier: 4.472A pdb=" N THR F 392 " --> pdb=" O ARG F 388 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N ARG F 400 " --> pdb=" O LYS F 396 " (cutoff:3.500A) removed outlier: 4.145A pdb=" N THR F 403 " --> pdb=" O ASP F 399 " (cutoff:3.500A) Processing helix chain 'F' and resid 407 through 423 removed outlier: 4.267A pdb=" N ILE F 411 " --> pdb=" O LYS F 407 " (cutoff:3.500A) removed outlier: 4.256A pdb=" N ASP F 412 " --> pdb=" O GLU F 408 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N ILE F 421 " --> pdb=" O LEU F 417 " (cutoff:3.500A) removed outlier: 5.108A pdb=" N GLY F 423 " --> pdb=" O LYS F 419 " (cutoff:3.500A) Processing helix chain 'F' and resid 428 through 444 Proline residue: F 436 - end of helix Processing helix chain 'F' and resid 445 through 459 Processing helix chain 'G' and resid 53 through 62 Processing helix chain 'G' and resid 111 through 130 removed outlier: 4.684A pdb=" N ASN G 128 " --> pdb=" O MET G 124 " (cutoff:3.500A) removed outlier: 4.353A pdb=" N HIS G 129 " --> pdb=" O MET G 125 " (cutoff:3.500A) Proline residue: G 130 - end of helix Processing helix chain 'G' and resid 142 through 151 removed outlier: 3.516A pdb=" N ASP G 146 " --> pdb=" O CYS G 142 " (cutoff:3.500A) Processing helix chain 'G' and resid 187 through 195 removed outlier: 3.572A pdb=" N ARG G 191 " --> pdb=" O THR G 187 " (cutoff:3.500A) Processing helix chain 'G' and resid 225 through 234 removed outlier: 4.319A pdb=" N VAL G 229 " --> pdb=" O LEU G 225 " (cutoff:3.500A) removed outlier: 4.441A pdb=" N ILE G 230 " --> pdb=" O SER G 226 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N ASP G 231 " --> pdb=" O GLY G 227 " (cutoff:3.500A) Proline residue: G 234 - end of helix Processing helix chain 'G' and resid 248 through 253 removed outlier: 4.183A pdb=" N LEU G 252 " --> pdb=" O ARG G 248 " (cutoff:3.500A) removed outlier: 5.873A pdb=" N LYS G 253 " --> pdb=" O PRO G 249 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 248 through 253' Processing helix chain 'G' and resid 294 through 307 removed outlier: 3.641A pdb=" N ARG G 298 " --> pdb=" O ASN G 294 " (cutoff:3.500A) removed outlier: 5.161A pdb=" N CYS G 301 " --> pdb=" O SER G 297 " (cutoff:3.500A) removed outlier: 6.342A pdb=" N ASP G 302 " --> pdb=" O ARG G 298 " (cutoff:3.500A) removed outlier: 5.319A pdb=" N GLY G 303 " --> pdb=" O PHE G 299 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N LEU G 304 " --> pdb=" O ALA G 300 " (cutoff:3.500A) removed outlier: 4.304A pdb=" N LYS G 305 " --> pdb=" O CYS G 301 " (cutoff:3.500A) removed outlier: 4.405A pdb=" N THR G 306 " --> pdb=" O ASP G 302 " (cutoff:3.500A) removed outlier: 5.760A pdb=" N GLN G 307 " --> pdb=" O GLY G 303 " (cutoff:3.500A) Processing helix chain 'G' and resid 324 through 340 Processing helix chain 'G' and resid 355 through 370 removed outlier: 4.211A pdb=" N MET G 359 " --> pdb=" O GLU G 355 " (cutoff:3.500A) Processing helix chain 'G' and resid 391 through 396 removed outlier: 4.427A pdb=" N TYR G 395 " --> pdb=" O PHE G 391 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N LEU G 396 " --> pdb=" O ARG G 392 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 391 through 396' Processing helix chain 'G' and resid 400 through 407 removed outlier: 3.876A pdb=" N ILE G 404 " --> pdb=" O SER G 400 " (cutoff:3.500A) removed outlier: 4.936A pdb=" N GLU G 405 " --> pdb=" O ILE G 401 " (cutoff:3.500A) removed outlier: 4.521A pdb=" N ASP G 406 " --> pdb=" O ALA G 402 " (cutoff:3.500A) Processing helix chain 'G' and resid 416 through 421 removed outlier: 3.659A pdb=" N ALA G 421 " --> pdb=" O PRO G 417 " (cutoff:3.500A) Processing helix chain 'G' and resid 422 through 435 removed outlier: 3.821A pdb=" N ARG G 434 " --> pdb=" O LYS G 430 " (cutoff:3.500A) Processing helix chain 'G' and resid 458 through 468 Processing helix chain 'G' and resid 469 through 477 Processing helix chain 'G' and resid 485 through 492 removed outlier: 4.129A pdb=" N THR G 489 " --> pdb=" O GLY G 485 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ARG G 491 " --> pdb=" O GLY G 487 " (cutoff:3.500A) removed outlier: 5.502A pdb=" N GLU G 492 " --> pdb=" O ILE G 488 " (cutoff:3.500A) Processing helix chain 'G' and resid 493 through 509 removed outlier: 4.438A pdb=" N PHE G 497 " --> pdb=" O ASP G 493 " (cutoff:3.500A) Proline residue: G 509 - end of helix Processing helix chain 'G' and resid 525 through 535 removed outlier: 4.928A pdb=" N ALA G 529 " --> pdb=" O SER G 525 " (cutoff:3.500A) removed outlier: 4.676A pdb=" N GLY G 530 " --> pdb=" O ALA G 526 " (cutoff:3.500A) Processing helix chain 'G' and resid 539 through 546 removed outlier: 3.852A pdb=" N LYS G 544 " --> pdb=" O ASP G 540 " (cutoff:3.500A) removed outlier: 4.185A pdb=" N THR G 545 " --> pdb=" O GLU G 541 " (cutoff:3.500A) removed outlier: 5.743A pdb=" N THR G 546 " --> pdb=" O ALA G 542 " (cutoff:3.500A) Processing helix chain 'G' and resid 559 through 564 removed outlier: 6.926A pdb=" N ILE G 563 " --> pdb=" O ALA G 559 " (cutoff:3.500A) Proline residue: G 564 - end of helix No H-bonds generated for 'chain 'G' and resid 559 through 564' Processing helix chain 'G' and resid 577 through 583 removed outlier: 5.870A pdb=" N GLN G 581 " --> pdb=" O ASP G 577 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N PHE G 582 " --> pdb=" O VAL G 578 " (cutoff:3.500A) Processing helix chain 'G' and resid 591 through 596 removed outlier: 3.629A pdb=" N LYS G 595 " --> pdb=" O ALA G 591 " (cutoff:3.500A) removed outlier: 5.783A pdb=" N ALA G 596 " --> pdb=" O TYR G 592 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 591 through 596' Processing helix chain 'G' and resid 621 through 634 removed outlier: 4.226A pdb=" N GLY G 634 " --> pdb=" O SER G 630 " (cutoff:3.500A) Processing helix chain 'G' and resid 641 through 653 Processing helix chain 'G' and resid 654 through 659 removed outlier: 3.911A pdb=" N ARG G 658 " --> pdb=" O PRO G 654 " (cutoff:3.500A) removed outlier: 5.342A pdb=" N TYR G 659 " --> pdb=" O SER G 655 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 654 through 659' Processing helix chain 'G' and resid 667 through 675 Processing helix chain 'G' and resid 701 through 708 removed outlier: 3.535A pdb=" N SER G 707 " --> pdb=" O ILE G 703 " (cutoff:3.500A) Proline residue: G 708 - end of helix Processing helix chain 'G' and resid 709 through 718 removed outlier: 4.097A pdb=" N PHE G 717 " --> pdb=" O SER G 713 " (cutoff:3.500A) removed outlier: 4.936A pdb=" N ASN G 718 " --> pdb=" O SER G 714 " (cutoff:3.500A) Processing helix chain 'G' and resid 721 through 726 removed outlier: 4.003A pdb=" N GLN G 725 " --> pdb=" O ASN G 721 " (cutoff:3.500A) removed outlier: 5.232A pdb=" N ALA G 726 " --> pdb=" O LYS G 722 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 721 through 726' Processing helix chain 'G' and resid 678 through 683 removed outlier: 3.652A pdb=" N GLY G 681 " --> pdb=" O GLY G 678 " (cutoff:3.500A) removed outlier: 4.964A pdb=" N SER G 682 " --> pdb=" O PRO G 679 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N VAL G 683 " --> pdb=" O ASN G 680 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 678 through 683' Processing helix chain 'H' and resid 1 through 35 removed outlier: 3.672A pdb=" N VAL H 24 " --> pdb=" O ALA H 20 " (cutoff:3.500A) Processing helix chain 'H' and resid 48 through 61 removed outlier: 5.859A pdb=" N GLU H 61 " --> pdb=" O LEU H 57 " (cutoff:3.500A) Processing helix chain 'H' and resid 69 through 92 removed outlier: 4.309A pdb=" N LEU H 73 " --> pdb=" O ASN H 69 " (cutoff:3.500A) Proline residue: H 77 - end of helix removed outlier: 3.788A pdb=" N GLY H 87 " --> pdb=" O THR H 83 " (cutoff:3.500A) removed outlier: 4.478A pdb=" N TRP H 88 " --> pdb=" O ALA H 84 " (cutoff:3.500A) removed outlier: 4.256A pdb=" N VAL H 89 " --> pdb=" O LEU H 85 " (cutoff:3.500A) removed outlier: 4.674A pdb=" N VAL H 90 " --> pdb=" O ILE H 86 " (cutoff:3.500A) removed outlier: 4.621A pdb=" N ILE H 91 " --> pdb=" O GLY H 87 " (cutoff:3.500A) Proline residue: H 92 - end of helix Processing helix chain 'H' and resid 104 through 128 removed outlier: 4.808A pdb=" N VAL H 117 " --> pdb=" O GLY H 113 " (cutoff:3.500A) removed outlier: 5.281A pdb=" N PHE H 118 " --> pdb=" O SER H 114 " (cutoff:3.500A) removed outlier: 5.212A pdb=" N GLY H 119 " --> pdb=" O LEU H 115 " (cutoff:3.500A) removed outlier: 4.809A pdb=" N SER H 120 " --> pdb=" O GLY H 116 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N GLY H 124 " --> pdb=" O SER H 120 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N TRP H 125 " --> pdb=" O LEU H 121 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N SER H 127 " --> pdb=" O SER H 123 " (cutoff:3.500A) removed outlier: 4.835A pdb=" N ASN H 128 " --> pdb=" O GLY H 124 " (cutoff:3.500A) Processing helix chain 'H' and resid 129 through 160 removed outlier: 4.134A pdb=" N LEU H 133 " --> pdb=" O SER H 129 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N LEU H 134 " --> pdb=" O LYS H 130 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N ILE H 137 " --> pdb=" O LEU H 133 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N LEU H 143 " --> pdb=" O SER H 139 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N LEU H 148 " --> pdb=" O ILE H 144 " (cutoff:3.500A) removed outlier: 4.522A pdb=" N ILE H 149 " --> pdb=" O SER H 145 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N ILE H 153 " --> pdb=" O ILE H 149 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N PHE H 160 " --> pdb=" O ILE H 156 " (cutoff:3.500A) Processing helix chain 'H' and resid 165 through 176 removed outlier: 3.830A pdb=" N GLN H 173 " --> pdb=" O ILE H 169 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N ARG H 174 " --> pdb=" O ILE H 170 " (cutoff:3.500A) removed outlier: 5.137A pdb=" N VAL H 175 " --> pdb=" O GLU H 171 " (cutoff:3.500A) removed outlier: 4.453A pdb=" N VAL H 176 " --> pdb=" O THR H 172 " (cutoff:3.500A) Processing helix chain 'H' and resid 177 through 183 Proline residue: H 181 - end of helix No H-bonds generated for 'chain 'H' and resid 177 through 183' Processing helix chain 'H' and resid 184 through 198 removed outlier: 3.540A pdb=" N ALA H 198 " --> pdb=" O VAL H 194 " (cutoff:3.500A) Processing helix chain 'H' and resid 203 through 213 removed outlier: 3.586A pdb=" N SER H 207 " --> pdb=" O ASP H 203 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N VAL H 212 " --> pdb=" O GLU H 208 " (cutoff:3.500A) removed outlier: 4.829A pdb=" N ALA H 213 " --> pdb=" O SER H 209 " (cutoff:3.500A) Processing helix chain 'H' and resid 221 through 246 removed outlier: 3.968A pdb=" N VAL H 225 " --> pdb=" O GLY H 221 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N TYR H 232 " --> pdb=" O PHE H 228 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N SER H 233 " --> pdb=" O LEU H 229 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N ILE H 236 " --> pdb=" O TYR H 232 " (cutoff:3.500A) Processing helix chain 'H' and resid 255 through 263 Processing helix chain 'H' and resid 267 through 300 removed outlier: 4.241A pdb=" N LEU H 272 " --> pdb=" O TYR H 268 " (cutoff:3.500A) Processing helix chain 'H' and resid 304 through 335 removed outlier: 5.436A pdb=" N LEU H 317 " --> pdb=" O TRP H 313 " (cutoff:3.500A) Proline residue: H 318 - end of helix removed outlier: 3.987A pdb=" N LEU H 325 " --> pdb=" O PHE H 321 " (cutoff:3.500A) Proline residue: H 328 - end of helix removed outlier: 3.832A pdb=" N PHE H 334 " --> pdb=" O THR H 330 " (cutoff:3.500A) Processing helix chain 'I' and resid 243 through 248 Proline residue: I 248 - end of helix Processing helix chain 'I' and resid 266 through 277 removed outlier: 3.629A pdb=" N LEU I 277 " --> pdb=" O LYS I 273 " (cutoff:3.500A) Processing helix chain 'I' and resid 278 through 294 removed outlier: 4.006A pdb=" N GLN I 290 " --> pdb=" O VAL I 286 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N PHE I 291 " --> pdb=" O VAL I 287 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N PHE I 292 " --> pdb=" O LEU I 288 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N ARG I 293 " --> pdb=" O GLU I 289 " (cutoff:3.500A) removed outlier: 5.429A pdb=" N ALA I 294 " --> pdb=" O GLN I 290 " (cutoff:3.500A) Processing helix chain 'I' and resid 331 through 337 removed outlier: 3.720A pdb=" N ALA I 335 " --> pdb=" O LYS I 331 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N CYS I 337 " --> pdb=" O CYS I 333 " (cutoff:3.500A) Processing helix chain 'I' and resid 362 through 367 removed outlier: 5.956A pdb=" N ILE I 367 " --> pdb=" O MET I 363 " (cutoff:3.500A) Processing helix chain 'I' and resid 370 through 376 removed outlier: 3.713A pdb=" N CYS I 376 " --> pdb=" O CYS I 372 " (cutoff:3.500A) Processing helix chain 'I' and resid 393 through 399 removed outlier: 4.530A pdb=" N LEU I 397 " --> pdb=" O THR I 393 " (cutoff:3.500A) removed outlier: 4.233A pdb=" N LEU I 398 " --> pdb=" O ARG I 394 " (cutoff:3.500A) removed outlier: 5.784A pdb=" N TYR I 399 " --> pdb=" O GLU I 395 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 393 through 399' Processing helix chain 'I' and resid 400 through 412 Processing helix chain 'I' and resid 413 through 423 Processing helix chain 'I' and resid 299 through 304 removed outlier: 4.667A pdb=" N LYS I 304 " --> pdb=" O TYR I 299 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 299 through 304' Processing helix chain 'J' and resid 1 through 26 removed outlier: 4.535A pdb=" N THR J 5 " --> pdb=" O FME J 1 " (cutoff:3.500A) removed outlier: 4.797A pdb=" N TYR J 6 " --> pdb=" O MET J 2 " (cutoff:3.500A) removed outlier: 5.036A pdb=" N TYR J 7 " --> pdb=" O TYR J 3 " (cutoff:3.500A) removed outlier: 5.829A pdb=" N PHE J 8 " --> pdb=" O LEU J 4 " (cutoff:3.500A) removed outlier: 6.552A pdb=" N ILE J 9 " --> pdb=" O THR J 5 " (cutoff:3.500A) removed outlier: 5.942A pdb=" N GLU J 10 " --> pdb=" O TYR J 6 " (cutoff:3.500A) Processing helix chain 'J' and resid 28 through 51 removed outlier: 3.654A pdb=" N SER J 32 " --> pdb=" O ASN J 28 " (cutoff:3.500A) Processing helix chain 'J' and resid 52 through 63 Processing helix chain 'J' and resid 65 through 78 removed outlier: 4.824A pdb=" N VAL J 69 " --> pdb=" O GLY J 65 " (cutoff:3.500A) removed outlier: 4.124A pdb=" N LEU J 77 " --> pdb=" O PHE J 73 " (cutoff:3.500A) Processing helix chain 'J' and resid 90 through 113 removed outlier: 4.425A pdb=" N LEU J 94 " --> pdb=" O ASN J 90 " (cutoff:3.500A) Proline residue: J 95 - end of helix removed outlier: 4.698A pdb=" N TYR J 112 " --> pdb=" O GLY J 108 " (cutoff:3.500A) removed outlier: 4.900A pdb=" N SER J 113 " --> pdb=" O LEU J 109 " (cutoff:3.500A) Processing helix chain 'J' and resid 117 through 128 removed outlier: 3.578A pdb=" N LEU J 122 " --> pdb=" O LEU J 118 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N ALA J 125 " --> pdb=" O LYS J 121 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N GLY J 127 " --> pdb=" O LEU J 123 " (cutoff:3.500A) removed outlier: 4.859A pdb=" N ASN J 128 " --> pdb=" O GLU J 124 " (cutoff:3.500A) Processing helix chain 'J' and resid 145 through 156 Processing helix chain 'J' and resid 158 through 181 removed outlier: 3.778A pdb=" N LEU J 162 " --> pdb=" O ASN J 158 " (cutoff:3.500A) removed outlier: 4.766A pdb=" N ILE J 167 " --> pdb=" O LEU J 163 " (cutoff:3.500A) Proline residue: J 176 - end of helix Processing helix chain 'K' and resid 1 through 18 removed outlier: 3.792A pdb=" N THR K 5 " --> pdb=" O FME K 1 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N ASN K 18 " --> pdb=" O GLY K 14 " (cutoff:3.500A) Processing helix chain 'K' and resid 21 through 48 removed outlier: 5.046A pdb=" N ALA K 25 " --> pdb=" O ASN K 21 " (cutoff:3.500A) Processing helix chain 'K' and resid 49 through 82 removed outlier: 5.035A pdb=" N SER K 53 " --> pdb=" O ASP K 49 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N VAL K 75 " --> pdb=" O LEU K 71 " (cutoff:3.500A) Processing helix chain 'L' and resid 708 through 727 Proline residue: L 717 - end of helix Proline residue: L 724 - end of helix Processing helix chain 'L' and resid 732 through 762 Processing helix chain 'L' and resid 787 through 812 removed outlier: 4.033A pdb=" N ILE L 809 " --> pdb=" O HIS L 805 " (cutoff:3.500A) removed outlier: 4.389A pdb=" N GLY L 810 " --> pdb=" O ILE L 806 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N MET L 812 " --> pdb=" O SER L 808 " (cutoff:3.500A) Processing helix chain 'L' and resid 817 through 838 Processing helix chain 'L' and resid 840 through 861 removed outlier: 3.545A pdb=" N GLY L 847 " --> pdb=" O VAL L 843 " (cutoff:3.500A) Processing helix chain 'L' and resid 865 through 897 removed outlier: 4.396A pdb=" N PHE L 885 " --> pdb=" O PHE L 881 " (cutoff:3.500A) Processing helix chain 'L' and resid 901 through 913 removed outlier: 5.507A pdb=" N TYR L 910 " --> pdb=" O PHE L 906 " (cutoff:3.500A) removed outlier: 6.571A pdb=" N LEU L 911 " --> pdb=" O ALA L 907 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N ILE L 912 " --> pdb=" O THR L 908 " (cutoff:3.500A) removed outlier: 6.160A pdb=" N ASN L 913 " --> pdb=" O ALA L 909 " (cutoff:3.500A) Processing helix chain 'L' and resid 914 through 933 Processing helix chain 'L' and resid 938 through 945 removed outlier: 4.091A pdb=" N THR L 942 " --> pdb=" O HIS L 938 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N LEU L 943 " --> pdb=" O ASN L 939 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N MET L 945 " --> pdb=" O LEU L 941 " (cutoff:3.500A) Processing helix chain 'L' and resid 948 through 955 Processing helix chain 'L' and resid 960 through 972 removed outlier: 4.808A pdb=" N GLY L 964 " --> pdb=" O LEU L 960 " (cutoff:3.500A) removed outlier: 4.474A pdb=" N ILE L 965 " --> pdb=" O VAL L 961 " (cutoff:3.500A) Processing helix chain 'L' and resid 973 through 979 removed outlier: 5.108A pdb=" N TYR L 977 " --> pdb=" O ASN L 973 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N THR L 978 " --> pdb=" O ILE L 974 " (cutoff:3.500A) Proline residue: L 979 - end of helix No H-bonds generated for 'chain 'L' and resid 973 through 979' Processing helix chain 'L' and resid 980 through 1003 removed outlier: 3.901A pdb=" N GLY L 997 " --> pdb=" O THR L 993 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N CYS L1002 " --> pdb=" O LEU L 998 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N SER L1003 " --> pdb=" O ILE L 999 " (cutoff:3.500A) Processing helix chain 'L' and resid 1005 through 1028 removed outlier: 3.686A pdb=" N ILE L1009 " --> pdb=" O ASP L1005 " (cutoff:3.500A) Processing helix chain 'L' and resid 1029 through 1059 removed outlier: 3.613A pdb=" N ALA L1033 " --> pdb=" O ALA L1029 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N LEU L1046 " --> pdb=" O PHE L1042 " (cutoff:3.500A) removed outlier: 4.575A pdb=" N LEU L1047 " --> pdb=" O PHE L1043 " (cutoff:3.500A) removed outlier: 5.291A pdb=" N LEU L1059 " --> pdb=" O ILE L1055 " (cutoff:3.500A) Processing helix chain 'L' and resid 1064 through 1069 removed outlier: 3.891A pdb=" N TYR L1068 " --> pdb=" O ASP L1064 " (cutoff:3.500A) removed outlier: 4.238A pdb=" N GLY L1069 " --> pdb=" O ILE L1065 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 1064 through 1069' Processing helix chain 'L' and resid 1075 through 1091 removed outlier: 3.559A pdb=" N TYR L1079 " --> pdb=" O LEU L1075 " (cutoff:3.500A) Processing helix chain 'L' and resid 1095 through 1111 removed outlier: 3.789A pdb=" N TYR L1099 " --> pdb=" O LEU L1095 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N ILE L1103 " --> pdb=" O TYR L1099 " (cutoff:3.500A) removed outlier: 4.730A pdb=" N ILE L1104 " --> pdb=" O THR L1100 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N TYR L1109 " --> pdb=" O ILE L1105 " (cutoff:3.500A) Processing helix chain 'L' and resid 1115 through 1142 removed outlier: 4.824A pdb=" N VAL L1119 " --> pdb=" O SER L1115 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N TYR L1120 " --> pdb=" O ASN L1116 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N TRP L1121 " --> pdb=" O TYR L1117 " (cutoff:3.500A) Processing helix chain 'L' and resid 1149 through 1156 removed outlier: 4.811A pdb=" N TYR L1153 " --> pdb=" O ASN L1149 " (cutoff:3.500A) Processing helix chain 'L' and resid 1160 through 1186 Proline residue: L1166 - end of helix removed outlier: 6.127A pdb=" N GLY L1178 " --> pdb=" O ALA L1174 " (cutoff:3.500A) removed outlier: 5.755A pdb=" N TRP L1179 " --> pdb=" O MET L1175 " (cutoff:3.500A) removed outlier: 5.011A pdb=" N ASP L1183 " --> pdb=" O TRP L1179 " (cutoff:3.500A) removed outlier: 5.627A pdb=" N ILE L1184 " --> pdb=" O ILE L1180 " (cutoff:3.500A) Processing helix chain 'L' and resid 1198 through 1210 removed outlier: 3.519A pdb=" N PHE L1202 " --> pdb=" O LEU L1198 " (cutoff:3.500A) removed outlier: 5.906A pdb=" N SER L1203 " --> pdb=" O PRO L1199 " (cutoff:3.500A) removed outlier: 8.780A pdb=" N TYR L1204 " --> pdb=" O ASN L1200 " (cutoff:3.500A) removed outlier: 8.386A pdb=" N PHE L1205 " --> pdb=" O ASN L1201 " (cutoff:3.500A) removed outlier: 6.109A pdb=" N ASP L1206 " --> pdb=" O PHE L1202 " (cutoff:3.500A) Processing helix chain 'L' and resid 1212 through 1236 Proline residue: L1219 - end of helix removed outlier: 3.782A pdb=" N SER L1227 " --> pdb=" O ALA L1223 " (cutoff:3.500A) Processing helix chain 'L' and resid 1237 through 1243 removed outlier: 4.733A pdb=" N PHE L1241 " --> pdb=" O PHE L1237 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N ASN L1242 " --> pdb=" O ALA L1238 " (cutoff:3.500A) Processing helix chain 'L' and resid 1245 through 1258 removed outlier: 3.723A pdb=" N VAL L1251 " --> pdb=" O TYR L1247 " (cutoff:3.500A) removed outlier: 4.503A pdb=" N GLN L1257 " --> pdb=" O SER L1253 " (cutoff:3.500A) removed outlier: 4.217A pdb=" N LYS L1258 " --> pdb=" O ILE L1254 " (cutoff:3.500A) Processing helix chain 'L' and resid 1259 through 1283 removed outlier: 6.603A pdb=" N GLN L1263 " --> pdb=" O LEU L1259 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N ASN L1266 " --> pdb=" O ASP L1262 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N HIS L1267 " --> pdb=" O GLN L1263 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N PHE L1271 " --> pdb=" O HIS L1267 " (cutoff:3.500A) removed outlier: 4.494A pdb=" N LYS L1272 " --> pdb=" O PHE L1268 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N THR L1276 " --> pdb=" O LYS L1272 " (cutoff:3.500A) Processing helix chain 'L' and resid 1287 through 1294 removed outlier: 4.488A pdb=" N GLY L1293 " --> pdb=" O LEU L1289 " (cutoff:3.500A) Proline residue: L1294 - end of helix Processing helix chain 'L' and resid 1295 through 1312 removed outlier: 4.008A pdb=" N LEU L1311 " --> pdb=" O ASN L1307 " (cutoff:3.500A) removed outlier: 4.928A pdb=" N SER L1312 " --> pdb=" O VAL L1308 " (cutoff:3.500A) Processing helix chain 'L' and resid 1317 through 1343 removed outlier: 3.942A pdb=" N MET L1321 " --> pdb=" O SER L1317 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N VAL L1342 " --> pdb=" O LEU L1338 " (cutoff:3.500A) Processing helix chain 'L' and resid 1344 through 1360 removed outlier: 3.910A pdb=" N ILE L1348 " --> pdb=" O PHE L1344 " (cutoff:3.500A) Proline residue: L1349 - end of helix Processing helix chain 'M' and resid 504 through 523 Processing helix chain 'M' and resid 526 through 548 Processing helix chain 'M' and resid 584 through 606 removed outlier: 3.590A pdb=" N PHE M 590 " --> pdb=" O LEU M 586 " (cutoff:3.500A) Proline residue: M 599 - end of helix removed outlier: 4.247A pdb=" N ASN M 605 " --> pdb=" O THR M 601 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N TRP M 606 " --> pdb=" O LEU M 602 " (cutoff:3.500A) Processing helix chain 'M' and resid 612 through 633 removed outlier: 3.527A pdb=" N TYR M 616 " --> pdb=" O ASN M 612 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N PHE M 631 " --> pdb=" O ILE M 627 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N TRP M 632 " --> pdb=" O LEU M 628 " (cutoff:3.500A) Processing helix chain 'M' and resid 635 through 657 removed outlier: 3.837A pdb=" N ALA M 645 " --> pdb=" O ILE M 641 " (cutoff:3.500A) removed outlier: 4.867A pdb=" N THR M 646 " --> pdb=" O LEU M 642 " (cutoff:3.500A) removed outlier: 5.324A pdb=" N LEU M 647 " --> pdb=" O PHE M 643 " (cutoff:3.500A) Proline residue: M 648 - end of helix Processing helix chain 'M' and resid 661 through 689 removed outlier: 3.593A pdb=" N THR M 673 " --> pdb=" O VAL M 669 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N PHE M 679 " --> pdb=" O SER M 675 " (cutoff:3.500A) Processing helix chain 'M' and resid 698 through 703 removed outlier: 4.219A pdb=" N PHE M 702 " --> pdb=" O ASN M 698 " (cutoff:3.500A) removed outlier: 5.885A pdb=" N VAL M 703 " --> pdb=" O HIS M 699 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 698 through 703' Processing helix chain 'M' and resid 705 through 724 removed outlier: 3.893A pdb=" N ILE M 711 " --> pdb=" O ASP M 707 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N LEU M 714 " --> pdb=" O THR M 710 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N GLY M 715 " --> pdb=" O ILE M 711 " (cutoff:3.500A) Processing helix chain 'M' and resid 730 through 740 Proline residue: M 734 - end of helix removed outlier: 3.509A pdb=" N SER M 740 " --> pdb=" O VAL M 736 " (cutoff:3.500A) Processing helix chain 'M' and resid 741 through 763 removed outlier: 4.915A pdb=" N LEU M 753 " --> pdb=" O ALA M 749 " (cutoff:3.500A) removed outlier: 5.076A pdb=" N LYS M 754 " --> pdb=" O GLY M 750 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N ALA M 756 " --> pdb=" O ILE M 752 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N LEU M 757 " --> pdb=" O LEU M 753 " (cutoff:3.500A) Processing helix chain 'M' and resid 768 through 776 Processing helix chain 'M' and resid 777 through 797 removed outlier: 4.151A pdb=" N ARG M 796 " --> pdb=" O LEU M 792 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N GLN M 797 " --> pdb=" O ALA M 793 " (cutoff:3.500A) Processing helix chain 'M' and resid 799 through 822 removed outlier: 3.525A pdb=" N ILE M 803 " --> pdb=" O ASP M 799 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ILE M 804 " --> pdb=" O LEU M 800 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N SER M 821 " --> pdb=" O LEU M 817 " (cutoff:3.500A) removed outlier: 4.662A pdb=" N ASN M 822 " --> pdb=" O GLY M 818 " (cutoff:3.500A) Processing helix chain 'M' and resid 823 through 849 Proline residue: M 842 - end of helix Processing helix chain 'M' and resid 851 through 856 Processing helix chain 'M' and resid 860 through 865 removed outlier: 3.861A pdb=" N TYR M 864 " --> pdb=" O ILE M 860 " (cutoff:3.500A) removed outlier: 4.975A pdb=" N LYS M 865 " --> pdb=" O VAL M 861 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 860 through 865' Processing helix chain 'M' and resid 866 through 871 removed outlier: 4.578A pdb=" N TYR M 870 " --> pdb=" O GLY M 866 " (cutoff:3.500A) Processing helix chain 'M' and resid 872 through 887 removed outlier: 3.684A pdb=" N GLY M 887 " --> pdb=" O PHE M 883 " (cutoff:3.500A) Processing helix chain 'M' and resid 891 through 908 removed outlier: 4.090A pdb=" N GLU M 897 " --> pdb=" O ASN M 893 " (cutoff:3.500A) Processing helix chain 'M' and resid 909 through 935 removed outlier: 4.309A pdb=" N CYS M 916 " --> pdb=" O GLY M 912 " (cutoff:3.500A) removed outlier: 4.528A pdb=" N ILE M 917 " --> pdb=" O GLY M 913 " (cutoff:3.500A) removed outlier: 5.390A pdb=" N SER M 918 " --> pdb=" O ILE M 914 " (cutoff:3.500A) removed outlier: 4.970A pdb=" N VAL M 919 " --> pdb=" O SER M 915 " (cutoff:3.500A) removed outlier: 4.246A pdb=" N LEU M 920 " --> pdb=" O CYS M 916 " (cutoff:3.500A) removed outlier: 4.097A pdb=" N ALA M 923 " --> pdb=" O VAL M 919 " (cutoff:3.500A) removed outlier: 4.459A pdb=" N LEU M 929 " --> pdb=" O TYR M 925 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N LYS M 932 " --> pdb=" O LYS M 928 " (cutoff:3.500A) Processing helix chain 'M' and resid 949 through 970 removed outlier: 3.730A pdb=" N THR M 963 " --> pdb=" O LEU M 959 " (cutoff:3.500A) Proline residue: M 970 - end of helix Processing helix chain 'M' and resid 971 through 978 removed outlier: 4.388A pdb=" N ASN M 975 " --> pdb=" O GLN M 971 " (cutoff:3.500A) removed outlier: 5.170A pdb=" N LEU M 976 " --> pdb=" O ILE M 972 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N LEU M 977 " --> pdb=" O MET M 973 " (cutoff:3.500A) Processing helix chain 'M' and resid 979 through 986 removed outlier: 4.197A pdb=" N TYR M 984 " --> pdb=" O THR M 980 " (cutoff:3.500A) removed outlier: 5.376A pdb=" N ILE M 985 " --> pdb=" O VAL M 981 " (cutoff:3.500A) removed outlier: 6.256A pdb=" N TYR M 986 " --> pdb=" O ASN M 982 " (cutoff:3.500A) Processing helix chain 'N' and resid 2403 through 2419 removed outlier: 3.599A pdb=" N THR N2413 " --> pdb=" O ILE N2409 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N SER N2418 " --> pdb=" O PHE N2414 " (cutoff:3.500A) removed outlier: 4.883A pdb=" N LYS N2419 " --> pdb=" O VAL N2415 " (cutoff:3.500A) Processing helix chain 'N' and resid 2422 through 2441 Processing helix chain 'N' and resid 2444 through 2449 removed outlier: 4.463A pdb=" N PHE N2448 " --> pdb=" O LEU N2444 " (cutoff:3.500A) removed outlier: 4.223A pdb=" N LEU N2449 " --> pdb=" O TYR N2445 " (cutoff:3.500A) No H-bonds generated for 'chain 'N' and resid 2444 through 2449' Processing helix chain 'N' and resid 2464 through 2487 removed outlier: 3.651A pdb=" N SER N2482 " --> pdb=" O MET N2478 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N SER N2483 " --> pdb=" O ILE N2479 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N TYR N2485 " --> pdb=" O ILE N2481 " (cutoff:3.500A) Processing helix chain 'N' and resid 2492 through 2500 removed outlier: 3.812A pdb=" N GLU N2500 " --> pdb=" O LYS N2496 " (cutoff:3.500A) Processing helix chain 'N' and resid 2504 through 2522 Processing helix chain 'N' and resid 2524 through 2545 Processing helix chain 'N' and resid 2549 through 2581 removed outlier: 3.556A pdb=" N SER N2553 " --> pdb=" O SER N2549 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N LEU N2566 " --> pdb=" O MET N2562 " (cutoff:3.500A) Processing helix chain 'N' and resid 2585 through 2590 removed outlier: 4.682A pdb=" N LEU N2589 " --> pdb=" O THR N2585 " (cutoff:3.500A) removed outlier: 5.465A pdb=" N ASP N2590 " --> pdb=" O LEU N2586 " (cutoff:3.500A) No H-bonds generated for 'chain 'N' and resid 2585 through 2590' Processing helix chain 'N' and resid 2591 through 2597 Processing helix chain 'N' and resid 2599 through 2615 removed outlier: 4.025A pdb=" N LEU N2606 " --> pdb=" O ILE N2602 " (cutoff:3.500A) removed outlier: 4.294A pdb=" N LYS N2613 " --> pdb=" O GLY N2609 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N ILE N2614 " --> pdb=" O LEU N2610 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N GLY N2615 " --> pdb=" O LEU N2611 " (cutoff:3.500A) Processing helix chain 'N' and resid 2619 through 2630 removed outlier: 4.972A pdb=" N LEU N2623 " --> pdb=" O LEU N2619 " (cutoff:3.500A) Processing helix chain 'N' and resid 2631 through 2654 removed outlier: 4.438A pdb=" N TYR N2637 " --> pdb=" O LEU N2633 " (cutoff:3.500A) removed outlier: 4.542A pdb=" N LEU N2640 " --> pdb=" O ILE N2636 " (cutoff:3.500A) Proline residue: N2642 - end of helix removed outlier: 4.675A pdb=" N ASN N2654 " --> pdb=" O LEU N2650 " (cutoff:3.500A) Processing helix chain 'N' and resid 2659 through 2681 removed outlier: 3.573A pdb=" N SER N2663 " --> pdb=" O SER N2659 " (cutoff:3.500A) removed outlier: 4.429A pdb=" N GLY N2677 " --> pdb=" O GLY N2673 " (cutoff:3.500A) removed outlier: 4.481A pdb=" N LEU N2678 " --> pdb=" O SER N2674 " (cutoff:3.500A) removed outlier: 4.794A pdb=" N LEU N2679 " --> pdb=" O VAL N2675 " (cutoff:3.500A) removed outlier: 4.702A pdb=" N GLN N2680 " --> pdb=" O GLY N2676 " (cutoff:3.500A) removed outlier: 6.603A pdb=" N ILE N2681 " --> pdb=" O GLY N2677 " (cutoff:3.500A) Processing helix chain 'N' and resid 2682 through 2705 removed outlier: 4.065A pdb=" N LEU N2701 " --> pdb=" O TYR N2697 " (cutoff:3.500A) removed outlier: 4.181A pdb=" N LEU N2702 " --> pdb=" O MET N2698 " (cutoff:3.500A) removed outlier: 4.608A pdb=" N LEU N2703 " --> pdb=" O MET N2699 " (cutoff:3.500A) removed outlier: 5.405A pdb=" N LEU N2704 " --> pdb=" O LEU N2700 " (cutoff:3.500A) removed outlier: 5.306A pdb=" N ASN N2705 " --> pdb=" O LEU N2701 " (cutoff:3.500A) Processing helix chain 'N' and resid 2707 through 2737 removed outlier: 3.832A pdb=" N ILE N2733 " --> pdb=" O ILE N2729 " (cutoff:3.500A) removed outlier: 4.984A pdb=" N TYR N2734 " --> pdb=" O ILE N2730 " (cutoff:3.500A) removed outlier: 4.917A pdb=" N TYR N2735 " --> pdb=" O PHE N2731 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N ILE N2736 " --> pdb=" O SER N2732 " (cutoff:3.500A) removed outlier: 5.981A pdb=" N ASN N2737 " --> pdb=" O ILE N2733 " (cutoff:3.500A) Processing helix chain 'N' and resid 2748 through 2759 removed outlier: 4.418A pdb=" N LEU N2752 " --> pdb=" O TYR N2748 " (cutoff:3.500A) removed outlier: 4.383A pdb=" N LYS N2753 " --> pdb=" O VAL N2749 " (cutoff:3.500A) removed outlier: 6.741A pdb=" N GLY N2754 " --> pdb=" O ASN N2750 " (cutoff:3.500A) removed outlier: 6.474A pdb=" N LEU N2755 " --> pdb=" O GLN N2751 " (cutoff:3.500A) removed outlier: 5.484A pdb=" N ILE N2756 " --> pdb=" O LEU N2752 " (cutoff:3.500A) removed outlier: 6.946A pdb=" N HIS N2757 " --> pdb=" O LYS N2753 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N ASP N2758 " --> pdb=" O GLY N2754 " (cutoff:3.500A) Processing helix chain 'N' and resid 2760 through 2775 Processing helix chain 'N' and resid 2779 through 2796 removed outlier: 3.993A pdb=" N PHE N2783 " --> pdb=" O LEU N2779 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N ASN N2787 " --> pdb=" O PHE N2783 " (cutoff:3.500A) Processing helix chain 'N' and resid 2797 through 2824 removed outlier: 4.179A pdb=" N SER N2801 " --> pdb=" O TYR N2797 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N LEU N2813 " --> pdb=" O LEU N2809 " (cutoff:3.500A) removed outlier: 4.260A pdb=" N TYR N2814 " --> pdb=" O ILE N2810 " (cutoff:3.500A) removed outlier: 4.599A pdb=" N LEU N2818 " --> pdb=" O TYR N2814 " (cutoff:3.500A) removed outlier: 4.191A pdb=" N LEU N2819 " --> pdb=" O TYR N2815 " (cutoff:3.500A) Processing helix chain 'N' and resid 2838 through 2860 removed outlier: 3.762A pdb=" N SER N2842 " --> pdb=" O SER N2838 " (cutoff:3.500A) removed outlier: 5.816A pdb=" N PHE N2856 " --> pdb=" O ILE N2852 " (cutoff:3.500A) removed outlier: 6.141A pdb=" N ILE N2857 " --> pdb=" O THR N2853 " (cutoff:3.500A) removed outlier: 4.723A pdb=" N TYR N2858 " --> pdb=" O PHE N2854 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N ASN N2859 " --> pdb=" O GLY N2855 " (cutoff:3.500A) removed outlier: 5.440A pdb=" N SER N2860 " --> pdb=" O PHE N2856 " (cutoff:3.500A) Processing helix chain 'N' and resid 2861 through 2870 Processing helix chain 'O' and resid 428 through 436 removed outlier: 3.891A pdb=" N MET O 436 " --> pdb=" O VAL O 432 " (cutoff:3.500A) Processing helix chain 'O' and resid 437 through 462 removed outlier: 3.615A pdb=" N TYR O 441 " --> pdb=" O ARG O 437 " (cutoff:3.500A) Proline residue: O 452 - end of helix Processing helix chain 'O' and resid 472 through 501 Processing helix chain 'O' and resid 505 through 523 Processing helix chain 'O' and resid 533 through 552 removed outlier: 6.761A pdb=" N HIS O 546 " --> pdb=" O LYS O 542 " (cutoff:3.500A) removed outlier: 5.537A pdb=" N SER O 547 " --> pdb=" O ASN O 543 " (cutoff:3.500A) removed outlier: 5.623A pdb=" N ILE O 548 " --> pdb=" O SER O 544 " (cutoff:3.500A) removed outlier: 7.010A pdb=" N ALA O 549 " --> pdb=" O ALA O 545 " (cutoff:3.500A) removed outlier: 4.772A pdb=" N GLY O 550 " --> pdb=" O HIS O 546 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N LEU O 551 " --> pdb=" O SER O 547 " (cutoff:3.500A) removed outlier: 5.251A pdb=" N PHE O 552 " --> pdb=" O ILE O 548 " (cutoff:3.500A) Processing helix chain 'P' and resid 63 through 77 removed outlier: 4.186A pdb=" N TYR P 68 " --> pdb=" O PHE P 64 " (cutoff:3.500A) removed outlier: 4.508A pdb=" N HIS P 76 " --> pdb=" O LYS P 72 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N GLY P 77 " --> pdb=" O LEU P 73 " (cutoff:3.500A) Processing helix chain 'P' and resid 86 through 98 removed outlier: 4.262A pdb=" N LYS P 90 " --> pdb=" O GLU P 86 " (cutoff:3.500A) removed outlier: 4.411A pdb=" N ARG P 91 " --> pdb=" O GLU P 87 " (cutoff:3.500A) removed outlier: 5.462A pdb=" N HIS P 92 " --> pdb=" O MET P 88 " (cutoff:3.500A) removed outlier: 5.651A pdb=" N LEU P 93 " --> pdb=" O ALA P 89 " (cutoff:3.500A) removed outlier: 4.238A pdb=" N LYS P 94 " --> pdb=" O LYS P 90 " (cutoff:3.500A) removed outlier: 4.304A pdb=" N VAL P 95 " --> pdb=" O ARG P 91 " (cutoff:3.500A) removed outlier: 5.237A pdb=" N THR P 96 " --> pdb=" O HIS P 92 " (cutoff:3.500A) removed outlier: 4.536A pdb=" N GLY P 97 " --> pdb=" O LEU P 93 " (cutoff:3.500A) removed outlier: 5.576A pdb=" N ASP P 98 " --> pdb=" O LYS P 94 " (cutoff:3.500A) No H-bonds generated for 'chain 'P' and resid 86 through 98' Processing helix chain 'P' and resid 111 through 120 removed outlier: 3.972A pdb=" N ILE P 115 " --> pdb=" O ASN P 111 " (cutoff:3.500A) Processing helix chain 'P' and resid 139 through 159 removed outlier: 3.811A pdb=" N GLU P 146 " --> pdb=" O ASP P 142 " (cutoff:3.500A) removed outlier: 4.424A pdb=" N GLY P 147 " --> pdb=" O VAL P 143 " (cutoff:3.500A) removed outlier: 4.740A pdb=" N ALA P 148 " --> pdb=" O HIS P 144 " (cutoff:3.500A) Processing helix chain 'P' and resid 177 through 194 Processing helix chain 'P' and resid 213 through 219 Processing helix chain 'P' and resid 237 through 251 removed outlier: 3.673A pdb=" N PHE P 250 " --> pdb=" O GLU P 246 " (cutoff:3.500A) removed outlier: 4.174A pdb=" N ASP P 251 " --> pdb=" O ARG P 247 " (cutoff:3.500A) Processing helix chain 'P' and resid 268 through 281 Processing helix chain 'P' and resid 290 through 304 removed outlier: 3.536A pdb=" N TYR P 294 " --> pdb=" O PRO P 290 " (cutoff:3.500A) removed outlier: 4.595A pdb=" N ALA P 303 " --> pdb=" O LYS P 299 " (cutoff:3.500A) removed outlier: 4.996A pdb=" N ILE P 304 " --> pdb=" O ALA P 300 " (cutoff:3.500A) Processing helix chain 'P' and resid 310 through 320 removed outlier: 3.872A pdb=" N VAL P 314 " --> pdb=" O SER P 310 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N GLU P 315 " --> pdb=" O PRO P 311 " (cutoff:3.500A) removed outlier: 4.292A pdb=" N PHE P 318 " --> pdb=" O VAL P 314 " (cutoff:3.500A) removed outlier: 4.333A pdb=" N LEU P 319 " --> pdb=" O GLU P 315 " (cutoff:3.500A) removed outlier: 5.079A pdb=" N SER P 320 " --> pdb=" O ARG P 316 " (cutoff:3.500A) Processing helix chain 'P' and resid 329 through 334 removed outlier: 4.073A pdb=" N LEU P 333 " --> pdb=" O THR P 329 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N ASP P 334 " --> pdb=" O PHE P 330 " (cutoff:3.500A) No H-bonds generated for 'chain 'P' and resid 329 through 334' Processing helix chain 'P' and resid 339 through 353 removed outlier: 5.024A pdb=" N PHE P 345 " --> pdb=" O PRO P 341 " (cutoff:3.500A) removed outlier: 4.707A pdb=" N LYS P 346 " --> pdb=" O ASP P 342 " (cutoff:3.500A) Proline residue: P 350 - end of helix removed outlier: 5.535A pdb=" N VAL P 353 " --> pdb=" O ARG P 349 " (cutoff:3.500A) Processing helix chain 'P' and resid 362 through 371 removed outlier: 5.517A pdb=" N LYS P 366 " --> pdb=" O GLN P 362 " (cutoff:3.500A) removed outlier: 4.161A pdb=" N THR P 369 " --> pdb=" O ASN P 365 " (cutoff:3.500A) removed outlier: 4.336A pdb=" N PHE P 370 " --> pdb=" O LYS P 366 " (cutoff:3.500A) removed outlier: 5.535A pdb=" N VAL P 371 " --> pdb=" O GLU P 367 " (cutoff:3.500A) Processing helix chain 'Q' and resid 41 through 47 removed outlier: 4.557A pdb=" N VAL Q 45 " --> pdb=" O ALA Q 41 " (cutoff:3.500A) removed outlier: 4.706A pdb=" N GLY Q 47 " --> pdb=" O GLU Q 43 " (cutoff:3.500A) Processing helix chain 'Q' and resid 49 through 55 removed outlier: 4.955A pdb=" N SER Q 53 " --> pdb=" O PRO Q 49 " (cutoff:3.500A) Processing helix chain 'Q' and resid 114 through 126 Processing helix chain 'Q' and resid 143 through 149 removed outlier: 4.630A pdb=" N ASN Q 147 " --> pdb=" O GLN Q 143 " (cutoff:3.500A) removed outlier: 4.546A pdb=" N PHE Q 148 " --> pdb=" O TYR Q 144 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N VAL Q 149 " --> pdb=" O ALA Q 145 " (cutoff:3.500A) No H-bonds generated for 'chain 'Q' and resid 143 through 149' Processing helix chain 'R' and resid 32 through 37 removed outlier: 3.623A pdb=" N THR R 36 " --> pdb=" O PRO R 32 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N LYS R 37 " --> pdb=" O GLU R 33 " (cutoff:3.500A) No H-bonds generated for 'chain 'R' and resid 32 through 37' Processing helix chain 'R' and resid 52 through 61 Processing helix chain 'R' and resid 68 through 73 removed outlier: 3.963A pdb=" N GLN R 72 " --> pdb=" O ASP R 68 " (cutoff:3.500A) Proline residue: R 73 - end of helix No H-bonds generated for 'chain 'R' and resid 68 through 73' Processing helix chain 'R' and resid 77 through 86 removed outlier: 3.767A pdb=" N LEU R 81 " --> pdb=" O ALA R 77 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N ALA R 83 " --> pdb=" O ILE R 79 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N GLN R 84 " --> pdb=" O GLU R 80 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N GLN R 85 " --> pdb=" O LEU R 81 " (cutoff:3.500A) Proline residue: R 86 - end of helix Processing helix chain 'S' and resid 19 through 29 Processing helix chain 'S' and resid 30 through 38 Proline residue: S 38 - end of helix Processing helix chain 'S' and resid 72 through 87 removed outlier: 3.518A pdb=" N VAL S 76 " --> pdb=" O SER S 72 " (cutoff:3.500A) removed outlier: 4.602A pdb=" N LYS S 87 " --> pdb=" O LEU S 83 " (cutoff:3.500A) Processing helix chain 'T' and resid 29 through 44 removed outlier: 3.810A pdb=" N LYS T 34 " --> pdb=" O PRO T 30 " (cutoff:3.500A) removed outlier: 4.772A pdb=" N ARG T 35 " --> pdb=" O ASP T 31 " (cutoff:3.500A) removed outlier: 5.200A pdb=" N ASP T 44 " --> pdb=" O LEU T 40 " (cutoff:3.500A) Processing helix chain 'T' and resid 57 through 62 removed outlier: 3.865A pdb=" N ASP T 61 " --> pdb=" O SER T 57 " (cutoff:3.500A) removed outlier: 4.677A pdb=" N LEU T 62 " --> pdb=" O PHE T 58 " (cutoff:3.500A) No H-bonds generated for 'chain 'T' and resid 57 through 62' Processing helix chain 'T' and resid 65 through 81 removed outlier: 3.603A pdb=" N VAL T 70 " --> pdb=" O SER T 66 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N VAL T 73 " --> pdb=" O THR T 69 " (cutoff:3.500A) Processing helix chain 'T' and resid 85 through 93 removed outlier: 5.984A pdb=" N LYS T 93 " --> pdb=" O ALA T 89 " (cutoff:3.500A) Processing helix chain 'T' and resid 94 through 105 removed outlier: 4.118A pdb=" N ALA T 104 " --> pdb=" O GLU T 100 " (cutoff:3.500A) removed outlier: 4.689A pdb=" N GLN T 105 " --> pdb=" O TYR T 101 " (cutoff:3.500A) Processing helix chain 'U' and resid 51 through 67 removed outlier: 3.777A pdb=" N PHE U 66 " --> pdb=" O LEU U 62 " (cutoff:3.500A) removed outlier: 5.660A pdb=" N ASP U 67 " --> pdb=" O LEU U 63 " (cutoff:3.500A) Processing helix chain 'U' and resid 88 through 104 removed outlier: 3.745A pdb=" N VAL U 92 " --> pdb=" O ASP U 88 " (cutoff:3.500A) removed outlier: 4.682A pdb=" N VAL U 93 " --> pdb=" O SER U 89 " (cutoff:3.500A) Processing helix chain 'U' and resid 108 through 116 removed outlier: 4.747A pdb=" N GLU U 114 " --> pdb=" O HIS U 110 " (cutoff:3.500A) removed outlier: 4.158A pdb=" N ILE U 115 " --> pdb=" O ASP U 111 " (cutoff:3.500A) removed outlier: 5.341A pdb=" N LYS U 116 " --> pdb=" O ALA U 112 " (cutoff:3.500A) Processing helix chain 'U' and resid 117 through 129 removed outlier: 3.634A pdb=" N GLN U 128 " --> pdb=" O TYR U 124 " (cutoff:3.500A) Proline residue: U 129 - end of helix Processing helix chain 'U' and resid 80 through 86 Processing helix chain 'V' and resid 41 through 60 removed outlier: 4.301A pdb=" N ALA V 45 " --> pdb=" O ASN V 41 " (cutoff:3.500A) Processing helix chain 'V' and resid 65 through 85 removed outlier: 3.535A pdb=" N ASN V 85 " --> pdb=" O ILE V 81 " (cutoff:3.500A) Processing helix chain 'V' and resid 87 through 96 removed outlier: 4.132A pdb=" N GLY V 96 " --> pdb=" O GLU V 92 " (cutoff:3.500A) Processing helix chain 'V' and resid 99 through 121 removed outlier: 3.810A pdb=" N ILE V 105 " --> pdb=" O GLU V 101 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N GLU V 119 " --> pdb=" O LYS V 115 " (cutoff:3.500A) removed outlier: 4.282A pdb=" N LYS V 121 " --> pdb=" O MET V 117 " (cutoff:3.500A) Processing helix chain 'W' and resid 17 through 44 removed outlier: 3.664A pdb=" N LEU W 21 " --> pdb=" O SER W 17 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N LYS W 23 " --> pdb=" O GLN W 19 " (cutoff:3.500A) Proline residue: W 37 - end of helix removed outlier: 3.809A pdb=" N TYR W 43 " --> pdb=" O PHE W 39 " (cutoff:3.500A) removed outlier: 4.610A pdb=" N GLU W 44 " --> pdb=" O ALA W 40 " (cutoff:3.500A) Processing helix chain 'W' and resid 48 through 65 removed outlier: 4.255A pdb=" N HIS W 63 " --> pdb=" O GLU W 59 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N ARG W 64 " --> pdb=" O PHE W 60 " (cutoff:3.500A) removed outlier: 5.130A pdb=" N PHE W 65 " --> pdb=" O GLU W 61 " (cutoff:3.500A) Processing helix chain 'W' and resid 68 through 89 removed outlier: 3.519A pdb=" N ASN W 88 " --> pdb=" O GLN W 84 " (cutoff:3.500A) removed outlier: 4.784A pdb=" N PHE W 89 " --> pdb=" O GLU W 85 " (cutoff:3.500A) Processing helix chain 'W' and resid 92 through 101 removed outlier: 4.853A pdb=" N TYR W 99 " --> pdb=" O GLN W 95 " (cutoff:3.500A) removed outlier: 4.255A pdb=" N PHE W 100 " --> pdb=" O PHE W 96 " (cutoff:3.500A) Proline residue: W 101 - end of helix Processing helix chain 'W' and resid 114 through 122 removed outlier: 3.623A pdb=" N LYS W 118 " --> pdb=" O ASN W 114 " (cutoff:3.500A) Processing helix chain 'X' and resid 31 through 40 removed outlier: 4.956A pdb=" N TYR X 40 " --> pdb=" O LEU X 36 " (cutoff:3.500A) Processing helix chain 'X' and resid 41 through 47 Processing helix chain 'X' and resid 48 through 61 removed outlier: 3.699A pdb=" N GLN X 61 " --> pdb=" O ARG X 57 " (cutoff:3.500A) Processing helix chain 'X' and resid 63 through 89 removed outlier: 5.236A pdb=" N LEU X 69 " --> pdb=" O ALA X 65 " (cutoff:3.500A) removed outlier: 6.756A pdb=" N LYS X 70 " --> pdb=" O ILE X 66 " (cutoff:3.500A) removed outlier: 5.857A pdb=" N GLU X 71 " --> pdb=" O ASP X 67 " (cutoff:3.500A) Processing helix chain 'X' and resid 90 through 105 removed outlier: 3.652A pdb=" N ASN X 104 " --> pdb=" O CYS X 100 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N ASN X 105 " --> pdb=" O LEU X 101 " (cutoff:3.500A) Processing helix chain 'X' and resid 107 through 112 removed outlier: 4.685A pdb=" N CYS X 111 " --> pdb=" O GLN X 107 " (cutoff:3.500A) removed outlier: 4.132A pdb=" N ARG X 112 " --> pdb=" O LEU X 108 " (cutoff:3.500A) No H-bonds generated for 'chain 'X' and resid 107 through 112' Processing helix chain 'X' and resid 113 through 126 Processing helix chain 'X' and resid 156 through 170 Processing helix chain 'Y' and resid 1207 through 1234 Processing helix chain 'Y' and resid 1241 through 1246 removed outlier: 4.025A pdb=" N SER Y1245 " --> pdb=" O LEU Y1241 " (cutoff:3.500A) Processing helix chain 'Y' and resid 1249 through 1273 Processing helix chain 'Y' and resid 1276 through 1296 removed outlier: 4.352A pdb=" N HIS Y1280 " --> pdb=" O ASP Y1276 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N ARG Y1294 " --> pdb=" O VAL Y1290 " (cutoff:3.500A) removed outlier: 4.388A pdb=" N THR Y1295 " --> pdb=" O LEU Y1291 " (cutoff:3.500A) removed outlier: 4.897A pdb=" N LYS Y1296 " --> pdb=" O GLY Y1292 " (cutoff:3.500A) Processing helix chain 'Y' and resid 1297 through 1319 removed outlier: 3.558A pdb=" N GLY Y1319 " --> pdb=" O PHE Y1315 " (cutoff:3.500A) Processing helix chain 'Y' and resid 1325 through 1330 removed outlier: 6.349A pdb=" N SER Y1329 " --> pdb=" O ASP Y1325 " (cutoff:3.500A) removed outlier: 7.327A pdb=" N LEU Y1330 " --> pdb=" O ARG Y1326 " (cutoff:3.500A) No H-bonds generated for 'chain 'Y' and resid 1325 through 1330' Processing helix chain 'Y' and resid 1354 through 1363 removed outlier: 3.575A pdb=" N THR Y1358 " --> pdb=" O PRO Y1354 " (cutoff:3.500A) Processing helix chain 'Y' and resid 1372 through 1378 Processing helix chain 'Z' and resid 29 through 71 removed outlier: 3.929A pdb=" N TYR Z 33 " --> pdb=" O ARG Z 29 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N GLU Z 54 " --> pdb=" O GLY Z 50 " (cutoff:3.500A) Proline residue: Z 71 - end of helix Processing helix chain 'Z' and resid 72 through 97 removed outlier: 3.788A pdb=" N LEU Z 89 " --> pdb=" O SER Z 85 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N GLU Z 94 " --> pdb=" O GLU Z 90 " (cutoff:3.500A) Processing helix chain 'a' and resid 6 through 34 Proline residue: a 10 - end of helix Processing helix chain 'a' and resid 43 through 58 removed outlier: 4.741A pdb=" N GLY a 58 " --> pdb=" O LEU a 54 " (cutoff:3.500A) Processing helix chain 'a' and resid 71 through 78 removed outlier: 4.531A pdb=" N LYS a 75 " --> pdb=" O PRO a 71 " (cutoff:3.500A) removed outlier: 4.309A pdb=" N HIS a 76 " --> pdb=" O GLU a 72 " (cutoff:3.500A) removed outlier: 4.187A pdb=" N HIS a 78 " --> pdb=" O PHE a 74 " (cutoff:3.500A) Processing helix chain 'b' and resid 7 through 12 removed outlier: 4.188A pdb=" N GLY b 11 " --> pdb=" O GLY b 7 " (cutoff:3.500A) Proline residue: b 12 - end of helix No H-bonds generated for 'chain 'b' and resid 7 through 12' Processing helix chain 'b' and resid 13 through 23 Processing helix chain 'b' and resid 24 through 50 removed outlier: 4.304A pdb=" N ALA b 29 " --> pdb=" O HIS b 25 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N GLY b 36 " --> pdb=" O ILE b 32 " (cutoff:3.500A) Proline residue: b 37 - end of helix removed outlier: 3.919A pdb=" N THR b 44 " --> pdb=" O ALA b 40 " (cutoff:3.500A) Proline residue: b 45 - end of helix Processing helix chain 'c' and resid 8 through 13 removed outlier: 4.064A pdb=" N LYS c 12 " --> pdb=" O PRO c 8 " (cutoff:3.500A) removed outlier: 5.301A pdb=" N TYR c 13 " --> pdb=" O VAL c 9 " (cutoff:3.500A) No H-bonds generated for 'chain 'c' and resid 8 through 13' Processing helix chain 'c' and resid 19 through 29 Processing helix chain 'c' and resid 53 through 58 removed outlier: 4.265A pdb=" N VAL c 57 " --> pdb=" O PRO c 53 " (cutoff:3.500A) Processing helix chain 'c' and resid 63 through 68 Processing helix chain 'c' and resid 73 through 78 removed outlier: 3.920A pdb=" N ARG c 77 " --> pdb=" O PRO c 73 " (cutoff:3.500A) Processing helix chain 'c' and resid 90 through 100 removed outlier: 3.802A pdb=" N LEU c 97 " --> pdb=" O THR c 93 " (cutoff:3.500A) Processing helix chain 'c' and resid 111 through 124 removed outlier: 3.667A pdb=" N ILE c 121 " --> pdb=" O ALA c 117 " (cutoff:3.500A) removed outlier: 4.505A pdb=" N GLY c 124 " --> pdb=" O ASN c 120 " (cutoff:3.500A) Processing helix chain 'c' and resid 127 through 135 removed outlier: 3.679A pdb=" N SER c 135 " --> pdb=" O ALA c 131 " (cutoff:3.500A) Processing helix chain 'c' and resid 136 through 142 removed outlier: 4.116A pdb=" N GLY c 142 " --> pdb=" O ASP c 138 " (cutoff:3.500A) Processing helix chain 'd' and resid 2 through 26 Processing helix chain 'd' and resid 32 through 68 removed outlier: 4.182A pdb=" N TYR d 36 " --> pdb=" O TYR d 32 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N VAL d 37 " --> pdb=" O PRO d 33 " (cutoff:3.500A) Processing helix chain 'e' and resid 15 through 30 removed outlier: 4.821A pdb=" N ASP e 30 " --> pdb=" O THR e 26 " (cutoff:3.500A) Processing helix chain 'e' and resid 37 through 50 Processing helix chain 'e' and resid 51 through 66 Processing helix chain 'f' and resid 4 through 16 removed outlier: 3.841A pdb=" N VAL f 8 " --> pdb=" O SER f 4 " (cutoff:3.500A) removed outlier: 4.371A pdb=" N GLY f 16 " --> pdb=" O ALA f 12 " (cutoff:3.500A) Processing helix chain 'f' and resid 17 through 27 Processing helix chain 'f' and resid 74 through 83 removed outlier: 6.269A pdb=" N PHE f 79 " --> pdb=" O PRO f 75 " (cutoff:3.500A) removed outlier: 4.796A pdb=" N GLY f 82 " --> pdb=" O HIS f 78 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N TYR f 83 " --> pdb=" O PHE f 79 " (cutoff:3.500A) Processing helix chain 'f' and resid 93 through 98 removed outlier: 3.850A pdb=" N LEU f 97 " --> pdb=" O PRO f 93 " (cutoff:3.500A) Proline residue: f 98 - end of helix No H-bonds generated for 'chain 'f' and resid 93 through 98' Processing helix chain 'g' and resid 52 through 67 removed outlier: 3.893A pdb=" N GLU g 56 " --> pdb=" O ASN g 52 " (cutoff:3.500A) removed outlier: 4.566A pdb=" N GLN g 61 " --> pdb=" O LEU g 57 " (cutoff:3.500A) removed outlier: 4.098A pdb=" N LEU g 66 " --> pdb=" O ARG g 62 " (cutoff:3.500A) Proline residue: g 67 - end of helix Processing helix chain 'g' and resid 69 through 75 removed outlier: 4.526A pdb=" N PHE g 73 " --> pdb=" O PRO g 69 " (cutoff:3.500A) removed outlier: 5.472A pdb=" N VAL g 74 " --> pdb=" O GLY g 70 " (cutoff:3.500A) Processing helix chain 'g' and resid 84 through 101 removed outlier: 3.695A pdb=" N LEU g 97 " --> pdb=" O GLU g 93 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N TYR g 98 " --> pdb=" O ILE g 94 " (cutoff:3.500A) removed outlier: 4.516A pdb=" N LYS g 99 " --> pdb=" O ALA g 95 " (cutoff:3.500A) removed outlier: 4.483A pdb=" N THR g 100 " --> pdb=" O ALA g 96 " (cutoff:3.500A) removed outlier: 5.669A pdb=" N ASP g 101 " --> pdb=" O LEU g 97 " (cutoff:3.500A) Processing helix chain 'g' and resid 104 through 111 removed outlier: 3.839A pdb=" N LEU g 110 " --> pdb=" O LEU g 106 " (cutoff:3.500A) Processing helix chain 'g' and resid 112 through 137 removed outlier: 3.653A pdb=" N LEU g 118 " --> pdb=" O LYS g 114 " (cutoff:3.500A) removed outlier: 4.170A pdb=" N LEU g 125 " --> pdb=" O ASP g 121 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N LEU g 126 " --> pdb=" O ASN g 122 " (cutoff:3.500A) Processing helix chain 'g' and resid 164 through 169 Processing helix chain 'g' and resid 171 through 208 removed outlier: 3.928A pdb=" N SER g 175 " --> pdb=" O LEU g 171 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N ARG g 188 " --> pdb=" O VAL g 184 " (cutoff:3.500A) removed outlier: 5.117A pdb=" N GLU g 189 " --> pdb=" O TYR g 185 " (cutoff:3.500A) removed outlier: 4.076A pdb=" N ASP g 190 " --> pdb=" O LYS g 186 " (cutoff:3.500A) removed outlier: 6.213A pdb=" N ILE g 191 " --> pdb=" O SER g 187 " (cutoff:3.500A) removed outlier: 7.197A pdb=" N THR g 192 " --> pdb=" O ARG g 188 " (cutoff:3.500A) removed outlier: 6.961A pdb=" N PHE g 193 " --> pdb=" O GLU g 189 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N TRP g 194 " --> pdb=" O ASP g 190 " (cutoff:3.500A) Proline residue: g 208 - end of helix Processing helix chain 'g' and resid 209 through 214 removed outlier: 4.177A pdb=" N ALA g 213 " --> pdb=" O GLU g 209 " (cutoff:3.500A) Proline residue: g 214 - end of helix No H-bonds generated for 'chain 'g' and resid 209 through 214' Processing helix chain 'g' and resid 217 through 229 removed outlier: 3.525A pdb=" N GLY g 229 " --> pdb=" O ARG g 225 " (cutoff:3.500A) Processing helix chain 'g' and resid 233 through 239 removed outlier: 4.691A pdb=" N LYS g 239 " --> pdb=" O ALA g 235 " (cutoff:3.500A) Processing helix chain 'h' and resid 48 through 75 Processing helix chain 'h' and resid 78 through 85 removed outlier: 3.820A pdb=" N THR h 82 " --> pdb=" O THR h 78 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N PHE h 83 " --> pdb=" O TRP h 79 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N PHE h 84 " --> pdb=" O VAL h 80 " (cutoff:3.500A) removed outlier: 5.966A pdb=" N HIS h 85 " --> pdb=" O GLU h 81 " (cutoff:3.500A) No H-bonds generated for 'chain 'h' and resid 78 through 85' Processing helix chain 'h' and resid 88 through 119 removed outlier: 4.653A pdb=" N ARG h 118 " --> pdb=" O HIS h 114 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N GLU h 119 " --> pdb=" O GLU h 115 " (cutoff:3.500A) Processing helix chain 'h' and resid 122 through 127 Processing helix chain 'i' and resid 25 through 50 removed outlier: 3.592A pdb=" N ASN i 29 " --> pdb=" O ASN i 25 " (cutoff:3.500A) Proline residue: i 50 - end of helix Processing helix chain 'i' and resid 60 through 79 Processing helix chain 'j' and resid 20 through 46 Processing helix chain 'k' and resid 9 through 19 removed outlier: 4.992A pdb=" N TRP k 15 " --> pdb=" O ARG k 11 " (cutoff:3.500A) removed outlier: 5.453A pdb=" N ARG k 16 " --> pdb=" O ARG k 12 " (cutoff:3.500A) removed outlier: 4.834A pdb=" N TYR k 17 " --> pdb=" O GLU k 13 " (cutoff:3.500A) removed outlier: 5.711A pdb=" N THR k 19 " --> pdb=" O TRP k 15 " (cutoff:3.500A) Processing helix chain 'k' and resid 22 through 29 removed outlier: 4.687A pdb=" N PHE k 27 " --> pdb=" O ARG k 23 " (cutoff:3.500A) removed outlier: 5.060A pdb=" N GLY k 29 " --> pdb=" O ASN k 25 " (cutoff:3.500A) Processing helix chain 'k' and resid 33 through 48 Processing helix chain 'l' and resid 27 through 38 removed outlier: 3.693A pdb=" N GLU l 33 " --> pdb=" O PHE l 29 " (cutoff:3.500A) removed outlier: 4.847A pdb=" N GLU l 34 " --> pdb=" O ASP l 30 " (cutoff:3.500A) Proline residue: l 35 - end of helix removed outlier: 4.996A pdb=" N GLY l 38 " --> pdb=" O GLU l 34 " (cutoff:3.500A) Processing helix chain 'l' and resid 47 through 52 removed outlier: 3.633A pdb=" N LYS l 51 " --> pdb=" O PRO l 47 " (cutoff:3.500A) removed outlier: 5.468A pdb=" N ASN l 52 " --> pdb=" O ALA l 48 " (cutoff:3.500A) No H-bonds generated for 'chain 'l' and resid 47 through 52' Processing helix chain 'l' and resid 73 through 78 removed outlier: 3.735A pdb=" N TYR l 77 " --> pdb=" O ASN l 73 " (cutoff:3.500A) Processing helix chain 'l' and resid 89 through 115 removed outlier: 4.186A pdb=" N THR l 112 " --> pdb=" O SER l 108 " (cutoff:3.500A) removed outlier: 4.111A pdb=" N TYR l 113 " --> pdb=" O TYR l 109 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N PHE l 114 " --> pdb=" O VAL l 110 " (cutoff:3.500A) removed outlier: 4.201A pdb=" N VAL l 115 " --> pdb=" O ALA l 111 " (cutoff:3.500A) Processing helix chain 'l' and resid 126 through 131 removed outlier: 6.029A pdb=" N LEU l 130 " --> pdb=" O PRO l 126 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N TRP l 131 " --> pdb=" O TYR l 127 " (cutoff:3.500A) No H-bonds generated for 'chain 'l' and resid 126 through 131' Processing helix chain 'l' and resid 140 through 145 Processing helix chain 'm' and resid 29 through 46 removed outlier: 6.075A pdb=" N ASP m 33 " --> pdb=" O ASP m 29 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N ARG m 34 " --> pdb=" O GLY m 30 " (cutoff:3.500A) removed outlier: 6.146A pdb=" N GLN m 43 " --> pdb=" O ARG m 39 " (cutoff:3.500A) removed outlier: 6.610A pdb=" N GLU m 44 " --> pdb=" O THR m 40 " (cutoff:3.500A) removed outlier: 4.067A pdb=" N ARG m 45 " --> pdb=" O PHE m 41 " (cutoff:3.500A) Processing helix chain 'm' and resid 49 through 75 removed outlier: 3.765A pdb=" N LYS m 54 " --> pdb=" O ARG m 50 " (cutoff:3.500A) removed outlier: 5.629A pdb=" N PHE m 63 " --> pdb=" O PHE m 59 " (cutoff:3.500A) Proline residue: m 64 - end of helix Processing helix chain 'n' and resid 8 through 30 Processing helix chain 'n' and resid 32 through 52 removed outlier: 3.769A pdb=" N PHE n 36 " --> pdb=" O ASN n 32 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N ASN n 50 " --> pdb=" O LYS n 46 " (cutoff:3.500A) removed outlier: 4.765A pdb=" N GLN n 52 " --> pdb=" O ASP n 48 " (cutoff:3.500A) Processing helix chain 'n' and resid 55 through 74 Processing helix chain 'o' and resid 9 through 17 Processing helix chain 'o' and resid 19 through 24 removed outlier: 5.211A pdb=" N ASP o 24 " --> pdb=" O LEU o 20 " (cutoff:3.500A) Processing helix chain 'o' and resid 26 through 41 removed outlier: 3.872A pdb=" N LEU o 30 " --> pdb=" O CYS o 26 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N VAL o 31 " --> pdb=" O ALA o 27 " (cutoff:3.500A) Proline residue: o 32 - end of helix Processing helix chain 'o' and resid 43 through 84 removed outlier: 4.727A pdb=" N CYS o 47 " --> pdb=" O MET o 43 " (cutoff:3.500A) removed outlier: 5.347A pdb=" N GLY o 48 " --> pdb=" O PRO o 44 " (cutoff:3.500A) removed outlier: 7.635A pdb=" N HIS o 49 " --> pdb=" O TRP o 45 " (cutoff:3.500A) removed outlier: 6.932A pdb=" N GLU o 50 " --> pdb=" O ALA o 46 " (cutoff:3.500A) Processing helix chain 'p' and resid 11 through 16 removed outlier: 3.773A pdb=" N ILE p 15 " --> pdb=" O SER p 11 " (cutoff:3.500A) removed outlier: 5.603A pdb=" N ASN p 16 " --> pdb=" O PHE p 12 " (cutoff:3.500A) No H-bonds generated for 'chain 'p' and resid 11 through 16' Processing helix chain 'p' and resid 19 through 55 removed outlier: 3.580A pdb=" N VAL p 23 " --> pdb=" O ASP p 19 " (cutoff:3.500A) Processing helix chain 'p' and resid 58 through 63 Processing helix chain 'p' and resid 64 through 77 Proline residue: p 75 - end of helix Processing helix chain 'p' and resid 82 through 88 removed outlier: 4.182A pdb=" N ASN p 88 " --> pdb=" O GLY p 84 " (cutoff:3.500A) Processing sheet with id= 1, first strand: chain 'B' and resid 116 through 119 removed outlier: 3.526A pdb=" N MET B 117 " --> pdb=" O TRP B 143 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N MET B 147 " --> pdb=" O VAL B 119 " (cutoff:3.500A) Processing sheet with id= 2, first strand: chain 'C' and resid 87 through 91 removed outlier: 3.675A pdb=" N GLY C 88 " --> pdb=" O HIS C 99 " (cutoff:3.500A) removed outlier: 5.178A pdb=" N LEU C 96 " --> pdb=" O ARG C 152 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N LEU C 98 " --> pdb=" O ARG C 154 " (cutoff:3.500A) removed outlier: 4.606A pdb=" N TYR C 158 " --> pdb=" O VAL C 100 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N VAL C 140 " --> pdb=" O THR C 157 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N PHE C 138 " --> pdb=" O ALA C 159 " (cutoff:3.500A) removed outlier: 6.717A pdb=" N ASN C 143 " --> pdb=" O ILE C 124 " (cutoff:3.500A) Processing sheet with id= 3, first strand: chain 'C' and resid 219 through 225 No H-bonds generated for sheet with id= 3 Processing sheet with id= 4, first strand: chain 'C' and resid 125 through 131 removed outlier: 3.860A pdb=" N ASP C 125 " --> pdb=" O ASN C 143 " (cutoff:3.500A) removed outlier: 4.393A pdb=" N ARG C 137 " --> pdb=" O TYR C 131 " (cutoff:3.500A) Processing sheet with id= 5, first strand: chain 'D' and resid 83 through 86 removed outlier: 3.590A pdb=" N ARG D 99 " --> pdb=" O HIS D 115 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N ILE D 101 " --> pdb=" O ASP D 113 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N ARG D 111 " --> pdb=" O GLU D 103 " (cutoff:3.500A) Processing sheet with id= 6, first strand: chain 'D' and resid 397 through 404 removed outlier: 3.835A pdb=" N GLY D 397 " --> pdb=" O SER D 416 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N LYS D 424 " --> pdb=" O VAL D 415 " (cutoff:3.500A) Processing sheet with id= 7, first strand: chain 'E' and resid 121 through 127 Processing sheet with id= 8, first strand: chain 'F' and resid 195 through 202 removed outlier: 3.829A pdb=" N ASP F 196 " --> pdb=" O THR F 154 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N ALA F 155 " --> pdb=" O ARG F 113 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N THR F 243 " --> pdb=" O TYR F 114 " (cutoff:3.500A) Processing sheet with id= 9, first strand: chain 'F' and resid 287 through 291 removed outlier: 3.686A pdb=" N CYS F 288 " --> pdb=" O ILE F 280 " (cutoff:3.500A) Processing sheet with id= 10, first strand: chain 'G' and resid 175 through 179 removed outlier: 8.050A pdb=" N LEU G 175 " --> pdb=" O LYS G 241 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N LYS G 241 " --> pdb=" O LEU G 175 " (cutoff:3.500A) removed outlier: 4.449A pdb=" N ALA G 237 " --> pdb=" O SER G 179 " (cutoff:3.500A) Processing sheet with id= 11, first strand: chain 'G' and resid 203 through 207 removed outlier: 4.325A pdb=" N ARG G 207 " --> pdb=" O ASP G 210 " (cutoff:3.500A) Processing sheet with id= 12, first strand: chain 'G' and resid 254 through 257 removed outlier: 3.576A pdb=" N SER G 257 " --> pdb=" O ILE G 268 " (cutoff:3.500A) removed outlier: 5.381A pdb=" N ASN G 267 " --> pdb=" O ARG G 283 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ARG G 279 " --> pdb=" O ASP G 271 " (cutoff:3.500A) Processing sheet with id= 13, first strand: chain 'G' and resid 320 through 323 removed outlier: 6.659A pdb=" N ASP G 584 " --> pdb=" O ARG G 315 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N MET G 549 " --> pdb=" O GLU G 345 " (cutoff:3.500A) removed outlier: 4.566A pdb=" N ASN G 373 " --> pdb=" O PHE G 346 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N ALA G 348 " --> pdb=" O ASN G 373 " (cutoff:3.500A) Processing sheet with id= 14, first strand: chain 'G' and resid 437 through 442 removed outlier: 4.341A pdb=" N ALA G 409 " --> pdb=" O ASN G 479 " (cutoff:3.500A) Processing sheet with id= 15, first strand: chain 'G' and resid 597 through 601 removed outlier: 4.843A pdb=" N GLY G 597 " --> pdb=" O SER G 609 " (cutoff:3.500A) removed outlier: 4.287A pdb=" N ARG G 605 " --> pdb=" O ASN G 601 " (cutoff:3.500A) Processing sheet with id= 16, first strand: chain 'I' and resid 314 through 318 removed outlier: 3.561A pdb=" N GLU I 314 " --> pdb=" O THR I 384 " (cutoff:3.500A) removed outlier: 6.522A pdb=" N ALA I 380 " --> pdb=" O ARG I 318 " (cutoff:3.500A) Processing sheet with id= 17, first strand: chain 'I' and resid 342 through 346 Processing sheet with id= 18, first strand: chain 'L' and resid 766 through 769 removed outlier: 3.772A pdb=" N LEU L 769 " --> pdb=" O TYR L 782 " (cutoff:3.500A) removed outlier: 4.363A pdb=" N TYR L 782 " --> pdb=" O LEU L 769 " (cutoff:3.500A) Processing sheet with id= 19, first strand: chain 'M' and resid 558 through 561 Processing sheet with id= 20, first strand: chain 'P' and resid 30 through 33 removed outlier: 7.184A pdb=" N ASP P 30 " --> pdb=" O ALA P 42 " (cutoff:3.500A) Processing sheet with id= 21, first strand: chain 'P' and resid 101 through 106 removed outlier: 6.406A pdb=" N VAL P 101 " --> pdb=" O THR P 78 " (cutoff:3.500A) removed outlier: 5.529A pdb=" N LEU P 128 " --> pdb=" O PHE P 59 " (cutoff:3.500A) Processing sheet with id= 22, first strand: chain 'P' and resid 222 through 226 removed outlier: 6.539A pdb=" N SER P 225 " --> pdb=" O ILE P 287 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N LEU P 289 " --> pdb=" O SER P 225 " (cutoff:3.500A) Processing sheet with id= 23, first strand: chain 'Q' and resid 90 through 93 removed outlier: 3.793A pdb=" N TRP Q 91 " --> pdb=" O SER Q 100 " (cutoff:3.500A) removed outlier: 4.800A pdb=" N TRP Q 98 " --> pdb=" O ASN Q 93 " (cutoff:3.500A) Processing sheet with id= 24, first strand: chain 'Q' and resid 109 through 113 removed outlier: 5.424A pdb=" N VAL Q 57 " --> pdb=" O ASP Q 83 " (cutoff:3.500A) removed outlier: 4.680A pdb=" N GLN Q 62 " --> pdb=" O GLN Q 132 " (cutoff:3.500A) Processing sheet with id= 25, first strand: chain 'R' and resid 19 through 23 removed outlier: 4.582A pdb=" N ASN R 27 " --> pdb=" O SER R 23 " (cutoff:3.500A) Processing sheet with id= 26, first strand: chain 'R' and resid 87 through 90 removed outlier: 5.105A pdb=" N THR R 130 " --> pdb=" O CYS R 125 " (cutoff:3.500A) Processing sheet with id= 27, first strand: chain 'S' and resid 41 through 47 removed outlier: 3.590A pdb=" N LEU S 12 " --> pdb=" O ARG S 45 " (cutoff:3.500A) Processing sheet with id= 28, first strand: chain 'f' and resid 43 through 48 removed outlier: 5.921A pdb=" N THR f 58 " --> pdb=" O THR f 48 " (cutoff:3.500A) Processing sheet with id= 29, first strand: chain 'g' and resid 139 through 143 removed outlier: 4.226A pdb=" N THR g 151 " --> pdb=" O VAL g 142 " (cutoff:3.500A) 3135 hydrogen bonds defined for protein. 9378 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: 49.08 Time building geometry restraints manager: 76.90 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.81 - 1.11: 64030 1.11 - 1.40: 27477 1.40 - 1.69: 38919 1.69 - 1.99: 473 1.99 - 2.28: 68 Bond restraints: 130967 Sorted by residual: bond pdb=" C3' FMN F 501 " pdb=" O3' FMN F 501 " ideal model delta sigma weight residual 1.410 1.184 0.226 2.00e-02 2.50e+03 1.28e+02 bond pdb=" C4 FMN F 501 " pdb=" C4A FMN F 501 " ideal model delta sigma weight residual 1.390 1.613 -0.223 2.00e-02 2.50e+03 1.24e+02 bond pdb=" OB3 CDL O 601 " pdb=" PB2 CDL O 601 " ideal model delta sigma weight residual 1.529 1.446 0.083 1.00e-02 1.00e+04 6.95e+01 bond pdb=" C2 FMN F 501 " pdb=" O2 FMN F 501 " ideal model delta sigma weight residual 1.230 1.392 -0.162 2.00e-02 2.50e+03 6.60e+01 bond pdb=" C4 FMN F 501 " pdb=" O4 FMN F 501 " ideal model delta sigma weight residual 1.230 1.388 -0.158 2.00e-02 2.50e+03 6.25e+01 ... (remaining 130962 not shown) Histogram of bond angle deviations from ideal: 6.45 - 33.26: 4 33.26 - 60.07: 10 60.07 - 86.87: 104 86.87 - 113.68: 156527 113.68 - 140.49: 79525 Bond angle restraints: 236170 Sorted by residual: angle pdb=" HZ1 LYS F 57 " pdb=" NZ LYS F 57 " pdb=" HZ2 LYS F 57 " ideal model delta sigma weight residual 109.00 6.45 102.55 3.00e+00 1.11e-01 1.17e+03 angle pdb=" HZ1 LYS F 221 " pdb=" NZ LYS F 221 " pdb=" HZ2 LYS F 221 " ideal model delta sigma weight residual 109.00 13.81 95.19 3.00e+00 1.11e-01 1.01e+03 angle pdb=" HZ1 LYS d 63 " pdb=" NZ LYS d 63 " pdb=" HZ2 LYS d 63 " ideal model delta sigma weight residual 109.00 21.43 87.57 3.00e+00 1.11e-01 8.52e+02 angle pdb=" HZ1 LYS o 17 " pdb=" NZ LYS o 17 " pdb=" HZ2 LYS o 17 " ideal model delta sigma weight residual 109.00 25.54 83.46 3.00e+00 1.11e-01 7.74e+02 angle pdb=" HZ1 LYS f 66 " pdb=" NZ LYS f 66 " pdb=" HZ2 LYS f 66 " ideal model delta sigma weight residual 109.00 38.06 70.94 3.00e+00 1.11e-01 5.59e+02 ... (remaining 236165 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 36.00: 60085 36.00 - 72.00: 2043 72.00 - 107.99: 105 107.99 - 143.99: 19 143.99 - 179.99: 13 Dihedral angle restraints: 62265 sinusoidal: 34005 harmonic: 28260 Sorted by residual: dihedral pdb=" C10 FMN F 501 " pdb=" C1' FMN F 501 " pdb=" N10 FMN F 501 " pdb=" C2' FMN F 501 " ideal model delta sinusoidal sigma weight residual -102.41 73.03 -175.44 1 2.00e+01 2.50e-03 4.79e+01 dihedral pdb=" C5' FMN F 501 " pdb=" O5' FMN F 501 " pdb=" P FMN F 501 " pdb=" O1P FMN F 501 " ideal model delta sinusoidal sigma weight residual 75.26 -109.92 -174.82 1 2.00e+01 2.50e-03 4.79e+01 dihedral pdb=" CA LYS o 81 " pdb=" C LYS o 81 " pdb=" N ALA o 82 " pdb=" CA ALA o 82 " ideal model delta harmonic sigma weight residual 180.00 151.70 28.30 0 5.00e+00 4.00e-02 3.20e+01 ... (remaining 62262 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 4.187: 10059 4.187 - 8.374: 12 8.374 - 12.561: 0 12.561 - 16.748: 0 16.748 - 20.935: 4 Chirality restraints: 10075 Sorted by residual: chirality pdb="FE4 SF4 F 502 " pdb=" S1 SF4 F 502 " pdb=" S2 SF4 F 502 " pdb=" S3 SF4 F 502 " both_signs ideal model delta sigma weight residual False 10.55 -10.38 20.93 2.00e-01 2.50e+01 1.10e+04 chirality pdb="FE3 SF4 F 502 " pdb=" S1 SF4 F 502 " pdb=" S2 SF4 F 502 " pdb=" S4 SF4 F 502 " both_signs ideal model delta sigma weight residual False -10.55 10.26 -20.81 2.00e-01 2.50e+01 1.08e+04 chirality pdb="FE1 SF4 F 502 " pdb=" S2 SF4 F 502 " pdb=" S3 SF4 F 502 " pdb=" S4 SF4 F 502 " both_signs ideal model delta sigma weight residual False -10.55 10.16 -20.71 2.00e-01 2.50e+01 1.07e+04 ... (remaining 10072 not shown) Planarity restraints: 19050 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LYS L1272 " 0.028 2.00e-02 2.50e+03 5.46e-02 2.98e+01 pdb=" N GLY L1273 " -0.094 2.00e-02 2.50e+03 pdb=" CA GLY L1273 " 0.025 2.00e-02 2.50e+03 pdb=" H GLY L1273 " 0.041 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ILE A 8 " -0.024 2.00e-02 2.50e+03 4.66e-02 2.17e+01 pdb=" N ILE A 9 " 0.080 2.00e-02 2.50e+03 pdb=" CA ILE A 9 " -0.022 2.00e-02 2.50e+03 pdb=" H ILE A 9 " -0.034 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LYS I 403 " -0.020 2.00e-02 2.50e+03 3.86e-02 1.49e+01 pdb=" N LEU I 404 " 0.066 2.00e-02 2.50e+03 pdb=" CA LEU I 404 " -0.018 2.00e-02 2.50e+03 pdb=" H LEU I 404 " -0.029 2.00e-02 2.50e+03 ... (remaining 19047 not shown) Histogram of nonbonded interaction distances: 0.02 - 0.93: 2 0.93 - 1.85: 428 1.85 - 2.77: 263854 2.77 - 3.68: 569149 3.68 - 4.60: 1053126 Warning: very small nonbonded interaction distances. Nonbonded interactions: 1886559 Sorted by model distance: nonbonded pdb=" OG SER T 66 " pdb=" O7 EHZ T 201 " model vdw 0.019 2.200 nonbonded pdb=" OG SER U 89 " pdb=" O7 EHZ U 201 " model vdw 0.116 2.200 nonbonded pdb=" CB SER T 66 " pdb=" O7 EHZ T 201 " model vdw 1.431 3.100 nonbonded pdb=" OE1 GLU N2533 " pdb=" HH TYR N2537 " model vdw 1.460 1.850 nonbonded pdb=" CB SER U 89 " pdb=" O7 EHZ U 201 " model vdw 1.474 3.100 ... (remaining 1886554 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.650 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 1.380 Extract box with map and model: 22.250 Check model and map are aligned: 1.390 Set scattering table: 0.860 Process input model: 391.070 Find NCS groups from input model: 2.290 Set up NCS constraints: 0.270 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.020 Load rotamer database and sin/cos tables:2.360 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 425.540 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7279 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 : 0.018 0.226 66880 Z= 1.195 Angle : 1.199 24.151 90646 Z= 0.607 Chirality : 0.455 20.935 10075 Planarity : 0.007 0.083 11400 Dihedral : 16.447 179.988 25018 Min Nonbonded Distance : 0.019 Molprobity Statistics. All-atom Clashscore : 3.79 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.51 % Favored : 94.39 % Rotamer: Outliers : 0.07 % Allowed : 0.86 % Favored : 99.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.92 (0.08), residues: 7999 helix: -2.15 (0.06), residues: 4144 sheet: -2.63 (0.21), residues: 399 loop : -1.34 (0.11), residues: 3456 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.003 TRP H 295 HIS 0.022 0.002 HIS Q 135 PHE 0.037 0.003 PHE L1043 TYR 0.036 0.003 TYR M 978 ARG 0.015 0.001 ARG P 216 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15998 Ramachandran restraints generated. 7999 Oldfield, 0 Emsley, 7999 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15998 Ramachandran restraints generated. 7999 Oldfield, 0 Emsley, 7999 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue VAL 97 is missing expected H atoms. Skipping. Residue MET 121 is missing expected H atoms. Skipping. Residue TYR 144 is missing expected H atoms. Skipping. Residue LEU 211 is missing expected H atoms. Skipping. Residue VAL 212 is missing expected H atoms. Skipping. Residue TYR 215 is missing expected H atoms. Skipping. Residue THR 217 is missing expected H atoms. Skipping. Residue TYR 219 is missing expected H atoms. Skipping. Residue VAL 353 is missing expected H atoms. Skipping. Residue THR 355 is missing expected H atoms. Skipping. Residue VAL 360 is missing expected H atoms. Skipping. Residue SER 361 is missing expected H atoms. Skipping. Residue LEU 363 is missing expected H atoms. Skipping. Residue SER 66 is missing expected H atoms. Skipping. Residue SER 89 is missing expected H atoms. Skipping. Residue THR 75 is missing expected H atoms. Skipping. Residue LYS 84 is missing expected H atoms. Skipping. Evaluate side-chains 1361 residues out of total 6918 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 1356 time to evaluate : 7.368 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash 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: B 115 ASP cc_start: 0.7196 (m-30) cc_final: 0.6787 (m-30) REVERT: B 174 ASP cc_start: 0.8160 (m-30) cc_final: 0.7682 (m-30) REVERT: B 185 GLU cc_start: 0.7985 (mt-10) cc_final: 0.7590 (mp0) REVERT: D 75 ASP cc_start: 0.6165 (m-30) cc_final: 0.5737 (p0) REVERT: D 83 PHE cc_start: 0.6447 (t80) cc_final: 0.6157 (t80) REVERT: D 140 ASP cc_start: 0.7048 (m-30) cc_final: 0.6514 (m-30) REVERT: D 188 MET cc_start: 0.6921 (tpp) cc_final: 0.6716 (ttm) REVERT: I 409 ASP cc_start: 0.7001 (m-30) cc_final: 0.6695 (m-30) REVERT: J 115 ASP cc_start: 0.3774 (t0) cc_final: 0.3531 (t0) REVERT: L 753 TYR cc_start: 0.7084 (t80) cc_final: 0.6804 (t80) REVERT: L 1104 ILE cc_start: 0.8058 (mt) cc_final: 0.7828 (mt) REVERT: L 1302 ASN cc_start: 0.7614 (OUTLIER) cc_final: 0.7095 (t0) REVERT: M 828 TYR cc_start: 0.8073 (t80) cc_final: 0.7390 (t80) REVERT: N 2535 GLN cc_start: 0.8236 (tt0) cc_final: 0.7911 (tt0) REVERT: N 2701 LEU cc_start: 0.8653 (pp) cc_final: 0.8451 (mp) REVERT: N 2748 TYR cc_start: 0.7957 (m-80) cc_final: 0.7722 (m-80) REVERT: O 409 VAL cc_start: 0.7795 (p) cc_final: 0.7544 (p) REVERT: O 426 ASP cc_start: 0.7618 (t0) cc_final: 0.7235 (m-30) REVERT: O 477 ARG cc_start: 0.6434 (mtt90) cc_final: 0.6168 (mmp-170) REVERT: P 209 GLU cc_start: 0.6486 (mp0) cc_final: 0.5711 (tp30) REVERT: P 219 ARG cc_start: 0.5565 (mtp180) cc_final: 0.5289 (ttt-90) REVERT: P 251 ASP cc_start: 0.6505 (t0) cc_final: 0.6101 (t0) REVERT: Q 94 ASP cc_start: 0.7212 (p0) cc_final: 0.6787 (p0) REVERT: R 135 GLU cc_start: 0.6312 (tp30) cc_final: 0.5436 (tp30) REVERT: S 73 GLU cc_start: 0.5813 (tt0) cc_final: 0.5118 (tm-30) REVERT: U 81 LEU cc_start: 0.6083 (mt) cc_final: 0.5786 (mp) REVERT: V 27 GLU cc_start: 0.6298 (OUTLIER) cc_final: 0.6056 (pt0) REVERT: X 60 SER cc_start: 0.6499 (t) cc_final: 0.6286 (m) REVERT: a 43 ASP cc_start: 0.7054 (p0) cc_final: 0.6553 (p0) REVERT: g 57 LEU cc_start: 0.7333 (tp) cc_final: 0.7128 (tt) REVERT: g 60 LYS cc_start: 0.6057 (tttt) cc_final: 0.5756 (ttpp) REVERT: h 91 ASP cc_start: 0.6229 (m-30) cc_final: 0.5548 (t0) REVERT: h 120 GLU cc_start: 0.5461 (tp30) cc_final: 0.5182 (tp30) REVERT: h 121 LYS cc_start: 0.5975 (mttt) cc_final: 0.5623 (mtmt) REVERT: k 45 LEU cc_start: 0.5393 (mt) cc_final: 0.5004 (mt) REVERT: l 31 LYS cc_start: 0.6389 (pttt) cc_final: 0.5658 (tttp) REVERT: l 62 ASP cc_start: 0.6747 (m-30) cc_final: 0.6458 (t0) REVERT: l 67 GLU cc_start: 0.6602 (mm-30) cc_final: 0.5668 (tm-30) REVERT: l 124 GLU cc_start: 0.5881 (mt-10) cc_final: 0.5581 (mt-10) REVERT: m 10 ILE cc_start: 0.8008 (mt) cc_final: 0.7710 (mt) REVERT: m 44 GLU cc_start: 0.7385 (mm-30) cc_final: 0.7059 (tm-30) outliers start: 5 outliers final: 0 residues processed: 1360 average time/residue: 1.9005 time to fit residues: 4088.7102 Evaluate side-chains 731 residues out of total 6918 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 729 time to evaluate : 7.693 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 1302 ASN Chi-restraints excluded: chain V residue 27 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 788 random chunks: chunk 665 optimal weight: 0.9990 chunk 597 optimal weight: 7.9990 chunk 331 optimal weight: 1.9990 chunk 204 optimal weight: 0.7980 chunk 402 optimal weight: 0.9980 chunk 319 optimal weight: 0.9990 chunk 617 optimal weight: 3.9990 chunk 239 optimal weight: 1.9990 chunk 375 optimal weight: 0.9980 chunk 459 optimal weight: 0.9980 chunk 715 optimal weight: 1.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 109 ASN B 73 GLN C 208 HIS ** D 57 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 77 ASN D 185 ASN G 56 GLN I 416 GLN J 114 ASN L 867 GLN L1155 ASN L1244 ASN M 523 GLN M 737 HIS N2488 ASN N2717 GLN N2740 ASN ** P 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 234 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 147 ASN R 91 HIS V 85 ASN ** V 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 64 GLN a 76 HIS a 77 ASN c 161 GLN ** i 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** j 11 ASN n 21 GLN o 16 HIS Total number of N/Q/H flips: 26 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7260 moved from start: 0.2253 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.225 66880 Z= 0.267 Angle : 0.855 50.086 90646 Z= 0.510 Chirality : 0.142 6.977 10075 Planarity : 0.005 0.065 11400 Dihedral : 12.623 166.417 9937 Min Nonbonded Distance : 1.841 Molprobity Statistics. All-atom Clashscore : 6.98 Ramachandran Plot: Outliers : 0.01 % Allowed : 3.55 % Favored : 96.44 % Rotamer: Outliers : 0.77 % Allowed : 6.22 % Favored : 93.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.29 (0.09), residues: 7999 helix: -0.29 (0.08), residues: 4202 sheet: -2.02 (0.23), residues: 386 loop : -1.33 (0.11), residues: 3411 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP X 98 HIS 0.008 0.001 HIS e 49 PHE 0.022 0.001 PHE H 41 TYR 0.017 0.001 TYR M 925 ARG 0.009 0.000 ARG g 156 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15998 Ramachandran restraints generated. 7999 Oldfield, 0 Emsley, 7999 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15998 Ramachandran restraints generated. 7999 Oldfield, 0 Emsley, 7999 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue VAL 97 is missing expected H atoms. Skipping. Residue MET 121 is missing expected H atoms. Skipping. Residue TYR 144 is missing expected H atoms. Skipping. Residue LEU 211 is missing expected H atoms. Skipping. Residue VAL 212 is missing expected H atoms. Skipping. Residue TYR 215 is missing expected H atoms. Skipping. Residue THR 217 is missing expected H atoms. Skipping. Residue TYR 219 is missing expected H atoms. Skipping. Residue VAL 353 is missing expected H atoms. Skipping. Residue THR 355 is missing expected H atoms. Skipping. Residue VAL 360 is missing expected H atoms. Skipping. Residue SER 361 is missing expected H atoms. Skipping. Residue LEU 363 is missing expected H atoms. Skipping. Residue SER 66 is missing expected H atoms. Skipping. Residue SER 89 is missing expected H atoms. Skipping. Residue THR 75 is missing expected H atoms. Skipping. Residue LYS 84 is missing expected H atoms. Skipping. Evaluate side-chains 868 residues out of total 6918 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 815 time to evaluate : 7.230 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 115 ASP cc_start: 0.7168 (m-30) cc_final: 0.6761 (m-30) REVERT: B 174 ASP cc_start: 0.8075 (m-30) cc_final: 0.7819 (m-30) REVERT: B 185 GLU cc_start: 0.7981 (mt-10) cc_final: 0.7532 (mp0) REVERT: D 75 ASP cc_start: 0.5951 (m-30) cc_final: 0.5675 (p0) REVERT: D 188 MET cc_start: 0.6989 (tpp) cc_final: 0.6650 (ttm) REVERT: D 209 GLU cc_start: 0.7148 (mm-30) cc_final: 0.6753 (mm-30) REVERT: G 278 MET cc_start: 0.7552 (mmm) cc_final: 0.7336 (mmt) REVERT: G 572 GLN cc_start: 0.7699 (OUTLIER) cc_final: 0.7264 (mm-40) REVERT: H 88 TRP cc_start: 0.7143 (m100) cc_final: 0.6854 (m100) REVERT: H 294 ILE cc_start: 0.8523 (mt) cc_final: 0.8292 (mm) REVERT: I 409 ASP cc_start: 0.6922 (m-30) cc_final: 0.6671 (m-30) REVERT: J 115 ASP cc_start: 0.3789 (t0) cc_final: 0.3582 (t0) REVERT: L 753 TYR cc_start: 0.7115 (t80) cc_final: 0.6868 (t80) REVERT: L 1006 LEU cc_start: 0.8114 (tp) cc_final: 0.7860 (tp) REVERT: N 2485 TYR cc_start: 0.7420 (m-80) cc_final: 0.7200 (m-80) REVERT: N 2701 LEU cc_start: 0.8666 (pp) cc_final: 0.8349 (mp) REVERT: N 2717 GLN cc_start: 0.8054 (OUTLIER) cc_final: 0.7813 (tm-30) REVERT: O 426 ASP cc_start: 0.7602 (t0) cc_final: 0.7188 (m-30) REVERT: O 511 LYS cc_start: 0.7581 (tttt) cc_final: 0.6906 (mtmt) REVERT: P 209 GLU cc_start: 0.6292 (mp0) cc_final: 0.5774 (tp30) REVERT: P 251 ASP cc_start: 0.6317 (t0) cc_final: 0.6040 (t0) REVERT: Q 94 ASP cc_start: 0.6964 (p0) cc_final: 0.6566 (p0) REVERT: R 135 GLU cc_start: 0.6335 (tp30) cc_final: 0.5423 (tp30) REVERT: S 73 GLU cc_start: 0.5907 (tt0) cc_final: 0.5130 (tm-30) REVERT: V 27 GLU cc_start: 0.6211 (OUTLIER) cc_final: 0.5842 (pt0) REVERT: X 60 SER cc_start: 0.6276 (t) cc_final: 0.6023 (m) REVERT: Y 1360 GLU cc_start: 0.6494 (tm-30) cc_final: 0.6246 (tm-30) REVERT: Z 123 LYS cc_start: 0.3600 (mmtm) cc_final: 0.3231 (mmmt) REVERT: a 51 GLU cc_start: 0.6392 (tt0) cc_final: 0.6164 (tt0) REVERT: c 44 TYR cc_start: 0.7946 (t80) cc_final: 0.7733 (t80) REVERT: c 161 GLN cc_start: 0.7089 (tm130) cc_final: 0.6634 (tp-100) REVERT: h 91 ASP cc_start: 0.6286 (m-30) cc_final: 0.5508 (t0) REVERT: l 31 LYS cc_start: 0.6012 (pttt) cc_final: 0.5540 (tttp) REVERT: l 67 GLU cc_start: 0.6401 (mm-30) cc_final: 0.5431 (tm-30) REVERT: p 82 TYR cc_start: 0.7278 (p90) cc_final: 0.6993 (p90) outliers start: 53 outliers final: 32 residues processed: 841 average time/residue: 1.4444 time to fit residues: 2020.9039 Evaluate side-chains 727 residues out of total 6918 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 692 time to evaluate : 7.188 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 109 ASN Chi-restraints excluded: chain A residue 121 THR Chi-restraints excluded: chain D residue 80 ILE Chi-restraints excluded: chain D residue 218 GLU Chi-restraints excluded: chain D residue 399 THR Chi-restraints excluded: chain F residue 277 LEU Chi-restraints excluded: chain G residue 137 ASP Chi-restraints excluded: chain G residue 572 GLN Chi-restraints excluded: chain H residue 80 THR Chi-restraints excluded: chain H residue 290 MET Chi-restraints excluded: chain J residue 101 LEU Chi-restraints excluded: chain L residue 718 CYS Chi-restraints excluded: chain L residue 867 GLN Chi-restraints excluded: chain L residue 1154 TYR Chi-restraints excluded: chain L residue 1231 VAL Chi-restraints excluded: chain M residue 612 ASN Chi-restraints excluded: chain N residue 2464 ASN Chi-restraints excluded: chain N residue 2526 ILE Chi-restraints excluded: chain N residue 2570 ILE Chi-restraints excluded: chain N residue 2717 GLN Chi-restraints excluded: chain O residue 446 LEU Chi-restraints excluded: chain O residue 533 THR Chi-restraints excluded: chain P residue 172 GLU Chi-restraints excluded: chain S residue 59 ASP Chi-restraints excluded: chain V residue 27 GLU Chi-restraints excluded: chain Y residue 1215 SER Chi-restraints excluded: chain Z residue 7 ASP Chi-restraints excluded: chain a residue 15 PHE Chi-restraints excluded: chain a residue 77 ASN Chi-restraints excluded: chain b residue 32 ILE Chi-restraints excluded: chain b residue 44 THR Chi-restraints excluded: chain b residue 51 LEU Chi-restraints excluded: chain c residue 14 THR Chi-restraints excluded: chain f residue 91 ASN Chi-restraints excluded: chain i residue 49 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 788 random chunks: chunk 397 optimal weight: 8.9990 chunk 222 optimal weight: 5.9990 chunk 595 optimal weight: 9.9990 chunk 487 optimal weight: 8.9990 chunk 197 optimal weight: 7.9990 chunk 716 optimal weight: 7.9990 chunk 774 optimal weight: 7.9990 chunk 638 optimal weight: 10.0000 chunk 710 optimal weight: 0.1980 chunk 244 optimal weight: 6.9990 chunk 575 optimal weight: 9.9990 overall best weight: 5.8388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 159 ASN F 283 ASN ** F 285 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 363 GLN G 398 ASN ** G 572 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 49 GLN J 120 ASN ** L1116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L1201 ASN L1266 ASN M 630 ASN ** N2492 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 188 GLN ** P 234 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 91 HIS U 120 GLN V 73 ASN W 63 HIS X 87 ASN a 77 ASN ** i 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 11 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** n 21 GLN n 50 ASN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7429 moved from start: 0.3018 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.239 66880 Z= 0.486 Angle : 0.929 50.280 90646 Z= 0.549 Chirality : 0.136 6.465 10075 Planarity : 0.005 0.065 11400 Dihedral : 12.183 156.675 9935 Min Nonbonded Distance : 1.716 Molprobity Statistics. All-atom Clashscore : 9.32 Ramachandran Plot: Outliers : 0.06 % Allowed : 6.10 % Favored : 93.84 % Rotamer: Outliers : 1.45 % Allowed : 9.33 % Favored : 89.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.22 (0.09), residues: 7999 helix: -0.00 (0.08), residues: 4212 sheet: -2.04 (0.24), residues: 396 loop : -1.63 (0.10), residues: 3391 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP X 98 HIS 0.016 0.001 HIS e 49 PHE 0.020 0.002 PHE D 177 TYR 0.030 0.002 TYR P 294 ARG 0.014 0.001 ARG E 103 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15998 Ramachandran restraints generated. 7999 Oldfield, 0 Emsley, 7999 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15998 Ramachandran restraints generated. 7999 Oldfield, 0 Emsley, 7999 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue VAL 97 is missing expected H atoms. Skipping. Residue MET 121 is missing expected H atoms. Skipping. Residue TYR 144 is missing expected H atoms. Skipping. Residue LEU 211 is missing expected H atoms. Skipping. Residue VAL 212 is missing expected H atoms. Skipping. Residue TYR 215 is missing expected H atoms. Skipping. Residue THR 217 is missing expected H atoms. Skipping. Residue TYR 219 is missing expected H atoms. Skipping. Residue VAL 353 is missing expected H atoms. Skipping. Residue THR 355 is missing expected H atoms. Skipping. Residue VAL 360 is missing expected H atoms. Skipping. Residue SER 361 is missing expected H atoms. Skipping. Residue LEU 363 is missing expected H atoms. Skipping. Residue SER 66 is missing expected H atoms. Skipping. Residue SER 89 is missing expected H atoms. Skipping. Residue THR 75 is missing expected H atoms. Skipping. Residue LYS 84 is missing expected H atoms. Skipping. Evaluate side-chains 828 residues out of total 6918 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 100 poor density : 728 time to evaluate : 7.534 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 115 ASP cc_start: 0.7154 (m-30) cc_final: 0.6585 (m-30) REVERT: B 185 GLU cc_start: 0.7943 (mt-10) cc_final: 0.7528 (mp0) REVERT: D 75 ASP cc_start: 0.6085 (m-30) cc_final: 0.5638 (p0) REVERT: D 83 PHE cc_start: 0.6312 (t80) cc_final: 0.5996 (t80) REVERT: E 157 LYS cc_start: 0.6099 (mmpt) cc_final: 0.5660 (mttp) REVERT: F 219 GLU cc_start: 0.6802 (mt-10) cc_final: 0.6547 (mt-10) REVERT: I 409 ASP cc_start: 0.7131 (m-30) cc_final: 0.6840 (m-30) REVERT: L 1020 MET cc_start: 0.7346 (mtp) cc_final: 0.6980 (tpp) REVERT: L 1302 ASN cc_start: 0.7775 (OUTLIER) cc_final: 0.7265 (t0) REVERT: M 739 GLU cc_start: 0.6752 (mt-10) cc_final: 0.6527 (mt-10) REVERT: M 828 TYR cc_start: 0.8452 (t80) cc_final: 0.7740 (t80) REVERT: N 2464 ASN cc_start: 0.9033 (OUTLIER) cc_final: 0.8605 (p0) REVERT: N 2657 ILE cc_start: 0.7291 (mm) cc_final: 0.6998 (mt) REVERT: O 511 LYS cc_start: 0.7759 (tttt) cc_final: 0.7084 (mtmt) REVERT: P 209 GLU cc_start: 0.6448 (mp0) cc_final: 0.5886 (tp30) REVERT: P 224 VAL cc_start: 0.6637 (t) cc_final: 0.6033 (t) REVERT: P 251 ASP cc_start: 0.6576 (t0) cc_final: 0.6332 (t0) REVERT: P 281 ARG cc_start: 0.5252 (mtp85) cc_final: 0.4922 (tmm160) REVERT: R 135 GLU cc_start: 0.6423 (tp30) cc_final: 0.5365 (tp30) REVERT: U 97 MET cc_start: 0.5981 (mmm) cc_final: 0.5262 (ppp) REVERT: V 27 GLU cc_start: 0.6363 (OUTLIER) cc_final: 0.6039 (pt0) REVERT: X 39 SER cc_start: 0.9042 (p) cc_final: 0.8787 (t) REVERT: X 111 CYS cc_start: 0.7149 (OUTLIER) cc_final: 0.6674 (m) REVERT: Y 1341 ASP cc_start: 0.5769 (m-30) cc_final: 0.5211 (t70) REVERT: Z 123 LYS cc_start: 0.3627 (mmtm) cc_final: 0.3334 (mmmt) REVERT: c 44 TYR cc_start: 0.7996 (t80) cc_final: 0.7778 (t80) REVERT: h 91 ASP cc_start: 0.6785 (m-30) cc_final: 0.6560 (m-30) REVERT: l 31 LYS cc_start: 0.6469 (pttt) cc_final: 0.5750 (tttp) REVERT: l 67 GLU cc_start: 0.6780 (mm-30) cc_final: 0.5778 (tm-30) REVERT: m 79 GLU cc_start: 0.5405 (pp20) cc_final: 0.5121 (pp20) outliers start: 100 outliers final: 75 residues processed: 789 average time/residue: 1.4325 time to fit residues: 1884.5037 Evaluate side-chains 709 residues out of total 6918 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 79 poor density : 630 time to evaluate : 7.723 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 121 THR Chi-restraints excluded: chain C residue 41 ASP Chi-restraints excluded: chain D residue 80 ILE Chi-restraints excluded: chain D residue 218 GLU Chi-restraints excluded: chain D residue 376 GLU Chi-restraints excluded: chain D residue 399 THR Chi-restraints excluded: chain E residue 200 CYS Chi-restraints excluded: chain E residue 207 THR Chi-restraints excluded: chain E residue 228 LEU Chi-restraints excluded: chain F residue 289 THR Chi-restraints excluded: chain F residue 387 CYS Chi-restraints excluded: chain G residue 137 ASP Chi-restraints excluded: chain G residue 294 ASN Chi-restraints excluded: chain G residue 344 ASP Chi-restraints excluded: chain G residue 469 GLU Chi-restraints excluded: chain G residue 476 ASN Chi-restraints excluded: chain G residue 489 THR Chi-restraints excluded: chain G residue 572 GLN Chi-restraints excluded: chain G residue 660 ASP Chi-restraints excluded: chain G residue 672 VAL Chi-restraints excluded: chain G residue 676 LEU Chi-restraints excluded: chain H residue 3 ILE Chi-restraints excluded: chain H residue 80 THR Chi-restraints excluded: chain H residue 147 GLU Chi-restraints excluded: chain H residue 274 GLU Chi-restraints excluded: chain H residue 290 MET Chi-restraints excluded: chain I residue 255 HIS Chi-restraints excluded: chain J residue 101 LEU Chi-restraints excluded: chain K residue 30 GLU Chi-restraints excluded: chain L residue 718 CYS Chi-restraints excluded: chain L residue 915 ASP Chi-restraints excluded: chain L residue 939 ASN Chi-restraints excluded: chain L residue 1154 TYR Chi-restraints excluded: chain L residue 1191 ASP Chi-restraints excluded: chain L residue 1231 VAL Chi-restraints excluded: chain L residue 1302 ASN Chi-restraints excluded: chain L residue 1332 SER Chi-restraints excluded: chain M residue 612 ASN Chi-restraints excluded: chain M residue 731 VAL Chi-restraints excluded: chain M residue 761 LEU Chi-restraints excluded: chain N residue 2464 ASN Chi-restraints excluded: chain N residue 2526 ILE Chi-restraints excluded: chain N residue 2543 THR Chi-restraints excluded: chain N residue 2570 ILE Chi-restraints excluded: chain N residue 2664 ILE Chi-restraints excluded: chain O residue 446 LEU Chi-restraints excluded: chain O residue 503 THR Chi-restraints excluded: chain O residue 529 THR Chi-restraints excluded: chain P residue 123 ASP Chi-restraints excluded: chain P residue 172 GLU Chi-restraints excluded: chain S residue 54 VAL Chi-restraints excluded: chain S residue 59 ASP Chi-restraints excluded: chain V residue 27 GLU Chi-restraints excluded: chain V residue 59 ASP Chi-restraints excluded: chain V residue 81 ILE Chi-restraints excluded: chain W residue 41 ASP Chi-restraints excluded: chain X residue 111 CYS Chi-restraints excluded: chain X residue 127 ASN Chi-restraints excluded: chain Y residue 1215 SER Chi-restraints excluded: chain Y residue 1240 ILE Chi-restraints excluded: chain Z residue 7 ASP Chi-restraints excluded: chain a residue 15 PHE Chi-restraints excluded: chain a residue 56 LEU Chi-restraints excluded: chain b residue 32 ILE Chi-restraints excluded: chain b residue 44 THR Chi-restraints excluded: chain b residue 51 LEU Chi-restraints excluded: chain c residue 136 SER Chi-restraints excluded: chain f residue 91 ASN Chi-restraints excluded: chain g residue 57 LEU Chi-restraints excluded: chain g residue 63 LEU Chi-restraints excluded: chain h residue 87 LYS Chi-restraints excluded: chain h residue 122 ASP Chi-restraints excluded: chain i residue 49 LEU Chi-restraints excluded: chain l residue 78 ASP Chi-restraints excluded: chain l residue 108 SER Chi-restraints excluded: chain m residue 10 ILE Chi-restraints excluded: chain o residue 7 LEU Chi-restraints excluded: chain p residue 55 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 788 random chunks: chunk 708 optimal weight: 5.9990 chunk 538 optimal weight: 9.9990 chunk 372 optimal weight: 2.9990 chunk 79 optimal weight: 7.9990 chunk 342 optimal weight: 7.9990 chunk 481 optimal weight: 7.9990 chunk 719 optimal weight: 6.9990 chunk 761 optimal weight: 0.9990 chunk 375 optimal weight: 5.9990 chunk 681 optimal weight: 4.9990 chunk 205 optimal weight: 9.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 73 GLN ** D 57 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 285 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 425 ASN ** G 572 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L1116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 630 ASN ** N2492 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 234 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 91 HIS b 22 ASN g 65 GLN i 25 ASN j 11 ASN k 20 ASN o 49 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7422 moved from start: 0.3474 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.240 66880 Z= 0.351 Angle : 0.846 50.623 90646 Z= 0.510 Chirality : 0.132 6.310 10075 Planarity : 0.005 0.064 11400 Dihedral : 11.481 153.083 9935 Min Nonbonded Distance : 1.877 Molprobity Statistics. All-atom Clashscore : 8.30 Ramachandran Plot: Outliers : 0.01 % Allowed : 4.43 % Favored : 95.56 % Rotamer: Outliers : 1.60 % Allowed : 10.93 % Favored : 87.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.01 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.86 (0.09), residues: 7999 helix: 0.36 (0.08), residues: 4220 sheet: -1.85 (0.24), residues: 385 loop : -1.58 (0.10), residues: 3394 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP X 98 HIS 0.005 0.001 HIS M 699 PHE 0.021 0.001 PHE L1043 TYR 0.018 0.002 TYR N2748 ARG 0.004 0.000 ARG W 24 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15998 Ramachandran restraints generated. 7999 Oldfield, 0 Emsley, 7999 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15998 Ramachandran restraints generated. 7999 Oldfield, 0 Emsley, 7999 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue VAL 97 is missing expected H atoms. Skipping. Residue MET 121 is missing expected H atoms. Skipping. Residue TYR 144 is missing expected H atoms. Skipping. Residue LEU 211 is missing expected H atoms. Skipping. Residue VAL 212 is missing expected H atoms. Skipping. Residue TYR 215 is missing expected H atoms. Skipping. Residue THR 217 is missing expected H atoms. Skipping. Residue TYR 219 is missing expected H atoms. Skipping. Residue VAL 353 is missing expected H atoms. Skipping. Residue THR 355 is missing expected H atoms. Skipping. Residue VAL 360 is missing expected H atoms. Skipping. Residue SER 361 is missing expected H atoms. Skipping. Residue LEU 363 is missing expected H atoms. Skipping. Residue SER 66 is missing expected H atoms. Skipping. Residue SER 89 is missing expected H atoms. Skipping. Residue THR 75 is missing expected H atoms. Skipping. Residue LYS 84 is missing expected H atoms. Skipping. Evaluate side-chains 792 residues out of total 6918 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 110 poor density : 682 time to evaluate : 7.632 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 117 ASN cc_start: 0.5926 (m-40) cc_final: 0.5698 (m-40) REVERT: B 185 GLU cc_start: 0.7889 (mt-10) cc_final: 0.7555 (mp0) REVERT: D 75 ASP cc_start: 0.6111 (m-30) cc_final: 0.5648 (p0) REVERT: D 83 PHE cc_start: 0.6169 (t80) cc_final: 0.5965 (t80) REVERT: E 157 LYS cc_start: 0.6093 (mmpt) cc_final: 0.5685 (mttt) REVERT: F 133 MET cc_start: 0.7680 (OUTLIER) cc_final: 0.7396 (mmm) REVERT: G 659 TYR cc_start: 0.8080 (m-80) cc_final: 0.7822 (m-80) REVERT: I 409 ASP cc_start: 0.7130 (m-30) cc_final: 0.6919 (m-30) REVERT: I 416 GLN cc_start: 0.7604 (OUTLIER) cc_final: 0.7202 (tp-100) REVERT: J 49 LEU cc_start: 0.8594 (OUTLIER) cc_final: 0.8344 (mt) REVERT: L 901 ASN cc_start: 0.7352 (OUTLIER) cc_final: 0.7141 (p0) REVERT: L 1020 MET cc_start: 0.7265 (mtp) cc_final: 0.6978 (tpp) REVERT: L 1302 ASN cc_start: 0.7735 (OUTLIER) cc_final: 0.7297 (t0) REVERT: M 828 TYR cc_start: 0.8383 (t80) cc_final: 0.7942 (t80) REVERT: N 2464 ASN cc_start: 0.9034 (OUTLIER) cc_final: 0.8655 (p0) REVERT: N 2657 ILE cc_start: 0.7394 (mm) cc_final: 0.7124 (mt) REVERT: O 511 LYS cc_start: 0.7790 (tttt) cc_final: 0.7089 (mtmt) REVERT: P 190 THR cc_start: 0.7836 (OUTLIER) cc_final: 0.7608 (t) REVERT: P 209 GLU cc_start: 0.6485 (mp0) cc_final: 0.5876 (tp30) REVERT: P 251 ASP cc_start: 0.6541 (t0) cc_final: 0.6327 (t0) REVERT: P 275 MET cc_start: 0.7463 (mtp) cc_final: 0.7229 (mtp) REVERT: P 281 ARG cc_start: 0.5176 (mtp85) cc_final: 0.4893 (tmm160) REVERT: Q 119 ILE cc_start: 0.8626 (mt) cc_final: 0.8336 (pt) REVERT: V 27 GLU cc_start: 0.6405 (OUTLIER) cc_final: 0.6162 (pt0) REVERT: X 39 SER cc_start: 0.8950 (p) cc_final: 0.8689 (t) REVERT: Y 1341 ASP cc_start: 0.5682 (m-30) cc_final: 0.5143 (t70) REVERT: Z 123 LYS cc_start: 0.3575 (mmtm) cc_final: 0.2971 (mmmt) REVERT: b 30 PHE cc_start: 0.7270 (OUTLIER) cc_final: 0.6721 (t80) REVERT: c 44 TYR cc_start: 0.8005 (t80) cc_final: 0.7796 (t80) REVERT: i 25 ASN cc_start: 0.7269 (OUTLIER) cc_final: 0.7007 (p0) REVERT: l 31 LYS cc_start: 0.6336 (pttt) cc_final: 0.5748 (tttp) REVERT: l 67 GLU cc_start: 0.6720 (mm-30) cc_final: 0.5821 (tm-30) REVERT: m 44 GLU cc_start: 0.6898 (tm-30) cc_final: 0.6612 (tm-30) REVERT: m 79 GLU cc_start: 0.5135 (pp20) cc_final: 0.4709 (pp20) REVERT: o 43 MET cc_start: 0.5722 (mmm) cc_final: 0.5017 (mtm) REVERT: o 81 LYS cc_start: 0.5184 (mmtm) cc_final: 0.3736 (mmmt) outliers start: 110 outliers final: 74 residues processed: 755 average time/residue: 1.5260 time to fit residues: 1948.1825 Evaluate side-chains 718 residues out of total 6918 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 84 poor density : 634 time to evaluate : 7.394 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 121 THR Chi-restraints excluded: chain C residue 41 ASP Chi-restraints excluded: chain D residue 80 ILE Chi-restraints excluded: chain D residue 155 SER Chi-restraints excluded: chain D residue 218 GLU Chi-restraints excluded: chain D residue 376 GLU Chi-restraints excluded: chain D residue 399 THR Chi-restraints excluded: chain D residue 449 ASP Chi-restraints excluded: chain E residue 200 CYS Chi-restraints excluded: chain E residue 205 MET Chi-restraints excluded: chain E residue 207 THR Chi-restraints excluded: chain E residue 228 LEU Chi-restraints excluded: chain F residue 77 ASP Chi-restraints excluded: chain F residue 133 MET Chi-restraints excluded: chain F residue 277 LEU Chi-restraints excluded: chain G residue 262 ASP Chi-restraints excluded: chain G residue 294 ASN Chi-restraints excluded: chain G residue 469 GLU Chi-restraints excluded: chain G residue 572 GLN Chi-restraints excluded: chain G residue 660 ASP Chi-restraints excluded: chain G residue 672 VAL Chi-restraints excluded: chain H residue 3 ILE Chi-restraints excluded: chain H residue 80 THR Chi-restraints excluded: chain H residue 147 GLU Chi-restraints excluded: chain I residue 416 GLN Chi-restraints excluded: chain J residue 49 LEU Chi-restraints excluded: chain J residue 93 ASP Chi-restraints excluded: chain J residue 101 LEU Chi-restraints excluded: chain J residue 181 MET Chi-restraints excluded: chain L residue 718 CYS Chi-restraints excluded: chain L residue 901 ASN Chi-restraints excluded: chain L residue 939 ASN Chi-restraints excluded: chain L residue 1154 TYR Chi-restraints excluded: chain L residue 1191 ASP Chi-restraints excluded: chain L residue 1231 VAL Chi-restraints excluded: chain L residue 1246 LYS Chi-restraints excluded: chain L residue 1302 ASN Chi-restraints excluded: chain L residue 1323 SER Chi-restraints excluded: chain L residue 1332 SER Chi-restraints excluded: chain M residue 583 ILE Chi-restraints excluded: chain M residue 612 ASN Chi-restraints excluded: chain M residue 731 VAL Chi-restraints excluded: chain M residue 761 LEU Chi-restraints excluded: chain N residue 2464 ASN Chi-restraints excluded: chain N residue 2472 MET Chi-restraints excluded: chain N residue 2526 ILE Chi-restraints excluded: chain N residue 2553 SER Chi-restraints excluded: chain N residue 2570 ILE Chi-restraints excluded: chain N residue 2626 ILE Chi-restraints excluded: chain N residue 2664 ILE Chi-restraints excluded: chain O residue 446 LEU Chi-restraints excluded: chain P residue 123 ASP Chi-restraints excluded: chain P residue 172 GLU Chi-restraints excluded: chain P residue 190 THR Chi-restraints excluded: chain R residue 74 MET Chi-restraints excluded: chain S residue 54 VAL Chi-restraints excluded: chain S residue 59 ASP Chi-restraints excluded: chain U residue 59 ILE Chi-restraints excluded: chain U residue 62 LEU Chi-restraints excluded: chain U residue 101 GLU Chi-restraints excluded: chain V residue 27 GLU Chi-restraints excluded: chain X residue 22 VAL Chi-restraints excluded: chain X residue 37 SER Chi-restraints excluded: chain Y residue 1215 SER Chi-restraints excluded: chain Y residue 1240 ILE Chi-restraints excluded: chain Z residue 7 ASP Chi-restraints excluded: chain a residue 15 PHE Chi-restraints excluded: chain a residue 56 LEU Chi-restraints excluded: chain b residue 22 ASN Chi-restraints excluded: chain b residue 30 PHE Chi-restraints excluded: chain b residue 32 ILE Chi-restraints excluded: chain b residue 44 THR Chi-restraints excluded: chain b residue 51 LEU Chi-restraints excluded: chain c residue 14 THR Chi-restraints excluded: chain c residue 136 SER Chi-restraints excluded: chain e residue 9 THR Chi-restraints excluded: chain g residue 63 LEU Chi-restraints excluded: chain g residue 100 THR Chi-restraints excluded: chain h residue 122 ASP Chi-restraints excluded: chain i residue 25 ASN Chi-restraints excluded: chain i residue 49 LEU Chi-restraints excluded: chain l residue 108 SER Chi-restraints excluded: chain o residue 7 LEU Chi-restraints excluded: chain p residue 33 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 788 random chunks: chunk 634 optimal weight: 9.9990 chunk 432 optimal weight: 2.9990 chunk 11 optimal weight: 0.9980 chunk 567 optimal weight: 10.0000 chunk 314 optimal weight: 9.9990 chunk 649 optimal weight: 5.9990 chunk 526 optimal weight: 5.9990 chunk 0 optimal weight: 10.0000 chunk 388 optimal weight: 5.9990 chunk 683 optimal weight: 9.9990 chunk 192 optimal weight: 3.9990 overall best weight: 3.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 73 GLN ** D 57 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 285 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 572 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 696 ASN L 757 GLN ** L1116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 630 ASN ** N2492 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 91 HIS V 19 GLN ** W 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 22 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7442 moved from start: 0.3730 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.243 66880 Z= 0.362 Angle : 0.844 50.573 90646 Z= 0.509 Chirality : 0.132 6.309 10075 Planarity : 0.005 0.064 11400 Dihedral : 11.076 152.106 9935 Min Nonbonded Distance : 1.863 Molprobity Statistics. All-atom Clashscore : 8.81 Ramachandran Plot: Outliers : 0.01 % Allowed : 5.88 % Favored : 94.11 % Rotamer: Outliers : 1.70 % Allowed : 12.00 % Favored : 86.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.01 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.73 (0.09), residues: 7999 helix: 0.50 (0.08), residues: 4219 sheet: -1.77 (0.24), residues: 382 loop : -1.57 (0.10), residues: 3398 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP X 98 HIS 0.005 0.001 HIS R 110 PHE 0.018 0.001 PHE L1043 TYR 0.019 0.002 TYR N2748 ARG 0.003 0.000 ARG I 312 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15998 Ramachandran restraints generated. 7999 Oldfield, 0 Emsley, 7999 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15998 Ramachandran restraints generated. 7999 Oldfield, 0 Emsley, 7999 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue VAL 97 is missing expected H atoms. Skipping. Residue MET 121 is missing expected H atoms. Skipping. Residue TYR 144 is missing expected H atoms. Skipping. Residue LEU 211 is missing expected H atoms. Skipping. Residue VAL 212 is missing expected H atoms. Skipping. Residue TYR 215 is missing expected H atoms. Skipping. Residue THR 217 is missing expected H atoms. Skipping. Residue TYR 219 is missing expected H atoms. Skipping. Residue VAL 353 is missing expected H atoms. Skipping. Residue THR 355 is missing expected H atoms. Skipping. Residue VAL 360 is missing expected H atoms. Skipping. Residue SER 361 is missing expected H atoms. Skipping. Residue LEU 363 is missing expected H atoms. Skipping. Residue SER 66 is missing expected H atoms. Skipping. Residue SER 89 is missing expected H atoms. Skipping. Residue THR 75 is missing expected H atoms. Skipping. Residue LYS 84 is missing expected H atoms. Skipping. Evaluate side-chains 778 residues out of total 6918 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 117 poor density : 661 time to evaluate : 7.658 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash 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 117 ASN cc_start: 0.5731 (m-40) cc_final: 0.5528 (m-40) REVERT: B 185 GLU cc_start: 0.7834 (mt-10) cc_final: 0.7549 (mp0) REVERT: C 227 GLU cc_start: 0.7519 (OUTLIER) cc_final: 0.6994 (mp0) REVERT: D 75 ASP cc_start: 0.6159 (m-30) cc_final: 0.5697 (p0) REVERT: E 157 LYS cc_start: 0.5939 (mmpt) cc_final: 0.5610 (mttt) REVERT: F 133 MET cc_start: 0.7662 (OUTLIER) cc_final: 0.7296 (mmm) REVERT: G 659 TYR cc_start: 0.8074 (m-80) cc_final: 0.7831 (m-80) REVERT: I 409 ASP cc_start: 0.7139 (m-30) cc_final: 0.6917 (m-30) REVERT: J 49 LEU cc_start: 0.8621 (OUTLIER) cc_final: 0.8392 (mt) REVERT: K 78 TYR cc_start: 0.7710 (t80) cc_final: 0.7456 (t80) REVERT: L 1020 MET cc_start: 0.7403 (mtp) cc_final: 0.7153 (tpp) REVERT: L 1096 THR cc_start: 0.7869 (p) cc_final: 0.7578 (t) REVERT: L 1302 ASN cc_start: 0.7682 (OUTLIER) cc_final: 0.7342 (t0) REVERT: M 739 GLU cc_start: 0.6701 (mt-10) cc_final: 0.6448 (mt-10) REVERT: M 764 LEU cc_start: 0.8457 (OUTLIER) cc_final: 0.8178 (tt) REVERT: M 828 TYR cc_start: 0.8447 (t80) cc_final: 0.7946 (t80) REVERT: N 2464 ASN cc_start: 0.9025 (OUTLIER) cc_final: 0.8650 (p0) REVERT: N 2657 ILE cc_start: 0.7397 (mm) cc_final: 0.7131 (mt) REVERT: N 2717 GLN cc_start: 0.8565 (tm-30) cc_final: 0.8251 (tm-30) REVERT: O 511 LYS cc_start: 0.7807 (tttt) cc_final: 0.7106 (mtmt) REVERT: P 190 THR cc_start: 0.7853 (OUTLIER) cc_final: 0.7650 (t) REVERT: P 209 GLU cc_start: 0.6486 (mp0) cc_final: 0.5849 (tp30) REVERT: P 251 ASP cc_start: 0.6669 (t0) cc_final: 0.6467 (t0) REVERT: P 281 ARG cc_start: 0.5175 (mtp85) cc_final: 0.4906 (tmm160) REVERT: Q 119 ILE cc_start: 0.8667 (mt) cc_final: 0.8355 (pt) REVERT: S 41 LYS cc_start: 0.6506 (mttt) cc_final: 0.5985 (mttp) REVERT: T 77 GLU cc_start: 0.5226 (pt0) cc_final: 0.4919 (pt0) REVERT: T 78 GLU cc_start: 0.4698 (pt0) cc_final: 0.4263 (mt-10) REVERT: T 88 GLU cc_start: 0.7420 (mm-30) cc_final: 0.6808 (mp0) REVERT: V 27 GLU cc_start: 0.6444 (OUTLIER) cc_final: 0.6202 (pt0) REVERT: X 39 SER cc_start: 0.8938 (p) cc_final: 0.8690 (t) REVERT: X 85 ASP cc_start: 0.6522 (m-30) cc_final: 0.6254 (t0) REVERT: X 111 CYS cc_start: 0.7130 (OUTLIER) cc_final: 0.6700 (m) REVERT: Y 1341 ASP cc_start: 0.5674 (m-30) cc_final: 0.5143 (t70) REVERT: Z 123 LYS cc_start: 0.3433 (mmtm) cc_final: 0.3046 (mmmt) REVERT: c 44 TYR cc_start: 0.8016 (t80) cc_final: 0.7810 (t80) REVERT: f 69 ASP cc_start: 0.8097 (t0) cc_final: 0.7498 (t70) REVERT: l 31 LYS cc_start: 0.6396 (pttt) cc_final: 0.5770 (tttp) REVERT: l 67 GLU cc_start: 0.6834 (mm-30) cc_final: 0.5884 (tm-30) REVERT: m 44 GLU cc_start: 0.6917 (tm-30) cc_final: 0.6662 (tm-30) REVERT: m 79 GLU cc_start: 0.5289 (pp20) cc_final: 0.4988 (pp20) REVERT: o 81 LYS cc_start: 0.5072 (mmtm) cc_final: 0.3700 (mmmt) outliers start: 117 outliers final: 86 residues processed: 744 average time/residue: 1.4124 time to fit residues: 1769.9562 Evaluate side-chains 724 residues out of total 6918 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 95 poor density : 629 time to evaluate : 7.314 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 121 THR Chi-restraints excluded: chain C residue 41 ASP Chi-restraints excluded: chain C residue 227 GLU Chi-restraints excluded: chain D residue 80 ILE Chi-restraints excluded: chain D residue 155 SER Chi-restraints excluded: chain D residue 376 GLU Chi-restraints excluded: chain D residue 399 THR Chi-restraints excluded: chain D residue 449 ASP Chi-restraints excluded: chain E residue 164 SER Chi-restraints excluded: chain E residue 200 CYS Chi-restraints excluded: chain E residue 205 MET Chi-restraints excluded: chain E residue 207 THR Chi-restraints excluded: chain E residue 218 CYS Chi-restraints excluded: chain E residue 228 LEU Chi-restraints excluded: chain F residue 77 ASP Chi-restraints excluded: chain F residue 133 MET Chi-restraints excluded: chain F residue 277 LEU Chi-restraints excluded: chain F residue 289 THR Chi-restraints excluded: chain F residue 387 CYS Chi-restraints excluded: chain F residue 399 ASP Chi-restraints excluded: chain F residue 470 ASP Chi-restraints excluded: chain G residue 294 ASN Chi-restraints excluded: chain G residue 556 ASP Chi-restraints excluded: chain G residue 572 GLN Chi-restraints excluded: chain G residue 660 ASP Chi-restraints excluded: chain G residue 672 VAL Chi-restraints excluded: chain H residue 3 ILE Chi-restraints excluded: chain H residue 4 ASN Chi-restraints excluded: chain H residue 26 GLU Chi-restraints excluded: chain H residue 80 THR Chi-restraints excluded: chain H residue 147 GLU Chi-restraints excluded: chain H residue 274 GLU Chi-restraints excluded: chain I residue 243 SER Chi-restraints excluded: chain I residue 255 HIS Chi-restraints excluded: chain J residue 49 LEU Chi-restraints excluded: chain J residue 101 LEU Chi-restraints excluded: chain J residue 174 ILE Chi-restraints excluded: chain L residue 718 CYS Chi-restraints excluded: chain L residue 752 TYR Chi-restraints excluded: chain L residue 939 ASN Chi-restraints excluded: chain L residue 1102 ASP Chi-restraints excluded: chain L residue 1130 THR Chi-restraints excluded: chain L residue 1154 TYR Chi-restraints excluded: chain L residue 1191 ASP Chi-restraints excluded: chain L residue 1302 ASN Chi-restraints excluded: chain L residue 1323 SER Chi-restraints excluded: chain L residue 1332 SER Chi-restraints excluded: chain M residue 583 ILE Chi-restraints excluded: chain M residue 612 ASN Chi-restraints excluded: chain M residue 731 VAL Chi-restraints excluded: chain M residue 761 LEU Chi-restraints excluded: chain M residue 764 LEU Chi-restraints excluded: chain N residue 2464 ASN Chi-restraints excluded: chain N residue 2472 MET Chi-restraints excluded: chain N residue 2526 ILE Chi-restraints excluded: chain N residue 2543 THR Chi-restraints excluded: chain N residue 2553 SER Chi-restraints excluded: chain N residue 2570 ILE Chi-restraints excluded: chain N residue 2626 ILE Chi-restraints excluded: chain N residue 2664 ILE Chi-restraints excluded: chain O residue 446 LEU Chi-restraints excluded: chain O residue 529 THR Chi-restraints excluded: chain P residue 172 GLU Chi-restraints excluded: chain P residue 190 THR Chi-restraints excluded: chain R residue 74 MET Chi-restraints excluded: chain S residue 54 VAL Chi-restraints excluded: chain S residue 59 ASP Chi-restraints excluded: chain U residue 59 ILE Chi-restraints excluded: chain U residue 62 LEU Chi-restraints excluded: chain U residue 101 GLU Chi-restraints excluded: chain V residue 27 GLU Chi-restraints excluded: chain X residue 22 VAL Chi-restraints excluded: chain X residue 111 CYS Chi-restraints excluded: chain Y residue 1215 SER Chi-restraints excluded: chain Y residue 1240 ILE Chi-restraints excluded: chain Z residue 7 ASP Chi-restraints excluded: chain Z residue 31 LEU Chi-restraints excluded: chain a residue 15 PHE Chi-restraints excluded: chain a residue 56 LEU Chi-restraints excluded: chain b residue 44 THR Chi-restraints excluded: chain b residue 51 LEU Chi-restraints excluded: chain c residue 136 SER Chi-restraints excluded: chain e residue 9 THR Chi-restraints excluded: chain e residue 47 CYS Chi-restraints excluded: chain f residue 91 ASN Chi-restraints excluded: chain g residue 57 LEU Chi-restraints excluded: chain g residue 63 LEU Chi-restraints excluded: chain g residue 100 THR Chi-restraints excluded: chain h residue 122 ASP Chi-restraints excluded: chain i residue 49 LEU Chi-restraints excluded: chain l residue 78 ASP Chi-restraints excluded: chain l residue 108 SER Chi-restraints excluded: chain m residue 10 ILE Chi-restraints excluded: chain o residue 7 LEU Chi-restraints excluded: chain p residue 33 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 788 random chunks: chunk 256 optimal weight: 6.9990 chunk 685 optimal weight: 7.9990 chunk 150 optimal weight: 3.9990 chunk 447 optimal weight: 6.9990 chunk 188 optimal weight: 6.9990 chunk 762 optimal weight: 8.9990 chunk 632 optimal weight: 9.9990 chunk 353 optimal weight: 10.0000 chunk 63 optimal weight: 4.9990 chunk 252 optimal weight: 8.9990 chunk 400 optimal weight: 6.9990 overall best weight: 5.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 73 GLN D 57 HIS E 115 ASN ** F 285 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 138 GLN ** G 572 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 696 ASN ** L1116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 630 ASN ** N2492 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 91 HIS V 19 GLN ** V 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 84 GLN Y1381 ASN ** g 211 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** p 16 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7495 moved from start: 0.4161 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.240 66880 Z= 0.464 Angle : 0.901 50.609 90646 Z= 0.538 Chirality : 0.133 6.328 10075 Planarity : 0.005 0.066 11400 Dihedral : 11.128 146.402 9935 Min Nonbonded Distance : 1.848 Molprobity Statistics. All-atom Clashscore : 10.14 Ramachandran Plot: Outliers : 0.01 % Allowed : 6.70 % Favored : 93.29 % Rotamer: Outliers : 2.18 % Allowed : 13.09 % Favored : 84.73 % Cbeta Deviations : 0.01 % Peptide Plane: Cis-proline : 3.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.01 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.03 (0.09), residues: 7999 helix: 0.30 (0.08), residues: 4218 sheet: -1.89 (0.25), residues: 370 loop : -1.78 (0.10), residues: 3411 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP X 98 HIS 0.009 0.001 HIS M 699 PHE 0.024 0.002 PHE P 330 TYR 0.029 0.002 TYR B 156 ARG 0.006 0.001 ARG I 312 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15998 Ramachandran restraints generated. 7999 Oldfield, 0 Emsley, 7999 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15998 Ramachandran restraints generated. 7999 Oldfield, 0 Emsley, 7999 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue VAL 97 is missing expected H atoms. Skipping. Residue MET 121 is missing expected H atoms. Skipping. Residue TYR 144 is missing expected H atoms. Skipping. Residue LEU 211 is missing expected H atoms. Skipping. Residue VAL 212 is missing expected H atoms. Skipping. Residue TYR 215 is missing expected H atoms. Skipping. Residue THR 217 is missing expected H atoms. Skipping. Residue TYR 219 is missing expected H atoms. Skipping. Residue VAL 353 is missing expected H atoms. Skipping. Residue THR 355 is missing expected H atoms. Skipping. Residue VAL 360 is missing expected H atoms. Skipping. Residue SER 361 is missing expected H atoms. Skipping. Residue LEU 363 is missing expected H atoms. Skipping. Residue SER 66 is missing expected H atoms. Skipping. Residue SER 89 is missing expected H atoms. Skipping. Residue THR 75 is missing expected H atoms. Skipping. Residue LYS 84 is missing expected H atoms. Skipping. Evaluate side-chains 805 residues out of total 6918 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 150 poor density : 655 time to evaluate : 7.424 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 117 ASN cc_start: 0.6019 (m-40) cc_final: 0.5731 (m-40) REVERT: B 115 ASP cc_start: 0.7126 (m-30) cc_final: 0.6608 (m-30) REVERT: B 185 GLU cc_start: 0.7824 (mt-10) cc_final: 0.7572 (mp0) REVERT: D 75 ASP cc_start: 0.6506 (m-30) cc_final: 0.5876 (p0) REVERT: D 86 ASN cc_start: 0.7901 (m-40) cc_final: 0.7491 (p0) REVERT: D 188 MET cc_start: 0.7864 (tpt) cc_final: 0.7589 (tpt) REVERT: D 258 LEU cc_start: 0.8160 (mt) cc_final: 0.7782 (mt) REVERT: E 157 LYS cc_start: 0.6242 (mmpt) cc_final: 0.5725 (mttt) REVERT: G 215 THR cc_start: 0.6261 (OUTLIER) cc_final: 0.5939 (t) REVERT: I 409 ASP cc_start: 0.7082 (m-30) cc_final: 0.6872 (m-30) REVERT: I 416 GLN cc_start: 0.7657 (OUTLIER) cc_final: 0.7219 (tp-100) REVERT: J 49 LEU cc_start: 0.8634 (OUTLIER) cc_final: 0.8417 (mt) REVERT: K 78 TYR cc_start: 0.7700 (t80) cc_final: 0.7497 (t80) REVERT: L 832 MET cc_start: 0.6390 (OUTLIER) cc_final: 0.6154 (ttt) REVERT: L 1020 MET cc_start: 0.7349 (mtp) cc_final: 0.6943 (tpp) REVERT: L 1302 ASN cc_start: 0.7755 (OUTLIER) cc_final: 0.7385 (t0) REVERT: M 739 GLU cc_start: 0.6703 (mt-10) cc_final: 0.6423 (mt-10) REVERT: M 764 LEU cc_start: 0.8590 (OUTLIER) cc_final: 0.8335 (tt) REVERT: M 828 TYR cc_start: 0.8634 (t80) cc_final: 0.8118 (t80) REVERT: N 2656 SER cc_start: 0.7503 (OUTLIER) cc_final: 0.7223 (t) REVERT: N 2657 ILE cc_start: 0.7478 (mm) cc_final: 0.7255 (mt) REVERT: N 2846 SER cc_start: 0.8944 (m) cc_final: 0.8605 (p) REVERT: O 511 LYS cc_start: 0.7808 (tttt) cc_final: 0.7094 (mtmt) REVERT: P 107 MET cc_start: 0.6597 (OUTLIER) cc_final: 0.6313 (tmm) REVERT: P 281 ARG cc_start: 0.5306 (mtp85) cc_final: 0.4959 (tmm160) REVERT: Q 72 GLU cc_start: 0.7179 (mm-30) cc_final: 0.6860 (mm-30) REVERT: Q 119 ILE cc_start: 0.8690 (mt) cc_final: 0.8363 (pt) REVERT: S 41 LYS cc_start: 0.6651 (mttt) cc_final: 0.6114 (mttp) REVERT: T 43 PHE cc_start: 0.4456 (OUTLIER) cc_final: 0.3791 (t80) REVERT: T 78 GLU cc_start: 0.4972 (pt0) cc_final: 0.4295 (mt-10) REVERT: T 88 GLU cc_start: 0.7527 (mm-30) cc_final: 0.6810 (mp0) REVERT: T 100 GLU cc_start: 0.6502 (tp30) cc_final: 0.5839 (tm-30) REVERT: X 39 SER cc_start: 0.8976 (p) cc_final: 0.8734 (t) REVERT: X 54 MET cc_start: 0.7699 (mmt) cc_final: 0.7289 (mmt) REVERT: X 85 ASP cc_start: 0.6545 (m-30) cc_final: 0.6228 (t0) REVERT: X 111 CYS cc_start: 0.7203 (OUTLIER) cc_final: 0.6650 (m) REVERT: X 142 VAL cc_start: 0.7593 (OUTLIER) cc_final: 0.7314 (p) REVERT: Y 1341 ASP cc_start: 0.5586 (m-30) cc_final: 0.5060 (t70) REVERT: Y 1364 GLU cc_start: 0.6048 (pm20) cc_final: 0.5661 (pm20) REVERT: Z 31 LEU cc_start: 0.7648 (OUTLIER) cc_final: 0.7306 (tt) REVERT: Z 123 LYS cc_start: 0.3427 (mmtm) cc_final: 0.2771 (mmmt) REVERT: b 72 LEU cc_start: 0.6522 (OUTLIER) cc_final: 0.6242 (mt) REVERT: c 44 TYR cc_start: 0.8060 (t80) cc_final: 0.7839 (t80) REVERT: f 69 ASP cc_start: 0.8233 (t0) cc_final: 0.7651 (t70) REVERT: g 153 GLU cc_start: 0.4841 (mm-30) cc_final: 0.4553 (mm-30) REVERT: l 31 LYS cc_start: 0.6697 (pttt) cc_final: 0.5874 (tttp) REVERT: l 67 GLU cc_start: 0.6843 (mm-30) cc_final: 0.5719 (tm-30) REVERT: m 44 GLU cc_start: 0.6938 (tm-30) cc_final: 0.6676 (tm-30) REVERT: m 73 GLN cc_start: 0.7564 (mm-40) cc_final: 0.7143 (mm-40) REVERT: m 79 GLU cc_start: 0.5422 (pp20) cc_final: 0.5097 (pp20) REVERT: o 43 MET cc_start: 0.5797 (mmm) cc_final: 0.5075 (mtm) REVERT: o 81 LYS cc_start: 0.4985 (mmtm) cc_final: 0.3722 (mmmt) outliers start: 150 outliers final: 105 residues processed: 764 average time/residue: 1.4268 time to fit residues: 1850.1768 Evaluate side-chains 724 residues out of total 6918 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 118 poor density : 606 time to evaluate : 8.389 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 103 VAL Chi-restraints excluded: chain A residue 121 THR Chi-restraints excluded: chain C residue 41 ASP Chi-restraints excluded: chain D residue 80 ILE Chi-restraints excluded: chain D residue 155 SER Chi-restraints excluded: chain D residue 376 GLU Chi-restraints excluded: chain D residue 399 THR Chi-restraints excluded: chain E residue 164 SER Chi-restraints excluded: chain E residue 200 CYS Chi-restraints excluded: chain E residue 205 MET Chi-restraints excluded: chain E residue 207 THR Chi-restraints excluded: chain E residue 218 CYS Chi-restraints excluded: chain E residue 228 LEU Chi-restraints excluded: chain F residue 77 ASP Chi-restraints excluded: chain F residue 243 THR Chi-restraints excluded: chain F residue 289 THR Chi-restraints excluded: chain F residue 387 CYS Chi-restraints excluded: chain F residue 470 ASP Chi-restraints excluded: chain G residue 112 GLU Chi-restraints excluded: chain G residue 215 THR Chi-restraints excluded: chain G residue 239 THR Chi-restraints excluded: chain G residue 294 ASN Chi-restraints excluded: chain G residue 344 ASP Chi-restraints excluded: chain G residue 400 SER Chi-restraints excluded: chain G residue 489 THR Chi-restraints excluded: chain G residue 501 ILE Chi-restraints excluded: chain G residue 556 ASP Chi-restraints excluded: chain G residue 572 GLN Chi-restraints excluded: chain G residue 660 ASP Chi-restraints excluded: chain G residue 672 VAL Chi-restraints excluded: chain H residue 3 ILE Chi-restraints excluded: chain H residue 4 ASN Chi-restraints excluded: chain H residue 26 GLU Chi-restraints excluded: chain H residue 80 THR Chi-restraints excluded: chain H residue 147 GLU Chi-restraints excluded: chain H residue 274 GLU Chi-restraints excluded: chain I residue 255 HIS Chi-restraints excluded: chain I residue 391 THR Chi-restraints excluded: chain I residue 416 GLN Chi-restraints excluded: chain J residue 49 LEU Chi-restraints excluded: chain J residue 93 ASP Chi-restraints excluded: chain J residue 101 LEU Chi-restraints excluded: chain K residue 30 GLU Chi-restraints excluded: chain L residue 718 CYS Chi-restraints excluded: chain L residue 752 TYR Chi-restraints excluded: chain L residue 832 MET Chi-restraints excluded: chain L residue 939 ASN Chi-restraints excluded: chain L residue 1064 ASP Chi-restraints excluded: chain L residue 1102 ASP Chi-restraints excluded: chain L residue 1130 THR Chi-restraints excluded: chain L residue 1154 TYR Chi-restraints excluded: chain L residue 1191 ASP Chi-restraints excluded: chain L residue 1246 LYS Chi-restraints excluded: chain L residue 1302 ASN Chi-restraints excluded: chain L residue 1323 SER Chi-restraints excluded: chain L residue 1332 SER Chi-restraints excluded: chain L residue 1334 LEU Chi-restraints excluded: chain M residue 583 ILE Chi-restraints excluded: chain M residue 612 ASN Chi-restraints excluded: chain M residue 731 VAL Chi-restraints excluded: chain M residue 761 LEU Chi-restraints excluded: chain M residue 764 LEU Chi-restraints excluded: chain N residue 2472 MET Chi-restraints excluded: chain N residue 2526 ILE Chi-restraints excluded: chain N residue 2543 THR Chi-restraints excluded: chain N residue 2553 SER Chi-restraints excluded: chain N residue 2570 ILE Chi-restraints excluded: chain N residue 2626 ILE Chi-restraints excluded: chain N residue 2656 SER Chi-restraints excluded: chain N residue 2664 ILE Chi-restraints excluded: chain N residue 2852 ILE Chi-restraints excluded: chain O residue 436 MET Chi-restraints excluded: chain O residue 446 LEU Chi-restraints excluded: chain O residue 529 THR Chi-restraints excluded: chain P residue 107 MET Chi-restraints excluded: chain P residue 123 ASP Chi-restraints excluded: chain P residue 172 GLU Chi-restraints excluded: chain R residue 74 MET Chi-restraints excluded: chain S residue 54 VAL Chi-restraints excluded: chain S residue 59 ASP Chi-restraints excluded: chain T residue 43 PHE Chi-restraints excluded: chain U residue 59 ILE Chi-restraints excluded: chain U residue 62 LEU Chi-restraints excluded: chain U residue 101 GLU Chi-restraints excluded: chain V residue 59 ASP Chi-restraints excluded: chain V residue 81 ILE Chi-restraints excluded: chain W residue 59 GLU Chi-restraints excluded: chain X residue 22 VAL Chi-restraints excluded: chain X residue 37 SER Chi-restraints excluded: chain X residue 111 CYS Chi-restraints excluded: chain X residue 127 ASN Chi-restraints excluded: chain X residue 142 VAL Chi-restraints excluded: chain Y residue 1240 ILE Chi-restraints excluded: chain Z residue 7 ASP Chi-restraints excluded: chain Z residue 31 LEU Chi-restraints excluded: chain a residue 15 PHE Chi-restraints excluded: chain a residue 56 LEU Chi-restraints excluded: chain b residue 44 THR Chi-restraints excluded: chain b residue 51 LEU Chi-restraints excluded: chain b residue 72 LEU Chi-restraints excluded: chain c residue 14 THR Chi-restraints excluded: chain c residue 136 SER Chi-restraints excluded: chain e residue 9 THR Chi-restraints excluded: chain e residue 47 CYS Chi-restraints excluded: chain f residue 58 THR Chi-restraints excluded: chain g residue 57 LEU Chi-restraints excluded: chain g residue 63 LEU Chi-restraints excluded: chain g residue 100 THR Chi-restraints excluded: chain h residue 122 ASP Chi-restraints excluded: chain i residue 49 LEU Chi-restraints excluded: chain i residue 68 ASN Chi-restraints excluded: chain l residue 78 ASP Chi-restraints excluded: chain l residue 108 SER Chi-restraints excluded: chain l residue 137 THR Chi-restraints excluded: chain m residue 10 ILE Chi-restraints excluded: chain n residue 62 THR Chi-restraints excluded: chain o residue 7 LEU Chi-restraints excluded: chain p residue 33 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 788 random chunks: chunk 735 optimal weight: 6.9990 chunk 85 optimal weight: 0.9980 chunk 434 optimal weight: 4.9990 chunk 556 optimal weight: 6.9990 chunk 431 optimal weight: 4.9990 chunk 641 optimal weight: 10.0000 chunk 425 optimal weight: 6.9990 chunk 759 optimal weight: 6.9990 chunk 475 optimal weight: 7.9990 chunk 463 optimal weight: 9.9990 chunk 350 optimal weight: 9.9990 overall best weight: 4.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 73 GLN D 308 ASN F 285 ASN ** G 572 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 696 ASN ** L1116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 630 ASN ** N2492 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N2705 ASN ** P 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** f 25 ASN ** g 211 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7487 moved from start: 0.4385 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.240 66880 Z= 0.395 Angle : 0.861 50.582 90646 Z= 0.518 Chirality : 0.132 6.317 10075 Planarity : 0.005 0.068 11400 Dihedral : 10.751 144.293 9932 Min Nonbonded Distance : 1.903 Molprobity Statistics. All-atom Clashscore : 9.66 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.10 % Favored : 93.87 % Rotamer: Outliers : 2.01 % Allowed : 14.05 % Favored : 83.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.89 (0.09), residues: 7999 helix: 0.43 (0.08), residues: 4210 sheet: -1.91 (0.25), residues: 373 loop : -1.74 (0.10), residues: 3416 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP X 98 HIS 0.007 0.001 HIS F 487 PHE 0.019 0.002 PHE S 25 TYR 0.022 0.002 TYR B 156 ARG 0.005 0.000 ARG I 312 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15998 Ramachandran restraints generated. 7999 Oldfield, 0 Emsley, 7999 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15998 Ramachandran restraints generated. 7999 Oldfield, 0 Emsley, 7999 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue VAL 97 is missing expected H atoms. Skipping. Residue MET 121 is missing expected H atoms. Skipping. Residue TYR 144 is missing expected H atoms. Skipping. Residue LEU 211 is missing expected H atoms. Skipping. Residue VAL 212 is missing expected H atoms. Skipping. Residue TYR 215 is missing expected H atoms. Skipping. Residue THR 217 is missing expected H atoms. Skipping. Residue TYR 219 is missing expected H atoms. Skipping. Residue VAL 353 is missing expected H atoms. Skipping. Residue THR 355 is missing expected H atoms. Skipping. Residue VAL 360 is missing expected H atoms. Skipping. Residue SER 361 is missing expected H atoms. Skipping. Residue LEU 363 is missing expected H atoms. Skipping. Residue SER 66 is missing expected H atoms. Skipping. Residue SER 89 is missing expected H atoms. Skipping. Residue THR 75 is missing expected H atoms. Skipping. Residue LYS 84 is missing expected H atoms. Skipping. Evaluate side-chains 773 residues out of total 6918 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 138 poor density : 635 time to evaluate : 7.408 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash 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 117 ASN cc_start: 0.5905 (m-40) cc_final: 0.5623 (m-40) REVERT: B 115 ASP cc_start: 0.7226 (m-30) cc_final: 0.6691 (m-30) REVERT: B 185 GLU cc_start: 0.7777 (mt-10) cc_final: 0.7557 (mp0) REVERT: D 86 ASN cc_start: 0.7844 (m-40) cc_final: 0.7578 (p0) REVERT: D 258 LEU cc_start: 0.8106 (mt) cc_final: 0.7806 (mt) REVERT: E 157 LYS cc_start: 0.6410 (mmpt) cc_final: 0.5937 (mttt) REVERT: H 88 TRP cc_start: 0.7805 (m100) cc_final: 0.7590 (m100) REVERT: L 832 MET cc_start: 0.6448 (OUTLIER) cc_final: 0.6225 (ttt) REVERT: L 1020 MET cc_start: 0.7347 (mtp) cc_final: 0.7048 (tpp) REVERT: L 1302 ASN cc_start: 0.7728 (OUTLIER) cc_final: 0.7393 (t0) REVERT: M 739 GLU cc_start: 0.6948 (mt-10) cc_final: 0.6632 (mt-10) REVERT: M 764 LEU cc_start: 0.8577 (OUTLIER) cc_final: 0.8315 (tt) REVERT: M 828 TYR cc_start: 0.8620 (t80) cc_final: 0.8068 (t80) REVERT: N 2657 ILE cc_start: 0.7446 (mm) cc_final: 0.7180 (mt) REVERT: N 2846 SER cc_start: 0.8944 (m) cc_final: 0.8586 (p) REVERT: O 436 MET cc_start: 0.6943 (OUTLIER) cc_final: 0.6108 (mtm) REVERT: O 446 LEU cc_start: 0.5895 (OUTLIER) cc_final: 0.5607 (mp) REVERT: O 511 LYS cc_start: 0.7884 (tttt) cc_final: 0.7050 (mtmt) REVERT: Q 72 GLU cc_start: 0.7152 (mm-30) cc_final: 0.6842 (mm-30) REVERT: Q 119 ILE cc_start: 0.8657 (mt) cc_final: 0.8333 (pt) REVERT: S 41 LYS cc_start: 0.6570 (mttt) cc_final: 0.6036 (mttp) REVERT: T 43 PHE cc_start: 0.4551 (OUTLIER) cc_final: 0.3907 (t80) REVERT: T 78 GLU cc_start: 0.5055 (pt0) cc_final: 0.4427 (mt-10) REVERT: T 88 GLU cc_start: 0.7581 (mm-30) cc_final: 0.6858 (mp0) REVERT: T 100 GLU cc_start: 0.6500 (tp30) cc_final: 0.5860 (tm-30) REVERT: X 39 SER cc_start: 0.8927 (p) cc_final: 0.8690 (t) REVERT: X 85 ASP cc_start: 0.6502 (m-30) cc_final: 0.6167 (t0) REVERT: Y 1339 GLN cc_start: 0.4895 (mm110) cc_final: 0.4548 (tp40) REVERT: Y 1341 ASP cc_start: 0.5625 (m-30) cc_final: 0.5145 (t70) REVERT: Z 31 LEU cc_start: 0.7646 (OUTLIER) cc_final: 0.7313 (tt) REVERT: Z 123 LYS cc_start: 0.3479 (mmtm) cc_final: 0.2823 (mmmt) REVERT: b 30 PHE cc_start: 0.7453 (OUTLIER) cc_final: 0.6766 (t80) REVERT: b 72 LEU cc_start: 0.6551 (OUTLIER) cc_final: 0.6242 (mt) REVERT: g 153 GLU cc_start: 0.4835 (mm-30) cc_final: 0.4550 (tp30) REVERT: k 17 TYR cc_start: 0.7104 (OUTLIER) cc_final: 0.5998 (m-80) REVERT: l 31 LYS cc_start: 0.6689 (pttt) cc_final: 0.5854 (tttp) REVERT: l 67 GLU cc_start: 0.6839 (mm-30) cc_final: 0.5786 (tm-30) REVERT: m 79 GLU cc_start: 0.5569 (pp20) cc_final: 0.5154 (pp20) REVERT: o 81 LYS cc_start: 0.4882 (mmtm) cc_final: 0.3649 (mmmt) outliers start: 138 outliers final: 99 residues processed: 728 average time/residue: 1.3975 time to fit residues: 1717.9643 Evaluate side-chains 716 residues out of total 6918 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 109 poor density : 607 time to evaluate : 7.267 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 103 VAL Chi-restraints excluded: chain A residue 121 THR Chi-restraints excluded: chain C residue 41 ASP Chi-restraints excluded: chain C residue 118 THR Chi-restraints excluded: chain D residue 58 MET Chi-restraints excluded: chain D residue 80 ILE Chi-restraints excluded: chain D residue 83 PHE Chi-restraints excluded: chain D residue 155 SER Chi-restraints excluded: chain D residue 376 GLU Chi-restraints excluded: chain D residue 399 THR Chi-restraints excluded: chain D residue 401 THR Chi-restraints excluded: chain E residue 164 SER Chi-restraints excluded: chain E residue 200 CYS Chi-restraints excluded: chain E residue 205 MET Chi-restraints excluded: chain E residue 207 THR Chi-restraints excluded: chain E residue 218 CYS Chi-restraints excluded: chain E residue 228 LEU Chi-restraints excluded: chain F residue 77 ASP Chi-restraints excluded: chain F residue 243 THR Chi-restraints excluded: chain F residue 387 CYS Chi-restraints excluded: chain F residue 470 ASP Chi-restraints excluded: chain G residue 294 ASN Chi-restraints excluded: chain G residue 331 THR Chi-restraints excluded: chain G residue 344 ASP Chi-restraints excluded: chain G residue 389 ILE Chi-restraints excluded: chain G residue 400 SER Chi-restraints excluded: chain G residue 501 ILE Chi-restraints excluded: chain G residue 556 ASP Chi-restraints excluded: chain G residue 572 GLN Chi-restraints excluded: chain G residue 608 ILE Chi-restraints excluded: chain G residue 660 ASP Chi-restraints excluded: chain G residue 672 VAL Chi-restraints excluded: chain G residue 676 LEU Chi-restraints excluded: chain G residue 696 ASN Chi-restraints excluded: chain H residue 3 ILE Chi-restraints excluded: chain H residue 4 ASN Chi-restraints excluded: chain H residue 26 GLU Chi-restraints excluded: chain H residue 78 LEU Chi-restraints excluded: chain H residue 80 THR Chi-restraints excluded: chain H residue 147 GLU Chi-restraints excluded: chain H residue 274 GLU Chi-restraints excluded: chain I residue 255 HIS Chi-restraints excluded: chain J residue 93 ASP Chi-restraints excluded: chain J residue 101 LEU Chi-restraints excluded: chain J residue 174 ILE Chi-restraints excluded: chain K residue 30 GLU Chi-restraints excluded: chain L residue 718 CYS Chi-restraints excluded: chain L residue 752 TYR Chi-restraints excluded: chain L residue 832 MET Chi-restraints excluded: chain L residue 915 ASP Chi-restraints excluded: chain L residue 939 ASN Chi-restraints excluded: chain L residue 1130 THR Chi-restraints excluded: chain L residue 1154 TYR Chi-restraints excluded: chain L residue 1191 ASP Chi-restraints excluded: chain L residue 1302 ASN Chi-restraints excluded: chain L residue 1323 SER Chi-restraints excluded: chain L residue 1332 SER Chi-restraints excluded: chain L residue 1334 LEU Chi-restraints excluded: chain L residue 1340 MET Chi-restraints excluded: chain M residue 583 ILE Chi-restraints excluded: chain M residue 612 ASN Chi-restraints excluded: chain M residue 669 VAL Chi-restraints excluded: chain M residue 731 VAL Chi-restraints excluded: chain M residue 761 LEU Chi-restraints excluded: chain M residue 764 LEU Chi-restraints excluded: chain N residue 2411 LEU Chi-restraints excluded: chain N residue 2465 SER Chi-restraints excluded: chain N residue 2472 MET Chi-restraints excluded: chain N residue 2543 THR Chi-restraints excluded: chain N residue 2553 SER Chi-restraints excluded: chain N residue 2570 ILE Chi-restraints excluded: chain N residue 2664 ILE Chi-restraints excluded: chain N residue 2852 ILE Chi-restraints excluded: chain O residue 436 MET Chi-restraints excluded: chain O residue 446 LEU Chi-restraints excluded: chain P residue 123 ASP Chi-restraints excluded: chain P residue 172 GLU Chi-restraints excluded: chain R residue 74 MET Chi-restraints excluded: chain S residue 54 VAL Chi-restraints excluded: chain T residue 43 PHE Chi-restraints excluded: chain U residue 59 ILE Chi-restraints excluded: chain U residue 101 GLU Chi-restraints excluded: chain W residue 59 GLU Chi-restraints excluded: chain X residue 22 VAL Chi-restraints excluded: chain X residue 37 SER Chi-restraints excluded: chain Y residue 1240 ILE Chi-restraints excluded: chain Y residue 1375 THR Chi-restraints excluded: chain Z residue 7 ASP Chi-restraints excluded: chain Z residue 31 LEU Chi-restraints excluded: chain a residue 56 LEU Chi-restraints excluded: chain b residue 30 PHE Chi-restraints excluded: chain b residue 44 THR Chi-restraints excluded: chain b residue 51 LEU Chi-restraints excluded: chain b residue 72 LEU Chi-restraints excluded: chain c residue 136 SER Chi-restraints excluded: chain e residue 9 THR Chi-restraints excluded: chain e residue 47 CYS Chi-restraints excluded: chain g residue 57 LEU Chi-restraints excluded: chain g residue 63 LEU Chi-restraints excluded: chain g residue 100 THR Chi-restraints excluded: chain h residue 122 ASP Chi-restraints excluded: chain i residue 49 LEU Chi-restraints excluded: chain i residue 68 ASN Chi-restraints excluded: chain i residue 81 ILE Chi-restraints excluded: chain k residue 17 TYR Chi-restraints excluded: chain l residue 108 SER Chi-restraints excluded: chain o residue 7 LEU Chi-restraints excluded: chain p residue 29 SER Chi-restraints excluded: chain p residue 33 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 788 random chunks: chunk 469 optimal weight: 4.9990 chunk 303 optimal weight: 7.9990 chunk 453 optimal weight: 4.9990 chunk 228 optimal weight: 6.9990 chunk 149 optimal weight: 0.9980 chunk 147 optimal weight: 7.9990 chunk 482 optimal weight: 3.9990 chunk 517 optimal weight: 10.0000 chunk 375 optimal weight: 5.9990 chunk 70 optimal weight: 0.0980 chunk 596 optimal weight: 6.9990 overall best weight: 3.0186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 73 GLN ** G 572 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L1116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 630 ASN ** N2492 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 211 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7465 moved from start: 0.4477 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.244 66880 Z= 0.314 Angle : 0.827 50.555 90646 Z= 0.501 Chirality : 0.131 6.315 10075 Planarity : 0.004 0.062 11400 Dihedral : 10.403 146.014 9932 Min Nonbonded Distance : 1.917 Molprobity Statistics. All-atom Clashscore : 9.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.61 % Favored : 94.39 % Rotamer: Outliers : 1.63 % Allowed : 14.73 % Favored : 83.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.01 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.63 (0.09), residues: 7999 helix: 0.65 (0.08), residues: 4216 sheet: -1.74 (0.25), residues: 370 loop : -1.63 (0.10), residues: 3413 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP X 98 HIS 0.005 0.001 HIS M 699 PHE 0.018 0.001 PHE L1043 TYR 0.021 0.001 TYR N2559 ARG 0.006 0.000 ARG h 149 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15998 Ramachandran restraints generated. 7999 Oldfield, 0 Emsley, 7999 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15998 Ramachandran restraints generated. 7999 Oldfield, 0 Emsley, 7999 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue VAL 97 is missing expected H atoms. Skipping. Residue MET 121 is missing expected H atoms. Skipping. Residue TYR 144 is missing expected H atoms. Skipping. Residue LEU 211 is missing expected H atoms. Skipping. Residue VAL 212 is missing expected H atoms. Skipping. Residue TYR 215 is missing expected H atoms. Skipping. Residue THR 217 is missing expected H atoms. Skipping. Residue TYR 219 is missing expected H atoms. Skipping. Residue VAL 353 is missing expected H atoms. Skipping. Residue THR 355 is missing expected H atoms. Skipping. Residue VAL 360 is missing expected H atoms. Skipping. Residue SER 361 is missing expected H atoms. Skipping. Residue LEU 363 is missing expected H atoms. Skipping. Residue SER 66 is missing expected H atoms. Skipping. Residue SER 89 is missing expected H atoms. Skipping. Residue THR 75 is missing expected H atoms. Skipping. Residue LYS 84 is missing expected H atoms. Skipping. Evaluate side-chains 738 residues out of total 6918 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 112 poor density : 626 time to evaluate : 6.845 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 117 ASN cc_start: 0.5915 (m-40) cc_final: 0.5620 (m-40) REVERT: B 115 ASP cc_start: 0.7293 (m-30) cc_final: 0.6740 (m-30) REVERT: B 185 GLU cc_start: 0.7751 (mt-10) cc_final: 0.7515 (mp0) REVERT: D 86 ASN cc_start: 0.7843 (m-40) cc_final: 0.7400 (p0) REVERT: D 258 LEU cc_start: 0.8086 (mt) cc_final: 0.7793 (mt) REVERT: E 67 LYS cc_start: 0.7823 (ptmt) cc_final: 0.7594 (pttt) REVERT: E 157 LYS cc_start: 0.6384 (mmpt) cc_final: 0.5903 (mttt) REVERT: H 88 TRP cc_start: 0.7770 (m100) cc_final: 0.7564 (m100) REVERT: L 832 MET cc_start: 0.6464 (OUTLIER) cc_final: 0.6200 (ttt) REVERT: L 1020 MET cc_start: 0.7413 (mtp) cc_final: 0.7182 (tpp) REVERT: L 1154 TYR cc_start: 0.7856 (OUTLIER) cc_final: 0.6746 (t80) REVERT: L 1302 ASN cc_start: 0.7662 (OUTLIER) cc_final: 0.7390 (t0) REVERT: L 1334 LEU cc_start: 0.7336 (OUTLIER) cc_final: 0.7115 (mt) REVERT: M 739 GLU cc_start: 0.6840 (mt-10) cc_final: 0.6468 (mt-10) REVERT: M 764 LEU cc_start: 0.8541 (OUTLIER) cc_final: 0.8265 (tt) REVERT: M 828 TYR cc_start: 0.8564 (t80) cc_final: 0.8077 (t80) REVERT: N 2846 SER cc_start: 0.8935 (m) cc_final: 0.8581 (p) REVERT: O 436 MET cc_start: 0.6884 (OUTLIER) cc_final: 0.5976 (mtm) REVERT: O 446 LEU cc_start: 0.5891 (OUTLIER) cc_final: 0.5621 (mp) REVERT: O 511 LYS cc_start: 0.7864 (tttt) cc_final: 0.7032 (mtmt) REVERT: P 294 TYR cc_start: 0.7575 (t80) cc_final: 0.6961 (t80) REVERT: Q 72 GLU cc_start: 0.7176 (mm-30) cc_final: 0.6852 (mm-30) REVERT: Q 119 ILE cc_start: 0.8620 (mt) cc_final: 0.8295 (pt) REVERT: S 41 LYS cc_start: 0.6574 (mttt) cc_final: 0.6064 (mttp) REVERT: T 78 GLU cc_start: 0.4997 (pt0) cc_final: 0.4393 (mt-10) REVERT: T 88 GLU cc_start: 0.7462 (mm-30) cc_final: 0.6839 (mp0) REVERT: T 100 GLU cc_start: 0.6471 (tp30) cc_final: 0.5823 (tm-30) REVERT: X 39 SER cc_start: 0.8925 (p) cc_final: 0.8651 (t) REVERT: X 85 ASP cc_start: 0.6448 (m-30) cc_final: 0.6139 (t0) REVERT: X 111 CYS cc_start: 0.7158 (OUTLIER) cc_final: 0.6787 (m) REVERT: Y 1341 ASP cc_start: 0.5582 (m-30) cc_final: 0.5104 (t70) REVERT: Z 31 LEU cc_start: 0.7632 (OUTLIER) cc_final: 0.7298 (tt) REVERT: Z 123 LYS cc_start: 0.3449 (mmtm) cc_final: 0.2967 (mmmt) REVERT: b 30 PHE cc_start: 0.7388 (OUTLIER) cc_final: 0.6715 (t80) REVERT: b 72 LEU cc_start: 0.6527 (OUTLIER) cc_final: 0.6212 (mt) REVERT: g 153 GLU cc_start: 0.4783 (mm-30) cc_final: 0.4494 (tp30) REVERT: l 31 LYS cc_start: 0.6664 (pttt) cc_final: 0.5833 (tttp) REVERT: l 67 GLU cc_start: 0.6860 (mm-30) cc_final: 0.5834 (tm-30) REVERT: m 79 GLU cc_start: 0.5602 (pp20) cc_final: 0.5180 (pp20) REVERT: o 43 MET cc_start: 0.5730 (mmm) cc_final: 0.4804 (mtm) REVERT: o 81 LYS cc_start: 0.5032 (mmtm) cc_final: 0.3722 (mmmt) outliers start: 112 outliers final: 93 residues processed: 703 average time/residue: 1.5112 time to fit residues: 1793.2716 Evaluate side-chains 712 residues out of total 6918 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 104 poor density : 608 time to evaluate : 7.268 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 103 VAL Chi-restraints excluded: chain A residue 121 THR Chi-restraints excluded: chain C residue 41 ASP Chi-restraints excluded: chain D residue 58 MET Chi-restraints excluded: chain D residue 80 ILE Chi-restraints excluded: chain D residue 155 SER Chi-restraints excluded: chain D residue 376 GLU Chi-restraints excluded: chain D residue 399 THR Chi-restraints excluded: chain D residue 401 THR Chi-restraints excluded: chain E residue 200 CYS Chi-restraints excluded: chain E residue 205 MET Chi-restraints excluded: chain E residue 207 THR Chi-restraints excluded: chain E residue 218 CYS Chi-restraints excluded: chain E residue 228 LEU Chi-restraints excluded: chain F residue 58 GLN Chi-restraints excluded: chain F residue 77 ASP Chi-restraints excluded: chain F residue 243 THR Chi-restraints excluded: chain F residue 289 THR Chi-restraints excluded: chain F residue 387 CYS Chi-restraints excluded: chain F residue 470 ASP Chi-restraints excluded: chain G residue 239 THR Chi-restraints excluded: chain G residue 294 ASN Chi-restraints excluded: chain G residue 331 THR Chi-restraints excluded: chain G residue 344 ASP Chi-restraints excluded: chain G residue 389 ILE Chi-restraints excluded: chain G residue 400 SER Chi-restraints excluded: chain G residue 501 ILE Chi-restraints excluded: chain G residue 556 ASP Chi-restraints excluded: chain G residue 572 GLN Chi-restraints excluded: chain G residue 660 ASP Chi-restraints excluded: chain G residue 672 VAL Chi-restraints excluded: chain G residue 676 LEU Chi-restraints excluded: chain H residue 3 ILE Chi-restraints excluded: chain H residue 63 VAL Chi-restraints excluded: chain H residue 78 LEU Chi-restraints excluded: chain H residue 80 THR Chi-restraints excluded: chain H residue 147 GLU Chi-restraints excluded: chain H residue 274 GLU Chi-restraints excluded: chain I residue 255 HIS Chi-restraints excluded: chain J residue 93 ASP Chi-restraints excluded: chain J residue 101 LEU Chi-restraints excluded: chain J residue 174 ILE Chi-restraints excluded: chain K residue 30 GLU Chi-restraints excluded: chain L residue 718 CYS Chi-restraints excluded: chain L residue 752 TYR Chi-restraints excluded: chain L residue 832 MET Chi-restraints excluded: chain L residue 939 ASN Chi-restraints excluded: chain L residue 1102 ASP Chi-restraints excluded: chain L residue 1154 TYR Chi-restraints excluded: chain L residue 1191 ASP Chi-restraints excluded: chain L residue 1302 ASN Chi-restraints excluded: chain L residue 1323 SER Chi-restraints excluded: chain L residue 1332 SER Chi-restraints excluded: chain L residue 1334 LEU Chi-restraints excluded: chain M residue 583 ILE Chi-restraints excluded: chain M residue 612 ASN Chi-restraints excluded: chain M residue 660 SER Chi-restraints excluded: chain M residue 661 ASP Chi-restraints excluded: chain M residue 669 VAL Chi-restraints excluded: chain M residue 731 VAL Chi-restraints excluded: chain M residue 761 LEU Chi-restraints excluded: chain M residue 764 LEU Chi-restraints excluded: chain N residue 2411 LEU Chi-restraints excluded: chain N residue 2465 SER Chi-restraints excluded: chain N residue 2543 THR Chi-restraints excluded: chain N residue 2553 SER Chi-restraints excluded: chain N residue 2570 ILE Chi-restraints excluded: chain N residue 2852 ILE Chi-restraints excluded: chain O residue 436 MET Chi-restraints excluded: chain O residue 446 LEU Chi-restraints excluded: chain P residue 123 ASP Chi-restraints excluded: chain P residue 172 GLU Chi-restraints excluded: chain S residue 54 VAL Chi-restraints excluded: chain U residue 62 LEU Chi-restraints excluded: chain U residue 101 GLU Chi-restraints excluded: chain W residue 59 GLU Chi-restraints excluded: chain X residue 22 VAL Chi-restraints excluded: chain X residue 37 SER Chi-restraints excluded: chain X residue 111 CYS Chi-restraints excluded: chain Y residue 1240 ILE Chi-restraints excluded: chain Z residue 7 ASP Chi-restraints excluded: chain Z residue 31 LEU Chi-restraints excluded: chain Z residue 107 VAL Chi-restraints excluded: chain a residue 15 PHE Chi-restraints excluded: chain a residue 56 LEU Chi-restraints excluded: chain b residue 30 PHE Chi-restraints excluded: chain b residue 44 THR Chi-restraints excluded: chain b residue 51 LEU Chi-restraints excluded: chain b residue 72 LEU Chi-restraints excluded: chain c residue 136 SER Chi-restraints excluded: chain e residue 9 THR Chi-restraints excluded: chain e residue 47 CYS Chi-restraints excluded: chain g residue 57 LEU Chi-restraints excluded: chain g residue 63 LEU Chi-restraints excluded: chain g residue 100 THR Chi-restraints excluded: chain h residue 122 ASP Chi-restraints excluded: chain i residue 49 LEU Chi-restraints excluded: chain i residue 68 ASN Chi-restraints excluded: chain l residue 108 SER Chi-restraints excluded: chain l residue 137 THR Chi-restraints excluded: chain o residue 7 LEU Chi-restraints excluded: chain p residue 29 SER Chi-restraints excluded: chain p residue 33 GLU Chi-restraints excluded: chain p residue 55 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 788 random chunks: chunk 690 optimal weight: 1.9990 chunk 727 optimal weight: 6.9990 chunk 663 optimal weight: 10.0000 chunk 707 optimal weight: 7.9990 chunk 425 optimal weight: 4.9990 chunk 308 optimal weight: 5.9990 chunk 555 optimal weight: 9.9990 chunk 217 optimal weight: 9.9990 chunk 639 optimal weight: 0.9990 chunk 669 optimal weight: 7.9990 chunk 705 optimal weight: 5.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 73 GLN ** G 572 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L1116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L1244 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 630 ASN ** N2492 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 29 GLN ** V 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 211 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7480 moved from start: 0.4593 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.243 66880 Z= 0.362 Angle : 0.840 50.567 90646 Z= 0.507 Chirality : 0.132 6.313 10075 Planarity : 0.005 0.061 11400 Dihedral : 10.248 145.333 9932 Min Nonbonded Distance : 1.908 Molprobity Statistics. All-atom Clashscore : 9.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.26 % Favored : 93.74 % Rotamer: Outliers : 1.77 % Allowed : 14.82 % Favored : 83.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.61 (0.09), residues: 7999 helix: 0.68 (0.08), residues: 4214 sheet: -1.85 (0.25), residues: 390 loop : -1.62 (0.10), residues: 3395 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP X 98 HIS 0.006 0.001 HIS F 487 PHE 0.019 0.001 PHE D 177 TYR 0.023 0.002 TYR N2748 ARG 0.003 0.000 ARG I 312 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15998 Ramachandran restraints generated. 7999 Oldfield, 0 Emsley, 7999 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15998 Ramachandran restraints generated. 7999 Oldfield, 0 Emsley, 7999 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue VAL 97 is missing expected H atoms. Skipping. Residue MET 121 is missing expected H atoms. Skipping. Residue TYR 144 is missing expected H atoms. Skipping. Residue LEU 211 is missing expected H atoms. Skipping. Residue VAL 212 is missing expected H atoms. Skipping. Residue TYR 215 is missing expected H atoms. Skipping. Residue THR 217 is missing expected H atoms. Skipping. Residue TYR 219 is missing expected H atoms. Skipping. Residue VAL 353 is missing expected H atoms. Skipping. Residue THR 355 is missing expected H atoms. Skipping. Residue VAL 360 is missing expected H atoms. Skipping. Residue SER 361 is missing expected H atoms. Skipping. Residue LEU 363 is missing expected H atoms. Skipping. Residue SER 66 is missing expected H atoms. Skipping. Residue SER 89 is missing expected H atoms. Skipping. Residue THR 75 is missing expected H atoms. Skipping. Residue LYS 84 is missing expected H atoms. Skipping. Evaluate side-chains 741 residues out of total 6918 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 122 poor density : 619 time to evaluate : 7.473 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash 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 117 ASN cc_start: 0.5972 (m-40) cc_final: 0.5681 (m-40) REVERT: B 115 ASP cc_start: 0.7286 (m-30) cc_final: 0.6734 (m-30) REVERT: B 185 GLU cc_start: 0.7771 (mt-10) cc_final: 0.7559 (mp0) REVERT: D 86 ASN cc_start: 0.7818 (m-40) cc_final: 0.7439 (p0) REVERT: D 258 LEU cc_start: 0.8098 (mt) cc_final: 0.7812 (mt) REVERT: E 157 LYS cc_start: 0.6357 (mmpt) cc_final: 0.5850 (mttt) REVERT: F 133 MET cc_start: 0.7637 (mtt) cc_final: 0.7157 (mmm) REVERT: I 347 GLU cc_start: 0.7061 (pt0) cc_final: 0.6775 (pt0) REVERT: L 832 MET cc_start: 0.6492 (OUTLIER) cc_final: 0.6183 (ttt) REVERT: L 1020 MET cc_start: 0.7357 (mtp) cc_final: 0.7139 (tpp) REVERT: L 1154 TYR cc_start: 0.7913 (OUTLIER) cc_final: 0.6793 (t80) REVERT: L 1302 ASN cc_start: 0.7682 (OUTLIER) cc_final: 0.7415 (t0) REVERT: L 1334 LEU cc_start: 0.7376 (OUTLIER) cc_final: 0.7152 (mt) REVERT: M 739 GLU cc_start: 0.6762 (mt-10) cc_final: 0.6381 (mt-10) REVERT: M 764 LEU cc_start: 0.8565 (OUTLIER) cc_final: 0.8298 (tt) REVERT: M 828 TYR cc_start: 0.8601 (t80) cc_final: 0.8095 (t80) REVERT: N 2846 SER cc_start: 0.8944 (m) cc_final: 0.8564 (p) REVERT: O 436 MET cc_start: 0.6923 (OUTLIER) cc_final: 0.6143 (mtm) REVERT: O 446 LEU cc_start: 0.5900 (OUTLIER) cc_final: 0.5637 (mp) REVERT: O 511 LYS cc_start: 0.7931 (tttt) cc_final: 0.7089 (mtmt) REVERT: Q 72 GLU cc_start: 0.7180 (mm-30) cc_final: 0.6857 (mm-30) REVERT: Q 119 ILE cc_start: 0.8643 (mt) cc_final: 0.8310 (pt) REVERT: T 43 PHE cc_start: 0.4524 (OUTLIER) cc_final: 0.3899 (t80) REVERT: T 78 GLU cc_start: 0.5027 (pt0) cc_final: 0.4394 (mt-10) REVERT: T 88 GLU cc_start: 0.7478 (mm-30) cc_final: 0.6827 (mp0) REVERT: T 100 GLU cc_start: 0.6518 (tp30) cc_final: 0.5883 (tm-30) REVERT: X 39 SER cc_start: 0.8925 (p) cc_final: 0.8652 (t) REVERT: X 85 ASP cc_start: 0.6504 (m-30) cc_final: 0.6201 (t0) REVERT: X 111 CYS cc_start: 0.7176 (OUTLIER) cc_final: 0.6748 (m) REVERT: X 142 VAL cc_start: 0.7636 (OUTLIER) cc_final: 0.7389 (p) REVERT: Y 1339 GLN cc_start: 0.4888 (mm110) cc_final: 0.4539 (tp40) REVERT: Y 1341 ASP cc_start: 0.5678 (m-30) cc_final: 0.5162 (t70) REVERT: Z 123 LYS cc_start: 0.3374 (mmtm) cc_final: 0.2753 (mmmt) REVERT: b 30 PHE cc_start: 0.7390 (OUTLIER) cc_final: 0.6719 (t80) REVERT: b 72 LEU cc_start: 0.6485 (OUTLIER) cc_final: 0.6197 (mt) REVERT: g 153 GLU cc_start: 0.4814 (mm-30) cc_final: 0.4537 (tp30) REVERT: l 31 LYS cc_start: 0.6697 (pttt) cc_final: 0.5860 (tttp) REVERT: l 67 GLU cc_start: 0.6863 (mm-30) cc_final: 0.5775 (tm-30) REVERT: m 79 GLU cc_start: 0.5552 (pp20) cc_final: 0.5246 (pp20) REVERT: o 43 MET cc_start: 0.5800 (mmm) cc_final: 0.4659 (mtm) REVERT: o 81 LYS cc_start: 0.4811 (mmtm) cc_final: 0.3663 (mmmt) outliers start: 122 outliers final: 99 residues processed: 706 average time/residue: 1.4082 time to fit residues: 1680.7470 Evaluate side-chains 717 residues out of total 6918 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 111 poor density : 606 time to evaluate : 7.344 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 103 VAL Chi-restraints excluded: chain A residue 121 THR Chi-restraints excluded: chain C residue 41 ASP Chi-restraints excluded: chain D residue 58 MET Chi-restraints excluded: chain D residue 80 ILE Chi-restraints excluded: chain D residue 155 SER Chi-restraints excluded: chain D residue 376 GLU Chi-restraints excluded: chain D residue 399 THR Chi-restraints excluded: chain D residue 401 THR Chi-restraints excluded: chain E residue 164 SER Chi-restraints excluded: chain E residue 200 CYS Chi-restraints excluded: chain E residue 205 MET Chi-restraints excluded: chain E residue 207 THR Chi-restraints excluded: chain E residue 218 CYS Chi-restraints excluded: chain E residue 228 LEU Chi-restraints excluded: chain F residue 77 ASP Chi-restraints excluded: chain F residue 243 THR Chi-restraints excluded: chain F residue 387 CYS Chi-restraints excluded: chain F residue 470 ASP Chi-restraints excluded: chain G residue 239 THR Chi-restraints excluded: chain G residue 294 ASN Chi-restraints excluded: chain G residue 331 THR Chi-restraints excluded: chain G residue 344 ASP Chi-restraints excluded: chain G residue 389 ILE Chi-restraints excluded: chain G residue 393 SER Chi-restraints excluded: chain G residue 400 SER Chi-restraints excluded: chain G residue 501 ILE Chi-restraints excluded: chain G residue 556 ASP Chi-restraints excluded: chain G residue 572 GLN Chi-restraints excluded: chain G residue 660 ASP Chi-restraints excluded: chain G residue 672 VAL Chi-restraints excluded: chain G residue 676 LEU Chi-restraints excluded: chain H residue 3 ILE Chi-restraints excluded: chain H residue 63 VAL Chi-restraints excluded: chain H residue 78 LEU Chi-restraints excluded: chain H residue 80 THR Chi-restraints excluded: chain H residue 147 GLU Chi-restraints excluded: chain H residue 274 GLU Chi-restraints excluded: chain I residue 255 HIS Chi-restraints excluded: chain I residue 391 THR Chi-restraints excluded: chain J residue 93 ASP Chi-restraints excluded: chain J residue 101 LEU Chi-restraints excluded: chain J residue 174 ILE Chi-restraints excluded: chain K residue 30 GLU Chi-restraints excluded: chain L residue 718 CYS Chi-restraints excluded: chain L residue 752 TYR Chi-restraints excluded: chain L residue 832 MET Chi-restraints excluded: chain L residue 939 ASN Chi-restraints excluded: chain L residue 1102 ASP Chi-restraints excluded: chain L residue 1130 THR Chi-restraints excluded: chain L residue 1154 TYR Chi-restraints excluded: chain L residue 1191 ASP Chi-restraints excluded: chain L residue 1302 ASN Chi-restraints excluded: chain L residue 1323 SER Chi-restraints excluded: chain L residue 1332 SER Chi-restraints excluded: chain L residue 1334 LEU Chi-restraints excluded: chain L residue 1340 MET Chi-restraints excluded: chain M residue 583 ILE Chi-restraints excluded: chain M residue 612 ASN Chi-restraints excluded: chain M residue 660 SER Chi-restraints excluded: chain M residue 669 VAL Chi-restraints excluded: chain M residue 731 VAL Chi-restraints excluded: chain M residue 761 LEU Chi-restraints excluded: chain M residue 764 LEU Chi-restraints excluded: chain N residue 2411 LEU Chi-restraints excluded: chain N residue 2465 SER Chi-restraints excluded: chain N residue 2543 THR Chi-restraints excluded: chain N residue 2553 SER Chi-restraints excluded: chain N residue 2570 ILE Chi-restraints excluded: chain N residue 2664 ILE Chi-restraints excluded: chain O residue 436 MET Chi-restraints excluded: chain O residue 446 LEU Chi-restraints excluded: chain P residue 123 ASP Chi-restraints excluded: chain P residue 172 GLU Chi-restraints excluded: chain P residue 185 LEU Chi-restraints excluded: chain P residue 199 ILE Chi-restraints excluded: chain P residue 309 TYR Chi-restraints excluded: chain S residue 54 VAL Chi-restraints excluded: chain T residue 43 PHE Chi-restraints excluded: chain U residue 101 GLU Chi-restraints excluded: chain W residue 59 GLU Chi-restraints excluded: chain X residue 22 VAL Chi-restraints excluded: chain X residue 37 SER Chi-restraints excluded: chain X residue 111 CYS Chi-restraints excluded: chain X residue 142 VAL Chi-restraints excluded: chain Y residue 1240 ILE Chi-restraints excluded: chain Y residue 1375 THR Chi-restraints excluded: chain Z residue 7 ASP Chi-restraints excluded: chain Z residue 31 LEU Chi-restraints excluded: chain Z residue 107 VAL Chi-restraints excluded: chain a residue 56 LEU Chi-restraints excluded: chain b residue 30 PHE Chi-restraints excluded: chain b residue 44 THR Chi-restraints excluded: chain b residue 51 LEU Chi-restraints excluded: chain b residue 72 LEU Chi-restraints excluded: chain c residue 136 SER Chi-restraints excluded: chain e residue 9 THR Chi-restraints excluded: chain e residue 47 CYS Chi-restraints excluded: chain g residue 57 LEU Chi-restraints excluded: chain g residue 63 LEU Chi-restraints excluded: chain g residue 100 THR Chi-restraints excluded: chain h residue 122 ASP Chi-restraints excluded: chain i residue 49 LEU Chi-restraints excluded: chain i residue 68 ASN Chi-restraints excluded: chain l residue 108 SER Chi-restraints excluded: chain l residue 137 THR Chi-restraints excluded: chain n residue 62 THR Chi-restraints excluded: chain o residue 7 LEU Chi-restraints excluded: chain p residue 29 SER Chi-restraints excluded: chain p residue 33 GLU Chi-restraints excluded: chain p residue 55 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 788 random chunks: chunk 464 optimal weight: 10.0000 chunk 748 optimal weight: 4.9990 chunk 456 optimal weight: 7.9990 chunk 355 optimal weight: 0.8980 chunk 520 optimal weight: 1.9990 chunk 785 optimal weight: 1.9990 chunk 722 optimal weight: 6.9990 chunk 625 optimal weight: 0.9990 chunk 64 optimal weight: 5.9990 chunk 482 optimal weight: 0.8980 chunk 383 optimal weight: 0.9980 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 73 GLN D 193 HIS ** G 572 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L1116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L1145 ASN ** L1244 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 630 ASN N2431 ASN ** N2492 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 543 ASN ** P 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y1231 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 211 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7428 moved from start: 0.4650 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.247 66880 Z= 0.263 Angle : 0.797 50.531 90646 Z= 0.486 Chirality : 0.131 6.306 10075 Planarity : 0.004 0.060 11400 Dihedral : 9.665 149.857 9932 Min Nonbonded Distance : 1.962 Molprobity Statistics. All-atom Clashscore : 8.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.75 % Favored : 96.25 % Rotamer: Outliers : 1.05 % Allowed : 15.71 % Favored : 83.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.01 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.17 (0.10), residues: 7999 helix: 1.00 (0.08), residues: 4242 sheet: -1.51 (0.26), residues: 352 loop : -1.40 (0.11), residues: 3405 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP F 61 HIS 0.005 0.001 HIS I 315 PHE 0.021 0.001 PHE L1043 TYR 0.019 0.001 TYR M 925 ARG 0.003 0.000 ARG E 216 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15998 Ramachandran restraints generated. 7999 Oldfield, 0 Emsley, 7999 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15998 Ramachandran restraints generated. 7999 Oldfield, 0 Emsley, 7999 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue VAL 97 is missing expected H atoms. Skipping. Residue MET 121 is missing expected H atoms. Skipping. Residue TYR 144 is missing expected H atoms. Skipping. Residue LEU 211 is missing expected H atoms. Skipping. Residue VAL 212 is missing expected H atoms. Skipping. Residue TYR 215 is missing expected H atoms. Skipping. Residue THR 217 is missing expected H atoms. Skipping. Residue TYR 219 is missing expected H atoms. Skipping. Residue VAL 353 is missing expected H atoms. Skipping. Residue THR 355 is missing expected H atoms. Skipping. Residue VAL 360 is missing expected H atoms. Skipping. Residue SER 361 is missing expected H atoms. Skipping. Residue LEU 363 is missing expected H atoms. Skipping. Residue SER 66 is missing expected H atoms. Skipping. Residue SER 89 is missing expected H atoms. Skipping. Residue THR 75 is missing expected H atoms. Skipping. Residue LYS 84 is missing expected H atoms. Skipping. Evaluate side-chains 728 residues out of total 6918 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 656 time to evaluate : 7.292 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 117 ASN cc_start: 0.5970 (m-40) cc_final: 0.5678 (m-40) REVERT: B 115 ASP cc_start: 0.7169 (m-30) cc_final: 0.6613 (m-30) REVERT: B 185 GLU cc_start: 0.7717 (mt-10) cc_final: 0.7480 (mp0) REVERT: D 258 LEU cc_start: 0.8059 (mt) cc_final: 0.7760 (mt) REVERT: D 378 MET cc_start: 0.8271 (tpt) cc_final: 0.7693 (tpt) REVERT: E 157 LYS cc_start: 0.6258 (mmpt) cc_final: 0.5761 (mttt) REVERT: F 140 LEU cc_start: 0.6839 (tp) cc_final: 0.6592 (tp) REVERT: G 261 MET cc_start: 0.8144 (mtm) cc_final: 0.7896 (mtm) REVERT: I 347 GLU cc_start: 0.6839 (pt0) cc_final: 0.6566 (pt0) REVERT: L 832 MET cc_start: 0.6399 (OUTLIER) cc_final: 0.6149 (ttt) REVERT: L 1154 TYR cc_start: 0.7845 (OUTLIER) cc_final: 0.6782 (t80) REVERT: M 764 LEU cc_start: 0.8469 (OUTLIER) cc_final: 0.8174 (tt) REVERT: M 828 TYR cc_start: 0.8504 (t80) cc_final: 0.7998 (t80) REVERT: N 2846 SER cc_start: 0.8937 (m) cc_final: 0.8564 (p) REVERT: O 446 LEU cc_start: 0.5808 (OUTLIER) cc_final: 0.5563 (mp) REVERT: O 511 LYS cc_start: 0.7822 (tttt) cc_final: 0.7019 (mtmt) REVERT: P 294 TYR cc_start: 0.7295 (t80) cc_final: 0.7085 (t80) REVERT: Q 72 GLU cc_start: 0.7180 (mm-30) cc_final: 0.6855 (mm-30) REVERT: Q 119 ILE cc_start: 0.8583 (mt) cc_final: 0.8260 (pt) REVERT: T 78 GLU cc_start: 0.5074 (pt0) cc_final: 0.4471 (mt-10) REVERT: T 88 GLU cc_start: 0.7510 (mm-30) cc_final: 0.6810 (mp0) REVERT: T 100 GLU cc_start: 0.6516 (tp30) cc_final: 0.5923 (tm-30) REVERT: X 37 SER cc_start: 0.8662 (OUTLIER) cc_final: 0.8370 (t) REVERT: X 39 SER cc_start: 0.8786 (p) cc_final: 0.8503 (t) REVERT: X 85 ASP cc_start: 0.6457 (m-30) cc_final: 0.6226 (t0) REVERT: Z 123 LYS cc_start: 0.3481 (mmtm) cc_final: 0.3063 (mmmt) REVERT: b 17 ARG cc_start: 0.7418 (mtp85) cc_final: 0.6818 (tpt170) REVERT: b 30 PHE cc_start: 0.7232 (OUTLIER) cc_final: 0.6594 (t80) REVERT: g 153 GLU cc_start: 0.4752 (mm-30) cc_final: 0.4477 (tp30) REVERT: l 31 LYS cc_start: 0.6550 (pttt) cc_final: 0.5806 (tttp) REVERT: l 67 GLU cc_start: 0.6831 (mm-30) cc_final: 0.5881 (tm-30) REVERT: m 79 GLU cc_start: 0.5690 (pp20) cc_final: 0.5341 (pp20) REVERT: o 43 MET cc_start: 0.5651 (mmm) cc_final: 0.4570 (mtm) REVERT: o 81 LYS cc_start: 0.4897 (mmtm) cc_final: 0.3697 (mmmt) REVERT: p 39 GLU cc_start: 0.6592 (tp30) cc_final: 0.6264 (tp30) outliers start: 72 outliers final: 60 residues processed: 702 average time/residue: 1.4330 time to fit residues: 1692.3454 Evaluate side-chains 695 residues out of total 6918 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 629 time to evaluate : 7.326 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 103 VAL Chi-restraints excluded: chain C residue 41 ASP Chi-restraints excluded: chain D residue 58 MET Chi-restraints excluded: chain D residue 80 ILE Chi-restraints excluded: chain D residue 399 THR Chi-restraints excluded: chain E residue 200 CYS Chi-restraints excluded: chain E residue 205 MET Chi-restraints excluded: chain E residue 207 THR Chi-restraints excluded: chain E residue 218 CYS Chi-restraints excluded: chain F residue 289 THR Chi-restraints excluded: chain F residue 387 CYS Chi-restraints excluded: chain G residue 344 ASP Chi-restraints excluded: chain G residue 389 ILE Chi-restraints excluded: chain G residue 393 SER Chi-restraints excluded: chain G residue 501 ILE Chi-restraints excluded: chain G residue 572 GLN Chi-restraints excluded: chain G residue 660 ASP Chi-restraints excluded: chain G residue 672 VAL Chi-restraints excluded: chain H residue 3 ILE Chi-restraints excluded: chain H residue 63 VAL Chi-restraints excluded: chain H residue 80 THR Chi-restraints excluded: chain J residue 93 ASP Chi-restraints excluded: chain J residue 101 LEU Chi-restraints excluded: chain J residue 174 ILE Chi-restraints excluded: chain L residue 718 CYS Chi-restraints excluded: chain L residue 832 MET Chi-restraints excluded: chain L residue 1130 THR Chi-restraints excluded: chain L residue 1154 TYR Chi-restraints excluded: chain M residue 583 ILE Chi-restraints excluded: chain M residue 660 SER Chi-restraints excluded: chain M residue 669 VAL Chi-restraints excluded: chain M residue 731 VAL Chi-restraints excluded: chain M residue 761 LEU Chi-restraints excluded: chain M residue 764 LEU Chi-restraints excluded: chain N residue 2411 LEU Chi-restraints excluded: chain N residue 2431 ASN Chi-restraints excluded: chain N residue 2570 ILE Chi-restraints excluded: chain O residue 436 MET Chi-restraints excluded: chain O residue 446 LEU Chi-restraints excluded: chain P residue 123 ASP Chi-restraints excluded: chain P residue 172 GLU Chi-restraints excluded: chain P residue 309 TYR Chi-restraints excluded: chain R residue 74 MET Chi-restraints excluded: chain S residue 54 VAL Chi-restraints excluded: chain U residue 101 GLU Chi-restraints excluded: chain W residue 59 GLU Chi-restraints excluded: chain X residue 37 SER Chi-restraints excluded: chain Y residue 1375 THR Chi-restraints excluded: chain Z residue 7 ASP Chi-restraints excluded: chain Z residue 31 LEU Chi-restraints excluded: chain a residue 56 LEU Chi-restraints excluded: chain b residue 30 PHE Chi-restraints excluded: chain b residue 44 THR Chi-restraints excluded: chain b residue 51 LEU Chi-restraints excluded: chain c residue 136 SER Chi-restraints excluded: chain g residue 57 LEU Chi-restraints excluded: chain g residue 63 LEU Chi-restraints excluded: chain g residue 100 THR Chi-restraints excluded: chain h residue 122 ASP Chi-restraints excluded: chain i residue 49 LEU Chi-restraints excluded: chain i residue 68 ASN Chi-restraints excluded: chain l residue 137 THR Chi-restraints excluded: chain o residue 7 LEU Chi-restraints excluded: chain p residue 29 SER Chi-restraints excluded: chain p residue 33 GLU Chi-restraints excluded: chain p residue 55 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 788 random chunks: chunk 496 optimal weight: 7.9990 chunk 665 optimal weight: 0.6980 chunk 191 optimal weight: 8.9990 chunk 576 optimal weight: 0.0980 chunk 92 optimal weight: 8.9990 chunk 173 optimal weight: 3.9990 chunk 626 optimal weight: 7.9990 chunk 262 optimal weight: 3.9990 chunk 642 optimal weight: 0.2980 chunk 79 optimal weight: 7.9990 chunk 115 optimal weight: 8.9990 overall best weight: 1.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 73 GLN F 272 ASN ** G 572 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L1116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L1244 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 630 ASN N2431 ASN ** N2492 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y1231 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 211 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3528 r_free = 0.3528 target = 0.107452 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.098320 restraints weight = 390088.760| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.099340 restraints weight = 267018.320| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.100564 restraints weight = 197519.811| |-----------------------------------------------------------------------------| r_work (final): 0.3414 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7449 moved from start: 0.4668 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.278 66880 Z= 0.290 Angle : 0.836 59.165 90646 Z= 0.513 Chirality : 0.131 6.311 10075 Planarity : 0.004 0.061 11400 Dihedral : 9.661 149.880 9932 Min Nonbonded Distance : 1.499 Molprobity Statistics. All-atom Clashscore : 9.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.89 % Favored : 96.11 % Rotamer: Outliers : 1.08 % Allowed : 15.71 % Favored : 83.22 % Cbeta Deviations : 0.01 % Peptide Plane: Cis-proline : 3.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.01 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.16 (0.10), residues: 7999 helix: 1.02 (0.08), residues: 4238 sheet: -1.50 (0.26), residues: 352 loop : -1.39 (0.11), residues: 3409 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP X 98 HIS 0.005 0.001 HIS I 315 PHE 0.021 0.001 PHE L1043 TYR 0.017 0.001 TYR M 925 ARG 0.002 0.000 ARG n 20 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 29432.48 seconds wall clock time: 507 minutes 14.09 seconds (30434.09 seconds total)