Starting phenix.real_space_refine (version: 1.21rc1) on Sat Oct 7 07:57:47 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ba0_15937/10_2023/8ba0_15937_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ba0_15937/10_2023/8ba0_15937.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ba0_15937/10_2023/8ba0_15937_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.68 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ba0_15937/10_2023/8ba0_15937_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ba0_15937/10_2023/8ba0_15937_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ba0_15937/10_2023/8ba0_15937.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ba0_15937/10_2023/8ba0_15937.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ba0_15937/10_2023/8ba0_15937_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ba0_15937/10_2023/8ba0_15937_updated.pdb" } resolution = 3.68 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= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Fe 28 7.16 5 Zn 1 6.06 5 P 19 5.49 5 S 478 5.16 5 C 42652 2.51 5 N 10947 2.21 5 O 11787 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 20": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 33": "NH1" <-> "NH2" Residue "A GLU 40": "OE1" <-> "OE2" Residue "A ARG 50": "NH1" <-> "NH2" Residue "A ARG 56": "NH1" <-> "NH2" Residue "A PHE 58": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 83": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 74": "NH1" <-> "NH2" Residue "B ASP 77": "OD1" <-> "OD2" Residue "B ARG 83": "NH1" <-> "NH2" Residue "B PHE 92": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 100": "OE1" <-> "OE2" Residue "B ARG 108": "NH1" <-> "NH2" Residue "B ASP 112": "OD1" <-> "OD2" Residue "B ARG 113": "NH1" <-> "NH2" Residue "B ARG 119": "NH1" <-> "NH2" Residue "B ARG 123": "NH1" <-> "NH2" Residue "B ARG 143": "NH1" <-> "NH2" Residue "B TYR 146": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 147": "OD1" <-> "OD2" Residue "B ARG 153": "NH1" <-> "NH2" Residue "B ARG 176": "NH1" <-> "NH2" Residue "B ARG 180": "NH1" <-> "NH2" Residue "B TYR 187": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 211": "NH1" <-> "NH2" Residue "B ARG 220": "NH1" <-> "NH2" Residue "C ARG 50": "NH1" <-> "NH2" Residue "C ARG 57": "NH1" <-> "NH2" Residue "C ARG 65": "NH1" <-> "NH2" Residue "C TYR 66": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 74": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 104": "OD1" <-> "OD2" Residue "C PHE 110": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 124": "NH1" <-> "NH2" Residue "C ARG 127": "NH1" <-> "NH2" Residue "C ARG 138": "NH1" <-> "NH2" Residue "C ARG 142": "NH1" <-> "NH2" Residue "C ARG 144": "NH1" <-> "NH2" Residue "C TYR 148": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 151": "OE1" <-> "OE2" Residue "C TYR 168": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 170": "NH1" <-> "NH2" Residue "C ARG 187": "NH1" <-> "NH2" Residue "C ARG 188": "NH1" <-> "NH2" Residue "C ARG 201": "NH1" <-> "NH2" Residue "C ARG 202": "NH1" <-> "NH2" Residue "C ARG 213": "NH1" <-> "NH2" Residue "C ARG 220": "NH1" <-> "NH2" Residue "C GLU 231": "OE1" <-> "OE2" Residue "C PHE 232": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 233": "NH1" <-> "NH2" Residue "C PHE 235": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 248": "NH1" <-> "NH2" Residue "D PHE 48": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 58": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 83": "NH1" <-> "NH2" Residue "D ARG 101": "NH1" <-> "NH2" Residue "D GLU 105": "OE1" <-> "OE2" Residue "D ARG 113": "NH1" <-> "NH2" Residue "D TYR 134": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 143": "NH1" <-> "NH2" Residue "D ARG 171": "NH1" <-> "NH2" Residue "D ARG 176": "NH1" <-> "NH2" Residue "D ARG 184": "NH1" <-> "NH2" Residue "D PHE 206": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 212": "NH1" <-> "NH2" Residue "D PHE 218": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 221": "NH1" <-> "NH2" Residue "D ARG 226": "NH1" <-> "NH2" Residue "D TYR 231": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 233": "NH1" <-> "NH2" Residue "D ARG 259": "NH1" <-> "NH2" Residue "D ARG 271": "NH1" <-> "NH2" Residue "D ARG 276": "NH1" <-> "NH2" Residue "D ASP 279": "OD1" <-> "OD2" Residue "D ARG 299": "NH1" <-> "NH2" Residue "D ARG 308": "NH1" <-> "NH2" Residue "D TYR 313": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 334": "NH1" <-> "NH2" Residue "D ARG 338": "NH1" <-> "NH2" Residue "D ARG 343": "NH1" <-> "NH2" Residue "D ARG 347": "NH1" <-> "NH2" Residue "D ARG 373": "NH1" <-> "NH2" Residue "D TYR 402": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 411": "OE1" <-> "OE2" Residue "D PHE 412": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 423": "NH1" <-> "NH2" Residue "D TYR 425": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 426": "NH1" <-> "NH2" Residue "D PHE 434": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 441": "OE1" <-> "OE2" Residue "D PHE 463": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 468": "NH1" <-> "NH2" Residue "E ARG 35": "NH1" <-> "NH2" Residue "E ASP 36": "OD1" <-> "OD2" Residue "E PHE 46": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 55": "NH1" <-> "NH2" Residue "E ARG 69": "NH1" <-> "NH2" Residue "E ARG 81": "NH1" <-> "NH2" Residue "E TYR 83": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 104": "NH1" <-> "NH2" Residue "E ARG 117": "NH1" <-> "NH2" Residue "E TYR 123": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 136": "NH1" <-> "NH2" Residue "E ARG 160": "NH1" <-> "NH2" Residue "E ARG 212": "NH1" <-> "NH2" Residue "E ARG 215": "NH1" <-> "NH2" Residue "F ARG 55": "NH1" <-> "NH2" Residue "F ARG 63": "NH1" <-> "NH2" Residue "F ASP 65": "OD1" <-> "OD2" Residue "F ARG 67": "NH1" <-> "NH2" Residue "F ARG 74": "NH1" <-> "NH2" Residue "F TYR 78": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 101": "NH1" <-> "NH2" Residue "F ARG 103": "NH1" <-> "NH2" Residue "F PHE 108": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 124": "NH1" <-> "NH2" Residue "F ASP 142": "OD1" <-> "OD2" Residue "F ARG 143": "NH1" <-> "NH2" Residue "F ARG 147": "NH1" <-> "NH2" Residue "F ARG 162": "NH1" <-> "NH2" Residue "F TYR 172": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 174": "NH1" <-> "NH2" Residue "F TYR 178": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 214": "NH1" <-> "NH2" Residue "F GLU 224": "OE1" <-> "OE2" Residue "F ARG 239": "NH1" <-> "NH2" Residue "F ARG 271": "NH1" <-> "NH2" Residue "F ARG 272": "NH1" <-> "NH2" Residue "F ARG 282": "NH1" <-> "NH2" Residue "F ARG 284": "NH1" <-> "NH2" Residue "F ARG 299": "NH1" <-> "NH2" Residue "F ARG 317": "NH1" <-> "NH2" Residue "F ARG 384": "NH1" <-> "NH2" Residue "F PHE 388": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 401": "NH1" <-> "NH2" Residue "F ARG 413": "NH1" <-> "NH2" Residue "F ARG 455": "NH1" <-> "NH2" Residue "F ARG 458": "NH1" <-> "NH2" Residue "F ARG 464": "NH1" <-> "NH2" Residue "F ARG 471": "NH1" <-> "NH2" Residue "G PHE 45": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ARG 72": "NH1" <-> "NH2" Residue "G ARG 78": "NH1" <-> "NH2" Residue "G ARG 86": "NH1" <-> "NH2" Residue "G GLU 91": "OE1" <-> "OE2" Residue "G GLU 93": "OE1" <-> "OE2" Residue "G ARG 111": "NH1" <-> "NH2" Residue "G ARG 120": "NH1" <-> "NH2" Residue "G ARG 123": "NH1" <-> "NH2" Residue "G ARG 160": "NH1" <-> "NH2" Residue "G ARG 162": "NH1" <-> "NH2" Residue "G TYR 168": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ARG 172": "NH1" <-> "NH2" Residue "G ARG 189": "NH1" <-> "NH2" Residue "G ARG 195": "NH1" <-> "NH2" Residue "G ARG 198": "NH1" <-> "NH2" Residue "G ARG 214": "NH1" <-> "NH2" Residue "G ARG 255": "NH1" <-> "NH2" Residue "G GLU 258": "OE1" <-> "OE2" Residue "G ARG 260": "NH1" <-> "NH2" Residue "G ARG 280": "NH1" <-> "NH2" Residue "G ARG 286": "NH1" <-> "NH2" Residue "G ARG 290": "NH1" <-> "NH2" Residue "G ASP 294": "OD1" <-> "OD2" Residue "G ARG 305": "NH1" <-> "NH2" Residue "G PHE 306": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ARG 313": "NH1" <-> "NH2" Residue "G ARG 315": "NH1" <-> "NH2" Residue "G ARG 322": "NH1" <-> "NH2" Residue "G ARG 373": "NH1" <-> "NH2" Residue "G GLU 377": "OE1" <-> "OE2" Residue "G ARG 393": "NH1" <-> "NH2" Residue "G TYR 396": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ARG 419": "NH1" <-> "NH2" Residue "G ARG 428": "NH1" <-> "NH2" Residue "G ARG 430": "NH1" <-> "NH2" Residue "G TYR 433": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 451": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ARG 494": "NH1" <-> "NH2" Residue "G ARG 563": "NH1" <-> "NH2" Residue "G TYR 602": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ARG 608": "NH1" <-> "NH2" Residue "G ARG 623": "NH1" <-> "NH2" Residue "G ARG 630": "NH1" <-> "NH2" Residue "G TYR 642": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ARG 649": "NH1" <-> "NH2" Residue "G ARG 651": "NH1" <-> "NH2" Residue "G ARG 661": "NH1" <-> "NH2" Residue "G ARG 694": "NH1" <-> "NH2" Residue "G ARG 704": "NH1" <-> "NH2" Residue "G ARG 721": "NH1" <-> "NH2" Residue "H GLU 5": "OE1" <-> "OE2" Residue "H ARG 32": "NH1" <-> "NH2" Residue "H ARG 41": "NH1" <-> "NH2" Residue "H ASP 58": "OD1" <-> "OD2" Residue "H TYR 79": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 105": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 111": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ARG 141": "NH1" <-> "NH2" Residue "H ARG 202": "NH1" <-> "NH2" Residue "H GLU 211": "OE1" <-> "OE2" Residue "H PHE 218": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 227": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 234": "OE1" <-> "OE2" Residue "H PHE 265": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ARG 274": "NH1" <-> "NH2" Residue "H ARG 279": "NH1" <-> "NH2" Residue "H PHE 280": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ARG 281": "NH1" <-> "NH2" Residue "H TYR 282": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 287": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 307": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 312": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ASP 35": "OD1" <-> "OD2" Residue "I ARG 61": "NH1" <-> "NH2" Residue "I PHE 68": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ARG 73": "NH1" <-> "NH2" Residue "I ARG 101": "NH1" <-> "NH2" Residue "I PHE 102": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ARG 103": "NH1" <-> "NH2" Residue "I ARG 109": "NH1" <-> "NH2" Residue "I ARG 110": "NH1" <-> "NH2" Residue "I ARG 117": "NH1" <-> "NH2" Residue "I GLU 139": "OE1" <-> "OE2" Residue "I ARG 140": "NH1" <-> "NH2" Residue "I ASP 142": "OD1" <-> "OD2" Residue "I ARG 145": "NH1" <-> "NH2" Residue "I ARG 146": "NH1" <-> "NH2" Residue "I ARG 149": "NH1" <-> "NH2" Residue "I ASP 170": "OD1" <-> "OD2" Residue "I ASP 213": "OD1" <-> "OD2" Residue "I TYR 216": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ARG 217": "NH1" <-> "NH2" Residue "J PHE 48": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 55": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 58": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 66": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 94": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 110": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 137": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 151": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ARG 25": "NH1" <-> "NH2" Residue "K GLU 36": "OE1" <-> "OE2" Residue "K PHE 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 47": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K GLU 56": "OE1" <-> "OE2" Residue "K PHE 66": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K GLU 70": "OE1" <-> "OE2" Residue "K ARG 83": "NH1" <-> "NH2" Residue "L ASP 32": "OD1" <-> "OD2" Residue "L PHE 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 75": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 76": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 80": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ARG 89": "NH1" <-> "NH2" Residue "L ASP 118": "OD1" <-> "OD2" Residue "L TYR 125": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ARG 148": "NH1" <-> "NH2" Residue "L TYR 164": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 172": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ARG 235": "NH1" <-> "NH2" Residue "L PHE 307": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 312": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ARG 329": "NH1" <-> "NH2" Residue "L PHE 345": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 382": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ARG 397": "NH1" <-> "NH2" Residue "L ARG 424": "NH1" <-> "NH2" Residue "L TYR 449": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 471": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 488": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 501": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 525": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ASP 526": "OD1" <-> "OD2" Residue "L PHE 564": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M PHE 35": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M GLU 47": "OE1" <-> "OE2" Residue "M TYR 50": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M TYR 132": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M ARG 136": "NH1" <-> "NH2" Residue "M TYR 171": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M PHE 176": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M PHE 185": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M GLU 210": "OE1" <-> "OE2" Residue "M ARG 233": "NH1" <-> "NH2" Residue "M PHE 247": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M ARG 266": "NH1" <-> "NH2" Residue "M GLU 323": "OE1" <-> "OE2" Residue "M ARG 324": "NH1" <-> "NH2" Residue "M ARG 328": "NH1" <-> "NH2" Residue "M PHE 339": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M PHE 348": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M TYR 368": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M PHE 386": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M TYR 394": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M TYR 399": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M TYR 412": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M ARG 420": "NH1" <-> "NH2" Residue "M PHE 442": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N PHE 41": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N PHE 112": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N ARG 172": "NH1" <-> "NH2" Residue "N PHE 203": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N PHE 209": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N PHE 230": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N PHE 287": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N PHE 288": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N ARG 291": "NH1" <-> "NH2" Residue "N TYR 317": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N PHE 325": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N PHE 337": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O ARG 46": "NH1" <-> "NH2" Residue "O ARG 50": "NH1" <-> "NH2" Residue "O TYR 57": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O ARG 77": "NH1" <-> "NH2" Residue "O GLU 88": "OE1" <-> "OE2" Residue "O PHE 98": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O TYR 124": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O TYR 126": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O ARG 129": "NH1" <-> "NH2" Residue "O ASP 132": "OD1" <-> "OD2" Residue "O ARG 140": "NH1" <-> "NH2" Residue "O TYR 142": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O ARG 145": "NH1" <-> "NH2" Residue "O ASP 154": "OD1" <-> "OD2" Residue "O ARG 162": "NH1" <-> "NH2" Residue "O ARG 167": "NH1" <-> "NH2" Residue "O ARG 189": "NH1" <-> "NH2" Residue "O PHE 197": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O ARG 203": "NH1" <-> "NH2" Residue "O ARG 209": "NH1" <-> "NH2" Residue "O ARG 212": "NH1" <-> "NH2" Residue "O ARG 219": "NH1" <-> "NH2" Residue "O ARG 249": "NH1" <-> "NH2" Residue "O TYR 289": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O GLU 302": "OE1" <-> "OE2" Residue "O ARG 306": "NH1" <-> "NH2" Residue "O PHE 309": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O ARG 325": "NH1" <-> "NH2" Residue "O GLU 334": "OE1" <-> "OE2" Residue "O ARG 336": "NH1" <-> "NH2" Residue "O ASP 345": "OD1" <-> "OD2" Residue "O ARG 354": "NH1" <-> "NH2" Residue "O ARG 362": "NH1" <-> "NH2" Residue "O ARG 371": "NH1" <-> "NH2" Residue "O ARG 383": "NH1" <-> "NH2" Residue "P ARG 41": "NH1" <-> "NH2" Residue "P ARG 53": "NH1" <-> "NH2" Residue "P ARG 58": "NH1" <-> "NH2" Residue "P ARG 77": "NH1" <-> "NH2" Residue "P TYR 78": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P ARG 95": "NH1" <-> "NH2" Residue "P ARG 103": "NH1" <-> "NH2" Residue "P ARG 127": "NH1" <-> "NH2" Residue "P ARG 142": "NH1" <-> "NH2" Residue "P PHE 144": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P PHE 149": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P ARG 161": "NH1" <-> "NH2" Residue "P ARG 164": "NH1" <-> "NH2" Residue "P ARG 167": "NH1" <-> "NH2" Residue "P GLU 168": "OE1" <-> "OE2" Residue "P ARG 173": "NH1" <-> "NH2" Residue "P GLU 183": "OE1" <-> "OE2" Residue "P ARG 207": "NH1" <-> "NH2" Residue "P ARG 209": "NH1" <-> "NH2" Residue "P PHE 212": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P ARG 219": "NH1" <-> "NH2" Residue "P ARG 229": "NH1" <-> "NH2" Residue "P PHE 230": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P ARG 232": "NH1" <-> "NH2" Residue "P TYR 233": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P ARG 239": "NH1" <-> "NH2" Residue "P ARG 240": "NH1" <-> "NH2" Residue "P PHE 242": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P ARG 243": "NH1" <-> "NH2" Residue "P ARG 280": "NH1" <-> "NH2" Residue "P ARG 289": "NH1" <-> "NH2" Residue "P ARG 301": "NH1" <-> "NH2" Residue "P ARG 304": "NH1" <-> "NH2" Residue "P ARG 309": "NH1" <-> "NH2" Residue "P ARG 314": "NH1" <-> "NH2" Residue "P ARG 318": "NH1" <-> "NH2" Residue "P ARG 346": "NH1" <-> "NH2" Residue "P ARG 349": "NH1" <-> "NH2" Residue "P GLU 374": "OE1" <-> "OE2" Residue "P ARG 382": "NH1" <-> "NH2" Residue "P ARG 385": "NH1" <-> "NH2" Residue "P TYR 389": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P TYR 390": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P ARG 409": "NH1" <-> "NH2" Residue "P ARG 413": "NH1" <-> "NH2" Residue "Q ARG 80": "NH1" <-> "NH2" Residue "Q ARG 82": "NH1" <-> "NH2" Residue "Q ARG 83": "NH1" <-> "NH2" Residue "Q ARG 85": "NH1" <-> "NH2" Residue "Q GLU 107": "OE1" <-> "OE2" Residue "Q PHE 108": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q ARG 111": "NH1" <-> "NH2" Residue "Q ARG 113": "NH1" <-> "NH2" Residue "Q PHE 135": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q GLU 140": "OE1" <-> "OE2" Residue "Q ARG 147": "NH1" <-> "NH2" Residue "Q ARG 151": "NH1" <-> "NH2" Residue "Q ARG 164": "NH1" <-> "NH2" Residue "Q ARG 177": "NH1" <-> "NH2" Residue "Q ARG 179": "NH1" <-> "NH2" Residue "R ARG 33": "NH1" <-> "NH2" Residue "R GLU 37": "OE1" <-> "OE2" Residue "R GLU 49": "OE1" <-> "OE2" Residue "R ARG 52": "NH1" <-> "NH2" Residue "R ARG 55": "NH1" <-> "NH2" Residue "R ARG 61": "NH1" <-> "NH2" Residue "R GLU 82": "OE1" <-> "OE2" Residue "R ARG 83": "NH1" <-> "NH2" Residue "R PHE 86": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R TYR 100": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R ARG 117": "NH1" <-> "NH2" Residue "R PHE 118": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T ARG 78": "NH1" <-> "NH2" Residue "T GLU 119": "OE1" <-> "OE2" Residue "U ARG 78": "NH1" <-> "NH2" Residue "U PHE 122": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V ARG 33": "NH1" <-> "NH2" Residue "V TYR 44": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V ARG 45": "NH1" <-> "NH2" Residue "V ARG 55": "NH1" <-> "NH2" Residue "V ASP 64": "OD1" <-> "OD2" Residue "V GLU 79": "OE1" <-> "OE2" Residue "V ARG 92": "NH1" <-> "NH2" Residue "W ARG 15": "NH1" <-> "NH2" Residue "W ASP 21": "OD1" <-> "OD2" Residue "W ARG 22": "NH1" <-> "NH2" Residue "W ARG 26": "NH1" <-> "NH2" Residue "W ARG 28": "NH1" <-> "NH2" Residue "W ARG 38": "NH1" <-> "NH2" Residue "W TYR 47": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W ARG 57": "NH1" <-> "NH2" Residue "W ARG 61": "NH1" <-> "NH2" Residue "W ARG 68": "NH1" <-> "NH2" Residue "W ARG 74": "NH1" <-> "NH2" Residue "W ARG 102": "NH1" <-> "NH2" Residue "W ASP 109": "OD1" <-> "OD2" Residue "W PHE 119": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X ARG 28": "NH1" <-> "NH2" Residue "X ARG 49": "NH1" <-> "NH2" Residue "X ARG 56": "NH1" <-> "NH2" Residue "X PHE 73": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X ARG 74": "NH1" <-> "NH2" Residue "X ARG 104": "NH1" <-> "NH2" Residue "X ARG 122": "NH1" <-> "NH2" Residue "X TYR 125": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X TYR 127": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X ARG 130": "NH1" <-> "NH2" Residue "X ARG 138": "NH1" <-> "NH2" Residue "X TYR 149": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X GLU 158": "OE1" <-> "OE2" Residue "X ASP 159": "OD1" <-> "OD2" Residue "X ARG 170": "NH1" <-> "NH2" Residue "Y ARG 5": "NH1" <-> "NH2" Residue "Y TYR 8": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y GLU 15": "OE1" <-> "OE2" Residue "Y ASP 16": "OD1" <-> "OD2" Residue "Y ARG 55": "NH1" <-> "NH2" Residue "Y PHE 70": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y ARG 81": "NH1" <-> "NH2" Residue "Y TYR 143": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z ARG 27": "NH1" <-> "NH2" Residue "Z TYR 33": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z TYR 54": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z ARG 63": "NH1" <-> "NH2" Residue "Z ARG 69": "NH1" <-> "NH2" Residue "Z GLU 82": "OE1" <-> "OE2" Residue "Z ARG 83": "NH1" <-> "NH2" Residue "Z ARG 85": "NH1" <-> "NH2" Residue "Z ARG 89": "NH1" <-> "NH2" Residue "Z ARG 92": "NH1" <-> "NH2" Residue "Z ARG 93": "NH1" <-> "NH2" Residue "Z ARG 95": "NH1" <-> "NH2" Residue "Z GLU 97": "OE1" <-> "OE2" Residue "Z GLU 116": "OE1" <-> "OE2" Residue "Z PHE 132": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z PHE 135": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z TYR 144": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z ARG 147": "NH1" <-> "NH2" Residue "a PHE 3": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a TYR 24": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a ARG 36": "NH1" <-> "NH2" Residue "a ARG 37": "NH1" <-> "NH2" Residue "a GLU 41": "OE1" <-> "OE2" Residue "a ARG 42": "NH1" <-> "NH2" Residue "a PHE 43": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a ARG 45": "NH1" <-> "NH2" Residue "a TYR 48": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a ARG 50": "NH1" <-> "NH2" Residue "a ARG 53": "NH1" <-> "NH2" Residue "a ASP 56": "OD1" <-> "OD2" Residue "b ARG 15": "NH1" <-> "NH2" Residue "b ARG 52": "NH1" <-> "NH2" Residue "b ARG 53": "NH1" <-> "NH2" Residue "b TYR 58": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b ARG 62": "NH1" <-> "NH2" Residue "b ARG 67": "NH1" <-> "NH2" Residue "b ARG 72": "NH1" <-> "NH2" Residue "d ASP 6": "OD1" <-> "OD2" Residue "d GLU 18": "OE1" <-> "OE2" Residue "d ARG 47": "NH1" <-> "NH2" Residue "d TYR 70": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d ARG 75": "NH1" <-> "NH2" Residue "d ARG 82": "NH1" <-> "NH2" Residue "d ASP 83": "OD1" <-> "OD2" Residue "d ARG 87": "NH1" <-> "NH2" Residue "d ARG 102": "NH1" <-> "NH2" Residue "d ARG 116": "NH1" <-> "NH2" Residue "e PHE 6": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "e ARG 8": "NH1" <-> "NH2" Residue "e PHE 38": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "e ARG 45": "NH1" <-> "NH2" Residue "e ARG 48": "NH1" <-> "NH2" Residue "e ARG 69": "NH1" <-> "NH2" Residue "e ARG 74": "NH1" <-> "NH2" Residue "e GLU 76": "OE1" <-> "OE2" Residue "e ARG 77": "NH1" <-> "NH2" Residue "e ARG 86": "NH1" <-> "NH2" Residue "e ARG 97": "NH1" <-> "NH2" Residue "f ARG 8": "NH1" <-> "NH2" Residue "f PHE 24": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "f ARG 32": "NH1" <-> "NH2" Residue "f PHE 36": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "f ARG 37": "NH1" <-> "NH2" Residue "f ARG 45": "NH1" <-> "NH2" Residue "g GLU 48": "OE1" <-> "OE2" Residue "g GLU 70": "OE1" <-> "OE2" Residue "g ARG 72": "NH1" <-> "NH2" Residue "g PHE 79": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "g PHE 80": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "g TYR 93": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "g ARG 103": "NH1" <-> "NH2" Residue "g ARG 108": "NH1" <-> "NH2" Residue "g GLU 113": "OE1" <-> "OE2" Residue "g ARG 116": "NH1" <-> "NH2" Residue "g ARG 117": "NH1" <-> "NH2" Residue "g GLU 141": "OE1" <-> "OE2" Residue "h ARG 52": "NH1" <-> "NH2" Residue "h PHE 53": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "h TYR 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "h ARG 110": "NH1" <-> "NH2" Residue "h ARG 114": "NH1" <-> "NH2" Residue "h TYR 124": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "h GLU 133": "OE1" <-> "OE2" Residue "h ARG 141": "NH1" <-> "NH2" Residue "h ARG 148": "NH1" <-> "NH2" Residue "h ARG 149": "NH1" <-> "NH2" Residue "h ARG 154": "NH1" <-> "NH2" Residue "h ARG 163": "NH1" <-> "NH2" Residue "h ARG 171": "NH1" <-> "NH2" Residue "h ARG 184": "NH1" <-> "NH2" Residue "i ARG 20": "NH1" <-> "NH2" Residue "i ARG 23": "NH1" <-> "NH2" Residue "i ARG 25": "NH1" <-> "NH2" Residue "i ARG 27": "NH1" <-> "NH2" Residue "i ARG 36": "NH1" <-> "NH2" Residue "i ARG 39": "NH1" <-> "NH2" Residue "i ARG 53": "NH1" <-> "NH2" Residue "i GLU 59": "OE1" <-> "OE2" Residue "i GLU 61": "OE1" <-> "OE2" Residue "i ARG 68": "NH1" <-> "NH2" Residue "i TYR 70": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "i ARG 71": "NH1" <-> "NH2" Residue "i ARG 89": "NH1" <-> "NH2" Residue "i ARG 94": "NH1" <-> "NH2" Residue "i PHE 95": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "i TYR 113": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "i PHE 114": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "i TYR 116": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "i ARG 123": "NH1" <-> "NH2" Residue "i ARG 128": "NH1" <-> "NH2" Residue "i ARG 149": "NH1" <-> "NH2" Residue "i ARG 158": "NH1" <-> "NH2" Residue "j TYR 33": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "j ARG 34": "NH1" <-> "NH2" Residue "j TYR 76": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "j ARG 80": "NH1" <-> "NH2" Residue "k ARG 34": "NH1" <-> "NH2" Residue "k ARG 43": "NH1" <-> "NH2" Residue "k ARG 48": "NH1" <-> "NH2" Residue "k TYR 49": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "k ARG 58": "NH1" <-> "NH2" Residue "k ARG 60": "NH1" <-> "NH2" Residue "k ARG 67": "NH1" <-> "NH2" Residue "k TYR 84": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "l TYR 36": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "l TYR 41": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "l GLU 45": "OE1" <-> "OE2" Residue "l GLU 47": "OE1" <-> "OE2" Residue "l ARG 48": "NH1" <-> "NH2" Residue "l TYR 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "l TYR 75": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "l ARG 100": "NH1" <-> "NH2" Residue "l GLU 115": "OE1" <-> "OE2" Residue "l ARG 117": "NH1" <-> "NH2" Residue "l ARG 125": "NH1" <-> "NH2" Residue "l TYR 131": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "l TYR 146": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "l TYR 155": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "l ARG 156": "NH1" <-> "NH2" Residue "l TYR 163": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "m ARG 13": "NH1" <-> "NH2" Residue "m ARG 22": "NH1" <-> "NH2" Residue "m TYR 33": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "m ARG 34": "NH1" <-> "NH2" Residue "m PHE 44": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "m ARG 50": "NH1" <-> "NH2" Residue "m ARG 55": "NH1" <-> "NH2" Residue "m GLU 60": "OE1" <-> "OE2" Residue "m PHE 69": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "m ARG 70": "NH1" <-> "NH2" Residue "m TYR 83": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "m ARG 91": "NH1" <-> "NH2" Residue "m ARG 94": "NH1" <-> "NH2" Residue "m ARG 99": "NH1" <-> "NH2" Residue "m ARG 108": "NH1" <-> "NH2" Residue "m PHE 110": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "n ARG 13": "NH1" <-> "NH2" Residue "n ARG 21": "NH1" <-> "NH2" Residue "n ARG 24": "NH1" <-> "NH2" Residue "n TYR 30": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "n ARG 32": "NH1" <-> "NH2" Residue "n ARG 33": "NH1" <-> "NH2" Residue "n ARG 37": "NH1" <-> "NH2" Residue "n ARG 39": "NH1" <-> "NH2" Residue "n ARG 44": "NH1" <-> "NH2" Residue "n ARG 46": "NH1" <-> "NH2" Residue "n ARG 51": "NH1" <-> "NH2" Residue "n ARG 60": "NH1" <-> "NH2" Residue "n ARG 67": "NH1" <-> "NH2" Residue "n PHE 70": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "n ARG 73": "NH1" <-> "NH2" Residue "n ARG 78": "NH1" <-> "NH2" Residue "n ARG 91": "NH1" <-> "NH2" Residue "n ASP 101": "OD1" <-> "OD2" Residue "n TYR 111": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "n ARG 118": "NH1" <-> "NH2" Residue "n ARG 121": "NH1" <-> "NH2" Residue "n TYR 133": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "o ARG 32": "NH1" <-> "NH2" Residue "o ARG 35": "NH1" <-> "NH2" Residue "o ARG 54": "NH1" <-> "NH2" Residue "o ASP 55": "OD1" <-> "OD2" Residue "o ARG 68": "NH1" <-> "NH2" Residue "o TYR 93": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "o ARG 96": "NH1" <-> "NH2" Residue "o ARG 102": "NH1" <-> "NH2" Residue "o ARG 104": "NH1" <-> "NH2" Residue "o ARG 105": "NH1" <-> "NH2" Residue "o ARG 109": "NH1" <-> "NH2" Residue "o ARG 112": "NH1" <-> "NH2" Residue "p ARG 5": "NH1" <-> "NH2" Residue "p ARG 27": "NH1" <-> "NH2" Residue "p ARG 44": "NH1" <-> "NH2" Residue "p ARG 46": "NH1" <-> "NH2" Residue "p ARG 47": "NH1" <-> "NH2" Residue "p ARG 62": "NH1" <-> "NH2" Residue "p PHE 63": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "p GLU 64": "OE1" <-> "OE2" Residue "p ARG 70": "NH1" <-> "NH2" Residue "p ARG 71": "NH1" <-> "NH2" Residue "p ARG 73": "NH1" <-> "NH2" Residue "p ARG 84": "NH1" <-> "NH2" Residue "p ARG 86": "NH1" <-> "NH2" Residue "p ARG 103": "NH1" <-> "NH2" Residue "p PHE 117": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "p TYR 126": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "p ARG 139": "NH1" <-> "NH2" Residue "p ARG 144": "NH1" <-> "NH2" Residue "p ARG 145": "NH1" <-> "NH2" Residue "q ARG 9": "NH1" <-> "NH2" Residue "q ARG 18": "NH1" <-> "NH2" Residue "q ARG 32": "NH1" <-> "NH2" Residue "q ASP 35": "OD1" <-> "OD2" Residue "q TYR 51": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "q ARG 61": "NH1" <-> "NH2" Residue "q ARG 63": "NH1" <-> "NH2" Residue "q GLU 66": "OE1" <-> "OE2" Residue "q TYR 75": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "q ASP 76": "OD1" <-> "OD2" Residue "q ARG 98": "NH1" <-> "NH2" Residue "q ARG 102": "NH1" <-> "NH2" Residue "q ASP 110": "OD1" <-> "OD2" Residue "q GLU 120": "OE1" <-> "OE2" Residue "r ARG 5": "NH1" <-> "NH2" Residue "r ARG 6": "NH1" <-> "NH2" Residue "r ASP 7": "OD1" <-> "OD2" Residue "r ARG 14": "NH1" <-> "NH2" Residue "r ARG 16": "NH1" <-> "NH2" Residue "r ARG 22": "NH1" <-> "NH2" Residue "r ARG 29": "NH1" <-> "NH2" Residue "r ASP 36": "OD1" <-> "OD2" Residue "r ARG 37": "NH1" <-> "NH2" Residue "r ASP 46": "OD1" <-> "OD2" Residue "r ARG 60": "NH1" <-> "NH2" Residue "r ARG 63": "NH1" <-> "NH2" Residue "r ARG 64": "NH1" <-> "NH2" Residue "r GLU 65": "OE1" <-> "OE2" Residue "s ARG 87": "NH1" <-> "NH2" Residue "s TYR 90": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "s TYR 100": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "s ARG 101": "NH1" <-> "NH2" Time to flip residues: 0.17s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/modules/chem_data/mon_lib" Total number of atoms: 65912 Number of models: 1 Model: "" Number of chains: 56 Chain: "A" Number of atoms: 956 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 956 Classifications: {'peptide': 117} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 112} Chain: "B" Number of atoms: 1435 Number of conformers: 1 Conformer: "" Number of residues, atoms: 182, 1435 Classifications: {'peptide': 182} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 11, 'TRANS': 168} Chain: "C" Number of atoms: 1726 Number of conformers: 1 Conformer: "" Number of residues, atoms: 209, 1726 Classifications: {'peptide': 209} Link IDs: {'PTRANS': 15, 'TRANS': 193} Chain: "D" Number of atoms: 3424 Number of conformers: 1 Conformer: "" Number of residues, atoms: 428, 3424 Classifications: {'peptide': 428} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 24, 'TRANS': 402} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'2MR:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "E" Number of atoms: 1679 Number of conformers: 1 Conformer: "" Number of residues, atoms: 214, 1679 Classifications: {'peptide': 214} Link IDs: {'PCIS': 2, 'PTRANS': 15, 'TRANS': 196} Chain: "F" Number of atoms: 3367 Number of conformers: 1 Conformer: "" Number of residues, atoms: 439, 3367 Classifications: {'peptide': 439} Link IDs: {'PCIS': 2, 'PTRANS': 24, 'TRANS': 412} Chain: "G" Number of atoms: 5146 Number of conformers: 1 Conformer: "" Number of residues, atoms: 677, 5146 Classifications: {'peptide': 677} Link IDs: {'PTRANS': 33, 'TRANS': 643} Chain breaks: 1 Chain: "H" Number of atoms: 2571 Number of conformers: 1 Conformer: "" Number of residues, atoms: 315, 2571 Classifications: {'peptide': 315} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 305} Chain: "I" Number of atoms: 1485 Number of conformers: 1 Conformer: "" Number of residues, atoms: 186, 1485 Classifications: {'peptide': 186} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 8, 'TRANS': 175} Chain: "J" Number of atoms: 1351 Number of conformers: 1 Conformer: "" Number of residues, atoms: 167, 1351 Classifications: {'peptide': 167} Link IDs: {'PCIS': 1, 'PTRANS': 1, 'TRANS': 164} Chain: "K" Number of atoms: 771 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 771 Classifications: {'peptide': 93} Link IDs: {'PTRANS': 1, 'TRANS': 91} Chain: "L" Number of atoms: 4606 Number of conformers: 1 Conformer: "" Number of residues, atoms: 577, 4606 Classifications: {'peptide': 577} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 564} Chain: "M" Number of atoms: 3617 Number of conformers: 1 Conformer: "" Number of residues, atoms: 446, 3617 Classifications: {'peptide': 446} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 9, 'TRANS': 434} Chain: "N" Number of atoms: 2796 Number of conformers: 1 Conformer: "" Number of residues, atoms: 341, 2796 Classifications: {'peptide': 341} Link IDs: {'PTRANS': 7, 'TRANS': 333} Chain: "O" Number of atoms: 3007 Number of conformers: 1 Conformer: "" Number of residues, atoms: 368, 3007 Classifications: {'peptide': 368} Link IDs: {'PTRANS': 19, 'TRANS': 348} Chain: "P" Number of atoms: 3032 Number of conformers: 1 Conformer: "" Number of residues, atoms: 377, 3032 Classifications: {'peptide': 377} Link IDs: {'PTRANS': 21, 'TRANS': 355} Chain: "Q" Number of atoms: 1054 Number of conformers: 1 Conformer: "" Number of residues, atoms: 130, 1054 Classifications: {'peptide': 130} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 120} Chain: "R" Number of atoms: 716 Number of conformers: 1 Conformer: "" Number of residues, atoms: 89, 716 Classifications: {'peptide': 89} Link IDs: {'PTRANS': 5, 'TRANS': 83} Chain: "T" Number of atoms: 615 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 615 Classifications: {'peptide': 77} Link IDs: {'PTRANS': 3, 'TRANS': 73} Chain: "U" Number of atoms: 684 Number of conformers: 1 Conformer: "" Number of residues, atoms: 85, 684 Classifications: {'peptide': 85} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 80} Chain: "V" Number of atoms: 922 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 922 Classifications: {'peptide': 118} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 110} Chain: "W" Number of atoms: 968 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 968 Classifications: {'peptide': 114} Link IDs: {'PTRANS': 5, 'TRANS': 108} Chain: "X" Number of atoms: 1383 Number of conformers: 1 Conformer: "" Number of residues, atoms: 174, 1383 Classifications: {'peptide': 174} Link IDs: {'PTRANS': 10, 'TRANS': 163} Chain: "Y" Number of atoms: 1277 Number of conformers: 1 Conformer: "" Number of residues, atoms: 167, 1277 Classifications: {'peptide': 167} Link IDs: {'PTRANS': 9, 'TRANS': 157} Chain: "Z" Number of atoms: 1201 Number of conformers: 1 Conformer: "" Number of residues, atoms: 146, 1201 Classifications: {'peptide': 146} Link IDs: {'PTRANS': 12, 'TRANS': 133} Chain: "a" Number of atoms: 601 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 601 Classifications: {'peptide': 73} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 68} Chain: "b" Number of atoms: 519 Number of conformers: 1 Conformer: "" Number of residues, atoms: 66, 519 Classifications: {'peptide': 66} Link IDs: {'PTRANS': 2, 'TRANS': 63} Chain: "d" Number of atoms: 907 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 907 Classifications: {'peptide': 115} Link IDs: {'PTRANS': 8, 'TRANS': 106} Chain: "e" Number of atoms: 828 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 828 Classifications: {'peptide': 100} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 95} Chain: "f" Number of atoms: 437 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 437 Classifications: {'peptide': 56} Link IDs: {'PTRANS': 3, 'TRANS': 52} Chain: "g" Number of atoms: 870 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 870 Classifications: {'peptide': 106} Link IDs: {'PTRANS': 6, 'TRANS': 99} Chain: "h" Number of atoms: 1234 Number of conformers: 1 Conformer: "" Number of residues, atoms: 145, 1234 Classifications: {'peptide': 145} Link IDs: {'PTRANS': 7, 'TRANS': 137} Chain: "i" Number of atoms: 1302 Number of conformers: 1 Conformer: "" Number of residues, atoms: 161, 1302 Classifications: {'peptide': 161} Link IDs: {'PTRANS': 11, 'TRANS': 149} Chain: "j" Number of atoms: 489 Number of conformers: 1 Conformer: "" Number of residues, atoms: 59, 489 Classifications: {'peptide': 59} Link IDs: {'PTRANS': 5, 'TRANS': 53} Chain: "k" Number of atoms: 671 Number of conformers: 1 Conformer: "" Number of residues, atoms: 84, 671 Classifications: {'peptide': 84} Link IDs: {'PTRANS': 5, 'TRANS': 78} Chain: "l" Number of atoms: 1201 Number of conformers: 1 Conformer: "" Number of residues, atoms: 144, 1201 Classifications: {'peptide': 144} Link IDs: {'PTRANS': 14, 'TRANS': 129} Chain: "m" Number of atoms: 892 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 892 Classifications: {'peptide': 108} Link IDs: {'PTRANS': 3, 'TRANS': 104} Chain: "n" Number of atoms: 1152 Number of conformers: 1 Conformer: "" Number of residues, atoms: 134, 1152 Classifications: {'peptide': 134} Link IDs: {'PTRANS': 6, 'TRANS': 127} Chain: "o" Number of atoms: 937 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 937 Classifications: {'peptide': 112} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 104} Chain: "p" Number of atoms: 1266 Number of conformers: 1 Conformer: "" Number of residues, atoms: 151, 1266 Classifications: {'peptide': 151} Link IDs: {'PTRANS': 7, 'TRANS': 143} Chain: "q" Number of atoms: 1130 Number of conformers: 1 Conformer: "" Number of residues, atoms: 135, 1130 Classifications: {'peptide': 135} Link IDs: {'PTRANS': 9, 'TRANS': 125} Chain: "r" Number of atoms: 724 Number of conformers: 1 Conformer: "" Number of residues, atoms: 89, 724 Classifications: {'peptide': 89} Link IDs: {'PTRANS': 9, 'TRANS': 79} Chain breaks: 1 Chain: "s" Number of atoms: 456 Number of conformers: 1 Conformer: "" Number of residues, atoms: 62, 456 Classifications: {'peptide': 62} Link IDs: {'PTRANS': 7, 'TRANS': 54} Chain: "B" Number of atoms: 76 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 76 Unusual residues: {'3PE': 2, 'SF4': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 34 Unresolved non-hydrogen angles: 34 Unresolved non-hydrogen dihedrals: 34 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: "I" Number of atoms: 16 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 16 Unusual residues: {'SF4': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "L" Number of atoms: 35 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 35 Unusual residues: {'3PE': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 16 Chain: "M" Number of atoms: 55 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 55 Unusual residues: {'CDL': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 45 Unresolved non-hydrogen angles: 45 Unresolved non-hydrogen dihedrals: 45 Chain: "O" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'DGT': 1} Classifications: {'undetermined': 1} Chain: "P" Number of atoms: 89 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 89 Unusual residues: {'CDL': 1, 'NDP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 59 Unresolved non-hydrogen angles: 59 Unresolved non-hydrogen dihedrals: 59 Chain: "R" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "T" Number of atoms: 37 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 37 Unusual residues: {'EHZ': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Chain: "U" Number of atoms: 37 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 37 Unusual residues: {'EHZ': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Chain: "Y" Number of atoms: 67 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 67 Unusual residues: {'3PE': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 86 Unresolved non-hydrogen angles: 86 Unresolved non-hydrogen dihedrals: 86 List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 1906 SG CYS B 161 79.515 86.314 100.840 1.00 68.05 S ATOM 2137 SG CYS B 191 83.060 88.040 96.254 1.00 65.77 S ATOM 1399 SG CYS B 96 85.871 88.755 101.561 1.00 76.48 S ATOM 1405 SG CYS B 97 81.020 91.643 102.003 1.00 74.58 S ATOM 8363 SG CYS E 128 103.322 57.930 32.368 1.00102.28 S ATOM 8397 SG CYS E 133 106.241 57.530 32.441 1.00107.82 S ATOM 8678 SG CYS E 169 103.401 53.222 36.502 1.00100.12 S ATOM 8701 SG CYS E 173 106.255 53.303 36.043 1.00107.87 S ATOM 11986 SG CYS F 397 93.413 50.769 57.274 1.00 66.39 S ATOM 12006 SG CYS F 400 96.750 54.370 53.647 1.00 67.40 S ATOM 12328 SG CYS F 440 96.485 48.533 52.168 1.00 74.05 S ATOM 11967 SG CYS F 394 91.065 51.400 51.691 1.00 68.67 S ATOM 13420 SG CYS G 147 83.231 64.025 70.503 1.00 65.07 S ATOM 13359 SG CYS G 138 85.226 70.270 70.391 1.00 66.85 S ATOM 13380 SG CYS G 141 79.648 68.280 67.992 1.00 65.08 S ATOM 13782 SG CYS G 193 81.522 55.671 63.294 1.00 62.36 S ATOM 13758 SG CYS G 190 82.150 60.546 58.877 1.00 63.04 S ATOM 13806 SG CYS G 196 77.385 56.412 58.839 1.00 64.96 S ATOM 14135 SG CYS G 240 78.154 60.533 63.874 1.00 62.30 S ATOM 12859 SG CYS G 74 86.285 50.013 64.072 1.00 66.19 S ATOM 12944 SG CYS G 85 89.036 52.353 66.152 1.00 63.16 S ATOM 12969 SG CYS G 88 90.683 47.925 67.561 1.00 67.33 S ATOM 13070 SG CYS G 102 88.303 46.301 66.187 1.00 66.37 S ATOM 21330 SG CYS I 160 84.691 83.573 88.750 1.00 64.52 S ATOM 21304 SG CYS I 157 79.656 87.764 89.116 1.00 63.43 S ATOM 21351 SG CYS I 163 82.003 85.488 83.706 1.00 61.87 S ATOM 21076 SG CYS I 128 78.694 81.626 87.777 1.00 58.36 S ATOM 21380 SG CYS I 167 82.426 83.479 75.429 1.00 65.27 S ATOM 21006 SG CYS I 118 75.987 83.232 74.147 1.00 67.80 S ATOM 21048 SG CYS I 124 78.189 81.381 79.769 1.00 61.52 S ATOM 21025 SG CYS I 121 80.403 78.189 75.192 1.00 67.56 S ATOM 42482 SG CYS R 87 84.482 83.815 59.736 1.00 65.11 S ATOM 42658 SG CYS R 111 81.667 81.502 60.955 1.00 65.23 S ATOM 42680 SG CYS R 114 81.461 84.735 61.198 1.00 64.88 S Time building chain proxies: 24.67, per 1000 atoms: 0.37 Number of scatterers: 65912 At special positions: 0 Unit cell: (140.432, 192.832, 300.776, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 1 29.99 Fe 28 26.01 S 478 16.00 P 19 15.00 O 11787 8.00 N 10947 7.00 C 42652 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS X 80 " - pdb=" SG CYS X 113 " distance=2.03 Simple disulfide: pdb=" SG CYS X 90 " - pdb=" SG CYS X 103 " distance=2.04 Simple disulfide: pdb=" SG CYS o 67 " - pdb=" SG CYS o 78 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=3, symmetry=0 Number of additional bonds: simple=3, symmetry=0 Coordination: Other bonds: Time building additional restraints: 21.93 Conformation dependent library (CDL) restraints added in 7.2 seconds Dynamic metal coordination Iron sulfur cluster coordination pdb=" FES E 301 " pdb="FE1 FES E 301 " - pdb=" SG CYS E 133 " pdb="FE2 FES E 301 " - pdb=" SG CYS E 173 " pdb="FE1 FES E 301 " - pdb=" SG CYS E 128 " pdb="FE2 FES E 301 " - pdb=" SG CYS E 169 " pdb=" FES G 803 " pdb="FE1 FES G 803 " - pdb=" SG CYS G 85 " pdb="FE1 FES G 803 " - pdb=" SG CYS G 74 " pdb="FE2 FES G 803 " - pdb=" SG CYS G 88 " pdb="FE2 FES G 803 " - pdb=" SG CYS G 102 " pdb=" SF4 B 301 " pdb="FE1 SF4 B 301 " - pdb=" SG CYS B 161 " pdb="FE3 SF4 B 301 " - pdb=" SG CYS B 96 " pdb="FE2 SF4 B 301 " - pdb=" SG CYS B 191 " pdb="FE4 SF4 B 301 " - pdb=" SG CYS B 97 " pdb=" SF4 F 502 " pdb="FE2 SF4 F 502 " - pdb=" SG CYS F 400 " pdb="FE3 SF4 F 502 " - pdb=" SG CYS F 440 " pdb="FE1 SF4 F 502 " - pdb=" SG CYS F 397 " pdb="FE4 SF4 F 502 " - pdb=" SG CYS F 394 " pdb=" SF4 G 801 " pdb="FE3 SF4 G 801 " - pdb=" NE2 HIS G 134 " pdb="FE1 SF4 G 801 " - pdb=" SG CYS G 147 " pdb="FE4 SF4 G 801 " - pdb=" SG CYS G 141 " pdb="FE2 SF4 G 801 " - pdb=" SG CYS G 138 " pdb=" SF4 G 802 " pdb="FE1 SF4 G 802 " - pdb=" SG CYS G 193 " pdb="FE3 SF4 G 802 " - pdb=" SG CYS G 196 " pdb="FE4 SF4 G 802 " - pdb=" SG CYS G 240 " pdb="FE2 SF4 G 802 " - pdb=" SG CYS G 190 " pdb=" SF4 I 301 " pdb="FE2 SF4 I 301 " - pdb=" SG CYS I 157 " pdb="FE3 SF4 I 301 " - pdb=" SG CYS I 163 " pdb="FE4 SF4 I 301 " - pdb=" SG CYS I 128 " pdb="FE1 SF4 I 301 " - pdb=" SG CYS I 160 " pdb=" SF4 I 302 " pdb="FE1 SF4 I 302 " - pdb=" SG CYS I 167 " pdb="FE4 SF4 I 302 " - pdb=" SG CYS I 121 " pdb="FE3 SF4 I 302 " - pdb=" SG CYS I 124 " pdb="FE2 SF4 I 302 " - pdb=" SG CYS I 118 " Number of angles added : 81 Zn2+ tetrahedral coordination pdb=" ZN R 201 " pdb="ZN ZN R 201 " - pdb=" NE2 HIS R 96 " pdb="ZN ZN R 201 " - pdb=" SG CYS R 114 " pdb="ZN ZN R 201 " - pdb=" SG CYS R 111 " pdb="ZN ZN R 201 " - pdb=" SG CYS R 87 " Number of angles added : 3 16086 Ramachandran restraints generated. 8043 Oldfield, 0 Emsley, 8043 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 15200 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 338 helices and 24 sheets defined 52.0% alpha, 3.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 6.58 Creating SS restraints... Processing helix chain 'A' and resid 2 through 25 Processing helix chain 'A' and resid 57 through 82 Proline residue: A 76 - end of helix removed outlier: 5.370A pdb=" N ILE A 79 " --> pdb=" O LEU A 75 " (cutoff:3.500A) removed outlier: 4.864A pdb=" N LYS A 82 " --> pdb=" O ILE A 78 " (cutoff:3.500A) Processing helix chain 'A' and resid 86 through 110 Processing helix chain 'B' and resid 46 through 51 Processing helix chain 'B' and resid 67 through 85 Processing helix chain 'B' and resid 96 through 103 removed outlier: 4.368A pdb=" N GLU B 100 " --> pdb=" O CYS B 96 " (cutoff:3.500A) Processing helix chain 'B' and resid 112 through 114 No H-bonds generated for 'chain 'B' and resid 112 through 114' Processing helix chain 'B' and resid 136 through 148 Proline residue: B 140 - end of helix Processing helix chain 'B' and resid 159 through 164 Processing helix chain 'B' and resid 166 through 168 No H-bonds generated for 'chain 'B' and resid 166 through 168' Processing helix chain 'B' and resid 195 through 211 Processing helix chain 'B' and resid 215 through 218 No H-bonds generated for 'chain 'B' and resid 215 through 218' Processing helix chain 'C' and resid 54 through 70 Processing helix chain 'C' and resid 92 through 104 removed outlier: 3.655A pdb=" N VAL C 95 " --> pdb=" O PRO C 92 " (cutoff:3.500A) removed outlier: 4.673A pdb=" N VAL C 96 " --> pdb=" O GLU C 93 " (cutoff:3.500A) Proline residue: C 97 - end of helix removed outlier: 3.556A pdb=" N GLN C 100 " --> pdb=" O PRO C 97 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N LYS C 103 " --> pdb=" O GLN C 100 " (cutoff:3.500A) Processing helix chain 'C' and resid 163 through 175 removed outlier: 4.287A pdb=" N TRP C 167 " --> pdb=" O ALA C 164 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N GLU C 169 " --> pdb=" O ASN C 166 " (cutoff:3.500A) Processing helix chain 'D' and resid 46 through 51 Processing helix chain 'D' and resid 125 through 131 Processing helix chain 'D' and resid 136 through 143 Proline residue: D 139 - end of helix Processing helix chain 'D' and resid 150 through 164 Processing helix chain 'D' and resid 170 through 199 Processing helix chain 'D' and resid 202 through 223 removed outlier: 3.747A pdb=" N GLU D 211 " --> pdb=" O TRP D 207 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N GLU D 213 " --> pdb=" O PHE D 209 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N LYS D 214 " --> pdb=" O GLU D 210 " (cutoff:3.500A) Processing helix chain 'D' and resid 245 through 267 removed outlier: 4.021A pdb=" N ALA D 257 " --> pdb=" O ALA D 253 " (cutoff:3.500A) removed outlier: 4.832A pdb=" N GLU D 258 " --> pdb=" O SER D 254 " (cutoff:3.500A) Processing helix chain 'D' and resid 271 through 277 Processing helix chain 'D' and resid 285 through 290 Processing helix chain 'D' and resid 295 through 301 Processing helix chain 'D' and resid 307 through 310 No H-bonds generated for 'chain 'D' and resid 307 through 310' Processing helix chain 'D' and resid 315 through 318 Processing helix chain 'D' and resid 331 through 354 Processing helix chain 'D' and resid 373 through 376 No H-bonds generated for 'chain 'D' and resid 373 through 376' Processing helix chain 'D' and resid 380 through 392 Processing helix chain 'D' and resid 432 through 443 removed outlier: 4.059A pdb=" N LEU D 440 " --> pdb=" O HIS D 436 " (cutoff:3.500A) removed outlier: 4.223A pdb=" N GLU D 441 " --> pdb=" O LEU D 437 " (cutoff:3.500A) removed outlier: 4.589A pdb=" N LYS D 442 " --> pdb=" O ALA D 438 " (cutoff:3.500A) Processing helix chain 'D' and resid 449 through 459 Processing helix chain 'E' and resid 50 through 62 removed outlier: 3.982A pdb=" N SER E 61 " --> pdb=" O GLU E 57 " (cutoff:3.500A) removed outlier: 4.481A pdb=" N ILE E 62 " --> pdb=" O ALA E 58 " (cutoff:3.500A) Processing helix chain 'E' and resid 68 through 83 removed outlier: 4.197A pdb=" N ILE E 73 " --> pdb=" O GLY E 70 " (cutoff:3.500A) Proline residue: E 74 - end of helix Processing helix chain 'E' and resid 88 through 98 Processing helix chain 'E' and resid 102 through 111 Processing helix chain 'E' and resid 138 through 149 removed outlier: 3.575A pdb=" N LEU E 142 " --> pdb=" O SER E 138 " (cutoff:3.500A) Processing helix chain 'E' and resid 173 through 175 No H-bonds generated for 'chain 'E' and resid 173 through 175' Processing helix chain 'E' and resid 191 through 203 Processing helix chain 'F' and resid 68 through 73 Processing helix chain 'F' and resid 80 through 86 Processing helix chain 'F' and resid 88 through 98 Processing helix chain 'F' and resid 110 through 117 removed outlier: 3.501A pdb=" N MET F 117 " --> pdb=" O LYS F 113 " (cutoff:3.500A) Processing helix chain 'F' and resid 141 through 163 removed outlier: 3.697A pdb=" N ILE F 145 " --> pdb=" O LYS F 141 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N MET F 146 " --> pdb=" O ASP F 142 " (cutoff:3.500A) Proline residue: F 150 - end of helix removed outlier: 3.564A pdb=" N LEU F 153 " --> pdb=" O ASP F 149 " (cutoff:3.500A) Processing helix chain 'F' and resid 178 through 194 Processing helix chain 'F' and resid 201 through 203 No H-bonds generated for 'chain 'F' and resid 201 through 203' Processing helix chain 'F' and resid 219 through 222 Processing helix chain 'F' and resid 224 through 232 Processing helix chain 'F' and resid 250 through 252 No H-bonds generated for 'chain 'F' and resid 250 through 252' Processing helix chain 'F' and resid 260 through 272 removed outlier: 3.598A pdb=" N ALA F 266 " --> pdb=" O THR F 262 " (cutoff:3.500A) Proline residue: F 267 - end of helix Processing helix chain 'F' and resid 274 through 279 Processing helix chain 'F' and resid 311 through 317 Processing helix chain 'F' and resid 344 through 347 No H-bonds generated for 'chain 'F' and resid 344 through 347' Processing helix chain 'F' and resid 354 through 357 No H-bonds generated for 'chain 'F' and resid 354 through 357' Processing helix chain 'F' and resid 378 through 391 Processing helix chain 'F' and resid 398 through 416 removed outlier: 3.827A pdb=" N GLU F 402 " --> pdb=" O THR F 398 " (cutoff:3.500A) removed outlier: 4.307A pdb=" N ILE F 404 " --> pdb=" O CYS F 400 " (cutoff:3.500A) removed outlier: 5.175A pdb=" N GLY F 405 " --> pdb=" O ARG F 401 " (cutoff:3.500A) Processing helix chain 'F' and resid 421 through 434 removed outlier: 3.520A pdb=" N MET F 426 " --> pdb=" O GLU F 423 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N LEU F 427 " --> pdb=" O ILE F 424 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N ILE F 430 " --> pdb=" O LEU F 427 " (cutoff:3.500A) Processing helix chain 'F' and resid 442 through 471 Proline residue: F 449 - end of helix removed outlier: 3.561A pdb=" N ARG F 458 " --> pdb=" O ILE F 454 " (cutoff:3.500A) Proline residue: F 459 - end of helix Processing helix chain 'G' and resid 59 through 66 Processing helix chain 'G' and resid 101 through 103 No H-bonds generated for 'chain 'G' and resid 101 through 103' Processing helix chain 'G' and resid 117 through 133 removed outlier: 4.664A pdb=" N ASN G 133 " --> pdb=" O PHE G 129 " (cutoff:3.500A) Processing helix chain 'G' and resid 148 through 156 Processing helix chain 'G' and resid 165 through 167 No H-bonds generated for 'chain 'G' and resid 165 through 167' Processing helix chain 'G' and resid 187 through 189 No H-bonds generated for 'chain 'G' and resid 187 through 189' Processing helix chain 'G' and resid 195 through 202 Processing helix chain 'G' and resid 215 through 217 No H-bonds generated for 'chain 'G' and resid 215 through 217' Processing helix chain 'G' and resid 233 through 239 Processing helix chain 'G' and resid 302 through 312 removed outlier: 4.736A pdb=" N CYS G 308 " --> pdb=" O SER G 304 " (cutoff:3.500A) removed outlier: 6.412A pdb=" N ASP G 309 " --> pdb=" O ARG G 305 " (cutoff:3.500A) removed outlier: 5.368A pdb=" N GLY G 310 " --> pdb=" O PHE G 306 " (cutoff:3.500A) removed outlier: 4.191A pdb=" N LEU G 311 " --> pdb=" O ALA G 307 " (cutoff:3.500A) removed outlier: 4.544A pdb=" N LYS G 312 " --> pdb=" O CYS G 308 " (cutoff:3.500A) Processing helix chain 'G' and resid 333 through 347 Processing helix chain 'G' and resid 361 through 374 Processing helix chain 'G' and resid 393 through 395 No H-bonds generated for 'chain 'G' and resid 393 through 395' Processing helix chain 'G' and resid 402 through 407 removed outlier: 4.155A pdb=" N GLU G 406 " --> pdb=" O ILE G 402 " (cutoff:3.500A) removed outlier: 4.202A pdb=" N GLU G 407 " --> pdb=" O ALA G 403 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 402 through 407' Processing helix chain 'G' and resid 418 through 421 No H-bonds generated for 'chain 'G' and resid 418 through 421' Processing helix chain 'G' and resid 423 through 435 Processing helix chain 'G' and resid 460 through 468 removed outlier: 3.532A pdb=" N VAL G 466 " --> pdb=" O VAL G 463 " (cutoff:3.500A) Processing helix chain 'G' and resid 472 through 479 Processing helix chain 'G' and resid 489 through 494 Processing helix chain 'G' and resid 498 through 511 removed outlier: 4.360A pdb=" N LYS G 510 " --> pdb=" O GLU G 506 " (cutoff:3.500A) Processing helix chain 'G' and resid 528 through 534 Processing helix chain 'G' and resid 540 through 546 Processing helix chain 'G' and resid 582 through 585 removed outlier: 3.601A pdb=" N ILE G 585 " --> pdb=" O GLY G 582 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 582 through 585' Processing helix chain 'G' and resid 595 through 597 No H-bonds generated for 'chain 'G' and resid 595 through 597' Processing helix chain 'G' and resid 625 through 636 Processing helix chain 'G' and resid 645 through 655 Processing helix chain 'G' and resid 657 through 660 No H-bonds generated for 'chain 'G' and resid 657 through 660' Processing helix chain 'G' and resid 693 through 697 Processing helix chain 'G' and resid 701 through 705 Processing helix chain 'G' and resid 707 through 725 Processing helix chain 'H' and resid 2 through 38 removed outlier: 4.420A pdb=" N LEU H 29 " --> pdb=" O ALA H 25 " (cutoff:3.500A) removed outlier: 4.051A pdb=" N LEU H 30 " --> pdb=" O PHE H 26 " (cutoff:3.500A) Processing helix chain 'H' and resid 52 through 64 Proline residue: H 55 - end of helix removed outlier: 3.609A pdb=" N PHE H 63 " --> pdb=" O ILE H 60 " (cutoff:3.500A) Processing helix chain 'H' and resid 72 through 95 removed outlier: 4.204A pdb=" N TYR H 75 " --> pdb=" O LEU H 72 " (cutoff:3.500A) removed outlier: 4.670A pdb=" N LEU H 76 " --> pdb=" O SER H 73 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N TYR H 78 " --> pdb=" O TYR H 75 " (cutoff:3.500A) removed outlier: 4.266A pdb=" N SER H 81 " --> pdb=" O TYR H 78 " (cutoff:3.500A) Proline residue: H 82 - end of helix removed outlier: 4.421A pdb=" N PHE H 87 " --> pdb=" O PHE H 84 " (cutoff:3.500A) removed outlier: 4.277A pdb=" N VAL H 92 " --> pdb=" O SER H 89 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N CYS H 95 " --> pdb=" O VAL H 92 " (cutoff:3.500A) Processing helix chain 'H' and resid 108 through 130 removed outlier: 3.808A pdb=" N GLY H 119 " --> pdb=" O CYS H 115 " (cutoff:3.500A) removed outlier: 5.308A pdb=" N VAL H 120 " --> pdb=" O THR H 116 " (cutoff:3.500A) removed outlier: 4.924A pdb=" N TYR H 121 " --> pdb=" O SER H 117 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N THR H 122 " --> pdb=" O LEU H 118 " (cutoff:3.500A) Processing helix chain 'H' and resid 133 through 164 removed outlier: 3.974A pdb=" N VAL H 151 " --> pdb=" O ILE H 147 " (cutoff:3.500A) removed outlier: 4.189A pdb=" N SER H 152 " --> pdb=" O SER H 148 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N LEU H 155 " --> pdb=" O VAL H 151 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N PHE H 160 " --> pdb=" O ILE H 156 " (cutoff:3.500A) Processing helix chain 'H' and resid 169 through 175 removed outlier: 3.635A pdb=" N TYR H 175 " --> pdb=" O PHE H 172 " (cutoff:3.500A) Processing helix chain 'H' and resid 186 through 199 Processing helix chain 'H' and resid 217 through 221 removed outlier: 3.974A pdb=" N GLU H 221 " --> pdb=" O PHE H 218 " (cutoff:3.500A) Processing helix chain 'H' and resid 224 through 249 Processing helix chain 'H' and resid 257 through 274 Processing helix chain 'H' and resid 282 through 290 Processing helix chain 'H' and resid 293 through 314 removed outlier: 3.772A pdb=" N GLY H 306 " --> pdb=" O LEU H 302 " (cutoff:3.500A) Processing helix chain 'I' and resid 55 through 67 Processing helix chain 'I' and resid 69 through 83 removed outlier: 4.113A pdb=" N PHE I 83 " --> pdb=" O LEU I 79 " (cutoff:3.500A) Processing helix chain 'I' and resid 123 through 127 Processing helix chain 'I' and resid 162 through 166 Processing helix chain 'I' and resid 185 through 188 Processing helix chain 'I' and resid 192 through 201 Processing helix chain 'I' and resid 203 through 213 Processing helix chain 'J' and resid 2 through 19 Processing helix chain 'J' and resid 23 through 43 Processing helix chain 'J' and resid 49 through 58 Processing helix chain 'J' and resid 62 through 69 removed outlier: 3.811A pdb=" N PHE J 66 " --> pdb=" O MET J 62 " (cutoff:3.500A) Processing helix chain 'J' and resid 73 through 75 No H-bonds generated for 'chain 'J' and resid 73 through 75' Processing helix chain 'J' and resid 82 through 101 Processing helix chain 'J' and resid 122 through 125 removed outlier: 3.652A pdb=" N TYR J 125 " --> pdb=" O MET J 122 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 122 through 125' Processing helix chain 'J' and resid 134 through 136 No H-bonds generated for 'chain 'J' and resid 134 through 136' Processing helix chain 'J' and resid 143 through 162 Processing helix chain 'K' and resid 2 through 5 No H-bonds generated for 'chain 'K' and resid 2 through 5' Processing helix chain 'K' and resid 8 through 22 Processing helix chain 'K' and resid 29 through 52 Processing helix chain 'K' and resid 56 through 85 removed outlier: 3.528A pdb=" N THR K 65 " --> pdb=" O MET K 62 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N VAL K 68 " --> pdb=" O THR K 65 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N SER K 80 " --> pdb=" O ILE K 77 " (cutoff:3.500A) Processing helix chain 'K' and resid 90 through 92 No H-bonds generated for 'chain 'K' and resid 90 through 92' Processing helix chain 'L' and resid 6 through 31 removed outlier: 3.832A pdb=" N ASN L 13 " --> pdb=" O ILE L 9 " (cutoff:3.500A) Processing helix chain 'L' and resid 57 through 80 removed outlier: 4.100A pdb=" N GLU L 79 " --> pdb=" O PHE L 75 " (cutoff:3.500A) Processing helix chain 'L' and resid 87 through 106 Processing helix chain 'L' and resid 110 through 128 removed outlier: 4.009A pdb=" N CYS L 126 " --> pdb=" O LEU L 122 " (cutoff:3.500A) Processing helix chain 'L' and resid 134 through 162 removed outlier: 3.788A pdb=" N ALA L 159 " --> pdb=" O LEU L 155 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N TRP L 160 " --> pdb=" O LEU L 156 " (cutoff:3.500A) Processing helix chain 'L' and resid 169 through 171 No H-bonds generated for 'chain 'L' and resid 169 through 171' Processing helix chain 'L' and resid 174 through 176 No H-bonds generated for 'chain 'L' and resid 174 through 176' Processing helix chain 'L' and resid 180 through 196 Processing helix chain 'L' and resid 207 through 209 No H-bonds generated for 'chain 'L' and resid 207 through 209' Processing helix chain 'L' and resid 214 through 221 Processing helix chain 'L' and resid 225 through 235 Processing helix chain 'L' and resid 238 through 242 Processing helix chain 'L' and resid 244 through 266 removed outlier: 4.832A pdb=" N ASN L 265 " --> pdb=" O GLY L 261 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N PHE L 266 " --> pdb=" O LEU L 262 " (cutoff:3.500A) Processing helix chain 'L' and resid 270 through 291 removed outlier: 3.653A pdb=" N LEU L 284 " --> pdb=" O SER L 280 " (cutoff:3.500A) Processing helix chain 'L' and resid 294 through 321 removed outlier: 3.696A pdb=" N PHE L 307 " --> pdb=" O THR L 303 " (cutoff:3.500A) Processing helix chain 'L' and resid 339 through 353 Processing helix chain 'L' and resid 359 through 373 removed outlier: 3.616A pdb=" N ASP L 365 " --> pdb=" O PHE L 361 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N MET L 366 " --> pdb=" O TYR L 362 " (cutoff:3.500A) Processing helix chain 'L' and resid 378 through 403 Processing helix chain 'L' and resid 420 through 441 removed outlier: 4.093A pdb=" N MET L 426 " --> pdb=" O MET L 422 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N GLY L 428 " --> pdb=" O ARG L 424 " (cutoff:3.500A) removed outlier: 4.587A pdb=" N LEU L 429 " --> pdb=" O GLY L 425 " (cutoff:3.500A) removed outlier: 5.184A pdb=" N GLY L 437 " --> pdb=" O SER L 433 " (cutoff:3.500A) removed outlier: 6.735A pdb=" N SER L 438 " --> pdb=" O ILE L 434 " (cutoff:3.500A) removed outlier: 4.918A pdb=" N MET L 439 " --> pdb=" O ILE L 435 " (cutoff:3.500A) removed outlier: 4.623A pdb=" N LEU L 440 " --> pdb=" O GLY L 436 " (cutoff:3.500A) Processing helix chain 'L' and resid 455 through 458 No H-bonds generated for 'chain 'L' and resid 455 through 458' Processing helix chain 'L' and resid 460 through 474 removed outlier: 3.931A pdb=" N CYS L 465 " --> pdb=" O THR L 461 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N GLY L 468 " --> pdb=" O VAL L 464 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N GLY L 469 " --> pdb=" O CYS L 465 " (cutoff:3.500A) Processing helix chain 'L' and resid 485 through 488 No H-bonds generated for 'chain 'L' and resid 485 through 488' Processing helix chain 'L' and resid 490 through 497 Processing helix chain 'L' and resid 499 through 524 Proline residue: L 503 - end of helix removed outlier: 4.299A pdb=" N TYR L 508 " --> pdb=" O ILE L 505 " (cutoff:3.500A) removed outlier: 5.938A pdb=" N GLY L 509 " --> pdb=" O SER L 506 " (cutoff:3.500A) removed outlier: 4.257A pdb=" N MET L 510 " --> pdb=" O THR L 507 " (cutoff:3.500A) removed outlier: 4.273A pdb=" N ILE L 511 " --> pdb=" O TYR L 508 " (cutoff:3.500A) removed outlier: 5.818A pdb=" N PHE L 512 " --> pdb=" O GLY L 509 " (cutoff:3.500A) removed outlier: 4.091A pdb=" N TYR L 513 " --> pdb=" O MET L 510 " (cutoff:3.500A) Proline residue: L 514 - end of helix Processing helix chain 'L' and resid 529 through 533 Processing helix chain 'L' and resid 535 through 553 removed outlier: 3.892A pdb=" N TYR L 539 " --> pdb=" O GLY L 535 " (cutoff:3.500A) Processing helix chain 'L' and resid 557 through 576 Processing helix chain 'M' and resid 2 through 16 Proline residue: M 13 - end of helix removed outlier: 4.213A pdb=" N PHE M 16 " --> pdb=" O ILE M 12 " (cutoff:3.500A) Processing helix chain 'M' and resid 21 through 37 Processing helix chain 'M' and resid 56 through 75 removed outlier: 3.586A pdb=" N GLY M 60 " --> pdb=" O MET M 56 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N LEU M 61 " --> pdb=" O LEU M 57 " (cutoff:3.500A) removed outlier: 4.574A pdb=" N LEU M 73 " --> pdb=" O CYS M 69 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N LEU M 74 " --> pdb=" O SER M 70 " (cutoff:3.500A) Processing helix chain 'M' and resid 78 through 82 Processing helix chain 'M' and resid 86 through 105 Processing helix chain 'M' and resid 109 through 130 removed outlier: 4.476A pdb=" N LEU M 120 " --> pdb=" O PHE M 116 " (cutoff:3.500A) removed outlier: 4.887A pdb=" N ILE M 121 " --> pdb=" O GLU M 117 " (cutoff:3.500A) Proline residue: M 122 - end of helix removed outlier: 3.747A pdb=" N TRP M 130 " --> pdb=" O LEU M 126 " (cutoff:3.500A) Processing helix chain 'M' and resid 134 through 151 removed outlier: 3.657A pdb=" N ALA M 139 " --> pdb=" O ARG M 136 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N LEU M 143 " --> pdb=" O GLY M 140 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N LEU M 144 " --> pdb=" O LEU M 141 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N TYR M 146 " --> pdb=" O LEU M 143 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N LEU M 148 " --> pdb=" O PHE M 145 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N LEU M 149 " --> pdb=" O TYR M 146 " (cutoff:3.500A) Processing helix chain 'M' and resid 153 through 165 removed outlier: 3.537A pdb=" N ILE M 158 " --> pdb=" O LEU M 155 " (cutoff:3.500A) Processing helix chain 'M' and resid 170 through 174 Processing helix chain 'M' and resid 183 through 194 removed outlier: 3.560A pdb=" N ALA M 190 " --> pdb=" O CYS M 186 " (cutoff:3.500A) removed outlier: 4.250A pdb=" N LYS M 194 " --> pdb=" O ALA M 190 " (cutoff:3.500A) Processing helix chain 'M' and resid 198 through 209 removed outlier: 4.860A pdb=" N LEU M 202 " --> pdb=" O LEU M 199 " (cutoff:3.500A) removed outlier: 4.228A pdb=" N TRP M 203 " --> pdb=" O VAL M 200 " (cutoff:3.500A) Proline residue: M 205 - end of helix Processing helix chain 'M' and resid 213 through 221 Processing helix chain 'M' and resid 223 through 237 removed outlier: 4.731A pdb=" N SER M 236 " --> pdb=" O LEU M 232 " (cutoff:3.500A) removed outlier: 5.835A pdb=" N PHE M 237 " --> pdb=" O ARG M 233 " (cutoff:3.500A) Processing helix chain 'M' and resid 239 through 244 Processing helix chain 'M' and resid 247 through 266 removed outlier: 3.534A pdb=" N VAL M 258 " --> pdb=" O LEU M 254 " (cutoff:3.500A) Processing helix chain 'M' and resid 270 through 291 Processing helix chain 'M' and resid 294 through 324 removed outlier: 3.667A pdb=" N THR M 302 " --> pdb=" O CYS M 298 " (cutoff:3.500A) Processing helix chain 'M' and resid 336 through 338 No H-bonds generated for 'chain 'M' and resid 336 through 338' Processing helix chain 'M' and resid 341 through 355 removed outlier: 4.056A pdb=" N TRP M 346 " --> pdb=" O SER M 342 " (cutoff:3.500A) Processing helix chain 'M' and resid 361 through 376 removed outlier: 3.617A pdb=" N TYR M 368 " --> pdb=" O LEU M 364 " (cutoff:3.500A) Processing helix chain 'M' and resid 378 through 403 removed outlier: 4.592A pdb=" N SER M 385 " --> pdb=" O ILE M 382 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N SER M 388 " --> pdb=" O SER M 385 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N PHE M 390 " --> pdb=" O LEU M 387 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N TYR M 394 " --> pdb=" O SER M 391 " (cutoff:3.500A) removed outlier: 4.135A pdb=" N PHE M 401 " --> pdb=" O LEU M 398 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N SER M 402 " --> pdb=" O TYR M 399 " (cutoff:3.500A) Processing helix chain 'M' and resid 419 through 443 Proline residue: M 431 - end of helix removed outlier: 5.159A pdb=" N ILE M 436 " --> pdb=" O LEU M 432 " (cutoff:3.500A) removed outlier: 4.643A pdb=" N LEU M 437 " --> pdb=" O ASN M 433 " (cutoff:3.500A) removed outlier: 4.354A pdb=" N LYS M 438 " --> pdb=" O LEU M 434 " (cutoff:3.500A) removed outlier: 5.997A pdb=" N GLU M 440 " --> pdb=" O ILE M 436 " (cutoff:3.500A) removed outlier: 7.646A pdb=" N SER M 441 " --> pdb=" O LEU M 437 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N PHE M 442 " --> pdb=" O LYS M 438 " (cutoff:3.500A) Processing helix chain 'N' and resid 6 through 22 Processing helix chain 'N' and resid 27 through 45 Proline residue: N 43 - end of helix Processing helix chain 'N' and resid 52 through 81 removed outlier: 4.137A pdb=" N LEU N 66 " --> pdb=" O LEU N 62 " (cutoff:3.500A) Processing helix chain 'N' and resid 92 through 105 removed outlier: 4.222A pdb=" N ILE N 96 " --> pdb=" O PHE N 92 " (cutoff:3.500A) removed outlier: 4.581A pdb=" N ILE N 97 " --> pdb=" O THR N 93 " (cutoff:3.500A) Processing helix chain 'N' and resid 112 through 120 removed outlier: 3.654A pdb=" N ASN N 116 " --> pdb=" O PHE N 112 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N GLU N 119 " --> pdb=" O PRO N 115 " (cutoff:3.500A) removed outlier: 4.214A pdb=" N GLY N 120 " --> pdb=" O ASN N 116 " (cutoff:3.500A) Processing helix chain 'N' and resid 123 through 143 removed outlier: 3.784A pdb=" N GLN N 133 " --> pdb=" O LEU N 129 " (cutoff:3.500A) removed outlier: 4.842A pdb=" N LYS N 134 " --> pdb=" O MET N 130 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N ILE N 135 " --> pdb=" O THR N 131 " (cutoff:3.500A) removed outlier: 4.571A pdb=" N ALA N 136 " --> pdb=" O TRP N 132 " (cutoff:3.500A) Proline residue: N 137 - end of helix removed outlier: 3.701A pdb=" N TYR N 143 " --> pdb=" O MET N 139 " (cutoff:3.500A) Processing helix chain 'N' and resid 147 through 163 removed outlier: 4.047A pdb=" N VAL N 158 " --> pdb=" O VAL N 154 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N ILE N 159 " --> pdb=" O ILE N 155 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N ILE N 160 " --> pdb=" O LEU N 156 " (cutoff:3.500A) removed outlier: 4.176A pdb=" N GLY N 161 " --> pdb=" O SER N 157 " (cutoff:3.500A) Processing helix chain 'N' and resid 171 through 192 Processing helix chain 'N' and resid 195 through 218 Processing helix chain 'N' and resid 223 through 228 Processing helix chain 'N' and resid 236 through 246 removed outlier: 3.958A pdb=" N PHE N 241 " --> pdb=" O LYS N 237 " (cutoff:3.500A) removed outlier: 5.116A pdb=" N ASN N 243 " --> pdb=" O THR N 239 " (cutoff:3.500A) removed outlier: 5.154A pdb=" N PHE N 244 " --> pdb=" O LEU N 240 " (cutoff:3.500A) removed outlier: 4.110A pdb=" N LEU N 245 " --> pdb=" O PHE N 241 " (cutoff:3.500A) Processing helix chain 'N' and resid 251 through 253 No H-bonds generated for 'chain 'N' and resid 251 through 253' Processing helix chain 'N' and resid 255 through 269 removed outlier: 3.638A pdb=" N LYS N 259 " --> pdb=" O GLY N 255 " (cutoff:3.500A) Processing helix chain 'N' and resid 272 through 295 removed outlier: 3.753A pdb=" N LEU N 283 " --> pdb=" O MET N 279 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N ILE N 284 " --> pdb=" O MET N 280 " (cutoff:3.500A) removed outlier: 5.326A pdb=" N SER N 295 " --> pdb=" O ARG N 291 " (cutoff:3.500A) Processing helix chain 'N' and resid 314 through 328 removed outlier: 3.870A pdb=" N ILE N 322 " --> pdb=" O ASN N 318 " (cutoff:3.500A) Processing helix chain 'N' and resid 331 through 335 removed outlier: 4.292A pdb=" N SER N 335 " --> pdb=" O PHE N 332 " (cutoff:3.500A) Processing helix chain 'O' and resid 43 through 46 No H-bonds generated for 'chain 'O' and resid 43 through 46' Processing helix chain 'O' and resid 66 through 71 Processing helix chain 'O' and resid 75 through 77 No H-bonds generated for 'chain 'O' and resid 75 through 77' Processing helix chain 'O' and resid 95 through 106 Processing helix chain 'O' and resid 116 through 119 Processing helix chain 'O' and resid 128 through 130 No H-bonds generated for 'chain 'O' and resid 128 through 130' Processing helix chain 'O' and resid 133 through 139 Proline residue: O 136 - end of helix removed outlier: 4.121A pdb=" N CYS O 139 " --> pdb=" O PRO O 136 " (cutoff:3.500A) No H-bonds generated for 'chain 'O' and resid 133 through 139' Processing helix chain 'O' and resid 144 through 149 Processing helix chain 'O' and resid 154 through 181 removed outlier: 4.282A pdb=" N MET O 163 " --> pdb=" O GLN O 160 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N LEU O 179 " --> pdb=" O GLN O 176 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N SER O 180 " --> pdb=" O HIS O 177 " (cutoff:3.500A) Processing helix chain 'O' and resid 191 through 204 removed outlier: 4.200A pdb=" N PHE O 195 " --> pdb=" O PRO O 191 " (cutoff:3.500A) removed outlier: 5.541A pdb=" N VAL O 196 " --> pdb=" O TYR O 192 " (cutoff:3.500A) removed outlier: 4.321A pdb=" N PHE O 197 " --> pdb=" O SER O 193 " (cutoff:3.500A) Processing helix chain 'O' and resid 209 through 225 removed outlier: 4.225A pdb=" N GLN O 220 " --> pdb=" O ASN O 216 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N ASN O 221 " --> pdb=" O GLU O 217 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N THR O 222 " --> pdb=" O LEU O 218 " (cutoff:3.500A) removed outlier: 5.042A pdb=" N GLU O 225 " --> pdb=" O ASN O 221 " (cutoff:3.500A) Processing helix chain 'O' and resid 239 through 249 Processing helix chain 'O' and resid 262 through 273 removed outlier: 3.666A pdb=" N LEU O 268 " --> pdb=" O TYR O 264 " (cutoff:3.500A) removed outlier: 4.267A pdb=" N GLU O 269 " --> pdb=" O LEU O 265 " (cutoff:3.500A) Processing helix chain 'O' and resid 275 through 283 removed outlier: 4.662A pdb=" N ASP O 279 " --> pdb=" O GLN O 275 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N ILE O 280 " --> pdb=" O TYR O 276 " (cutoff:3.500A) Processing helix chain 'O' and resid 297 through 306 Processing helix chain 'O' and resid 310 through 312 No H-bonds generated for 'chain 'O' and resid 310 through 312' Processing helix chain 'O' and resid 322 through 324 No H-bonds generated for 'chain 'O' and resid 322 through 324' Processing helix chain 'O' and resid 329 through 340 Processing helix chain 'O' and resid 343 through 350 removed outlier: 4.407A pdb=" N PHE O 350 " --> pdb=" O LEU O 346 " (cutoff:3.500A) Processing helix chain 'O' and resid 364 through 376 Processing helix chain 'P' and resid 48 through 50 No H-bonds generated for 'chain 'P' and resid 48 through 50' Processing helix chain 'P' and resid 76 through 86 Processing helix chain 'P' and resid 98 through 100 No H-bonds generated for 'chain 'P' and resid 98 through 100' Processing helix chain 'P' and resid 102 through 107 Processing helix chain 'P' and resid 123 through 130 Processing helix chain 'P' and resid 151 through 155 Processing helix chain 'P' and resid 157 through 169 Processing helix chain 'P' and resid 196 through 211 Processing helix chain 'P' and resid 229 through 235 Processing helix chain 'P' and resid 248 through 251 Processing helix chain 'P' and resid 261 through 273 Processing helix chain 'P' and resid 292 through 302 Processing helix chain 'P' and resid 322 through 333 Processing helix chain 'P' and resid 339 through 341 No H-bonds generated for 'chain 'P' and resid 339 through 341' Processing helix chain 'P' and resid 344 through 351 Processing helix chain 'P' and resid 373 through 384 Proline residue: P 378 - end of helix Proline residue: P 383 - end of helix Processing helix chain 'P' and resid 408 through 415 Processing helix chain 'Q' and resid 69 through 72 No H-bonds generated for 'chain 'Q' and resid 69 through 72' Processing helix chain 'Q' and resid 76 through 81 Processing helix chain 'Q' and resid 127 through 129 No H-bonds generated for 'chain 'Q' and resid 127 through 129' Processing helix chain 'Q' and resid 138 through 147 Processing helix chain 'Q' and resid 169 through 171 No H-bonds generated for 'chain 'Q' and resid 169 through 171' Processing helix chain 'R' and resid 35 through 37 No H-bonds generated for 'chain 'R' and resid 35 through 37' Processing helix chain 'R' and resid 51 through 56 removed outlier: 3.638A pdb=" N ARG R 55 " --> pdb=" O ARG R 52 " (cutoff:3.500A) Processing helix chain 'R' and resid 68 through 74 Processing helix chain 'R' and resid 92 through 94 No H-bonds generated for 'chain 'R' and resid 92 through 94' Processing helix chain 'T' and resid 72 through 84 removed outlier: 3.906A pdb=" N LEU T 83 " --> pdb=" O VAL T 79 " (cutoff:3.500A) Processing helix chain 'T' and resid 108 through 122 Processing helix chain 'T' and resid 129 through 133 Processing helix chain 'T' and resid 137 through 145 Processing helix chain 'U' and resid 72 through 85 Processing helix chain 'U' and resid 108 through 122 removed outlier: 4.427A pdb=" N VAL U 112 " --> pdb=" O SER U 108 " (cutoff:3.500A) Processing helix chain 'U' and resid 128 through 133 removed outlier: 4.260A pdb=" N GLU U 132 " --> pdb=" O ASP U 128 " (cutoff:3.500A) Processing helix chain 'U' and resid 137 through 148 Processing helix chain 'V' and resid 20 through 36 Processing helix chain 'V' and resid 43 through 61 removed outlier: 4.168A pdb=" N GLN V 50 " --> pdb=" O LYS V 46 " (cutoff:3.500A) removed outlier: 4.771A pdb=" N ALA V 60 " --> pdb=" O ALA V 56 " (cutoff:3.500A) removed outlier: 4.473A pdb=" N GLN V 61 " --> pdb=" O ASP V 57 " (cutoff:3.500A) Processing helix chain 'V' and resid 65 through 72 Processing helix chain 'V' and resid 77 through 97 removed outlier: 3.907A pdb=" N VAL V 82 " --> pdb=" O GLU V 78 " (cutoff:3.500A) Processing helix chain 'W' and resid 22 through 46 Proline residue: W 41 - end of helix Processing helix chain 'W' and resid 53 through 67 removed outlier: 4.704A pdb=" N HIS W 67 " --> pdb=" O GLU W 63 " (cutoff:3.500A) Processing helix chain 'W' and resid 73 through 91 Processing helix chain 'W' and resid 97 through 103 removed outlier: 4.765A pdb=" N TYR W 103 " --> pdb=" O HIS W 99 " (cutoff:3.500A) Processing helix chain 'W' and resid 115 through 121 Processing helix chain 'X' and resid 12 through 15 No H-bonds generated for 'chain 'X' and resid 12 through 15' Processing helix chain 'X' and resid 24 through 29 Processing helix chain 'X' and resid 31 through 35 Processing helix chain 'X' and resid 40 through 51 Processing helix chain 'X' and resid 55 through 79 removed outlier: 3.536A pdb=" N LEU X 59 " --> pdb=" O PRO X 55 " (cutoff:3.500A) removed outlier: 5.624A pdb=" N ALA X 60 " --> pdb=" O ARG X 56 " (cutoff:3.500A) removed outlier: 4.970A pdb=" N GLU X 61 " --> pdb=" O ALA X 57 " (cutoff:3.500A) Processing helix chain 'X' and resid 82 through 93 Processing helix chain 'X' and resid 100 through 102 No H-bonds generated for 'chain 'X' and resid 100 through 102' Processing helix chain 'X' and resid 104 through 117 Processing helix chain 'Y' and resid 8 through 10 No H-bonds generated for 'chain 'Y' and resid 8 through 10' Processing helix chain 'Y' and resid 17 through 39 removed outlier: 4.260A pdb=" N TYR Y 27 " --> pdb=" O ALA Y 23 " (cutoff:3.500A) removed outlier: 4.254A pdb=" N ALA Y 31 " --> pdb=" O TYR Y 27 " (cutoff:3.500A) Processing helix chain 'Y' and resid 49 through 80 Proline residue: Y 62 - end of helix Processing helix chain 'Y' and resid 86 through 104 Processing helix chain 'Y' and resid 107 through 130 Processing helix chain 'Y' and resid 146 through 149 removed outlier: 4.387A pdb=" N ALA Y 149 " --> pdb=" O LEU Y 146 " (cutoff:3.500A) No H-bonds generated for 'chain 'Y' and resid 146 through 149' Processing helix chain 'Z' and resid 36 through 101 Proline residue: Z 77 - end of helix removed outlier: 3.700A pdb=" N ARG Z 85 " --> pdb=" O ALA Z 81 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N GLU Z 86 " --> pdb=" O GLU Z 82 " (cutoff:3.500A) Processing helix chain 'Z' and resid 132 through 135 No H-bonds generated for 'chain 'Z' and resid 132 through 135' Processing helix chain 'Z' and resid 141 through 150 removed outlier: 3.763A pdb=" N ARG Z 147 " --> pdb=" O SER Z 143 " (cutoff:3.500A) removed outlier: 5.018A pdb=" N LEU Z 150 " --> pdb=" O LYS Z 146 " (cutoff:3.500A) Processing helix chain 'a' and resid 3 through 30 Proline residue: a 7 - end of helix Proline residue: a 19 - end of helix Processing helix chain 'a' and resid 42 through 54 Processing helix chain 'a' and resid 64 through 66 No H-bonds generated for 'chain 'a' and resid 64 through 66' Processing helix chain 'b' and resid 12 through 19 Processing helix chain 'b' and resid 21 through 46 Processing helix chain 'b' and resid 66 through 70 Processing helix chain 'd' and resid 7 through 11 Processing helix chain 'd' and resid 25 through 45 removed outlier: 4.292A pdb=" N VAL d 33 " --> pdb=" O ILE d 29 " (cutoff:3.500A) Processing helix chain 'd' and resid 54 through 92 Processing helix chain 'd' and resid 105 through 107 No H-bonds generated for 'chain 'd' and resid 105 through 107' Processing helix chain 'e' and resid 12 through 15 No H-bonds generated for 'chain 'e' and resid 12 through 15' Processing helix chain 'e' and resid 26 through 40 removed outlier: 3.947A pdb=" N PHE e 30 " --> pdb=" O LYS e 26 " (cutoff:3.500A) removed outlier: 4.179A pdb=" N CYS e 37 " --> pdb=" O LYS e 33 " (cutoff:3.500A) Processing helix chain 'e' and resid 45 through 48 No H-bonds generated for 'chain 'e' and resid 45 through 48' Processing helix chain 'e' and resid 51 through 62 Processing helix chain 'e' and resid 64 through 83 Processing helix chain 'f' and resid 8 through 32 removed outlier: 4.513A pdb=" N LEU f 14 " --> pdb=" O LEU f 10 " (cutoff:3.500A) Proline residue: f 15 - end of helix Processing helix chain 'g' and resid 47 through 51 Processing helix chain 'g' and resid 68 through 87 removed outlier: 4.085A pdb=" N LEU g 85 " --> pdb=" O VAL g 81 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N CYS g 86 " --> pdb=" O THR g 82 " (cutoff:3.500A) Processing helix chain 'g' and resid 89 through 95 Processing helix chain 'g' and resid 103 through 120 removed outlier: 3.766A pdb=" N PHE g 111 " --> pdb=" O GLN g 107 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N LEU g 114 " --> pdb=" O GLY g 110 " (cutoff:3.500A) Processing helix chain 'g' and resid 140 through 143 No H-bonds generated for 'chain 'g' and resid 140 through 143' Processing helix chain 'h' and resid 53 through 83 Proline residue: h 72 - end of helix Processing helix chain 'h' and resid 100 through 103 Processing helix chain 'h' and resid 107 through 115 Processing helix chain 'h' and resid 120 through 154 removed outlier: 4.176A pdb=" N SER h 127 " --> pdb=" O ASN h 123 " (cutoff:3.500A) Processing helix chain 'h' and resid 168 through 183 removed outlier: 3.612A pdb=" N ALA h 182 " --> pdb=" O ASP h 178 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N LEU h 183 " --> pdb=" O GLU h 179 " (cutoff:3.500A) Processing helix chain 'i' and resid 20 through 22 No H-bonds generated for 'chain 'i' and resid 20 through 22' Processing helix chain 'i' and resid 24 through 29 Processing helix chain 'i' and resid 33 through 44 Processing helix chain 'i' and resid 56 through 61 removed outlier: 4.041A pdb=" N LEU i 60 " --> pdb=" O PRO i 56 " (cutoff:3.500A) Processing helix chain 'i' and resid 65 through 116 removed outlier: 4.047A pdb=" N TYR i 70 " --> pdb=" O ILE i 66 " (cutoff:3.500A) Proline residue: i 73 - end of helix removed outlier: 4.515A pdb=" N VAL i 77 " --> pdb=" O PRO i 73 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N CYS i 78 " --> pdb=" O LEU i 74 " (cutoff:3.500A) removed outlier: 4.071A pdb=" N VAL i 80 " --> pdb=" O LYS i 76 " (cutoff:3.500A) Proline residue: i 83 - end of helix removed outlier: 6.586A pdb=" N PHE i 87 " --> pdb=" O PRO i 83 " (cutoff:3.500A) removed outlier: 9.523A pdb=" N GLN i 88 " --> pdb=" O VAL i 84 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N ARG i 89 " --> pdb=" O LEU i 85 " (cutoff:3.500A) Processing helix chain 'j' and resid 42 through 65 removed outlier: 3.554A pdb=" N MET j 55 " --> pdb=" O VAL j 51 " (cutoff:3.500A) Processing helix chain 'j' and resid 67 through 69 No H-bonds generated for 'chain 'j' and resid 67 through 69' Processing helix chain 'k' and resid 25 through 33 Processing helix chain 'k' and resid 42 through 48 removed outlier: 3.723A pdb=" N TRP k 47 " --> pdb=" O ASN k 44 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ARG k 48 " --> pdb=" O GLU k 45 " (cutoff:3.500A) Processing helix chain 'k' and resid 57 through 65 Processing helix chain 'k' and resid 69 through 85 Processing helix chain 'l' and resid 33 through 36 Processing helix chain 'l' and resid 45 through 54 Processing helix chain 'l' and resid 96 through 98 No H-bonds generated for 'chain 'l' and resid 96 through 98' Processing helix chain 'l' and resid 128 through 150 removed outlier: 3.895A pdb=" N VAL l 138 " --> pdb=" O CYS l 134 " (cutoff:3.500A) Processing helix chain 'm' and resid 10 through 18 removed outlier: 4.393A pdb=" N ALA m 17 " --> pdb=" O ARG m 13 " (cutoff:3.500A) Processing helix chain 'm' and resid 20 through 30 removed outlier: 3.575A pdb=" N GLU m 24 " --> pdb=" O LYS m 20 " (cutoff:3.500A) Processing helix chain 'm' and resid 32 through 37 Processing helix chain 'm' and resid 46 through 56 Processing helix chain 'm' and resid 66 through 75 Processing helix chain 'm' and resid 77 through 100 Processing helix chain 'n' and resid 11 through 29 removed outlier: 3.950A pdb=" N LEU n 18 " --> pdb=" O GLN n 14 " (cutoff:3.500A) Processing helix chain 'n' and resid 33 through 46 removed outlier: 3.724A pdb=" N TYR n 38 " --> pdb=" O ASN n 34 " (cutoff:3.500A) Processing helix chain 'n' and resid 55 through 71 removed outlier: 4.221A pdb=" N ARG n 67 " --> pdb=" O ALA n 63 " (cutoff:3.500A) Processing helix chain 'n' and resid 97 through 102 Processing helix chain 'n' and resid 105 through 110 removed outlier: 4.012A pdb=" N GLN n 110 " --> pdb=" O LEU n 106 " (cutoff:3.500A) Processing helix chain 'n' and resid 112 through 132 Processing helix chain 'o' and resid 5 through 9 Processing helix chain 'o' and resid 41 through 47 Processing helix chain 'o' and resid 59 through 70 Processing helix chain 'o' and resid 72 through 77 removed outlier: 6.360A pdb=" N TYR o 76 " --> pdb=" O PRO o 73 " (cutoff:3.500A) Processing helix chain 'o' and resid 80 through 111 removed outlier: 4.130A pdb=" N GLN o 110 " --> pdb=" O LEU o 106 " (cutoff:3.500A) Processing helix chain 'p' and resid 7 through 29 removed outlier: 4.401A pdb=" N SER p 14 " --> pdb=" O SER p 10 " (cutoff:3.500A) Proline residue: p 22 - end of helix Processing helix chain 'p' and resid 32 through 34 No H-bonds generated for 'chain 'p' and resid 32 through 34' Processing helix chain 'p' and resid 59 through 93 removed outlier: 3.786A pdb=" N ASN p 81 " --> pdb=" O ASN p 77 " (cutoff:3.500A) Processing helix chain 'p' and resid 102 through 120 removed outlier: 4.945A pdb=" N GLN p 108 " --> pdb=" O PRO p 104 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N TYR p 109 " --> pdb=" O LEU p 105 " (cutoff:3.500A) Processing helix chain 'p' and resid 129 through 146 Processing helix chain 'q' and resid 10 through 20 Processing helix chain 'q' and resid 23 through 33 removed outlier: 4.207A pdb=" N LYS q 29 " --> pdb=" O GLN q 25 " (cutoff:3.500A) Processing helix chain 'q' and resid 59 through 62 No H-bonds generated for 'chain 'q' and resid 59 through 62' Processing helix chain 'q' and resid 77 through 79 No H-bonds generated for 'chain 'q' and resid 77 through 79' Processing helix chain 'q' and resid 82 through 89 removed outlier: 4.161A pdb=" N GLY q 86 " --> pdb=" O ALA q 82 " (cutoff:3.500A) removed outlier: 5.004A pdb=" N TRP q 87 " --> pdb=" O GLU q 83 " (cutoff:3.500A) Processing helix chain 'r' and resid 10 through 20 Processing helix chain 'r' and resid 72 through 78 Processing helix chain 's' and resid 80 through 84 Processing helix chain 's' and resid 89 through 98 Processing sheet with id= A, first strand: chain 'B' and resid 127 through 131 removed outlier: 6.710A pdb=" N TRP B 154 " --> pdb=" O ILE B 128 " (cutoff:3.500A) removed outlier: 7.367A pdb=" N VAL B 130 " --> pdb=" O TRP B 154 " (cutoff:3.500A) removed outlier: 6.300A pdb=" N ILE B 156 " --> pdb=" O VAL B 130 " (cutoff:3.500A) removed outlier: 6.624A pdb=" N ILE B 186 " --> pdb=" O SER B 157 " (cutoff:3.500A) No H-bonds generated for sheet with id= A Processing sheet with id= B, first strand: chain 'C' and resid 112 through 119 removed outlier: 3.680A pdb=" N ASN C 112 " --> pdb=" O LEU C 135 " (cutoff:3.500A) removed outlier: 6.973A pdb=" N ASN C 133 " --> pdb=" O VAL C 114 " (cutoff:3.500A) removed outlier: 4.222A pdb=" N ILE C 116 " --> pdb=" O VAL C 131 " (cutoff:3.500A) removed outlier: 5.961A pdb=" N VAL C 131 " --> pdb=" O ILE C 116 " (cutoff:3.500A) removed outlier: 4.782A pdb=" N GLY C 118 " --> pdb=" O GLU C 129 " (cutoff:3.500A) removed outlier: 6.826A pdb=" N GLU C 129 " --> pdb=" O GLY C 118 " (cutoff:3.500A) removed outlier: 4.608A pdb=" N LEU C 86 " --> pdb=" O ARG C 142 " (cutoff:3.500A) removed outlier: 4.834A pdb=" N TYR C 148 " --> pdb=" O ILE C 90 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'C' and resid 210 through 215 Processing sheet with id= D, first strand: chain 'D' and resid 85 through 89 removed outlier: 6.915A pdb=" N ASP D 107 " --> pdb=" O VAL D 111 " (cutoff:3.500A) removed outlier: 5.799A pdb=" N VAL D 111 " --> pdb=" O ASP D 107 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'D' and resid 399 through 407 Processing sheet with id= F, first strand: chain 'E' and resid 125 through 127 Processing sheet with id= G, first strand: chain 'F' and resid 255 through 259 removed outlier: 7.516A pdb=" N TYR F 127 " --> pdb=" O THR F 256 " (cutoff:3.500A) removed outlier: 8.560A pdb=" N THR F 258 " --> pdb=" O TYR F 127 " (cutoff:3.500A) removed outlier: 6.527A pdb=" N VAL F 129 " --> pdb=" O THR F 258 " (cutoff:3.500A) removed outlier: 6.611A pdb=" N ALA F 168 " --> pdb=" O LEU F 128 " (cutoff:3.500A) removed outlier: 7.997A pdb=" N VAL F 130 " --> pdb=" O ALA F 168 " (cutoff:3.500A) removed outlier: 6.674A pdb=" N TYR F 170 " --> pdb=" O VAL F 130 " (cutoff:3.500A) removed outlier: 6.433A pdb=" N ASP F 209 " --> pdb=" O ALA F 169 " (cutoff:3.500A) removed outlier: 7.796A pdb=" N ILE F 171 " --> pdb=" O ASP F 209 " (cutoff:3.500A) removed outlier: 7.123A pdb=" N PHE F 211 " --> pdb=" O ILE F 171 " (cutoff:3.500A) removed outlier: 7.716A pdb=" N ILE F 173 " --> pdb=" O PHE F 211 " (cutoff:3.500A) removed outlier: 6.474A pdb=" N HIS F 213 " --> pdb=" O ILE F 173 " (cutoff:3.500A) No H-bonds generated for sheet with id= G Processing sheet with id= H, first strand: chain 'F' and resid 301 through 306 removed outlier: 3.630A pdb=" N GLY F 331 " --> pdb=" O MET F 372 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'G' and resid 41 through 45 Processing sheet with id= J, first strand: chain 'G' and resid 183 through 185 Processing sheet with id= K, first strand: chain 'G' and resid 210 through 212 Processing sheet with id= L, first strand: chain 'G' and resid 260 through 265 removed outlier: 3.854A pdb=" N ARG G 286 " --> pdb=" O SER G 278 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'G' and resid 379 through 381 removed outlier: 8.354A pdb=" N ALA G 380 " --> pdb=" O ILE G 351 " (cutoff:3.500A) removed outlier: 6.237A pdb=" N GLY G 353 " --> pdb=" O ALA G 380 " (cutoff:3.500A) removed outlier: 6.469A pdb=" N VAL G 550 " --> pdb=" O ALA G 352 " (cutoff:3.500A) removed outlier: 7.922A pdb=" N ILE G 354 " --> pdb=" O VAL G 550 " (cutoff:3.500A) removed outlier: 6.274A pdb=" N PHE G 552 " --> pdb=" O ILE G 354 " (cutoff:3.500A) removed outlier: 6.808A pdb=" N PHE G 571 " --> pdb=" O LEU G 551 " (cutoff:3.500A) removed outlier: 8.175A pdb=" N LEU G 553 " --> pdb=" O PHE G 571 " (cutoff:3.500A) removed outlier: 7.114A pdb=" N VAL G 573 " --> pdb=" O LEU G 553 " (cutoff:3.500A) No H-bonds generated for sheet with id= M Processing sheet with id= N, first strand: chain 'G' and resid 439 through 442 removed outlier: 4.248A pdb=" N GLY G 488 " --> pdb=" O VAL G 414 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N LEU G 522 " --> pdb=" O ILE G 487 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'G' and resid 601 through 603 Processing sheet with id= P, first strand: chain 'I' and resid 106 through 108 Processing sheet with id= Q, first strand: chain 'I' and resid 133 through 139 removed outlier: 5.513A pdb=" N GLU I 138 " --> pdb=" O THR I 147 " (cutoff:3.500A) removed outlier: 5.005A pdb=" N THR I 147 " --> pdb=" O GLU I 138 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'L' and resid 35 through 42 removed outlier: 7.063A pdb=" N ILE L 49 " --> pdb=" O LEU L 41 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'O' and resid 185 through 187 removed outlier: 6.666A pdb=" N LEU O 231 " --> pdb=" O CYS O 86 " (cutoff:3.500A) removed outlier: 8.147A pdb=" N GLU O 88 " --> pdb=" O LEU O 231 " (cutoff:3.500A) removed outlier: 6.471A pdb=" N ILE O 233 " --> pdb=" O GLU O 88 " (cutoff:3.500A) removed outlier: 5.985A pdb=" N GLU O 285 " --> pdb=" O VAL O 232 " (cutoff:3.500A) removed outlier: 7.484A pdb=" N TYR O 234 " --> pdb=" O GLU O 285 " (cutoff:3.500A) removed outlier: 6.518A pdb=" N LEU O 287 " --> pdb=" O TYR O 234 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'P' and resid 66 through 69 removed outlier: 6.576A pdb=" N VAL P 135 " --> pdb=" O THR P 67 " (cutoff:3.500A) removed outlier: 7.856A pdb=" N PHE P 69 " --> pdb=" O VAL P 135 " (cutoff:3.500A) removed outlier: 6.557A pdb=" N ILE P 137 " --> pdb=" O PHE P 69 " (cutoff:3.500A) removed outlier: 6.551A pdb=" N ARG P 173 " --> pdb=" O VAL P 136 " (cutoff:3.500A) removed outlier: 8.065A pdb=" N ASN P 138 " --> pdb=" O ARG P 173 " (cutoff:3.500A) removed outlier: 7.204A pdb=" N ILE P 175 " --> pdb=" O ASN P 138 " (cutoff:3.500A) removed outlier: 6.350A pdb=" N THR P 216 " --> pdb=" O HIS P 176 " (cutoff:3.500A) No H-bonds generated for sheet with id= T Processing sheet with id= U, first strand: chain 'P' and resid 244 through 247 removed outlier: 6.539A pdb=" N MET P 313 " --> pdb=" O MET P 245 " (cutoff:3.500A) removed outlier: 7.347A pdb=" N LEU P 247 " --> pdb=" O MET P 313 " (cutoff:3.500A) removed outlier: 5.902A pdb=" N TYR P 315 " --> pdb=" O LEU P 247 " (cutoff:3.500A) No H-bonds generated for sheet with id= U Processing sheet with id= V, first strand: chain 'Q' and resid 104 through 107 Processing sheet with id= W, first strand: chain 'R' and resid 84 through 87 Processing sheet with id= X, first strand: chain 'q' and resid 63 through 66 removed outlier: 3.772A pdb=" N GLY q 43 " --> pdb=" O TYR q 51 " (cutoff:3.500A) removed outlier: 6.971A pdb=" N GLU q 53 " --> pdb=" O LEU q 41 " (cutoff:3.500A) removed outlier: 6.019A pdb=" N LEU q 41 " --> pdb=" O GLU q 53 " (cutoff:3.500A) 2751 hydrogen bonds defined for protein. 7671 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: 18.58 Time building geometry restraints manager: 23.90 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.14 - 1.37: 22385 1.37 - 1.60: 44344 1.60 - 1.83: 794 1.83 - 2.05: 1 2.05 - 2.28: 80 Bond restraints: 67604 Sorted by residual: bond pdb=" C1' DGT O 501 " pdb=" O4' DGT O 501 " ideal model delta sigma weight residual 1.536 1.306 0.230 2.00e-02 2.50e+03 1.32e+02 bond pdb=" C5N NDP P 501 " pdb=" C6N NDP P 501 " ideal model delta sigma weight residual 1.337 1.543 -0.206 2.40e-02 1.74e+03 7.34e+01 bond pdb=" C1' DGT O 501 " pdb=" C2' DGT O 501 " ideal model delta sigma weight residual 1.362 1.532 -0.170 2.00e-02 2.50e+03 7.26e+01 bond pdb=" C1B NDP P 501 " pdb=" C2B NDP P 501 " ideal model delta sigma weight residual 1.575 1.298 0.277 3.70e-02 7.30e+02 5.62e+01 bond pdb=" C1D NDP P 501 " pdb=" C2D NDP P 501 " ideal model delta sigma weight residual 1.560 1.299 0.261 3.70e-02 7.30e+02 4.96e+01 ... (remaining 67599 not shown) Histogram of bond angle deviations from ideal: 71.02 - 84.50: 76 84.50 - 97.99: 11 97.99 - 111.47: 30479 111.47 - 124.95: 59592 124.95 - 138.43: 1371 Bond angle restraints: 91529 Sorted by residual: angle pdb=" C11 CDL M 501 " pdb=" CA5 CDL M 501 " pdb=" OA6 CDL M 501 " ideal model delta sigma weight residual 111.33 120.79 -9.46 1.32e+00 5.72e-01 5.12e+01 angle pdb=" C1' DGT O 501 " pdb=" N9 DGT O 501 " pdb=" C8 DGT O 501 " ideal model delta sigma weight residual 116.68 137.64 -20.96 3.00e+00 1.11e-01 4.88e+01 angle pdb=" C5B NDP P 501 " pdb=" O5B NDP P 501 " pdb=" PA NDP P 501 " ideal model delta sigma weight residual 103.84 116.99 -13.15 1.91e+00 2.73e-01 4.72e+01 angle pdb=" C11 CDL P 502 " pdb=" CA5 CDL P 502 " pdb=" OA6 CDL P 502 " ideal model delta sigma weight residual 111.33 120.38 -9.05 1.32e+00 5.72e-01 4.69e+01 angle pdb=" O1X NDP P 501 " pdb=" P2B NDP P 501 " pdb=" O3X NDP P 501 " ideal model delta sigma weight residual 117.46 110.11 7.35 1.17e+00 7.36e-01 3.97e+01 ... (remaining 91524 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.48: 39561 35.48 - 70.97: 619 70.97 - 106.45: 45 106.45 - 141.93: 9 141.93 - 177.42: 1 Dihedral angle restraints: 40235 sinusoidal: 16561 harmonic: 23674 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 75.01 -177.42 1 2.00e+01 2.50e-03 4.80e+01 dihedral pdb=" CB CYS X 90 " pdb=" SG CYS X 90 " pdb=" SG CYS X 103 " pdb=" CB CYS X 103 " ideal model delta sinusoidal sigma weight residual 93.00 33.99 59.01 1 1.00e+01 1.00e-02 4.66e+01 dihedral pdb=" CA MET N 79 " pdb=" C MET N 79 " pdb=" N LEU N 80 " pdb=" CA LEU N 80 " ideal model delta harmonic sigma weight residual 180.00 152.05 27.95 0 5.00e+00 4.00e-02 3.12e+01 ... (remaining 40232 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 4.194: 9861 4.194 - 8.388: 0 8.388 - 12.581: 0 12.581 - 16.775: 0 16.775 - 20.969: 16 Chirality restraints: 9877 Sorted by residual: chirality pdb="FE1 SF4 I 301 " pdb=" S2 SF4 I 301 " pdb=" S3 SF4 I 301 " pdb=" S4 SF4 I 301 " both_signs ideal model delta sigma weight residual False -10.55 10.41 -20.97 2.00e-01 2.50e+01 1.10e+04 chirality pdb="FE2 SF4 G 801 " pdb=" S1 SF4 G 801 " pdb=" S3 SF4 G 801 " pdb=" S4 SF4 G 801 " both_signs ideal model delta sigma weight residual False 10.55 -10.40 20.96 2.00e-01 2.50e+01 1.10e+04 chirality pdb="FE2 SF4 G 802 " pdb=" S1 SF4 G 802 " pdb=" S3 SF4 G 802 " pdb=" S4 SF4 G 802 " both_signs ideal model delta sigma weight residual False 10.55 -10.40 20.95 2.00e-01 2.50e+01 1.10e+04 ... (remaining 9874 not shown) Planarity restraints: 11543 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' DGT O 501 " 0.398 2.00e-02 2.50e+03 4.72e-01 4.45e+03 pdb=" C2' DGT O 501 " -0.480 2.00e-02 2.50e+03 pdb=" C3' DGT O 501 " -0.391 2.00e-02 2.50e+03 pdb=" C4' DGT O 501 " 0.317 2.00e-02 2.50e+03 pdb=" C5' DGT O 501 " -0.499 2.00e-02 2.50e+03 pdb=" N9 DGT O 501 " -0.424 2.00e-02 2.50e+03 pdb=" O3' DGT O 501 " 0.288 2.00e-02 2.50e+03 pdb=" O4' DGT O 501 " 0.791 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2N NDP P 501 " -0.287 2.00e-02 2.50e+03 1.80e-01 4.04e+02 pdb=" C3N NDP P 501 " -0.059 2.00e-02 2.50e+03 pdb=" C4N NDP P 501 " -0.032 2.00e-02 2.50e+03 pdb=" C7N NDP P 501 " 0.152 2.00e-02 2.50e+03 pdb=" N1N NDP P 501 " 0.227 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C4N NDP P 501 " 0.041 2.00e-02 2.50e+03 6.71e-02 4.50e+01 pdb=" C5N NDP P 501 " -0.082 2.00e-02 2.50e+03 pdb=" C6N NDP P 501 " 0.086 2.00e-02 2.50e+03 pdb=" N1N NDP P 501 " -0.045 2.00e-02 2.50e+03 ... (remaining 11540 not shown) Histogram of nonbonded interaction distances: 1.82 - 2.44: 459 2.44 - 3.05: 50363 3.05 - 3.67: 104782 3.67 - 4.28: 158311 4.28 - 4.90: 251620 Nonbonded interactions: 565535 Sorted by model distance: nonbonded pdb=" OG1 THR D 203 " pdb=" O GLY H 275 " model vdw 1.823 2.440 nonbonded pdb=" O ALA L 198 " pdb=" OG SER L 203 " model vdw 1.926 2.440 nonbonded pdb=" OE2 GLU O 254 " pdb=" O3' DGT O 501 " model vdw 1.955 3.040 nonbonded pdb=" O LEU L 219 " pdb=" OG1 THR L 224 " model vdw 1.960 2.440 nonbonded pdb=" O PHE L 525 " pdb=" OG SER L 530 " model vdw 1.960 2.440 ... (remaining 565530 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'T' selection = (chain 'U' and (resid 70 through 146 or resid 201)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 3.990 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.040 Extract box with map and model: 20.300 Check model and map are aligned: 0.720 Set scattering table: 0.450 Process input model: 145.340 Find NCS groups from input model: 2.000 Set up NCS constraints: 0.230 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.390 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 175.470 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7875 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 : 0.007 0.277 67604 Z= 0.484 Angle : 0.829 20.963 91529 Z= 0.428 Chirality : 0.843 20.969 9877 Planarity : 0.007 0.472 11543 Dihedral : 14.159 177.417 25026 Min Nonbonded Distance : 1.823 Molprobity Statistics. All-atom Clashscore : 11.05 Ramachandran Plot: Outliers : 0.02 % Allowed : 8.01 % Favored : 91.97 % Rotamer: Outliers : 0.00 % Allowed : 0.60 % Favored : 99.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.69 % 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: -1.67 (0.09), residues: 8043 helix: -0.36 (0.08), residues: 4172 sheet: -1.79 (0.26), residues: 342 loop : -1.91 (0.10), residues: 3529 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16086 Ramachandran restraints generated. 8043 Oldfield, 0 Emsley, 8043 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16086 Ramachandran restraints generated. 8043 Oldfield, 0 Emsley, 8043 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 677 residues out of total 7047 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 677 time to evaluate : 5.787 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 outliers start: 0 outliers final: 0 residues processed: 677 average time/residue: 0.6150 time to fit residues: 722.1881 Evaluate side-chains 506 residues out of total 7047 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 506 time to evaluate : 5.886 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 7.7643 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 791 random chunks: chunk 667 optimal weight: 10.0000 chunk 599 optimal weight: 5.9990 chunk 332 optimal weight: 7.9990 chunk 204 optimal weight: 8.9990 chunk 404 optimal weight: 5.9990 chunk 320 optimal weight: 6.9990 chunk 619 optimal weight: 0.0670 chunk 239 optimal weight: 5.9990 chunk 376 optimal weight: 1.9990 chunk 461 optimal weight: 10.0000 chunk 718 optimal weight: 7.9990 overall best weight: 4.0126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 152 ASN E 126 GLN ** E 195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 437 HIS G 84 ASN ** G 372 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 439 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 54 GLN ** J 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 326 GLN L 349 ASN ** L 527 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 536 GLN M 82 HIS M 138 GLN M 333 ASN ** N 304 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 316 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 160 GLN ** O 230 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 138 ASN P 155 HIS P 291 GLN R 64 ASN V 83 GLN ** W 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 172 HIS ** b 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** h 63 HIS ** h 106 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** i 131 HIS ** l 98 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** o 41 GLN p 42 HIS p 43 GLN Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7853 moved from start: 0.1323 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.245 67604 Z= 0.472 Angle : 1.398 51.060 91529 Z= 0.880 Chirality : 0.258 6.477 9877 Planarity : 0.005 0.062 11543 Dihedral : 9.476 178.674 9166 Min Nonbonded Distance : 2.049 Molprobity Statistics. All-atom Clashscore : 12.13 Ramachandran Plot: Outliers : 0.04 % Allowed : 6.04 % Favored : 93.92 % Rotamer: Outliers : 0.88 % Allowed : 8.00 % Favored : 91.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.69 % 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: -0.97 (0.09), residues: 8043 helix: 0.24 (0.08), residues: 4212 sheet: -1.43 (0.26), residues: 370 loop : -1.63 (0.11), residues: 3461 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16086 Ramachandran restraints generated. 8043 Oldfield, 0 Emsley, 8043 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16086 Ramachandran restraints generated. 8043 Oldfield, 0 Emsley, 8043 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 649 residues out of total 7047 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 587 time to evaluate : 5.827 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 62 outliers final: 30 residues processed: 620 average time/residue: 0.6016 time to fit residues: 661.9897 Evaluate side-chains 535 residues out of total 7047 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 505 time to evaluate : 5.751 Switching outliers to nearest non-outliers outliers start: 30 outliers final: 0 residues processed: 30 average time/residue: 0.5230 time to fit residues: 36.8111 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 791 random chunks: chunk 399 optimal weight: 10.0000 chunk 222 optimal weight: 8.9990 chunk 597 optimal weight: 8.9990 chunk 489 optimal weight: 4.9990 chunk 198 optimal weight: 5.9990 chunk 719 optimal weight: 8.9990 chunk 777 optimal weight: 30.0000 chunk 640 optimal weight: 5.9990 chunk 713 optimal weight: 10.0000 chunk 245 optimal weight: 10.0000 chunk 577 optimal weight: 6.9990 overall best weight: 6.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 200 GLN ** E 195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 84 ASN ** G 372 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 383 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 439 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 145 GLN ** J 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 163 ASN ** L 326 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 349 ASN ** L 413 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 527 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 138 GLN N 243 ASN ** N 304 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 316 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 230 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** W 69 ASN X 42 ASN ** b 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 106 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** m 35 HIS ** n 104 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** q 33 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7898 moved from start: 0.1598 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.232 67604 Z= 0.547 Angle : 1.413 50.998 91529 Z= 0.886 Chirality : 0.257 6.364 9877 Planarity : 0.005 0.062 11543 Dihedral : 9.358 178.361 9166 Min Nonbonded Distance : 2.052 Molprobity Statistics. All-atom Clashscore : 14.67 Ramachandran Plot: Outliers : 0.04 % Allowed : 7.01 % Favored : 92.95 % Rotamer: Outliers : 1.69 % Allowed : 12.16 % Favored : 86.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.99 (0.09), residues: 8043 helix: 0.20 (0.08), residues: 4203 sheet: -1.38 (0.26), residues: 385 loop : -1.62 (0.11), residues: 3455 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16086 Ramachandran restraints generated. 8043 Oldfield, 0 Emsley, 8043 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16086 Ramachandran restraints generated. 8043 Oldfield, 0 Emsley, 8043 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 660 residues out of total 7047 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 119 poor density : 541 time to evaluate : 6.345 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 119 outliers final: 56 residues processed: 639 average time/residue: 0.5905 time to fit residues: 672.2286 Evaluate side-chains 551 residues out of total 7047 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 495 time to evaluate : 5.741 Switching outliers to nearest non-outliers outliers start: 56 outliers final: 0 residues processed: 56 average time/residue: 0.4784 time to fit residues: 58.8026 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 791 random chunks: chunk 710 optimal weight: 4.9990 chunk 541 optimal weight: 5.9990 chunk 373 optimal weight: 9.9990 chunk 79 optimal weight: 4.9990 chunk 343 optimal weight: 6.9990 chunk 483 optimal weight: 4.9990 chunk 722 optimal weight: 0.9990 chunk 764 optimal weight: 6.9990 chunk 377 optimal weight: 1.9990 chunk 684 optimal weight: 8.9990 chunk 206 optimal weight: 9.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 112 ASN ** E 195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 84 ASN ** G 372 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 383 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 439 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 145 GLN ** J 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 51 ASN ** L 237 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 326 GLN L 349 ASN ** L 527 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 536 GLN M 138 GLN M 242 ASN ** N 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 270 ASN ** N 304 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 316 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 68 ASN ** O 230 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 348 ASN R 64 ASN X 102 HIS Y 147 ASN ** b 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 43 ASN ** h 106 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** k 13 HIS ** n 104 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7862 moved from start: 0.1904 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.240 67604 Z= 0.461 Angle : 1.371 50.723 91529 Z= 0.867 Chirality : 0.257 6.364 9877 Planarity : 0.004 0.060 11543 Dihedral : 9.144 178.443 9166 Min Nonbonded Distance : 2.084 Molprobity Statistics. All-atom Clashscore : 13.36 Ramachandran Plot: Outliers : 0.01 % Allowed : 5.66 % Favored : 94.33 % Rotamer: Outliers : 1.55 % Allowed : 13.95 % Favored : 84.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.69 % 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: -0.68 (0.09), residues: 8043 helix: 0.45 (0.08), residues: 4188 sheet: -1.23 (0.27), residues: 373 loop : -1.46 (0.11), residues: 3482 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16086 Ramachandran restraints generated. 8043 Oldfield, 0 Emsley, 8043 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16086 Ramachandran restraints generated. 8043 Oldfield, 0 Emsley, 8043 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 679 residues out of total 7047 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 109 poor density : 570 time to evaluate : 5.715 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 109 outliers final: 45 residues processed: 656 average time/residue: 0.5949 time to fit residues: 692.6979 Evaluate side-chains 557 residues out of total 7047 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 512 time to evaluate : 5.710 Switching outliers to nearest non-outliers outliers start: 45 outliers final: 0 residues processed: 45 average time/residue: 0.4995 time to fit residues: 50.0810 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 791 random chunks: chunk 636 optimal weight: 5.9990 chunk 434 optimal weight: 9.9990 chunk 11 optimal weight: 8.9990 chunk 569 optimal weight: 0.0770 chunk 315 optimal weight: 6.9990 chunk 652 optimal weight: 6.9990 chunk 528 optimal weight: 2.9990 chunk 0 optimal weight: 10.0000 chunk 390 optimal weight: 0.9980 chunk 686 optimal weight: 0.0670 chunk 192 optimal weight: 20.0000 overall best weight: 2.0280 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 446 GLN ** G 372 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 383 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 439 GLN H 74 ASN ** J 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 147 ASN L 237 ASN L 326 GLN ** L 527 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 536 GLN M 138 GLN M 242 ASN M 333 ASN ** N 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 167 ASN N 270 ASN ** N 304 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 316 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 230 HIS ** X 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 42 ASN Z 72 GLN ** b 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 106 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 104 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7834 moved from start: 0.2193 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.243 67604 Z= 0.437 Angle : 1.357 50.817 91529 Z= 0.860 Chirality : 0.257 6.408 9877 Planarity : 0.004 0.055 11543 Dihedral : 8.911 179.936 9166 Min Nonbonded Distance : 2.091 Molprobity Statistics. All-atom Clashscore : 13.23 Ramachandran Plot: Outliers : 0.01 % Allowed : 5.47 % Favored : 94.52 % Rotamer: Outliers : 1.39 % Allowed : 15.16 % Favored : 83.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.69 % 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: -0.41 (0.10), residues: 8043 helix: 0.66 (0.08), residues: 4179 sheet: -1.17 (0.27), residues: 379 loop : -1.28 (0.11), residues: 3485 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16086 Ramachandran restraints generated. 8043 Oldfield, 0 Emsley, 8043 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16086 Ramachandran restraints generated. 8043 Oldfield, 0 Emsley, 8043 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 672 residues out of total 7047 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 98 poor density : 574 time to evaluate : 5.776 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 outliers start: 98 outliers final: 36 residues processed: 649 average time/residue: 0.6209 time to fit residues: 713.6193 Evaluate side-chains 557 residues out of total 7047 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 521 time to evaluate : 5.728 Switching outliers to nearest non-outliers outliers start: 36 outliers final: 0 residues processed: 36 average time/residue: 0.5045 time to fit residues: 42.1883 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 791 random chunks: chunk 257 optimal weight: 0.9990 chunk 688 optimal weight: 7.9990 chunk 151 optimal weight: 1.9990 chunk 448 optimal weight: 9.9990 chunk 188 optimal weight: 0.6980 chunk 765 optimal weight: 10.0000 chunk 635 optimal weight: 0.8980 chunk 354 optimal weight: 10.0000 chunk 63 optimal weight: 9.9990 chunk 253 optimal weight: 4.9990 chunk 401 optimal weight: 4.9990 overall best weight: 1.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 148 GLN ** G 372 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 383 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 209 ASN J 33 GLN ** J 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 326 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 536 GLN M 138 GLN ** N 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 304 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 316 ASN O 153 HIS O 387 ASN ** X 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 42 ASN ** b 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 106 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 104 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7822 moved from start: 0.2429 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.243 67604 Z= 0.434 Angle : 1.352 50.625 91529 Z= 0.858 Chirality : 0.256 6.358 9877 Planarity : 0.004 0.055 11543 Dihedral : 8.753 179.267 9166 Min Nonbonded Distance : 2.092 Molprobity Statistics. All-atom Clashscore : 13.24 Ramachandran Plot: Outliers : 0.01 % Allowed : 5.27 % Favored : 94.72 % Rotamer: Outliers : 1.12 % Allowed : 16.01 % Favored : 82.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.69 % 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: -0.24 (0.10), residues: 8043 helix: 0.77 (0.08), residues: 4171 sheet: -1.09 (0.27), residues: 378 loop : -1.17 (0.11), residues: 3494 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16086 Ramachandran restraints generated. 8043 Oldfield, 0 Emsley, 8043 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16086 Ramachandran restraints generated. 8043 Oldfield, 0 Emsley, 8043 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 657 residues out of total 7047 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 79 poor density : 578 time to evaluate : 5.830 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 79 outliers final: 25 residues processed: 633 average time/residue: 0.6183 time to fit residues: 694.5174 Evaluate side-chains 548 residues out of total 7047 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 523 time to evaluate : 5.738 Switching outliers to nearest non-outliers outliers start: 25 outliers final: 0 residues processed: 25 average time/residue: 0.4931 time to fit residues: 31.2627 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 791 random chunks: chunk 737 optimal weight: 0.9990 chunk 86 optimal weight: 9.9990 chunk 436 optimal weight: 9.9990 chunk 558 optimal weight: 9.9990 chunk 433 optimal weight: 0.0270 chunk 644 optimal weight: 0.9990 chunk 427 optimal weight: 20.0000 chunk 762 optimal weight: 10.0000 chunk 477 optimal weight: 10.0000 chunk 464 optimal weight: 5.9990 chunk 351 optimal weight: 7.9990 overall best weight: 3.2046 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 372 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 383 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 33 GLN ** J 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 326 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 304 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 153 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 42 ASN X 172 HIS ** b 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 106 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 104 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** p 115 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7843 moved from start: 0.2496 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.238 67604 Z= 0.452 Angle : 1.365 50.766 91529 Z= 0.862 Chirality : 0.256 6.346 9877 Planarity : 0.004 0.067 11543 Dihedral : 8.732 179.996 9166 Min Nonbonded Distance : 2.082 Molprobity Statistics. All-atom Clashscore : 13.96 Ramachandran Plot: Outliers : 0.01 % Allowed : 5.63 % Favored : 94.36 % Rotamer: Outliers : 1.06 % Allowed : 17.09 % Favored : 81.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.69 % 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: -0.25 (0.10), residues: 8043 helix: 0.78 (0.08), residues: 4180 sheet: -1.14 (0.27), residues: 381 loop : -1.18 (0.11), residues: 3482 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16086 Ramachandran restraints generated. 8043 Oldfield, 0 Emsley, 8043 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16086 Ramachandran restraints generated. 8043 Oldfield, 0 Emsley, 8043 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 620 residues out of total 7047 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 545 time to evaluate : 5.933 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 75 outliers final: 37 residues processed: 596 average time/residue: 0.6288 time to fit residues: 667.2865 Evaluate side-chains 553 residues out of total 7047 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 516 time to evaluate : 5.693 Switching outliers to nearest non-outliers outliers start: 37 outliers final: 0 residues processed: 37 average time/residue: 0.4958 time to fit residues: 42.6672 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 791 random chunks: chunk 471 optimal weight: 0.9980 chunk 304 optimal weight: 9.9990 chunk 455 optimal weight: 8.9990 chunk 229 optimal weight: 4.9990 chunk 149 optimal weight: 0.9990 chunk 147 optimal weight: 0.8980 chunk 484 optimal weight: 8.9990 chunk 519 optimal weight: 9.9990 chunk 376 optimal weight: 6.9990 chunk 71 optimal weight: 0.9990 chunk 599 optimal weight: 2.9990 overall best weight: 1.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 372 ASN ** G 383 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 33 GLN J 117 GLN L 326 GLN ** N 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 304 ASN O 153 HIS ** O 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** g 128 ASN ** h 106 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** n 3 GLN ** n 104 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7809 moved from start: 0.2702 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.245 67604 Z= 0.432 Angle : 1.360 50.626 91529 Z= 0.859 Chirality : 0.256 6.335 9877 Planarity : 0.004 0.056 11543 Dihedral : 8.597 178.114 9166 Min Nonbonded Distance : 2.055 Molprobity Statistics. All-atom Clashscore : 13.53 Ramachandran Plot: Outliers : 0.01 % Allowed : 4.90 % Favored : 95.09 % Rotamer: Outliers : 0.62 % Allowed : 17.34 % Favored : 82.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.69 % 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: -0.15 (0.10), residues: 8043 helix: 0.84 (0.08), residues: 4180 sheet: -1.01 (0.27), residues: 377 loop : -1.13 (0.11), residues: 3486 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16086 Ramachandran restraints generated. 8043 Oldfield, 0 Emsley, 8043 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16086 Ramachandran restraints generated. 8043 Oldfield, 0 Emsley, 8043 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 619 residues out of total 7047 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 575 time to evaluate : 5.778 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 44 outliers final: 12 residues processed: 609 average time/residue: 0.6384 time to fit residues: 688.8930 Evaluate side-chains 536 residues out of total 7047 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 524 time to evaluate : 6.593 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 0 residues processed: 12 average time/residue: 0.5747 time to fit residues: 19.8888 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 791 random chunks: chunk 693 optimal weight: 4.9990 chunk 730 optimal weight: 9.9990 chunk 666 optimal weight: 0.9990 chunk 710 optimal weight: 5.9990 chunk 427 optimal weight: 0.9990 chunk 309 optimal weight: 3.9990 chunk 557 optimal weight: 5.9990 chunk 218 optimal weight: 6.9990 chunk 641 optimal weight: 9.9990 chunk 671 optimal weight: 6.9990 chunk 707 optimal weight: 0.0770 overall best weight: 2.2146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 383 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 33 GLN L 326 GLN ** N 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 153 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 172 HIS Y 151 ASN ** b 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 106 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** k 13 HIS ** m 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 104 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7818 moved from start: 0.2775 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.242 67604 Z= 0.439 Angle : 1.367 50.861 91529 Z= 0.862 Chirality : 0.256 6.425 9877 Planarity : 0.004 0.056 11543 Dihedral : 8.545 178.411 9166 Min Nonbonded Distance : 2.053 Molprobity Statistics. All-atom Clashscore : 13.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.28 % Favored : 94.72 % Rotamer: Outliers : 0.58 % Allowed : 17.82 % Favored : 81.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.69 % 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: -0.13 (0.10), residues: 8043 helix: 0.85 (0.08), residues: 4176 sheet: -0.99 (0.27), residues: 377 loop : -1.11 (0.11), residues: 3490 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16086 Ramachandran restraints generated. 8043 Oldfield, 0 Emsley, 8043 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16086 Ramachandran restraints generated. 8043 Oldfield, 0 Emsley, 8043 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 595 residues out of total 7047 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 554 time to evaluate : 5.981 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 41 outliers final: 19 residues processed: 582 average time/residue: 0.6149 time to fit residues: 636.8901 Evaluate side-chains 542 residues out of total 7047 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 523 time to evaluate : 5.818 Switching outliers to nearest non-outliers outliers start: 19 outliers final: 0 residues processed: 19 average time/residue: 0.5547 time to fit residues: 27.2773 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 791 random chunks: chunk 466 optimal weight: 2.9990 chunk 751 optimal weight: 5.9990 chunk 458 optimal weight: 9.9990 chunk 356 optimal weight: 8.9990 chunk 522 optimal weight: 6.9990 chunk 788 optimal weight: 4.9990 chunk 725 optimal weight: 4.9990 chunk 627 optimal weight: 9.9990 chunk 65 optimal weight: 0.4980 chunk 484 optimal weight: 5.9990 chunk 384 optimal weight: 6.9990 overall best weight: 3.8988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 383 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 81 HIS J 33 GLN L 326 GLN ** L 413 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 50 ASN ** N 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 153 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 172 HIS ** b 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 106 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 104 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7849 moved from start: 0.2736 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.238 67604 Z= 0.467 Angle : 1.386 50.690 91529 Z= 0.869 Chirality : 0.257 6.395 9877 Planarity : 0.004 0.061 11543 Dihedral : 8.608 179.673 9166 Min Nonbonded Distance : 2.041 Molprobity Statistics. All-atom Clashscore : 15.01 Ramachandran Plot: Outliers : 0.01 % Allowed : 6.02 % Favored : 93.97 % Rotamer: Outliers : 0.37 % Allowed : 18.12 % Favored : 81.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.69 % 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: -0.19 (0.10), residues: 8043 helix: 0.79 (0.08), residues: 4168 sheet: -1.08 (0.27), residues: 384 loop : -1.11 (0.11), residues: 3491 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16086 Ramachandran restraints generated. 8043 Oldfield, 0 Emsley, 8043 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16086 Ramachandran restraints generated. 8043 Oldfield, 0 Emsley, 8043 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 555 residues out of total 7047 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 529 time to evaluate : 5.753 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 26 outliers final: 14 residues processed: 542 average time/residue: 0.6159 time to fit residues: 593.7216 Evaluate side-chains 528 residues out of total 7047 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 514 time to evaluate : 5.819 Switching outliers to nearest non-outliers outliers start: 14 outliers final: 0 residues processed: 14 average time/residue: 0.5161 time to fit residues: 21.2606 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 791 random chunks: chunk 498 optimal weight: 3.9990 chunk 668 optimal weight: 5.9990 chunk 192 optimal weight: 10.0000 chunk 578 optimal weight: 1.9990 chunk 92 optimal weight: 9.9990 chunk 174 optimal weight: 0.5980 chunk 628 optimal weight: 9.9990 chunk 263 optimal weight: 4.9990 chunk 645 optimal weight: 10.0000 chunk 79 optimal weight: 0.9990 chunk 115 optimal weight: 8.9990 overall best weight: 2.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 192 HIS ** G 383 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 326 GLN ** L 413 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 153 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 130 ASN ** R 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 172 HIS ** b 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 106 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 104 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** p 67 GLN ** p 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3453 r_free = 0.3453 target = 0.053126 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3230 r_free = 0.3230 target = 0.046249 restraints weight = 420887.424| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.047390 restraints weight = 202060.897| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.047765 restraints weight = 124755.932| |-----------------------------------------------------------------------------| r_work (final): 0.3267 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7910 moved from start: 0.2833 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.241 67604 Z= 0.444 Angle : 1.377 50.657 91529 Z= 0.865 Chirality : 0.257 6.367 9877 Planarity : 0.004 0.058 11543 Dihedral : 8.567 178.544 9166 Min Nonbonded Distance : 2.057 Molprobity Statistics. All-atom Clashscore : 14.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.62 % Favored : 94.38 % Rotamer: Outliers : 0.18 % Allowed : 18.32 % Favored : 81.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.69 % 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: -0.14 (0.10), residues: 8043 helix: 0.84 (0.08), residues: 4155 sheet: -1.04 (0.27), residues: 385 loop : -1.09 (0.11), residues: 3503 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11667.33 seconds wall clock time: 209 minutes 30.46 seconds (12570.46 seconds total)