Starting phenix.real_space_refine on Tue Apr 16 09:06:05 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8h9u_34582/04_2024/8h9u_34582_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8h9u_34582/04_2024/8h9u_34582.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.61 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8h9u_34582/04_2024/8h9u_34582.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8h9u_34582/04_2024/8h9u_34582.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8h9u_34582/04_2024/8h9u_34582_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8h9u_34582/04_2024/8h9u_34582_updated.pdb" } resolution = 2.61 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= 0.007 sd= 1.078 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: 6 Type Number sf(0) Gaussians P 13 5.49 5 Mg 5 5.21 5 S 159 5.16 5 C 24558 2.51 5 N 6524 2.21 5 O 7222 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 50": "OE1" <-> "OE2" Residue "A GLU 54": "OE1" <-> "OE2" Residue "A PHE 55": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 79": "OD1" <-> "OD2" Residue "A GLU 102": "OE1" <-> "OE2" Residue "A GLU 144": "OE1" <-> "OE2" Residue "A GLU 165": "OE1" <-> "OE2" Residue "A ARG 171": "NH1" <-> "NH2" Residue "A TYR 203": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 228": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 255": "OE1" <-> "OE2" Residue "A TYR 256": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 278": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 300": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 307": "OE1" <-> "OE2" Residue "A PHE 316": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 328": "OE1" <-> "OE2" Residue "A PHE 351": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 393": "OE1" <-> "OE2" Residue "A TYR 397": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 409": "OD1" <-> "OD2" Residue "A GLU 439": "OE1" <-> "OE2" Residue "A GLU 440": "OE1" <-> "OE2" Residue "A PHE 464": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 468": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 486": "OD1" <-> "OD2" Residue "A GLU 491": "OE1" <-> "OE2" Residue "A ASP 494": "OD1" <-> "OD2" Residue "A PHE 508": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 509": "OE1" <-> "OE2" Residue "B GLU 50": "OE1" <-> "OE2" Residue "B PHE 55": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 102": "OE1" <-> "OE2" Residue "B GLU 165": "OE1" <-> "OE2" Residue "B TYR 203": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 224": "OD1" <-> "OD2" Residue "B TYR 228": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 255": "OE1" <-> "OE2" Residue "B TYR 256": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 278": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 299": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 300": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 314": "OD1" <-> "OD2" Residue "B PHE 316": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 328": "OE1" <-> "OE2" Residue "B TYR 337": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 357": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 373": "NH1" <-> "NH2" Residue "B TYR 397": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 399": "OE1" <-> "OE2" Residue "B GLU 440": "OE1" <-> "OE2" Residue "B TYR 452": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 457": "OE1" <-> "OE2" Residue "B PHE 464": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 468": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 499": "OE1" <-> "OE2" Residue "B PHE 508": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 509": "OE1" <-> "OE2" Residue "C GLU 26": "OE1" <-> "OE2" Residue "C GLU 27": "OE1" <-> "OE2" Residue "C ARG 30": "NH1" <-> "NH2" Residue "C GLU 54": "OE1" <-> "OE2" Residue "C PHE 55": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 67": "OE1" <-> "OE2" Residue "C GLU 165": "OE1" <-> "OE2" Residue "C ASP 194": "OD1" <-> "OD2" Residue "C GLU 195": "OE1" <-> "OE2" Residue "C TYR 200": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 203": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 228": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 255": "OE1" <-> "OE2" Residue "C TYR 256": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 278": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 292": "OE1" <-> "OE2" Residue "C PHE 299": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 300": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 307": "OE1" <-> "OE2" Residue "C PHE 316": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 333": "OD1" <-> "OD2" Residue "C TYR 337": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 393": "OE1" <-> "OE2" Residue "C TYR 397": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 426": "OE1" <-> "OE2" Residue "C GLU 440": "OE1" <-> "OE2" Residue "C GLU 457": "OE1" <-> "OE2" Residue "C PHE 464": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 468": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 486": "OD1" <-> "OD2" Residue "C ASP 494": "OD1" <-> "OD2" Residue "C PHE 504": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 508": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 28": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 29": "OD1" <-> "OD2" Residue "E GLU 30": "OE1" <-> "OE2" Residue "E GLU 45": "OE1" <-> "OE2" Residue "E GLU 58": "OE1" <-> "OE2" Residue "E GLU 107": "OE1" <-> "OE2" Residue "E PHE 116": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 122": "OE1" <-> "OE2" Residue "E PHE 126": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 158": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 171": "OE1" <-> "OE2" Residue "E GLU 195": "OE1" <-> "OE2" Residue "E TYR 200": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 202": "OE1" <-> "OE2" Residue "E GLU 227": "OE1" <-> "OE2" Residue "E GLU 244": "OE1" <-> "OE2" Residue "E PHE 257": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 262": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 264": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 270": "OE1" <-> "OE2" Residue "E GLU 297": "OE1" <-> "OE2" Residue "E TYR 314": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 318": "OD1" <-> "OD2" Residue "E ARG 359": "NH1" <-> "NH2" Residue "E TYR 371": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 384": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 389": "OD1" <-> "OD2" Residue "E GLU 401": "OE1" <-> "OE2" Residue "E GLU 402": "OE1" <-> "OE2" Residue "E ASP 403": "OD1" <-> "OD2" Residue "E ARG 411": "NH1" <-> "NH2" Residue "E PHE 416": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 425": "OE1" <-> "OE2" Residue "E GLU 451": "OE1" <-> "OE2" Residue "E ASP 453": "OD1" <-> "OD2" Residue "E PHE 460": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 461": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 468": "OE1" <-> "OE2" Residue "F PHE 28": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 29": "OD1" <-> "OD2" Residue "F GLU 30": "OE1" <-> "OE2" Residue "F ARG 74": "NH1" <-> "NH2" Residue "F GLU 92": "OE1" <-> "OE2" Residue "F GLU 103": "OE1" <-> "OE2" Residue "F GLU 107": "OE1" <-> "OE2" Residue "F ARG 108": "NH1" <-> "NH2" Residue "F PHE 116": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 126": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 134": "OE1" <-> "OE2" Residue "F PHE 158": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 171": "OE1" <-> "OE2" Residue "F ARG 192": "NH1" <-> "NH2" Residue "F GLU 195": "OE1" <-> "OE2" Residue "F TYR 200": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 222": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 227": "OE1" <-> "OE2" Residue "F ARG 232": "NH1" <-> "NH2" Residue "F ARG 247": "NH1" <-> "NH2" Residue "F PHE 262": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 263": "NH1" <-> "NH2" Residue "F PHE 264": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 314": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 329": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 369": "OE1" <-> "OE2" Residue "F TYR 371": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 384": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 389": "OD1" <-> "OD2" Residue "F ASP 397": "OD1" <-> "OD2" Residue "F ASP 403": "OD1" <-> "OD2" Residue "F PHE 416": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 425": "OE1" <-> "OE2" Residue "F GLU 451": "OE1" <-> "OE2" Residue "F PHE 460": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 461": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 468": "OE1" <-> "OE2" Residue "D PHE 28": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 29": "OD1" <-> "OD2" Residue "D GLU 45": "OE1" <-> "OE2" Residue "D GLU 58": "OE1" <-> "OE2" Residue "D ASP 67": "OD1" <-> "OD2" Residue "D GLU 103": "OE1" <-> "OE2" Residue "D GLU 107": "OE1" <-> "OE2" Residue "D PHE 116": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 125": "OE1" <-> "OE2" Residue "D PHE 126": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 134": "OE1" <-> "OE2" Residue "D PHE 158": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 171": "OE1" <-> "OE2" Residue "D PHE 186": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 195": "OE1" <-> "OE2" Residue "D ASP 198": "OD1" <-> "OD2" Residue "D ASP 213": "OD1" <-> "OD2" Residue "D TYR 222": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 244": "OE1" <-> "OE2" Residue "D PHE 246": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 247": "NH1" <-> "NH2" Residue "D ASP 248": "OD1" <-> "OD2" Residue "D ASP 253": "OD1" <-> "OD2" Residue "D PHE 262": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 264": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 277": "NH1" <-> "NH2" Residue "D TYR 314": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 340": "NH1" <-> "NH2" Residue "D GLU 344": "OE1" <-> "OE2" Residue "D TYR 371": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 384": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 398": "OE1" <-> "OE2" Residue "D GLU 402": "OE1" <-> "OE2" Residue "D ASP 403": "OD1" <-> "OD2" Residue "D PHE 416": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 425": "OE1" <-> "OE2" Residue "D TYR 461": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 468": "OE1" <-> "OE2" Residue "G ASP 5": "OD1" <-> "OD2" Residue "G ARG 33": "NH1" <-> "NH2" Residue "G GLU 37": "OE1" <-> "OE2" Residue "G TYR 44": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 61": "OE1" <-> "OE2" Residue "G ASP 122": "OD1" <-> "OD2" Residue "G GLU 154": "OE1" <-> "OE2" Residue "G ASP 156": "OD1" <-> "OD2" Residue "G ASP 195": "OD1" <-> "OD2" Residue "G ASP 244": "OD1" <-> "OD2" Residue "G PHE 250": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 261": "OE1" <-> "OE2" Residue "O GLU 38": "OE1" <-> "OE2" Residue "O PHE 105": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O GLU 128": "OE1" <-> "OE2" Residue "O ASP 172": "OD1" <-> "OD2" Residue "K GLU 7": "OE1" <-> "OE2" Residue "K TYR 8": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K GLU 19": "OE1" <-> "OE2" Residue "K GLU 49": "OE1" <-> "OE2" Residue "K TYR 51": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 69": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ASP 83": "OD1" <-> "OD2" Residue "K ASP 109": "OD1" <-> "OD2" Residue "K TYR 123": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 125": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ASP 156": "OD1" <-> "OD2" Residue "K TYR 157": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K GLU 171": "OE1" <-> "OE2" Residue "L GLU 72": "OE1" <-> "OE2" Residue "M ASP 11": "OD1" <-> "OD2" Residue "M PHE 15": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M GLU 17": "OE1" <-> "OE2" Residue "M ASP 52": "OD1" <-> "OD2" Residue "M TYR 56": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M ASP 67": "OD1" <-> "OD2" Residue "M ASP 83": "OD1" <-> "OD2" Residue "M ASP 90": "OD1" <-> "OD2" Residue "M GLU 92": "OE1" <-> "OE2" Residue "M GLU 93": "OE1" <-> "OE2" Residue "M ASP 96": "OD1" <-> "OD2" Residue "M GLU 115": "OE1" <-> "OE2" Residue "M PHE 127": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M ASP 128": "OD1" <-> "OD2" Residue "M ASP 134": "OD1" <-> "OD2" Residue "M GLU 137": "OE1" <-> "OE2" Residue "3 ASP 3": "OD1" <-> "OD2" Residue "3 ARG 38": "NH1" <-> "NH2" Residue "3 PHE 47": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "3 PHE 69": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "4 ASP 3": "OD1" <-> "OD2" Residue "4 PHE 47": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "4 PHE 69": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5 ASP 3": "OD1" <-> "OD2" Residue "5 ARG 38": "NH1" <-> "NH2" Residue "5 PHE 47": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5 PHE 69": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "6 ASP 3": "OD1" <-> "OD2" Residue "6 ARG 38": "NH1" <-> "NH2" Residue "6 PHE 47": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "6 PHE 69": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "7 ASP 3": "OD1" <-> "OD2" Residue "7 PHE 47": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "7 PHE 69": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "8 ASP 3": "OD1" <-> "OD2" Residue "8 PHE 47": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "8 PHE 69": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "1 ASP 3": "OD1" <-> "OD2" Residue "1 ARG 38": "NH1" <-> "NH2" Residue "1 PHE 47": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "1 PHE 69": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "2 ASP 3": "OD1" <-> "OD2" Residue "2 ARG 38": "NH1" <-> "NH2" Residue "2 PHE 47": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "2 PHE 69": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 45": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 75": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 118": "OE1" <-> "OE2" Residue "H ASP 124": "OD1" <-> "OD2" Residue "H GLU 125": "OE1" <-> "OE2" Residue "H GLU 136": "OE1" <-> "OE2" Residue "H GLU 139": "OE1" <-> "OE2" Residue "H GLU 146": "OE1" <-> "OE2" Residue "I TYR 15": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N PHE 9": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N PHE 26": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N TYR 36": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N PHE 128": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N GLU 203": "OE1" <-> "OE2" Residue "N ASP 224": "OD1" <-> "OD2" Residue "Q TYR 47": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R GLU 24": "OE1" <-> "OE2" Residue "R ASP 33": "OD1" <-> "OD2" Residue "R ARG 45": "NH1" <-> "NH2" Residue "R TYR 50": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R TYR 54": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R TYR 77": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R PHE 79": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R TYR 92": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S GLU 71": "OE1" <-> "OE2" Residue "S GLU 81": "OE1" <-> "OE2" Residue "S ASP 101": "OD1" <-> "OD2" Residue "T PHE 20": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T TYR 25": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T TYR 30": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T GLU 38": "OE1" <-> "OE2" Residue "T GLU 40": "OE1" <-> "OE2" Residue "J ARG 16": "NH1" <-> "NH2" Residue "J PHE 22": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ARG 32": "NH1" <-> "NH2" Residue "J TYR 33": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 34": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ARG 35": "NH1" <-> "NH2" Residue "J ARG 39": "NH1" <-> "NH2" Residue "J GLU 40": "OE1" <-> "OE2" Time to flip residues: 0.13s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 38481 Number of models: 1 Model: "" Number of chains: 33 Chain: "A" Number of atoms: 3706 Number of conformers: 1 Conformer: "" Number of residues, atoms: 486, 3706 Classifications: {'peptide': 486} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 16, 'TRANS': 467} Chain: "B" Number of atoms: 3639 Number of conformers: 1 Conformer: "" Number of residues, atoms: 477, 3639 Classifications: {'peptide': 477} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 16, 'TRANS': 458} Chain breaks: 1 Chain: "C" Number of atoms: 3587 Number of conformers: 1 Conformer: "" Number of residues, atoms: 470, 3587 Classifications: {'peptide': 470} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 16, 'TRANS': 451} Chain breaks: 1 Chain: "E" Number of atoms: 3458 Number of conformers: 1 Conformer: "" Number of residues, atoms: 456, 3458 Classifications: {'peptide': 456} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 23, 'TRANS': 430} Chain breaks: 1 Chain: "F" Number of atoms: 3529 Number of conformers: 1 Conformer: "" Number of residues, atoms: 466, 3529 Classifications: {'peptide': 466} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 23, 'TRANS': 440} Chain: "D" Number of atoms: 3562 Number of conformers: 1 Conformer: "" Number of residues, atoms: 470, 3562 Classifications: {'peptide': 470} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 23, 'TRANS': 444} Chain: "G" Number of atoms: 2103 Number of conformers: 1 Conformer: "" Number of residues, atoms: 271, 2103 Classifications: {'peptide': 271} Link IDs: {'PTRANS': 5, 'TRANS': 265} Chain: "O" Number of atoms: 1437 Number of conformers: 1 Conformer: "" Number of residues, atoms: 187, 1437 Classifications: {'peptide': 187} Link IDs: {'PTRANS': 8, 'TRANS': 178} Chain: "K" Number of atoms: 1573 Number of conformers: 1 Conformer: "" Number of residues, atoms: 198, 1573 Classifications: {'peptide': 198} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PTRANS': 6, 'TRANS': 191} Chain breaks: 1 Unresolved non-hydrogen bonds: 37 Unresolved non-hydrogen angles: 44 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "L" Number of atoms: 549 Number of conformers: 1 Conformer: "" Number of residues, atoms: 67, 549 Classifications: {'peptide': 67} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 4, 'TRANS': 62} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 12 Planarities with less than four sites: {'TYR:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "M" Number of atoms: 1259 Number of conformers: 1 Conformer: "" Number of residues, atoms: 156, 1259 Classifications: {'peptide': 156} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 144} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 8 Chain: "3" Number of atoms: 534 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 534 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 1, 'TRANS': 73} Chain: "4" Number of atoms: 534 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 534 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 1, 'TRANS': 73} Chain: "5" Number of atoms: 534 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 534 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 1, 'TRANS': 73} Chain: "6" Number of atoms: 534 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 534 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 1, 'TRANS': 73} Chain: "7" Number of atoms: 534 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 534 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 1, 'TRANS': 73} Chain: "8" Number of atoms: 534 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 534 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 1, 'TRANS': 73} Chain: "1" Number of atoms: 534 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 534 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 1, 'TRANS': 73} Chain: "2" Number of atoms: 534 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 534 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 1, 'TRANS': 73} Chain: "H" Number of atoms: 975 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 975 Classifications: {'peptide': 132} Link IDs: {'PTRANS': 4, 'TRANS': 127} Chain: "I" Number of atoms: 354 Number of conformers: 1 Conformer: "" Number of residues, atoms: 45, 354 Classifications: {'peptide': 45} Link IDs: {'TRANS': 44} Chain: "N" Number of atoms: 1718 Number of conformers: 1 Conformer: "" Number of residues, atoms: 223, 1718 Classifications: {'peptide': 223} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 14, 'TRANS': 208} Chain: "P" Number of atoms: 344 Number of conformers: 1 Conformer: "" Number of residues, atoms: 41, 344 Classifications: {'peptide': 41} Link IDs: {'PTRANS': 2, 'TRANS': 38} Chain: "Q" Number of atoms: 422 Number of conformers: 1 Conformer: "" Number of residues, atoms: 51, 422 Classifications: {'peptide': 51} Link IDs: {'PTRANS': 8, 'TRANS': 42} Chain: "R" Number of atoms: 621 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 621 Classifications: {'peptide': 74} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 71} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Chain: "S" Number of atoms: 605 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 605 Classifications: {'peptide': 77} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 72} Chain: "T" Number of atoms: 346 Number of conformers: 1 Conformer: "" Number of residues, atoms: 44, 346 Classifications: {'peptide': 44} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 4, 'TRANS': 39} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Chain: "J" Number of atoms: 270 Number of conformers: 1 Conformer: "" Number of residues, atoms: 35, 270 Classifications: {'peptide': 35} Link IDs: {'TRANS': 34} Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 19.85, per 1000 atoms: 0.52 Number of scatterers: 38481 At special positions: 0 Unit cell: (144.54, 135.05, 247.47, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 159 16.00 P 13 15.00 Mg 5 11.99 O 7222 8.00 N 6524 7.00 C 24558 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 17.38 Conformation dependent library (CDL) restraints added in 7.2 seconds 9924 Ramachandran restraints generated. 4962 Oldfield, 0 Emsley, 4962 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 9170 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 191 helices and 26 sheets defined 53.9% alpha, 9.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 7.89 Creating SS restraints... Processing helix chain 'A' and resid 79 through 81 No H-bonds generated for 'chain 'A' and resid 79 through 81' Processing helix chain 'A' and resid 101 through 103 No H-bonds generated for 'chain 'A' and resid 101 through 103' Processing helix chain 'A' and resid 151 through 156 Processing helix chain 'A' and resid 175 through 191 removed outlier: 3.762A pdb=" N GLN A 186 " --> pdb=" O THR A 182 " (cutoff:3.500A) removed outlier: 4.549A pdb=" N LYS A 187 " --> pdb=" O ILE A 183 " (cutoff:3.500A) removed outlier: 5.087A pdb=" N ARG A 188 " --> pdb=" O ILE A 184 " (cutoff:3.500A) removed outlier: 4.698A pdb=" N PHE A 189 " --> pdb=" O ASN A 185 " (cutoff:3.500A) Processing helix chain 'A' and resid 195 through 197 No H-bonds generated for 'chain 'A' and resid 195 through 197' Processing helix chain 'A' and resid 210 through 222 Processing helix chain 'A' and resid 240 through 260 Proline residue: A 247 - end of helix removed outlier: 3.953A pdb=" N PHE A 257 " --> pdb=" O MET A 253 " (cutoff:3.500A) Processing helix chain 'A' and resid 271 through 284 Processing helix chain 'A' and resid 291 through 293 No H-bonds generated for 'chain 'A' and resid 291 through 293' Processing helix chain 'A' and resid 298 through 308 removed outlier: 4.525A pdb=" N ARG A 308 " --> pdb=" O ARG A 304 " (cutoff:3.500A) Processing helix chain 'A' and resid 314 through 316 No H-bonds generated for 'chain 'A' and resid 314 through 316' Processing helix chain 'A' and resid 337 through 345 Processing helix chain 'A' and resid 354 through 358 Processing helix chain 'A' and resid 375 through 378 Processing helix chain 'A' and resid 381 through 403 removed outlier: 3.970A pdb=" N THR A 389 " --> pdb=" O GLN A 385 " (cutoff:3.500A) removed outlier: 4.855A pdb=" N ALA A 402 " --> pdb=" O ARG A 398 " (cutoff:3.500A) removed outlier: 5.980A pdb=" N PHE A 403 " --> pdb=" O GLU A 399 " (cutoff:3.500A) Processing helix chain 'A' and resid 407 through 409 No H-bonds generated for 'chain 'A' and resid 407 through 409' Processing helix chain 'A' and resid 412 through 428 Processing helix chain 'A' and resid 438 through 449 Processing helix chain 'A' and resid 458 through 475 removed outlier: 4.601A pdb=" N THR A 462 " --> pdb=" O PRO A 458 " (cutoff:3.500A) removed outlier: 5.339A pdb=" N LYS A 463 " --> pdb=" O SER A 459 " (cutoff:3.500A) Processing helix chain 'A' and resid 477 through 486 Processing helix chain 'A' and resid 491 through 506 Processing helix chain 'B' and resid 79 through 81 No H-bonds generated for 'chain 'B' and resid 79 through 81' Processing helix chain 'B' and resid 101 through 103 No H-bonds generated for 'chain 'B' and resid 101 through 103' Processing helix chain 'B' and resid 151 through 156 Processing helix chain 'B' and resid 175 through 190 removed outlier: 4.300A pdb=" N LYS B 187 " --> pdb=" O ILE B 183 " (cutoff:3.500A) removed outlier: 4.914A pdb=" N ARG B 188 " --> pdb=" O ILE B 184 " (cutoff:3.500A) removed outlier: 4.663A pdb=" N PHE B 189 " --> pdb=" O ASN B 185 " (cutoff:3.500A) Processing helix chain 'B' and resid 195 through 197 No H-bonds generated for 'chain 'B' and resid 195 through 197' Processing helix chain 'B' and resid 210 through 222 Processing helix chain 'B' and resid 226 through 228 No H-bonds generated for 'chain 'B' and resid 226 through 228' Processing helix chain 'B' and resid 240 through 260 Proline residue: B 247 - end of helix removed outlier: 4.053A pdb=" N PHE B 257 " --> pdb=" O MET B 253 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N ASN B 260 " --> pdb=" O TYR B 256 " (cutoff:3.500A) Processing helix chain 'B' and resid 271 through 284 Processing helix chain 'B' and resid 291 through 293 No H-bonds generated for 'chain 'B' and resid 291 through 293' Processing helix chain 'B' and resid 296 through 308 removed outlier: 4.280A pdb=" N PHE B 299 " --> pdb=" O GLY B 296 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N TYR B 300 " --> pdb=" O ASP B 297 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N LEU B 301 " --> pdb=" O VAL B 298 " (cutoff:3.500A) removed outlier: 4.350A pdb=" N ARG B 304 " --> pdb=" O LEU B 301 " (cutoff:3.500A) removed outlier: 4.255A pdb=" N GLU B 307 " --> pdb=" O ARG B 304 " (cutoff:3.500A) Processing helix chain 'B' and resid 337 through 345 Processing helix chain 'B' and resid 354 through 358 Processing helix chain 'B' and resid 376 through 378 No H-bonds generated for 'chain 'B' and resid 376 through 378' Processing helix chain 'B' and resid 381 through 400 removed outlier: 4.498A pdb=" N THR B 389 " --> pdb=" O GLN B 385 " (cutoff:3.500A) Processing helix chain 'B' and resid 413 through 428 Processing helix chain 'B' and resid 438 through 449 Processing helix chain 'B' and resid 458 through 474 removed outlier: 4.504A pdb=" N THR B 462 " --> pdb=" O PRO B 458 " (cutoff:3.500A) removed outlier: 5.287A pdb=" N LYS B 463 " --> pdb=" O SER B 459 " (cutoff:3.500A) Processing helix chain 'B' and resid 477 through 486 Processing helix chain 'B' and resid 491 through 506 Processing helix chain 'C' and resid 79 through 81 No H-bonds generated for 'chain 'C' and resid 79 through 81' Processing helix chain 'C' and resid 151 through 156 Processing helix chain 'C' and resid 175 through 190 removed outlier: 3.732A pdb=" N GLN C 186 " --> pdb=" O THR C 182 " (cutoff:3.500A) removed outlier: 4.547A pdb=" N LYS C 187 " --> pdb=" O ILE C 183 " (cutoff:3.500A) removed outlier: 5.039A pdb=" N ARG C 188 " --> pdb=" O ILE C 184 " (cutoff:3.500A) removed outlier: 4.630A pdb=" N PHE C 189 " --> pdb=" O ASN C 185 " (cutoff:3.500A) Processing helix chain 'C' and resid 210 through 222 Processing helix chain 'C' and resid 226 through 228 No H-bonds generated for 'chain 'C' and resid 226 through 228' Processing helix chain 'C' and resid 240 through 260 Proline residue: C 247 - end of helix removed outlier: 3.998A pdb=" N PHE C 257 " --> pdb=" O MET C 253 " (cutoff:3.500A) Processing helix chain 'C' and resid 271 through 284 Processing helix chain 'C' and resid 291 through 293 No H-bonds generated for 'chain 'C' and resid 291 through 293' Processing helix chain 'C' and resid 298 through 308 removed outlier: 4.008A pdb=" N LEU C 305 " --> pdb=" O LEU C 301 " (cutoff:3.500A) removed outlier: 4.448A pdb=" N ARG C 308 " --> pdb=" O ARG C 304 " (cutoff:3.500A) Processing helix chain 'C' and resid 314 through 316 No H-bonds generated for 'chain 'C' and resid 314 through 316' Processing helix chain 'C' and resid 337 through 345 Processing helix chain 'C' and resid 354 through 358 Processing helix chain 'C' and resid 375 through 378 Processing helix chain 'C' and resid 381 through 399 removed outlier: 3.599A pdb=" N THR C 389 " --> pdb=" O GLN C 385 " (cutoff:3.500A) Processing helix chain 'C' and resid 418 through 428 Processing helix chain 'C' and resid 438 through 449 Processing helix chain 'C' and resid 458 through 475 removed outlier: 4.314A pdb=" N THR C 462 " --> pdb=" O PRO C 458 " (cutoff:3.500A) removed outlier: 4.962A pdb=" N LYS C 463 " --> pdb=" O SER C 459 " (cutoff:3.500A) Processing helix chain 'C' and resid 477 through 486 Processing helix chain 'C' and resid 491 through 507 Processing helix chain 'E' and resid 91 through 93 No H-bonds generated for 'chain 'E' and resid 91 through 93' Processing helix chain 'E' and resid 126 through 128 No H-bonds generated for 'chain 'E' and resid 126 through 128' Processing helix chain 'E' and resid 141 through 146 Processing helix chain 'E' and resid 165 through 179 Processing helix chain 'E' and resid 193 through 205 Processing helix chain 'E' and resid 229 through 248 removed outlier: 4.887A pdb=" N ALA E 236 " --> pdb=" O ARG E 232 " (cutoff:3.500A) removed outlier: 4.894A pdb=" N LEU E 237 " --> pdb=" O ALA E 233 " (cutoff:3.500A) Processing helix chain 'E' and resid 261 through 274 Processing helix chain 'E' and resid 281 through 283 No H-bonds generated for 'chain 'E' and resid 281 through 283' Processing helix chain 'E' and resid 288 through 298 removed outlier: 4.717A pdb=" N ARG E 298 " --> pdb=" O THR E 294 " (cutoff:3.500A) Processing helix chain 'E' and resid 316 through 318 No H-bonds generated for 'chain 'E' and resid 316 through 318' Processing helix chain 'E' and resid 323 through 328 Processing helix chain 'E' and resid 340 through 344 Processing helix chain 'E' and resid 368 through 390 removed outlier: 4.136A pdb=" N ILE E 390 " --> pdb=" O SER E 386 " (cutoff:3.500A) Processing helix chain 'E' and resid 403 through 417 Processing helix chain 'E' and resid 422 through 428 removed outlier: 5.200A pdb=" N VAL E 426 " --> pdb=" O VAL E 423 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N THR E 428 " --> pdb=" O GLU E 425 " (cutoff:3.500A) Processing helix chain 'E' and resid 437 through 448 Processing helix chain 'E' and resid 457 through 459 No H-bonds generated for 'chain 'E' and resid 457 through 459' Processing helix chain 'E' and resid 466 through 474 Processing helix chain 'F' and resid 91 through 93 No H-bonds generated for 'chain 'F' and resid 91 through 93' Processing helix chain 'F' and resid 126 through 128 No H-bonds generated for 'chain 'F' and resid 126 through 128' Processing helix chain 'F' and resid 141 through 146 Processing helix chain 'F' and resid 165 through 175 Processing helix chain 'F' and resid 193 through 205 Processing helix chain 'F' and resid 229 through 248 removed outlier: 4.914A pdb=" N ALA F 236 " --> pdb=" O ARG F 232 " (cutoff:3.500A) removed outlier: 4.886A pdb=" N LEU F 237 " --> pdb=" O ALA F 233 " (cutoff:3.500A) Processing helix chain 'F' and resid 261 through 272 removed outlier: 3.720A pdb=" N THR F 265 " --> pdb=" O ILE F 261 " (cutoff:3.500A) Processing helix chain 'F' and resid 281 through 283 No H-bonds generated for 'chain 'F' and resid 281 through 283' Processing helix chain 'F' and resid 288 through 296 Processing helix chain 'F' and resid 316 through 318 No H-bonds generated for 'chain 'F' and resid 316 through 318' Processing helix chain 'F' and resid 323 through 331 removed outlier: 4.615A pdb=" N ALA F 330 " --> pdb=" O ALA F 326 " (cutoff:3.500A) removed outlier: 4.560A pdb=" N HIS F 331 " --> pdb=" O THR F 327 " (cutoff:3.500A) Processing helix chain 'F' and resid 340 through 344 Processing helix chain 'F' and resid 363 through 366 No H-bonds generated for 'chain 'F' and resid 363 through 366' Processing helix chain 'F' and resid 368 through 394 removed outlier: 4.818A pdb=" N ASP F 389 " --> pdb=" O LYS F 385 " (cutoff:3.500A) removed outlier: 5.223A pdb=" N ILE F 390 " --> pdb=" O SER F 386 " (cutoff:3.500A) Processing helix chain 'F' and resid 396 through 398 No H-bonds generated for 'chain 'F' and resid 396 through 398' Processing helix chain 'F' and resid 401 through 417 Processing helix chain 'F' and resid 422 through 427 removed outlier: 3.751A pdb=" N GLU F 425 " --> pdb=" O GLN F 422 " (cutoff:3.500A) removed outlier: 4.699A pdb=" N VAL F 426 " --> pdb=" O VAL F 423 " (cutoff:3.500A) Processing helix chain 'F' and resid 437 through 449 Processing helix chain 'F' and resid 457 through 460 removed outlier: 3.527A pdb=" N PHE F 460 " --> pdb=" O GLU F 457 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 457 through 460' Processing helix chain 'F' and resid 466 through 476 Processing helix chain 'D' and resid 91 through 93 No H-bonds generated for 'chain 'D' and resid 91 through 93' Processing helix chain 'D' and resid 141 through 146 Processing helix chain 'D' and resid 165 through 179 Processing helix chain 'D' and resid 193 through 204 Processing helix chain 'D' and resid 229 through 248 removed outlier: 4.964A pdb=" N ALA D 236 " --> pdb=" O ARG D 232 " (cutoff:3.500A) removed outlier: 4.928A pdb=" N LEU D 237 " --> pdb=" O ALA D 233 " (cutoff:3.500A) Processing helix chain 'D' and resid 261 through 275 removed outlier: 3.609A pdb=" N THR D 265 " --> pdb=" O ILE D 261 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N VAL D 271 " --> pdb=" O ALA D 267 " (cutoff:3.500A) removed outlier: 4.361A pdb=" N ALA D 273 " --> pdb=" O SER D 269 " (cutoff:3.500A) removed outlier: 5.684A pdb=" N LEU D 274 " --> pdb=" O GLU D 270 " (cutoff:3.500A) Processing helix chain 'D' and resid 281 through 283 No H-bonds generated for 'chain 'D' and resid 281 through 283' Processing helix chain 'D' and resid 288 through 298 removed outlier: 4.440A pdb=" N ARG D 298 " --> pdb=" O THR D 294 " (cutoff:3.500A) Processing helix chain 'D' and resid 316 through 318 No H-bonds generated for 'chain 'D' and resid 316 through 318' Processing helix chain 'D' and resid 323 through 331 removed outlier: 4.481A pdb=" N ALA D 330 " --> pdb=" O ALA D 326 " (cutoff:3.500A) removed outlier: 4.457A pdb=" N HIS D 331 " --> pdb=" O THR D 327 " (cutoff:3.500A) Processing helix chain 'D' and resid 340 through 345 removed outlier: 3.757A pdb=" N LEU D 345 " --> pdb=" O ALA D 341 " (cutoff:3.500A) Processing helix chain 'D' and resid 363 through 366 No H-bonds generated for 'chain 'D' and resid 363 through 366' Processing helix chain 'D' and resid 368 through 394 removed outlier: 4.121A pdb=" N ASP D 389 " --> pdb=" O LYS D 385 " (cutoff:3.500A) removed outlier: 4.378A pdb=" N ILE D 390 " --> pdb=" O SER D 386 " (cutoff:3.500A) Processing helix chain 'D' and resid 401 through 417 Processing helix chain 'D' and resid 425 through 428 No H-bonds generated for 'chain 'D' and resid 425 through 428' Processing helix chain 'D' and resid 437 through 449 Processing helix chain 'D' and resid 466 through 479 Processing helix chain 'G' and resid 3 through 31 Processing helix chain 'G' and resid 36 through 48 Proline residue: G 40 - end of helix Processing helix chain 'G' and resid 50 through 54 Processing helix chain 'G' and resid 81 through 98 Processing helix chain 'G' and resid 110 through 116 Processing helix chain 'G' and resid 138 through 149 Processing helix chain 'G' and resid 181 through 185 Processing helix chain 'G' and resid 200 through 220 removed outlier: 3.521A pdb=" N ILE G 212 " --> pdb=" O ASN G 208 " (cutoff:3.500A) Processing helix chain 'G' and resid 224 through 270 removed outlier: 3.724A pdb=" N MET G 229 " --> pdb=" O GLN G 225 " (cutoff:3.500A) Processing helix chain 'O' and resid 14 through 29 removed outlier: 3.618A pdb=" N GLN O 29 " --> pdb=" O ALA O 25 " (cutoff:3.500A) Processing helix chain 'O' and resid 32 through 46 Processing helix chain 'O' and resid 49 through 56 Processing helix chain 'O' and resid 62 through 74 Processing helix chain 'O' and resid 80 through 92 Processing helix chain 'O' and resid 95 through 112 removed outlier: 4.764A pdb=" N GLN O 99 " --> pdb=" O SER O 96 " (cutoff:3.500A) Processing helix chain 'O' and resid 128 through 138 Processing helix chain 'O' and resid 156 through 158 No H-bonds generated for 'chain 'O' and resid 156 through 158' Processing helix chain 'O' and resid 175 through 187 Processing helix chain 'K' and resid 19 through 29 Proline residue: K 27 - end of helix Processing helix chain 'K' and resid 33 through 47 Processing helix chain 'K' and resid 55 through 182 Proline residue: K 76 - end of helix removed outlier: 3.831A pdb=" N SER K 100 " --> pdb=" O ALA K 96 " (cutoff:3.500A) removed outlier: 4.775A pdb=" N HIS K 122 " --> pdb=" O VAL K 118 " (cutoff:3.500A) removed outlier: 6.226A pdb=" N TYR K 123 " --> pdb=" O GLN K 119 " (cutoff:3.500A) removed outlier: 5.392A pdb=" N LEU K 124 " --> pdb=" O LYS K 120 " (cutoff:3.500A) removed outlier: 4.854A pdb=" N PHE K 125 " --> pdb=" O ARG K 121 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ASP K 126 " --> pdb=" O HIS K 122 " (cutoff:3.500A) Processing helix chain 'K' and resid 194 through 205 removed outlier: 3.512A pdb=" N LEU K 201 " --> pdb=" O CYS K 197 " (cutoff:3.500A) Processing helix chain 'L' and resid 41 through 54 Processing helix chain 'L' and resid 68 through 82 removed outlier: 4.492A pdb=" N ARG L 73 " --> pdb=" O GLN L 69 " (cutoff:3.500A) Processing helix chain 'M' and resid 13 through 18 removed outlier: 3.934A pdb=" N ILE M 18 " --> pdb=" O ALA M 14 " (cutoff:3.500A) Processing helix chain 'M' and resid 21 through 42 removed outlier: 3.775A pdb=" N LYS M 24 " --> pdb=" O GLN M 21 " (cutoff:3.500A) removed outlier: 5.681A pdb=" N ALA M 25 " --> pdb=" O ASN M 22 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N ILE M 26 " --> pdb=" O GLN M 23 " (cutoff:3.500A) removed outlier: 4.239A pdb=" N TRP M 33 " --> pdb=" O LEU M 30 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N LEU M 37 " --> pdb=" O ASN M 34 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N ARG M 40 " --> pdb=" O LEU M 37 " (cutoff:3.500A) Processing helix chain 'M' and resid 53 through 57 Processing helix chain 'M' and resid 65 through 74 Processing helix chain 'M' and resid 86 through 122 Processing helix chain 'M' and resid 127 through 129 No H-bonds generated for 'chain 'M' and resid 127 through 129' Processing helix chain 'M' and resid 132 through 138 Processing helix chain '3' and resid 2 through 38 removed outlier: 3.888A pdb=" N PHE 3 8 " --> pdb=" O THR 3 4 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ILE 3 9 " --> pdb=" O ALA 3 5 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N THR 3 15 " --> pdb=" O ALA 3 11 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N VAL 3 16 " --> pdb=" O GLY 3 12 " (cutoff:3.500A) removed outlier: 4.185A pdb=" N GLY 3 17 " --> pdb=" O ALA 3 13 " (cutoff:3.500A) removed outlier: 4.594A pdb=" N VAL 3 18 " --> pdb=" O ALA 3 14 " (cutoff:3.500A) removed outlier: 4.355A pdb=" N ALA 3 19 " --> pdb=" O THR 3 15 " (cutoff:3.500A) removed outlier: 4.319A pdb=" N GLY 3 20 " --> pdb=" O VAL 3 16 " (cutoff:3.500A) removed outlier: 4.362A pdb=" N SER 3 21 " --> pdb=" O GLY 3 17 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N GLY 3 26 " --> pdb=" O GLY 3 22 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N ILE 3 33 " --> pdb=" O PHE 3 29 " (cutoff:3.500A) Processing helix chain '3' and resid 40 through 72 removed outlier: 5.057A pdb=" N GLN 3 44 " --> pdb=" O SER 3 41 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N LEU 3 46 " --> pdb=" O LYS 3 43 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N PHE 3 47 " --> pdb=" O GLN 3 44 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N ILE 3 51 " --> pdb=" O SER 3 48 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N LEU 3 52 " --> pdb=" O TYR 3 49 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N ALA 3 55 " --> pdb=" O LEU 3 52 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N PHE 3 63 " --> pdb=" O MET 3 60 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N MET 3 66 " --> pdb=" O PHE 3 63 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N ALA 3 68 " --> pdb=" O LEU 3 65 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N ILE 3 71 " --> pdb=" O ALA 3 68 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N LEU 3 72 " --> pdb=" O PHE 3 69 " (cutoff:3.500A) Processing helix chain '4' and resid 2 through 38 removed outlier: 3.887A pdb=" N PHE 4 8 " --> pdb=" O THR 4 4 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ILE 4 9 " --> pdb=" O ALA 4 5 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N THR 4 15 " --> pdb=" O ALA 4 11 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N VAL 4 16 " --> pdb=" O GLY 4 12 " (cutoff:3.500A) removed outlier: 4.184A pdb=" N GLY 4 17 " --> pdb=" O ALA 4 13 " (cutoff:3.500A) removed outlier: 4.594A pdb=" N VAL 4 18 " --> pdb=" O ALA 4 14 " (cutoff:3.500A) removed outlier: 4.355A pdb=" N ALA 4 19 " --> pdb=" O THR 4 15 " (cutoff:3.500A) removed outlier: 4.319A pdb=" N GLY 4 20 " --> pdb=" O VAL 4 16 " (cutoff:3.500A) removed outlier: 4.362A pdb=" N SER 4 21 " --> pdb=" O GLY 4 17 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N GLY 4 26 " --> pdb=" O GLY 4 22 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N ILE 4 33 " --> pdb=" O PHE 4 29 " (cutoff:3.500A) Processing helix chain '4' and resid 40 through 72 removed outlier: 5.057A pdb=" N GLN 4 44 " --> pdb=" O SER 4 41 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N LEU 4 46 " --> pdb=" O LYS 4 43 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N PHE 4 47 " --> pdb=" O GLN 4 44 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N ILE 4 51 " --> pdb=" O SER 4 48 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N LEU 4 52 " --> pdb=" O TYR 4 49 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N ALA 4 55 " --> pdb=" O LEU 4 52 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N PHE 4 63 " --> pdb=" O MET 4 60 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N MET 4 66 " --> pdb=" O PHE 4 63 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N ALA 4 68 " --> pdb=" O LEU 4 65 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N ILE 4 71 " --> pdb=" O ALA 4 68 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N LEU 4 72 " --> pdb=" O PHE 4 69 " (cutoff:3.500A) Processing helix chain '5' and resid 2 through 38 removed outlier: 3.887A pdb=" N PHE 5 8 " --> pdb=" O THR 5 4 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N ILE 5 9 " --> pdb=" O ALA 5 5 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N THR 5 15 " --> pdb=" O ALA 5 11 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N VAL 5 16 " --> pdb=" O GLY 5 12 " (cutoff:3.500A) removed outlier: 4.184A pdb=" N GLY 5 17 " --> pdb=" O ALA 5 13 " (cutoff:3.500A) removed outlier: 4.594A pdb=" N VAL 5 18 " --> pdb=" O ALA 5 14 " (cutoff:3.500A) removed outlier: 4.355A pdb=" N ALA 5 19 " --> pdb=" O THR 5 15 " (cutoff:3.500A) removed outlier: 4.319A pdb=" N GLY 5 20 " --> pdb=" O VAL 5 16 " (cutoff:3.500A) removed outlier: 4.362A pdb=" N SER 5 21 " --> pdb=" O GLY 5 17 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N GLY 5 26 " --> pdb=" O GLY 5 22 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N ILE 5 33 " --> pdb=" O PHE 5 29 " (cutoff:3.500A) Processing helix chain '5' and resid 40 through 72 removed outlier: 5.058A pdb=" N GLN 5 44 " --> pdb=" O SER 5 41 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N LEU 5 46 " --> pdb=" O LYS 5 43 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N PHE 5 47 " --> pdb=" O GLN 5 44 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N ILE 5 51 " --> pdb=" O SER 5 48 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N LEU 5 52 " --> pdb=" O TYR 5 49 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N ALA 5 55 " --> pdb=" O LEU 5 52 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N PHE 5 63 " --> pdb=" O MET 5 60 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N MET 5 66 " --> pdb=" O PHE 5 63 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N ALA 5 68 " --> pdb=" O LEU 5 65 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N ILE 5 71 " --> pdb=" O ALA 5 68 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N LEU 5 72 " --> pdb=" O PHE 5 69 " (cutoff:3.500A) Processing helix chain '6' and resid 2 through 38 removed outlier: 3.887A pdb=" N PHE 6 8 " --> pdb=" O THR 6 4 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ILE 6 9 " --> pdb=" O ALA 6 5 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N THR 6 15 " --> pdb=" O ALA 6 11 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N VAL 6 16 " --> pdb=" O GLY 6 12 " (cutoff:3.500A) removed outlier: 4.184A pdb=" N GLY 6 17 " --> pdb=" O ALA 6 13 " (cutoff:3.500A) removed outlier: 4.594A pdb=" N VAL 6 18 " --> pdb=" O ALA 6 14 " (cutoff:3.500A) removed outlier: 4.355A pdb=" N ALA 6 19 " --> pdb=" O THR 6 15 " (cutoff:3.500A) removed outlier: 4.319A pdb=" N GLY 6 20 " --> pdb=" O VAL 6 16 " (cutoff:3.500A) removed outlier: 4.363A pdb=" N SER 6 21 " --> pdb=" O GLY 6 17 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N GLY 6 26 " --> pdb=" O GLY 6 22 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N ILE 6 33 " --> pdb=" O PHE 6 29 " (cutoff:3.500A) Processing helix chain '6' and resid 40 through 72 removed outlier: 5.057A pdb=" N GLN 6 44 " --> pdb=" O SER 6 41 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N LEU 6 46 " --> pdb=" O LYS 6 43 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N PHE 6 47 " --> pdb=" O GLN 6 44 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N ILE 6 51 " --> pdb=" O SER 6 48 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N LEU 6 52 " --> pdb=" O TYR 6 49 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N ALA 6 55 " --> pdb=" O LEU 6 52 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N PHE 6 63 " --> pdb=" O MET 6 60 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N MET 6 66 " --> pdb=" O PHE 6 63 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N ALA 6 68 " --> pdb=" O LEU 6 65 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N ILE 6 71 " --> pdb=" O ALA 6 68 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N LEU 6 72 " --> pdb=" O PHE 6 69 " (cutoff:3.500A) Processing helix chain '7' and resid 2 through 38 removed outlier: 3.887A pdb=" N PHE 7 8 " --> pdb=" O THR 7 4 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ILE 7 9 " --> pdb=" O ALA 7 5 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N THR 7 15 " --> pdb=" O ALA 7 11 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N VAL 7 16 " --> pdb=" O GLY 7 12 " (cutoff:3.500A) removed outlier: 4.184A pdb=" N GLY 7 17 " --> pdb=" O ALA 7 13 " (cutoff:3.500A) removed outlier: 4.593A pdb=" N VAL 7 18 " --> pdb=" O ALA 7 14 " (cutoff:3.500A) removed outlier: 4.354A pdb=" N ALA 7 19 " --> pdb=" O THR 7 15 " (cutoff:3.500A) removed outlier: 4.320A pdb=" N GLY 7 20 " --> pdb=" O VAL 7 16 " (cutoff:3.500A) removed outlier: 4.363A pdb=" N SER 7 21 " --> pdb=" O GLY 7 17 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N GLY 7 26 " --> pdb=" O GLY 7 22 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N ILE 7 33 " --> pdb=" O PHE 7 29 " (cutoff:3.500A) Processing helix chain '7' and resid 40 through 72 removed outlier: 5.057A pdb=" N GLN 7 44 " --> pdb=" O SER 7 41 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N LEU 7 46 " --> pdb=" O LYS 7 43 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N PHE 7 47 " --> pdb=" O GLN 7 44 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N ILE 7 51 " --> pdb=" O SER 7 48 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N LEU 7 52 " --> pdb=" O TYR 7 49 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N ALA 7 55 " --> pdb=" O LEU 7 52 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N PHE 7 63 " --> pdb=" O MET 7 60 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N MET 7 66 " --> pdb=" O PHE 7 63 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N ALA 7 68 " --> pdb=" O LEU 7 65 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N ILE 7 71 " --> pdb=" O ALA 7 68 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N LEU 7 72 " --> pdb=" O PHE 7 69 " (cutoff:3.500A) Processing helix chain '8' and resid 2 through 38 removed outlier: 3.887A pdb=" N PHE 8 8 " --> pdb=" O THR 8 4 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N ILE 8 9 " --> pdb=" O ALA 8 5 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N THR 8 15 " --> pdb=" O ALA 8 11 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N VAL 8 16 " --> pdb=" O GLY 8 12 " (cutoff:3.500A) removed outlier: 4.183A pdb=" N GLY 8 17 " --> pdb=" O ALA 8 13 " (cutoff:3.500A) removed outlier: 4.595A pdb=" N VAL 8 18 " --> pdb=" O ALA 8 14 " (cutoff:3.500A) removed outlier: 4.355A pdb=" N ALA 8 19 " --> pdb=" O THR 8 15 " (cutoff:3.500A) removed outlier: 4.319A pdb=" N GLY 8 20 " --> pdb=" O VAL 8 16 " (cutoff:3.500A) removed outlier: 4.363A pdb=" N SER 8 21 " --> pdb=" O GLY 8 17 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N GLY 8 26 " --> pdb=" O GLY 8 22 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N ILE 8 33 " --> pdb=" O PHE 8 29 " (cutoff:3.500A) Processing helix chain '8' and resid 40 through 72 removed outlier: 5.056A pdb=" N GLN 8 44 " --> pdb=" O SER 8 41 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N LEU 8 46 " --> pdb=" O LYS 8 43 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N PHE 8 47 " --> pdb=" O GLN 8 44 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N ILE 8 51 " --> pdb=" O SER 8 48 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N LEU 8 52 " --> pdb=" O TYR 8 49 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N ALA 8 55 " --> pdb=" O LEU 8 52 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N PHE 8 63 " --> pdb=" O MET 8 60 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N MET 8 66 " --> pdb=" O PHE 8 63 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N ALA 8 68 " --> pdb=" O LEU 8 65 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N ILE 8 71 " --> pdb=" O ALA 8 68 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N LEU 8 72 " --> pdb=" O PHE 8 69 " (cutoff:3.500A) Processing helix chain '1' and resid 2 through 38 removed outlier: 3.887A pdb=" N PHE 1 8 " --> pdb=" O THR 1 4 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ILE 1 9 " --> pdb=" O ALA 1 5 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N THR 1 15 " --> pdb=" O ALA 1 11 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N VAL 1 16 " --> pdb=" O GLY 1 12 " (cutoff:3.500A) removed outlier: 4.183A pdb=" N GLY 1 17 " --> pdb=" O ALA 1 13 " (cutoff:3.500A) removed outlier: 4.594A pdb=" N VAL 1 18 " --> pdb=" O ALA 1 14 " (cutoff:3.500A) removed outlier: 4.355A pdb=" N ALA 1 19 " --> pdb=" O THR 1 15 " (cutoff:3.500A) removed outlier: 4.319A pdb=" N GLY 1 20 " --> pdb=" O VAL 1 16 " (cutoff:3.500A) removed outlier: 4.362A pdb=" N SER 1 21 " --> pdb=" O GLY 1 17 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N GLY 1 26 " --> pdb=" O GLY 1 22 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N ILE 1 33 " --> pdb=" O PHE 1 29 " (cutoff:3.500A) Processing helix chain '1' and resid 40 through 72 removed outlier: 5.057A pdb=" N GLN 1 44 " --> pdb=" O SER 1 41 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N LEU 1 46 " --> pdb=" O LYS 1 43 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N PHE 1 47 " --> pdb=" O GLN 1 44 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N ILE 1 51 " --> pdb=" O SER 1 48 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N LEU 1 52 " --> pdb=" O TYR 1 49 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N ALA 1 55 " --> pdb=" O LEU 1 52 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N PHE 1 63 " --> pdb=" O MET 1 60 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N MET 1 66 " --> pdb=" O PHE 1 63 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N ALA 1 68 " --> pdb=" O LEU 1 65 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N ILE 1 71 " --> pdb=" O ALA 1 68 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N LEU 1 72 " --> pdb=" O PHE 1 69 " (cutoff:3.500A) Processing helix chain '2' and resid 2 through 38 removed outlier: 3.888A pdb=" N PHE 2 8 " --> pdb=" O THR 2 4 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N ILE 2 9 " --> pdb=" O ALA 2 5 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N THR 2 15 " --> pdb=" O ALA 2 11 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N VAL 2 16 " --> pdb=" O GLY 2 12 " (cutoff:3.500A) removed outlier: 4.184A pdb=" N GLY 2 17 " --> pdb=" O ALA 2 13 " (cutoff:3.500A) removed outlier: 4.594A pdb=" N VAL 2 18 " --> pdb=" O ALA 2 14 " (cutoff:3.500A) removed outlier: 4.355A pdb=" N ALA 2 19 " --> pdb=" O THR 2 15 " (cutoff:3.500A) removed outlier: 4.320A pdb=" N GLY 2 20 " --> pdb=" O VAL 2 16 " (cutoff:3.500A) removed outlier: 4.363A pdb=" N SER 2 21 " --> pdb=" O GLY 2 17 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N GLY 2 26 " --> pdb=" O GLY 2 22 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N ILE 2 33 " --> pdb=" O PHE 2 29 " (cutoff:3.500A) Processing helix chain '2' and resid 40 through 72 removed outlier: 5.058A pdb=" N GLN 2 44 " --> pdb=" O SER 2 41 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N LEU 2 46 " --> pdb=" O LYS 2 43 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N PHE 2 47 " --> pdb=" O GLN 2 44 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N ILE 2 51 " --> pdb=" O SER 2 48 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N LEU 2 52 " --> pdb=" O TYR 2 49 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N ALA 2 55 " --> pdb=" O LEU 2 52 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N PHE 2 63 " --> pdb=" O MET 2 60 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N MET 2 66 " --> pdb=" O PHE 2 63 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N ALA 2 68 " --> pdb=" O LEU 2 65 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N ILE 2 71 " --> pdb=" O ALA 2 68 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N LEU 2 72 " --> pdb=" O PHE 2 69 " (cutoff:3.500A) Processing helix chain 'H' and resid 100 through 102 No H-bonds generated for 'chain 'H' and resid 100 through 102' Processing helix chain 'H' and resid 105 through 121 Processing helix chain 'H' and resid 125 through 145 Processing helix chain 'I' and resid 4 through 8 Processing helix chain 'I' and resid 12 through 25 Processing helix chain 'I' and resid 29 through 37 removed outlier: 4.272A pdb=" N ALA I 33 " --> pdb=" O THR I 29 " (cutoff:3.500A) removed outlier: 5.606A pdb=" N ASN I 34 " --> pdb=" O GLU I 30 " (cutoff:3.500A) Processing helix chain 'N' and resid 6 through 9 Processing helix chain 'N' and resid 19 through 30 removed outlier: 4.030A pdb=" N ILE N 24 " --> pdb=" O VAL N 21 " (cutoff:3.500A) Proline residue: N 27 - end of helix Processing helix chain 'N' and resid 41 through 58 Processing helix chain 'N' and resid 65 through 87 removed outlier: 4.448A pdb=" N LEU N 70 " --> pdb=" O THR N 67 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N LEU N 72 " --> pdb=" O SER N 69 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N VAL N 73 " --> pdb=" O LEU N 70 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N ILE N 76 " --> pdb=" O VAL N 73 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N ILE N 77 " --> pdb=" O SER N 74 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N ILE N 79 " --> pdb=" O ILE N 76 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N ALA N 80 " --> pdb=" O ILE N 77 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N ASN N 83 " --> pdb=" O ALA N 80 " (cutoff:3.500A) Processing helix chain 'N' and resid 98 through 118 Proline residue: N 107 - end of helix Processing helix chain 'N' and resid 121 through 127 Processing helix chain 'N' and resid 140 through 180 removed outlier: 4.068A pdb=" N GLU N 145 " --> pdb=" O LEU N 141 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N ILE N 147 " --> pdb=" O ILE N 143 " (cutoff:3.500A) Proline residue: N 153 - end of helix removed outlier: 3.715A pdb=" N ASN N 163 " --> pdb=" O ARG N 159 " (cutoff:3.500A) Processing helix chain 'N' and resid 186 through 225 Processing helix chain 'P' and resid 10 through 17 Proline residue: P 15 - end of helix Processing helix chain 'P' and resid 22 through 40 Processing helix chain 'Q' and resid 2 through 4 No H-bonds generated for 'chain 'Q' and resid 2 through 4' Processing helix chain 'Q' and resid 9 through 20 removed outlier: 3.627A pdb=" N THR Q 14 " --> pdb=" O PRO Q 10 " (cutoff:3.500A) Proline residue: Q 15 - end of helix Processing helix chain 'Q' and resid 23 through 28 Processing helix chain 'R' and resid 28 through 31 No H-bonds generated for 'chain 'R' and resid 28 through 31' Processing helix chain 'R' and resid 36 through 54 Processing helix chain 'R' and resid 63 through 84 removed outlier: 4.480A pdb=" N VAL R 68 " --> pdb=" O GLY R 64 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N PHE R 79 " --> pdb=" O PHE R 75 " (cutoff:3.500A) removed outlier: 4.709A pdb=" N LYS R 82 " --> pdb=" O SER R 78 " (cutoff:3.500A) removed outlier: 5.030A pdb=" N HIS R 83 " --> pdb=" O PHE R 79 " (cutoff:3.500A) Processing helix chain 'S' and resid 28 through 36 removed outlier: 4.297A pdb=" N VAL S 35 " --> pdb=" O TYR S 31 " (cutoff:3.500A) Processing helix chain 'S' and resid 45 through 61 Processing helix chain 'S' and resid 63 through 66 Processing helix chain 'S' and resid 69 through 93 Processing helix chain 'T' and resid 9 through 44 Proline residue: T 35 - end of helix Processing helix chain 'J' and resid 14 through 17 No H-bonds generated for 'chain 'J' and resid 14 through 17' Processing helix chain 'J' and resid 20 through 42 removed outlier: 3.520A pdb=" N GLU J 26 " --> pdb=" O PHE J 22 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 28 through 30 removed outlier: 6.476A pdb=" N GLY A 72 " --> pdb=" O LEU A 64 " (cutoff:3.500A) removed outlier: 5.931A pdb=" N HIS A 42 " --> pdb=" O VAL A 31 " (cutoff:3.500A) removed outlier: 5.583A pdb=" N VAL A 31 " --> pdb=" O HIS A 42 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 96 through 99 removed outlier: 4.040A pdb=" N THR A 125 " --> pdb=" O VAL A 99 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 349 through 352 removed outlier: 6.592A pdb=" N LEU A 166 " --> pdb=" O ILE A 350 " (cutoff:3.500A) removed outlier: 7.546A pdb=" N LEU A 352 " --> pdb=" O LEU A 166 " (cutoff:3.500A) removed outlier: 7.091A pdb=" N ILE A 168 " --> pdb=" O LEU A 352 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 229 through 234 removed outlier: 6.718A pdb=" N CYS A 201 " --> pdb=" O ILE A 230 " (cutoff:3.500A) removed outlier: 7.967A pdb=" N VAL A 232 " --> pdb=" O CYS A 201 " (cutoff:3.500A) removed outlier: 6.283A pdb=" N TYR A 203 " --> pdb=" O VAL A 232 " (cutoff:3.500A) removed outlier: 7.453A pdb=" N ALA A 234 " --> pdb=" O TYR A 203 " (cutoff:3.500A) removed outlier: 6.008A pdb=" N ALA A 205 " --> pdb=" O ALA A 234 " (cutoff:3.500A) removed outlier: 6.255A pdb=" N SER A 320 " --> pdb=" O ALA A 264 " (cutoff:3.500A) removed outlier: 7.969A pdb=" N ILE A 266 " --> pdb=" O SER A 320 " (cutoff:3.500A) removed outlier: 6.354A pdb=" N THR A 322 " --> pdb=" O ILE A 266 " (cutoff:3.500A) removed outlier: 7.638A pdb=" N TYR A 268 " --> pdb=" O THR A 322 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 87 through 89 removed outlier: 6.563A pdb=" N ARG B 40 " --> pdb=" O LEU B 32 " (cutoff:3.500A) removed outlier: 4.553A pdb=" N ILE B 34 " --> pdb=" O ILE B 38 " (cutoff:3.500A) removed outlier: 6.849A pdb=" N ILE B 38 " --> pdb=" O ILE B 34 " (cutoff:3.500A) removed outlier: 6.708A pdb=" N VAL B 74 " --> pdb=" O SER B 63 " (cutoff:3.500A) removed outlier: 5.723A pdb=" N SER B 63 " --> pdb=" O VAL B 74 " (cutoff:3.500A) removed outlier: 4.126A pdb=" N GLU B 51 " --> pdb=" O SER B 63 " (cutoff:3.500A) removed outlier: 4.877A pdb=" N ALA B 93 " --> pdb=" O MET B 52 " (cutoff:3.500A) removed outlier: 8.448A pdb=" N GLU B 54 " --> pdb=" O THR B 91 " (cutoff:3.500A) removed outlier: 6.924A pdb=" N THR B 91 " --> pdb=" O GLU B 54 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 96 through 99 removed outlier: 4.153A pdb=" N THR B 125 " --> pdb=" O VAL B 99 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 107 through 109 removed outlier: 8.110A pdb=" N VAL B 108 " --> pdb=" O THR B 229 " (cutoff:3.500A) removed outlier: 6.087A pdb=" N VAL B 231 " --> pdb=" O VAL B 108 " (cutoff:3.500A) removed outlier: 6.708A pdb=" N CYS B 201 " --> pdb=" O ILE B 230 " (cutoff:3.500A) removed outlier: 7.905A pdb=" N VAL B 232 " --> pdb=" O CYS B 201 " (cutoff:3.500A) removed outlier: 6.300A pdb=" N TYR B 203 " --> pdb=" O VAL B 232 " (cutoff:3.500A) removed outlier: 7.549A pdb=" N ALA B 234 " --> pdb=" O TYR B 203 " (cutoff:3.500A) removed outlier: 6.011A pdb=" N ALA B 205 " --> pdb=" O ALA B 234 " (cutoff:3.500A) removed outlier: 6.153A pdb=" N SER B 320 " --> pdb=" O ALA B 264 " (cutoff:3.500A) removed outlier: 7.997A pdb=" N ILE B 266 " --> pdb=" O SER B 320 " (cutoff:3.500A) removed outlier: 6.282A pdb=" N THR B 322 " --> pdb=" O ILE B 266 " (cutoff:3.500A) removed outlier: 7.640A pdb=" N TYR B 268 " --> pdb=" O THR B 322 " (cutoff:3.500A) removed outlier: 6.766A pdb=" N LEU B 324 " --> pdb=" O TYR B 268 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 349 through 352 removed outlier: 6.732A pdb=" N LEU B 166 " --> pdb=" O ILE B 350 " (cutoff:3.500A) removed outlier: 7.194A pdb=" N LEU B 352 " --> pdb=" O LEU B 166 " (cutoff:3.500A) removed outlier: 6.727A pdb=" N ILE B 168 " --> pdb=" O LEU B 352 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'C' and resid 28 through 30 removed outlier: 6.449A pdb=" N GLY C 72 " --> pdb=" O LEU C 64 " (cutoff:3.500A) removed outlier: 5.737A pdb=" N HIS C 42 " --> pdb=" O VAL C 31 " (cutoff:3.500A) removed outlier: 5.541A pdb=" N VAL C 31 " --> pdb=" O HIS C 42 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'C' and resid 96 through 99 removed outlier: 4.330A pdb=" N THR C 125 " --> pdb=" O VAL C 99 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'C' and resid 349 through 352 removed outlier: 6.717A pdb=" N LEU C 166 " --> pdb=" O ILE C 350 " (cutoff:3.500A) removed outlier: 7.489A pdb=" N LEU C 352 " --> pdb=" O LEU C 166 " (cutoff:3.500A) removed outlier: 6.788A pdb=" N ILE C 168 " --> pdb=" O LEU C 352 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'C' and resid 229 through 234 removed outlier: 6.826A pdb=" N CYS C 201 " --> pdb=" O ILE C 230 " (cutoff:3.500A) removed outlier: 8.078A pdb=" N VAL C 232 " --> pdb=" O CYS C 201 " (cutoff:3.500A) removed outlier: 6.416A pdb=" N TYR C 203 " --> pdb=" O VAL C 232 " (cutoff:3.500A) removed outlier: 7.571A pdb=" N ALA C 234 " --> pdb=" O TYR C 203 " (cutoff:3.500A) removed outlier: 6.267A pdb=" N ALA C 205 " --> pdb=" O ALA C 234 " (cutoff:3.500A) removed outlier: 6.196A pdb=" N SER C 320 " --> pdb=" O ALA C 264 " (cutoff:3.500A) removed outlier: 7.897A pdb=" N ILE C 266 " --> pdb=" O SER C 320 " (cutoff:3.500A) removed outlier: 6.314A pdb=" N THR C 322 " --> pdb=" O ILE C 266 " (cutoff:3.500A) removed outlier: 7.736A pdb=" N TYR C 268 " --> pdb=" O THR C 322 " (cutoff:3.500A) removed outlier: 6.970A pdb=" N LEU C 324 " --> pdb=" O TYR C 268 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'E' and resid 13 through 15 removed outlier: 6.725A pdb=" N ARG E 62 " --> pdb=" O ALA E 53 " (cutoff:3.500A) removed outlier: 5.038A pdb=" N HIS E 55 " --> pdb=" O THR E 60 " (cutoff:3.500A) removed outlier: 7.195A pdb=" N THR E 60 " --> pdb=" O HIS E 55 " (cutoff:3.500A) removed outlier: 6.037A pdb=" N GLN E 27 " --> pdb=" O ILE E 16 " (cutoff:3.500A) removed outlier: 5.587A pdb=" N ILE E 16 " --> pdb=" O GLN E 27 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'E' and resid 86 through 89 removed outlier: 4.257A pdb=" N GLN E 115 " --> pdb=" O VAL E 89 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'E' and resid 334 through 337 removed outlier: 8.433A pdb=" N ILE E 155 " --> pdb=" O ILE E 307 " (cutoff:3.500A) removed outlier: 6.646A pdb=" N SER E 309 " --> pdb=" O ILE E 155 " (cutoff:3.500A) removed outlier: 7.145A pdb=" N LEU E 157 " --> pdb=" O SER E 309 " (cutoff:3.500A) removed outlier: 6.331A pdb=" N GLN E 311 " --> pdb=" O LEU E 157 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'F' and resid 13 through 15 removed outlier: 6.645A pdb=" N ARG F 62 " --> pdb=" O ALA F 53 " (cutoff:3.500A) removed outlier: 4.963A pdb=" N HIS F 55 " --> pdb=" O THR F 60 " (cutoff:3.500A) removed outlier: 7.189A pdb=" N THR F 60 " --> pdb=" O HIS F 55 " (cutoff:3.500A) removed outlier: 5.966A pdb=" N GLN F 27 " --> pdb=" O ILE F 16 " (cutoff:3.500A) removed outlier: 5.547A pdb=" N ILE F 16 " --> pdb=" O GLN F 27 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'F' and resid 86 through 89 removed outlier: 4.214A pdb=" N GLN F 115 " --> pdb=" O VAL F 89 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'F' and resid 334 through 337 removed outlier: 7.480A pdb=" N ILE F 155 " --> pdb=" O ILE F 307 " (cutoff:3.500A) removed outlier: 6.069A pdb=" N SER F 309 " --> pdb=" O ILE F 155 " (cutoff:3.500A) removed outlier: 7.354A pdb=" N LEU F 157 " --> pdb=" O SER F 309 " (cutoff:3.500A) removed outlier: 6.692A pdb=" N GLN F 311 " --> pdb=" O LEU F 157 " (cutoff:3.500A) removed outlier: 7.989A pdb=" N GLY F 159 " --> pdb=" O GLN F 311 " (cutoff:3.500A) removed outlier: 6.159A pdb=" N ILE F 313 " --> pdb=" O GLY F 159 " (cutoff:3.500A) removed outlier: 6.950A pdb=" N TYR F 183 " --> pdb=" O LEU F 255 " (cutoff:3.500A) removed outlier: 8.453A pdb=" N PHE F 257 " --> pdb=" O TYR F 183 " (cutoff:3.500A) removed outlier: 6.506A pdb=" N VAL F 185 " --> pdb=" O PHE F 257 " (cutoff:3.500A) removed outlier: 8.039A pdb=" N ASP F 259 " --> pdb=" O VAL F 185 " (cutoff:3.500A) removed outlier: 6.293A pdb=" N ALA F 187 " --> pdb=" O ASP F 259 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'D' and resid 13 through 15 removed outlier: 6.685A pdb=" N ARG D 62 " --> pdb=" O ALA D 53 " (cutoff:3.500A) removed outlier: 4.920A pdb=" N HIS D 55 " --> pdb=" O THR D 60 " (cutoff:3.500A) removed outlier: 7.051A pdb=" N THR D 60 " --> pdb=" O HIS D 55 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N ALA D 18 " --> pdb=" O ASP D 25 " (cutoff:3.500A) removed outlier: 6.143A pdb=" N GLN D 27 " --> pdb=" O ILE D 16 " (cutoff:3.500A) removed outlier: 5.838A pdb=" N ILE D 16 " --> pdb=" O GLN D 27 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'D' and resid 86 through 89 removed outlier: 4.155A pdb=" N GLN D 115 " --> pdb=" O VAL D 89 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'D' and resid 157 through 159 Processing sheet with id= V, first strand: chain 'D' and resid 218 through 223 removed outlier: 7.024A pdb=" N SER D 184 " --> pdb=" O ALA D 219 " (cutoff:3.500A) removed outlier: 8.479A pdb=" N VAL D 221 " --> pdb=" O SER D 184 " (cutoff:3.500A) removed outlier: 6.404A pdb=" N PHE D 186 " --> pdb=" O VAL D 221 " (cutoff:3.500A) removed outlier: 8.028A pdb=" N GLY D 223 " --> pdb=" O PHE D 186 " (cutoff:3.500A) removed outlier: 6.084A pdb=" N GLY D 188 " --> pdb=" O GLY D 223 " (cutoff:3.500A) removed outlier: 6.479A pdb=" N SER D 306 " --> pdb=" O VAL D 254 " (cutoff:3.500A) removed outlier: 7.501A pdb=" N LEU D 256 " --> pdb=" O SER D 306 " (cutoff:3.500A) removed outlier: 6.564A pdb=" N THR D 308 " --> pdb=" O LEU D 256 " (cutoff:3.500A) removed outlier: 7.795A pdb=" N ILE D 258 " --> pdb=" O THR D 308 " (cutoff:3.500A) removed outlier: 6.499A pdb=" N VAL D 310 " --> pdb=" O ILE D 258 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'G' and resid 171 through 179 removed outlier: 5.231A pdb=" N ASN G 163 " --> pdb=" O VAL G 71 " (cutoff:3.500A) removed outlier: 6.224A pdb=" N GLU G 102 " --> pdb=" O HIS G 66 " (cutoff:3.500A) removed outlier: 7.798A pdb=" N LEU G 68 " --> pdb=" O GLU G 102 " (cutoff:3.500A) removed outlier: 6.607A pdb=" N MET G 104 " --> pdb=" O LEU G 68 " (cutoff:3.500A) removed outlier: 7.824A pdb=" N GLY G 70 " --> pdb=" O MET G 104 " (cutoff:3.500A) removed outlier: 6.610A pdb=" N VAL G 106 " --> pdb=" O GLY G 70 " (cutoff:3.500A) removed outlier: 7.243A pdb=" N VAL G 126 " --> pdb=" O GLY G 107 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain 'O' and resid 147 through 154 Processing sheet with id= Y, first strand: chain 'H' and resid 20 through 22 removed outlier: 8.087A pdb=" N ALA H 21 " --> pdb=" O VAL H 90 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N LEU H 92 " --> pdb=" O ALA H 21 " (cutoff:3.500A) Processing sheet with id= Z, first strand: chain 'H' and resid 45 through 47 removed outlier: 6.834A pdb=" N HIS H 66 " --> pdb=" O ARG H 34 " (cutoff:3.500A) removed outlier: 4.312A pdb=" N VAL H 36 " --> pdb=" O VAL H 64 " (cutoff:3.500A) removed outlier: 6.498A pdb=" N VAL H 64 " --> pdb=" O VAL H 36 " (cutoff:3.500A) removed outlier: 5.063A pdb=" N VAL H 38 " --> pdb=" O LEU H 62 " (cutoff:3.500A) removed outlier: 7.352A pdb=" N LEU H 62 " --> pdb=" O VAL H 38 " (cutoff:3.500A) 1924 hydrogen bonds defined for protein. 5088 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 15.62 Time building geometry restraints manager: 18.37 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 6450 1.32 - 1.44: 9470 1.44 - 1.56: 22878 1.56 - 1.68: 21 1.68 - 1.81: 299 Bond restraints: 39118 Sorted by residual: bond pdb=" C6 ATP C 601 " pdb=" N6 ATP C 601 " ideal model delta sigma weight residual 1.337 1.461 -0.124 1.10e-02 8.26e+03 1.27e+02 bond pdb=" C6 ATP A 601 " pdb=" N6 ATP A 601 " ideal model delta sigma weight residual 1.337 1.459 -0.122 1.10e-02 8.26e+03 1.23e+02 bond pdb=" C6 ATP B 601 " pdb=" N6 ATP B 601 " ideal model delta sigma weight residual 1.337 1.459 -0.122 1.10e-02 8.26e+03 1.22e+02 bond pdb=" C4 ATP B 601 " pdb=" N9 ATP B 601 " ideal model delta sigma weight residual 1.374 1.285 0.089 1.00e-02 1.00e+04 7.85e+01 bond pdb=" C4 ATP A 601 " pdb=" N9 ATP A 601 " ideal model delta sigma weight residual 1.374 1.286 0.088 1.00e-02 1.00e+04 7.75e+01 ... (remaining 39113 not shown) Histogram of bond angle deviations from ideal: 98.73 - 106.41: 1009 106.41 - 114.10: 23134 114.10 - 121.78: 21072 121.78 - 129.47: 7583 129.47 - 137.16: 129 Bond angle restraints: 52927 Sorted by residual: angle pdb=" PB ATP A 601 " pdb=" O3B ATP A 601 " pdb=" PG ATP A 601 " ideal model delta sigma weight residual 139.87 123.11 16.76 1.00e+00 1.00e+00 2.81e+02 angle pdb=" PB ATP B 601 " pdb=" O3B ATP B 601 " pdb=" PG ATP B 601 " ideal model delta sigma weight residual 139.87 123.23 16.64 1.00e+00 1.00e+00 2.77e+02 angle pdb=" PB ATP C 601 " pdb=" O3B ATP C 601 " pdb=" PG ATP C 601 " ideal model delta sigma weight residual 139.87 124.79 15.08 1.00e+00 1.00e+00 2.27e+02 angle pdb=" PA ATP C 601 " pdb=" O3A ATP C 601 " pdb=" PB ATP C 601 " ideal model delta sigma weight residual 136.83 122.90 13.93 1.00e+00 1.00e+00 1.94e+02 angle pdb=" PA ATP A 601 " pdb=" O3A ATP A 601 " pdb=" PB ATP A 601 " ideal model delta sigma weight residual 136.83 125.53 11.30 1.00e+00 1.00e+00 1.28e+02 ... (remaining 52922 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 28.06: 22732 28.06 - 56.12: 850 56.12 - 84.19: 109 84.19 - 112.25: 17 112.25 - 140.31: 3 Dihedral angle restraints: 23711 sinusoidal: 9380 harmonic: 14331 Sorted by residual: dihedral pdb=" O2A ADP D 501 " pdb=" O3A ADP D 501 " pdb=" PA ADP D 501 " pdb=" PB ADP D 501 " ideal model delta sinusoidal sigma weight residual -60.00 80.31 -140.31 1 2.00e+01 2.50e-03 4.25e+01 dihedral pdb=" O1B ADP D 501 " pdb=" O3A ADP D 501 " pdb=" PB ADP D 501 " pdb=" PA ADP D 501 " ideal model delta sinusoidal sigma weight residual -60.00 74.99 -134.99 1 2.00e+01 2.50e-03 4.10e+01 dihedral pdb=" C5' ADP D 501 " pdb=" O5' ADP D 501 " pdb=" PA ADP D 501 " pdb=" O2A ADP D 501 " ideal model delta sinusoidal sigma weight residual -60.00 -176.35 116.35 1 2.00e+01 2.50e-03 3.47e+01 ... (remaining 23708 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.056: 5077 0.056 - 0.112: 942 0.112 - 0.169: 133 0.169 - 0.225: 5 0.225 - 0.281: 2 Chirality restraints: 6159 Sorted by residual: chirality pdb=" CB ILE S 98 " pdb=" CA ILE S 98 " pdb=" CG1 ILE S 98 " pdb=" CG2 ILE S 98 " both_signs ideal model delta sigma weight residual False 2.64 2.36 0.28 2.00e-01 2.50e+01 1.97e+00 chirality pdb=" C2' ATP A 601 " pdb=" C1' ATP A 601 " pdb=" C3' ATP A 601 " pdb=" O2' ATP A 601 " both_signs ideal model delta sigma weight residual False -2.68 -2.45 -0.23 2.00e-01 2.50e+01 1.29e+00 chirality pdb=" C2' ATP C 601 " pdb=" C1' ATP C 601 " pdb=" C3' ATP C 601 " pdb=" O2' ATP C 601 " both_signs ideal model delta sigma weight residual False -2.68 -2.46 -0.22 2.00e-01 2.50e+01 1.22e+00 ... (remaining 6156 not shown) Planarity restraints: 6753 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG 4 38 " 0.721 9.50e-02 1.11e+02 3.23e-01 6.36e+01 pdb=" NE ARG 4 38 " -0.043 2.00e-02 2.50e+03 pdb=" CZ ARG 4 38 " -0.007 2.00e-02 2.50e+03 pdb=" NH1 ARG 4 38 " -0.003 2.00e-02 2.50e+03 pdb=" NH2 ARG 4 38 " 0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG J 16 " -0.712 9.50e-02 1.11e+02 3.19e-01 6.21e+01 pdb=" NE ARG J 16 " 0.041 2.00e-02 2.50e+03 pdb=" CZ ARG J 16 " 0.011 2.00e-02 2.50e+03 pdb=" NH1 ARG J 16 " 0.002 2.00e-02 2.50e+03 pdb=" NH2 ARG J 16 " -0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP M 53 " 0.007 2.00e-02 2.50e+03 1.75e-02 7.69e+00 pdb=" CG TRP M 53 " -0.017 2.00e-02 2.50e+03 pdb=" CD1 TRP M 53 " 0.025 2.00e-02 2.50e+03 pdb=" CD2 TRP M 53 " 0.005 2.00e-02 2.50e+03 pdb=" NE1 TRP M 53 " 0.003 2.00e-02 2.50e+03 pdb=" CE2 TRP M 53 " -0.027 2.00e-02 2.50e+03 pdb=" CE3 TRP M 53 " -0.019 2.00e-02 2.50e+03 pdb=" CZ2 TRP M 53 " -0.014 2.00e-02 2.50e+03 pdb=" CZ3 TRP M 53 " 0.011 2.00e-02 2.50e+03 pdb=" CH2 TRP M 53 " 0.026 2.00e-02 2.50e+03 ... (remaining 6750 not shown) Histogram of nonbonded interaction distances: 1.92 - 2.52: 231 2.52 - 3.11: 30160 3.11 - 3.71: 59684 3.71 - 4.30: 91415 4.30 - 4.90: 147361 Nonbonded interactions: 328851 Sorted by model distance: nonbonded pdb=" OG1 THR A 176 " pdb="MG MG A 602 " model vdw 1.921 2.170 nonbonded pdb=" OG1 THR B 176 " pdb="MG MG B 602 " model vdw 2.009 2.170 nonbonded pdb=" O1B ATP B 601 " pdb="MG MG B 602 " model vdw 2.030 2.170 nonbonded pdb=" OG1 THR F 166 " pdb="MG MG F 502 " model vdw 2.037 2.170 nonbonded pdb=" O1B ATP A 601 " pdb="MG MG A 602 " model vdw 2.087 2.170 ... (remaining 328846 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 '1' selection = chain '2' selection = chain '3' selection = chain '4' selection = chain '5' selection = chain '6' selection = chain '7' selection = chain '8' } ncs_group { reference = (chain 'A' and (resid 24 through 401 or resid 417 through 508 or resid 601 throu \ gh 602)) selection = (chain 'B' and (resid 24 through 401 or resid 417 through 508 or resid 601 throu \ gh 602)) selection = chain 'C' } ncs_group { reference = (chain 'D' and (resid 12 through 391 or resid 400 through 475)) selection = chain 'E' selection = (chain 'F' and (resid 12 through 391 or resid 400 through 475)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 9.030 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 29.890 Check model and map are aligned: 0.560 Set scattering table: 0.390 Process input model: 106.290 Find NCS groups from input model: 2.570 Set up NCS constraints: 0.310 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.020 Load rotamer database and sin/cos tables:13.230 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 162.320 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7962 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.145 39118 Z= 0.407 Angle : 0.715 16.757 52927 Z= 0.447 Chirality : 0.044 0.281 6159 Planarity : 0.007 0.323 6753 Dihedral : 14.856 140.310 14541 Min Nonbonded Distance : 1.921 Molprobity Statistics. All-atom Clashscore : 8.72 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.04 % Favored : 96.90 % Rotamer: Outliers : 0.05 % Allowed : 4.79 % Favored : 95.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.13 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.00 (0.10), residues: 4962 helix: -2.10 (0.08), residues: 2713 sheet: -1.49 (0.20), residues: 560 loop : -1.58 (0.14), residues: 1689 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP M 53 HIS 0.005 0.001 HIS H 51 PHE 0.025 0.001 PHE J 34 TYR 0.023 0.001 TYR G 193 ARG 0.005 0.000 ARG F 108 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9924 Ramachandran restraints generated. 4962 Oldfield, 0 Emsley, 4962 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9924 Ramachandran restraints generated. 4962 Oldfield, 0 Emsley, 4962 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 779 residues out of total 4065 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 777 time to evaluate : 4.157 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 498 LYS cc_start: 0.8241 (tppt) cc_final: 0.7870 (tptt) REVERT: B 498 LYS cc_start: 0.7964 (ttmt) cc_final: 0.7723 (tptt) REVERT: C 124 LYS cc_start: 0.7898 (mmtm) cc_final: 0.7684 (mttm) REVERT: C 471 HIS cc_start: 0.6327 (t70) cc_final: 0.5995 (t-170) REVERT: D 475 LYS cc_start: 0.8144 (ttmt) cc_final: 0.7666 (tmtt) REVERT: 4 38 ARG cc_start: 0.7430 (OUTLIER) cc_final: 0.6849 (ttm170) REVERT: N 66 ARG cc_start: 0.8170 (mtt180) cc_final: 0.7836 (mtt180) REVERT: R 32 ARG cc_start: 0.5789 (mmp-170) cc_final: 0.5450 (mmm160) outliers start: 2 outliers final: 4 residues processed: 779 average time/residue: 1.7703 time to fit residues: 1631.4075 Evaluate side-chains 586 residues out of total 4065 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 581 time to evaluate : 4.770 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 169 ILE Chi-restraints excluded: chain G residue 197 ASP Chi-restraints excluded: chain 4 residue 38 ARG Chi-restraints excluded: chain 2 residue 25 ILE Chi-restraints excluded: chain R residue 77 TYR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 490 random chunks: chunk 413 optimal weight: 0.6980 chunk 371 optimal weight: 8.9990 chunk 206 optimal weight: 0.5980 chunk 126 optimal weight: 0.7980 chunk 250 optimal weight: 10.0000 chunk 198 optimal weight: 0.6980 chunk 384 optimal weight: 0.9980 chunk 148 optimal weight: 1.9990 chunk 233 optimal weight: 0.6980 chunk 285 optimal weight: 2.9990 chunk 444 optimal weight: 1.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 349 GLN A 396 GLN A 477 GLN A 503 ASN B 48 GLN ** B 385 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 432 GLN C 208 GLN C 385 GLN E 210 ASN E 370 HIS E 458 GLN ** F 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 180 HIS F 197 ASN F 296 GLN F 331 HIS F 458 GLN ** D 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 180 HIS D 201 HIS D 266 GLN G 120 HIS G 123 GLN G 150 ASN G 163 ASN O 84 ASN O 92 ASN O 97 ASN K 86 ASN K 92 GLN K 102 GLN ** K 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 180 HIS K 183 GLN M 34 ASN M 159 ASN 6 45 GLN 2 45 GLN H 35 GLN H 85 ASN H 111 ASN H 138 ASN I 34 ASN ** N 61 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 127 HIS ** N 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 172 HIS N 225 ASN Q 5 ASN Q 25 GLN Q 46 ASN ** T 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 46 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7923 moved from start: 0.1545 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.070 39118 Z= 0.172 Angle : 0.562 10.327 52927 Z= 0.288 Chirality : 0.042 0.169 6159 Planarity : 0.005 0.174 6753 Dihedral : 7.224 142.689 5530 Min Nonbonded Distance : 2.008 Molprobity Statistics. All-atom Clashscore : 8.44 Ramachandran Plot: Outliers : 0.06 % Allowed : 1.95 % Favored : 97.98 % Rotamer: Outliers : 1.95 % Allowed : 13.62 % Favored : 84.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.13 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.98 (0.11), residues: 4962 helix: -0.29 (0.10), residues: 2685 sheet: -0.96 (0.21), residues: 558 loop : -0.85 (0.15), residues: 1719 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP M 12 HIS 0.006 0.001 HIS B 476 PHE 0.025 0.001 PHE L 43 TYR 0.020 0.001 TYR C 397 ARG 0.015 0.000 ARG H 128 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9924 Ramachandran restraints generated. 4962 Oldfield, 0 Emsley, 4962 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9924 Ramachandran restraints generated. 4962 Oldfield, 0 Emsley, 4962 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 728 residues out of total 4065 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 79 poor density : 649 time to evaluate : 4.501 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 498 LYS cc_start: 0.8209 (tppt) cc_final: 0.7996 (tptt) REVERT: B 67 GLU cc_start: 0.7853 (OUTLIER) cc_final: 0.7567 (mt-10) REVERT: B 496 LYS cc_start: 0.8045 (OUTLIER) cc_final: 0.7827 (ttmm) REVERT: C 26 GLU cc_start: 0.8056 (mt-10) cc_final: 0.7845 (mp0) REVERT: C 471 HIS cc_start: 0.6173 (t70) cc_final: 0.5537 (t-170) REVERT: F 249 GLN cc_start: 0.7829 (OUTLIER) cc_final: 0.7465 (mp10) REVERT: D 475 LYS cc_start: 0.8106 (ttmt) cc_final: 0.7637 (tmtt) REVERT: O 150 LEU cc_start: 0.7143 (OUTLIER) cc_final: 0.6925 (mm) REVERT: K 174 ILE cc_start: 0.7442 (tp) cc_final: 0.7155 (tt) REVERT: L 69 GLN cc_start: 0.7779 (pm20) cc_final: 0.7508 (pt0) REVERT: 8 7 LYS cc_start: 0.7272 (OUTLIER) cc_final: 0.6978 (mttp) REVERT: I 30 GLU cc_start: 0.7598 (OUTLIER) cc_final: 0.7226 (tm-30) REVERT: S 84 MET cc_start: 0.7177 (mmp) cc_final: 0.6377 (mmp) outliers start: 79 outliers final: 24 residues processed: 684 average time/residue: 1.6991 time to fit residues: 1387.8493 Evaluate side-chains 601 residues out of total 4065 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 571 time to evaluate : 4.367 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 270 ASP Chi-restraints excluded: chain A residue 411 ASP Chi-restraints excluded: chain B residue 67 GLU Chi-restraints excluded: chain B residue 496 LYS Chi-restraints excluded: chain C residue 155 SER Chi-restraints excluded: chain C residue 371 VAL Chi-restraints excluded: chain F residue 46 THR Chi-restraints excluded: chain F residue 215 THR Chi-restraints excluded: chain F residue 249 GLN Chi-restraints excluded: chain D residue 46 THR Chi-restraints excluded: chain D residue 212 LYS Chi-restraints excluded: chain D residue 434 LEU Chi-restraints excluded: chain G residue 169 ILE Chi-restraints excluded: chain O residue 107 THR Chi-restraints excluded: chain O residue 150 LEU Chi-restraints excluded: chain K residue 46 LEU Chi-restraints excluded: chain K residue 181 VAL Chi-restraints excluded: chain M residue 89 VAL Chi-restraints excluded: chain 3 residue 41 SER Chi-restraints excluded: chain 8 residue 7 LYS Chi-restraints excluded: chain 1 residue 57 SER Chi-restraints excluded: chain 2 residue 62 LEU Chi-restraints excluded: chain H residue 143 LYS Chi-restraints excluded: chain I residue 30 GLU Chi-restraints excluded: chain I residue 38 THR Chi-restraints excluded: chain Q residue 6 THR Chi-restraints excluded: chain Q residue 32 ASN Chi-restraints excluded: chain Q residue 42 MET Chi-restraints excluded: chain Q residue 47 TYR Chi-restraints excluded: chain R residue 80 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 490 random chunks: chunk 247 optimal weight: 8.9990 chunk 138 optimal weight: 6.9990 chunk 370 optimal weight: 0.8980 chunk 303 optimal weight: 8.9990 chunk 122 optimal weight: 4.9990 chunk 445 optimal weight: 3.9990 chunk 481 optimal weight: 20.0000 chunk 397 optimal weight: 0.4980 chunk 442 optimal weight: 4.9990 chunk 151 optimal weight: 0.6980 chunk 357 optimal weight: 10.0000 overall best weight: 2.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 475 GLN A 477 GLN ** B 385 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 78 ASN ** E 458 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 224 GLN F 458 GLN ** D 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 150 ASN ** K 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 158 HIS L 40 GLN 4 39 ASN I 34 ASN ** N 61 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 8 ASN P 22 GLN ** T 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7990 moved from start: 0.1841 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 39118 Z= 0.301 Angle : 0.596 9.197 52927 Z= 0.304 Chirality : 0.044 0.167 6159 Planarity : 0.004 0.070 6753 Dihedral : 7.099 150.295 5520 Min Nonbonded Distance : 1.921 Molprobity Statistics. All-atom Clashscore : 8.54 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.34 % Favored : 97.60 % Rotamer: Outliers : 2.74 % Allowed : 15.84 % Favored : 81.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.13 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.39 (0.12), residues: 4962 helix: 0.17 (0.10), residues: 2676 sheet: -0.71 (0.21), residues: 568 loop : -0.54 (0.15), residues: 1718 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP M 12 HIS 0.006 0.001 HIS H 51 PHE 0.031 0.002 PHE R 79 TYR 0.018 0.001 TYR G 44 ARG 0.011 0.000 ARG H 128 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9924 Ramachandran restraints generated. 4962 Oldfield, 0 Emsley, 4962 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9924 Ramachandran restraints generated. 4962 Oldfield, 0 Emsley, 4962 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 708 residues out of total 4065 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 111 poor density : 597 time to evaluate : 4.680 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 52 MET cc_start: 0.8139 (tpp) cc_final: 0.7937 (tpp) REVERT: B 67 GLU cc_start: 0.7884 (OUTLIER) cc_final: 0.7563 (mt-10) REVERT: B 475 GLN cc_start: 0.8409 (OUTLIER) cc_final: 0.6985 (mp10) REVERT: B 496 LYS cc_start: 0.8057 (OUTLIER) cc_final: 0.7840 (ttmm) REVERT: C 30 ARG cc_start: 0.7936 (mtp85) cc_final: 0.7733 (mmm-85) REVERT: C 471 HIS cc_start: 0.6124 (t70) cc_final: 0.5588 (t-170) REVERT: C 496 LYS cc_start: 0.6971 (tttm) cc_final: 0.6502 (tppt) REVERT: E 128 GLU cc_start: 0.7312 (OUTLIER) cc_final: 0.7047 (mt-10) REVERT: E 224 GLN cc_start: 0.8384 (OUTLIER) cc_final: 0.7355 (mm-40) REVERT: F 217 LYS cc_start: 0.8172 (OUTLIER) cc_final: 0.7724 (mptm) REVERT: F 249 GLN cc_start: 0.7855 (OUTLIER) cc_final: 0.7479 (mp10) REVERT: D 475 LYS cc_start: 0.8117 (ttmt) cc_final: 0.7686 (tmtt) REVERT: G 53 GLU cc_start: 0.6496 (OUTLIER) cc_final: 0.5787 (mp0) REVERT: O 150 LEU cc_start: 0.7336 (OUTLIER) cc_final: 0.6965 (mm) REVERT: L 52 SER cc_start: 0.7615 (p) cc_final: 0.7409 (p) REVERT: L 69 GLN cc_start: 0.7754 (pm20) cc_final: 0.7445 (pt0) REVERT: 4 38 ARG cc_start: 0.7301 (OUTLIER) cc_final: 0.6183 (ttm-80) REVERT: 4 75 MET cc_start: 0.5892 (OUTLIER) cc_final: 0.5261 (mpm) REVERT: I 44 LYS cc_start: 0.7989 (OUTLIER) cc_final: 0.7772 (mttm) REVERT: S 84 MET cc_start: 0.7215 (mmp) cc_final: 0.6357 (mmp) outliers start: 111 outliers final: 38 residues processed: 655 average time/residue: 1.6804 time to fit residues: 1326.0033 Evaluate side-chains 612 residues out of total 4065 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 562 time to evaluate : 4.629 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 125 THR Chi-restraints excluded: chain A residue 270 ASP Chi-restraints excluded: chain A residue 411 ASP Chi-restraints excluded: chain B residue 38 ILE Chi-restraints excluded: chain B residue 67 GLU Chi-restraints excluded: chain B residue 87 ILE Chi-restraints excluded: chain B residue 137 ILE Chi-restraints excluded: chain B residue 475 GLN Chi-restraints excluded: chain B residue 496 LYS Chi-restraints excluded: chain C residue 25 LEU Chi-restraints excluded: chain C residue 124 LYS Chi-restraints excluded: chain C residue 125 THR Chi-restraints excluded: chain C residue 157 VAL Chi-restraints excluded: chain E residue 114 LYS Chi-restraints excluded: chain E residue 128 GLU Chi-restraints excluded: chain E residue 224 GLN Chi-restraints excluded: chain E residue 225 MET Chi-restraints excluded: chain F residue 46 THR Chi-restraints excluded: chain F residue 215 THR Chi-restraints excluded: chain F residue 217 LYS Chi-restraints excluded: chain F residue 249 GLN Chi-restraints excluded: chain F residue 271 VAL Chi-restraints excluded: chain F residue 290 THR Chi-restraints excluded: chain F residue 467 GLU Chi-restraints excluded: chain D residue 46 THR Chi-restraints excluded: chain D residue 212 LYS Chi-restraints excluded: chain D residue 434 LEU Chi-restraints excluded: chain D residue 467 GLU Chi-restraints excluded: chain G residue 53 GLU Chi-restraints excluded: chain G residue 169 ILE Chi-restraints excluded: chain G residue 241 GLU Chi-restraints excluded: chain O residue 150 LEU Chi-restraints excluded: chain K residue 67 MET Chi-restraints excluded: chain K residue 100 SER Chi-restraints excluded: chain K residue 145 TYR Chi-restraints excluded: chain K residue 181 VAL Chi-restraints excluded: chain L residue 71 LEU Chi-restraints excluded: chain M residue 89 VAL Chi-restraints excluded: chain 3 residue 41 SER Chi-restraints excluded: chain 4 residue 38 ARG Chi-restraints excluded: chain 4 residue 75 MET Chi-restraints excluded: chain 7 residue 21 SER Chi-restraints excluded: chain 7 residue 41 SER Chi-restraints excluded: chain 8 residue 7 LYS Chi-restraints excluded: chain 1 residue 57 SER Chi-restraints excluded: chain I residue 30 GLU Chi-restraints excluded: chain I residue 44 LYS Chi-restraints excluded: chain Q residue 8 VAL Chi-restraints excluded: chain Q residue 47 TYR Chi-restraints excluded: chain S residue 29 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 490 random chunks: chunk 440 optimal weight: 2.9990 chunk 335 optimal weight: 7.9990 chunk 231 optimal weight: 0.9980 chunk 49 optimal weight: 7.9990 chunk 212 optimal weight: 3.9990 chunk 299 optimal weight: 0.3980 chunk 447 optimal weight: 0.5980 chunk 473 optimal weight: 5.9990 chunk 233 optimal weight: 0.9980 chunk 424 optimal weight: 0.8980 chunk 127 optimal weight: 4.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 475 GLN A 477 GLN ** B 385 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 432 GLN ** E 458 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 224 GLN F 458 GLN ** D 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 150 ASN ** K 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 34 ASN ** N 61 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 8 ASN P 22 GLN ** T 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7931 moved from start: 0.2196 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 39118 Z= 0.163 Angle : 0.533 10.310 52927 Z= 0.271 Chirality : 0.041 0.161 6159 Planarity : 0.004 0.041 6753 Dihedral : 6.653 151.714 5520 Min Nonbonded Distance : 2.024 Molprobity Statistics. All-atom Clashscore : 8.17 Ramachandran Plot: Outliers : 0.04 % Allowed : 2.04 % Favored : 97.92 % Rotamer: Outliers : 2.27 % Allowed : 17.82 % Favored : 79.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.13 % 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 (0.12), residues: 4962 helix: 0.60 (0.10), residues: 2672 sheet: -0.54 (0.21), residues: 577 loop : -0.29 (0.16), residues: 1713 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP M 12 HIS 0.003 0.001 HIS D 180 PHE 0.028 0.001 PHE R 79 TYR 0.013 0.001 TYR G 44 ARG 0.007 0.000 ARG S 95 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9924 Ramachandran restraints generated. 4962 Oldfield, 0 Emsley, 4962 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9924 Ramachandran restraints generated. 4962 Oldfield, 0 Emsley, 4962 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 705 residues out of total 4065 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 92 poor density : 613 time to evaluate : 4.216 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 52 MET cc_start: 0.8101 (tpp) cc_final: 0.7889 (tpp) REVERT: B 67 GLU cc_start: 0.7845 (OUTLIER) cc_final: 0.7565 (mt-10) REVERT: C 471 HIS cc_start: 0.6018 (t70) cc_final: 0.5454 (t-170) REVERT: F 210 ASN cc_start: 0.8126 (t0) cc_final: 0.7901 (t0) REVERT: D 475 LYS cc_start: 0.8119 (ttmt) cc_final: 0.7686 (tmtt) REVERT: O 150 LEU cc_start: 0.7338 (OUTLIER) cc_final: 0.6941 (mm) REVERT: L 52 SER cc_start: 0.7725 (p) cc_final: 0.7467 (p) REVERT: L 69 GLN cc_start: 0.7754 (pm20) cc_final: 0.7514 (pt0) REVERT: 4 38 ARG cc_start: 0.7243 (OUTLIER) cc_final: 0.6573 (ttm-80) REVERT: 4 66 MET cc_start: 0.6957 (OUTLIER) cc_final: 0.6135 (mpp) REVERT: 4 75 MET cc_start: 0.5824 (OUTLIER) cc_final: 0.5201 (mpm) REVERT: 1 75 MET cc_start: 0.6528 (OUTLIER) cc_final: 0.4858 (mpp) REVERT: N 169 LEU cc_start: 0.8100 (OUTLIER) cc_final: 0.7879 (tt) REVERT: S 84 MET cc_start: 0.7166 (mmp) cc_final: 0.6304 (mmp) REVERT: J 40 GLU cc_start: 0.7125 (OUTLIER) cc_final: 0.6220 (mp0) outliers start: 92 outliers final: 28 residues processed: 665 average time/residue: 1.5868 time to fit residues: 1273.0745 Evaluate side-chains 595 residues out of total 4065 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 559 time to evaluate : 4.669 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 270 ASP Chi-restraints excluded: chain A residue 354 THR Chi-restraints excluded: chain A residue 411 ASP Chi-restraints excluded: chain B residue 38 ILE Chi-restraints excluded: chain B residue 67 GLU Chi-restraints excluded: chain B residue 411 ASP Chi-restraints excluded: chain C residue 124 LYS Chi-restraints excluded: chain C residue 157 VAL Chi-restraints excluded: chain F residue 46 THR Chi-restraints excluded: chain F residue 215 THR Chi-restraints excluded: chain F residue 467 GLU Chi-restraints excluded: chain D residue 46 THR Chi-restraints excluded: chain D residue 434 LEU Chi-restraints excluded: chain G residue 241 GLU Chi-restraints excluded: chain O residue 138 LEU Chi-restraints excluded: chain O residue 150 LEU Chi-restraints excluded: chain K residue 145 TYR Chi-restraints excluded: chain K residue 181 VAL Chi-restraints excluded: chain L residue 82 PHE Chi-restraints excluded: chain M residue 44 LEU Chi-restraints excluded: chain M residue 89 VAL Chi-restraints excluded: chain 3 residue 41 SER Chi-restraints excluded: chain 4 residue 38 ARG Chi-restraints excluded: chain 4 residue 66 MET Chi-restraints excluded: chain 4 residue 75 MET Chi-restraints excluded: chain 7 residue 41 SER Chi-restraints excluded: chain 8 residue 7 LYS Chi-restraints excluded: chain 1 residue 72 LEU Chi-restraints excluded: chain 1 residue 75 MET Chi-restraints excluded: chain I residue 30 GLU Chi-restraints excluded: chain I residue 38 THR Chi-restraints excluded: chain N residue 169 LEU Chi-restraints excluded: chain Q residue 8 VAL Chi-restraints excluded: chain R residue 19 GLU Chi-restraints excluded: chain R residue 74 LEU Chi-restraints excluded: chain J residue 40 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 490 random chunks: chunk 394 optimal weight: 4.9990 chunk 268 optimal weight: 5.9990 chunk 6 optimal weight: 4.9990 chunk 352 optimal weight: 5.9990 chunk 195 optimal weight: 5.9990 chunk 404 optimal weight: 2.9990 chunk 327 optimal weight: 9.9990 chunk 0 optimal weight: 4.9990 chunk 241 optimal weight: 7.9990 chunk 425 optimal weight: 3.9990 chunk 119 optimal weight: 1.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 172 GLN A 475 GLN A 477 GLN ** B 385 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 385 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 432 GLN E 224 GLN ** E 458 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 224 GLN F 458 GLN ** D 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 150 ASN O 34 GLN ** K 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 158 HIS ** K 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 2 45 GLN ** N 61 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 22 GLN ** S 75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8040 moved from start: 0.2227 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.075 39118 Z= 0.462 Angle : 0.662 11.461 52927 Z= 0.337 Chirality : 0.048 0.176 6159 Planarity : 0.005 0.071 6753 Dihedral : 7.376 155.056 5518 Min Nonbonded Distance : 1.895 Molprobity Statistics. All-atom Clashscore : 9.48 Ramachandran Plot: Outliers : 0.04 % Allowed : 2.98 % Favored : 96.98 % Rotamer: Outliers : 3.14 % Allowed : 18.19 % Favored : 78.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.13 % 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: -0.10 (0.12), residues: 4962 helix: 0.41 (0.10), residues: 2620 sheet: -0.56 (0.21), residues: 577 loop : -0.39 (0.15), residues: 1765 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP M 12 HIS 0.008 0.001 HIS H 51 PHE 0.034 0.002 PHE H 45 TYR 0.023 0.002 TYR M 56 ARG 0.015 0.001 ARG R 32 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9924 Ramachandran restraints generated. 4962 Oldfield, 0 Emsley, 4962 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9924 Ramachandran restraints generated. 4962 Oldfield, 0 Emsley, 4962 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 708 residues out of total 4065 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 127 poor density : 581 time to evaluate : 4.735 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 52 MET cc_start: 0.8111 (tpp) cc_final: 0.7888 (tpp) REVERT: B 67 GLU cc_start: 0.7908 (OUTLIER) cc_final: 0.7573 (mt-10) REVERT: B 475 GLN cc_start: 0.8223 (OUTLIER) cc_final: 0.6836 (mp10) REVERT: C 471 HIS cc_start: 0.6052 (t70) cc_final: 0.5475 (t-170) REVERT: C 496 LYS cc_start: 0.7007 (tttm) cc_final: 0.6660 (tppt) REVERT: E 15 ARG cc_start: 0.7971 (OUTLIER) cc_final: 0.7361 (ptm-80) REVERT: E 29 ASP cc_start: 0.7346 (OUTLIER) cc_final: 0.6845 (p0) REVERT: E 128 GLU cc_start: 0.7305 (OUTLIER) cc_final: 0.7047 (mt-10) REVERT: F 249 GLN cc_start: 0.7890 (OUTLIER) cc_final: 0.7501 (mp10) REVERT: D 475 LYS cc_start: 0.8146 (ttmt) cc_final: 0.7707 (tmtt) REVERT: G 53 GLU cc_start: 0.6476 (OUTLIER) cc_final: 0.5617 (mp0) REVERT: O 15 GLU cc_start: 0.7151 (mp0) cc_final: 0.6893 (mp0) REVERT: O 150 LEU cc_start: 0.7454 (OUTLIER) cc_final: 0.7061 (mm) REVERT: L 69 GLN cc_start: 0.7747 (pm20) cc_final: 0.7452 (pt0) REVERT: M 40 ARG cc_start: 0.7714 (mmm-85) cc_final: 0.7477 (mtp180) REVERT: 4 38 ARG cc_start: 0.7363 (OUTLIER) cc_final: 0.6637 (ttm-80) REVERT: 4 75 MET cc_start: 0.6174 (OUTLIER) cc_final: 0.5465 (mpm) REVERT: 1 75 MET cc_start: 0.7127 (OUTLIER) cc_final: 0.5814 (mpp) REVERT: N 169 LEU cc_start: 0.8181 (OUTLIER) cc_final: 0.7974 (tt) REVERT: S 84 MET cc_start: 0.7256 (mmp) cc_final: 0.6300 (mmp) outliers start: 127 outliers final: 62 residues processed: 654 average time/residue: 1.4878 time to fit residues: 1174.9429 Evaluate side-chains 625 residues out of total 4065 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 551 time to evaluate : 3.265 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 125 THR Chi-restraints excluded: chain A residue 354 THR Chi-restraints excluded: chain A residue 411 ASP Chi-restraints excluded: chain B residue 38 ILE Chi-restraints excluded: chain B residue 67 GLU Chi-restraints excluded: chain B residue 411 ASP Chi-restraints excluded: chain B residue 475 GLN Chi-restraints excluded: chain C residue 25 LEU Chi-restraints excluded: chain C residue 124 LYS Chi-restraints excluded: chain C residue 125 THR Chi-restraints excluded: chain C residue 155 SER Chi-restraints excluded: chain C residue 157 VAL Chi-restraints excluded: chain E residue 15 ARG Chi-restraints excluded: chain E residue 29 ASP Chi-restraints excluded: chain E residue 114 LYS Chi-restraints excluded: chain E residue 128 GLU Chi-restraints excluded: chain E residue 224 GLN Chi-restraints excluded: chain E residue 290 THR Chi-restraints excluded: chain E residue 335 THR Chi-restraints excluded: chain F residue 46 THR Chi-restraints excluded: chain F residue 215 THR Chi-restraints excluded: chain F residue 249 GLN Chi-restraints excluded: chain F residue 271 VAL Chi-restraints excluded: chain F residue 282 VAL Chi-restraints excluded: chain F residue 290 THR Chi-restraints excluded: chain F residue 467 GLU Chi-restraints excluded: chain D residue 46 THR Chi-restraints excluded: chain D residue 184 SER Chi-restraints excluded: chain D residue 202 GLU Chi-restraints excluded: chain D residue 212 LYS Chi-restraints excluded: chain D residue 434 LEU Chi-restraints excluded: chain D residue 467 GLU Chi-restraints excluded: chain G residue 53 GLU Chi-restraints excluded: chain G residue 104 MET Chi-restraints excluded: chain G residue 197 ASP Chi-restraints excluded: chain O residue 138 LEU Chi-restraints excluded: chain O residue 150 LEU Chi-restraints excluded: chain K residue 67 MET Chi-restraints excluded: chain K residue 100 SER Chi-restraints excluded: chain K residue 124 LEU Chi-restraints excluded: chain K residue 145 TYR Chi-restraints excluded: chain K residue 151 VAL Chi-restraints excluded: chain K residue 181 VAL Chi-restraints excluded: chain L residue 71 LEU Chi-restraints excluded: chain L residue 82 PHE Chi-restraints excluded: chain L residue 100 PHE Chi-restraints excluded: chain M residue 44 LEU Chi-restraints excluded: chain M residue 89 VAL Chi-restraints excluded: chain M residue 131 THR Chi-restraints excluded: chain M residue 145 ASP Chi-restraints excluded: chain 3 residue 41 SER Chi-restraints excluded: chain 4 residue 38 ARG Chi-restraints excluded: chain 4 residue 52 LEU Chi-restraints excluded: chain 4 residue 75 MET Chi-restraints excluded: chain 7 residue 4 THR Chi-restraints excluded: chain 7 residue 41 SER Chi-restraints excluded: chain 8 residue 21 SER Chi-restraints excluded: chain 8 residue 41 SER Chi-restraints excluded: chain 1 residue 72 LEU Chi-restraints excluded: chain 1 residue 75 MET Chi-restraints excluded: chain H residue 24 THR Chi-restraints excluded: chain I residue 30 GLU Chi-restraints excluded: chain I residue 38 THR Chi-restraints excluded: chain I residue 41 SER Chi-restraints excluded: chain N residue 39 ASN Chi-restraints excluded: chain N residue 91 SER Chi-restraints excluded: chain N residue 169 LEU Chi-restraints excluded: chain N residue 182 SER Chi-restraints excluded: chain N residue 206 VAL Chi-restraints excluded: chain Q residue 8 VAL Chi-restraints excluded: chain Q residue 42 MET Chi-restraints excluded: chain R residue 74 LEU Chi-restraints excluded: chain S residue 69 VAL Chi-restraints excluded: chain S residue 77 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 490 random chunks: chunk 159 optimal weight: 5.9990 chunk 426 optimal weight: 5.9990 chunk 93 optimal weight: 0.9980 chunk 278 optimal weight: 6.9990 chunk 116 optimal weight: 4.9990 chunk 474 optimal weight: 2.9990 chunk 393 optimal weight: 0.8980 chunk 219 optimal weight: 4.9990 chunk 39 optimal weight: 6.9990 chunk 156 optimal weight: 2.9990 chunk 248 optimal weight: 1.9990 overall best weight: 1.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Sorry: Reduce crashed with command 'molprobity.reduce -quiet -trim -'. Dumping stdin to file 'reduce_failure.pdb'. Return code: -15 Dumping stderr: