Starting phenix.real_space_refine (version: 1.21rc1) on Tue Apr 25 02:22:18 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6qdv_4525/04_2023/6qdv_4525_neut_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6qdv_4525/04_2023/6qdv_4525.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6qdv_4525/04_2023/6qdv_4525.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6qdv_4525/04_2023/6qdv_4525.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6qdv_4525/04_2023/6qdv_4525_neut_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6qdv_4525/04_2023/6qdv_4525_neut_updated.pdb" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.005 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 8 Type Number sf(0) Gaussians K 1 8.98 5 Zn 7 6.06 5 P 362 5.49 5 Mg 7 5.21 5 S 552 5.16 5 C 75163 2.51 5 N 21501 2.21 5 O 23559 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "7 GLU 59": "OE1" <-> "OE2" Residue "7 GLU 106": "OE1" <-> "OE2" Residue "7 ARG 173": "NH1" <-> "NH2" Residue "7 GLU 188": "OE1" <-> "OE2" Residue "7 GLU 224": "OE1" <-> "OE2" Residue "7 GLU 227": "OE1" <-> "OE2" Residue "7 GLU 259": "OE1" <-> "OE2" Residue "7 GLU 261": "OE1" <-> "OE2" Residue "7 ARG 324": "NH1" <-> "NH2" Residue "7 ARG 390": "NH1" <-> "NH2" Residue "7 GLU 393": "OE1" <-> "OE2" Residue "7 GLU 402": "OE1" <-> "OE2" Residue "8 GLU 83": "OE1" <-> "OE2" Residue "8 GLU 126": "OE1" <-> "OE2" Residue "9 GLU 27": "OE1" <-> "OE2" Residue "9 PHE 28": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "9 TYR 36": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "9 GLU 51": "OE1" <-> "OE2" Residue "A GLU 32": "OE1" <-> "OE2" Residue "A GLU 47": "OE1" <-> "OE2" Residue "A ARG 86": "NH1" <-> "NH2" Residue "A GLU 131": "OE1" <-> "OE2" Residue "A ARG 165": "NH1" <-> "NH2" Residue "A ARG 214": "NH1" <-> "NH2" Residue "A GLU 291": "OE1" <-> "OE2" Residue "A GLU 382": "OE1" <-> "OE2" Residue "A ARG 474": "NH1" <-> "NH2" Residue "A ARG 548": "NH1" <-> "NH2" Residue "A ARG 663": "NH1" <-> "NH2" Residue "A ARG 758": "NH1" <-> "NH2" Residue "A ARG 762": "NH1" <-> "NH2" Residue "A ARG 845": "NH1" <-> "NH2" Residue "A GLU 848": "OE1" <-> "OE2" Residue "A GLU 862": "OE1" <-> "OE2" Residue "A GLU 970": "OE1" <-> "OE2" Residue "A ARG 980": "NH1" <-> "NH2" Residue "A ARG 995": "NH1" <-> "NH2" Residue "A GLU 1116": "OE1" <-> "OE2" Residue "A GLU 1123": "OE1" <-> "OE2" Residue "A GLU 1361": "OE1" <-> "OE2" Residue "A ARG 1370": "NH1" <-> "NH2" Residue "A GLU 1376": "OE1" <-> "OE2" Residue "A ARG 1402": "NH1" <-> "NH2" Residue "A GLU 1406": "OE1" <-> "OE2" Residue "A ARG 1414": "NH1" <-> "NH2" Residue "A ARG 1427": "NH1" <-> "NH2" Residue "A ARG 1471": "NH1" <-> "NH2" Residue "A GLU 1486": "OE1" <-> "OE2" Residue "A ARG 1523": "NH1" <-> "NH2" Residue "A GLU 1587": "OE1" <-> "OE2" Residue "A GLU 1677": "OE1" <-> "OE2" Residue "A TYR 1715": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1719": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1770": "OE1" <-> "OE2" Residue "A ARG 1832": "NH1" <-> "NH2" Residue "A GLU 1844": "OE1" <-> "OE2" Residue "A ARG 1850": "NH1" <-> "NH2" Residue "A GLU 1856": "OE1" <-> "OE2" Residue "A ARG 1865": "NH1" <-> "NH2" Residue "A TYR 1930": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1974": "OE1" <-> "OE2" Residue "A GLU 2072": "OE1" <-> "OE2" Residue "A GLU 2141": "OE1" <-> "OE2" Residue "A GLU 2171": "OE1" <-> "OE2" Residue "A PHE 2267": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 2303": "OE1" <-> "OE2" Residue "A GLU 2307": "OE1" <-> "OE2" Residue "A ARG 2330": "NH1" <-> "NH2" Residue "A GLU 2331": "OE1" <-> "OE2" Residue "B GLU 465": "OE1" <-> "OE2" Residue "B ARG 483": "NH1" <-> "NH2" Residue "B ARG 490": "NH1" <-> "NH2" Residue "B GLU 494": "OE1" <-> "OE2" Residue "B ARG 519": "NH1" <-> "NH2" Residue "B GLU 550": "OE1" <-> "OE2" Residue "B ARG 558": "NH1" <-> "NH2" Residue "B GLU 579": "OE1" <-> "OE2" Residue "B GLU 591": "OE1" <-> "OE2" Residue "B ARG 610": "NH1" <-> "NH2" Residue "B GLU 629": "OE1" <-> "OE2" Residue "B GLU 659": "OE1" <-> "OE2" Residue "B ARG 666": "NH1" <-> "NH2" Residue "B GLU 686": "OE1" <-> "OE2" Residue "B GLU 744": "OE1" <-> "OE2" Residue "B GLU 760": "OE1" <-> "OE2" Residue "B GLU 767": "OE1" <-> "OE2" Residue "B GLU 843": "OE1" <-> "OE2" Residue "B GLU 866": "OE1" <-> "OE2" Residue "B ARG 952": "NH1" <-> "NH2" Residue "B GLU 983": "OE1" <-> "OE2" Residue "B ARG 986": "NH1" <-> "NH2" Residue "B GLU 1013": "OE1" <-> "OE2" Residue "B GLU 1023": "OE1" <-> "OE2" Residue "B ARG 1030": "NH1" <-> "NH2" Residue "B GLU 1054": "OE1" <-> "OE2" Residue "B ARG 1090": "NH1" <-> "NH2" Residue "B ARG 1093": "NH1" <-> "NH2" Residue "B ARG 1121": "NH1" <-> "NH2" Residue "B GLU 1144": "OE1" <-> "OE2" Residue "B GLU 1151": "OE1" <-> "OE2" Residue "B GLU 1185": "OE1" <-> "OE2" Residue "B GLU 1226": "OE1" <-> "OE2" Residue "B GLU 1237": "OE1" <-> "OE2" Residue "B ARG 1274": "NH1" <-> "NH2" Residue "B ARG 1287": "NH1" <-> "NH2" Residue "B GLU 1387": "OE1" <-> "OE2" Residue "B GLU 1411": "OE1" <-> "OE2" Residue "B GLU 1430": "OE1" <-> "OE2" Residue "B GLU 1455": "OE1" <-> "OE2" Residue "B GLU 1468": "OE1" <-> "OE2" Residue "B GLU 1482": "OE1" <-> "OE2" Residue "B ARG 1570": "NH1" <-> "NH2" Residue "B ARG 1588": "NH1" <-> "NH2" Residue "B GLU 1602": "OE1" <-> "OE2" Residue "B GLU 1622": "OE1" <-> "OE2" Residue "B GLU 1628": "OE1" <-> "OE2" Residue "B ARG 1648": "NH1" <-> "NH2" Residue "B TYR 1682": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 1693": "NH1" <-> "NH2" Residue "B ARG 1762": "NH1" <-> "NH2" Residue "B GLU 1787": "OE1" <-> "OE2" Residue "B GLU 1805": "OE1" <-> "OE2" Residue "B GLU 1907": "OE1" <-> "OE2" Residue "B GLU 1913": "OE1" <-> "OE2" Residue "B GLU 1944": "OE1" <-> "OE2" Residue "B GLU 1969": "OE1" <-> "OE2" Residue "B GLU 1980": "OE1" <-> "OE2" Residue "B ARG 1993": "NH1" <-> "NH2" Residue "B ARG 2030": "NH1" <-> "NH2" Residue "B GLU 2042": "OE1" <-> "OE2" Residue "B GLU 2044": "OE1" <-> "OE2" Residue "B GLU 2046": "OE1" <-> "OE2" Residue "B ARG 2081": "NH1" <-> "NH2" Residue "C ARG 160": "NH1" <-> "NH2" Residue "C GLU 233": "OE1" <-> "OE2" Residue "C GLU 240": "OE1" <-> "OE2" Residue "C GLU 284": "OE1" <-> "OE2" Residue "C PHE 318": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 512": "OE1" <-> "OE2" Residue "C TYR 514": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 520": "OE1" <-> "OE2" Residue "C ARG 569": "NH1" <-> "NH2" Residue "C GLU 572": "OE1" <-> "OE2" Residue "C GLU 623": "OE1" <-> "OE2" Residue "C GLU 690": "OE1" <-> "OE2" Residue "C ARG 711": "NH1" <-> "NH2" Residue "C GLU 716": "OE1" <-> "OE2" Residue "C ARG 730": "NH1" <-> "NH2" Residue "C GLU 753": "OE1" <-> "OE2" Residue "C ARG 775": "NH1" <-> "NH2" Residue "C GLU 776": "OE1" <-> "OE2" Residue "C GLU 782": "OE1" <-> "OE2" Residue "C GLU 884": "OE1" <-> "OE2" Residue "C ARG 919": "NH1" <-> "NH2" Residue "C GLU 922": "OE1" <-> "OE2" Residue "D GLU 30": "OE1" <-> "OE2" Residue "D ASP 43": "OD1" <-> "OD2" Residue "D GLU 78": "OE1" <-> "OE2" Residue "D ARG 86": "NH1" <-> "NH2" Residue "D GLU 101": "OE1" <-> "OE2" Residue "D GLU 108": "OE1" <-> "OE2" Residue "D ARG 131": "NH1" <-> "NH2" Residue "F ARG 644": "NH1" <-> "NH2" Residue "F ARG 726": "NH1" <-> "NH2" Residue "F ARG 733": "NH1" <-> "NH2" Residue "F ARG 737": "NH1" <-> "NH2" Residue "F ARG 753": "NH1" <-> "NH2" Residue "F ARG 757": "NH1" <-> "NH2" Residue "G GLU 66": "OE1" <-> "OE2" Residue "H ARG 457": "NH1" <-> "NH2" Residue "H GLU 483": "OE1" <-> "OE2" Residue "H ARG 538": "NH1" <-> "NH2" Residue "H GLU 540": "OE1" <-> "OE2" Residue "H ARG 545": "NH1" <-> "NH2" Residue "H ARG 625": "NH1" <-> "NH2" Residue "H GLU 642": "OE1" <-> "OE2" Residue "J ARG 383": "NH1" <-> "NH2" Residue "J PHE 447": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 46": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ARG 53": "NH1" <-> "NH2" Residue "K ARG 78": "NH1" <-> "NH2" Residue "K GLU 123": "OE1" <-> "OE2" Residue "K GLU 137": "OE1" <-> "OE2" Residue "K GLU 201": "OE1" <-> "OE2" Residue "K GLU 303": "OE1" <-> "OE2" Residue "L ARG 8": "NH1" <-> "NH2" Residue "L GLU 19": "OE1" <-> "OE2" Residue "L GLU 98": "OE1" <-> "OE2" Residue "M PHE 55": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M ARG 64": "NH1" <-> "NH2" Residue "M ARG 132": "NH1" <-> "NH2" Residue "M GLU 177": "OE1" <-> "OE2" Residue "M ARG 216": "NH1" <-> "NH2" Residue "M GLU 257": "OE1" <-> "OE2" Residue "M ARG 297": "NH1" <-> "NH2" Residue "N ARG 52": "NH1" <-> "NH2" Residue "N GLU 114": "OE1" <-> "OE2" Residue "N GLU 142": "OE1" <-> "OE2" Residue "N ARG 162": "NH1" <-> "NH2" Residue "N GLU 246": "OE1" <-> "OE2" Residue "N GLU 285": "OE1" <-> "OE2" Residue "N GLU 355": "OE1" <-> "OE2" Residue "O ARG 12": "NH1" <-> "NH2" Residue "O ARG 83": "NH1" <-> "NH2" Residue "O GLU 177": "OE1" <-> "OE2" Residue "O ARG 180": "NH1" <-> "NH2" Residue "O GLU 250": "OE1" <-> "OE2" Residue "O ASP 740": "OD1" <-> "OD2" Residue "O PHE 752": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O ASP 773": "OD1" <-> "OD2" Residue "O GLU 781": "OE1" <-> "OE2" Residue "P ARG 16": "NH1" <-> "NH2" Residue "P ARG 60": "NH1" <-> "NH2" Residue "P ARG 72": "NH1" <-> "NH2" Residue "S GLU 186": "OE1" <-> "OE2" Residue "S GLU 218": "OE1" <-> "OE2" Residue "S GLU 284": "OE1" <-> "OE2" Residue "S GLU 404": "OE1" <-> "OE2" Residue "T GLU 536": "OE1" <-> "OE2" Residue "T ARG 567": "NH1" <-> "NH2" Residue "T GLU 617": "OE1" <-> "OE2" Residue "T GLU 624": "OE1" <-> "OE2" Residue "T GLU 675": "OE1" <-> "OE2" Residue "T ARG 698": "NH1" <-> "NH2" Residue "T ARG 727": "NH1" <-> "NH2" Residue "U GLU 51": "OE1" <-> "OE2" Residue "U ARG 182": "NH1" <-> "NH2" Residue "U GLU 205": "OE1" <-> "OE2" Residue "U GLU 210": "OE1" <-> "OE2" Residue "U GLU 218": "OE1" <-> "OE2" Residue "U GLU 261": "OE1" <-> "OE2" Residue "U ARG 291": "NH1" <-> "NH2" Residue "U GLU 347": "OE1" <-> "OE2" Residue "U GLU 358": "OE1" <-> "OE2" Residue "U GLU 363": "OE1" <-> "OE2" Residue "U PHE 470": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U ARG 619": "NH1" <-> "NH2" Residue "U TYR 790": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U GLU 873": "OE1" <-> "OE2" Residue "U GLU 885": "OE1" <-> "OE2" Residue "U GLU 1009": "OE1" <-> "OE2" Residue "U GLU 1190": "OE1" <-> "OE2" Residue "W TYR 15": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W ASP 21": "OD1" <-> "OD2" Residue "W PHE 49": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W ASP 51": "OD1" <-> "OD2" Residue "W ASP 58": "OD1" <-> "OD2" Residue "W GLU 81": "OE1" <-> "OE2" Residue "W GLU 92": "OE1" <-> "OE2" Residue "W TYR 117": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W TYR 137": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W ASP 146": "OD1" <-> "OD2" Residue "W GLU 157": "OE1" <-> "OE2" Residue "Y TYR 10": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y GLU 21": "OE1" <-> "OE2" Residue "Y GLU 22": "OE1" <-> "OE2" Residue "Y PHE 34": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y ASP 39": "OD1" <-> "OD2" Residue "Y ASP 87": "OD1" <-> "OD2" Residue "Z ARG 330": "NH1" <-> "NH2" Residue "Z GLU 336": "OE1" <-> "OE2" Residue "Z ARG 358": "NH1" <-> "NH2" Residue "b ARG 16": "NH1" <-> "NH2" Residue "b PHE 48": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b GLU 75": "OE1" <-> "OE2" Residue "c GLU 38": "OE1" <-> "OE2" Residue "c ARG 86": "NH1" <-> "NH2" Residue "c GLU 90": "OE1" <-> "OE2" Residue "c ARG 136": "NH1" <-> "NH2" Residue "c ARG 139": "NH1" <-> "NH2" Residue "c GLU 176": "OE1" <-> "OE2" Residue "c GLU 340": "OE1" <-> "OE2" Residue "d ASP 37": "OD1" <-> "OD2" Residue "d TYR 62": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "e ARG 23": "NH1" <-> "NH2" Residue "e GLU 44": "OE1" <-> "OE2" Residue "e ARG 76": "NH1" <-> "NH2" Residue "f GLU 28": "OE1" <-> "OE2" Residue "f TYR 29": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "f ASP 52": "OD1" <-> "OD2" Residue "f TYR 71": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "f ARG 73": "NH1" <-> "NH2" Residue "g PHE 12": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "g ARG 32": "NH1" <-> "NH2" Residue "g GLU 44": "OE1" <-> "OE2" Residue "h GLU 13": "OE1" <-> "OE2" Residue "h ARG 61": "NH1" <-> "NH2" Residue "h PHE 68": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "h ASP 77": "OD1" <-> "OD2" Residue "i ARG 72": "NH1" <-> "NH2" Residue "j GLU 15": "OE1" <-> "OE2" Residue "j GLU 21": "OE1" <-> "OE2" Residue "j ARG 61": "NH1" <-> "NH2" Residue "j ASP 93": "OD1" <-> "OD2" Residue "j TYR 95": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "j PHE 100": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "j ARG 102": "NH1" <-> "NH2" Residue "k PHE 48": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "k GLU 62": "OE1" <-> "OE2" Residue "k GLU 63": "OE1" <-> "OE2" Residue "k GLU 83": "OE1" <-> "OE2" Residue "l GLU 18": "OE1" <-> "OE2" Residue "l ARG 61": "NH1" <-> "NH2" Residue "m GLU 21": "OE1" <-> "OE2" Residue "m GLU 22": "OE1" <-> "OE2" Residue "m ARG 61": "NH1" <-> "NH2" Residue "m GLU 68": "OE1" <-> "OE2" Residue "m PHE 100": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "m ARG 102": "NH1" <-> "NH2" Residue "n TYR 28": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "n ASP 37": "OD1" <-> "OD2" Residue "n TYR 62": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "n PHE 70": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "n ASP 75": "OD1" <-> "OD2" Residue "o GLU 96": "OE1" <-> "OE2" Residue "o ARG 108": "NH1" <-> "NH2" Residue "o GLU 158": "OE1" <-> "OE2" Residue "o ARG 178": "NH1" <-> "NH2" Residue "o GLU 202": "OE1" <-> "OE2" Residue "o TYR 249": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "o PHE 347": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "o GLU 429": "OE1" <-> "OE2" Residue "o ARG 495": "NH1" <-> "NH2" Residue "o GLU 562": "OE1" <-> "OE2" Residue "p ARG 23": "NH1" <-> "NH2" Residue "p GLU 52": "OE1" <-> "OE2" Residue "p TYR 53": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "p ARG 76": "NH1" <-> "NH2" Residue "q TYR 29": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "q ARG 73": "NH1" <-> "NH2" Residue "r GLU 8": "OE1" <-> "OE2" Residue "r ARG 32": "NH1" <-> "NH2" Residue "r PHE 34": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "r ASP 43": "OD1" <-> "OD2" Residue "r ARG 75": "NH1" <-> "NH2" Residue "s PHE 19": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "s GLU 38": "OE1" <-> "OE2" Residue "s ARG 42": "NH1" <-> "NH2" Residue "s GLU 140": "OE1" <-> "OE2" Residue "s TYR 193": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "t GLU 10": "OE1" <-> "OE2" Residue "t GLU 26": "OE1" <-> "OE2" Residue "t ARG 27": "NH1" <-> "NH2" Residue "t ARG 28": "NH1" <-> "NH2" Residue "t GLU 31": "OE1" <-> "OE2" Residue "t TYR 33": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "t ARG 115": "NH1" <-> "NH2" Residue "t GLU 123": "OE1" <-> "OE2" Residue "t GLU 129": "OE1" <-> "OE2" Residue "u TYR 25": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "u ARG 27": "NH1" <-> "NH2" Residue "u ARG 28": "NH1" <-> "NH2" Residue "u GLU 31": "OE1" <-> "OE2" Residue "u TYR 33": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "u TYR 108": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "u ARG 115": "NH1" <-> "NH2" Residue "v GLU 13": "OE1" <-> "OE2" Residue "v TYR 25": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "v ARG 27": "NH1" <-> "NH2" Residue "v ARG 28": "NH1" <-> "NH2" Residue "v GLU 31": "OE1" <-> "OE2" Residue "v ARG 115": "NH1" <-> "NH2" Residue "v GLU 129": "OE1" <-> "OE2" Residue "w ARG 27": "NH1" <-> "NH2" Residue "w ARG 28": "NH1" <-> "NH2" Residue "w GLU 31": "OE1" <-> "OE2" Residue "w GLU 81": "OE1" <-> "OE2" Residue "w ARG 115": "NH1" <-> "NH2" Residue "y ARG 117": "NH1" <-> "NH2" Residue "y GLU 147": "OE1" <-> "OE2" Residue "y ARG 181": "NH1" <-> "NH2" Residue "y GLU 191": "OE1" <-> "OE2" Residue "y GLU 223": "OE1" <-> "OE2" Time to flip residues: 0.25s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4938/modules/chem_data/mon_lib" Total number of atoms: 121152 Number of models: 1 Model: "" Number of chains: 60 Chain: "2" Number of atoms: 2535 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 2535 Classifications: {'RNA': 120} Modifications used: {'rna2p_pur': 9, 'rna2p_pyr': 17, 'rna3p_pur': 46, 'rna3p_pyr': 48} Link IDs: {'rna2p': 26, 'rna3p': 93} Chain breaks: 2 Chain: "5" Number of atoms: 1579 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 1579 Classifications: {'RNA': 75} Modifications used: {'rna2p_pur': 5, 'rna2p_pyr': 8, 'rna3p_pur': 28, 'rna3p_pyr': 34} Link IDs: {'rna2p': 13, 'rna3p': 61} Chain breaks: 1 Chain: "6" Number of atoms: 2075 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 2075 Classifications: {'RNA': 97} Modifications used: {'rna2p_pur': 10, 'rna2p_pyr': 6, 'rna3p_pur': 45, 'rna3p_pyr': 36} Link IDs: {'rna2p': 16, 'rna3p': 80} Chain: "7" Number of atoms: 3130 Number of conformers: 1 Conformer: "" Number of residues, atoms: 390, 3130 Classifications: {'peptide': 390} Link IDs: {'PTRANS': 12, 'TRANS': 377} Chain: "8" Number of atoms: 730 Number of conformers: 1 Conformer: "" Number of residues, atoms: 91, 730 Classifications: {'peptide': 91} Link IDs: {'PTRANS': 3, 'TRANS': 87} Chain: "9" Number of atoms: 1196 Number of conformers: 1 Conformer: "" Number of residues, atoms: 144, 1196 Classifications: {'peptide': 144} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 137} Chain: "A" Number of atoms: 18655 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2250, 18655 Classifications: {'peptide': 2250} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 126, 'TRANS': 2122} Chain breaks: 2 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "B" Number of atoms: 13846 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1722, 13846 Classifications: {'peptide': 1722} Link IDs: {'PTRANS': 79, 'TRANS': 1642} Chain: "C" Number of atoms: 7116 Number of conformers: 1 Conformer: "" Number of residues, atoms: 899, 7116 Classifications: {'peptide': 899} Link IDs: {'PTRANS': 54, 'TRANS': 844} Chain: "D" Number of atoms: 1013 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 1013 Classifications: {'peptide': 123} Link IDs: {'PTRANS': 8, 'TRANS': 114} Chain: "E" Number of atoms: 296 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 296 Classifications: {'RNA': 14} Modifications used: {'rna2p_pur': 2, 'rna2p_pyr': 4, 'rna3p_pur': 4, 'rna3p_pyr': 4} Link IDs: {'rna2p': 6, 'rna3p': 7} Chain: "F" Number of atoms: 1084 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 1084 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 9, 'TRANS': 112} Chain: "G" Number of atoms: 504 Number of conformers: 1 Conformer: "" Number of residues, atoms: 60, 504 Classifications: {'peptide': 60} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 57} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "H" Number of atoms: 3713 Number of conformers: 1 Conformer: "" Number of residues, atoms: 459, 3713 Classifications: {'peptide': 459} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 14, 'TRANS': 444} Chain breaks: 1 Unresolved non-hydrogen bonds: 30 Unresolved non-hydrogen angles: 39 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'GLU:plan': 3} Unresolved non-hydrogen planarities: 12 Chain: "I" Number of atoms: 872 Number of conformers: 1 Conformer: "" Number of residues, atoms: 42, 872 Classifications: {'RNA': 42} Modifications used: {'rna2p_pur': 7, 'rna2p_pyr': 1, 'rna3p_pur': 15, 'rna3p_pyr': 19} Link IDs: {'rna2p': 7, 'rna3p': 34} Chain breaks: 2 Unresolved non-hydrogen bonds: 25 Unresolved non-hydrogen angles: 40 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {' G%rna3p_pur:plan2': 1, ' G%rna3p_pur:plan': 1, ' A%rna3p_pur:plan2': 1, ' A%rna3p_pur:plan': 1} Unresolved non-hydrogen planarities: 25 Chain: "J" Number of atoms: 2523 Number of conformers: 1 Conformer: "" Number of residues, atoms: 320, 2523 Classifications: {'peptide': 320} Link IDs: {'PCIS': 2, 'PTRANS': 11, 'TRANS': 306} Chain: "K" Number of atoms: 2360 Number of conformers: 1 Conformer: "" Number of residues, atoms: 295, 2360 Classifications: {'peptide': 295} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 24, 'TRANS': 270} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "L" Number of atoms: 1188 Number of conformers: 1 Conformer: "" Number of residues, atoms: 144, 1188 Classifications: {'peptide': 144} Link IDs: {'PTRANS': 7, 'TRANS': 136} Chain: "M" Number of atoms: 2318 Number of conformers: 1 Conformer: "" Number of residues, atoms: 289, 2318 Classifications: {'peptide': 289} Link IDs: {'PTRANS': 17, 'TRANS': 271} Chain: "N" Number of atoms: 2394 Number of conformers: 1 Conformer: "" Number of residues, atoms: 306, 2394 Classifications: {'peptide': 306} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 10, 'TRANS': 295} Chain: "O" Number of atoms: 3416 Number of conformers: 1 Conformer: "" Number of residues, atoms: 441, 3416 Classifications: {'peptide': 441} Incomplete info: {'truncation_to_alanine': 64} Link IDs: {'PTRANS': 12, 'TRANS': 428} Chain breaks: 5 Unresolved non-hydrogen bonds: 237 Unresolved non-hydrogen angles: 290 Unresolved non-hydrogen dihedrals: 197 Unresolved non-hydrogen chiralities: 17 Planarities with less than four sites: {'GLN:plan1': 5, 'ASP:plan': 5, 'TYR:plan': 1, 'HIS:plan': 5, 'GLU:plan': 9, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 123 Chain: "P" Number of atoms: 888 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 888 Classifications: {'peptide': 106} Link IDs: {'PTRANS': 4, 'TRANS': 101} Chain breaks: 2 Chain: "R" Number of atoms: 193 Number of conformers: 1 Conformer: "" Number of residues, atoms: 26, 193 Classifications: {'peptide': 26} Link IDs: {'PTRANS': 2, 'TRANS': 23} Chain: "S" Number of atoms: 3965 Number of conformers: 1 Conformer: "" Number of residues, atoms: 570, 3965 Classifications: {'peptide': 570} Incomplete info: {'backbone_only': 8, 'truncation_to_alanine': 234} Link IDs: {'PTRANS': 16, 'TRANS': 553} Chain breaks: 19 Unresolved chain link angles: 8 Unresolved non-hydrogen bonds: 979 Unresolved non-hydrogen angles: 1242 Unresolved non-hydrogen dihedrals: 823 Unresolved non-hydrogen chiralities: 73 Planarities with less than four sites: {'GLN:plan1': 11, 'HIS:plan': 3, 'TYR:plan': 9, 'ASN:plan1': 6, 'TRP:plan': 6, 'ASP:plan': 13, 'PHE:plan': 12, 'GLU:plan': 40, 'ARG:plan': 25} Unresolved non-hydrogen planarities: 593 Chain: "T" Number of atoms: 4003 Number of conformers: 1 Conformer: "" Number of residues, atoms: 639, 4003 Classifications: {'peptide': 639} Incomplete info: {'truncation_to_alanine': 354} Link IDs: {'PTRANS': 16, 'TRANS': 622} Chain breaks: 20 Unresolved chain link angles: 10 Unresolved non-hydrogen bonds: 1442 Unresolved non-hydrogen angles: 1855 Unresolved non-hydrogen dihedrals: 1226 Unresolved non-hydrogen chiralities: 106 Planarities with less than four sites: {'GLN:plan1': 17, 'HIS:plan': 13, 'TYR:plan': 21, 'ASN:plan1': 13, 'TRP:plan': 10, 'ASP:plan': 25, 'PHE:plan': 14, 'GLU:plan': 35, 'ARG:plan': 40} Unresolved non-hydrogen planarities: 908 Chain: "U" Number of atoms: 10885 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 1322, 10862 Classifications: {'peptide': 1322} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 67, 'TRANS': 1254} Chain breaks: 8 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Conformer: "B" Number of residues, atoms: 1322, 10862 Classifications: {'peptide': 1322} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 67, 'TRANS': 1254} Chain breaks: 8 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 bond proxies already assigned to first conformer: 11093 Chain: "V" Number of atoms: 2995 Number of conformers: 1 Conformer: "" Number of residues, atoms: 713, 2995 Classifications: {'peptide': 713} Incomplete info: {'backbone_only': 639, 'truncation_to_alanine': 1} Link IDs: {'PTRANS': 40, 'TRANS': 672} Chain breaks: 1 Unresolved chain link angles: 37 Unresolved non-hydrogen bonds: 2776 Unresolved non-hydrogen angles: 4006 Unresolved non-hydrogen dihedrals: 1770 Unresolved non-hydrogen chiralities: 843 Planarities with less than four sites: {'GLN:plan1': 36, 'HIS:plan': 11, 'TYR:plan': 28, 'ASN:plan1': 17, 'TRP:plan': 5, 'ASP:plan': 38, 'PHE:plan': 23, 'GLU:plan': 45, 'ARG:plan': 37} Unresolved non-hydrogen planarities: 1229 Chain: "W" Number of atoms: 1282 Number of conformers: 1 Conformer: "" Number of residues, atoms: 162, 1282 Classifications: {'peptide': 162} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 6, 'TRANS': 155} Unresolved non-hydrogen bonds: 32 Unresolved non-hydrogen angles: 36 Unresolved non-hydrogen dihedrals: 28 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 14 Chain: "Y" Number of atoms: 745 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 745 Classifications: {'peptide': 92} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 3, 'TRANS': 88} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "Z" Number of atoms: 230 Number of conformers: 1 Conformer: "" Number of residues, atoms: 30, 230 Classifications: {'peptide': 30} Link IDs: {'PTRANS': 1, 'TRANS': 28} Chain: "b" Number of atoms: 545 Number of conformers: 1 Conformer: "" Number of residues, atoms: 68, 545 Classifications: {'peptide': 68} Link IDs: {'PTRANS': 3, 'TRANS': 64} Chain breaks: 1 Chain: "c" Number of atoms: 2215 Number of conformers: 1 Conformer: "" Number of residues, atoms: 269, 2215 Classifications: {'peptide': 269} Link IDs: {'PTRANS': 17, 'TRANS': 251} Chain breaks: 1 Chain: "d" Number of atoms: 658 Number of conformers: 1 Conformer: "" Number of residues, atoms: 84, 658 Classifications: {'peptide': 84} Link IDs: {'PTRANS': 3, 'TRANS': 80} Chain: "e" Number of atoms: 651 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 651 Classifications: {'peptide': 79} Link IDs: {'PTRANS': 1, 'TRANS': 77} Chain: "f" Number of atoms: 562 Number of conformers: 1 Conformer: "" Number of residues, atoms: 72, 562 Classifications: {'peptide': 72} Link IDs: {'PTRANS': 3, 'TRANS': 68} Chain: "g" Number of atoms: 568 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 568 Classifications: {'peptide': 73} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 69} Chain: "h" Number of atoms: 634 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 634 Classifications: {'peptide': 80} Link IDs: {'PTRANS': 3, 'TRANS': 76} Chain: "i" Number of atoms: 1270 Number of conformers: 1 Conformer: "" Number of residues, atoms: 164, 1270 Classifications: {'peptide': 164} Link IDs: {'PTRANS': 11, 'TRANS': 152} Chain: "j" Number of atoms: 774 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 774 Classifications: {'peptide': 95} Link IDs: {'PTRANS': 4, 'TRANS': 90} Chain breaks: 1 Chain: "k" Number of atoms: 664 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 664 Classifications: {'peptide': 82} Link IDs: {'PTRANS': 4, 'TRANS': 77} Chain: "l" Number of atoms: 634 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 634 Classifications: {'peptide': 80} Link IDs: {'PTRANS': 3, 'TRANS': 76} Chain: "m" Number of atoms: 774 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 774 Classifications: {'peptide': 95} Link IDs: {'PTRANS': 4, 'TRANS': 90} Chain breaks: 1 Chain: "n" Number of atoms: 652 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 652 Classifications: {'peptide': 83} Link IDs: {'PTRANS': 3, 'TRANS': 79} Chain: "o" Number of atoms: 4157 Number of conformers: 1 Conformer: "" Number of residues, atoms: 513, 4157 Classifications: {'peptide': 513} Link IDs: {'PTRANS': 24, 'TRANS': 488} Chain: "p" Number of atoms: 669 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 669 Classifications: {'peptide': 81} Link IDs: {'PTRANS': 1, 'TRANS': 79} Chain: "q" Number of atoms: 562 Number of conformers: 1 Conformer: "" Number of residues, atoms: 72, 562 Classifications: {'peptide': 72} Link IDs: {'PTRANS': 3, 'TRANS': 68} Chain: "r" Number of atoms: 568 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 568 Classifications: {'peptide': 73} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 69} Chain: "s" Number of atoms: 1402 Number of conformers: 1 Conformer: "" Number of residues, atoms: 169, 1402 Classifications: {'peptide': 169} Link IDs: {'PTRANS': 4, 'TRANS': 164} Chain breaks: 3 Chain: "t" Number of atoms: 988 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 988 Classifications: {'peptide': 125} Link IDs: {'PTRANS': 7, 'TRANS': 117} Chain breaks: 1 Chain: "u" Number of atoms: 938 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 938 Classifications: {'peptide': 118} Link IDs: {'PTRANS': 6, 'TRANS': 111} Chain breaks: 1 Chain: "v" Number of atoms: 988 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 988 Classifications: {'peptide': 125} Link IDs: {'PTRANS': 7, 'TRANS': 117} Chain breaks: 1 Chain: "w" Number of atoms: 938 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 938 Classifications: {'peptide': 118} Link IDs: {'PTRANS': 6, 'TRANS': 111} Chain breaks: 1 Chain: "y" Number of atoms: 1218 Number of conformers: 1 Conformer: "" Number of residues, atoms: 144, 1218 Classifications: {'peptide': 144} Link IDs: {'PTRANS': 5, 'TRANS': 138} Chain: "z" Number of atoms: 280 Number of conformers: 1 Conformer: "" Number of residues, atoms: 34, 280 Classifications: {'peptide': 34} Link IDs: {'TRANS': 33} Chain: "6" Number of atoms: 6 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 6 Unusual residues: {' K': 1, ' MG': 5} Classifications: {'undetermined': 6} Link IDs: {None: 5} Chain: "7" 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: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {' MG': 1, 'GTP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "L" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' ZN': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "M" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' ZN': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "c" Number of atoms: 37 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 37 Unusual residues: {' ZN': 1, 'IHP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 64124 SG CYS L 105 210.154 169.005 184.365 1.00 24.33 S ATOM 64218 SG CYS L 117 211.096 165.980 182.413 1.00 27.46 S ATOM 64232 SG CYS L 119 213.786 168.263 183.644 1.00 32.97 S ATOM 64351 SG CYS L 134 211.485 169.341 180.847 1.00 29.32 S ATOM 64093 SG CYS L 101 212.827 171.071 185.944 1.00 25.99 S ATOM 64099 SG CYS L 102 209.268 171.444 187.085 1.00 23.57 S ATOM 64124 SG CYS L 105 210.154 169.005 184.365 1.00 24.33 S ATOM 64374 SG CYS L 137 210.326 172.689 183.687 1.00 25.79 S ATOM 64093 SG CYS L 101 212.827 171.071 185.944 1.00 25.99 S ATOM 64232 SG CYS L 119 213.786 168.263 183.644 1.00 32.97 S ATOM 64384 SG CYS L 139 213.605 171.769 182.346 1.00 29.19 S ATOM 64405 SG CYS L 142 216.338 170.808 184.694 1.00 36.70 S ATOM 64468 SG CYS M 24 201.251 148.922 157.867 1.00 31.04 S ATOM 64490 SG CYS M 27 202.240 150.450 161.185 1.00 31.24 S ATOM 64933 SG CYS M 81 198.623 149.992 160.311 1.00 28.71 S ATOM 64955 SG CYS M 84 200.701 152.590 158.515 1.00 31.22 S ATOM 64639 SG CYS M 45 187.060 151.286 163.617 1.00 25.25 S ATOM 64662 SG CYS M 48 183.842 149.580 164.536 1.00 27.79 S ATOM 64858 SG CYS M 71 187.119 147.773 164.975 1.00 25.57 S ATOM 64880 SG CYS M 74 185.792 148.419 161.513 1.00 27.72 S ATOM 65592 SG CYS M 165 204.095 175.319 162.975 1.00 37.95 S ATOM 65658 SG CYS M 173 206.339 177.159 165.361 1.00 42.02 S ATOM 65706 SG CYS M 179 206.203 173.393 165.422 1.00 39.52 S ATOM 99024 SG CYS c 120 182.330 184.669 238.662 1.00 32.50 S ATOM 99047 SG CYS c 123 184.100 187.477 236.894 1.00 29.56 S ATOM 99122 SG CYS c 133 183.525 184.248 235.096 1.00 20.76 S Residues with excluded nonbonded symmetry interactions: 3 residue: pdb=" N HIS B1502 " occ=0.92 ... (8 atoms not shown) pdb=" NE2 HIS B1502 " occ=0.92 residue: pdb=" N MET U 79 " occ=0.50 ... (6 atoms not shown) pdb=" CE MET U 79 " occ=0.50 residue: pdb=" N MET U 326 " occ=0.58 ... (6 atoms not shown) pdb=" CE MET U 326 " occ=0.58 Time building chain proxies: 47.75, per 1000 atoms: 0.39 Number of scatterers: 121152 At special positions: 0 Unit cell: (279.6, 355.2, 342, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 8 Type Number sf(0) Zn 7 29.99 K 1 19.00 S 552 16.00 P 362 15.00 Mg 7 11.99 O 23559 8.00 N 21501 7.00 C 75163 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=2, symmetry=0 Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 38.58 Conformation dependent library (CDL) restraints added in 14.6 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN L 201 " pdb="ZN ZN L 201 " - pdb=" SG CYS L 117 " pdb="ZN ZN L 201 " - pdb=" SG CYS L 105 " pdb="ZN ZN L 201 " - pdb=" SG CYS L 134 " pdb="ZN ZN L 201 " - pdb=" SG CYS L 119 " pdb=" ZN L 202 " pdb="ZN ZN L 202 " - pdb=" SG CYS L 101 " pdb="ZN ZN L 202 " - pdb=" SG CYS L 105 " pdb="ZN ZN L 202 " - pdb=" SG CYS L 137 " pdb="ZN ZN L 202 " - pdb=" SG CYS L 102 " pdb=" ZN L 203 " pdb="ZN ZN L 203 " - pdb=" SG CYS L 142 " pdb="ZN ZN L 203 " - pdb=" SG CYS L 139 " pdb="ZN ZN L 203 " - pdb=" SG CYS L 101 " pdb="ZN ZN L 203 " - pdb=" SG CYS L 119 " pdb=" ZN M 501 " pdb="ZN ZN M 501 " - pdb=" SG CYS M 81 " pdb="ZN ZN M 501 " - pdb=" SG CYS M 27 " pdb="ZN ZN M 501 " - pdb=" SG CYS M 24 " pdb="ZN ZN M 501 " - pdb=" SG CYS M 84 " pdb=" ZN M 502 " pdb="ZN ZN M 502 " - pdb=" SG CYS M 45 " pdb="ZN ZN M 502 " - pdb=" SG CYS M 74 " pdb="ZN ZN M 502 " - pdb=" SG CYS M 48 " pdb="ZN ZN M 502 " - pdb=" SG CYS M 71 " pdb=" ZN M 503 " pdb="ZN ZN M 503 " - pdb=" SG CYS M 173 " pdb="ZN ZN M 503 " - pdb=" SG CYS M 165 " pdb="ZN ZN M 503 " - pdb=" NE2 HIS M 183 " pdb="ZN ZN M 503 " - pdb=" SG CYS M 179 " pdb=" ZN c 602 " pdb="ZN ZN c 602 " - pdb=" NE2 HIS c 128 " pdb="ZN ZN c 602 " - pdb=" SG CYS c 133 " pdb="ZN ZN c 602 " - pdb=" SG CYS c 123 " pdb="ZN ZN c 602 " - pdb=" SG CYS c 120 " Number of angles added : 36 28748 Ramachandran restraints generated. 14374 Oldfield, 0 Emsley, 14374 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 26512 Finding SS restraints... Warning!!! ksdssp method is not applicable forstructures with more than 99999 atoms! Switching to from_ca. running find_ss_from_ca liberal... Secondary structure from input PDB file: 535 helices and 106 sheets defined 50.8% alpha, 13.5% beta 74 base pairs and 184 stacking pairs defined. Time for finding SS restraints: 79.19 Creating SS restraints... Processing helix chain '7' and resid 39 through 44 removed outlier: 3.876A pdb=" N MET 7 43 " --> pdb=" O THR 7 39 " (cutoff:3.500A) removed outlier: 4.673A pdb=" N GLY 7 44 " --> pdb=" O PHE 7 40 " (cutoff:3.500A) No H-bonds generated for 'chain '7' and resid 39 through 44' Processing helix chain '7' and resid 46 through 57 Processing helix chain '7' and resid 62 through 75 removed outlier: 3.678A pdb=" N ILE 7 69 " --> pdb=" O GLN 7 65 " (cutoff:3.500A) removed outlier: 5.712A pdb=" N LYS 7 70 " --> pdb=" O GLN 7 66 " (cutoff:3.500A) removed outlier: 4.116A pdb=" N GLN 7 71 " --> pdb=" O ARG 7 67 " (cutoff:3.500A) Processing helix chain '7' and resid 87 through 100 Processing helix chain '7' and resid 115 through 131 Processing helix chain '7' and resid 145 through 156 Processing helix chain '7' and resid 163 through 174 Processing helix chain '7' and resid 188 through 194 Processing helix chain '7' and resid 195 through 209 removed outlier: 7.460A pdb=" N GLU 7 199 " --> pdb=" O LYS 7 195 " (cutoff:3.500A) removed outlier: 5.076A pdb=" N GLN 7 200 " --> pdb=" O GLY 7 196 " (cutoff:3.500A) removed outlier: 4.172A pdb=" N TYR 7 207 " --> pdb=" O ASP 7 203 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N LEU 7 208 " --> pdb=" O VAL 7 204 " (cutoff:3.500A) Proline residue: 7 209 - end of helix Processing helix chain '7' and resid 222 through 233 removed outlier: 3.559A pdb=" N MET 7 228 " --> pdb=" O GLU 7 224 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N THR 7 229 " --> pdb=" O ILE 7 225 " (cutoff:3.500A) removed outlier: 5.052A pdb=" N ASN 7 230 " --> pdb=" O LEU 7 226 " (cutoff:3.500A) removed outlier: 6.073A pdb=" N LYS 7 231 " --> pdb=" O GLU 7 227 " (cutoff:3.500A) removed outlier: 4.674A pdb=" N PHE 7 232 " --> pdb=" O MET 7 228 " (cutoff:3.500A) Processing helix chain '7' and resid 242 through 247 removed outlier: 4.582A pdb=" N THR 7 247 " --> pdb=" O ARG 7 243 " (cutoff:3.500A) Processing helix chain '7' and resid 260 through 276 removed outlier: 3.926A pdb=" N LYS 7 264 " --> pdb=" O ARG 7 260 " (cutoff:3.500A) removed outlier: 4.145A pdb=" N PHE 7 265 " --> pdb=" O GLU 7 261 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N ASP 7 266 " --> pdb=" O GLU 7 262 " (cutoff:3.500A) removed outlier: 4.302A pdb=" N ASP 7 273 " --> pdb=" O CYS 7 269 " (cutoff:3.500A) removed outlier: 4.851A pdb=" N THR 7 274 " --> pdb=" O ASP 7 270 " (cutoff:3.500A) Processing helix chain '7' and resid 286 through 301 Processing helix chain '7' and resid 312 through 326 Processing helix chain '7' and resid 334 through 339 removed outlier: 4.040A pdb=" N ALA 7 338 " --> pdb=" O THR 7 334 " (cutoff:3.500A) removed outlier: 4.273A pdb=" N ARG 7 339 " --> pdb=" O ASP 7 335 " (cutoff:3.500A) No H-bonds generated for 'chain '7' and resid 334 through 339' Processing helix chain '7' and resid 357 through 370 removed outlier: 3.630A pdb=" N TYR 7 361 " --> pdb=" O ASN 7 357 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ILE 7 362 " --> pdb=" O ARG 7 358 " (cutoff:3.500A) removed outlier: 4.619A pdb=" N SER 7 368 " --> pdb=" O ARG 7 364 " (cutoff:3.500A) removed outlier: 5.072A pdb=" N GLY 7 369 " --> pdb=" O ILE 7 365 " (cutoff:3.500A) removed outlier: 5.176A pdb=" N ARG 7 370 " --> pdb=" O GLY 7 366 " (cutoff:3.500A) Processing helix chain '7' and resid 384 through 397 removed outlier: 4.300A pdb=" N ILE 7 388 " --> pdb=" O ASP 7 384 " (cutoff:3.500A) Processing helix chain '8' and resid 85 through 94 Processing helix chain '8' and resid 123 through 134 Processing helix chain '9' and resid 55 through 70 Processing helix chain '9' and resid 108 through 115 Processing helix chain '9' and resid 117 through 144 removed outlier: 4.109A pdb=" N VAL 9 123 " --> pdb=" O GLU 9 119 " (cutoff:3.500A) Processing helix chain 'A' and resid 26 through 45 removed outlier: 3.910A pdb=" N LEU A 30 " --> pdb=" O SER A 26 " (cutoff:3.500A) removed outlier: 4.234A pdb=" N LYS A 33 " --> pdb=" O LYS A 29 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ALA A 34 " --> pdb=" O LEU A 30 " (cutoff:3.500A) removed outlier: 4.569A pdb=" N LYS A 43 " --> pdb=" O GLN A 39 " (cutoff:3.500A) Processing helix chain 'A' and resid 62 through 74 removed outlier: 4.187A pdb=" N VAL A 66 " --> pdb=" O PRO A 62 " (cutoff:3.500A) Processing helix chain 'A' and resid 78 through 83 removed outlier: 4.085A pdb=" N ARG A 82 " --> pdb=" O ASN A 78 " (cutoff:3.500A) removed outlier: 5.458A pdb=" N HIS A 83 " --> pdb=" O ARG A 79 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 78 through 83' Processing helix chain 'A' and resid 84 through 95 removed outlier: 3.935A pdb=" N LEU A 92 " --> pdb=" O TYR A 88 " (cutoff:3.500A) removed outlier: 4.265A pdb=" N LYS A 93 " --> pdb=" O LEU A 89 " (cutoff:3.500A) removed outlier: 4.669A pdb=" N TYR A 94 " --> pdb=" O GLY A 90 " (cutoff:3.500A) Processing helix chain 'A' and resid 96 through 106 removed outlier: 3.635A pdb=" N LYS A 101 " --> pdb=" O HIS A 97 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N ASN A 105 " --> pdb=" O LYS A 101 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N MET A 106 " --> pdb=" O LEU A 102 " (cutoff:3.500A) Processing helix chain 'A' and resid 136 through 158 Processing helix chain 'A' and resid 180 through 185 removed outlier: 6.050A pdb=" N ASP A 184 " --> pdb=" O ASP A 180 " (cutoff:3.500A) removed outlier: 5.389A pdb=" N VAL A 185 " --> pdb=" O ASN A 181 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 180 through 185' Processing helix chain 'A' and resid 231 through 243 removed outlier: 3.897A pdb=" N ASN A 243 " --> pdb=" O TYR A 239 " (cutoff:3.500A) Processing helix chain 'A' and resid 259 through 270 Processing helix chain 'A' and resid 309 through 317 Proline residue: A 317 - end of helix Processing helix chain 'A' and resid 397 through 407 removed outlier: 3.568A pdb=" N TRP A 406 " --> pdb=" O ILE A 402 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N ALA A 407 " --> pdb=" O ALA A 403 " (cutoff:3.500A) Processing helix chain 'A' and resid 408 through 413 removed outlier: 4.450A pdb=" N LEU A 413 " --> pdb=" O ARG A 409 " (cutoff:3.500A) Processing helix chain 'A' and resid 427 through 434 removed outlier: 3.823A pdb=" N TYR A 431 " --> pdb=" O VAL A 427 " (cutoff:3.500A) removed outlier: 4.413A pdb=" N GLU A 433 " --> pdb=" O ASN A 429 " (cutoff:3.500A) removed outlier: 5.138A pdb=" N HIS A 434 " --> pdb=" O TRP A 430 " (cutoff:3.500A) Processing helix chain 'A' and resid 440 through 461 Processing helix chain 'A' and resid 471 through 480 removed outlier: 3.944A pdb=" N SER A 475 " --> pdb=" O TYR A 471 " (cutoff:3.500A) removed outlier: 4.451A pdb=" N THR A 479 " --> pdb=" O SER A 475 " (cutoff:3.500A) removed outlier: 5.456A pdb=" N LYS A 480 " --> pdb=" O PHE A 476 " (cutoff:3.500A) Processing helix chain 'A' and resid 488 through 512 removed outlier: 3.551A pdb=" N ASN A 512 " --> pdb=" O ILE A 508 " (cutoff:3.500A) Processing helix chain 'A' and resid 531 through 539 removed outlier: 3.517A pdb=" N ARG A 539 " --> pdb=" O ARG A 535 " (cutoff:3.500A) Processing helix chain 'A' and resid 541 through 567 removed outlier: 3.554A pdb=" N LEU A 546 " --> pdb=" O ASN A 542 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N GLY A 567 " --> pdb=" O GLN A 563 " (cutoff:3.500A) Processing helix chain 'A' and resid 570 through 585 Processing helix chain 'A' and resid 590 through 596 removed outlier: 4.785A pdb=" N TYR A 594 " --> pdb=" O GLY A 590 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N TYR A 596 " --> pdb=" O TYR A 592 " (cutoff:3.500A) Processing helix chain 'A' and resid 597 through 617 removed outlier: 3.877A pdb=" N GLN A 601 " --> pdb=" O LYS A 597 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N MET A 604 " --> pdb=" O ARG A 600 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N LYS A 609 " --> pdb=" O CYS A 605 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N TYR A 614 " --> pdb=" O HIS A 610 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N ARG A 615 " --> pdb=" O LEU A 611 " (cutoff:3.500A) Processing helix chain 'A' and resid 631 through 660 removed outlier: 3.822A pdb=" N VAL A 636 " --> pdb=" O ALA A 632 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N GLY A 643 " --> pdb=" O PHE A 639 " (cutoff:3.500A) Proline residue: A 646 - end of helix Processing helix chain 'A' and resid 673 through 697 removed outlier: 3.604A pdb=" N VAL A 677 " --> pdb=" O THR A 673 " (cutoff:3.500A) removed outlier: 5.556A pdb=" N GLU A 678 " --> pdb=" O LYS A 674 " (cutoff:3.500A) removed outlier: 5.069A pdb=" N SER A 679 " --> pdb=" O GLN A 675 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N HIS A 680 " --> pdb=" O ARG A 676 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N ASP A 682 " --> pdb=" O GLU A 678 " (cutoff:3.500A) removed outlier: 4.667A pdb=" N ARG A 686 " --> pdb=" O ASP A 682 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N ALA A 687 " --> pdb=" O LEU A 683 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N MET A 690 " --> pdb=" O ARG A 686 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N ASP A 692 " --> pdb=" O ALA A 688 " (cutoff:3.500A) removed outlier: 4.313A pdb=" N LEU A 694 " --> pdb=" O MET A 690 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N ASP A 695 " --> pdb=" O HIS A 691 " (cutoff:3.500A) removed outlier: 4.298A pdb=" N MET A 697 " --> pdb=" O ILE A 693 " (cutoff:3.500A) Processing helix chain 'A' and resid 705 through 723 removed outlier: 3.582A pdb=" N ILE A 709 " --> pdb=" O LYS A 705 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N LEU A 710 " --> pdb=" O ALA A 706 " (cutoff:3.500A) Processing helix chain 'A' and resid 732 through 764 removed outlier: 3.509A pdb=" N ARG A 763 " --> pdb=" O GLU A 759 " (cutoff:3.500A) Processing helix chain 'A' and resid 768 through 797 removed outlier: 3.812A pdb=" N LEU A 776 " --> pdb=" O CYS A 772 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N ARG A 781 " --> pdb=" O GLY A 777 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N GLU A 789 " --> pdb=" O LYS A 785 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N LEU A 795 " --> pdb=" O GLN A 791 " (cutoff:3.500A) Processing helix chain 'A' and resid 802 through 821 removed outlier: 3.823A pdb=" N ARG A 821 " --> pdb=" O LEU A 817 " (cutoff:3.500A) Processing helix chain 'A' and resid 834 through 851 removed outlier: 3.618A pdb=" N ARG A 845 " --> pdb=" O LEU A 841 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N ALA A 849 " --> pdb=" O ARG A 845 " (cutoff:3.500A) removed outlier: 4.743A pdb=" N TYR A 850 " --> pdb=" O LEU A 846 " (cutoff:3.500A) removed outlier: 5.181A pdb=" N SER A 851 " --> pdb=" O LYS A 847 " (cutoff:3.500A) Processing helix chain 'A' and resid 857 through 874 removed outlier: 3.974A pdb=" N GLU A 862 " --> pdb=" O GLN A 858 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N GLU A 863 " --> pdb=" O SER A 859 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N GLY A 865 " --> pdb=" O ARG A 861 " (cutoff:3.500A) Proline residue: A 874 - end of helix Processing helix chain 'A' and resid 875 through 887 removed outlier: 3.647A pdb=" N LEU A 886 " --> pdb=" O LYS A 882 " (cutoff:3.500A) Processing helix chain 'A' and resid 913 through 934 removed outlier: 3.702A pdb=" N ILE A 917 " --> pdb=" O PRO A 913 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N THR A 918 " --> pdb=" O LEU A 914 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N ARG A 933 " --> pdb=" O GLU A 929 " (cutoff:3.500A) Processing helix chain 'A' and resid 947 through 962 removed outlier: 3.741A pdb=" N TYR A 953 " --> pdb=" O PRO A 949 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N LEU A 962 " --> pdb=" O GLY A 958 " (cutoff:3.500A) Processing helix chain 'A' and resid 983 through 988 removed outlier: 3.705A pdb=" N LYS A 987 " --> pdb=" O LYS A 983 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N ILE A 988 " --> pdb=" O MET A 984 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 983 through 988' Processing helix chain 'A' and resid 989 through 1001 removed outlier: 3.584A pdb=" N ARG A 995 " --> pdb=" O THR A 991 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N LEU A 999 " --> pdb=" O ARG A 995 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N ILE A1000 " --> pdb=" O LEU A 996 " (cutoff:3.500A) Processing helix chain 'A' and resid 1002 through 1015 removed outlier: 3.914A pdb=" N ASN A1014 " --> pdb=" O THR A1010 " (cutoff:3.500A) removed outlier: 4.680A pdb=" N VAL A1015 " --> pdb=" O ALA A1011 " (cutoff:3.500A) Processing helix chain 'A' and resid 1036 through 1054 removed outlier: 3.548A pdb=" N MET A1048 " --> pdb=" O TYR A1044 " (cutoff:3.500A) Processing helix chain 'A' and resid 1055 through 1063 Processing helix chain 'A' and resid 1076 through 1084 removed outlier: 4.456A pdb=" N GLU A1080 " --> pdb=" O ASP A1076 " (cutoff:3.500A) removed outlier: 4.314A pdb=" N ALA A1081 " --> pdb=" O ILE A1077 " (cutoff:3.500A) removed outlier: 4.608A pdb=" N HIS A1083 " --> pdb=" O THR A1079 " (cutoff:3.500A) Proline residue: A1084 - end of helix Processing helix chain 'A' and resid 1102 through 1117 Processing helix chain 'A' and resid 1122 through 1128 removed outlier: 3.825A pdb=" N VAL A1126 " --> pdb=" O ASN A1122 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N TYR A1128 " --> pdb=" O ASN A1124 " (cutoff:3.500A) Processing helix chain 'A' and resid 1143 through 1162 removed outlier: 3.816A pdb=" N LEU A1161 " --> pdb=" O ILE A1157 " (cutoff:3.500A) Proline residue: A1162 - end of helix Processing helix chain 'A' and resid 1169 through 1174 removed outlier: 3.768A pdb=" N SER A1173 " --> pdb=" O GLN A1169 " (cutoff:3.500A) removed outlier: 5.199A pdb=" N PHE A1174 " --> pdb=" O TRP A1170 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1169 through 1174' Processing helix chain 'A' and resid 1198 through 1203 removed outlier: 6.093A pdb=" N SER A1203 " --> pdb=" O LYS A1199 " (cutoff:3.500A) Processing helix chain 'A' and resid 1233 through 1252 removed outlier: 4.183A pdb=" N SER A1251 " --> pdb=" O ILE A1247 " (cutoff:3.500A) removed outlier: 5.623A pdb=" N GLY A1252 " --> pdb=" O LEU A1248 " (cutoff:3.500A) Processing helix chain 'A' and resid 1255 through 1275 removed outlier: 3.635A pdb=" N THR A1272 " --> pdb=" O ILE A1268 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N TYR A1273 " --> pdb=" O GLY A1269 " (cutoff:3.500A) Processing helix chain 'A' and resid 1276 through 1282 removed outlier: 3.991A pdb=" N ASN A1280 " --> pdb=" O GLU A1276 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N THR A1281 " --> pdb=" O ALA A1277 " (cutoff:3.500A) removed outlier: 5.135A pdb=" N GLN A1282 " --> pdb=" O VAL A1278 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1276 through 1282' Processing helix chain 'A' and resid 1283 through 1304 removed outlier: 3.645A pdb=" N VAL A1289 " --> pdb=" O LEU A1285 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N LYS A1290 " --> pdb=" O ASP A1286 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N ASN A1304 " --> pdb=" O LYS A1300 " (cutoff:3.500A) Processing helix chain 'A' and resid 1307 through 1312 removed outlier: 3.548A pdb=" N PHE A1311 " --> pdb=" O MET A1307 " (cutoff:3.500A) Proline residue: A1312 - end of helix No H-bonds generated for 'chain 'A' and resid 1307 through 1312' Processing helix chain 'A' and resid 1339 through 1346 removed outlier: 3.725A pdb=" N LYS A1344 " --> pdb=" O LEU A1340 " (cutoff:3.500A) removed outlier: 4.454A pdb=" N GLN A1345 " --> pdb=" O ARG A1341 " (cutoff:3.500A) Processing helix chain 'A' and resid 1367 through 1373 removed outlier: 4.551A pdb=" N TYR A1371 " --> pdb=" O ASN A1367 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N ILE A1372 " --> pdb=" O LEU A1368 " (cutoff:3.500A) removed outlier: 5.092A pdb=" N GLN A1373 " --> pdb=" O TYR A1369 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1367 through 1373' Processing helix chain 'A' and resid 1374 through 1400 removed outlier: 3.713A pdb=" N ALA A1398 " --> pdb=" O GLN A1394 " (cutoff:3.500A) Processing helix chain 'A' and resid 1404 through 1409 removed outlier: 6.305A pdb=" N LEU A1408 " --> pdb=" O THR A1404 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N GLU A1409 " --> pdb=" O LEU A1405 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1404 through 1409' Processing helix chain 'A' and resid 1418 through 1424 removed outlier: 4.262A pdb=" N LEU A1422 " --> pdb=" O ARG A1418 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N PHE A1423 " --> pdb=" O ILE A1419 " (cutoff:3.500A) Processing helix chain 'A' and resid 1426 through 1434 removed outlier: 3.512A pdb=" N ALA A1431 " --> pdb=" O ARG A1427 " (cutoff:3.500A) removed outlier: 5.187A pdb=" N TYR A1432 " --> pdb=" O HIS A1428 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N ASP A1433 " --> pdb=" O THR A1429 " (cutoff:3.500A) removed outlier: 5.540A pdb=" N LYS A1434 " --> pdb=" O LEU A1430 " (cutoff:3.500A) Processing helix chain 'A' and resid 1435 through 1447 removed outlier: 3.673A pdb=" N ASP A1441 " --> pdb=" O ARG A1437 " (cutoff:3.500A) removed outlier: 4.977A pdb=" N GLN A1444 " --> pdb=" O THR A1440 " (cutoff:3.500A) removed outlier: 5.442A pdb=" N TYR A1445 " --> pdb=" O ASP A1441 " (cutoff:3.500A) removed outlier: 4.140A pdb=" N GLN A1446 " --> pdb=" O PHE A1442 " (cutoff:3.500A) Processing helix chain 'A' and resid 1467 through 1479 removed outlier: 4.066A pdb=" N ARG A1471 " --> pdb=" O LEU A1467 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N THR A1472 " --> pdb=" O ASN A1468 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N ILE A1475 " --> pdb=" O ARG A1471 " (cutoff:3.500A) Processing helix chain 'A' and resid 1480 through 1489 removed outlier: 3.699A pdb=" N GLU A1486 " --> pdb=" O GLU A1482 " (cutoff:3.500A) removed outlier: 4.813A pdb=" N HIS A1487 " --> pdb=" O GLY A1483 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N THR A1488 " --> pdb=" O ILE A1484 " (cutoff:3.500A) removed outlier: 5.401A pdb=" N LEU A1489 " --> pdb=" O LEU A1485 " (cutoff:3.500A) Processing helix chain 'A' and resid 1519 through 1539 Proline residue: A1530 - end of helix Processing helix chain 'A' and resid 1566 through 1578 removed outlier: 3.830A pdb=" N SER A1572 " --> pdb=" O THR A1568 " (cutoff:3.500A) Processing helix chain 'A' and resid 1580 through 1605 removed outlier: 3.801A pdb=" N GLN A1599 " --> pdb=" O GLN A1595 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N GLU A1600 " --> pdb=" O VAL A1596 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N LEU A1601 " --> pdb=" O PHE A1597 " (cutoff:3.500A) removed outlier: 6.408A pdb=" N ASP A1602 " --> pdb=" O ASP A1598 " (cutoff:3.500A) removed outlier: 5.648A pdb=" N ALA A1603 " --> pdb=" O GLN A1599 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N GLU A1605 " --> pdb=" O LEU A1601 " (cutoff:3.500A) Processing helix chain 'A' and resid 1615 through 1621 removed outlier: 4.348A pdb=" N SER A1619 " --> pdb=" O HIS A1615 " (cutoff:3.500A) removed outlier: 4.152A pdb=" N TYR A1620 " --> pdb=" O PRO A1616 " (cutoff:3.500A) Processing helix chain 'A' and resid 1675 through 1690 Processing helix chain 'A' and resid 1721 through 1736 removed outlier: 3.650A pdb=" N LEU A1725 " --> pdb=" O GLY A1721 " (cutoff:3.500A) removed outlier: 4.886A pdb=" N ALA A1736 " --> pdb=" O LYS A1732 " (cutoff:3.500A) Processing helix chain 'A' and resid 1737 through 1752 Processing helix chain 'A' and resid 1764 through 1774 removed outlier: 6.005A pdb=" N GLY A1769 " --> pdb=" O SER A1765 " (cutoff:3.500A) removed outlier: 6.100A pdb=" N GLU A1770 " --> pdb=" O GLN A1766 " (cutoff:3.500A) removed outlier: 4.792A pdb=" N LEU A1771 " --> pdb=" O ASN A1767 " (cutoff:3.500A) removed outlier: 4.485A pdb=" N PHE A1772 " --> pdb=" O TYR A1768 " (cutoff:3.500A) removed outlier: 4.411A pdb=" N SER A1773 " --> pdb=" O GLY A1769 " (cutoff:3.500A) removed outlier: 6.305A pdb=" N ASN A1774 " --> pdb=" O GLU A1770 " (cutoff:3.500A) Processing helix chain 'A' and resid 1823 through 1828 removed outlier: 4.333A pdb=" N TRP A1827 " --> pdb=" O HIS A1823 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N ALA A1828 " --> pdb=" O THR A1824 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1823 through 1828' Processing helix chain 'A' and resid 1834 through 1853 removed outlier: 4.474A pdb=" N LYS A1838 " --> pdb=" O GLY A1834 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N TRP A1839 " --> pdb=" O GLN A1835 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N GLU A1843 " --> pdb=" O TRP A1839 " (cutoff:3.500A) Proline residue: A1853 - end of helix Processing helix chain 'A' and resid 1865 through 1877 removed outlier: 4.058A pdb=" N LEU A1869 " --> pdb=" O ARG A1865 " (cutoff:3.500A) removed outlier: 4.439A pdb=" N ASP A1870 " --> pdb=" O LYS A1866 " (cutoff:3.500A) Proline residue: A1871 - end of helix removed outlier: 4.059A pdb=" N LEU A1877 " --> pdb=" O GLU A1873 " (cutoff:3.500A) Processing helix chain 'A' and resid 1892 through 1899 removed outlier: 4.079A pdb=" N CYS A1896 " --> pdb=" O PRO A1892 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N LEU A1897 " --> pdb=" O PHE A1893 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N LYS A1898 " --> pdb=" O GLN A1894 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N VAL A1899 " --> pdb=" O ALA A1895 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1892 through 1899' Processing helix chain 'A' and resid 1900 through 1909 removed outlier: 3.508A pdb=" N ALA A1909 " --> pdb=" O LEU A1905 " (cutoff:3.500A) Processing helix chain 'A' and resid 1922 through 1927 removed outlier: 4.660A pdb=" N THR A1926 " --> pdb=" O ASP A1922 " (cutoff:3.500A) Processing helix chain 'A' and resid 1928 through 1946 Processing helix chain 'A' and resid 1947 through 1956 removed outlier: 4.639A pdb=" N LYS A1951 " --> pdb=" O ASN A1947 " (cutoff:3.500A) Proline residue: A1956 - end of helix Processing helix chain 'A' and resid 1972 through 1996 removed outlier: 3.659A pdb=" N ILE A1977 " --> pdb=" O ASP A1973 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N GLN A1982 " --> pdb=" O LYS A1978 " (cutoff:3.500A) Processing helix chain 'A' and resid 2003 through 2013 removed outlier: 3.708A pdb=" N ASP A2009 " --> pdb=" O SER A2005 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N LEU A2012 " --> pdb=" O ARG A2008 " (cutoff:3.500A) Processing helix chain 'A' and resid 2070 through 2090 removed outlier: 3.666A pdb=" N ARG A2074 " --> pdb=" O LYS A2070 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N ARG A2076 " --> pdb=" O GLU A2072 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N ALA A2081 " --> pdb=" O ALA A2077 " (cutoff:3.500A) removed outlier: 4.452A pdb=" N ASN A2082 " --> pdb=" O ILE A2078 " (cutoff:3.500A) removed outlier: 4.245A pdb=" N LEU A2083 " --> pdb=" O SER A2079 " (cutoff:3.500A) removed outlier: 4.903A pdb=" N HIS A2084 " --> pdb=" O ALA A2080 " (cutoff:3.500A) removed outlier: 6.162A pdb=" N LEU A2085 " --> pdb=" O ALA A2081 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N ARG A2086 " --> pdb=" O ASN A2082 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N THR A2087 " --> pdb=" O LEU A2083 " (cutoff:3.500A) removed outlier: 4.340A pdb=" N ASN A2088 " --> pdb=" O HIS A2084 " (cutoff:3.500A) removed outlier: 4.384A pdb=" N HIS A2089 " --> pdb=" O LEU A2085 " (cutoff:3.500A) removed outlier: 4.594A pdb=" N ILE A2090 " --> pdb=" O ARG A2086 " (cutoff:3.500A) Processing helix chain 'A' and resid 2107 through 2119 removed outlier: 3.675A pdb=" N LEU A2111 " --> pdb=" O PRO A2107 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N SER A2118 " --> pdb=" O PHE A2114 " (cutoff:3.500A) removed outlier: 5.410A pdb=" N ASP A2119 " --> pdb=" O ILE A2115 " (cutoff:3.500A) Processing helix chain 'A' and resid 2166 through 2171 removed outlier: 4.456A pdb=" N GLU A2171 " --> pdb=" O GLU A2167 " (cutoff:3.500A) Processing helix chain 'A' and resid 2189 through 2203 removed outlier: 3.651A pdb=" N ASP A2202 " --> pdb=" O LYS A2198 " (cutoff:3.500A) Processing helix chain 'A' and resid 2231 through 2241 Processing helix chain 'A' and resid 2252 through 2257 removed outlier: 4.682A pdb=" N TYR A2256 " --> pdb=" O LEU A2252 " (cutoff:3.500A) removed outlier: 5.593A pdb=" N GLU A2257 " --> pdb=" O PRO A2253 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 2252 through 2257' Processing helix chain 'A' and resid 2284 through 2289 removed outlier: 4.128A pdb=" N HIS A2288 " --> pdb=" O MET A2284 " (cutoff:3.500A) removed outlier: 5.588A pdb=" N ASP A2289 " --> pdb=" O GLY A2285 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 2284 through 2289' Processing helix chain 'A' and resid 2306 through 2311 removed outlier: 3.785A pdb=" N ARG A2310 " --> pdb=" O HIS A2306 " (cutoff:3.500A) Proline residue: A2311 - end of helix No H-bonds generated for 'chain 'A' and resid 2306 through 2311' Processing helix chain 'A' and resid 2321 through 2326 removed outlier: 4.663A pdb=" N VAL A2325 " --> pdb=" O GLN A2321 " (cutoff:3.500A) removed outlier: 4.151A pdb=" N TYR A2326 " --> pdb=" O GLU A2322 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 2321 through 2326' Processing helix chain 'A' and resid 196 through 201 removed outlier: 3.783A pdb=" N ALA A 201 " --> pdb=" O ASP A 196 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 196 through 201' Processing helix chain 'A' and resid 1457 through 1462 Processing helix chain 'B' and resid 410 through 415 removed outlier: 3.915A pdb=" N LEU B 414 " --> pdb=" O ASP B 410 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N VAL B 415 " --> pdb=" O LEU B 411 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 410 through 415' Processing helix chain 'B' and resid 468 through 473 removed outlier: 3.560A pdb=" N GLN B 472 " --> pdb=" O PRO B 468 " (cutoff:3.500A) removed outlier: 4.449A pdb=" N ALA B 473 " --> pdb=" O LYS B 469 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 468 through 473' Processing helix chain 'B' and resid 482 through 494 removed outlier: 5.460A pdb=" N ARG B 490 " --> pdb=" O SER B 486 " (cutoff:3.500A) removed outlier: 5.757A pdb=" N ALA B 491 " --> pdb=" O LYS B 487 " (cutoff:3.500A) Processing helix chain 'B' and resid 508 through 525 removed outlier: 4.315A pdb=" N VAL B 512 " --> pdb=" O GLY B 508 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N MET B 515 " --> pdb=" O ASN B 511 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N GLU B 520 " --> pdb=" O CYS B 516 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N HIS B 524 " --> pdb=" O GLU B 520 " (cutoff:3.500A) removed outlier: 4.918A pdb=" N ILE B 525 " --> pdb=" O ILE B 521 " (cutoff:3.500A) Processing helix chain 'B' and resid 544 through 559 removed outlier: 3.672A pdb=" N LYS B 557 " --> pdb=" O GLY B 553 " (cutoff:3.500A) Processing helix chain 'B' and resid 576 through 584 removed outlier: 4.897A pdb=" N ILE B 580 " --> pdb=" O CYS B 576 " (cutoff:3.500A) removed outlier: 4.620A pdb=" N ALA B 582 " --> pdb=" O GLU B 578 " (cutoff:3.500A) removed outlier: 4.202A pdb=" N THR B 583 " --> pdb=" O GLU B 579 " (cutoff:3.500A) removed outlier: 5.308A pdb=" N GLN B 584 " --> pdb=" O ILE B 580 " (cutoff:3.500A) Processing helix chain 'B' and resid 589 through 600 Processing helix chain 'B' and resid 601 through 606 removed outlier: 4.196A pdb=" N TYR B 605 " --> pdb=" O GLY B 601 " (cutoff:3.500A) Processing helix chain 'B' and resid 618 through 623 removed outlier: 4.385A pdb=" N ASP B 622 " --> pdb=" O HIS B 618 " (cutoff:3.500A) removed outlier: 5.348A pdb=" N ASP B 623 " --> pdb=" O LEU B 619 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 618 through 623' Processing helix chain 'B' and resid 624 through 643 removed outlier: 3.994A pdb=" N LEU B 628 " --> pdb=" O ARG B 624 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N MET B 641 " --> pdb=" O ARG B 637 " (cutoff:3.500A) Processing helix chain 'B' and resid 657 through 666 Processing helix chain 'B' and resid 696 through 717 removed outlier: 4.102A pdb=" N GLN B 702 " --> pdb=" O ILE B 698 " (cutoff:3.500A) removed outlier: 4.499A pdb=" N ASN B 705 " --> pdb=" O PHE B 701 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N HIS B 715 " --> pdb=" O LYS B 711 " (cutoff:3.500A) removed outlier: 4.802A pdb=" N GLY B 717 " --> pdb=" O MET B 713 " (cutoff:3.500A) Processing helix chain 'B' and resid 728 through 746 removed outlier: 4.957A pdb=" N GLY B 732 " --> pdb=" O ARG B 728 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N ALA B 735 " --> pdb=" O THR B 731 " (cutoff:3.500A) removed outlier: 4.445A pdb=" N ARG B 736 " --> pdb=" O GLY B 732 " (cutoff:3.500A) removed outlier: 4.107A pdb=" N ALA B 737 " --> pdb=" O LYS B 733 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ILE B 738 " --> pdb=" O THR B 734 " (cutoff:3.500A) removed outlier: 5.928A pdb=" N ARG B 739 " --> pdb=" O ALA B 735 " (cutoff:3.500A) removed outlier: 4.161A pdb=" N ASP B 746 " --> pdb=" O CYS B 742 " (cutoff:3.500A) Processing helix chain 'B' and resid 760 through 768 removed outlier: 3.802A pdb=" N THR B 764 " --> pdb=" O GLU B 760 " (cutoff:3.500A) removed outlier: 5.063A pdb=" N GLN B 768 " --> pdb=" O THR B 764 " (cutoff:3.500A) Processing helix chain 'B' and resid 773 through 781 removed outlier: 3.895A pdb=" N LEU B 777 " --> pdb=" O GLU B 773 " (cutoff:3.500A) Proline residue: B 779 - end of helix Processing helix chain 'B' and resid 790 through 804 removed outlier: 5.142A pdb=" N ARG B 794 " --> pdb=" O THR B 790 " (cutoff:3.500A) removed outlier: 4.226A pdb=" N THR B 795 " --> pdb=" O ARG B 791 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N LEU B 800 " --> pdb=" O LEU B 796 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N LYS B 804 " --> pdb=" O LEU B 800 " (cutoff:3.500A) Processing helix chain 'B' and resid 812 through 818 removed outlier: 3.984A pdb=" N ALA B 816 " --> pdb=" O THR B 812 " (cutoff:3.500A) Processing helix chain 'B' and resid 845 through 856 removed outlier: 3.590A pdb=" N ILE B 849 " --> pdb=" O GLY B 845 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ARG B 855 " --> pdb=" O GLN B 851 " (cutoff:3.500A) removed outlier: 4.572A pdb=" N ALA B 856 " --> pdb=" O MET B 852 " (cutoff:3.500A) Processing helix chain 'B' and resid 872 through 885 removed outlier: 4.305A pdb=" N GLN B 877 " --> pdb=" O HIS B 873 " (cutoff:3.500A) removed outlier: 5.179A pdb=" N TYR B 878 " --> pdb=" O GLY B 874 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N LEU B 880 " --> pdb=" O LEU B 876 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N LEU B 883 " --> pdb=" O TYR B 879 " (cutoff:3.500A) removed outlier: 4.717A pdb=" N GLN B 885 " --> pdb=" O SER B 881 " (cutoff:3.500A) Processing helix chain 'B' and resid 892 through 908 removed outlier: 4.115A pdb=" N LYS B 896 " --> pdb=" O GLN B 892 " (cutoff:3.500A) Proline residue: B 898 - end of helix Processing helix chain 'B' and resid 912 through 924 removed outlier: 3.720A pdb=" N TYR B 922 " --> pdb=" O ASN B 918 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N ALA B 923 " --> pdb=" O TRP B 919 " (cutoff:3.500A) removed outlier: 5.754A pdb=" N TYR B 924 " --> pdb=" O LEU B 920 " (cutoff:3.500A) Processing helix chain 'B' and resid 925 through 932 Processing helix chain 'B' and resid 939 through 947 Proline residue: B 947 - end of helix Processing helix chain 'B' and resid 949 through 968 removed outlier: 4.423A pdb=" N VAL B 957 " --> pdb=" O ARG B 953 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N HIS B 958 " --> pdb=" O LEU B 954 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N THR B 959 " --> pdb=" O ASP B 955 " (cutoff:3.500A) removed outlier: 6.214A pdb=" N ALA B 960 " --> pdb=" O LEU B 956 " (cutoff:3.500A) Processing helix chain 'B' and resid 982 through 992 Processing helix chain 'B' and resid 994 through 1005 removed outlier: 3.737A pdb=" N GLN B 999 " --> pdb=" O ASN B 995 " (cutoff:3.500A) Processing helix chain 'B' and resid 1010 through 1026 removed outlier: 3.853A pdb=" N ARG B1016 " --> pdb=" O ILE B1012 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N SER B1021 " --> pdb=" O VAL B1017 " (cutoff:3.500A) removed outlier: 6.168A pdb=" N SER B1022 " --> pdb=" O PHE B1018 " (cutoff:3.500A) removed outlier: 7.270A pdb=" N GLU B1023 " --> pdb=" O SER B1019 " (cutoff:3.500A) removed outlier: 6.329A pdb=" N PHE B1024 " --> pdb=" O LEU B1020 " (cutoff:3.500A) removed outlier: 4.140A pdb=" N LYS B1025 " --> pdb=" O SER B1021 " (cutoff:3.500A) removed outlier: 5.558A pdb=" N ASN B1026 " --> pdb=" O SER B1022 " (cutoff:3.500A) Processing helix chain 'B' and resid 1031 through 1042 removed outlier: 4.202A pdb=" N LEU B1035 " --> pdb=" O GLU B1031 " (cutoff:3.500A) removed outlier: 4.832A pdb=" N GLU B1036 " --> pdb=" O GLU B1032 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N GLN B1038 " --> pdb=" O LYS B1034 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N LYS B1039 " --> pdb=" O LEU B1035 " (cutoff:3.500A) Processing helix chain 'B' and resid 1054 through 1069 Processing helix chain 'B' and resid 1078 through 1103 removed outlier: 3.749A pdb=" N GLY B1089 " --> pdb=" O THR B1085 " (cutoff:3.500A) removed outlier: 4.702A pdb=" N ARG B1090 " --> pdb=" O GLN B1086 " (cutoff:3.500A) Processing helix chain 'B' and resid 1104 through 1121 Processing helix chain 'B' and resid 1127 through 1133 removed outlier: 4.694A pdb=" N GLN B1131 " --> pdb=" O CYS B1127 " (cutoff:3.500A) removed outlier: 4.319A pdb=" N PHE B1132 " --> pdb=" O PRO B1128 " (cutoff:3.500A) removed outlier: 5.054A pdb=" N ARG B1133 " --> pdb=" O LEU B1129 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 1127 through 1133' Processing helix chain 'B' and resid 1136 through 1147 removed outlier: 3.671A pdb=" N LYS B1146 " --> pdb=" O LYS B1142 " (cutoff:3.500A) removed outlier: 4.900A pdb=" N ASN B1147 " --> pdb=" O ILE B1143 " (cutoff:3.500A) Processing helix chain 'B' and resid 1149 through 1157 removed outlier: 4.136A pdb=" N LEU B1153 " --> pdb=" O PRO B1149 " (cutoff:3.500A) removed outlier: 4.630A pdb=" N TYR B1154 " --> pdb=" O PHE B1150 " (cutoff:3.500A) removed outlier: 5.090A pdb=" N ASP B1155 " --> pdb=" O GLU B1151 " (cutoff:3.500A) removed outlier: 4.475A pdb=" N LEU B1156 " --> pdb=" O ARG B1152 " (cutoff:3.500A) removed outlier: 5.504A pdb=" N ASN B1157 " --> pdb=" O LEU B1153 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 1149 through 1157' Processing helix chain 'B' and resid 1158 through 1166 removed outlier: 3.877A pdb=" N GLY B1162 " --> pdb=" O HIS B1158 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N LEU B1164 " --> pdb=" O GLU B1160 " (cutoff:3.500A) removed outlier: 4.195A pdb=" N ILE B1165 " --> pdb=" O ILE B1161 " (cutoff:3.500A) Processing helix chain 'B' and resid 1167 through 1182 removed outlier: 3.867A pdb=" N GLY B1171 " --> pdb=" O MET B1167 " (cutoff:3.500A) removed outlier: 4.717A pdb=" N LYS B1172 " --> pdb=" O PRO B1168 " (cutoff:3.500A) removed outlier: 5.433A pdb=" N THR B1173 " --> pdb=" O LYS B1169 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N HIS B1175 " --> pdb=" O GLY B1171 " (cutoff:3.500A) Proline residue: B1182 - end of helix Processing helix chain 'B' and resid 1314 through 1322 removed outlier: 4.446A pdb=" N LEU B1320 " --> pdb=" O ALA B1316 " (cutoff:3.500A) removed outlier: 4.189A pdb=" N TYR B1321 " --> pdb=" O PHE B1317 " (cutoff:3.500A) Processing helix chain 'B' and resid 1329 through 1340 removed outlier: 4.788A pdb=" N ASN B1337 " --> pdb=" O THR B1333 " (cutoff:3.500A) removed outlier: 5.262A pdb=" N THR B1338 " --> pdb=" O GLN B1334 " (cutoff:3.500A) Processing helix chain 'B' and resid 1355 through 1371 removed outlier: 3.664A pdb=" N CYS B1359 " --> pdb=" O GLY B1355 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ALA B1363 " --> pdb=" O CYS B1359 " (cutoff:3.500A) Processing helix chain 'B' and resid 1382 through 1397 removed outlier: 3.773A pdb=" N ASP B1392 " --> pdb=" O GLN B1388 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N GLU B1395 " --> pdb=" O MET B1391 " (cutoff:3.500A) Processing helix chain 'B' and resid 1411 through 1422 removed outlier: 4.907A pdb=" N GLY B1420 " --> pdb=" O LEU B1416 " (cutoff:3.500A) removed outlier: 4.272A pdb=" N LYS B1421 " --> pdb=" O LYS B1417 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N GLY B1422 " --> pdb=" O LEU B1418 " (cutoff:3.500A) Processing helix chain 'B' and resid 1428 through 1437 removed outlier: 3.666A pdb=" N LEU B1435 " --> pdb=" O LYS B1431 " (cutoff:3.500A) removed outlier: 4.552A pdb=" N SER B1436 " --> pdb=" O TRP B1432 " (cutoff:3.500A) Processing helix chain 'B' and resid 1438 through 1443 removed outlier: 3.889A pdb=" N ARG B1442 " --> pdb=" O ARG B1438 " (cutoff:3.500A) removed outlier: 4.731A pdb=" N LYS B1443 " --> pdb=" O TRP B1439 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 1438 through 1443' Processing helix chain 'B' and resid 1455 through 1462 removed outlier: 4.803A pdb=" N ILE B1459 " --> pdb=" O GLU B1455 " (cutoff:3.500A) removed outlier: 4.830A pdb=" N GLY B1460 " --> pdb=" O VAL B1456 " (cutoff:3.500A) removed outlier: 4.527A pdb=" N GLY B1461 " --> pdb=" O HIS B1457 " (cutoff:3.500A) removed outlier: 5.069A pdb=" N GLU B1462 " --> pdb=" O LEU B1458 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 1455 through 1462' Processing helix chain 'B' and resid 1463 through 1482 removed outlier: 4.104A pdb=" N LEU B1467 " --> pdb=" O ASN B1463 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N GLU B1482 " --> pdb=" O SER B1478 " (cutoff:3.500A) Processing helix chain 'B' and resid 1496 through 1505 removed outlier: 3.661A pdb=" N VAL B1500 " --> pdb=" O ASN B1496 " (cutoff:3.500A) Processing helix chain 'B' and resid 1507 through 1512 removed outlier: 5.530A pdb=" N PHE B1512 " --> pdb=" O ALA B1508 " (cutoff:3.500A) Processing helix chain 'B' and resid 1534 through 1553 removed outlier: 3.839A pdb=" N ALA B1543 " --> pdb=" O LEU B1539 " (cutoff:3.500A) removed outlier: 4.840A pdb=" N LYS B1544 " --> pdb=" O LEU B1540 " (cutoff:3.500A) Proline residue: B1545 - end of helix Processing helix chain 'B' and resid 1566 through 1584 removed outlier: 4.900A pdb=" N ARG B1570 " --> pdb=" O ARG B1566 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N LEU B1571 " --> pdb=" O LYS B1567 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N ALA B1582 " --> pdb=" O THR B1578 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N ASP B1583 " --> pdb=" O THR B1579 " (cutoff:3.500A) removed outlier: 4.249A pdb=" N ILE B1584 " --> pdb=" O CYS B1580 " (cutoff:3.500A) Processing helix chain 'B' and resid 1593 through 1604 removed outlier: 3.850A pdb=" N LEU B1597 " --> pdb=" O THR B1593 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N ILE B1598 " --> pdb=" O GLU B1594 " (cutoff:3.500A) Proline residue: B1599 - end of helix removed outlier: 4.737A pdb=" N LYS B1603 " --> pdb=" O PRO B1599 " (cutoff:3.500A) removed outlier: 4.595A pdb=" N LEU B1604 " --> pdb=" O TYR B1600 " (cutoff:3.500A) Processing helix chain 'B' and resid 1606 through 1616 removed outlier: 3.580A pdb=" N LYS B1610 " --> pdb=" O ASP B1606 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N GLU B1611 " --> pdb=" O SER B1607 " (cutoff:3.500A) Processing helix chain 'B' and resid 1625 through 1639 Processing helix chain 'B' and resid 1647 through 1652 removed outlier: 4.180A pdb=" N CYS B1651 " --> pdb=" O SER B1647 " (cutoff:3.500A) removed outlier: 4.866A pdb=" N TRP B1652 " --> pdb=" O ARG B1648 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 1647 through 1652' Processing helix chain 'B' and resid 1680 through 1691 removed outlier: 4.110A pdb=" N ALA B1691 " --> pdb=" O MET B1687 " (cutoff:3.500A) Processing helix chain 'B' and resid 1707 through 1720 removed outlier: 4.559A pdb=" N ASP B1712 " --> pdb=" O GLY B1708 " (cutoff:3.500A) removed outlier: 4.766A pdb=" N PHE B1713 " --> pdb=" O SER B1709 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N PHE B1714 " --> pdb=" O LYS B1710 " (cutoff:3.500A) removed outlier: 4.789A pdb=" N TYR B1719 " --> pdb=" O LYS B1715 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N GLU B1720 " --> pdb=" O LYS B1716 " (cutoff:3.500A) Processing helix chain 'B' and resid 1727 through 1732 removed outlier: 3.811A pdb=" N MET B1732 " --> pdb=" O LEU B1728 " (cutoff:3.500A) Processing helix chain 'B' and resid 1733 through 1743 Processing helix chain 'B' and resid 1747 through 1758 removed outlier: 3.619A pdb=" N TRP B1757 " --> pdb=" O ASP B1753 " (cutoff:3.500A) removed outlier: 4.188A pdb=" N THR B1758 " --> pdb=" O TYR B1754 " (cutoff:3.500A) Processing helix chain 'B' and resid 1759 through 1767 removed outlier: 4.502A pdb=" N THR B1765 " --> pdb=" O TYR B1761 " (cutoff:3.500A) removed outlier: 4.160A pdb=" N GLN B1766 " --> pdb=" O ARG B1762 " (cutoff:3.500A) Processing helix chain 'B' and resid 1777 through 1800 removed outlier: 3.547A pdb=" N LYS B1800 " --> pdb=" O LEU B1796 " (cutoff:3.500A) Processing helix chain 'B' and resid 1813 through 1823 Processing helix chain 'B' and resid 1825 through 1836 Processing helix chain 'B' and resid 1841 through 1852 removed outlier: 3.677A pdb=" N GLU B1847 " --> pdb=" O ARG B1843 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N ALA B1852 " --> pdb=" O ILE B1848 " (cutoff:3.500A) Processing helix chain 'B' and resid 1853 through 1858 removed outlier: 4.284A pdb=" N ASN B1857 " --> pdb=" O ALA B1853 " (cutoff:3.500A) removed outlier: 5.055A pdb=" N ILE B1858 " --> pdb=" O GLU B1854 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 1853 through 1858' Processing helix chain 'B' and resid 1863 through 1876 removed outlier: 4.379A pdb=" N LEU B1867 " --> pdb=" O HIS B1863 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N LEU B1868 " --> pdb=" O GLU B1864 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N ARG B1869 " --> pdb=" O ASP B1865 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N LYS B1874 " --> pdb=" O GLN B1870 " (cutoff:3.500A) Proline residue: B1876 - end of helix Processing helix chain 'B' and resid 1886 through 1901 Processing helix chain 'B' and resid 1905 through 1934 removed outlier: 3.744A pdb=" N ASP B1911 " --> pdb=" O GLU B1907 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N LYS B1918 " --> pdb=" O GLU B1914 " (cutoff:3.500A) removed outlier: 4.351A pdb=" N ILE B1920 " --> pdb=" O LEU B1916 " (cutoff:3.500A) removed outlier: 5.899A pdb=" N ARG B1921 " --> pdb=" O SER B1917 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N LEU B1922 " --> pdb=" O LYS B1918 " (cutoff:3.500A) Processing helix chain 'B' and resid 1935 through 1952 removed outlier: 3.560A pdb=" N ALA B1939 " --> pdb=" O TRP B1935 " (cutoff:3.500A) Processing helix chain 'B' and resid 1967 through 1978 removed outlier: 3.785A pdb=" N ILE B1971 " --> pdb=" O THR B1967 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N LYS B1972 " --> pdb=" O SER B1968 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N ARG B1973 " --> pdb=" O GLU B1969 " (cutoff:3.500A) Processing helix chain 'B' and resid 1981 through 1989 removed outlier: 3.588A pdb=" N ILE B1985 " --> pdb=" O SER B1981 " (cutoff:3.500A) removed outlier: 4.599A pdb=" N GLU B1987 " --> pdb=" O PHE B1983 " (cutoff:3.500A) removed outlier: 4.696A pdb=" N MET B1988 " --> pdb=" O ASP B1984 " (cutoff:3.500A) removed outlier: 6.315A pdb=" N GLU B1989 " --> pdb=" O ILE B1985 " (cutoff:3.500A) Processing helix chain 'B' and resid 1990 through 1998 removed outlier: 5.123A pdb=" N ASN B1994 " --> pdb=" O ASP B1990 " (cutoff:3.500A) removed outlier: 4.200A pdb=" N ALA B1995 " --> pdb=" O GLU B1991 " (cutoff:3.500A) removed outlier: 5.369A pdb=" N LEU B1997 " --> pdb=" O ARG B1993 " (cutoff:3.500A) removed outlier: 4.287A pdb=" N GLN B1998 " --> pdb=" O ASN B1994 " (cutoff:3.500A) Processing helix chain 'B' and resid 2000 through 2014 removed outlier: 3.716A pdb=" N PHE B2010 " --> pdb=" O ASP B2006 " (cutoff:3.500A) Processing helix chain 'B' and resid 1308 through 1313 removed outlier: 3.989A pdb=" N LEU B1312 " --> pdb=" O VAL B1309 " (cutoff:3.500A) removed outlier: 5.021A pdb=" N ARG B1313 " --> pdb=" O SER B1310 " (cutoff:3.500A) Processing helix chain 'B' and resid 1958 through 1964 removed outlier: 3.658A pdb=" N LYS B1961 " --> pdb=" O SER B1958 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N GLN B1962 " --> pdb=" O TYR B1959 " (cutoff:3.500A) Proline residue: B1964 - end of helix Processing helix chain 'B' and resid 668 through 673 Processing helix chain 'B' and resid 1211 through 1216 removed outlier: 3.696A pdb=" N GLY B1216 " --> pdb=" O ASP B1211 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 1211 through 1216' Processing helix chain 'C' and resid 68 through 74 removed outlier: 4.154A pdb=" N GLY C 74 " --> pdb=" O GLU C 70 " (cutoff:3.500A) Processing helix chain 'C' and resid 115 through 126 removed outlier: 3.788A pdb=" N ASP C 124 " --> pdb=" O ALA C 120 " (cutoff:3.500A) removed outlier: 4.273A pdb=" N ASN C 125 " --> pdb=" O ASP C 121 " (cutoff:3.500A) removed outlier: 4.329A pdb=" N SER C 126 " --> pdb=" O LEU C 122 " (cutoff:3.500A) Processing helix chain 'C' and resid 141 through 155 removed outlier: 3.670A pdb=" N GLN C 152 " --> pdb=" O CYS C 148 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N THR C 153 " --> pdb=" O LEU C 149 " (cutoff:3.500A) Proline residue: C 155 - end of helix Processing helix chain 'C' and resid 171 through 178 Processing helix chain 'C' and resid 208 through 222 removed outlier: 4.881A pdb=" N ASP C 213 " --> pdb=" O VAL C 209 " (cutoff:3.500A) removed outlier: 5.988A pdb=" N GLU C 214 " --> pdb=" O ASN C 210 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N VAL C 215 " --> pdb=" O PHE C 211 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ALA C 217 " --> pdb=" O ASP C 213 " (cutoff:3.500A) removed outlier: 4.147A pdb=" N GLY C 218 " --> pdb=" O GLU C 214 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N ILE C 221 " --> pdb=" O ALA C 217 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N SER C 222 " --> pdb=" O GLY C 218 " (cutoff:3.500A) Processing helix chain 'C' and resid 236 through 250 removed outlier: 3.635A pdb=" N GLU C 249 " --> pdb=" O HIS C 245 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N ARG C 250 " --> pdb=" O ALA C 246 " (cutoff:3.500A) Processing helix chain 'C' and resid 259 through 265 removed outlier: 4.403A pdb=" N LEU C 263 " --> pdb=" O LYS C 259 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N ILE C 264 " --> pdb=" O ILE C 260 " (cutoff:3.500A) Processing helix chain 'C' and resid 270 through 293 removed outlier: 3.662A pdb=" N TYR C 276 " --> pdb=" O THR C 272 " (cutoff:3.500A) Processing helix chain 'C' and resid 319 through 331 removed outlier: 4.072A pdb=" N ILE C 326 " --> pdb=" O SER C 322 " (cutoff:3.500A) Processing helix chain 'C' and resid 335 through 344 removed outlier: 3.682A pdb=" N LYS C 341 " --> pdb=" O GLN C 337 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N ARG C 342 " --> pdb=" O GLU C 338 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N LEU C 343 " --> pdb=" O PHE C 339 " (cutoff:3.500A) removed outlier: 5.459A pdb=" N TRP C 344 " --> pdb=" O ALA C 340 " (cutoff:3.500A) Processing helix chain 'C' and resid 367 through 386 removed outlier: 4.977A pdb=" N GLU C 375 " --> pdb=" O GLU C 371 " (cutoff:3.500A) Proline residue: C 376 - end of helix Processing helix chain 'C' and resid 391 through 400 removed outlier: 3.696A pdb=" N THR C 395 " --> pdb=" O SER C 391 " (cutoff:3.500A) Processing helix chain 'C' and resid 404 through 410 removed outlier: 3.756A pdb=" N LYS C 409 " --> pdb=" O LYS C 405 " (cutoff:3.500A) removed outlier: 4.576A pdb=" N LEU C 410 " --> pdb=" O GLU C 406 " (cutoff:3.500A) Processing helix chain 'C' and resid 411 through 425 Processing helix chain 'C' and resid 427 through 437 removed outlier: 4.310A pdb=" N VAL C 431 " --> pdb=" O PHE C 427 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N GLN C 436 " --> pdb=" O ASP C 432 " (cutoff:3.500A) Processing helix chain 'C' and resid 440 through 453 removed outlier: 4.836A pdb=" N LYS C 446 " --> pdb=" O LYS C 442 " (cutoff:3.500A) Proline residue: C 447 - end of helix removed outlier: 3.883A pdb=" N GLU C 450 " --> pdb=" O LYS C 446 " (cutoff:3.500A) removed outlier: 4.107A pdb=" N HIS C 451 " --> pdb=" O PRO C 447 " (cutoff:3.500A) Processing helix chain 'C' and resid 461 through 468 removed outlier: 3.667A pdb=" N SER C 466 " --> pdb=" O GLY C 462 " (cutoff:3.500A) removed outlier: 4.849A pdb=" N CYS C 468 " --> pdb=" O ALA C 464 " (cutoff:3.500A) Processing helix chain 'C' and resid 596 through 614 removed outlier: 4.176A pdb=" N LEU C 600 " --> pdb=" O ASN C 596 " (cutoff:3.500A) Proline residue: C 601 - end of helix removed outlier: 3.548A pdb=" N VAL C 610 " --> pdb=" O GLY C 606 " (cutoff:3.500A) Processing helix chain 'C' and resid 633 through 646 Processing helix chain 'C' and resid 695 through 703 removed outlier: 4.203A pdb=" N ASP C 699 " --> pdb=" O GLY C 695 " (cutoff:3.500A) removed outlier: 4.463A pdb=" N GLU C 703 " --> pdb=" O ASP C 699 " (cutoff:3.500A) Processing helix chain 'C' and resid 706 through 711 removed outlier: 4.773A pdb=" N ASN C 710 " --> pdb=" O GLN C 706 " (cutoff:3.500A) removed outlier: 6.383A pdb=" N ARG C 711 " --> pdb=" O ILE C 707 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 706 through 711' Processing helix chain 'C' and resid 712 through 722 removed outlier: 3.569A pdb=" N GLU C 716 " --> pdb=" O LYS C 712 " (cutoff:3.500A) removed outlier: 4.441A pdb=" N THR C 720 " --> pdb=" O GLU C 716 " (cutoff:3.500A) Processing helix chain 'C' and resid 726 through 732 removed outlier: 5.200A pdb=" N ARG C 730 " --> pdb=" O LEU C 726 " (cutoff:3.500A) removed outlier: 4.698A pdb=" N SER C 731 " --> pdb=" O LEU C 727 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N ILE C 732 " --> pdb=" O ALA C 728 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 726 through 732' Processing helix chain 'C' and resid 755 through 777 removed outlier: 4.437A pdb=" N LEU C 759 " --> pdb=" O ASP C 755 " (cutoff:3.500A) removed outlier: 4.370A pdb=" N SER C 761 " --> pdb=" O ALA C 757 " (cutoff:3.500A) removed outlier: 5.271A pdb=" N VAL C 762 " --> pdb=" O LEU C 758 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N LYS C 763 " --> pdb=" O LEU C 759 " (cutoff:3.500A) removed outlier: 5.648A pdb=" N ASP C 764 " --> pdb=" O GLY C 760 " (cutoff:3.500A) removed outlier: 5.716A pdb=" N SER C 765 " --> pdb=" O SER C 761 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N GLN C 768 " --> pdb=" O ASP C 764 " (cutoff:3.500A) removed outlier: 4.179A pdb=" N TRP C 772 " --> pdb=" O GLN C 768 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N GLU C 776 " --> pdb=" O TRP C 772 " (cutoff:3.500A) Processing helix chain 'C' and resid 800 through 805 removed outlier: 4.728A pdb=" N GLY C 804 " --> pdb=" O PRO C 800 " (cutoff:3.500A) removed outlier: 6.020A pdb=" N GLY C 805 " --> pdb=" O LEU C 801 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 800 through 805' Processing helix chain 'C' and resid 806 through 822 Proline residue: C 810 - end of helix removed outlier: 4.131A pdb=" N MET C 822 " --> pdb=" O SER C 818 " (cutoff:3.500A) Processing helix chain 'C' and resid 839 through 854 removed outlier: 5.626A pdb=" N SER C 844 " --> pdb=" O ALA C 840 " (cutoff:3.500A) removed outlier: 5.061A pdb=" N ALA C 845 " --> pdb=" O ASP C 841 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N VAL C 849 " --> pdb=" O ALA C 845 " (cutoff:3.500A) Processing helix chain 'C' and resid 876 through 892 removed outlier: 4.636A pdb=" N PHE C 881 " --> pdb=" O ALA C 877 " (cutoff:3.500A) removed outlier: 6.098A pdb=" N GLY C 882 " --> pdb=" O ILE C 878 " (cutoff:3.500A) removed outlier: 4.989A pdb=" N PHE C 883 " --> pdb=" O ASP C 879 " (cutoff:3.500A) removed outlier: 5.422A pdb=" N GLU C 884 " --> pdb=" O SER C 880 " (cutoff:3.500A) removed outlier: 6.917A pdb=" N THR C 885 " --> pdb=" O PHE C 881 " (cutoff:3.500A) Processing helix chain 'C' and resid 928 through 942 removed outlier: 3.726A pdb=" N GLU C 932 " --> pdb=" O HIS C 928 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N THR C 937 " --> pdb=" O PHE C 933 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N ARG C 940 " --> pdb=" O LYS C 936 " (cutoff:3.500A) Processing helix chain 'C' and resid 553 through 558 removed outlier: 6.512A pdb=" N ASP C 556 " --> pdb=" O GLU C 553 " (cutoff:3.500A) removed outlier: 5.099A pdb=" N GLN C 557 " --> pdb=" O GLY C 554 " (cutoff:3.500A) Proline residue: C 558 - end of helix No H-bonds generated for 'chain 'C' and resid 553 through 558' Processing helix chain 'D' and resid 26 through 40 removed outlier: 3.964A pdb=" N GLU D 30 " --> pdb=" O ASN D 26 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N GLN D 31 " --> pdb=" O ALA D 27 " (cutoff:3.500A) Processing helix chain 'D' and resid 77 through 140 removed outlier: 3.899A pdb=" N TYR D 82 " --> pdb=" O GLU D 78 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N ARG D 87 " --> pdb=" O ARG D 83 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N ASP D 97 " --> pdb=" O GLN D 93 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N ALA D 98 " --> pdb=" O ASP D 94 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N ALA D 100 " --> pdb=" O MET D 96 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N ARG D 127 " --> pdb=" O GLN D 123 " (cutoff:3.500A) Processing helix chain 'F' and resid 656 through 663 Processing helix chain 'G' and resid 59 through 73 Processing helix chain 'G' and resid 74 through 83 removed outlier: 4.095A pdb=" N LYS G 83 " --> pdb=" O LYS G 79 " (cutoff:3.500A) Processing helix chain 'G' and resid 84 through 100 removed outlier: 5.676A pdb=" N THR G 100 " --> pdb=" O LEU G 96 " (cutoff:3.500A) Processing helix chain 'H' and resid 149 through 173 Processing helix chain 'H' and resid 177 through 189 removed outlier: 3.522A pdb=" N GLN H 187 " --> pdb=" O GLN H 183 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N GLU H 188 " --> pdb=" O GLU H 184 " (cutoff:3.500A) removed outlier: 5.166A pdb=" N ASN H 189 " --> pdb=" O LEU H 185 " (cutoff:3.500A) Processing helix chain 'H' and resid 193 through 209 Proline residue: H 209 - end of helix Processing helix chain 'H' and resid 210 through 226 removed outlier: 6.157A pdb=" N VAL H 214 " --> pdb=" O ILE H 210 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N LYS H 225 " --> pdb=" O ILE H 221 " (cutoff:3.500A) Processing helix chain 'H' and resid 227 through 248 Processing helix chain 'H' and resid 249 through 267 Processing helix chain 'H' and resid 270 through 285 removed outlier: 4.475A pdb=" N CYS H 274 " --> pdb=" O HIS H 270 " (cutoff:3.500A) removed outlier: 4.558A pdb=" N ARG H 284 " --> pdb=" O LEU H 280 " (cutoff:3.500A) Proline residue: H 285 - end of helix Processing helix chain 'H' and resid 286 through 301 removed outlier: 3.551A pdb=" N GLU H 299 " --> pdb=" O GLY H 295 " (cutoff:3.500A) Processing helix chain 'H' and resid 302 through 308 Processing helix chain 'H' and resid 309 through 325 Processing helix chain 'H' and resid 329 through 346 Processing helix chain 'H' and resid 379 through 385 removed outlier: 4.482A pdb=" N ASN H 383 " --> pdb=" O GLU H 379 " (cutoff:3.500A) removed outlier: 4.201A pdb=" N VAL H 384 " --> pdb=" O ASP H 380 " (cutoff:3.500A) removed outlier: 5.600A pdb=" N PHE H 385 " --> pdb=" O VAL H 381 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 379 through 385' Processing helix chain 'H' and resid 390 through 406 removed outlier: 3.578A pdb=" N GLU H 404 " --> pdb=" O ALA H 400 " (cutoff:3.500A) Processing helix chain 'H' and resid 448 through 467 removed outlier: 3.627A pdb=" N SER H 466 " --> pdb=" O ALA H 462 " (cutoff:3.500A) removed outlier: 5.530A pdb=" N LEU H 467 " --> pdb=" O ILE H 463 " (cutoff:3.500A) Processing helix chain 'H' and resid 468 through 480 removed outlier: 3.998A pdb=" N GLU H 480 " --> pdb=" O LEU H 476 " (cutoff:3.500A) Processing helix chain 'H' and resid 482 through 501 removed outlier: 4.157A pdb=" N THR H 486 " --> pdb=" O PRO H 482 " (cutoff:3.500A) removed outlier: 5.256A pdb=" N LYS H 487 " --> pdb=" O GLU H 483 " (cutoff:3.500A) removed outlier: 5.517A pdb=" N GLU H 488 " --> pdb=" O SER H 484 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N CYS H 490 " --> pdb=" O THR H 486 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N GLN H 500 " --> pdb=" O CYS H 496 " (cutoff:3.500A) removed outlier: 5.894A pdb=" N ARG H 501 " --> pdb=" O CYS H 497 " (cutoff:3.500A) Processing helix chain 'H' and resid 504 through 518 removed outlier: 4.156A pdb=" N GLY H 508 " --> pdb=" O GLU H 504 " (cutoff:3.500A) Processing helix chain 'H' and resid 519 through 536 removed outlier: 3.686A pdb=" N ILE H 536 " --> pdb=" O GLN H 532 " (cutoff:3.500A) Processing helix chain 'H' and resid 540 through 558 removed outlier: 4.061A pdb=" N ASP H 558 " --> pdb=" O LEU H 554 " (cutoff:3.500A) Processing helix chain 'H' and resid 564 through 569 removed outlier: 4.596A pdb=" N ILE H 568 " --> pdb=" O VAL H 564 " (cutoff:3.500A) removed outlier: 5.408A pdb=" N LYS H 569 " --> pdb=" O LEU H 565 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 564 through 569' Processing helix chain 'H' and resid 576 through 595 removed outlier: 3.567A pdb=" N ARG H 580 " --> pdb=" O THR H 576 " (cutoff:3.500A) removed outlier: 4.076A pdb=" N ILE H 581 " --> pdb=" O SER H 577 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N VAL H 583 " --> pdb=" O SER H 579 " (cutoff:3.500A) removed outlier: 4.383A pdb=" N GLY H 595 " --> pdb=" O CYS H 591 " (cutoff:3.500A) Processing helix chain 'H' and resid 596 through 605 removed outlier: 3.641A pdb=" N ASP H 605 " --> pdb=" O ALA H 601 " (cutoff:3.500A) Processing helix chain 'H' and resid 606 through 613 Proline residue: H 610 - end of helix removed outlier: 3.881A pdb=" N GLU H 613 " --> pdb=" O GLN H 609 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 606 through 613' Processing helix chain 'H' and resid 620 through 635 removed outlier: 3.685A pdb=" N THR H 624 " --> pdb=" O ASN H 620 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N GLY H 635 " --> pdb=" O PHE H 631 " (cutoff:3.500A) Processing helix chain 'H' and resid 640 through 648 removed outlier: 3.648A pdb=" N GLU H 645 " --> pdb=" O ASP H 641 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N HIS H 646 " --> pdb=" O GLU H 642 " (cutoff:3.500A) removed outlier: 4.153A pdb=" N LEU H 647 " --> pdb=" O LEU H 643 " (cutoff:3.500A) removed outlier: 4.854A pdb=" N LYS H 648 " --> pdb=" O ARG H 644 " (cutoff:3.500A) Processing helix chain 'J' and resid 496 through 501 Proline residue: J 501 - end of helix Processing helix chain 'K' and resid 97 through 104 removed outlier: 5.246A pdb=" N ILE K 101 " --> pdb=" O LYS K 97 " (cutoff:3.500A) removed outlier: 4.188A pdb=" N ALA K 102 " --> pdb=" O TYR K 98 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N GLN K 104 " --> pdb=" O ALA K 100 " (cutoff:3.500A) Processing helix chain 'K' and resid 115 through 120 removed outlier: 3.921A pdb=" N LEU K 119 " --> pdb=" O LYS K 115 " (cutoff:3.500A) Processing helix chain 'K' and resid 136 through 159 removed outlier: 3.800A pdb=" N ILE K 140 " --> pdb=" O ASP K 136 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N LYS K 141 " --> pdb=" O GLU K 137 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N SER K 154 " --> pdb=" O ALA K 150 " (cutoff:3.500A) removed outlier: 4.076A pdb=" N GLN K 157 " --> pdb=" O LYS K 153 " (cutoff:3.500A) Processing helix chain 'K' and resid 185 through 190 removed outlier: 4.508A pdb=" N ASN K 189 " --> pdb=" O GLY K 185 " (cutoff:3.500A) removed outlier: 5.186A pdb=" N SER K 190 " --> pdb=" O VAL K 186 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 185 through 190' Processing helix chain 'K' and resid 238 through 246 removed outlier: 3.662A pdb=" N TRP K 245 " --> pdb=" O GLU K 241 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N LYS K 246 " --> pdb=" O GLN K 242 " (cutoff:3.500A) Processing helix chain 'K' and resid 263 through 270 removed outlier: 4.603A pdb=" N ALA K 270 " --> pdb=" O LYS K 266 " (cutoff:3.500A) Processing helix chain 'K' and resid 281 through 335 removed outlier: 4.381A pdb=" N ALA K 285 " --> pdb=" O ASN K 281 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N GLN K 307 " --> pdb=" O GLU K 303 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N ARG K 310 " --> pdb=" O ALA K 306 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N ALA K 313 " --> pdb=" O GLU K 309 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N ARG K 334 " --> pdb=" O LYS K 330 " (cutoff:3.500A) removed outlier: 4.850A pdb=" N ARG K 335 " --> pdb=" O ALA K 331 " (cutoff:3.500A) Processing helix chain 'K' and resid 54 through 59 removed outlier: 4.452A pdb=" N PHE K 58 " --> pdb=" O LEU K 55 " (cutoff:3.500A) removed outlier: 5.590A pdb=" N GLY K 59 " --> pdb=" O GLU K 56 " (cutoff:3.500A) Processing helix chain 'L' and resid 14 through 35 removed outlier: 3.841A pdb=" N ILE L 18 " --> pdb=" O GLY L 14 " (cutoff:3.500A) Proline residue: L 20 - end of helix removed outlier: 3.514A pdb=" N GLU L 35 " --> pdb=" O GLU L 31 " (cutoff:3.500A) Processing helix chain 'L' and resid 41 through 65 removed outlier: 3.701A pdb=" N SER L 45 " --> pdb=" O ARG L 41 " (cutoff:3.500A) removed outlier: 5.082A pdb=" N LEU L 46 " --> pdb=" O LYS L 42 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N TRP L 47 " --> pdb=" O VAL L 43 " (cutoff:3.500A) Proline residue: L 48 - end of helix removed outlier: 3.647A pdb=" N ILE L 60 " --> pdb=" O LYS L 56 " (cutoff:3.500A) Processing helix chain 'L' and resid 71 through 82 removed outlier: 4.025A pdb=" N GLY L 82 " --> pdb=" O CYS L 78 " (cutoff:3.500A) Processing helix chain 'L' and resid 85 through 95 removed outlier: 4.127A pdb=" N LYS L 94 " --> pdb=" O ALA L 90 " (cutoff:3.500A) removed outlier: 5.370A pdb=" N GLN L 95 " --> pdb=" O LYS L 91 " (cutoff:3.500A) Processing helix chain 'L' and resid 102 through 108 removed outlier: 4.323A pdb=" N ILE L 106 " --> pdb=" O CYS L 102 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N GLN L 107 " --> pdb=" O LEU L 103 " (cutoff:3.500A) removed outlier: 5.862A pdb=" N THR L 108 " --> pdb=" O ARG L 104 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 102 through 108' Processing helix chain 'L' and resid 117 through 122 removed outlier: 3.898A pdb=" N VAL L 121 " --> pdb=" O CYS L 117 " (cutoff:3.500A) Proline residue: L 122 - end of helix No H-bonds generated for 'chain 'L' and resid 117 through 122' Processing helix chain 'M' and resid 24 through 29 removed outlier: 4.234A pdb=" N LEU M 28 " --> pdb=" O CYS M 24 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N GLY M 29 " --> pdb=" O GLN M 25 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 24 through 29' Processing helix chain 'M' and resid 71 through 79 removed outlier: 3.933A pdb=" N LYS M 78 " --> pdb=" O CYS M 74 " (cutoff:3.500A) Processing helix chain 'M' and resid 93 through 102 removed outlier: 3.748A pdb=" N LEU M 101 " --> pdb=" O ARG M 97 " (cutoff:3.500A) Processing helix chain 'M' and resid 111 through 129 removed outlier: 4.576A pdb=" N GLU M 115 " --> pdb=" O ASP M 111 " (cutoff:3.500A) removed outlier: 4.158A pdb=" N SER M 128 " --> pdb=" O GLU M 124 " (cutoff:3.500A) removed outlier: 4.756A pdb=" N ASP M 129 " --> pdb=" O ILE M 125 " (cutoff:3.500A) Processing helix chain 'M' and resid 136 through 141 removed outlier: 4.638A pdb=" N ALA M 140 " --> pdb=" O MET M 136 " (cutoff:3.500A) removed outlier: 6.781A pdb=" N THR M 141 " --> pdb=" O LEU M 137 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 136 through 141' Processing helix chain 'M' and resid 144 through 151 removed outlier: 3.641A pdb=" N LEU M 150 " --> pdb=" O ALA M 146 " (cutoff:3.500A) Processing helix chain 'M' and resid 156 through 162 removed outlier: 4.562A pdb=" N ASN M 160 " --> pdb=" O TYR M 156 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N ARG M 161 " --> pdb=" O TYR M 157 " (cutoff:3.500A) Proline residue: M 162 - end of helix No H-bonds generated for 'chain 'M' and resid 156 through 162' Processing helix chain 'M' and resid 165 through 171 removed outlier: 3.557A pdb=" N LYS M 170 " --> pdb=" O SER M 166 " (cutoff:3.500A) Processing helix chain 'M' and resid 197 through 204 Processing helix chain 'M' and resid 207 through 220 Processing helix chain 'M' and resid 244 through 253 removed outlier: 4.362A pdb=" N LEU M 248 " --> pdb=" O THR M 244 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N HIS M 251 " --> pdb=" O ASP M 247 " (cutoff:3.500A) Processing helix chain 'M' and resid 276 through 288 removed outlier: 3.624A pdb=" N GLU M 285 " --> pdb=" O GLU M 281 " (cutoff:3.500A) Processing helix chain 'M' and resid 191 through 196 removed outlier: 4.105A pdb=" N ASP M 195 " --> pdb=" O PRO M 192 " (cutoff:3.500A) removed outlier: 5.427A pdb=" N GLN M 196 " --> pdb=" O LEU M 193 " (cutoff:3.500A) Processing helix chain 'O' and resid 12 through 26 removed outlier: 4.416A pdb=" N GLU O 17 " --> pdb=" O ASN O 13 " (cutoff:3.500A) Processing helix chain 'O' and resid 30 through 39 removed outlier: 4.093A pdb=" N LEU O 37 " --> pdb=" O ARG O 33 " (cutoff:3.500A) removed outlier: 4.269A pdb=" N HIS O 39 " --> pdb=" O ALA O 35 " (cutoff:3.500A) Processing helix chain 'O' and resid 42 through 53 Processing helix chain 'O' and resid 64 through 79 removed outlier: 3.829A pdb=" N LYS O 76 " --> pdb=" O LEU O 72 " (cutoff:3.500A) Proline residue: O 79 - end of helix Processing helix chain 'O' and resid 81 through 90 Proline residue: O 87 - end of helix Processing helix chain 'O' and resid 92 through 109 removed outlier: 3.987A pdb=" N GLN O 109 " --> pdb=" O ASP O 105 " (cutoff:3.500A) Processing helix chain 'O' and resid 131 through 136 removed outlier: 4.194A pdb=" N LYS O 135 " --> pdb=" O ASN O 131 " (cutoff:3.500A) Proline residue: O 136 - end of helix No H-bonds generated for 'chain 'O' and resid 131 through 136' Processing helix chain 'O' and resid 145 through 161 removed outlier: 3.635A pdb=" N ALA O 160 " --> pdb=" O ARG O 156 " (cutoff:3.500A) Processing helix chain 'O' and resid 164 through 195 removed outlier: 3.920A pdb=" N GLN O 175 " --> pdb=" O ALA O 171 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N LYS O 187 " --> pdb=" O ALA O 183 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N ALA O 193 " --> pdb=" O ARG O 189 " (cutoff:3.500A) Processing helix chain 'O' and resid 243 through 249 removed outlier: 4.207A pdb=" N LEU O 247 " --> pdb=" O ARG O 243 " (cutoff:3.500A) Processing helix chain 'O' and resid 251 through 274 Processing helix chain 'O' and resid 275 through 283 removed outlier: 3.762A pdb=" N THR O 282 " --> pdb=" O ALA O 278 " (cutoff:3.500A) Processing helix chain 'O' and resid 516 through 538 removed outlier: 3.598A pdb=" N GLU O 529 " --> pdb=" O ILE O 525 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N ARG O 536 " --> pdb=" O LYS O 532 " (cutoff:3.500A) removed outlier: 4.885A pdb=" N HIS O 538 " --> pdb=" O MET O 534 " (cutoff:3.500A) Processing helix chain 'O' and resid 568 through 590 removed outlier: 3.695A pdb=" N ILE O 575 " --> pdb=" O SER O 571 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N LYS O 576 " --> pdb=" O GLU O 572 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N HIS O 589 " --> pdb=" O TYR O 585 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N HIS O 590 " --> pdb=" O ASP O 586 " (cutoff:3.500A) Processing helix chain 'O' and resid 626 through 645 removed outlier: 3.927A pdb=" N GLU O 641 " --> pdb=" O VAL O 637 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N VAL O 642 " --> pdb=" O GLN O 638 " (cutoff:3.500A) Processing helix chain 'O' and resid 691 through 726 removed outlier: 4.237A pdb=" N ARG O 695 " --> pdb=" O SER O 691 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N LEU O 696 " --> pdb=" O LEU O 692 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N GLU O 697 " --> pdb=" O GLU O 693 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N ILE O 719 " --> pdb=" O LYS O 715 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N LEU O 720 " --> pdb=" O LYS O 716 " (cutoff:3.500A) removed outlier: 4.140A pdb=" N GLY O 723 " --> pdb=" O ILE O 719 " (cutoff:3.500A) removed outlier: 4.398A pdb=" N TYR O 724 " --> pdb=" O LEU O 720 " (cutoff:3.500A) Processing helix chain 'O' and resid 727 through 740 removed outlier: 3.953A pdb=" N ASP O 740 " --> pdb=" O ASN O 736 " (cutoff:3.500A) Processing helix chain 'O' and resid 742 through 789 removed outlier: 4.070A pdb=" N ARG O 750 " --> pdb=" O HIS O 746 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N PHE O 752 " --> pdb=" O GLU O 748 " (cutoff:3.500A) Proline residue: O 764 - end of helix removed outlier: 3.545A pdb=" N CYS O 769 " --> pdb=" O ARG O 765 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N LEU O 770 " --> pdb=" O ARG O 766 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N GLU O 772 " --> pdb=" O GLU O 768 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N GLN O 777 " --> pdb=" O ASP O 773 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N LYS O 782 " --> pdb=" O GLN O 778 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N GLU O 783 " --> pdb=" O GLU O 779 " (cutoff:3.500A) Processing helix chain 'O' and resid 791 through 800 removed outlier: 3.771A pdb=" N LYS O 795 " --> pdb=" O LEU O 791 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N GLU O 796 " --> pdb=" O LEU O 792 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N THR O 797 " --> pdb=" O LEU O 793 " (cutoff:3.500A) Processing helix chain 'P' and resid 50 through 58 removed outlier: 4.067A pdb=" N ARG P 55 " --> pdb=" O PRO P 51 " (cutoff:3.500A) removed outlier: 4.643A pdb=" N ASN P 56 " --> pdb=" O GLU P 52 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N ARG P 57 " --> pdb=" O GLU P 53 " (cutoff:3.500A) removed outlier: 5.714A pdb=" N ASP P 58 " --> pdb=" O VAL P 54 " (cutoff:3.500A) Processing helix chain 'P' and resid 59 through 75 Processing helix chain 'P' and resid 187 through 192 removed outlier: 5.708A pdb=" N ASP P 191 " --> pdb=" O ARG P 187 " (cutoff:3.500A) removed outlier: 4.759A pdb=" N VAL P 192 " --> pdb=" O TRP P 188 " (cutoff:3.500A) No H-bonds generated for 'chain 'P' and resid 187 through 192' Processing helix chain 'P' and resid 217 through 228 removed outlier: 3.927A pdb=" N ILE P 228 " --> pdb=" O MET P 224 " (cutoff:3.500A) Processing helix chain 'S' and resid 190 through 202 removed outlier: 3.535A pdb=" N ARG S 196 " --> pdb=" O GLU S 192 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N ARG S 201 " --> pdb=" O GLU S 197 " (cutoff:3.500A) removed outlier: 4.123A pdb=" N GLU S 202 " --> pdb=" O ALA S 198 " (cutoff:3.500A) Processing helix chain 'S' and resid 216 through 239 Processing helix chain 'S' and resid 241 through 256 removed outlier: 4.341A pdb=" N TRP S 245 " --> pdb=" O VAL S 241 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N TYR S 248 " --> pdb=" O ASN S 244 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N LYS S 256 " --> pdb=" O GLU S 252 " (cutoff:3.500A) Processing helix chain 'S' and resid 257 through 272 removed outlier: 3.692A pdb=" N VAL S 271 " --> pdb=" O ARG S 267 " (cutoff:3.500A) Processing helix chain 'S' and resid 275 through 290 removed outlier: 3.922A pdb=" N TRP S 279 " --> pdb=" O ASN S 275 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N TYR S 282 " --> pdb=" O LEU S 278 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ASN S 289 " --> pdb=" O MET S 285 " (cutoff:3.500A) Processing helix chain 'S' and resid 291 through 306 Processing helix chain 'S' and resid 309 through 324 removed outlier: 4.043A pdb=" N TRP S 313 " --> pdb=" O VAL S 309 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N TYR S 316 " --> pdb=" O PHE S 312 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N TYR S 318 " --> pdb=" O TYR S 314 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N GLY S 324 " --> pdb=" O GLU S 320 " (cutoff:3.500A) Processing helix chain 'S' and resid 325 through 340 removed outlier: 3.685A pdb=" N GLU S 338 " --> pdb=" O GLU S 334 " (cutoff:3.500A) removed outlier: 4.280A pdb=" N TRP S 339 " --> pdb=" O ARG S 335 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N GLN S 340 " --> pdb=" O TRP S 336 " (cutoff:3.500A) Processing helix chain 'S' and resid 342 through 357 removed outlier: 3.640A pdb=" N TYR S 349 " --> pdb=" O ALA S 345 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N TYR S 356 " --> pdb=" O PHE S 352 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N LYS S 357 " --> pdb=" O GLU S 353 " (cutoff:3.500A) Processing helix chain 'S' and resid 358 through 374 removed outlier: 3.992A pdb=" N THR S 364 " --> pdb=" O ASP S 360 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ILE S 365 " --> pdb=" O ARG S 361 " (cutoff:3.500A) Proline residue: S 374 - end of helix Processing helix chain 'S' and resid 375 through 390 Processing helix chain 'S' and resid 391 through 407 Processing helix chain 'S' and resid 412 through 427 removed outlier: 4.313A pdb=" N TYR S 416 " --> pdb=" O ASP S 412 " (cutoff:3.500A) Processing helix chain 'S' and resid 428 through 442 removed outlier: 3.658A pdb=" N ASP S 441 " --> pdb=" O LYS S 437 " (cutoff:3.500A) Processing helix chain 'S' and resid 448 through 463 removed outlier: 6.611A pdb=" N PHE S 452 " --> pdb=" O ALA S 448 " (cutoff:3.500A) removed outlier: 4.310A pdb=" N LYS S 453 " --> pdb=" O GLN S 449 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N THR S 456 " --> pdb=" O PHE S 452 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N GLY S 463 " --> pdb=" O GLU S 459 " (cutoff:3.500A) Processing helix chain 'S' and resid 464 through 480 removed outlier: 3.869A pdb=" N ILE S 468 " --> pdb=" O ASP S 464 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N ILE S 471 " --> pdb=" O GLY S 467 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N TYR S 480 " --> pdb=" O ARG S 476 " (cutoff:3.500A) Processing helix chain 'S' and resid 495 through 513 removed outlier: 4.560A pdb=" N ARG S 499 " --> pdb=" O PHE S 495 " (cutoff:3.500A) Processing helix chain 'S' and resid 520 through 535 removed outlier: 3.851A pdb=" N TYR S 535 " --> pdb=" O LYS S 531 " (cutoff:3.500A) Processing helix chain 'S' and resid 538 through 555 removed outlier: 4.107A pdb=" N LEU S 542 " --> pdb=" O ILE S 538 " (cutoff:3.500A) removed outlier: 4.820A pdb=" N TYR S 543 " --> pdb=" O ASN S 539 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N LEU S 546 " --> pdb=" O LEU S 542 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N GLU S 547 " --> pdb=" O TYR S 543 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N ALA S 548 " --> pdb=" O GLU S 544 " (cutoff:3.500A) removed outlier: 4.143A pdb=" N ASP S 550 " --> pdb=" O LEU S 546 " (cutoff:3.500A) Proline residue: S 551 - end of helix Processing helix chain 'S' and resid 559 through 569 Proline residue: S 566 - end of helix Processing helix chain 'S' and resid 573 through 586 removed outlier: 3.725A pdb=" N PHE S 582 " --> pdb=" O LEU S 578 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N GLU S 583 " --> pdb=" O TYR S 579 " (cutoff:3.500A) removed outlier: 5.874A pdb=" N ARG S 585 " --> pdb=" O GLN S 581 " (cutoff:3.500A) removed outlier: 5.229A pdb=" N GLN S 586 " --> pdb=" O PHE S 582 " (cutoff:3.500A) Processing helix chain 'S' and resid 592 through 605 removed outlier: 3.949A pdb=" N THR S 598 " --> pdb=" O ARG S 594 " (cutoff:3.500A) Proline residue: S 604 - end of helix Processing helix chain 'S' and resid 609 through 624 removed outlier: 3.501A pdb=" N ASP S 623 " --> pdb=" O LEU S 619 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ARG S 624 " --> pdb=" O ARG S 620 " (cutoff:3.500A) Processing helix chain 'S' and resid 631 through 644 removed outlier: 3.837A pdb=" N PHE S 635 " --> pdb=" O LYS S 631 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N GLY S 636 " --> pdb=" O PHE S 632 " (cutoff:3.500A) Proline residue: S 637 - end of helix removed outlier: 3.895A pdb=" N TRP S 643 " --> pdb=" O ASN S 639 " (cutoff:3.500A) removed outlier: 4.121A pdb=" N ILE S 644 " --> pdb=" O CYS S 640 " (cutoff:3.500A) Processing helix chain 'S' and resid 648 through 660 removed outlier: 3.950A pdb=" N ILE S 652 " --> pdb=" O GLU S 648 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N LEU S 653 " --> pdb=" O LEU S 649 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N ALA S 659 " --> pdb=" O ASP S 655 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N ARG S 660 " --> pdb=" O ILE S 656 " (cutoff:3.500A) Processing helix chain 'S' and resid 666 through 679 Proline residue: S 670 - end of helix removed outlier: 3.671A pdb=" N MET S 674 " --> pdb=" O PRO S 670 " (cutoff:3.500A) Proline residue: S 675 - end of helix removed outlier: 3.677A pdb=" N LEU S 678 " --> pdb=" O MET S 674 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N TRP S 679 " --> pdb=" O PRO S 675 " (cutoff:3.500A) Processing helix chain 'S' and resid 683 through 697 removed outlier: 4.134A pdb=" N ASN S 697 " --> pdb=" O GLU S 693 " (cutoff:3.500A) Processing helix chain 'S' and resid 699 through 710 removed outlier: 3.805A pdb=" N LEU S 703 " --> pdb=" O TYR S 699 " (cutoff:3.500A) Processing helix chain 'S' and resid 718 through 731 Processing helix chain 'S' and resid 740 through 756 removed outlier: 3.695A pdb=" N ASN S 744 " --> pdb=" O LYS S 740 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N LEU S 755 " --> pdb=" O ARG S 751 " (cutoff:3.500A) Processing helix chain 'S' and resid 762 through 776 removed outlier: 4.077A pdb=" N GLY S 766 " --> pdb=" O GLU S 762 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N THR S 767 " --> pdb=" O GLU S 763 " (cutoff:3.500A) Processing helix chain 'S' and resid 780 through 802 removed outlier: 3.797A pdb=" N LYS S 784 " --> pdb=" O GLU S 780 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N TYR S 801 " --> pdb=" O GLY S 797 " (cutoff:3.500A) removed outlier: 5.391A pdb=" N PHE S 802 " --> pdb=" O TRP S 798 " (cutoff:3.500A) Processing helix chain 'T' and resid 19 through 30 Proline residue: T 23 - end of helix Processing helix chain 'T' and resid 34 through 46 Processing helix chain 'T' and resid 50 through 63 Processing helix chain 'T' and resid 66 through 85 Processing helix chain 'T' and resid 87 through 105 Processing helix chain 'T' and resid 109 through 122 Processing helix chain 'T' and resid 126 through 139 Processing helix chain 'T' and resid 145 through 158 Proline residue: T 150 - end of helix Processing helix chain 'T' and resid 161 through 175 Processing helix chain 'T' and resid 179 through 190 Processing helix chain 'T' and resid 193 through 205 Processing helix chain 'T' and resid 217 through 233 Proline residue: T 232 - end of helix Processing helix chain 'T' and resid 239 through 250 Processing helix chain 'T' and resid 253 through 268 Processing helix chain 'T' and resid 271 through 286 Processing helix chain 'T' and resid 289 through 312 Processing helix chain 'T' and resid 322 through 341 Processing helix chain 'T' and resid 342 through 354 removed outlier: 3.555A pdb=" N LEU T 349 " --> pdb=" O LEU T 345 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N ARG T 351 " --> pdb=" O SER T 347 " (cutoff:3.500A) Proline residue: T 354 - end of helix Processing helix chain 'T' and resid 356 through 368 removed outlier: 3.925A pdb=" N GLN T 368 " --> pdb=" O VAL T 364 " (cutoff:3.500A) Processing helix chain 'T' and resid 372 through 384 Processing helix chain 'T' and resid 395 through 409 Processing helix chain 'T' and resid 410 through 423 removed outlier: 4.481A pdb=" N ALA T 414 " --> pdb=" O GLN T 410 " (cutoff:3.500A) Processing helix chain 'T' and resid 429 through 447 removed outlier: 4.157A pdb=" N SER T 434 " --> pdb=" O ASP T 430 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N VAL T 435 " --> pdb=" O ASP T 431 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N LEU T 444 " --> pdb=" O GLY T 440 " (cutoff:3.500A) Processing helix chain 'T' and resid 448 through 460 removed outlier: 3.592A pdb=" N ALA T 452 " --> pdb=" O ASN T 448 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N LYS T 458 " --> pdb=" O ARG T 454 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N ALA T 459 " --> pdb=" O LEU T 455 " (cutoff:3.500A) Processing helix chain 'T' and resid 476 through 481 removed outlier: 3.722A pdb=" N VAL T 480 " --> pdb=" O VAL T 476 " (cutoff:3.500A) removed outlier: 5.611A pdb=" N TYR T 481 " --> pdb=" O GLN T 477 " (cutoff:3.500A) No H-bonds generated for 'chain 'T' and resid 476 through 481' Processing helix chain 'T' and resid 483 through 497 removed outlier: 3.734A pdb=" N TRP T 487 " --> pdb=" O SER T 483 " (cutoff:3.500A) Processing helix chain 'T' and resid 502 through 514 removed outlier: 3.731A pdb=" N TYR T 507 " --> pdb=" O THR T 503 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N ASP T 508 " --> pdb=" O LYS T 504 " (cutoff:3.500A) removed outlier: 5.055A pdb=" N ARG T 514 " --> pdb=" O ILE T 510 " (cutoff:3.500A) Processing helix chain 'T' and resid 517 through 532 removed outlier: 3.585A pdb=" N ALA T 525 " --> pdb=" O VAL T 521 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N HIS T 531 " --> pdb=" O PHE T 527 " (cutoff:3.500A) Processing helix chain 'T' and resid 533 through 548 removed outlier: 6.004A pdb=" N SER T 537 " --> pdb=" O TYR T 533 " (cutoff:3.500A) removed outlier: 4.905A pdb=" N PHE T 538 " --> pdb=" O PHE T 534 " (cutoff:3.500A) removed outlier: 4.411A pdb=" N PHE T 548 " --> pdb=" O GLY T 544 " (cutoff:3.500A) Processing helix chain 'T' and resid 549 through 568 removed outlier: 4.407A pdb=" N VAL T 553 " --> pdb=" O LYS T 549 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N SER T 554 " --> pdb=" O TRP T 550 " (cutoff:3.500A) removed outlier: 7.473A pdb=" N ASP T 555 " --> pdb=" O PRO T 551 " (cutoff:3.500A) removed outlier: 5.781A pdb=" N ILE T 556 " --> pdb=" O ASN T 552 " (cutoff:3.500A) Processing helix chain 'T' and resid 572 through 585 removed outlier: 4.167A pdb=" N ALA T 576 " --> pdb=" O LYS T 572 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N GLN T 582 " --> pdb=" O ASP T 578 " (cutoff:3.500A) removed outlier: 4.243A pdb=" N ALA T 583 " --> pdb=" O LEU T 579 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N LEU T 584 " --> pdb=" O PHE T 580 " (cutoff:3.500A) removed outlier: 4.234A pdb=" N ASP T 585 " --> pdb=" O GLU T 581 " (cutoff:3.500A) Processing helix chain 'T' and resid 588 through 606 removed outlier: 4.053A pdb=" N ALA T 592 " --> pdb=" O PRO T 588 " (cutoff:3.500A) removed outlier: 5.988A pdb=" N LYS T 593 " --> pdb=" O PRO T 589 " (cutoff:3.500A) removed outlier: 6.726A pdb=" N THR T 594 " --> pdb=" O LYS T 590 " (cutoff:3.500A) removed outlier: 5.696A pdb=" N LEU T 595 " --> pdb=" O TYR T 591 " (cutoff:3.500A) Processing helix chain 'T' and resid 608 through 623 removed outlier: 3.845A pdb=" N ALA T 612 " --> pdb=" O LEU T 608 " (cutoff:3.500A) removed outlier: 4.469A pdb=" N VAL T 615 " --> pdb=" O HIS T 611 " (cutoff:3.500A) removed outlier: 5.098A pdb=" N TYR T 616 " --> pdb=" O ALA T 612 " (cutoff:3.500A) removed outlier: 4.246A pdb=" N GLU T 617 " --> pdb=" O MET T 613 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N ARG T 621 " --> pdb=" O GLU T 617 " (cutoff:3.500A) removed outlier: 4.355A pdb=" N ALA T 622 " --> pdb=" O ARG T 618 " (cutoff:3.500A) Processing helix chain 'T' and resid 625 through 643 removed outlier: 4.544A pdb=" N GLU T 641 " --> pdb=" O LYS T 637 " (cutoff:3.500A) removed outlier: 4.569A pdb=" N ILE T 642 " --> pdb=" O ARG T 638 " (cutoff:3.500A) Processing helix chain 'T' and resid 644 through 659 removed outlier: 4.310A pdb=" N THR T 648 " --> pdb=" O GLY T 644 " (cutoff:3.500A) removed outlier: 4.294A pdb=" N ARG T 649 " --> pdb=" O VAL T 645 " (cutoff:3.500A) removed outlier: 6.417A pdb=" N GLY T 650 " --> pdb=" O THR T 646 " (cutoff:3.500A) removed outlier: 5.079A pdb=" N ILE T 651 " --> pdb=" O HIS T 647 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N LYS T 654 " --> pdb=" O GLY T 650 " (cutoff:3.500A) removed outlier: 4.207A pdb=" N GLU T 657 " --> pdb=" O GLN T 653 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N VAL T 658 " --> pdb=" O LYS T 654 " (cutoff:3.500A) removed outlier: 4.290A pdb=" N LEU T 659 " --> pdb=" O ALA T 655 " (cutoff:3.500A) Processing helix chain 'T' and resid 662 through 679 removed outlier: 4.250A pdb=" N GLU T 666 " --> pdb=" O GLU T 662 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N LEU T 669 " --> pdb=" O ARG T 665 " (cutoff:3.500A) Processing helix chain 'T' and resid 680 through 695 removed outlier: 3.705A pdb=" N ALA T 684 " --> pdb=" O GLU T 680 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N SER T 692 " --> pdb=" O TYR T 688 " (cutoff:3.500A) removed outlier: 4.076A pdb=" N ILE T 694 " --> pdb=" O PHE T 690 " (cutoff:3.500A) Processing helix chain 'T' and resid 700 through 715 removed outlier: 6.815A pdb=" N TRP T 704 " --> pdb=" O THR T 700 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N GLN T 705 " --> pdb=" O GLY T 701 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N PHE T 710 " --> pdb=" O THR T 706 " (cutoff:3.500A) Processing helix chain 'T' and resid 716 through 736 removed outlier: 3.708A pdb=" N ILE T 720 " --> pdb=" O ASN T 716 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N ASN T 735 " --> pdb=" O GLN T 731 " (cutoff:3.500A) removed outlier: 4.881A pdb=" N THR T 736 " --> pdb=" O ALA T 732 " (cutoff:3.500A) Processing helix chain 'T' and resid 737 through 749 removed outlier: 3.811A pdb=" N SER T 749 " --> pdb=" O MET T 745 " (cutoff:3.500A) Processing helix chain 'U' and resid 19 through 30 Processing helix chain 'U' and resid 42 through 58 removed outlier: 4.049A pdb=" N ILE U 46 " --> pdb=" O ASP U 42 " (cutoff:3.500A) removed outlier: 4.060A pdb=" N VAL U 55 " --> pdb=" O GLU U 51 " (cutoff:3.500A) removed outlier: 4.572A pdb=" N LYS U 56 " --> pdb=" O LYS U 52 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N SER U 57 " --> pdb=" O GLU U 53 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ARG U 58 " --> pdb=" O ILE U 54 " (cutoff:3.500A) Processing helix chain 'U' and resid 60 through 71 Processing helix chain 'U' and resid 76 through 81 removed outlier: 3.638A pdb=" N ASN U 80 " --> pdb=" O TYR U 76 " (cutoff:3.500A) Processing helix chain 'U' and resid 87 through 105 Processing helix chain 'U' and resid 109 through 116 Proline residue: U 116 - end of helix Processing helix chain 'U' and resid 118 through 132 Processing helix chain 'U' and resid 139 through 157 removed outlier: 3.738A pdb=" N LEU U 157 " --> pdb=" O CYS U 153 " (cutoff:3.500A) Processing helix chain 'U' and resid 160 through 170 removed outlier: 3.939A pdb=" N GLN U 165 " --> pdb=" O LEU U 161 " (cutoff:3.500A) removed outlier: 5.343A pdb=" N GLN U 168 " --> pdb=" O SER U 164 " (cutoff:3.500A) removed outlier: 4.657A pdb=" N LEU U 169 " --> pdb=" O GLN U 165 " (cutoff:3.500A) Processing helix chain 'U' and resid 171 through 179 removed outlier: 4.486A pdb=" N TRP U 175 " --> pdb=" O SER U 171 " (cutoff:3.500A) removed outlier: 4.828A pdb=" N MET U 176 " --> pdb=" O LEU U 172 " (cutoff:3.500A) removed outlier: 4.996A pdb=" N GLY U 177 " --> pdb=" O PRO U 173 " (cutoff:3.500A) removed outlier: 4.511A pdb=" N LEU U 178 " --> pdb=" O MET U 174 " (cutoff:3.500A) removed outlier: 5.674A pdb=" N GLN U 179 " --> pdb=" O TRP U 175 " (cutoff:3.500A) No H-bonds generated for 'chain 'U' and resid 171 through 179' Processing helix chain 'U' and resid 180 through 191 Proline residue: U 191 - end of helix Processing helix chain 'U' and resid 192 through 208 removed outlier: 4.357A pdb=" N PHE U 196 " --> pdb=" O LYS U 192 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N GLU U 205 " --> pdb=" O LYS U 201 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N LYS U 206 " --> pdb=" O LYS U 202 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N MET U 207 " --> pdb=" O ASN U 203 " (cutoff:3.500A) removed outlier: 5.752A pdb=" N ASP U 208 " --> pdb=" O ASP U 204 " (cutoff:3.500A) Processing helix chain 'U' and resid 209 through 236 removed outlier: 4.869A pdb=" N LEU U 222 " --> pdb=" O GLU U 218 " (cutoff:3.500A) removed outlier: 5.508A pdb=" N SER U 223 " --> pdb=" O ARG U 219 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N VAL U 236 " --> pdb=" O VAL U 232 " (cutoff:3.500A) Processing helix chain 'U' and resid 243 through 264 removed outlier: 3.684A pdb=" N VAL U 247 " --> pdb=" O THR U 243 " (cutoff:3.500A) removed outlier: 5.391A pdb=" N LEU U 264 " --> pdb=" O LEU U 260 " (cutoff:3.500A) Processing helix chain 'U' and resid 265 through 278 removed outlier: 5.205A pdb=" N TRP U 269 " --> pdb=" O PRO U 265 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N PHE U 270 " --> pdb=" O THR U 266 " (cutoff:3.500A) removed outlier: 5.449A pdb=" N THR U 272 " --> pdb=" O ARG U 268 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N ILE U 273 " --> pdb=" O TRP U 269 " (cutoff:3.500A) Processing helix chain 'U' and resid 279 through 286 Processing helix chain 'U' and resid 287 through 292 removed outlier: 5.409A pdb=" N GLU U 292 " --> pdb=" O LEU U 288 " (cutoff:3.500A) Processing helix chain 'U' and resid 295 through 311 Processing helix chain 'U' and resid 322 through 344 Processing helix chain 'U' and resid 345 through 354 removed outlier: 3.624A pdb=" N TYR U 349 " --> pdb=" O PHE U 345 " (cutoff:3.500A) removed outlier: 5.274A pdb=" N ASP U 350 " --> pdb=" O PRO U 346 " (cutoff:3.500A) removed outlier: 5.817A pdb=" N PHE U 351 " --> pdb=" O GLU U 347 " (cutoff:3.500A) Processing helix chain 'U' and resid 355 through 360 removed outlier: 3.590A pdb=" N VAL U 359 " --> pdb=" O ASN U 355 " (cutoff:3.500A) Processing helix chain 'U' and resid 361 through 370 Processing helix chain 'U' and resid 373 through 385 Processing helix chain 'U' and resid 399 through 412 Processing helix chain 'U' and resid 416 through 424 removed outlier: 3.792A pdb=" N MET U 424 " --> pdb=" O GLN U 420 " (cutoff:3.500A) Processing helix chain 'U' and resid 429 through 435 removed outlier: 4.454A pdb=" N TRP U 434 " --> pdb=" O GLU U 430 " (cutoff:3.500A) removed outlier: 4.946A pdb=" N ASP U 435 " --> pdb=" O LYS U 431 " (cutoff:3.500A) Processing helix chain 'U' and resid 461 through 493 removed outlier: 3.513A pdb=" N TYR U 479 " --> pdb=" O LEU U 475 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N GLU U 480 " --> pdb=" O GLU U 476 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N LYS U 493 " --> pdb=" O VAL U 489 " (cutoff:3.500A) Processing helix chain 'U' and resid 546 through 556 removed outlier: 3.658A pdb=" N LEU U 556 " --> pdb=" O GLU U 552 " (cutoff:3.500A) Processing helix chain 'U' and resid 582 through 588 Processing helix chain 'U' and resid 630 through 644 Processing helix chain 'U' and resid 648 through 653 removed outlier: 4.256A pdb=" N THR U 652 " --> pdb=" O ASP U 648 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N PHE U 653 " --> pdb=" O VAL U 649 " (cutoff:3.500A) No H-bonds generated for 'chain 'U' and resid 648 through 653' Processing helix chain 'U' and resid 660 through 680 removed outlier: 4.308A pdb=" N ASN U 665 " --> pdb=" O PRO U 661 " (cutoff:3.500A) removed outlier: 7.502A pdb=" N PHE U 666 " --> pdb=" O LYS U 662 " (cutoff:3.500A) removed outlier: 7.797A pdb=" N LYS U 667 " --> pdb=" O GLU U 663 " (cutoff:3.500A) removed outlier: 5.888A pdb=" N ALA U 668 " --> pdb=" O ASN U 664 " (cutoff:3.500A) removed outlier: 4.882A pdb=" N ASP U 680 " --> pdb=" O LEU U 676 " (cutoff:3.500A) Processing helix chain 'U' and resid 684 through 693 removed outlier: 4.792A pdb=" N ASP U 689 " --> pdb=" O ASP U 685 " (cutoff:3.500A) removed outlier: 5.391A pdb=" N ILE U 690 " --> pdb=" O TRP U 686 " (cutoff:3.500A) Processing helix chain 'U' and resid 701 through 706 Proline residue: U 706 - end of helix Processing helix chain 'U' and resid 720 through 729 removed outlier: 3.550A pdb=" N PHE U 728 " --> pdb=" O LEU U 724 " (cutoff:3.500A) Proline residue: U 729 - end of helix Processing helix chain 'U' and resid 803 through 816 Proline residue: U 816 - end of helix Processing helix chain 'U' and resid 828 through 844 Processing helix chain 'U' and resid 855 through 870 removed outlier: 3.578A pdb=" N LEU U 859 " --> pdb=" O SER U 855 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N ALA U 868 " --> pdb=" O GLU U 864 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N LEU U 869 " --> pdb=" O LYS U 865 " (cutoff:3.500A) removed outlier: 4.994A pdb=" N ASP U 870 " --> pdb=" O ILE U 866 " (cutoff:3.500A) Processing helix chain 'U' and resid 872 through 877 removed outlier: 3.982A pdb=" N LEU U 876 " --> pdb=" O ASP U 872 " (cutoff:3.500A) removed outlier: 5.698A pdb=" N LEU U 877 " --> pdb=" O GLU U 873 " (cutoff:3.500A) No H-bonds generated for 'chain 'U' and resid 872 through 877' Processing helix chain 'U' and resid 893 through 920 Processing helix chain 'U' and resid 928 through 952 removed outlier: 4.173A pdb=" N MET U 941 " --> pdb=" O LEU U 937 " (cutoff:3.500A) removed outlier: 4.764A pdb=" N SER U 942 " --> pdb=" O TYR U 938 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N ARG U 943 " --> pdb=" O GLN U 939 " (cutoff:3.500A) Processing helix chain 'U' and resid 960 through 968 removed outlier: 3.873A pdb=" N SER U 965 " --> pdb=" O VAL U 961 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N PHE U 968 " --> pdb=" O VAL U 964 " (cutoff:3.500A) Processing helix chain 'U' and resid 970 through 975 Processing helix chain 'U' and resid 986 through 1018 removed outlier: 4.837A pdb=" N ALA U1013 " --> pdb=" O GLU U1009 " (cutoff:3.500A) removed outlier: 5.332A pdb=" N SER U1014 " --> pdb=" O GLU U1010 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N GLU U1015 " --> pdb=" O PHE U1011 " (cutoff:3.500A) removed outlier: 4.818A pdb=" N ARG U1018 " --> pdb=" O SER U1014 " (cutoff:3.500A) Processing helix chain 'U' and resid 1019 through 1030 Processing helix chain 'U' and resid 1038 through 1046 Processing helix chain 'U' and resid 1047 through 1053 Processing helix chain 'U' and resid 1063 through 1068 removed outlier: 3.619A pdb=" N ILE U1067 " --> pdb=" O GLU U1063 " (cutoff:3.500A) removed outlier: 5.692A pdb=" N LEU U1068 " --> pdb=" O ALA U1064 " (cutoff:3.500A) No H-bonds generated for 'chain 'U' and resid 1063 through 1068' Processing helix chain 'U' and resid 1069 through 1078 Proline residue: U1075 - end of helix removed outlier: 3.914A pdb=" N LEU U1078 " --> pdb=" O ILE U1074 " (cutoff:3.500A) Processing helix chain 'U' and resid 1106 through 1113 removed outlier: 4.219A pdb=" N GLN U1110 " --> pdb=" O ASN U1106 " (cutoff:3.500A) Processing helix chain 'U' and resid 1118 through 1127 Processing helix chain 'U' and resid 1140 through 1148 removed outlier: 4.199A pdb=" N LEU U1146 " --> pdb=" O SER U1142 " (cutoff:3.500A) removed outlier: 4.249A pdb=" N TYR U1147 " --> pdb=" O LEU U1143 " (cutoff:3.500A) Processing helix chain 'U' and resid 1157 through 1163 Processing helix chain 'U' and resid 1200 through 1218 Processing helix chain 'U' and resid 1220 through 1225 removed outlier: 3.765A pdb=" N ILE U1224 " --> pdb=" O PRO U1220 " (cutoff:3.500A) removed outlier: 5.275A pdb=" N SER U1225 " --> pdb=" O ALA U1221 " (cutoff:3.500A) No H-bonds generated for 'chain 'U' and resid 1220 through 1225' Processing helix chain 'U' and resid 1230 through 1245 Processing helix chain 'U' and resid 1259 through 1264 removed outlier: 3.745A pdb=" N GLN U1264 " --> pdb=" O VAL U1260 " (cutoff:3.500A) Processing helix chain 'U' and resid 1286 through 1296 removed outlier: 3.683A pdb=" N ARG U1296 " --> pdb=" O VAL U1292 " (cutoff:3.500A) Processing helix chain 'U' and resid 1306 through 1314 removed outlier: 3.754A pdb=" N PHE U1310 " --> pdb=" O ARG U1306 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N CYS U1313 " --> pdb=" O LEU U1309 " (cutoff:3.500A) removed outlier: 5.630A pdb=" N PHE U1314 " --> pdb=" O PHE U1310 " (cutoff:3.500A) Processing helix chain 'U' and resid 1316 through 1327 removed outlier: 4.235A pdb=" N GLN U1322 " --> pdb=" O PRO U1318 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N ALA U1325 " --> pdb=" O SER U1321 " (cutoff:3.500A) removed outlier: 4.241A pdb=" N ARG U1326 " --> pdb=" O GLN U1322 " (cutoff:3.500A) Proline residue: U1327 - end of helix Processing helix chain 'U' and resid 1357 through 1376 removed outlier: 3.618A pdb=" N GLN U1374 " --> pdb=" O MET U1370 " (cutoff:3.500A) Processing helix chain 'V' and resid 395 through 409 removed outlier: 4.514A pdb=" N LYS V 399 " --> pdb=" O SER V 395 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N TRP V 400 " --> pdb=" O ASP V 396 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N ASN V 409 " --> pdb=" O MET V 405 " (cutoff:3.500A) Processing helix chain 'V' and resid 534 through 544 Processing helix chain 'V' and resid 552 through 566 removed outlier: 4.117A pdb=" N LEU V 565 " --> pdb=" O GLN V 561 " (cutoff:3.500A) Proline residue: V 566 - end of helix Processing helix chain 'V' and resid 570 through 581 Processing helix chain 'V' and resid 595 through 606 removed outlier: 3.899A pdb=" N THR V 599 " --> pdb=" O THR V 595 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N GLN V 600 " --> pdb=" O THR V 596 " (cutoff:3.500A) Processing helix chain 'V' and resid 619 through 635 Processing helix chain 'V' and resid 662 through 674 removed outlier: 5.372A pdb=" N LEU V 667 " --> pdb=" O ASP V 663 " (cutoff:3.500A) Proline residue: V 674 - end of helix Processing helix chain 'V' and resid 691 through 708 Processing helix chain 'V' and resid 722 through 730 Processing helix chain 'V' and resid 755 through 770 Processing helix chain 'V' and resid 782 through 802 Proline residue: V 802 - end of helix Processing helix chain 'V' and resid 817 through 826 removed outlier: 3.625A pdb=" N ILE V 824 " --> pdb=" O MET V 820 " (cutoff:3.500A) removed outlier: 4.421A pdb=" N PHE V 825 " --> pdb=" O GLN V 821 " (cutoff:3.500A) removed outlier: 4.108A pdb=" N ASP V 826 " --> pdb=" O THR V 822 " (cutoff:3.500A) Processing helix chain 'V' and resid 839 through 845 removed outlier: 4.700A pdb=" N GLU V 843 " --> pdb=" O THR V 839 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N THR V 844 " --> pdb=" O ASN V 840 " (cutoff:3.500A) removed outlier: 4.187A pdb=" N SER V 845 " --> pdb=" O ILE V 841 " (cutoff:3.500A) No H-bonds generated for 'chain 'V' and resid 839 through 845' Processing helix chain 'V' and resid 880 through 893 removed outlier: 3.992A pdb=" N ALA V 891 " --> pdb=" O ARG V 887 " (cutoff:3.500A) removed outlier: 4.220A pdb=" N GLY V 892 " --> pdb=" O ALA V 888 " (cutoff:3.500A) removed outlier: 4.147A pdb=" N ARG V 893 " --> pdb=" O GLY V 889 " (cutoff:3.500A) Processing helix chain 'V' and resid 904 through 910 Processing helix chain 'V' and resid 918 through 923 removed outlier: 3.959A pdb=" N ARG V 922 " --> pdb=" O PRO V 918 " (cutoff:3.500A) Processing helix chain 'V' and resid 925 through 936 Processing helix chain 'V' and resid 950 through 965 removed outlier: 4.467A pdb=" N GLY V 965 " --> pdb=" O LEU V 961 " (cutoff:3.500A) Processing helix chain 'V' and resid 974 through 984 removed outlier: 3.913A pdb=" N PHE V 983 " --> pdb=" O ARG V 979 " (cutoff:3.500A) Proline residue: V 984 - end of helix Processing helix chain 'V' and resid 986 through 1000 removed outlier: 4.327A pdb=" N VAL V 997 " --> pdb=" O LEU V 993 " (cutoff:3.500A) removed outlier: 6.426A pdb=" N HIS V 998 " --> pdb=" O ILE V 994 " (cutoff:3.500A) Processing helix chain 'V' and resid 1001 through 1015 removed outlier: 3.664A pdb=" N VAL V1014 " --> pdb=" O SER V1010 " (cutoff:3.500A) removed outlier: 5.001A pdb=" N GLN V1015 " --> pdb=" O MET V1011 " (cutoff:3.500A) Processing helix chain 'V' and resid 1024 through 1036 removed outlier: 5.508A pdb=" N GLN V1030 " --> pdb=" O ALA V1026 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N PHE V1035 " --> pdb=" O LYS V1031 " (cutoff:3.500A) Processing helix chain 'V' and resid 1040 through 1054 Processing helix chain 'V' and resid 1058 through 1066 Processing helix chain 'V' and resid 1068 through 1090 removed outlier: 3.555A pdb=" N LYS V1090 " --> pdb=" O MET V1086 " (cutoff:3.500A) Processing helix chain 'V' and resid 1099 through 1112 Processing helix chain 'V' and resid 1169 through 1177 Processing helix chain 'V' and resid 1182 through 1187 Proline residue: V1186 - end of helix No H-bonds generated for 'chain 'V' and resid 1182 through 1187' Processing helix chain 'W' and resid 5 through 12 removed outlier: 3.800A pdb=" N ILE W 9 " --> pdb=" O THR W 5 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N ALA W 12 " --> pdb=" O LEU W 8 " (cutoff:3.500A) Processing helix chain 'W' and resid 82 through 88 removed outlier: 4.428A pdb=" N ALA W 86 " --> pdb=" O GLY W 82 " (cutoff:3.500A) Proline residue: W 88 - end of helix Processing helix chain 'W' and resid 102 through 108 removed outlier: 4.047A pdb=" N LEU W 106 " --> pdb=" O GLU W 102 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N ASP W 107 " --> pdb=" O LEU W 103 " (cutoff:3.500A) Proline residue: W 108 - end of helix No H-bonds generated for 'chain 'W' and resid 102 through 108' Processing helix chain 'W' and resid 123 through 128 removed outlier: 3.956A pdb=" N ASN W 127 " --> pdb=" O ASN W 123 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N LYS W 128 " --> pdb=" O PRO W 124 " (cutoff:3.500A) No H-bonds generated for 'chain 'W' and resid 123 through 128' Processing helix chain 'W' and resid 130 through 139 removed outlier: 3.588A pdb=" N TYR W 134 " --> pdb=" O HIS W 130 " (cutoff:3.500A) Processing helix chain 'W' and resid 151 through 162 removed outlier: 3.724A pdb=" N MET W 161 " --> pdb=" O GLU W 157 " (cutoff:3.500A) removed outlier: 5.789A pdb=" N PHE W 162 " --> pdb=" O ALA W 158 " (cutoff:3.500A) Processing helix chain 'W' and resid 36 through 41 removed outlier: 4.313A pdb=" N ALA W 39 " --> pdb=" O ASN W 36 " (cutoff:3.500A) Processing helix chain 'Y' and resid 19 through 32 Processing helix chain 'Y' and resid 58 through 69 removed outlier: 3.890A pdb=" N SER Y 62 " --> pdb=" O GLU Y 58 " (cutoff:3.500A) Processing helix chain 'Y' and resid 88 through 94 removed outlier: 3.728A pdb=" N SER Y 92 " --> pdb=" O SER Y 88 " (cutoff:3.500A) Processing helix chain 'Z' and resid 340 through 351 Processing helix chain 'b' and resid 6 through 13 removed outlier: 4.354A pdb=" N LEU b 10 " --> pdb=" O SER b 6 " (cutoff:3.500A) removed outlier: 4.432A pdb=" N GLN b 11 " --> pdb=" O SER b 7 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N HIS b 12 " --> pdb=" O LYS b 8 " (cutoff:3.500A) Processing helix chain 'b' and resid 73 through 78 removed outlier: 3.790A pdb=" N LEU b 77 " --> pdb=" O ARG b 73 " (cutoff:3.500A) removed outlier: 5.532A pdb=" N VAL b 78 " --> pdb=" O GLY b 74 " (cutoff:3.500A) No H-bonds generated for 'chain 'b' and resid 73 through 78' Processing helix chain 'c' and resid 31 through 46 Processing helix chain 'c' and resid 64 through 69 Processing helix chain 'c' and resid 88 through 93 removed outlier: 5.652A pdb=" N LYS c 93 " --> pdb=" O PRO c 89 " (cutoff:3.500A) Processing helix chain 'c' and resid 162 through 168 removed outlier: 3.579A pdb=" N ASP c 168 " --> pdb=" O ASP c 164 " (cutoff:3.500A) Processing helix chain 'c' and resid 174 through 200 removed outlier: 4.432A pdb=" N HIS c 178 " --> pdb=" O ASN c 174 " (cutoff:3.500A) removed outlier: 4.676A pdb=" N MET c 179 " --> pdb=" O PRO c 175 " (cutoff:3.500A) removed outlier: 4.543A pdb=" N LYS c 180 " --> pdb=" O GLU c 176 " (cutoff:3.500A) removed outlier: 4.245A pdb=" N ILE c 181 " --> pdb=" O GLU c 177 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N GLU c 184 " --> pdb=" O LYS c 180 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N LYS c 187 " --> pdb=" O GLU c 183 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N LEU c 190 " --> pdb=" O ALA c 186 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N THR c 194 " --> pdb=" O LEU c 190 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N LEU c 195 " --> pdb=" O ALA c 191 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N LYS c 196 " --> pdb=" O LYS c 192 " (cutoff:3.500A) Processing helix chain 'c' and resid 272 through 278 removed outlier: 3.553A pdb=" N ARG c 276 " --> pdb=" O ALA c 272 " (cutoff:3.500A) removed outlier: 4.662A pdb=" N ASN c 277 " --> pdb=" O LYS c 273 " (cutoff:3.500A) removed outlier: 4.600A pdb=" N LEU c 278 " --> pdb=" O TYR c 274 " (cutoff:3.500A) No H-bonds generated for 'chain 'c' and resid 272 through 278' Processing helix chain 'c' and resid 311 through 319 removed outlier: 4.010A pdb=" N VAL c 315 " --> pdb=" O GLY c 311 " (cutoff:3.500A) removed outlier: 4.418A pdb=" N TYR c 317 " --> pdb=" O ASN c 313 " (cutoff:3.500A) removed outlier: 4.749A pdb=" N THR c 318 " --> pdb=" O PHE c 314 " (cutoff:3.500A) removed outlier: 5.280A pdb=" N GLY c 319 " --> pdb=" O VAL c 315 " (cutoff:3.500A) Processing helix chain 'c' and resid 320 through 338 removed outlier: 3.517A pdb=" N THR c 327 " --> pdb=" O SER c 323 " (cutoff:3.500A) Processing helix chain 'c' and resid 346 through 363 removed outlier: 3.613A pdb=" N VAL c 359 " --> pdb=" O LYS c 355 " (cutoff:3.500A) removed outlier: 4.367A pdb=" N ASP c 363 " --> pdb=" O VAL c 359 " (cutoff:3.500A) Processing helix chain 'd' and resid 4 through 14 removed outlier: 3.702A pdb=" N GLU d 14 " --> pdb=" O LEU d 10 " (cutoff:3.500A) Processing helix chain 'd' and resid 74 through 81 removed outlier: 4.683A pdb=" N LYS d 78 " --> pdb=" O PRO d 74 " (cutoff:3.500A) removed outlier: 5.020A pdb=" N ASN d 79 " --> pdb=" O ASP d 75 " (cutoff:3.500A) removed outlier: 4.482A pdb=" N ALA d 80 " --> pdb=" O MET d 76 " (cutoff:3.500A) Proline residue: d 81 - end of helix No H-bonds generated for 'chain 'd' and resid 74 through 81' Processing helix chain 'e' and resid 16 through 28 removed outlier: 3.657A pdb=" N ASN e 27 " --> pdb=" O ARG e 23 " (cutoff:3.500A) Processing helix chain 'f' and resid 6 through 15 removed outlier: 3.536A pdb=" N GLY f 13 " --> pdb=" O PRO f 9 " (cutoff:3.500A) Processing helix chain 'q' and resid 6 through 15 Processing helix chain 'h' and resid 2 through 10 removed outlier: 4.091A pdb=" N PHE h 6 " --> pdb=" O LYS h 2 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N LEU h 7 " --> pdb=" O LEU h 3 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N LYS h 9 " --> pdb=" O ARG h 5 " (cutoff:3.500A) removed outlier: 4.839A pdb=" N LEU h 10 " --> pdb=" O PHE h 6 " (cutoff:3.500A) Processing helix chain 'h' and resid 75 through 80 removed outlier: 3.791A pdb=" N LEU h 79 " --> pdb=" O PRO h 75 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N LEU h 80 " --> pdb=" O LEU h 76 " (cutoff:3.500A) No H-bonds generated for 'chain 'h' and resid 75 through 80' Processing helix chain 'l' and resid 2 through 10 removed outlier: 4.174A pdb=" N PHE l 6 " --> pdb=" O LYS l 2 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N LYS l 9 " --> pdb=" O ARG l 5 " (cutoff:3.500A) removed outlier: 4.513A pdb=" N LEU l 10 " --> pdb=" O PHE l 6 " (cutoff:3.500A) Processing helix chain 'l' and resid 75 through 80 Processing helix chain 'i' and resid 32 through 46 removed outlier: 3.601A pdb=" N LYS i 37 " --> pdb=" O PRO i 33 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N ASN i 38 " --> pdb=" O LYS i 34 " (cutoff:3.500A) Processing helix chain 'i' and resid 119 through 126 removed outlier: 4.145A pdb=" N ASP i 123 " --> pdb=" O THR i 119 " (cutoff:3.500A) removed outlier: 4.974A pdb=" N GLY i 124 " --> pdb=" O GLN i 120 " (cutoff:3.500A) removed outlier: 4.875A pdb=" N LYS i 125 " --> pdb=" O TRP i 121 " (cutoff:3.500A) Processing helix chain 'i' and resid 135 through 145 removed outlier: 3.944A pdb=" N VAL i 145 " --> pdb=" O ARG i 141 " (cutoff:3.500A) Processing helix chain 'j' and resid 13 through 27 removed outlier: 3.506A pdb=" N GLN j 17 " --> pdb=" O PRO j 13 " (cutoff:3.500A) removed outlier: 4.549A pdb=" N LYS j 18 " --> pdb=" O GLU j 14 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N GLU j 21 " --> pdb=" O GLN j 17 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N THR j 26 " --> pdb=" O GLU j 22 " (cutoff:3.500A) Processing helix chain 'j' and resid 29 through 39 removed outlier: 3.842A pdb=" N VAL j 36 " --> pdb=" O LEU j 32 " (cutoff:3.500A) Processing helix chain 'j' and resid 102 through 107 removed outlier: 4.238A pdb=" N VAL j 106 " --> pdb=" O ARG j 102 " (cutoff:3.500A) removed outlier: 5.663A pdb=" N ILE j 107 " --> pdb=" O GLY j 103 " (cutoff:3.500A) No H-bonds generated for 'chain 'j' and resid 102 through 107' Processing helix chain 'm' and resid 13 through 27 Processing helix chain 'm' and resid 29 through 39 removed outlier: 3.535A pdb=" N ASN m 39 " --> pdb=" O SER m 35 " (cutoff:3.500A) Processing helix chain 'm' and resid 102 through 107 removed outlier: 4.210A pdb=" N VAL m 106 " --> pdb=" O ARG m 102 " (cutoff:3.500A) removed outlier: 5.847A pdb=" N ILE m 107 " --> pdb=" O GLY m 103 " (cutoff:3.500A) No H-bonds generated for 'chain 'm' and resid 102 through 107' Processing helix chain 'k' and resid 7 through 13 removed outlier: 4.217A pdb=" N GLN k 11 " --> pdb=" O SER k 7 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N HIS k 12 " --> pdb=" O LYS k 8 " (cutoff:3.500A) Processing helix chain 'k' and resid 73 through 78 removed outlier: 3.912A pdb=" N LEU k 77 " --> pdb=" O ARG k 73 " (cutoff:3.500A) removed outlier: 5.707A pdb=" N VAL k 78 " --> pdb=" O GLY k 74 " (cutoff:3.500A) No H-bonds generated for 'chain 'k' and resid 73 through 78' Processing helix chain 'n' and resid 4 through 14 Processing helix chain 'n' and resid 64 through 69 removed outlier: 3.632A pdb=" N ILE n 68 " --> pdb=" O ARG n 64 " (cutoff:3.500A) removed outlier: 5.867A pdb=" N ARG n 69 " --> pdb=" O GLY n 65 " (cutoff:3.500A) No H-bonds generated for 'chain 'n' and resid 64 through 69' Processing helix chain 'n' and resid 74 through 79 removed outlier: 4.602A pdb=" N LYS n 78 " --> pdb=" O PRO n 74 " (cutoff:3.500A) removed outlier: 5.016A pdb=" N ASN n 79 " --> pdb=" O ASP n 75 " (cutoff:3.500A) No H-bonds generated for 'chain 'n' and resid 74 through 79' Processing helix chain 'o' and resid 84 through 89 removed outlier: 3.569A pdb=" N MET o 88 " --> pdb=" O THR o 84 " (cutoff:3.500A) Processing helix chain 'o' and resid 101 through 107 removed outlier: 3.939A pdb=" N ALA o 106 " --> pdb=" O GLN o 102 " (cutoff:3.500A) Proline residue: o 107 - end of helix Processing helix chain 'o' and resid 121 through 135 Processing helix chain 'o' and resid 155 through 163 Processing helix chain 'o' and resid 209 through 228 removed outlier: 3.909A pdb=" N GLY o 227 " --> pdb=" O ARG o 223 " (cutoff:3.500A) removed outlier: 5.585A pdb=" N LYS o 228 " --> pdb=" O GLN o 224 " (cutoff:3.500A) Processing helix chain 'p' and resid 16 through 28 removed outlier: 3.608A pdb=" N LEU p 20 " --> pdb=" O GLN p 16 " (cutoff:3.500A) Processing helix chain 's' and resid 28 through 42 removed outlier: 3.594A pdb=" N LEU s 35 " --> pdb=" O ALA s 31 " (cutoff:3.500A) removed outlier: 4.335A pdb=" N GLU s 39 " --> pdb=" O LEU s 35 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N THR s 40 " --> pdb=" O VAL s 36 " (cutoff:3.500A) removed outlier: 4.293A pdb=" N ARG s 41 " --> pdb=" O GLU s 37 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N ARG s 42 " --> pdb=" O GLU s 38 " (cutoff:3.500A) Processing helix chain 's' and resid 65 through 78 removed outlier: 4.136A pdb=" N GLU s 69 " --> pdb=" O ILE s 65 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N ARG s 76 " --> pdb=" O ARG s 72 " (cutoff:3.500A) Proline residue: s 78 - end of helix Processing helix chain 's' and resid 84 through 90 removed outlier: 4.328A pdb=" N GLU s 88 " --> pdb=" O MET s 84 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N LEU s 89 " --> pdb=" O LYS s 85 " (cutoff:3.500A) Proline residue: s 90 - end of helix No H-bonds generated for 'chain 's' and resid 84 through 90' Processing helix chain 's' and resid 101 through 131 removed outlier: 4.197A pdb=" N GLU s 105 " --> pdb=" O THR s 101 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N SER s 110 " --> pdb=" O CYS s 106 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N ALA s 112 " --> pdb=" O ASN s 108 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N GLN s 117 " --> pdb=" O GLN s 113 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N GLN s 129 " --> pdb=" O GLU s 125 " (cutoff:3.500A) Processing helix chain 's' and resid 132 through 176 removed outlier: 3.606A pdb=" N LEU s 142 " --> pdb=" O TYR s 138 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N HIS s 148 " --> pdb=" O HIS s 144 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N LEU s 156 " --> pdb=" O GLU s 152 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N HIS s 159 " --> pdb=" O LYS s 155 " (cutoff:3.500A) Processing helix chain 's' and resid 178 through 213 removed outlier: 3.798A pdb=" N TYR s 207 " --> pdb=" O GLU s 203 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N ILE s 209 " --> pdb=" O GLU s 205 " (cutoff:3.500A) Processing helix chain 't' and resid 26 through 37 Processing helix chain 't' and resid 48 through 53 removed outlier: 3.810A pdb=" N LEU t 52 " --> pdb=" O SER t 48 " (cutoff:3.500A) removed outlier: 5.402A pdb=" N ILE t 53 " --> pdb=" O GLU t 49 " (cutoff:3.500A) No H-bonds generated for 'chain 't' and resid 48 through 53' Processing helix chain 't' and resid 70 through 138 removed outlier: 4.139A pdb=" N ARG t 115 " --> pdb=" O ASP t 111 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N LYS t 122 " --> pdb=" O ALA t 118 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N GLU t 123 " --> pdb=" O ARG t 119 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N LEU t 134 " --> pdb=" O ALA t 130 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N LYS t 135 " --> pdb=" O LEU t 131 " (cutoff:3.500A) Proline residue: t 136 - end of helix Processing helix chain 'v' and resid 26 through 37 Processing helix chain 'v' and resid 48 through 53 removed outlier: 5.483A pdb=" N ILE v 53 " --> pdb=" O GLU v 49 " (cutoff:3.500A) Processing helix chain 'v' and resid 71 through 122 removed outlier: 3.520A pdb=" N GLN v 79 " --> pdb=" O LEU v 75 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N LEU v 92 " --> pdb=" O HIS v 88 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N GLN v 97 " --> pdb=" O ARG v 93 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N SER v 104 " --> pdb=" O ARG v 100 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N TYR v 108 " --> pdb=" O SER v 104 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N GLN v 109 " --> pdb=" O HIS v 105 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N LYS v 122 " --> pdb=" O ALA v 118 " (cutoff:3.500A) Processing helix chain 'v' and resid 124 through 136 removed outlier: 3.613A pdb=" N LEU v 134 " --> pdb=" O ALA v 130 " (cutoff:3.500A) removed outlier: 4.780A pdb=" N LYS v 135 " --> pdb=" O LEU v 131 " (cutoff:3.500A) Proline residue: v 136 - end of helix Processing helix chain 'u' and resid 26 through 37 removed outlier: 3.525A pdb=" N LYS u 32 " --> pdb=" O ARG u 28 " (cutoff:3.500A) Processing helix chain 'u' and resid 48 through 53 removed outlier: 3.567A pdb=" N LEU u 52 " --> pdb=" O SER u 48 " (cutoff:3.500A) removed outlier: 5.358A pdb=" N ILE u 53 " --> pdb=" O GLU u 49 " (cutoff:3.500A) No H-bonds generated for 'chain 'u' and resid 48 through 53' Processing helix chain 'u' and resid 70 through 131 removed outlier: 3.577A pdb=" N ALA u 77 " --> pdb=" O ALA u 73 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N ASP u 80 " --> pdb=" O LYS u 76 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N ASP u 83 " --> pdb=" O GLN u 79 " (cutoff:3.500A) removed outlier: 4.339A pdb=" N VAL u 85 " --> pdb=" O GLU u 81 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N MET u 86 " --> pdb=" O TRP u 82 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N LEU u 92 " --> pdb=" O HIS u 88 " (cutoff:3.500A) removed outlier: 4.250A pdb=" N THR u 99 " --> pdb=" O GLN u 95 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N LEU u 103 " --> pdb=" O THR u 99 " (cutoff:3.500A) removed outlier: 4.142A pdb=" N LYS u 122 " --> pdb=" O ALA u 118 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N GLU u 123 " --> pdb=" O ARG u 119 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N LEU u 131 " --> pdb=" O ALA u 127 " (cutoff:3.500A) Processing helix chain 'w' and resid 26 through 37 removed outlier: 3.732A pdb=" N ILE w 30 " --> pdb=" O GLU w 26 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N GLU w 31 " --> pdb=" O ARG w 27 " (cutoff:3.500A) Processing helix chain 'w' and resid 48 through 53 removed outlier: 3.735A pdb=" N LEU w 52 " --> pdb=" O SER w 48 " (cutoff:3.500A) removed outlier: 5.463A pdb=" N ILE w 53 " --> pdb=" O GLU w 49 " (cutoff:3.500A) No H-bonds generated for 'chain 'w' and resid 48 through 53' Processing helix chain 'w' and resid 71 through 121 removed outlier: 3.645A pdb=" N ASP w 80 " --> pdb=" O LYS w 76 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N GLN w 97 " --> pdb=" O ARG w 93 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N GLN w 101 " --> pdb=" O GLN w 97 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N HIS w 105 " --> pdb=" O GLN w 101 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N ALA w 106 " --> pdb=" O GLU w 102 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N LEU w 107 " --> pdb=" O LEU w 103 " (cutoff:3.500A) removed outlier: 4.658A pdb=" N TYR w 108 " --> pdb=" O SER w 104 " (cutoff:3.500A) removed outlier: 4.724A pdb=" N GLN w 109 " --> pdb=" O HIS w 105 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N ASP w 111 " --> pdb=" O LEU w 107 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ARG w 119 " --> pdb=" O ARG w 115 " (cutoff:3.500A) Processing helix chain 'w' and resid 124 through 131 removed outlier: 3.599A pdb=" N LEU w 131 " --> pdb=" O ALA w 127 " (cutoff:3.500A) Processing helix chain 'y' and resid 100 through 108 removed outlier: 4.616A pdb=" N SER y 104 " --> pdb=" O LEU y 100 " (cutoff:3.500A) removed outlier: 4.195A pdb=" N ALA y 105 " --> pdb=" O LEU y 101 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ASP y 107 " --> pdb=" O ILE y 103 " (cutoff:3.500A) removed outlier: 6.063A pdb=" N ALA y 108 " --> pdb=" O SER y 104 " (cutoff:3.500A) Processing helix chain 'y' and resid 126 through 142 removed outlier: 3.647A pdb=" N GLN y 141 " --> pdb=" O ARG y 137 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N ILE y 142 " --> pdb=" O LEU y 138 " (cutoff:3.500A) Processing helix chain 'y' and resid 145 through 157 removed outlier: 3.538A pdb=" N LYS y 155 " --> pdb=" O ARG y 151 " (cutoff:3.500A) Processing helix chain 'y' and resid 175 through 197 removed outlier: 4.298A pdb=" N ARG y 181 " --> pdb=" O GLU y 177 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N LYS y 195 " --> pdb=" O GLU y 191 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N TYR y 196 " --> pdb=" O LYS y 192 " (cutoff:3.500A) removed outlier: 5.263A pdb=" N SER y 197 " --> pdb=" O ARG y 193 " (cutoff:3.500A) Processing helix chain 'y' and resid 212 through 226 Processing helix chain 'y' and resid 227 through 240 removed outlier: 3.767A pdb=" N ALA y 231 " --> pdb=" O GLY y 227 " (cutoff:3.500A) removed outlier: 7.080A pdb=" N GLU y 232 " --> pdb=" O LYS y 228 " (cutoff:3.500A) removed outlier: 5.422A pdb=" N ILE y 233 " --> pdb=" O TYR y 229 " (cutoff:3.500A) Processing helix chain 'z' and resid 108 through 126 removed outlier: 3.570A pdb=" N LYS z 123 " --> pdb=" O ALA z 119 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N GLN z 125 " --> pdb=" O TRP z 121 " (cutoff:3.500A) removed outlier: 4.207A pdb=" N ALA z 126 " --> pdb=" O VAL z 122 " (cutoff:3.500A) Processing sheet with id= 1, first strand: chain '7' and resid 136 through 140 Processing sheet with id= 2, first strand: chain '7' and resid 304 through 307 removed outlier: 5.729A pdb=" N SER 7 347 " --> pdb=" O LYS 7 374 " (cutoff:3.500A) removed outlier: 5.017A pdb=" N ALA 7 257 " --> pdb=" O MET 7 403 " (cutoff:3.500A) Processing sheet with id= 3, first strand: chain '8' and resid 101 through 104 removed outlier: 3.744A pdb=" N ASN 8 101 " --> pdb=" O GLU 8 120 " (cutoff:3.500A) Processing sheet with id= 4, first strand: chain '9' and resid 46 through 54 removed outlier: 3.552A pdb=" N VAL 9 46 " --> pdb=" O SER 9 40 " (cutoff:3.500A) removed outlier: 4.498A pdb=" N SER 9 40 " --> pdb=" O VAL 9 46 " (cutoff:3.500A) removed outlier: 5.191A pdb=" N GLY 9 32 " --> pdb=" O VAL 9 54 " (cutoff:3.500A) Processing sheet with id= 5, first strand: chain 'A' and resid 226 through 230 removed outlier: 6.266A pdb=" N GLN A 226 " --> pdb=" O THR A 418 " (cutoff:3.500A) removed outlier: 5.672A pdb=" N THR A 418 " --> pdb=" O GLN A 226 " (cutoff:3.500A) removed outlier: 5.519A pdb=" N ARG A 414 " --> pdb=" O PHE A 230 " (cutoff:3.500A) Processing sheet with id= 6, first strand: chain 'A' and resid 904 through 911 removed outlier: 4.602A pdb=" N HIS A 904 " --> pdb=" O LEU A 901 " (cutoff:3.500A) removed outlier: 4.403A pdb=" N MET A1022 " --> pdb=" O TYR A1019 " (cutoff:3.500A) Processing sheet with id= 7, first strand: chain 'A' and resid 1086 through 1091 removed outlier: 4.236A pdb=" N ARG A1094 " --> pdb=" O TYR A1091 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N CYS A 973 " --> pdb=" O PHE A1101 " (cutoff:3.500A) Processing sheet with id= 8, first strand: chain 'A' and resid 1184 through 1189 removed outlier: 6.053A pdb=" N GLY A1212 " --> pdb=" O LEU A1230 " (cutoff:3.500A) Processing sheet with id= 9, first strand: chain 'A' and resid 1333 through 1338 removed outlier: 6.199A pdb=" N VAL A1333 " --> pdb=" O GLY A1356 " (cutoff:3.500A) Processing sheet with id= 10, first strand: chain 'A' and resid 1607 through 1612 removed outlier: 3.587A pdb=" N THR A1608 " --> pdb=" O PHE A1632 " (cutoff:3.500A) removed outlier: 6.229A pdb=" N ASP A1628 " --> pdb=" O GLU A1612 " (cutoff:3.500A) removed outlier: 5.285A pdb=" N THR A1699 " --> pdb=" O LYS A1659 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N TRP A1661 " --> pdb=" O THR A1699 " (cutoff:3.500A) removed outlier: 4.926A pdb=" N GLY A1700 " --> pdb=" O ASN A1717 " (cutoff:3.500A) Processing sheet with id= 11, first strand: chain 'A' and resid 1624 through 1627 removed outlier: 5.610A pdb=" N SER A1625 " --> pdb=" O MET A1692 " (cutoff:3.500A) Processing sheet with id= 12, first strand: chain 'A' and resid 1636 through 1640 Processing sheet with id= 13, first strand: chain 'A' and resid 1787 through 1792 removed outlier: 4.524A pdb=" N ARG A1787 " --> pdb=" O ILE A1803 " (cutoff:3.500A) Processing sheet with id= 14, first strand: chain 'A' and resid 1883 through 1887 removed outlier: 3.664A pdb=" N SER A1887 " --> pdb=" O VAL A1863 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N VAL A1780 " --> pdb=" O ILE A1862 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N THR A1864 " --> pdb=" O VAL A1780 " (cutoff:3.500A) removed outlier: 8.387A pdb=" N ASP A1782 " --> pdb=" O THR A1864 " (cutoff:3.500A) removed outlier: 8.734A pdb=" N ILE A1777 " --> pdb=" O PRO A1812 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N GLN A1816 " --> pdb=" O ASN A1811 " (cutoff:3.500A) removed outlier: 7.560A pdb=" N GLY A1815 " --> pdb=" O LEU A1919 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N GLN A1913 " --> pdb=" O ILE A1821 " (cutoff:3.500A) Processing sheet with id= 15, first strand: chain 'A' and resid 2222 through 2229 removed outlier: 3.872A pdb=" N GLY A2176 " --> pdb=" O LEU A2128 " (cutoff:3.500A) removed outlier: 4.619A pdb=" N ILE A2124 " --> pdb=" O THR A2180 " (cutoff:3.500A) removed outlier: 6.771A pdb=" N TYR A2129 " --> pdb=" O ARG A2143 " (cutoff:3.500A) removed outlier: 4.459A pdb=" N GLN A2260 " --> pdb=" O TYR A2102 " (cutoff:3.500A) Processing sheet with id= 16, first strand: chain 'A' and resid 2270 through 2274 Processing sheet with id= 17, first strand: chain 'A' and resid 2126 through 2129 Processing sheet with id= 18, first strand: chain 'B' and resid 434 through 438 removed outlier: 3.981A pdb=" N ALA B 449 " --> pdb=" O LEU B 685 " (cutoff:3.500A) removed outlier: 6.386A pdb=" N LEU B 685 " --> pdb=" O ALA B 449 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N VAL B 826 " --> pdb=" O GLU B 866 " (cutoff:3.500A) Processing sheet with id= 19, first strand: chain 'B' and resid 498 through 503 removed outlier: 3.961A pdb=" N ALA B 567 " --> pdb=" O ILE B 585 " (cutoff:3.500A) Processing sheet with id= 20, first strand: chain 'B' and resid 831 through 835 removed outlier: 7.964A pdb=" N THR B 831 " --> pdb=" O LEU B 844 " (cutoff:3.500A) Processing sheet with id= 21, first strand: chain 'B' and resid 1183 through 1192 removed outlier: 5.509A pdb=" N LYS B1183 " --> pdb=" O ASP B1207 " (cutoff:3.500A) Processing sheet with id= 22, first strand: chain 'B' and resid 1235 through 1242 removed outlier: 7.926A pdb=" N ALA B1220 " --> pdb=" O ASP B1273 " (cutoff:3.500A) Processing sheet with id= 23, first strand: chain 'B' and resid 1345 through 1350 removed outlier: 3.552A pdb=" N ILE B1424 " --> pdb=" O LYS B1404 " (cutoff:3.500A) Processing sheet with id= 24, first strand: chain 'B' and resid 1522 through 1529 removed outlier: 4.327A pdb=" N GLY B1618 " --> pdb=" O VAL B1643 " (cutoff:3.500A) Processing sheet with id= 25, first strand: chain 'B' and resid 1666 through 1671 removed outlier: 7.946A pdb=" N THR B1666 " --> pdb=" O TYR B1679 " (cutoff:3.500A) Processing sheet with id= 26, first strand: chain 'B' and resid 1802 through 1805 Processing sheet with id= 27, first strand: chain 'B' and resid 2017 through 2024 removed outlier: 4.963A pdb=" N VAL B2036 " --> pdb=" O VAL B2024 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ARG B2043 " --> pdb=" O GLN B2086 " (cutoff:3.500A) removed outlier: 5.438A pdb=" N GLN B2086 " --> pdb=" O ARG B2043 " (cutoff:3.500A) Processing sheet with id= 28, first strand: chain 'B' and resid 2078 through 2083 removed outlier: 6.755A pdb=" N GLY B2063 " --> pdb=" O ASP B2111 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N HIS B2102 " --> pdb=" O VAL B2124 " (cutoff:3.500A) Processing sheet with id= 29, first strand: chain 'C' and resid 183 through 189 removed outlier: 5.573A pdb=" N GLY C 136 " --> pdb=" O THR C 205 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N ALA C 252 " --> pdb=" O ASP C 223 " (cutoff:3.500A) removed outlier: 7.168A pdb=" N ASN C 306 " --> pdb=" O VAL C 253 " (cutoff:3.500A) Processing sheet with id= 30, first strand: chain 'C' and resid 347 through 351 Processing sheet with id= 31, first strand: chain 'C' and resid 475 through 479 removed outlier: 7.989A pdb=" N ASP C 521 " --> pdb=" O GLY C 511 " (cutoff:3.500A) Processing sheet with id= 32, first strand: chain 'C' and resid 480 through 484 removed outlier: 6.287A pdb=" N THR C 484 " --> pdb=" O GLN C 489 " (cutoff:3.500A) removed outlier: 5.731A pdb=" N GLN C 489 " --> pdb=" O THR C 484 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N ASN C 548 " --> pdb=" O VAL C 496 " (cutoff:3.500A) Processing sheet with id= 33, first strand: chain 'C' and resid 530 through 533 removed outlier: 3.871A pdb=" N LEU C 530 " --> pdb=" O VAL C 541 " (cutoff:3.500A) Processing sheet with id= 34, first strand: chain 'C' and resid 588 through 592 removed outlier: 3.672A pdb=" N HIS C 627 " --> pdb=" O VAL C 592 " (cutoff:3.500A) removed outlier: 4.542A pdb=" N GLU C 626 " --> pdb=" O GLU C 622 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N GLU C 622 " --> pdb=" O GLU C 626 " (cutoff:3.500A) Processing sheet with id= 35, first strand: chain 'C' and resid 662 through 666 Processing sheet with id= 36, first strand: chain 'C' and resid 673 through 678 removed outlier: 3.507A pdb=" N CYS C 674 " --> pdb=" O MET C 687 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N ILE C 685 " --> pdb=" O ALA C 676 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N THR C 678 " --> pdb=" O ASN C 683 " (cutoff:3.500A) removed outlier: 5.042A pdb=" N ASN C 683 " --> pdb=" O THR C 678 " (cutoff:3.500A) removed outlier: 6.708A pdb=" N THR C 686 " --> pdb=" O LEU C 792 " (cutoff:3.500A) Processing sheet with id= 37, first strand: chain 'C' and resid 683 through 686 removed outlier: 3.676A pdb=" N ASP C 793 " --> pdb=" O THR C 686 " (cutoff:3.500A) Processing sheet with id= 38, first strand: chain 'C' and resid 832 through 838 Processing sheet with id= 39, first strand: chain 'C' and resid 828 through 832 No H-bonds generated for sheet with id= 39 Processing sheet with id= 40, first strand: chain 'F' and resid 644 through 651 removed outlier: 3.998A pdb=" N ARG F 644 " --> pdb=" O PHE F 681 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N ASN F 679 " --> pdb=" O PHE F 646 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N LYS F 677 " --> pdb=" O ARG F 648 " (cutoff:3.500A) removed outlier: 7.619A pdb=" N GLN F 674 " --> pdb=" O PHE F 751 " (cutoff:3.500A) removed outlier: 4.285A pdb=" N GLY F 743 " --> pdb=" O TYR F 682 " (cutoff:3.500A) Processing sheet with id= 41, first strand: chain 'F' and resid 692 through 698 Processing sheet with id= 42, first strand: chain 'J' and resid 193 through 197 removed outlier: 6.788A pdb=" N VAL J 488 " --> pdb=" O TYR J 197 " (cutoff:3.500A) Processing sheet with id= 43, first strand: chain 'J' and resid 208 through 213 removed outlier: 3.667A pdb=" N CYS J 209 " --> pdb=" O GLY J 222 " (cutoff:3.500A) removed outlier: 5.923A pdb=" N TRP J 218 " --> pdb=" O GLU J 213 " (cutoff:3.500A) removed outlier: 4.371A pdb=" N THR J 227 " --> pdb=" O SER J 223 " (cutoff:3.500A) removed outlier: 6.636A pdb=" N ILE J 230 " --> pdb=" O LYS J 239 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N LYS J 237 " --> pdb=" O ASP J 232 " (cutoff:3.500A) Processing sheet with id= 44, first strand: chain 'J' and resid 250 through 255 removed outlier: 4.790A pdb=" N TYR J 260 " --> pdb=" O SER J 255 " (cutoff:3.500A) Processing sheet with id= 45, first strand: chain 'J' and resid 292 through 297 removed outlier: 4.882A pdb=" N VAL J 302 " --> pdb=" O HIS J 297 " (cutoff:3.500A) removed outlier: 4.100A pdb=" N THR J 311 " --> pdb=" O SER J 307 " (cutoff:3.500A) removed outlier: 6.716A pdb=" N ILE J 314 " --> pdb=" O VAL J 323 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N ALA J 321 " --> pdb=" O ASP J 316 " (cutoff:3.500A) Processing sheet with id= 46, first strand: chain 'J' and resid 334 through 339 removed outlier: 4.819A pdb=" N GLN J 344 " --> pdb=" O GLN J 339 " (cutoff:3.500A) removed outlier: 4.297A pdb=" N ILE J 345 " --> pdb=" O TRP J 357 " (cutoff:3.500A) removed outlier: 6.507A pdb=" N LEU J 356 " --> pdb=" O ARG J 365 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N LYS J 363 " --> pdb=" O ASP J 358 " (cutoff:3.500A) Processing sheet with id= 47, first strand: chain 'J' and resid 377 through 381 removed outlier: 3.673A pdb=" N ALA J 377 " --> pdb=" O GLY J 390 " (cutoff:3.500A) removed outlier: 5.409A pdb=" N THR J 386 " --> pdb=" O HIS J 381 " (cutoff:3.500A) Processing sheet with id= 48, first strand: chain 'J' and resid 418 through 421 Processing sheet with id= 49, first strand: chain 'J' and resid 467 through 471 removed outlier: 5.909A pdb=" N ARG J 476 " --> pdb=" O ASP J 471 " (cutoff:3.500A) Processing sheet with id= 50, first strand: chain 'J' and resid 227 through 230 Processing sheet with id= 51, first strand: chain 'J' and resid 311 through 314 removed outlier: 3.641A pdb=" N HIS J 324 " --> pdb=" O ILE J 314 " (cutoff:3.500A) Processing sheet with id= 52, first strand: chain 'J' and resid 353 through 356 Processing sheet with id= 53, first strand: chain 'J' and resid 476 through 481 removed outlier: 4.609A pdb=" N THR J 485 " --> pdb=" O GLU J 481 " (cutoff:3.500A) Processing sheet with id= 54, first strand: chain 'K' and resid 175 through 180 removed outlier: 4.531A pdb=" N GLN K 175 " --> pdb=" O MET K 199 " (cutoff:3.500A) Processing sheet with id= 55, first strand: chain 'M' and resid 36 through 40 removed outlier: 5.268A pdb=" N PHE M 55 " --> pdb=" O THR M 68 " (cutoff:3.500A) Processing sheet with id= 56, first strand: chain 'M' and resid 260 through 265 removed outlier: 3.953A pdb=" N CYS M 269 " --> pdb=" O VAL M 264 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ALA M 270 " --> pdb=" O VAL M 236 " (cutoff:3.500A) removed outlier: 5.318A pdb=" N THR M 232 " --> pdb=" O PHE M 274 " (cutoff:3.500A) Processing sheet with id= 57, first strand: chain 'N' and resid 59 through 63 removed outlier: 3.843A pdb=" N MET N 60 " --> pdb=" O MET N 353 " (cutoff:3.500A) removed outlier: 5.269A pdb=" N ILE N 341 " --> pdb=" O HIS N 336 " (cutoff:3.500A) Processing sheet with id= 58, first strand: chain 'N' and resid 70 through 75 removed outlier: 5.476A pdb=" N THR N 80 " --> pdb=" O HIS N 75 " (cutoff:3.500A) removed outlier: 7.881A pdb=" N SER N 79 " --> pdb=" O VAL N 95 " (cutoff:3.500A) removed outlier: 4.595A pdb=" N GLY N 85 " --> pdb=" O LEU N 89 " (cutoff:3.500A) removed outlier: 4.921A pdb=" N LEU N 89 " --> pdb=" O GLY N 85 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ALA N 103 " --> pdb=" O LEU N 92 " (cutoff:3.500A) Processing sheet with id= 59, first strand: chain 'N' and resid 113 through 117 removed outlier: 4.514A pdb=" N THR N 132 " --> pdb=" O SER N 128 " (cutoff:3.500A) Processing sheet with id= 60, first strand: chain 'N' and resid 156 through 160 removed outlier: 4.389A pdb=" N LEU N 166 " --> pdb=" O ALA N 160 " (cutoff:3.500A) removed outlier: 4.529A pdb=" N GLY N 174 " --> pdb=" O ASN N 192 " (cutoff:3.500A) removed outlier: 4.308A pdb=" N GLN N 188 " --> pdb=" O LEU N 178 " (cutoff:3.500A) Processing sheet with id= 61, first strand: chain 'N' and resid 197 through 202 removed outlier: 6.476A pdb=" N GLN N 207 " --> pdb=" O ASN N 202 " (cutoff:3.500A) removed outlier: 8.418A pdb=" N ASP N 206 " --> pdb=" O LEU N 222 " (cutoff:3.500A) Processing sheet with id= 62, first strand: chain 'N' and resid 239 through 244 removed outlier: 6.511A pdb=" N TYR N 249 " --> pdb=" O SER N 244 " (cutoff:3.500A) removed outlier: 4.813A pdb=" N SER N 248 " --> pdb=" O VAL N 264 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N ALA N 254 " --> pdb=" O THR N 258 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N THR N 258 " --> pdb=" O ALA N 254 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N LYS N 275 " --> pdb=" O VAL N 261 " (cutoff:3.500A) Processing sheet with id= 63, first strand: chain 'N' and resid 290 through 294 removed outlier: 4.863A pdb=" N ARG N 290 " --> pdb=" O GLY N 303 " (cutoff:3.500A) removed outlier: 5.638A pdb=" N LYS N 299 " --> pdb=" O SER N 294 " (cutoff:3.500A) removed outlier: 8.492A pdb=" N SER N 298 " --> pdb=" O THR N 314 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N ALA N 302 " --> pdb=" O TYR N 310 " (cutoff:3.500A) removed outlier: 4.226A pdb=" N TYR N 310 " --> pdb=" O ALA N 302 " (cutoff:3.500A) removed outlier: 6.653A pdb=" N VAL N 311 " --> pdb=" O LEU N 320 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N ARG N 318 " --> pdb=" O ASP N 313 " (cutoff:3.500A) Processing sheet with id= 64, first strand: chain 'N' and resid 308 through 311 Processing sheet with id= 65, first strand: chain 'U' and resid 494 through 497 removed outlier: 3.503A pdb=" N GLY U 501 " --> pdb=" O SER U 497 " (cutoff:3.500A) Processing sheet with id= 66, first strand: chain 'U' and resid 511 through 514 removed outlier: 5.793A pdb=" N ASN U 654 " --> pdb=" O ILE U 514 " (cutoff:3.500A) removed outlier: 4.233A pdb=" N VAL U 535 " --> pdb=" O LEU U 629 " (cutoff:3.500A) removed outlier: 6.390A pdb=" N ARG U 536 " --> pdb=" O VAL U 520 " (cutoff:3.500A) Processing sheet with id= 67, first strand: chain 'U' and resid 711 through 714 removed outlier: 5.713A pdb=" N PHE U 747 " --> pdb=" O PHE U 714 " (cutoff:3.500A) Processing sheet with id= 68, first strand: chain 'U' and resid 1033 through 1037 Processing sheet with id= 69, first strand: chain 'U' and resid 1176 through 1181 Processing sheet with id= 70, first strand: chain 'U' and resid 1329 through 1333 Processing sheet with id= 71, first strand: chain 'V' and resid 641 through 645 removed outlier: 3.880A pdb=" N ILE V 681 " --> pdb=" O LYS V 612 " (cutoff:3.500A) removed outlier: 6.088A pdb=" N GLN V 582 " --> pdb=" O MET V 711 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N SER V 717 " --> pdb=" O VAL V 586 " (cutoff:3.500A) Processing sheet with id= 72, first strand: chain 'V' and resid 743 through 749 removed outlier: 6.859A pdb=" N TYR V 852 " --> pdb=" O PRO V 896 " (cutoff:3.500A) removed outlier: 6.416A pdb=" N PHE V 779 " --> pdb=" O VAL V 855 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N ARG V 833 " --> pdb=" O GLU V 806 " (cutoff:3.500A) Processing sheet with id= 73, first strand: chain 'V' and resid 861 through 867 Processing sheet with id= 74, first strand: chain 'V' and resid 1130 through 1134 removed outlier: 4.341A pdb=" N GLN V1131 " --> pdb=" O THR V1126 " (cutoff:3.500A) removed outlier: 6.572A pdb=" N GLY V1123 " --> pdb=" O ASP V1119 " (cutoff:3.500A) removed outlier: 7.173A pdb=" N ALA V1115 " --> pdb=" O LEU V1127 " (cutoff:3.500A) removed outlier: 5.654A pdb=" N ASN V1114 " --> pdb=" O TYR V1151 " (cutoff:3.500A) removed outlier: 7.091A pdb=" N GLU V1147 " --> pdb=" O LYS V1118 " (cutoff:3.500A) removed outlier: 4.458A pdb=" N TRP V1148 " --> pdb=" O ILE V1168 " (cutoff:3.500A) removed outlier: 6.998A pdb=" N GLU V1164 " --> pdb=" O HIS V1152 " (cutoff:3.500A) Processing sheet with id= 75, first strand: chain 'V' and resid 1153 through 1157 removed outlier: 6.758A pdb=" N GLU V1153 " --> pdb=" O MET V1162 " (cutoff:3.500A) removed outlier: 4.627A pdb=" N MET V1162 " --> pdb=" O GLU V1153 " (cutoff:3.500A) removed outlier: 6.746A pdb=" N VAL V1155 " --> pdb=" O GLU V1160 " (cutoff:3.500A) removed outlier: 4.660A pdb=" N GLU V1160 " --> pdb=" O VAL V1155 " (cutoff:3.500A) removed outlier: 5.645A pdb=" N THR V1157 " --> pdb=" O THR V1158 " (cutoff:3.500A) Processing sheet with id= 76, first strand: chain 'W' and resid 13 through 16 removed outlier: 4.335A pdb=" N ALA W 13 " --> pdb=" O ASP W 25 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N LEU W 26 " --> pdb=" O ASP W 48 " (cutoff:3.500A) removed outlier: 4.136A pdb=" N SER W 50 " --> pdb=" O LEU W 26 " (cutoff:3.500A) removed outlier: 4.306A pdb=" N ASN W 72 " --> pdb=" O PHE W 49 " (cutoff:3.500A) removed outlier: 4.232A pdb=" N THR W 96 " --> pdb=" O VAL W 71 " (cutoff:3.500A) removed outlier: 4.397A pdb=" N LEU W 121 " --> pdb=" O LEU W 95 " (cutoff:3.500A) Processing sheet with id= 77, first strand: chain 'Y' and resid 39 through 42 removed outlier: 3.600A pdb=" N ASP Y 39 " --> pdb=" O ILE Y 55 " (cutoff:3.500A) removed outlier: 6.471A pdb=" N THR Y 8 " --> pdb=" O ALA Y 84 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N PHE Y 72 " --> pdb=" O MET Y 79 " (cutoff:3.500A) Processing sheet with id= 78, first strand: chain 'b' and resid 40 through 43 Processing sheet with id= 79, first strand: chain 'b' and resid 44 through 48 removed outlier: 5.421A pdb=" N ASP b 44 " --> pdb=" O THR b 30 " (cutoff:3.500A) removed outlier: 4.582A pdb=" N THR b 30 " --> pdb=" O ASP b 44 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ILE b 26 " --> pdb=" O PHE b 48 " (cutoff:3.500A) Processing sheet with id= 80, first strand: chain 'd' and resid 55 through 59 removed outlier: 3.503A pdb=" N ALA d 56 " --> pdb=" O VAL d 48 " (cutoff:3.500A) removed outlier: 5.395A pdb=" N ASN d 45 " --> pdb=" O LYS d 31 " (cutoff:3.500A) removed outlier: 4.803A pdb=" N LYS d 31 " --> pdb=" O ASN d 45 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N ARG d 29 " --> pdb=" O THR d 47 " (cutoff:3.500A) removed outlier: 5.662A pdb=" N VAL d 27 " --> pdb=" O THR d 49 " (cutoff:3.500A) removed outlier: 4.216A pdb=" N HIS d 16 " --> pdb=" O LEU d 32 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N PHE d 70 " --> pdb=" O GLU d 21 " (cutoff:3.500A) Processing sheet with id= 81, first strand: chain 'e' and resid 54 through 58 removed outlier: 6.466A pdb=" N MET e 54 " --> pdb=" O GLY e 81 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N GLY e 81 " --> pdb=" O MET e 54 " (cutoff:3.500A) Processing sheet with id= 82, first strand: chain 'e' and resid 71 through 74 removed outlier: 3.840A pdb=" N LYS e 72 " --> pdb=" O GLU e 63 " (cutoff:3.500A) removed outlier: 5.485A pdb=" N ALA e 61 " --> pdb=" O LEU e 74 " (cutoff:3.500A) removed outlier: 8.102A pdb=" N ASN e 40 " --> pdb=" O SER e 66 " (cutoff:3.500A) Processing sheet with id= 83, first strand: chain 'f' and resid 56 through 59 removed outlier: 5.614A pdb=" N THR f 47 " --> pdb=" O LEU f 59 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N LYS f 30 " --> pdb=" O GLU f 48 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N TYR f 50 " --> pdb=" O GLU f 28 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N GLU f 28 " --> pdb=" O TYR f 50 " (cutoff:3.500A) removed outlier: 4.460A pdb=" N MET f 27 " --> pdb=" O LEU f 23 " (cutoff:3.500A) Processing sheet with id= 84, first strand: chain 'q' and resid 56 through 59 removed outlier: 5.674A pdb=" N THR q 47 " --> pdb=" O LEU q 59 " (cutoff:3.500A) removed outlier: 4.582A pdb=" N MET q 27 " --> pdb=" O LEU q 23 " (cutoff:3.500A) Processing sheet with id= 85, first strand: chain 'g' and resid 54 through 57 removed outlier: 3.512A pdb=" N ASN g 55 " --> pdb=" O GLU g 47 " (cutoff:3.500A) removed outlier: 5.594A pdb=" N CYS g 45 " --> pdb=" O ILE g 57 " (cutoff:3.500A) removed outlier: 4.040A pdb=" N HIS g 26 " --> pdb=" O MET g 48 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N ARG g 25 " --> pdb=" O LEU g 21 " (cutoff:3.500A) removed outlier: 6.978A pdb=" N LYS g 16 " --> pdb=" O LEU g 73 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N MET g 69 " --> pdb=" O LYS g 20 " (cutoff:3.500A) Processing sheet with id= 86, first strand: chain 'r' and resid 54 through 57 removed outlier: 5.765A pdb=" N CYS r 45 " --> pdb=" O ILE r 57 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N HIS r 26 " --> pdb=" O MET r 48 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N VAL r 27 " --> pdb=" O LEU r 19 " (cutoff:3.500A) removed outlier: 6.253A pdb=" N LYS r 16 " --> pdb=" O LEU r 73 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N MET r 69 " --> pdb=" O LYS r 20 " (cutoff:3.500A) Processing sheet with id= 87, first strand: chain 'h' and resid 52 through 55 removed outlier: 4.315A pdb=" N THR h 23 " --> pdb=" O LEU h 19 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N TYR h 67 " --> pdb=" O GLU h 18 " (cutoff:3.500A) Processing sheet with id= 88, first strand: chain 'l' and resid 52 through 55 removed outlier: 4.212A pdb=" N THR l 23 " --> pdb=" O LEU l 19 " (cutoff:3.500A) Processing sheet with id= 89, first strand: chain 'i' and resid 54 through 57 removed outlier: 5.261A pdb=" N GLN i 111 " --> pdb=" O ALA i 101 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N ILE i 97 " --> pdb=" O THR i 115 " (cutoff:3.500A) removed outlier: 8.395A pdb=" N GLY i 96 " --> pdb=" O ARG i 131 " (cutoff:3.500A) removed outlier: 4.486A pdb=" N ARG i 131 " --> pdb=" O GLY i 96 " (cutoff:3.500A) removed outlier: 6.383A pdb=" N LEU i 98 " --> pdb=" O PHE i 129 " (cutoff:3.500A) removed outlier: 4.156A pdb=" N THR i 127 " --> pdb=" O MET i 100 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N GLY i 21 " --> pdb=" O THR i 18 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N TYR i 15 " --> pdb=" O TYR i 163 " (cutoff:3.500A) Processing sheet with id= 90, first strand: chain 'j' and resid 89 through 96 removed outlier: 3.622A pdb=" N LYS j 50 " --> pdb=" O CYS j 46 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N LEU j 43 " --> pdb=" O LEU j 110 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N VAL j 108 " --> pdb=" O ASN j 45 " (cutoff:3.500A) Processing sheet with id= 91, first strand: chain 'm' and resid 89 through 96 removed outlier: 4.033A pdb=" N LYS m 50 " --> pdb=" O CYS m 46 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N VAL m 108 " --> pdb=" O ASN m 45 " (cutoff:3.500A) Processing sheet with id= 92, first strand: chain 'k' and resid 40 through 43 Processing sheet with id= 93, first strand: chain 'k' and resid 59 through 68 removed outlier: 5.924A pdb=" N ALA k 59 " --> pdb=" O PRO k 53 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N ARG k 61 " --> pdb=" O ILE k 51 " (cutoff:3.500A) removed outlier: 6.100A pdb=" N CYS k 45 " --> pdb=" O LEU k 67 " (cutoff:3.500A) removed outlier: 5.793A pdb=" N ASP k 44 " --> pdb=" O THR k 30 " (cutoff:3.500A) removed outlier: 5.132A pdb=" N THR k 30 " --> pdb=" O ASP k 44 " (cutoff:3.500A) removed outlier: 4.233A pdb=" N TYR k 15 " --> pdb=" O PHE k 31 " (cutoff:3.500A) removed outlier: 6.418A pdb=" N ARG k 16 " --> pdb=" O GLU k 83 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N SER k 79 " --> pdb=" O ILE k 20 " (cutoff:3.500A) Processing sheet with id= 94, first strand: chain 'n' and resid 41 through 44 Processing sheet with id= 95, first strand: chain 'n' and resid 54 through 59 removed outlier: 5.209A pdb=" N ARG n 54 " --> pdb=" O TYR n 50 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N TYR n 50 " --> pdb=" O ARG n 54 " (cutoff:3.500A) removed outlier: 5.436A pdb=" N ASN n 45 " --> pdb=" O LYS n 31 " (cutoff:3.500A) removed outlier: 4.685A pdb=" N LYS n 31 " --> pdb=" O ASN n 45 " (cutoff:3.500A) removed outlier: 6.038A pdb=" N VAL n 27 " --> pdb=" O THR n 49 " (cutoff:3.500A) removed outlier: 4.131A pdb=" N HIS n 16 " --> pdb=" O LEU n 32 " (cutoff:3.500A) Processing sheet with id= 96, first strand: chain 'o' and resid 237 through 241 removed outlier: 3.556A pdb=" N ARG o 326 " --> pdb=" O LEU o 315 " (cutoff:3.500A) removed outlier: 4.166A pdb=" N LYS o 312 " --> pdb=" O SER o 308 " (cutoff:3.500A) removed outlier: 7.341A pdb=" N HIS o 302 " --> pdb=" O VAL o 318 " (cutoff:3.500A) removed outlier: 6.001A pdb=" N LEU o 303 " --> pdb=" O PHE o 297 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N ALA o 293 " --> pdb=" O CYS o 307 " (cutoff:3.500A) Processing sheet with id= 97, first strand: chain 'o' and resid 281 through 284 removed outlier: 3.918A pdb=" N HIS o 282 " --> pdb=" O LEU o 577 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N TRP o 284 " --> pdb=" O ILE o 575 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N ILE o 575 " --> pdb=" O TRP o 284 " (cutoff:3.500A) Processing sheet with id= 98, first strand: chain 'o' and resid 336 through 341 removed outlier: 5.870A pdb=" N GLN o 346 " --> pdb=" O ASN o 341 " (cutoff:3.500A) removed outlier: 8.582A pdb=" N THR o 345 " --> pdb=" O THR o 361 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N THR o 361 " --> pdb=" O THR o 345 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N ALA o 351 " --> pdb=" O TYR o 355 " (cutoff:3.500A) removed outlier: 4.505A pdb=" N TYR o 355 " --> pdb=" O ALA o 351 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N SER o 368 " --> pdb=" O LEU o 358 " (cutoff:3.500A) Processing sheet with id= 99, first strand: chain 'o' and resid 378 through 381 removed outlier: 3.579A pdb=" N CYS o 378 " --> pdb=" O GLY o 394 " (cutoff:3.500A) removed outlier: 8.161A pdb=" N ASN o 389 " --> pdb=" O ILE o 405 " (cutoff:3.500A) removed outlier: 5.053A pdb=" N LYS o 399 " --> pdb=" O MET o 395 " (cutoff:3.500A) Processing sheet with id=100, first strand: chain 'o' and resid 423 through 427 removed outlier: 3.697A pdb=" N LYS o 454 " --> pdb=" O VAL o 444 " (cutoff:3.500A) Processing sheet with id=101, first strand: chain 'o' and resid 466 through 470 removed outlier: 4.739A pdb=" N ALA o 466 " --> pdb=" O GLN o 479 " (cutoff:3.500A) removed outlier: 5.737A pdb=" N TRP o 475 " --> pdb=" O SER o 470 " (cutoff:3.500A) removed outlier: 5.121A pdb=" N LYS o 474 " --> pdb=" O ALA o 490 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N GLN o 484 " --> pdb=" O SER o 480 " (cutoff:3.500A) Processing sheet with id=102, first strand: chain 'o' and resid 514 through 517 removed outlier: 5.150A pdb=" N TYR o 522 " --> pdb=" O SER o 517 " (cutoff:3.500A) removed outlier: 7.684A pdb=" N SER o 521 " --> pdb=" O TRP o 537 " (cutoff:3.500A) removed outlier: 5.099A pdb=" N LYS o 531 " --> pdb=" O ASP o 527 " (cutoff:3.500A) removed outlier: 6.590A pdb=" N ILE o 534 " --> pdb=" O TYR o 543 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N LYS o 541 " --> pdb=" O ASP o 536 " (cutoff:3.500A) Processing sheet with id=103, first strand: chain 'o' and resid 530 through 533 removed outlier: 4.561A pdb=" N GLY o 530 " --> pdb=" O ALA o 548 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N PHE o 546 " --> pdb=" O LEU o 532 " (cutoff:3.500A) Processing sheet with id=104, first strand: chain 'p' and resid 69 through 75 removed outlier: 3.550A pdb=" N SER p 70 " --> pdb=" O HIS p 65 " (cutoff:3.500A) removed outlier: 5.670A pdb=" N ALA p 61 " --> pdb=" O LEU p 74 " (cutoff:3.500A) removed outlier: 5.508A pdb=" N ASP p 60 " --> pdb=" O CYS p 46 " (cutoff:3.500A) removed outlier: 4.911A pdb=" N CYS p 46 " --> pdb=" O ASP p 60 " (cutoff:3.500A) removed outlier: 7.841A pdb=" N ASN p 40 " --> pdb=" O SER p 66 " (cutoff:3.500A) removed outlier: 7.104A pdb=" N MET p 41 " --> pdb=" O LEU p 35 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N LEU p 35 " --> pdb=" O MET p 41 " (cutoff:3.500A) Processing sheet with id=105, first strand: chain 'u' and resid 15 through 18 removed outlier: 6.388A pdb=" N CYS u 16 " --> pdb=" O VAL u 24 " (cutoff:3.500A) removed outlier: 4.290A pdb=" N VAL u 24 " --> pdb=" O CYS u 16 " (cutoff:3.500A) removed outlier: 6.037A pdb=" N SER u 18 " --> pdb=" O ASN u 22 " (cutoff:3.500A) Processing sheet with id=106, first strand: chain 'w' and resid 16 through 19 removed outlier: 3.655A pdb=" N HIS w 23 " --> pdb=" O SER w 18 " (cutoff:3.500A) 5439 hydrogen bonds defined for protein. 16111 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 181 hydrogen bonds 322 hydrogen bond angles 0 basepair planarities 74 basepair parallelities 184 stacking parallelities Total time for adding SS restraints: 67.61 Time building geometry restraints manager: 42.47 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.34: 38504 1.34 - 1.49: 35943 1.49 - 1.65: 48958 1.65 - 1.80: 676 1.80 - 1.96: 225 Bond restraints: 124306 Sorted by residual: bond pdb=" C4 ATP 7 702 " pdb=" N9 ATP 7 702 " ideal model delta sigma weight residual 1.374 1.306 0.068 1.00e-02 1.00e+04 4.63e+01 bond pdb=" SD MET U 867 " pdb=" CE MET U 867 " ideal model delta sigma weight residual 1.791 1.954 -0.163 2.50e-02 1.60e+03 4.27e+01 bond pdb=" SD MET U1093 " pdb=" CE MET U1093 " ideal model delta sigma weight residual 1.791 1.953 -0.162 2.50e-02 1.60e+03 4.19e+01 bond pdb=" SD MET U1368 " pdb=" CE MET U1368 " ideal model delta sigma weight residual 1.791 1.951 -0.160 2.50e-02 1.60e+03 4.11e+01 bond pdb=" SD MET U 79 " pdb=" CE MET U 79 " ideal model delta sigma weight residual 1.791 1.951 -0.160 2.50e-02 1.60e+03 4.11e+01 ... (remaining 124301 not shown) Histogram of bond angle deviations from ideal: 93.67 - 102.00: 730 102.00 - 110.33: 32291 110.33 - 118.66: 67883 118.66 - 126.99: 66316 126.99 - 135.32: 2277 Bond angle restraints: 169497 Sorted by residual: angle pdb=" PB ATP 7 702 " pdb=" O3B ATP 7 702 " pdb=" PG ATP 7 702 " ideal model delta sigma weight residual 139.87 117.95 21.92 1.00e+00 1.00e+00 4.81e+02 angle pdb=" PA ATP 7 702 " pdb=" O3A ATP 7 702 " pdb=" PB ATP 7 702 " ideal model delta sigma weight residual 136.83 123.47 13.36 1.00e+00 1.00e+00 1.78e+02 angle pdb=" O HIS T 84 " pdb=" C HIS T 84 " pdb=" N ARG T 85 " ideal model delta sigma weight residual 122.07 109.67 12.40 1.03e+00 9.43e-01 1.45e+02 angle pdb=" O LYS T 83 " pdb=" C LYS T 83 " pdb=" N HIS T 84 " ideal model delta sigma weight residual 122.07 109.73 12.34 1.03e+00 9.43e-01 1.44e+02 angle pdb=" O ALA T 309 " pdb=" C ALA T 309 " pdb=" N LYS T 310 " ideal model delta sigma weight residual 122.07 109.76 12.31 1.03e+00 9.43e-01 1.43e+02 ... (remaining 169492 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.86: 71851 35.86 - 71.72: 1787 71.72 - 107.58: 117 107.58 - 143.44: 10 143.44 - 179.30: 17 Dihedral angle restraints: 73782 sinusoidal: 32275 harmonic: 41507 Sorted by residual: dihedral pdb=" CA PRO V 811 " pdb=" C PRO V 811 " pdb=" N VAL V 812 " pdb=" CA VAL V 812 " ideal model delta harmonic sigma weight residual 180.00 101.86 78.14 0 5.00e+00 4.00e-02 2.44e+02 dihedral pdb=" CA GLN s 77 " pdb=" C GLN s 77 " pdb=" N PRO s 78 " pdb=" CA PRO s 78 " ideal model delta harmonic sigma weight residual -180.00 -122.80 -57.20 0 5.00e+00 4.00e-02 1.31e+02 dihedral pdb=" CA VAL V 855 " pdb=" C VAL V 855 " pdb=" N ASP V 856 " pdb=" CA ASP V 856 " ideal model delta harmonic sigma weight residual 180.00 126.48 53.52 0 5.00e+00 4.00e-02 1.15e+02 ... (remaining 73779 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.986: 18652 0.986 - 1.973: 0 1.973 - 2.959: 0 2.959 - 3.946: 0 3.946 - 4.932: 2 Chirality restraints: 18654 Sorted by residual: chirality pdb=" C2 IHP c 601 " pdb=" C1 IHP c 601 " pdb=" C3 IHP c 601 " pdb=" O12 IHP c 601 " both_signs ideal model delta sigma weight residual False -2.52 2.41 -4.93 2.00e-01 2.50e+01 6.08e+02 chirality pdb=" C3 IHP c 601 " pdb=" C2 IHP c 601 " pdb=" C4 IHP c 601 " pdb=" O13 IHP c 601 " both_signs ideal model delta sigma weight residual False -2.34 2.34 -4.68 2.00e-01 2.50e+01 5.48e+02 chirality pdb=" CA VAL T 476 " pdb=" N VAL T 476 " pdb=" C VAL T 476 " pdb=" CB VAL T 476 " both_signs ideal model delta sigma weight residual False 2.44 1.82 0.62 2.00e-01 2.50e+01 9.51e+00 ... (remaining 18651 not shown) Planarity restraints: 20807 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LYS T 83 " 0.067 2.00e-02 2.50e+03 1.25e-01 1.56e+02 pdb=" C LYS T 83 " -0.216 2.00e-02 2.50e+03 pdb=" O LYS T 83 " 0.080 2.00e-02 2.50e+03 pdb=" N HIS T 84 " 0.069 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA MET T 311 " -0.067 2.00e-02 2.50e+03 1.25e-01 1.56e+02 pdb=" C MET T 311 " 0.216 2.00e-02 2.50e+03 pdb=" O MET T 311 " -0.080 2.00e-02 2.50e+03 pdb=" N GLU T 312 " -0.069 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA HIS T 84 " 0.067 2.00e-02 2.50e+03 1.25e-01 1.55e+02 pdb=" C HIS T 84 " -0.216 2.00e-02 2.50e+03 pdb=" O HIS T 84 " 0.080 2.00e-02 2.50e+03 pdb=" N ARG T 85 " 0.069 2.00e-02 2.50e+03 ... (remaining 20804 not shown) Histogram of nonbonded interaction distances: 0.96 - 1.80: 46 1.80 - 2.63: 1995 2.63 - 3.47: 184564 3.47 - 4.30: 386643 4.30 - 5.14: 662928 Warning: very small nonbonded interaction distances. Nonbonded interactions: 1236176 Sorted by model distance: nonbonded pdb=" O PRO N 266 " pdb=" CE2 TYR O 788 " model vdw 0.962 3.340 nonbonded pdb=" CZ PHE N 267 " pdb=" CD1 ILE s 195 " model vdw 1.040 3.760 nonbonded pdb=" CE2 TYR A2168 " pdb=" CZ ARG B1287 " model vdw 1.095 3.570 nonbonded pdb=" O ARG V 393 " pdb=" CA GLN V1145 " model vdw 1.106 3.470 nonbonded pdb=" CE2 PHE N 267 " pdb=" CD1 ILE s 195 " model vdw 1.186 3.760 ... (remaining 1236171 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 'd' and resid 2 through 84) selection = chain 'n' } ncs_group { reference = chain 'e' selection = (chain 'p' and resid 13 through 91) } ncs_group { reference = chain 'f' selection = chain 'q' } ncs_group { reference = chain 'g' selection = chain 'r' } ncs_group { reference = chain 'h' selection = chain 'l' } ncs_group { reference = chain 'j' selection = chain 'm' } ncs_group { reference = (chain 't' and resid 2 through 131) selection = chain 'u' selection = (chain 'v' and resid 2 through 131) selection = chain 'w' } 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=0.42 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: 3.890 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.070 Extract box with map and model: 22.040 Check model and map are aligned: 1.280 Set scattering table: 0.760 Process input model: 349.970 Find NCS groups from input model: 3.510 Set up NCS constraints: 0.690 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.230 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 384.460 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6994 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.008 0.163 124306 Z= 0.537 Angle : 1.149 21.924 169497 Z= 0.733 Chirality : 0.082 4.932 18654 Planarity : 0.007 0.125 20807 Dihedral : 15.816 179.300 47270 Min Nonbonded Distance : 0.962 Molprobity Statistics. All-atom Clashscore : 10.58 Ramachandran Plot: Outliers : 0.34 % Allowed : 5.03 % Favored : 94.63 % Rotamer Outliers : 2.45 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 0.44 % Cis-general : 0.00 % Twisted Proline : 0.74 % Twisted General : 0.17 % 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: -3.15 (0.06), residues: 14374 helix: -2.30 (0.05), residues: 6113 sheet: -1.38 (0.11), residues: 1809 loop : -1.95 (0.07), residues: 6452 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 28748 Ramachandran restraints generated. 14374 Oldfield, 0 Emsley, 14374 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 28748 Ramachandran restraints generated. 14374 Oldfield, 0 Emsley, 14374 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2758 residues out of total 13025 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 288 poor density : 2470 time to evaluate : 11.318 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 288 outliers final: 50 residues processed: 2714 average time/residue: 1.1291 time to fit residues: 5194.3473 Evaluate side-chains 1487 residues out of total 13025 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 1437 time to evaluate : 9.907 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash outliers start: 50 outliers final: 3 residues processed: 50 average time/residue: 0.9706 time to fit residues: 102.1075 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1475 random chunks: chunk 1245 optimal weight: 0.5980 chunk 1117 optimal weight: 40.0000 chunk 620 optimal weight: 7.9990 chunk 381 optimal weight: 1.9990 chunk 754 optimal weight: 20.0000 chunk 597 optimal weight: 0.9990 chunk 1156 optimal weight: 7.9990 chunk 447 optimal weight: 0.6980 chunk 702 optimal weight: 4.9990 chunk 860 optimal weight: 0.9990 chunk 1339 optimal weight: 7.9990 overall best weight: 1.0586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 7 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 138 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 7 399 GLN A 210 HIS A 270 ASN ** A 321 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 325 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 326 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 328 HIS A 361 HIS A 363 HIS A 434 HIS A 505 ASN A 664 HIS A 755 HIS A 775 ASN A 792 HIS A 834 HIS A 994 ASN A1014 ASN A1023 ASN A1024 HIS A1096 HIS A1159 ASN A1169 GLN ** A1296 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1337 GLN A1345 GLN ** A1468 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1476 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1586 HIS A1615 HIS ** A1717 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1890 GLN A1946 ASN A1947 ASN A1996 ASN A2123 GLN A2260 GLN A2300 ASN A2306 HIS ** B 425 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 446 HIS B 720 GLN B1113 ASN B1179 HIS B1191 GLN B1281 GLN B1444 ASN B1447 ASN B1502 HIS B1591 HIS B1667 GLN B1784 HIS B1970 HIS ** C 137 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 154 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 163 GLN C 175 GLN C 477 HIS C 513 ASN C 557 GLN C 859 GLN C 890 HIS ** C 903 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 31 GLN F 660 GLN G 87 GLN ** H 266 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 474 HIS H 499 GLN H 500 GLN H 553 HIS H 600 ASN J 191 HIS ** J 269 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 446 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 500 HIS K 84 ASN M 82 GLN M 127 ASN N 101 ASN N 116 HIS N 225 ASN ** N 253 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 282 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 13 ASN ** O 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 245 GLN ** O 785 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 56 ASN S 221 ASN S 244 ASN S 250 GLN S 373 HIS T 601 GLN T 628 GLN T 714 HIS ** T 739 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 744 GLN U 165 GLN U 287 ASN U 375 ASN ** U 411 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** U 544 ASN U1199 GLN U1231 ASN U1235 HIS ** W 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 72 ASN W 130 HIS Y 15 ASN ** c 84 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 154 HIS c 171 ASN c 344 GLN ** e 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** f 41 ASN ** f 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** h 54 GLN h 64 ASN i 31 HIS ** i 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** i 140 ASN i 148 ASN j 39 ASN j 69 ASN k 55 ASN ** k 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** m 34 GLN m 49 ASN ** n 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** o 80 GLN o 145 ASN o 146 HIS o 147 GLN o 462 HIS ** o 479 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 492 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** p 26 GLN ** p 65 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 83 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** s 123 ASN s 159 HIS ** s 192 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** t 9 ASN u 45 GLN ** u 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** u 88 HIS u 105 HIS v 43 ASN v 105 HIS w 22 ASN y 131 GLN y 156 HIS y 169 HIS y 172 HIS y 215 ASN Total number of N/Q/H flips: 123 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7031 moved from start: 0.2252 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.008 2.343 124306 Z= 0.617 Angle : 0.673 21.114 169497 Z= 0.355 Chirality : 0.045 0.593 18654 Planarity : 0.005 0.104 20807 Dihedral : 11.153 177.076 20023 Min Nonbonded Distance : 1.910 Molprobity Statistics. All-atom Clashscore : 13.96 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.92 % Favored : 96.00 % Rotamer Outliers : 2.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.44 % Cis-general : 0.00 % Twisted Proline : 0.30 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.47 (0.07), residues: 14374 helix: -0.47 (0.06), residues: 6198 sheet: -1.01 (0.11), residues: 1862 loop : -1.37 (0.07), residues: 6314 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 28748 Ramachandran restraints generated. 14374 Oldfield, 0 Emsley, 14374 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 28748 Ramachandran restraints generated. 14374 Oldfield, 0 Emsley, 14374 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1946 residues out of total 13025 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 294 poor density : 1652 time to evaluate : 9.194 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 294 outliers final: 133 residues processed: 1854 average time/residue: 1.0603 time to fit residues: 3401.0226 Evaluate side-chains 1532 residues out of total 13025 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 133 poor density : 1399 time to evaluate : 9.965 Switching outliers to nearest non-outliers outliers start: 133 outliers final: 2 residues processed: 133 average time/residue: 0.8758 time to fit residues: 234.4400 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1475 random chunks: chunk 744 optimal weight: 3.9990 chunk 415 optimal weight: 6.9990 chunk 1114 optimal weight: 50.0000 chunk 912 optimal weight: 0.0870 chunk 369 optimal weight: 1.9990 chunk 1341 optimal weight: 0.0040 chunk 1449 optimal weight: 5.9990 chunk 1195 optimal weight: 6.9990 chunk 1330 optimal weight: 5.9990 chunk 457 optimal weight: 20.0000 chunk 1076 optimal weight: 40.0000 overall best weight: 2.4176 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 7 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 41 GLN ** A 326 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 505 ASN ** A 675 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1066 GLN A1117 HIS ** A1296 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1359 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1476 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1583 GLN A1665 GLN A1717 ASN A1944 HIS A1946 ASN A1947 ASN B 446 HIS B 824 HIS B1147 ASN B1189 HIS B1191 GLN B1281 GLN B1548 HIS B1659 HIS ** C 137 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 154 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 548 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 859 GLN C 924 GLN F 660 GLN ** F 739 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 87 GLN ** H 171 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 620 ASN J 417 ASN J 446 ASN ** L 116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 196 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 206 ASN O 13 ASN O 30 GLN O 161 ASN ** O 785 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 275 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 693 GLN T 737 GLN ** T 739 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 71 GLN ** U 411 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** V 404 GLN W 14 GLN ** W 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 148 GLN Y 13 ASN ** c 84 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** j 91 ASN k 11 GLN k 55 ASN ** k 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** m 34 GLN ** n 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** n 42 GLN ** o 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** o 256 HIS ** o 479 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 492 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 83 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** p 88 GLN ** r 22 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** u 105 HIS ** v 105 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** w 22 ASN Total number of N/Q/H flips: 45 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7111 moved from start: 0.2940 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.008 2.304 124306 Z= 0.638 Angle : 0.652 19.141 169497 Z= 0.339 Chirality : 0.045 0.453 18654 Planarity : 0.005 0.099 20807 Dihedral : 10.911 176.781 20023 Min Nonbonded Distance : 1.916 Molprobity Statistics. All-atom Clashscore : 14.26 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.41 % Favored : 95.51 % Rotamer Outliers : 2.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.44 % Cis-general : 0.00 % Twisted Proline : 0.30 % Twisted General : 0.02 % 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: -0.76 (0.07), residues: 14374 helix: 0.29 (0.07), residues: 6231 sheet: -0.80 (0.11), residues: 1863 loop : -1.15 (0.08), residues: 6280 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 28748 Ramachandran restraints generated. 14374 Oldfield, 0 Emsley, 14374 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 28748 Ramachandran restraints generated. 14374 Oldfield, 0 Emsley, 14374 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1837 residues out of total 13025 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 305 poor density : 1532 time to evaluate : 10.096 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 305 outliers final: 119 residues processed: 1746 average time/residue: 1.0908 time to fit residues: 3319.2015 Evaluate side-chains 1456 residues out of total 13025 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 119 poor density : 1337 time to evaluate : 9.904 Switching outliers to nearest non-outliers outliers start: 119 outliers final: 2 residues processed: 119 average time/residue: 0.8945 time to fit residues: 213.8639 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1475 random chunks: chunk 1325 optimal weight: 0.9990 chunk 1008 optimal weight: 50.0000 chunk 696 optimal weight: 0.4980 chunk 148 optimal weight: 0.9990 chunk 640 optimal weight: 2.9990 chunk 901 optimal weight: 9.9990 chunk 1346 optimal weight: 1.9990 chunk 1425 optimal weight: 9.9990 chunk 703 optimal weight: 0.4980 chunk 1276 optimal weight: 0.0980 chunk 384 optimal weight: 10.0000 overall best weight: 0.6184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 7 83 GLN ** 7 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 7 138 HIS 7 345 GLN A 160 HIS A 326 HIS A 675 GLN ** A1296 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1359 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1363 GLN ** A1476 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1528 GLN A1946 ASN A1947 ASN A2166 HIS B 446 HIS B1147 ASN B1235 HIS B1548 HIS ** B1659 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 137 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 154 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 548 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 924 GLN ** D 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 171 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 620 ASN H 623 ASN ** L 116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 127 ASN O 13 ASN ** O 785 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 238 ASN S 244 ASN S 410 HIS U 296 HIS U 316 GLN U1097 HIS W 14 GLN ** W 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 84 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** f 67 ASN ** h 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** j 91 ASN ** k 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** m 34 GLN m 69 ASN ** n 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** o 492 ASN q 46 ASN ** q 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 22 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** v 105 HIS w 22 ASN y 165 ASN Total number of N/Q/H flips: 36 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7034 moved from start: 0.3284 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.068 124306 Z= 0.169 Angle : 0.584 12.756 169497 Z= 0.302 Chirality : 0.043 0.329 18654 Planarity : 0.004 0.095 20807 Dihedral : 10.751 177.123 20023 Min Nonbonded Distance : 1.916 Molprobity Statistics. All-atom Clashscore : 13.38 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.08 % Favored : 95.85 % Rotamer Outliers : 1.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.44 % Cis-general : 0.00 % Twisted Proline : 0.30 % Twisted General : 0.01 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.30 (0.07), residues: 14374 helix: 0.76 (0.07), residues: 6225 sheet: -0.61 (0.11), residues: 1866 loop : -0.98 (0.08), residues: 6283 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 28748 Ramachandran restraints generated. 14374 Oldfield, 0 Emsley, 14374 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 28748 Ramachandran restraints generated. 14374 Oldfield, 0 Emsley, 14374 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1725 residues out of total 13025 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 219 poor density : 1506 time to evaluate : 10.025 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 219 outliers final: 90 residues processed: 1655 average time/residue: 1.0735 time to fit residues: 3101.1388 Evaluate side-chains 1418 residues out of total 13025 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 90 poor density : 1328 time to evaluate : 9.960 Switching outliers to nearest non-outliers outliers start: 90 outliers final: 2 residues processed: 90 average time/residue: 0.8978 time to fit residues: 166.0438 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1475 random chunks: chunk 1187 optimal weight: 6.9990 chunk 809 optimal weight: 6.9990 chunk 20 optimal weight: 10.0000 chunk 1061 optimal weight: 9.9990 chunk 588 optimal weight: 6.9990 chunk 1216 optimal weight: 6.9990 chunk 985 optimal weight: 9.9990 chunk 1 optimal weight: 6.9990 chunk 728 optimal weight: 0.5980 chunk 1279 optimal weight: 4.9990 chunk 359 optimal weight: 6.9990 overall best weight: 5.3188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 7 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 584 HIS A 963 GLN ** A1296 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1359 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1476 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1857 GLN A1947 ASN A2300 ASN ** B 425 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 446 HIS B 940 HIS ** B1124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1147 ASN B1191 GLN B1591 HIS B1659 HIS ** B1892 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1896 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 137 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 154 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 548 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 116 ASN G 102 HIS ** H 171 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 620 ASN H 623 ASN ** J 344 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 242 GLN ** M 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 287 ASN N 357 GLN ** O 785 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 238 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 244 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 275 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 347 HIS ** T 693 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 152 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** U 296 HIS ** W 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 84 HIS ** c 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** e 16 GLN ** e 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** f 67 ASN ** h 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** j 91 ASN ** k 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** l 26 HIS ** l 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** o 71 HIS ** o 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** o 256 HIS ** o 430 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 479 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** p 26 GLN ** p 83 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 22 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 116 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** t 95 GLN ** u 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** u 43 ASN u 88 HIS v 43 ASN w 22 ASN Total number of N/Q/H flips: 33 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7227 moved from start: 0.3854 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.008 0.147 124306 Z= 0.541 Angle : 0.758 13.914 169497 Z= 0.389 Chirality : 0.050 0.599 18654 Planarity : 0.006 0.096 20807 Dihedral : 10.971 179.427 20023 Min Nonbonded Distance : 1.843 Molprobity Statistics. All-atom Clashscore : 16.70 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.29 % Favored : 94.63 % Rotamer Outliers : 2.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.44 % Cis-general : 0.00 % Twisted Proline : 0.30 % Twisted General : 0.02 % 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: -0.55 (0.07), residues: 14374 helix: 0.51 (0.07), residues: 6224 sheet: -0.75 (0.11), residues: 1943 loop : -1.07 (0.08), residues: 6207 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 28748 Ramachandran restraints generated. 14374 Oldfield, 0 Emsley, 14374 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 28748 Ramachandran restraints generated. 14374 Oldfield, 0 Emsley, 14374 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1692 residues out of total 13025 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 287 poor density : 1405 time to evaluate : 10.088 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 287 outliers final: 144 residues processed: 1613 average time/residue: 1.1092 time to fit residues: 3128.3797 Evaluate side-chains 1418 residues out of total 13025 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 144 poor density : 1274 time to evaluate : 9.983 Switching outliers to nearest non-outliers outliers start: 144 outliers final: 2 residues processed: 144 average time/residue: 0.9038 time to fit residues: 259.0313 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1475 random chunks: chunk 479 optimal weight: 0.8980 chunk 1283 optimal weight: 4.9990 chunk 281 optimal weight: 1.9990 chunk 837 optimal weight: 1.9990 chunk 351 optimal weight: 6.9990 chunk 1427 optimal weight: 5.9990 chunk 1184 optimal weight: 9.9990 chunk 660 optimal weight: 0.6980 chunk 118 optimal weight: 0.6980 chunk 472 optimal weight: 0.5980 chunk 749 optimal weight: 0.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 7 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 157 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 8 103 HIS ** A1296 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1352 HIS A1468 ASN ** A1476 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1528 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1623 ASN A1947 ASN ** B 425 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 446 HIS B 638 ASN B 720 GLN B1147 ASN ** B1332 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1784 HIS ** B1877 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 137 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 154 HIS ** C 548 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 171 ASN H 267 ASN K 320 HIS ** L 116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 206 ASN ** O 785 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 275 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 693 GLN U 542 ASN U 544 ASN V 404 GLN ** W 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** e 16 GLN ** e 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** j 91 ASN ** k 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** m 62 HIS ** n 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 430 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 83 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 22 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 116 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** u 14 HIS u 45 GLN u 88 HIS u 95 GLN Total number of N/Q/H flips: 26 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7103 moved from start: 0.3937 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.061 124306 Z= 0.182 Angle : 0.603 14.434 169497 Z= 0.309 Chirality : 0.043 0.345 18654 Planarity : 0.004 0.093 20807 Dihedral : 10.787 179.224 20023 Min Nonbonded Distance : 1.911 Molprobity Statistics. All-atom Clashscore : 14.93 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.07 % Favored : 95.85 % Rotamer Outliers : 1.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.44 % Cis-general : 0.00 % Twisted Proline : 0.30 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.16 (0.07), residues: 14374 helix: 0.92 (0.07), residues: 6251 sheet: -0.64 (0.11), residues: 1934 loop : -0.94 (0.08), residues: 6189 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 28748 Ramachandran restraints generated. 14374 Oldfield, 0 Emsley, 14374 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 28748 Ramachandran restraints generated. 14374 Oldfield, 0 Emsley, 14374 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1552 residues out of total 13025 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 143 poor density : 1409 time to evaluate : 10.078 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 143 outliers final: 57 residues processed: 1499 average time/residue: 1.0383 time to fit residues: 2717.6236 Evaluate side-chains 1363 residues out of total 13025 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 1306 time to evaluate : 9.985 Switching outliers to nearest non-outliers outliers start: 57 outliers final: 2 residues processed: 57 average time/residue: 0.9130 time to fit residues: 111.1605 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1475 random chunks: chunk 1375 optimal weight: 5.9990 chunk 160 optimal weight: 0.7980 chunk 813 optimal weight: 10.0000 chunk 1042 optimal weight: 30.0000 chunk 807 optimal weight: 4.9990 chunk 1201 optimal weight: 9.9990 chunk 796 optimal weight: 0.6980 chunk 1421 optimal weight: 7.9990 chunk 889 optimal weight: 10.0000 chunk 866 optimal weight: 7.9990 chunk 656 optimal weight: 1.9990 overall best weight: 2.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 7 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 326 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 505 ASN ** A1023 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1056 HIS ** A1296 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1468 ASN ** A1476 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1947 ASN A2246 ASN ** B 425 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 446 HIS ** B 786 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1124 GLN B1147 ASN ** B1332 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1877 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 137 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 548 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 171 ASN K 307 GLN ** L 116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 206 ASN M 251 HIS N 215 ASN ** S 275 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 693 GLN U 296 HIS U 544 ASN V 404 GLN ** W 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** e 16 GLN ** e 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** j 91 ASN ** k 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 479 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 83 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 22 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 116 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** u 88 HIS u 95 GLN ** y 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** y 156 HIS Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7174 moved from start: 0.4181 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.062 124306 Z= 0.331 Angle : 0.652 14.472 169497 Z= 0.333 Chirality : 0.046 0.416 18654 Planarity : 0.005 0.093 20807 Dihedral : 10.770 179.553 20023 Min Nonbonded Distance : 1.903 Molprobity Statistics. All-atom Clashscore : 15.35 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.03 % Favored : 94.89 % Rotamer Outliers : 1.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.44 % Cis-general : 0.00 % Twisted Proline : 0.30 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.16 (0.07), residues: 14374 helix: 0.94 (0.07), residues: 6241 sheet: -0.64 (0.11), residues: 1951 loop : -0.95 (0.08), residues: 6182 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 28748 Ramachandran restraints generated. 14374 Oldfield, 0 Emsley, 14374 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 28748 Ramachandran restraints generated. 14374 Oldfield, 0 Emsley, 14374 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1503 residues out of total 13025 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 157 poor density : 1346 time to evaluate : 10.129 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 157 outliers final: 79 residues processed: 1458 average time/residue: 1.1073 time to fit residues: 2814.1400 Evaluate side-chains 1353 residues out of total 13025 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 79 poor density : 1274 time to evaluate : 9.992 Switching outliers to nearest non-outliers outliers start: 79 outliers final: 2 residues processed: 79 average time/residue: 0.8917 time to fit residues: 147.4755 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1475 random chunks: chunk 879 optimal weight: 30.0000 chunk 567 optimal weight: 0.0470 chunk 849 optimal weight: 0.9980 chunk 428 optimal weight: 1.9990 chunk 279 optimal weight: 1.9990 chunk 275 optimal weight: 0.1980 chunk 903 optimal weight: 40.0000 chunk 968 optimal weight: 10.0000 chunk 702 optimal weight: 6.9990 chunk 132 optimal weight: 0.6980 chunk 1117 optimal weight: 2.9990 overall best weight: 0.7880 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 7 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 294 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 326 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1296 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1468 ASN ** A1476 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1528 GLN A1944 HIS A1947 ASN ** B 425 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 446 HIS B1124 GLN B1147 ASN ** B1332 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1877 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 137 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 548 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 807 GLN F 746 GLN ** L 116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 275 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 404 GLN ** W 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 126 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** o 561 HIS ** p 83 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 22 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** s 201 GLN ** t 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** u 88 HIS Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7092 moved from start: 0.4282 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.052 124306 Z= 0.177 Angle : 0.592 15.333 169497 Z= 0.302 Chirality : 0.043 0.299 18654 Planarity : 0.004 0.093 20807 Dihedral : 10.651 179.296 20023 Min Nonbonded Distance : 1.910 Molprobity Statistics. All-atom Clashscore : 14.58 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.35 % Favored : 95.57 % Rotamer Outliers : 0.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.44 % Cis-general : 0.00 % Twisted Proline : 0.30 % Twisted General : 0.01 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.09 (0.07), residues: 14374 helix: 1.21 (0.07), residues: 6214 sheet: -0.57 (0.12), residues: 1866 loop : -0.87 (0.08), residues: 6294 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 28748 Ramachandran restraints generated. 14374 Oldfield, 0 Emsley, 14374 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 28748 Ramachandran restraints generated. 14374 Oldfield, 0 Emsley, 14374 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1476 residues out of total 13025 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 87 poor density : 1389 time to evaluate : 9.930 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 87 outliers final: 33 residues processed: 1446 average time/residue: 1.0785 time to fit residues: 2725.2428 Evaluate side-chains 1326 residues out of total 13025 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 1293 time to evaluate : 9.999 Switching outliers to nearest non-outliers outliers start: 33 outliers final: 2 residues processed: 33 average time/residue: 0.9380 time to fit residues: 71.3697 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1475 random chunks: chunk 1293 optimal weight: 9.9990 chunk 1361 optimal weight: 0.5980 chunk 1242 optimal weight: 20.0000 chunk 1324 optimal weight: 0.0010 chunk 797 optimal weight: 2.9990 chunk 577 optimal weight: 10.0000 chunk 1040 optimal weight: 8.9990 chunk 406 optimal weight: 5.9990 chunk 1197 optimal weight: 0.7980 chunk 1252 optimal weight: 20.0000 chunk 1320 optimal weight: 0.9980 overall best weight: 1.0788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 7 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 294 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 326 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1042 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1296 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1400 ASN A1468 ASN ** A1476 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1947 ASN A2255 HIS ** B 425 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 446 HIS B 786 HIS B1147 ASN ** B1332 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1877 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 137 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 139 HIS ** C 548 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 807 GLN ** L 116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 275 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 404 GLN ** W 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 83 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 22 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** u 88 HIS ** u 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** y 131 GLN ** y 219 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7093 moved from start: 0.4405 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.047 124306 Z= 0.193 Angle : 0.597 15.368 169497 Z= 0.303 Chirality : 0.043 0.372 18654 Planarity : 0.004 0.093 20807 Dihedral : 10.569 178.661 20023 Min Nonbonded Distance : 1.914 Molprobity Statistics. All-atom Clashscore : 14.44 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.52 % Favored : 95.41 % Rotamer Outliers : 0.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.44 % Cis-general : 0.00 % Twisted Proline : 0.30 % Twisted General : 0.01 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.21 (0.07), residues: 14374 helix: 1.32 (0.07), residues: 6222 sheet: -0.52 (0.12), residues: 1887 loop : -0.81 (0.08), residues: 6265 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 28748 Ramachandran restraints generated. 14374 Oldfield, 0 Emsley, 14374 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 28748 Ramachandran restraints generated. 14374 Oldfield, 0 Emsley, 14374 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1413 residues out of total 13025 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 1340 time to evaluate : 10.098 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 73 outliers final: 32 residues processed: 1377 average time/residue: 1.0949 time to fit residues: 2639.2360 Evaluate side-chains 1296 residues out of total 13025 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 1264 time to evaluate : 10.073 Switching outliers to nearest non-outliers outliers start: 32 outliers final: 2 residues processed: 32 average time/residue: 0.9380 time to fit residues: 70.4982 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1475 random chunks: chunk 869 optimal weight: 0.9990 chunk 1400 optimal weight: 0.9990 chunk 855 optimal weight: 2.9990 chunk 664 optimal weight: 0.9990 chunk 973 optimal weight: 0.3980 chunk 1469 optimal weight: 3.9990 chunk 1352 optimal weight: 0.8980 chunk 1170 optimal weight: 20.0000 chunk 121 optimal weight: 0.0060 chunk 903 optimal weight: 40.0000 chunk 717 optimal weight: 2.9990 overall best weight: 0.6600 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 7 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 289 GLN ** A 294 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 326 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1042 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1296 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1468 ASN ** A1476 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1767 ASN A1797 ASN A1947 ASN ** B 425 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 446 HIS B 715 HIS B1147 ASN ** B1332 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1877 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 137 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 548 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 31 GLN ** H 265 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 620 ASN H 623 ASN J 451 HIS ** L 116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 275 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 404 GLN ** W 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** h 26 HIS ** i 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 126 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** j 34 GLN ** j 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** l 24 GLN ** l 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 430 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 533 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 83 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 22 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** t 79 GLN u 88 HIS ** u 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** v 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** w 22 ASN y 131 GLN ** y 219 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7057 moved from start: 0.4547 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.067 124306 Z= 0.166 Angle : 0.589 15.090 169497 Z= 0.298 Chirality : 0.043 0.309 18654 Planarity : 0.004 0.092 20807 Dihedral : 10.500 178.188 20023 Min Nonbonded Distance : 1.909 Molprobity Statistics. All-atom Clashscore : 14.16 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.38 % Favored : 95.55 % Rotamer Outliers : 0.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.44 % Cis-general : 0.00 % Twisted Proline : 0.30 % Twisted General : 0.01 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.33 (0.07), residues: 14374 helix: 1.45 (0.07), residues: 6246 sheet: -0.45 (0.12), residues: 1892 loop : -0.80 (0.08), residues: 6236 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 28748 Ramachandran restraints generated. 14374 Oldfield, 0 Emsley, 14374 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 28748 Ramachandran restraints generated. 14374 Oldfield, 0 Emsley, 14374 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1400 residues out of total 13025 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 1357 time to evaluate : 10.042 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 43 outliers final: 18 residues processed: 1379 average time/residue: 1.0944 time to fit residues: 2641.2748 Evaluate side-chains 1283 residues out of total 13025 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 1265 time to evaluate : 9.987 Switching outliers to nearest non-outliers outliers start: 18 outliers final: 2 residues processed: 18 average time/residue: 0.9907 time to fit residues: 46.7524 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1475 random chunks: chunk 929 optimal weight: 50.0000 chunk 1246 optimal weight: 0.4980 chunk 358 optimal weight: 20.0000 chunk 1078 optimal weight: 0.9990 chunk 172 optimal weight: 0.7980 chunk 325 optimal weight: 0.0770 chunk 1172 optimal weight: 6.9990 chunk 490 optimal weight: 2.9990 chunk 1203 optimal weight: 6.9990 chunk 148 optimal weight: 2.9990 chunk 215 optimal weight: 3.9990 overall best weight: 1.0742 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 7 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 9 41 ASN ** A 294 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 326 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 873 ASN ** A1042 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1296 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1468 ASN ** A1476 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1947 ASN ** B 425 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1147 ASN ** B1332 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1877 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 137 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 548 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 807 GLN ** H 265 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 451 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 165 GLN O 786 HIS ** S 275 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 296 HIS V 404 GLN ** W 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** e 40 ASN ** i 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 126 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** l 24 GLN ** l 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** n 11 HIS ** n 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** o 529 ASN o 533 ASN ** p 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** p 38 GLN p 65 HIS ** p 83 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** q 58 HIS ** r 22 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** u 88 HIS ** u 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** w 22 ASN y 131 GLN ** y 219 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4648 r_free = 0.4648 target = 0.227010 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4464 r_free = 0.4464 target = 0.209040 restraints weight = 232229.679| |-----------------------------------------------------------------------------| r_work (start): 0.4464 rms_B_bonded: 1.37 r_work: 0.4271 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.4233 rms_B_bonded: 3.23 restraints_weight: 0.2500 r_work (final): 0.4233 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4233 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4233 r_free = 0.4233 target_work(ls_wunit_k1) = 0.189 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4233 r_free = 0.4233 target_work(ls_wunit_k1) = 0.189 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 25 | |-----------------------------------------------------------------------------| r_final: 0.4233 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6441 moved from start: 0.4648 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.047 124306 Z= 0.188 Angle : 0.593 14.943 169497 Z= 0.300 Chirality : 0.043 0.322 18654 Planarity : 0.004 0.092 20807 Dihedral : 10.453 177.491 20023 Min Nonbonded Distance : 1.913 Molprobity Statistics. All-atom Clashscore : 14.47 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.54 % Favored : 95.39 % Rotamer Outliers : 0.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.44 % Cis-general : 0.00 % Twisted Proline : 0.30 % Twisted General : 0.01 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.41 (0.07), residues: 14374 helix: 1.52 (0.07), residues: 6242 sheet: -0.35 (0.12), residues: 1903 loop : -0.77 (0.08), residues: 6229 =============================================================================== Job complete usr+sys time: 43986.52 seconds wall clock time: 762 minutes 1.93 seconds (45721.93 seconds total)