Starting phenix.real_space_refine on Tue Feb 13 03:13:22 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7z13_14439/02_2024/7z13_14439_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7z13_14439/02_2024/7z13_14439.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7z13_14439/02_2024/7z13_14439.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7z13_14439/02_2024/7z13_14439.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7z13_14439/02_2024/7z13_14439_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7z13_14439/02_2024/7z13_14439_updated.pdb" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.081 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Zn 14 6.06 5 P 138 5.49 5 Mg 6 5.21 5 S 482 5.16 5 C 67692 2.51 5 N 18485 2.21 5 O 20564 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "2 GLU 180": "OE1" <-> "OE2" Residue "2 GLU 210": "OE1" <-> "OE2" Residue "2 GLU 221": "OE1" <-> "OE2" Residue "2 GLU 266": "OE1" <-> "OE2" Residue "2 TYR 304": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "2 PHE 339": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "2 GLU 407": "OE1" <-> "OE2" Residue "2 ASP 416": "OD1" <-> "OD2" Residue "2 GLU 425": "OE1" <-> "OE2" Residue "2 GLU 483": "OE1" <-> "OE2" Residue "2 GLU 588": "OE1" <-> "OE2" Residue "2 PHE 609": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "2 ASP 610": "OD1" <-> "OD2" Residue "2 ASP 688": "OD1" <-> "OD2" Residue "2 ASP 701": "OD1" <-> "OD2" Residue "2 GLU 752": "OE1" <-> "OE2" Residue "2 TYR 775": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "2 GLU 827": "OE1" <-> "OE2" Residue "2 ASP 847": "OD1" <-> "OD2" Residue "3 ASP 33": "OD1" <-> "OD2" Residue "3 PHE 35": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "3 ASP 101": "OD1" <-> "OD2" Residue "3 PHE 106": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "3 PHE 157": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "3 GLU 183": "OE1" <-> "OE2" Residue "3 GLU 237": "OE1" <-> "OE2" Residue "3 TYR 247": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "3 ASP 361": "OD1" <-> "OD2" Residue "3 GLU 458": "OE1" <-> "OE2" Residue "3 PHE 520": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "3 TYR 523": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "3 ASP 537": "OD1" <-> "OD2" Residue "4 GLU 213": "OE1" <-> "OE2" Residue "4 TYR 264": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "4 ASP 286": "OD1" <-> "OD2" Residue "4 GLU 295": "OE1" <-> "OE2" Residue "4 GLU 316": "OE1" <-> "OE2" Residue "4 ASP 341": "OD1" <-> "OD2" Residue "4 GLU 367": "OE1" <-> "OE2" Residue "4 GLU 372": "OE1" <-> "OE2" Residue "4 TYR 420": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "4 GLU 422": "OE1" <-> "OE2" Residue "4 GLU 511": "OE1" <-> "OE2" Residue "4 TYR 531": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "4 ASP 632": "OD1" <-> "OD2" Residue "4 ASP 635": "OD1" <-> "OD2" Residue "4 ASP 703": "OD1" <-> "OD2" Residue "4 TYR 706": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "4 ASP 717": "OD1" <-> "OD2" Residue "4 GLU 745": "OE1" <-> "OE2" Residue "4 GLU 764": "OE1" <-> "OE2" Residue "4 GLU 806": "OE1" <-> "OE2" Residue "4 GLU 824": "OE1" <-> "OE2" Residue "5 GLU 73": "OE1" <-> "OE2" Residue "5 ASP 74": "OD1" <-> "OD2" Residue "5 GLU 154": "OE1" <-> "OE2" Residue "5 TYR 241": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5 GLU 246": "OE1" <-> "OE2" Residue "5 GLU 269": "OE1" <-> "OE2" Residue "5 ASP 336": "OD1" <-> "OD2" Residue "5 GLU 354": "OE1" <-> "OE2" Residue "5 ASP 383": "OD1" <-> "OD2" Residue "5 PHE 428": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5 ASP 541": "OD1" <-> "OD2" Residue "5 GLU 717": "OE1" <-> "OE2" Residue "6 GLU 113": "OE1" <-> "OE2" Residue "6 GLU 116": "OE1" <-> "OE2" Residue "6 GLU 141": "OE1" <-> "OE2" Residue "6 ASP 154": "OD1" <-> "OD2" Residue "6 GLU 162": "OE1" <-> "OE2" Residue "6 TYR 175": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "6 GLU 260": "OE1" <-> "OE2" Residue "6 GLU 303": "OE1" <-> "OE2" Residue "6 GLU 329": "OE1" <-> "OE2" Residue "6 PHE 332": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "6 GLU 339": "OE1" <-> "OE2" Residue "6 GLU 367": "OE1" <-> "OE2" Residue "6 GLU 401": "OE1" <-> "OE2" Residue "6 PHE 454": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "6 GLU 518": "OE1" <-> "OE2" Residue "6 TYR 526": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "6 GLU 541": "OE1" <-> "OE2" Residue "6 TYR 597": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "6 GLU 617": "OE1" <-> "OE2" Residue "6 ASP 632": "OD1" <-> "OD2" Residue "6 PHE 712": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "6 PHE 713": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "6 GLU 775": "OE1" <-> "OE2" Residue "6 TYR 793": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "7 TYR 14": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "7 ASP 81": "OD1" <-> "OD2" Residue "7 ASP 136": "OD1" <-> "OD2" Residue "7 ASP 140": "OD1" <-> "OD2" Residue "7 PHE 192": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "7 TYR 215": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "7 GLU 256": "OE1" <-> "OE2" Residue "7 PHE 270": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "7 GLU 283": "OE1" <-> "OE2" Residue "7 GLU 373": "OE1" <-> "OE2" Residue "7 ASP 427": "OD1" <-> "OD2" Residue "7 TYR 482": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "7 ASP 500": "OD1" <-> "OD2" Residue "7 TYR 571": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "7 ASP 627": "OD1" <-> "OD2" Residue "7 ASP 629": "OD1" <-> "OD2" Residue "7 TYR 641": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "7 ASP 709": "OD1" <-> "OD2" Residue "7 GLU 714": "OE1" <-> "OE2" Residue "C ASP 8": "OD1" <-> "OD2" Residue "C GLU 171": "OE1" <-> "OE2" Residue "D GLU 75": "OE1" <-> "OE2" Residue "D GLU 130": "OE1" <-> "OE2" Residue "D TYR 182": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 196": "OD1" <-> "OD2" Residue "D GLU 204": "OE1" <-> "OE2" Residue "D PHE 229": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 256": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 289": "OD1" <-> "OD2" Residue "E TYR 2": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 10": "OE1" <-> "OE2" Residue "E GLU 113": "OE1" <-> "OE2" Residue "E GLU 157": "OE1" <-> "OE2" Residue "E GLU 239": "OE1" <-> "OE2" Residue "E ASP 281": "OD1" <-> "OD2" Residue "E TYR 284": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 298": "OE1" <-> "OE2" Residue "E GLU 353": "OE1" <-> "OE2" Residue "E TYR 379": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 424": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 426": "OE1" <-> "OE2" Residue "E PHE 477": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 490": "OE1" <-> "OE2" Residue "E ASP 501": "OD1" <-> "OD2" Residue "E PHE 507": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 515": "OE1" <-> "OE2" Residue "E PHE 640": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 62": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 64": "OE1" <-> "OE2" Residue "F TYR 183": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 233": "OE1" <-> "OE2" Residue "F ASP 278": "OD1" <-> "OD2" Residue "F PHE 292": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 308": "OD1" <-> "OD2" Residue "F GLU 329": "OE1" <-> "OE2" Residue "F GLU 353": "OE1" <-> "OE2" Residue "F ASP 380": "OD1" <-> "OD2" Residue "F PHE 399": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 438": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 512": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 557": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ASP 95": "OD1" <-> "OD2" Residue "H GLU 133": "OE1" <-> "OE2" Residue "H ASP 148": "OD1" <-> "OD2" Residue "I GLU 14": "OE1" <-> "OE2" Residue "I GLU 21": "OE1" <-> "OE2" Residue "I GLU 23": "OE1" <-> "OE2" Residue "I GLU 97": "OE1" <-> "OE2" Residue "I GLU 150": "OE1" <-> "OE2" Residue "I GLU 194": "OE1" <-> "OE2" Residue "J ASP 8": "OD1" <-> "OD2" Residue "J GLU 171": "OE1" <-> "OE2" Residue "K GLU 75": "OE1" <-> "OE2" Residue "K GLU 130": "OE1" <-> "OE2" Residue "K TYR 182": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ASP 196": "OD1" <-> "OD2" Residue "K GLU 204": "OE1" <-> "OE2" Residue "K PHE 229": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 256": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ASP 289": "OD1" <-> "OD2" Residue "L TYR 2": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L GLU 10": "OE1" <-> "OE2" Residue "L GLU 113": "OE1" <-> "OE2" Residue "L GLU 157": "OE1" <-> "OE2" Residue "L GLU 239": "OE1" <-> "OE2" Residue "L ASP 281": "OD1" <-> "OD2" Residue "L TYR 284": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L GLU 298": "OE1" <-> "OE2" Residue "L GLU 353": "OE1" <-> "OE2" Residue "L TYR 379": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 424": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L GLU 426": "OE1" <-> "OE2" Residue "L PHE 477": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L GLU 490": "OE1" <-> "OE2" Residue "L ASP 501": "OD1" <-> "OD2" Residue "L PHE 507": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L GLU 515": "OE1" <-> "OE2" Residue "L PHE 640": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M PHE 62": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M GLU 64": "OE1" <-> "OE2" Residue "M TYR 183": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M GLU 233": "OE1" <-> "OE2" Residue "M ASP 278": "OD1" <-> "OD2" Residue "M PHE 292": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M ASP 308": "OD1" <-> "OD2" Residue "M GLU 329": "OE1" <-> "OE2" Residue "M GLU 353": "OE1" <-> "OE2" Residue "M ASP 380": "OD1" <-> "OD2" Residue "M PHE 399": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M PHE 438": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M PHE 512": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M PHE 557": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N PHE 1339": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N TYR 1358": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N PHE 1361": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N PHE 1398": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N GLU 1428": "OE1" <-> "OE2" Residue "N PHE 1463": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N GLU 1472": "OE1" <-> "OE2" Residue "N ASP 1669": "OD1" <-> "OD2" Residue "N GLU 1683": "OE1" <-> "OE2" Residue "N GLU 1691": "OE1" <-> "OE2" Residue "N PHE 1705": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N ASP 1733": "OD1" <-> "OD2" Residue "N PHE 1778": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N GLU 1801": "OE1" <-> "OE2" Residue "N GLU 1805": "OE1" <-> "OE2" Residue "N TYR 1879": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N TYR 1881": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N TYR 1897": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N PHE 2007": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N GLU 2024": "OE1" <-> "OE2" Residue "N ASP 2028": "OD1" <-> "OD2" Residue "N GLU 2053": "OE1" <-> "OE2" Residue "N GLU 2084": "OE1" <-> "OE2" Residue "N ASP 2096": "OD1" <-> "OD2" Residue "N PHE 2106": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N ASP 2219": "OD1" <-> "OD2" Residue "O TYR 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O ASP 95": "OD1" <-> "OD2" Residue "O GLU 133": "OE1" <-> "OE2" Residue "O ASP 148": "OD1" <-> "OD2" Residue "P GLU 14": "OE1" <-> "OE2" Residue "P GLU 21": "OE1" <-> "OE2" Residue "P GLU 23": "OE1" <-> "OE2" Residue "P GLU 97": "OE1" <-> "OE2" Residue "P GLU 150": "OE1" <-> "OE2" Residue "P GLU 194": "OE1" <-> "OE2" Residue "Q PHE 1339": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q TYR 1358": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q PHE 1361": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q PHE 1398": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q GLU 1428": "OE1" <-> "OE2" Residue "Q PHE 1463": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q GLU 1472": "OE1" <-> "OE2" Residue "Q ASP 1669": "OD1" <-> "OD2" Residue "Q GLU 1683": "OE1" <-> "OE2" Residue "Q GLU 1691": "OE1" <-> "OE2" Residue "Q PHE 1705": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q ASP 1733": "OD1" <-> "OD2" Residue "Q PHE 1778": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q GLU 1801": "OE1" <-> "OE2" Residue "Q GLU 1805": "OE1" <-> "OE2" Residue "Q TYR 1879": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q TYR 1881": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q TYR 1897": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q PHE 2007": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q GLU 2024": "OE1" <-> "OE2" Residue "Q ASP 2028": "OD1" <-> "OD2" Residue "Q GLU 2053": "OE1" <-> "OE2" Residue "Q GLU 2084": "OE1" <-> "OE2" Residue "Q ASP 2096": "OD1" <-> "OD2" Residue "Q PHE 2106": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q ASP 2219": "OD1" <-> "OD2" Residue "a GLU 180": "OE1" <-> "OE2" Residue "a GLU 210": "OE1" <-> "OE2" Residue "a GLU 221": "OE1" <-> "OE2" Residue "a GLU 266": "OE1" <-> "OE2" Residue "a TYR 304": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a PHE 339": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a GLU 407": "OE1" <-> "OE2" Residue "a ASP 416": "OD1" <-> "OD2" Residue "a GLU 425": "OE1" <-> "OE2" Residue "a GLU 483": "OE1" <-> "OE2" Residue "a GLU 588": "OE1" <-> "OE2" Residue "a PHE 609": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a ASP 610": "OD1" <-> "OD2" Residue "a ASP 688": "OD1" <-> "OD2" Residue "a ASP 701": "OD1" <-> "OD2" Residue "a GLU 752": "OE1" <-> "OE2" Residue "a TYR 775": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a GLU 827": "OE1" <-> "OE2" Residue "a ASP 847": "OD1" <-> "OD2" Residue "b ASP 33": "OD1" <-> "OD2" Residue "b PHE 35": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b ASP 101": "OD1" <-> "OD2" Residue "b PHE 106": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b PHE 157": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b GLU 183": "OE1" <-> "OE2" Residue "b GLU 237": "OE1" <-> "OE2" Residue "b TYR 247": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b ASP 361": "OD1" <-> "OD2" Residue "b GLU 458": "OE1" <-> "OE2" Residue "b PHE 520": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b TYR 523": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b ASP 537": "OD1" <-> "OD2" Residue "c GLU 213": "OE1" <-> "OE2" Residue "c TYR 264": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c ASP 286": "OD1" <-> "OD2" Residue "c GLU 295": "OE1" <-> "OE2" Residue "c GLU 316": "OE1" <-> "OE2" Residue "c ASP 341": "OD1" <-> "OD2" Residue "c GLU 367": "OE1" <-> "OE2" Residue "c GLU 372": "OE1" <-> "OE2" Residue "c TYR 420": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c GLU 422": "OE1" <-> "OE2" Residue "c GLU 511": "OE1" <-> "OE2" Residue "c TYR 531": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c ASP 632": "OD1" <-> "OD2" Residue "c ASP 635": "OD1" <-> "OD2" Residue "c ASP 703": "OD1" <-> "OD2" Residue "c TYR 706": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c ASP 717": "OD1" <-> "OD2" Residue "c GLU 745": "OE1" <-> "OE2" Residue "c GLU 764": "OE1" <-> "OE2" Residue "c GLU 806": "OE1" <-> "OE2" Residue "c GLU 824": "OE1" <-> "OE2" Residue "d GLU 73": "OE1" <-> "OE2" Residue "d ASP 74": "OD1" <-> "OD2" Residue "d GLU 154": "OE1" <-> "OE2" Residue "d TYR 241": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d GLU 246": "OE1" <-> "OE2" Residue "d GLU 269": "OE1" <-> "OE2" Residue "d ASP 336": "OD1" <-> "OD2" Residue "d GLU 354": "OE1" <-> "OE2" Residue "d ASP 383": "OD1" <-> "OD2" Residue "d PHE 428": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d ASP 541": "OD1" <-> "OD2" Residue "d GLU 717": "OE1" <-> "OE2" Residue "e GLU 113": "OE1" <-> "OE2" Residue "e GLU 116": "OE1" <-> "OE2" Residue "e GLU 141": "OE1" <-> "OE2" Residue "e ASP 154": "OD1" <-> "OD2" Residue "e GLU 162": "OE1" <-> "OE2" Residue "e TYR 175": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "e GLU 260": "OE1" <-> "OE2" Residue "e GLU 303": "OE1" <-> "OE2" Residue "e GLU 329": "OE1" <-> "OE2" Residue "e PHE 332": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "e GLU 339": "OE1" <-> "OE2" Residue "e GLU 367": "OE1" <-> "OE2" Residue "e GLU 401": "OE1" <-> "OE2" Residue "e PHE 454": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "e GLU 518": "OE1" <-> "OE2" Residue "e TYR 526": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "e GLU 541": "OE1" <-> "OE2" Residue "e TYR 597": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "e GLU 617": "OE1" <-> "OE2" Residue "e ASP 632": "OD1" <-> "OD2" Residue "e PHE 712": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "e PHE 713": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "e GLU 775": "OE1" <-> "OE2" Residue "e TYR 793": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "f TYR 14": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "f ASP 81": "OD1" <-> "OD2" Residue "f ASP 136": "OD1" <-> "OD2" Residue "f ASP 140": "OD1" <-> "OD2" Residue "f PHE 192": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "f TYR 215": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "f GLU 256": "OE1" <-> "OE2" Residue "f PHE 270": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "f GLU 283": "OE1" <-> "OE2" Residue "f GLU 373": "OE1" <-> "OE2" Residue "f ASP 427": "OD1" <-> "OD2" Residue "f TYR 482": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "f ASP 500": "OD1" <-> "OD2" Residue "f ASP 627": "OD1" <-> "OD2" Residue "f ASP 629": "OD1" <-> "OD2" Residue "f TYR 641": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "f ASP 709": "OD1" <-> "OD2" Residue "f GLU 714": "OE1" <-> "OE2" Time to flip residues: 0.26s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 107381 Number of models: 1 Model: "" Number of chains: 42 Chain: "2" Number of atoms: 5231 Number of conformers: 1 Conformer: "" Number of residues, atoms: 660, 5231 Classifications: {'peptide': 660} Link IDs: {'PTRANS': 25, 'TRANS': 634} Chain breaks: 1 Chain: "3" Number of atoms: 4958 Number of conformers: 1 Conformer: "" Number of residues, atoms: 633, 4958 Classifications: {'peptide': 633} Link IDs: {'PTRANS': 29, 'TRANS': 603} Chain breaks: 3 Chain: "4" Number of atoms: 4850 Number of conformers: 1 Conformer: "" Number of residues, atoms: 609, 4850 Classifications: {'peptide': 609} Link IDs: {'PTRANS': 22, 'TRANS': 586} Chain breaks: 3 Chain: "5" Number of atoms: 5450 Number of conformers: 1 Conformer: "" Number of residues, atoms: 690, 5450 Classifications: {'peptide': 690} Link IDs: {'PTRANS': 26, 'TRANS': 663} Chain breaks: 4 Chain: "6" Number of atoms: 4972 Number of conformers: 1 Conformer: "" Number of residues, atoms: 629, 4972 Classifications: {'peptide': 629} Link IDs: {'PTRANS': 22, 'TRANS': 606} Chain breaks: 4 Chain: "7" Number of atoms: 5181 Number of conformers: 1 Conformer: "" Number of residues, atoms: 658, 5181 Classifications: {'peptide': 658} Link IDs: {'PTRANS': 30, 'TRANS': 627} Chain breaks: 3 Chain: "A" Number of atoms: 1087 Number of conformers: 1 Conformer: "" Number of residues, atoms: 53, 1087 Classifications: {'DNA': 53} Link IDs: {'rna3p': 52} Chain: "B" Number of atoms: 1086 Number of conformers: 1 Conformer: "" Number of residues, atoms: 53, 1086 Classifications: {'DNA': 53} Link IDs: {'rna3p': 52} Chain: "C" Number of atoms: 1398 Number of conformers: 1 Conformer: "" Number of residues, atoms: 173, 1398 Classifications: {'peptide': 173} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 10, 'TRANS': 162} Chain breaks: 2 Chain: "D" Number of atoms: 1990 Number of conformers: 1 Conformer: "" Number of residues, atoms: 242, 1990 Classifications: {'peptide': 242} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 15, 'TRANS': 226} Chain: "E" Number of atoms: 4599 Number of conformers: 1 Conformer: "" Number of residues, atoms: 566, 4599 Classifications: {'peptide': 566} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 14, 'TRANS': 550} Chain breaks: 3 Chain: "F" Number of atoms: 4396 Number of conformers: 1 Conformer: "" Number of residues, atoms: 551, 4396 Classifications: {'peptide': 551} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 30, 'TRANS': 520} Chain breaks: 3 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: 1697 Number of conformers: 1 Conformer: "" Number of residues, atoms: 208, 1697 Classifications: {'peptide': 208} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 204} Chain: "I" Number of atoms: 1581 Number of conformers: 1 Conformer: "" Number of residues, atoms: 189, 1581 Classifications: {'peptide': 189} Link IDs: {'PTRANS': 9, 'TRANS': 179} Chain breaks: 1 Chain: "J" Number of atoms: 1398 Number of conformers: 1 Conformer: "" Number of residues, atoms: 173, 1398 Classifications: {'peptide': 173} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 10, 'TRANS': 162} Chain breaks: 2 Chain: "K" Number of atoms: 1990 Number of conformers: 1 Conformer: "" Number of residues, atoms: 242, 1990 Classifications: {'peptide': 242} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 15, 'TRANS': 226} Chain: "L" Number of atoms: 4599 Number of conformers: 1 Conformer: "" Number of residues, atoms: 566, 4599 Classifications: {'peptide': 566} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 14, 'TRANS': 550} Chain breaks: 3 Chain: "M" Number of atoms: 4396 Number of conformers: 1 Conformer: "" Number of residues, atoms: 551, 4396 Classifications: {'peptide': 551} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 30, 'TRANS': 520} Chain breaks: 3 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: "N" Number of atoms: 6113 Number of conformers: 1 Conformer: "" Number of residues, atoms: 756, 6113 Classifications: {'peptide': 756} Link IDs: {'PTRANS': 32, 'TRANS': 723} Chain breaks: 3 Chain: "O" Number of atoms: 1697 Number of conformers: 1 Conformer: "" Number of residues, atoms: 208, 1697 Classifications: {'peptide': 208} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 204} Chain: "P" Number of atoms: 1581 Number of conformers: 1 Conformer: "" Number of residues, atoms: 189, 1581 Classifications: {'peptide': 189} Link IDs: {'PTRANS': 9, 'TRANS': 179} Chain breaks: 1 Chain: "Q" Number of atoms: 6113 Number of conformers: 1 Conformer: "" Number of residues, atoms: 756, 6113 Classifications: {'peptide': 756} Link IDs: {'PTRANS': 32, 'TRANS': 723} Chain breaks: 3 Chain: "a" Number of atoms: 5231 Number of conformers: 1 Conformer: "" Number of residues, atoms: 660, 5231 Classifications: {'peptide': 660} Link IDs: {'PTRANS': 25, 'TRANS': 634} Chain breaks: 1 Chain: "b" Number of atoms: 4958 Number of conformers: 1 Conformer: "" Number of residues, atoms: 633, 4958 Classifications: {'peptide': 633} Link IDs: {'PTRANS': 29, 'TRANS': 603} Chain breaks: 3 Chain: "c" Number of atoms: 4850 Number of conformers: 1 Conformer: "" Number of residues, atoms: 609, 4850 Classifications: {'peptide': 609} Link IDs: {'PTRANS': 22, 'TRANS': 586} Chain breaks: 3 Chain: "d" Number of atoms: 5450 Number of conformers: 1 Conformer: "" Number of residues, atoms: 690, 5450 Classifications: {'peptide': 690} Link IDs: {'PTRANS': 26, 'TRANS': 663} Chain breaks: 4 Chain: "e" Number of atoms: 4972 Number of conformers: 1 Conformer: "" Number of residues, atoms: 629, 4972 Classifications: {'peptide': 629} Link IDs: {'PTRANS': 22, 'TRANS': 606} Chain breaks: 4 Chain: "f" Number of atoms: 5181 Number of conformers: 1 Conformer: "" Number of residues, atoms: 658, 5181 Classifications: {'peptide': 658} Link IDs: {'PTRANS': 30, 'TRANS': 627} Chain breaks: 3 Chain: "2" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' ZN': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "3" 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: "4" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' ZN': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "5" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' MG': 1, ' ZN': 1, 'ATP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "6" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' ZN': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "7" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' MG': 1, ' ZN': 1, 'ATP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "N" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "Q" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "a" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' ZN': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "b" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "c" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' ZN': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "d" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' MG': 1, ' ZN': 1, 'ATP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "e" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' ZN': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "f" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' MG': 1, ' ZN': 1, 'ATP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 1311 SG CYS 2 341 118.737 177.119 77.740 1.00 80.00 S ATOM 1334 SG CYS 2 344 116.580 179.796 76.508 1.00 76.23 S ATOM 1492 SG CYS 2 364 119.289 178.031 73.913 1.00 83.78 S ATOM 1513 SG CYS 2 367 120.238 180.786 76.875 1.00 79.04 S ATOM 11625 SG CYS 4 349 153.888 180.342 58.940 1.00 65.57 S ATOM 11646 SG CYS 4 352 156.174 181.856 56.479 1.00 73.26 S ATOM 11793 SG CYS 4 371 157.310 182.170 60.057 1.00 69.90 S ATOM 11835 SG CYS 4 376 154.183 184.147 58.563 1.00 81.39 S ATOM 16154 SG CYS 5 183 124.699 173.038 103.180 1.00 52.08 S ATOM 16179 SG CYS 5 186 123.555 175.784 105.358 1.00 63.95 S ATOM 16329 SG CYS 5 211 122.944 175.906 101.638 1.00 43.30 S ATOM 16357 SG CYS 5 236 126.421 176.443 102.727 1.00 58.27 S ATOM 21693 SG CYS 6 311 130.763 179.640 61.336 1.00 61.22 S ATOM 21715 SG CYS 6 314 130.074 183.244 60.088 1.00 71.11 S ATOM 21872 SG CYS 6 333 133.909 181.361 59.957 1.00 53.84 S ATOM 21906 SG CYS 6 338 131.631 183.248 62.750 1.00 75.99 S ATOM 27069 SG CYS 7 262 168.586 176.995 86.689 1.00 81.40 S ATOM 27092 SG CYS 7 265 169.853 179.499 84.376 1.00 78.94 S ATOM 27246 SG CYS 7 284 165.848 179.370 86.305 1.00 79.63 S ATOM 27283 SG CYS 7 289 168.968 180.615 88.079 1.00 81.82 S ATOM 66065 SG CYS N2108 212.157 321.747 66.432 1.00 52.35 S ATOM 66092 SG CYS N2111 209.691 322.833 63.331 1.00 60.65 S ATOM 66241 SG CYS N2130 211.233 319.280 63.806 1.00 44.31 S ATOM 66265 SG CYS N2133 213.445 322.310 62.965 1.00 54.00 S ATOM 66528 SG CYS N2164 180.124 289.964 87.726 1.00 23.09 S ATOM 66551 SG CYS N2167 176.092 290.656 86.921 1.00 27.49 S ATOM 66652 SG CYS N2179 177.709 291.053 90.665 1.00 18.71 S ATOM 66665 SG CYS N2181 176.527 287.536 88.300 1.00 23.33 S ATOM 75456 SG CYS Q2108 60.803 54.567 67.406 1.00 52.35 S ATOM 75483 SG CYS Q2111 63.218 53.438 64.281 1.00 60.65 S ATOM 75632 SG CYS Q2130 61.728 57.011 64.760 1.00 44.31 S ATOM 75656 SG CYS Q2133 59.469 54.007 63.956 1.00 54.00 S ATOM 75919 SG CYS Q2164 93.488 86.004 88.216 1.00 23.09 S ATOM 75942 SG CYS Q2167 97.501 85.257 87.367 1.00 27.49 S ATOM 76043 SG CYS Q2179 95.920 84.894 91.131 1.00 18.71 S ATOM 76056 SG CYS Q2181 97.122 88.388 88.739 1.00 23.33 S ATOM 77674 SG CYS a 341 155.948 198.490 77.864 1.00 80.00 S ATOM 77697 SG CYS a 344 158.127 195.837 76.616 1.00 76.23 S ATOM 77855 SG CYS a 364 155.365 197.557 74.047 1.00 83.78 S ATOM 77876 SG CYS a 367 154.487 194.801 77.029 1.00 79.04 S ATOM 87988 SG CYS c 349 120.630 194.740 59.478 1.00 65.57 S ATOM 88009 SG CYS c 352 118.337 193.189 57.049 1.00 73.26 S ATOM 88156 SG CYS c 371 117.246 192.872 60.641 1.00 69.90 S ATOM 88198 SG CYS c 376 120.381 190.931 59.118 1.00 81.39 S ATOM 92517 SG CYS d 183 150.223 202.587 103.356 1.00 52.08 S ATOM 92542 SG CYS d 186 151.427 199.865 105.531 1.00 63.95 S ATOM 92692 SG CYS d 211 151.997 199.737 101.803 1.00 43.30 S ATOM 92720 SG CYS d 236 148.540 199.158 102.935 1.00 58.27 S ATOM 98056 SG CYS e 311 143.770 195.753 61.607 1.00 61.22 S ATOM 98078 SG CYS e 314 144.491 192.153 60.364 1.00 71.11 S ATOM 98235 SG CYS e 333 140.653 194.215 60.322 1.00 53.84 S ATOM 98269 SG CYS e 338 143.191 192.348 63.168 1.00 75.99 S ATOM A02NC SG CYS f 262 106.207 197.999 87.381 1.00 81.40 S ATOM A02NZ SG CYS f 265 104.947 195.472 85.092 1.00 78.94 S ATOM A02S9 SG CYS f 284 108.971 195.658 86.975 1.00 79.63 S ATOM A02TA SG CYS f 289 105.888 194.379 88.789 1.00 81.82 S Time building chain proxies: 39.96, per 1000 atoms: 0.37 Number of scatterers: 107381 At special positions: 0 Unit cell: (274.32, 378, 166.32, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 14 29.99 S 482 16.00 P 138 15.00 Mg 6 11.99 O 20564 8.00 N 18485 7.00 C 67692 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 29.86 Conformation dependent library (CDL) restraints added in 14.0 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN 2 902 " pdb="ZN ZN 2 902 " - pdb=" SG CYS 2 344 " pdb="ZN ZN 2 902 " - pdb=" SG CYS 2 341 " pdb="ZN ZN 2 902 " - pdb=" SG CYS 2 367 " pdb="ZN ZN 2 902 " - pdb=" SG CYS 2 364 " pdb=" ZN 41002 " pdb="ZN ZN 41002 " - pdb=" SG CYS 4 352 " pdb="ZN ZN 41002 " - pdb=" SG CYS 4 376 " pdb="ZN ZN 41002 " - pdb=" SG CYS 4 349 " pdb="ZN ZN 41002 " - pdb=" SG CYS 4 371 " pdb=" ZN 51703 " pdb="ZN ZN 51703 " - pdb=" SG CYS 5 211 " pdb="ZN ZN 51703 " - pdb=" SG CYS 5 183 " pdb="ZN ZN 51703 " - pdb=" SG CYS 5 186 " pdb="ZN ZN 51703 " - pdb=" SG CYS 5 236 " pdb=" ZN 61202 " pdb="ZN ZN 61202 " - pdb=" SG CYS 6 314 " pdb="ZN ZN 61202 " - pdb=" SG CYS 6 338 " pdb="ZN ZN 61202 " - pdb=" SG CYS 6 311 " pdb="ZN ZN 61202 " - pdb=" SG CYS 6 333 " pdb=" ZN 7 903 " pdb="ZN ZN 7 903 " - pdb=" SG CYS 7 262 " pdb="ZN ZN 7 903 " - pdb=" SG CYS 7 289 " pdb="ZN ZN 7 903 " - pdb=" SG CYS 7 284 " pdb="ZN ZN 7 903 " - pdb=" SG CYS 7 265 " pdb=" ZN N4001 " pdb="ZN ZN N4001 " - pdb=" SG CYS N2133 " pdb="ZN ZN N4001 " - pdb=" SG CYS N2130 " pdb="ZN ZN N4001 " - pdb=" SG CYS N2108 " pdb="ZN ZN N4001 " - pdb=" SG CYS N2111 " pdb=" ZN N4002 " pdb="ZN ZN N4002 " - pdb=" SG CYS N2167 " pdb="ZN ZN N4002 " - pdb=" SG CYS N2181 " pdb="ZN ZN N4002 " - pdb=" SG CYS N2179 " pdb="ZN ZN N4002 " - pdb=" SG CYS N2164 " pdb=" ZN Q4001 " pdb="ZN ZN Q4001 " - pdb=" SG CYS Q2133 " pdb="ZN ZN Q4001 " - pdb=" SG CYS Q2130 " pdb="ZN ZN Q4001 " - pdb=" SG CYS Q2108 " pdb="ZN ZN Q4001 " - pdb=" SG CYS Q2111 " pdb=" ZN Q4002 " pdb="ZN ZN Q4002 " - pdb=" SG CYS Q2167 " pdb="ZN ZN Q4002 " - pdb=" SG CYS Q2181 " pdb="ZN ZN Q4002 " - pdb=" SG CYS Q2179 " pdb="ZN ZN Q4002 " - pdb=" SG CYS Q2164 " pdb=" ZN a 902 " pdb="ZN ZN a 902 " - pdb=" SG CYS a 344 " pdb="ZN ZN a 902 " - pdb=" SG CYS a 341 " pdb="ZN ZN a 902 " - pdb=" SG CYS a 367 " pdb="ZN ZN a 902 " - pdb=" SG CYS a 364 " pdb=" ZN c1002 " pdb="ZN ZN c1002 " - pdb=" SG CYS c 352 " pdb="ZN ZN c1002 " - pdb=" SG CYS c 376 " pdb="ZN ZN c1002 " - pdb=" SG CYS c 349 " pdb="ZN ZN c1002 " - pdb=" SG CYS c 371 " pdb=" ZN d1703 " pdb="ZN ZN d1703 " - pdb=" SG CYS d 211 " pdb="ZN ZN d1703 " - pdb=" SG CYS d 183 " pdb="ZN ZN d1703 " - pdb=" SG CYS d 186 " pdb="ZN ZN d1703 " - pdb=" SG CYS d 236 " pdb=" ZN e1202 " pdb="ZN ZN e1202 " - pdb=" SG CYS e 314 " pdb="ZN ZN e1202 " - pdb=" SG CYS e 338 " pdb="ZN ZN e1202 " - pdb=" SG CYS e 311 " pdb="ZN ZN e1202 " - pdb=" SG CYS e 333 " pdb=" ZN f 903 " pdb="ZN ZN f 903 " - pdb=" SG CYS f 262 " pdb="ZN ZN f 903 " - pdb=" SG CYS f 289 " pdb="ZN ZN f 903 " - pdb=" SG CYS f 284 " pdb="ZN ZN f 903 " - pdb=" SG CYS f 265 " Number of angles added : 84 25912 Ramachandran restraints generated. 12956 Oldfield, 0 Emsley, 12956 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 24996 Finding SS restraints... Warning!!! ksdssp method is not applicable for structures that cannot fit in PDB format. Switching to from_ca. running find_ss_from_ca liberal... Secondary structure from input PDB file: 480 helices and 118 sheets defined 49.6% alpha, 13.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 34.55 Creating SS restraints... Processing helix chain '2' and resid 182 through 188 removed outlier: 4.211A pdb=" N SER 2 187 " --> pdb=" O LEU 2 183 " (cutoff:3.500A) removed outlier: 4.582A pdb=" N ASN 2 188 " --> pdb=" O GLU 2 184 " (cutoff:3.500A) Processing helix chain '2' and resid 193 through 200 Processing helix chain '2' and resid 201 through 217 removed outlier: 3.535A pdb=" N ARG 2 205 " --> pdb=" O PRO 2 201 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N THR 2 206 " --> pdb=" O ASN 2 202 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ALA 2 208 " --> pdb=" O SER 2 204 " (cutoff:3.500A) Processing helix chain '2' and resid 225 through 238 removed outlier: 3.786A pdb=" N ALA 2 229 " --> pdb=" O SER 2 225 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N GLU 2 236 " --> pdb=" O ARG 2 232 " (cutoff:3.500A) Processing helix chain '2' and resid 245 through 253 removed outlier: 3.564A pdb=" N LEU 2 249 " --> pdb=" O ASN 2 245 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N SER 2 252 " --> pdb=" O HIS 2 248 " (cutoff:3.500A) removed outlier: 4.404A pdb=" N LYS 2 253 " --> pdb=" O LEU 2 249 " (cutoff:3.500A) Processing helix chain '2' and resid 254 through 263 Processing helix chain '2' and resid 265 through 283 removed outlier: 3.544A pdb=" N LYS 2 269 " --> pdb=" O GLU 2 265 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N ILE 2 270 " --> pdb=" O GLU 2 266 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N LEU 2 281 " --> pdb=" O GLU 2 277 " (cutoff:3.500A) removed outlier: 4.256A pdb=" N HIS 2 282 " --> pdb=" O ALA 2 278 " (cutoff:3.500A) Processing helix chain '2' and resid 285 through 290 removed outlier: 4.748A pdb=" N ILE 2 289 " --> pdb=" O ASP 2 285 " (cutoff:3.500A) Processing helix chain '2' and resid 393 through 398 Proline residue: 2 398 - end of helix Processing helix chain '2' and resid 435 through 443 Processing helix chain '2' and resid 477 through 490 removed outlier: 4.011A pdb=" N ARG 2 489 " --> pdb=" O ARG 2 485 " (cutoff:3.500A) removed outlier: 4.392A pdb=" N ASP 2 490 " --> pdb=" O LYS 2 486 " (cutoff:3.500A) Processing helix chain '2' and resid 492 through 501 removed outlier: 3.523A pdb=" N MET 2 501 " --> pdb=" O ILE 2 497 " (cutoff:3.500A) Processing helix chain '2' and resid 508 through 521 Processing helix chain '2' and resid 548 through 560 removed outlier: 3.507A pdb=" N ILE 2 552 " --> pdb=" O ALA 2 548 " (cutoff:3.500A) Processing helix chain '2' and resid 572 through 577 removed outlier: 3.581A pdb=" N LEU 2 576 " --> pdb=" O SER 2 572 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N THR 2 577 " --> pdb=" O ALA 2 573 " (cutoff:3.500A) No H-bonds generated for 'chain '2' and resid 572 through 577' Processing helix chain '2' and resid 594 through 600 removed outlier: 3.785A pdb=" N ASP 2 600 " --> pdb=" O LEU 2 596 " (cutoff:3.500A) Processing helix chain '2' and resid 613 through 626 removed outlier: 3.851A pdb=" N SER 2 619 " --> pdb=" O GLN 2 615 " (cutoff:3.500A) removed outlier: 4.640A pdb=" N ILE 2 620 " --> pdb=" O ASP 2 616 " (cutoff:3.500A) removed outlier: 4.705A pdb=" N HIS 2 621 " --> pdb=" O ARG 2 617 " (cutoff:3.500A) removed outlier: 5.280A pdb=" N GLU 2 622 " --> pdb=" O THR 2 618 " (cutoff:3.500A) removed outlier: 4.942A pdb=" N ALA 2 623 " --> pdb=" O SER 2 619 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N GLU 2 625 " --> pdb=" O HIS 2 621 " (cutoff:3.500A) Processing helix chain '2' and resid 662 through 668 removed outlier: 3.712A pdb=" N ASN 2 666 " --> pdb=" O PRO 2 662 " (cutoff:3.500A) removed outlier: 5.511A pdb=" N SER 2 668 " --> pdb=" O ALA 2 664 " (cutoff:3.500A) Processing helix chain '2' and resid 670 through 677 removed outlier: 4.167A pdb=" N ARG 2 676 " --> pdb=" O PRO 2 672 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N PHE 2 677 " --> pdb=" O ILE 2 673 " (cutoff:3.500A) Processing helix chain '2' and resid 688 through 707 Processing helix chain '2' and resid 739 through 756 removed outlier: 3.807A pdb=" N LEU 2 745 " --> pdb=" O ARG 2 741 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N GLU 2 754 " --> pdb=" O LYS 2 750 " (cutoff:3.500A) removed outlier: 4.547A pdb=" N ILE 2 755 " --> pdb=" O LYS 2 751 " (cutoff:3.500A) Processing helix chain '2' and resid 759 through 773 removed outlier: 3.570A pdb=" N LYS 2 765 " --> pdb=" O GLU 2 761 " (cutoff:3.500A) Processing helix chain '2' and resid 782 through 800 removed outlier: 3.803A pdb=" N VAL 2 786 " --> pdb=" O ASP 2 782 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N SER 2 797 " --> pdb=" O LEU 2 793 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N ILE 2 798 " --> pdb=" O ARG 2 794 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N SER 2 799 " --> pdb=" O ARG 2 795 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N THR 2 800 " --> pdb=" O GLU 2 796 " (cutoff:3.500A) Processing helix chain '2' and resid 806 through 825 removed outlier: 3.941A pdb=" N LEU 2 810 " --> pdb=" O THR 2 806 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N GLU 2 811 " --> pdb=" O VAL 2 807 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N SER 2 812 " --> pdb=" O ARG 2 808 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N ILE 2 813 " --> pdb=" O HIS 2 809 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N LEU 2 814 " --> pdb=" O LEU 2 810 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N ARG 2 824 " --> pdb=" O PHE 2 820 " (cutoff:3.500A) Processing helix chain '2' and resid 830 through 849 removed outlier: 3.555A pdb=" N LEU 2 834 " --> pdb=" O SER 2 830 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N ASP 2 847 " --> pdb=" O ASP 2 843 " (cutoff:3.500A) removed outlier: 4.545A pdb=" N ALA 2 848 " --> pdb=" O SER 2 844 " (cutoff:3.500A) removed outlier: 4.427A pdb=" N GLN 2 849 " --> pdb=" O PHE 2 845 " (cutoff:3.500A) Processing helix chain '2' and resid 850 through 866 removed outlier: 4.667A pdb=" N ARG 2 855 " --> pdb=" O VAL 2 851 " (cutoff:3.500A) removed outlier: 5.081A pdb=" N GLN 2 856 " --> pdb=" O SER 2 852 " (cutoff:3.500A) removed outlier: 4.648A pdb=" N ILE 2 863 " --> pdb=" O ARG 2 859 " (cutoff:3.500A) removed outlier: 5.860A pdb=" N TYR 2 864 " --> pdb=" O SER 2 860 " (cutoff:3.500A) removed outlier: 4.331A pdb=" N THR 2 865 " --> pdb=" O PHE 2 861 " (cutoff:3.500A) removed outlier: 4.229A pdb=" N LEU 2 866 " --> pdb=" O ALA 2 862 " (cutoff:3.500A) Processing helix chain '2' and resid 462 through 467 removed outlier: 4.668A pdb=" N ASN 2 465 " --> pdb=" O ASN 2 462 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N GLU 2 466 " --> pdb=" O THR 2 463 " (cutoff:3.500A) Processing helix chain 'a' and resid 182 through 188 removed outlier: 4.212A pdb=" N SER a 187 " --> pdb=" O LEU a 183 " (cutoff:3.500A) removed outlier: 4.582A pdb=" N ASN a 188 " --> pdb=" O GLU a 184 " (cutoff:3.500A) Processing helix chain 'a' and resid 193 through 200 Processing helix chain 'a' and resid 201 through 217 removed outlier: 3.532A pdb=" N ARG a 205 " --> pdb=" O PRO a 201 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N THR a 206 " --> pdb=" O ASN a 202 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ALA a 208 " --> pdb=" O SER a 204 " (cutoff:3.500A) Processing helix chain 'a' and resid 225 through 238 removed outlier: 3.787A pdb=" N ALA a 229 " --> pdb=" O SER a 225 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N GLU a 236 " --> pdb=" O ARG a 232 " (cutoff:3.500A) Processing helix chain 'a' and resid 245 through 253 removed outlier: 3.563A pdb=" N LEU a 249 " --> pdb=" O ASN a 245 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N SER a 252 " --> pdb=" O HIS a 248 " (cutoff:3.500A) removed outlier: 4.405A pdb=" N LYS a 253 " --> pdb=" O LEU a 249 " (cutoff:3.500A) Processing helix chain 'a' and resid 254 through 263 Processing helix chain 'a' and resid 265 through 283 removed outlier: 3.545A pdb=" N LYS a 269 " --> pdb=" O GLU a 265 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N ILE a 270 " --> pdb=" O GLU a 266 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N LEU a 281 " --> pdb=" O GLU a 277 " (cutoff:3.500A) removed outlier: 4.257A pdb=" N HIS a 282 " --> pdb=" O ALA a 278 " (cutoff:3.500A) Processing helix chain 'a' and resid 285 through 290 removed outlier: 4.747A pdb=" N ILE a 289 " --> pdb=" O ASP a 285 " (cutoff:3.500A) Processing helix chain 'a' and resid 393 through 398 Proline residue: a 398 - end of helix Processing helix chain 'a' and resid 435 through 443 Processing helix chain 'a' and resid 477 through 490 removed outlier: 4.010A pdb=" N ARG a 489 " --> pdb=" O ARG a 485 " (cutoff:3.500A) removed outlier: 4.392A pdb=" N ASP a 490 " --> pdb=" O LYS a 486 " (cutoff:3.500A) Processing helix chain 'a' and resid 492 through 501 removed outlier: 3.523A pdb=" N MET a 501 " --> pdb=" O ILE a 497 " (cutoff:3.500A) Processing helix chain 'a' and resid 508 through 521 Processing helix chain 'a' and resid 548 through 560 removed outlier: 3.507A pdb=" N ILE a 552 " --> pdb=" O ALA a 548 " (cutoff:3.500A) Processing helix chain 'a' and resid 572 through 577 removed outlier: 3.581A pdb=" N LEU a 576 " --> pdb=" O SER a 572 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N THR a 577 " --> pdb=" O ALA a 573 " (cutoff:3.500A) No H-bonds generated for 'chain 'a' and resid 572 through 577' Processing helix chain 'a' and resid 594 through 600 removed outlier: 3.783A pdb=" N ASP a 600 " --> pdb=" O LEU a 596 " (cutoff:3.500A) Processing helix chain 'a' and resid 613 through 626 removed outlier: 3.853A pdb=" N SER a 619 " --> pdb=" O GLN a 615 " (cutoff:3.500A) removed outlier: 4.639A pdb=" N ILE a 620 " --> pdb=" O ASP a 616 " (cutoff:3.500A) removed outlier: 4.705A pdb=" N HIS a 621 " --> pdb=" O ARG a 617 " (cutoff:3.500A) removed outlier: 5.279A pdb=" N GLU a 622 " --> pdb=" O THR a 618 " (cutoff:3.500A) removed outlier: 4.943A pdb=" N ALA a 623 " --> pdb=" O SER a 619 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N GLU a 625 " --> pdb=" O HIS a 621 " (cutoff:3.500A) Processing helix chain 'a' and resid 662 through 668 removed outlier: 3.712A pdb=" N ASN a 666 " --> pdb=" O PRO a 662 " (cutoff:3.500A) removed outlier: 5.511A pdb=" N SER a 668 " --> pdb=" O ALA a 664 " (cutoff:3.500A) Processing helix chain 'a' and resid 670 through 677 removed outlier: 4.165A pdb=" N ARG a 676 " --> pdb=" O PRO a 672 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N PHE a 677 " --> pdb=" O ILE a 673 " (cutoff:3.500A) Processing helix chain 'a' and resid 688 through 707 Processing helix chain 'a' and resid 739 through 756 removed outlier: 3.806A pdb=" N LEU a 745 " --> pdb=" O ARG a 741 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N GLU a 754 " --> pdb=" O LYS a 750 " (cutoff:3.500A) removed outlier: 4.547A pdb=" N ILE a 755 " --> pdb=" O LYS a 751 " (cutoff:3.500A) Processing helix chain 'a' and resid 759 through 773 removed outlier: 3.570A pdb=" N LYS a 765 " --> pdb=" O GLU a 761 " (cutoff:3.500A) Processing helix chain 'a' and resid 782 through 800 removed outlier: 3.803A pdb=" N VAL a 786 " --> pdb=" O ASP a 782 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N SER a 797 " --> pdb=" O LEU a 793 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N ILE a 798 " --> pdb=" O ARG a 794 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N SER a 799 " --> pdb=" O ARG a 795 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N THR a 800 " --> pdb=" O GLU a 796 " (cutoff:3.500A) Processing helix chain 'a' and resid 806 through 825 removed outlier: 3.940A pdb=" N LEU a 810 " --> pdb=" O THR a 806 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N GLU a 811 " --> pdb=" O VAL a 807 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N SER a 812 " --> pdb=" O ARG a 808 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N ILE a 813 " --> pdb=" O HIS a 809 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N LEU a 814 " --> pdb=" O LEU a 810 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N ARG a 824 " --> pdb=" O PHE a 820 " (cutoff:3.500A) Processing helix chain 'a' and resid 830 through 849 removed outlier: 3.554A pdb=" N LEU a 834 " --> pdb=" O SER a 830 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ASP a 847 " --> pdb=" O ASP a 843 " (cutoff:3.500A) removed outlier: 4.545A pdb=" N ALA a 848 " --> pdb=" O SER a 844 " (cutoff:3.500A) removed outlier: 4.427A pdb=" N GLN a 849 " --> pdb=" O PHE a 845 " (cutoff:3.500A) Processing helix chain 'a' and resid 850 through 866 removed outlier: 4.666A pdb=" N ARG a 855 " --> pdb=" O VAL a 851 " (cutoff:3.500A) removed outlier: 5.080A pdb=" N GLN a 856 " --> pdb=" O SER a 852 " (cutoff:3.500A) removed outlier: 4.648A pdb=" N ILE a 863 " --> pdb=" O ARG a 859 " (cutoff:3.500A) removed outlier: 5.860A pdb=" N TYR a 864 " --> pdb=" O SER a 860 " (cutoff:3.500A) removed outlier: 4.331A pdb=" N THR a 865 " --> pdb=" O PHE a 861 " (cutoff:3.500A) removed outlier: 4.228A pdb=" N LEU a 866 " --> pdb=" O ALA a 862 " (cutoff:3.500A) Processing helix chain 'a' and resid 462 through 467 removed outlier: 4.669A pdb=" N ASN a 465 " --> pdb=" O ASN a 462 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N GLU a 466 " --> pdb=" O THR a 463 " (cutoff:3.500A) Processing helix chain '3' and resid 18 through 36 removed outlier: 4.547A pdb=" N THR 3 36 " --> pdb=" O LEU 3 32 " (cutoff:3.500A) Processing helix chain '3' and resid 37 through 56 removed outlier: 3.568A pdb=" N ALA 3 54 " --> pdb=" O SER 3 50 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N ASN 3 55 " --> pdb=" O ASN 3 51 " (cutoff:3.500A) removed outlier: 5.554A pdb=" N TYR 3 56 " --> pdb=" O ASN 3 52 " (cutoff:3.500A) Processing helix chain '3' and resid 99 through 107 removed outlier: 3.637A pdb=" N LEU 3 103 " --> pdb=" O SER 3 99 " (cutoff:3.500A) Processing helix chain '3' and resid 108 through 117 Processing helix chain '3' and resid 118 through 138 Proline residue: 3 123 - end of helix removed outlier: 5.240A pdb=" N ASP 3 138 " --> pdb=" O ASP 3 134 " (cutoff:3.500A) Processing helix chain '3' and resid 145 through 150 removed outlier: 3.923A pdb=" N SER 3 149 " --> pdb=" O SER 3 145 " (cutoff:3.500A) removed outlier: 4.447A pdb=" N ARG 3 150 " --> pdb=" O ALA 3 146 " (cutoff:3.500A) No H-bonds generated for 'chain '3' and resid 145 through 150' Processing helix chain '3' and resid 216 through 221 removed outlier: 5.323A pdb=" N LEU 3 221 " --> pdb=" O ALA 3 217 " (cutoff:3.500A) Processing helix chain '3' and resid 343 through 356 removed outlier: 3.749A pdb=" N LYS 3 355 " --> pdb=" O ASN 3 351 " (cutoff:3.500A) removed outlier: 4.217A pdb=" N LYS 3 356 " --> pdb=" O LYS 3 352 " (cutoff:3.500A) Processing helix chain '3' and resid 358 through 367 removed outlier: 3.826A pdb=" N ILE 3 362 " --> pdb=" O ASP 3 358 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N LEU 3 367 " --> pdb=" O LEU 3 363 " (cutoff:3.500A) Processing helix chain '3' and resid 374 through 387 removed outlier: 4.033A pdb=" N GLY 3 387 " --> pdb=" O LEU 3 383 " (cutoff:3.500A) Processing helix chain '3' and resid 414 through 426 removed outlier: 3.928A pdb=" N LEU 3 418 " --> pdb=" O ALA 3 414 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N LEU 3 419 " --> pdb=" O LYS 3 415 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N PHE 3 421 " --> pdb=" O GLN 3 417 " (cutoff:3.500A) Processing helix chain '3' and resid 438 through 444 removed outlier: 3.701A pdb=" N ALA 3 444 " --> pdb=" O VAL 3 440 " (cutoff:3.500A) Processing helix chain '3' and resid 460 through 466 removed outlier: 4.106A pdb=" N ASP 3 466 " --> pdb=" O MET 3 462 " (cutoff:3.500A) Processing helix chain '3' and resid 479 through 492 removed outlier: 4.457A pdb=" N ALA 3 485 " --> pdb=" O VAL 3 481 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N ILE 3 486 " --> pdb=" O ASP 3 482 " (cutoff:3.500A) Processing helix chain '3' and resid 528 through 534 removed outlier: 4.936A pdb=" N ALA 3 534 " --> pdb=" O HIS 3 530 " (cutoff:3.500A) Processing helix chain '3' and resid 536 through 543 removed outlier: 3.991A pdb=" N ARG 3 542 " --> pdb=" O SER 3 538 " (cutoff:3.500A) removed outlier: 4.394A pdb=" N PHE 3 543 " --> pdb=" O LEU 3 539 " (cutoff:3.500A) Processing helix chain '3' and resid 554 through 571 removed outlier: 3.848A pdb=" N ARG 3 570 " --> pdb=" O LEU 3 566 " (cutoff:3.500A) removed outlier: 4.547A pdb=" N TYR 3 571 " --> pdb=" O ARG 3 567 " (cutoff:3.500A) Processing helix chain '3' and resid 652 through 666 Processing helix chain '3' and resid 672 through 689 removed outlier: 3.607A pdb=" N VAL 3 678 " --> pdb=" O GLU 3 674 " (cutoff:3.500A) removed outlier: 4.232A pdb=" N ASP 3 689 " --> pdb=" O ASP 3 685 " (cutoff:3.500A) Processing helix chain '3' and resid 698 through 717 removed outlier: 4.794A pdb=" N LEU 3 702 " --> pdb=" O THR 3 698 " (cutoff:3.500A) removed outlier: 4.581A pdb=" N GLU 3 703 " --> pdb=" O ALA 3 699 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N LEU 3 717 " --> pdb=" O ALA 3 713 " (cutoff:3.500A) Processing helix chain '3' and resid 722 through 738 removed outlier: 3.538A pdb=" N ALA 3 726 " --> pdb=" O ASN 3 722 " (cutoff:3.500A) Processing helix chain 'b' and resid 18 through 36 removed outlier: 4.545A pdb=" N THR b 36 " --> pdb=" O LEU b 32 " (cutoff:3.500A) Processing helix chain 'b' and resid 37 through 56 removed outlier: 3.568A pdb=" N ALA b 54 " --> pdb=" O SER b 50 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N ASN b 55 " --> pdb=" O ASN b 51 " (cutoff:3.500A) removed outlier: 5.554A pdb=" N TYR b 56 " --> pdb=" O ASN b 52 " (cutoff:3.500A) Processing helix chain 'b' and resid 99 through 107 removed outlier: 3.637A pdb=" N LEU b 103 " --> pdb=" O SER b 99 " (cutoff:3.500A) Processing helix chain 'b' and resid 108 through 117 Processing helix chain 'b' and resid 118 through 138 Proline residue: b 123 - end of helix removed outlier: 5.240A pdb=" N ASP b 138 " --> pdb=" O ASP b 134 " (cutoff:3.500A) Processing helix chain 'b' and resid 145 through 150 removed outlier: 3.924A pdb=" N SER b 149 " --> pdb=" O SER b 145 " (cutoff:3.500A) removed outlier: 4.448A pdb=" N ARG b 150 " --> pdb=" O ALA b 146 " (cutoff:3.500A) No H-bonds generated for 'chain 'b' and resid 145 through 150' Processing helix chain 'b' and resid 216 through 221 removed outlier: 5.321A pdb=" N LEU b 221 " --> pdb=" O ALA b 217 " (cutoff:3.500A) Processing helix chain 'b' and resid 343 through 356 removed outlier: 3.751A pdb=" N LYS b 355 " --> pdb=" O ASN b 351 " (cutoff:3.500A) removed outlier: 4.215A pdb=" N LYS b 356 " --> pdb=" O LYS b 352 " (cutoff:3.500A) Processing helix chain 'b' and resid 358 through 367 removed outlier: 3.827A pdb=" N ILE b 362 " --> pdb=" O ASP b 358 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N LEU b 367 " --> pdb=" O LEU b 363 " (cutoff:3.500A) Processing helix chain 'b' and resid 374 through 387 removed outlier: 4.034A pdb=" N GLY b 387 " --> pdb=" O LEU b 383 " (cutoff:3.500A) Processing helix chain 'b' and resid 414 through 426 removed outlier: 3.926A pdb=" N LEU b 418 " --> pdb=" O ALA b 414 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N LEU b 419 " --> pdb=" O LYS b 415 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N PHE b 421 " --> pdb=" O GLN b 417 " (cutoff:3.500A) Processing helix chain 'b' and resid 438 through 444 removed outlier: 3.700A pdb=" N ALA b 444 " --> pdb=" O VAL b 440 " (cutoff:3.500A) Processing helix chain 'b' and resid 460 through 466 removed outlier: 4.106A pdb=" N ASP b 466 " --> pdb=" O MET b 462 " (cutoff:3.500A) Processing helix chain 'b' and resid 479 through 492 removed outlier: 4.456A pdb=" N ALA b 485 " --> pdb=" O VAL b 481 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N ILE b 486 " --> pdb=" O ASP b 482 " (cutoff:3.500A) Processing helix chain 'b' and resid 528 through 534 removed outlier: 4.935A pdb=" N ALA b 534 " --> pdb=" O HIS b 530 " (cutoff:3.500A) Processing helix chain 'b' and resid 536 through 543 removed outlier: 3.992A pdb=" N ARG b 542 " --> pdb=" O SER b 538 " (cutoff:3.500A) removed outlier: 4.394A pdb=" N PHE b 543 " --> pdb=" O LEU b 539 " (cutoff:3.500A) Processing helix chain 'b' and resid 554 through 571 removed outlier: 3.849A pdb=" N ARG b 570 " --> pdb=" O LEU b 566 " (cutoff:3.500A) removed outlier: 4.546A pdb=" N TYR b 571 " --> pdb=" O ARG b 567 " (cutoff:3.500A) Processing helix chain 'b' and resid 652 through 666 Processing helix chain 'b' and resid 672 through 689 removed outlier: 3.606A pdb=" N VAL b 678 " --> pdb=" O GLU b 674 " (cutoff:3.500A) removed outlier: 4.232A pdb=" N ASP b 689 " --> pdb=" O ASP b 685 " (cutoff:3.500A) Processing helix chain 'b' and resid 698 through 717 removed outlier: 4.794A pdb=" N LEU b 702 " --> pdb=" O THR b 698 " (cutoff:3.500A) removed outlier: 4.580A pdb=" N GLU b 703 " --> pdb=" O ALA b 699 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N LEU b 717 " --> pdb=" O ALA b 713 " (cutoff:3.500A) Processing helix chain 'b' and resid 722 through 738 removed outlier: 3.537A pdb=" N ALA b 726 " --> pdb=" O ASN b 722 " (cutoff:3.500A) Processing helix chain '4' and resid 186 through 200 removed outlier: 3.628A pdb=" N CYS 4 190 " --> pdb=" O SER 4 186 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N THR 4 192 " --> pdb=" O GLN 4 188 " (cutoff:3.500A) Processing helix chain '4' and resid 202 through 211 Processing helix chain '4' and resid 219 through 237 removed outlier: 3.697A pdb=" N GLU 4 223 " --> pdb=" O THR 4 219 " (cutoff:3.500A) removed outlier: 4.893A pdb=" N LEU 4 224 " --> pdb=" O THR 4 220 " (cutoff:3.500A) removed outlier: 7.197A pdb=" N TYR 4 225 " --> pdb=" O ASP 4 221 " (cutoff:3.500A) removed outlier: 8.866A pdb=" N TYR 4 226 " --> pdb=" O GLU 4 222 " (cutoff:3.500A) removed outlier: 6.210A pdb=" N ILE 4 227 " --> pdb=" O GLU 4 223 " (cutoff:3.500A) Processing helix chain '4' and resid 244 through 251 removed outlier: 4.159A pdb=" N TYR 4 251 " --> pdb=" O ASN 4 247 " (cutoff:3.500A) Processing helix chain '4' and resid 254 through 264 removed outlier: 3.807A pdb=" N TYR 4 258 " --> pdb=" O THR 4 254 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N HIS 4 259 " --> pdb=" O GLU 4 255 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N LEU 4 262 " --> pdb=" O TYR 4 258 " (cutoff:3.500A) removed outlier: 4.200A pdb=" N ASN 4 263 " --> pdb=" O HIS 4 259 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N TYR 4 264 " --> pdb=" O GLN 4 260 " (cutoff:3.500A) Processing helix chain '4' and resid 265 through 288 removed outlier: 3.924A pdb=" N ASP 4 278 " --> pdb=" O GLN 4 274 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N MET 4 280 " --> pdb=" O ILE 4 276 " (cutoff:3.500A) removed outlier: 4.631A pdb=" N VAL 4 281 " --> pdb=" O LYS 4 277 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N LEU 4 283 " --> pdb=" O CYS 4 279 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N VAL 4 285 " --> pdb=" O VAL 4 281 " (cutoff:3.500A) removed outlier: 4.777A pdb=" N ASP 4 286 " --> pdb=" O SER 4 282 " (cutoff:3.500A) removed outlier: 5.084A pdb=" N ASN 4 287 " --> pdb=" O LEU 4 283 " (cutoff:3.500A) removed outlier: 4.210A pdb=" N ASN 4 288 " --> pdb=" O ILE 4 284 " (cutoff:3.500A) Processing helix chain '4' and resid 293 through 300 removed outlier: 4.984A pdb=" N PHE 4 300 " --> pdb=" O ILE 4 296 " (cutoff:3.500A) Processing helix chain '4' and resid 402 through 407 removed outlier: 3.672A pdb=" N VAL 4 406 " --> pdb=" O THR 4 402 " (cutoff:3.500A) Proline residue: 4 407 - end of helix No H-bonds generated for 'chain '4' and resid 402 through 407' Processing helix chain '4' and resid 502 through 515 removed outlier: 3.905A pdb=" N ARG 4 515 " --> pdb=" O GLU 4 511 " (cutoff:3.500A) Processing helix chain '4' and resid 517 through 528 removed outlier: 3.850A pdb=" N LEU 4 521 " --> pdb=" O ASP 4 517 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N LEU 4 522 " --> pdb=" O LEU 4 518 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N ILE 4 526 " --> pdb=" O LEU 4 522 " (cutoff:3.500A) removed outlier: 4.735A pdb=" N ALA 4 527 " --> pdb=" O ALA 4 523 " (cutoff:3.500A) Proline residue: 4 528 - end of helix Processing helix chain '4' and resid 533 through 546 removed outlier: 3.854A pdb=" N PHE 4 545 " --> pdb=" O LEU 4 541 " (cutoff:3.500A) Processing helix chain '4' and resid 573 through 586 removed outlier: 3.859A pdb=" N LYS 4 583 " --> pdb=" O GLN 4 579 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N ILE 4 584 " --> pdb=" O TYR 4 580 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N THR 4 585 " --> pdb=" O VAL 4 581 " (cutoff:3.500A) Proline residue: 4 586 - end of helix Processing helix chain '4' and resid 619 through 625 removed outlier: 3.678A pdb=" N ASP 4 625 " --> pdb=" O LEU 4 621 " (cutoff:3.500A) Processing helix chain '4' and resid 638 through 651 removed outlier: 4.227A pdb=" N SER 4 643 " --> pdb=" O ASP 4 639 " (cutoff:3.500A) removed outlier: 4.468A pdb=" N VAL 4 644 " --> pdb=" O SER 4 640 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N LEU 4 645 " --> pdb=" O THR 4 641 " (cutoff:3.500A) Processing helix chain '4' and resid 687 through 693 removed outlier: 4.181A pdb=" N ASN 4 691 " --> pdb=" O PRO 4 687 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N ASP 4 693 " --> pdb=" O THR 4 689 " (cutoff:3.500A) Processing helix chain '4' and resid 695 through 702 removed outlier: 3.807A pdb=" N PHE 4 702 " --> pdb=" O LEU 4 698 " (cutoff:3.500A) Processing helix chain '4' and resid 713 through 730 removed outlier: 4.901A pdb=" N GLU 4 730 " --> pdb=" O ASN 4 726 " (cutoff:3.500A) Processing helix chain '4' and resid 745 through 757 removed outlier: 3.578A pdb=" N MET 4 749 " --> pdb=" O GLU 4 745 " (cutoff:3.500A) Processing helix chain '4' and resid 763 through 779 removed outlier: 3.559A pdb=" N GLU 4 769 " --> pdb=" O ALA 4 765 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N ARG 4 772 " --> pdb=" O THR 4 768 " (cutoff:3.500A) Processing helix chain '4' and resid 794 through 813 removed outlier: 4.214A pdb=" N LEU 4 798 " --> pdb=" O THR 4 794 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N GLU 4 799 " --> pdb=" O THR 4 795 " (cutoff:3.500A) removed outlier: 4.438A pdb=" N LYS 4 812 " --> pdb=" O HIS 4 808 " (cutoff:3.500A) removed outlier: 5.109A pdb=" N LEU 4 813 " --> pdb=" O ALA 4 809 " (cutoff:3.500A) Processing helix chain '4' and resid 818 through 835 removed outlier: 3.502A pdb=" N VAL 4 822 " --> pdb=" O GLU 4 818 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N ASP 4 835 " --> pdb=" O SER 4 831 " (cutoff:3.500A) Processing helix chain 'c' and resid 186 through 200 removed outlier: 3.627A pdb=" N CYS c 190 " --> pdb=" O SER c 186 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N THR c 192 " --> pdb=" O GLN c 188 " (cutoff:3.500A) Processing helix chain 'c' and resid 202 through 211 Processing helix chain 'c' and resid 219 through 237 removed outlier: 3.696A pdb=" N GLU c 223 " --> pdb=" O THR c 219 " (cutoff:3.500A) removed outlier: 4.893A pdb=" N LEU c 224 " --> pdb=" O THR c 220 " (cutoff:3.500A) removed outlier: 7.199A pdb=" N TYR c 225 " --> pdb=" O ASP c 221 " (cutoff:3.500A) removed outlier: 8.867A pdb=" N TYR c 226 " --> pdb=" O GLU c 222 " (cutoff:3.500A) removed outlier: 6.210A pdb=" N ILE c 227 " --> pdb=" O GLU c 223 " (cutoff:3.500A) Processing helix chain 'c' and resid 244 through 251 removed outlier: 4.159A pdb=" N TYR c 251 " --> pdb=" O ASN c 247 " (cutoff:3.500A) Processing helix chain 'c' and resid 254 through 264 removed outlier: 3.808A pdb=" N TYR c 258 " --> pdb=" O THR c 254 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N HIS c 259 " --> pdb=" O GLU c 255 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N LEU c 262 " --> pdb=" O TYR c 258 " (cutoff:3.500A) removed outlier: 4.199A pdb=" N ASN c 263 " --> pdb=" O HIS c 259 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N TYR c 264 " --> pdb=" O GLN c 260 " (cutoff:3.500A) Processing helix chain 'c' and resid 265 through 288 removed outlier: 3.924A pdb=" N ASP c 278 " --> pdb=" O GLN c 274 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N MET c 280 " --> pdb=" O ILE c 276 " (cutoff:3.500A) removed outlier: 4.631A pdb=" N VAL c 281 " --> pdb=" O LYS c 277 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N LEU c 283 " --> pdb=" O CYS c 279 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N VAL c 285 " --> pdb=" O VAL c 281 " (cutoff:3.500A) removed outlier: 4.777A pdb=" N ASP c 286 " --> pdb=" O SER c 282 " (cutoff:3.500A) removed outlier: 5.084A pdb=" N ASN c 287 " --> pdb=" O LEU c 283 " (cutoff:3.500A) removed outlier: 4.211A pdb=" N ASN c 288 " --> pdb=" O ILE c 284 " (cutoff:3.500A) Processing helix chain 'c' and resid 293 through 300 removed outlier: 4.984A pdb=" N PHE c 300 " --> pdb=" O ILE c 296 " (cutoff:3.500A) Processing helix chain 'c' and resid 402 through 407 removed outlier: 3.672A pdb=" N VAL c 406 " --> pdb=" O THR c 402 " (cutoff:3.500A) Proline residue: c 407 - end of helix No H-bonds generated for 'chain 'c' and resid 402 through 407' Processing helix chain 'c' and resid 502 through 515 removed outlier: 3.905A pdb=" N ARG c 515 " --> pdb=" O GLU c 511 " (cutoff:3.500A) Processing helix chain 'c' and resid 517 through 528 removed outlier: 3.848A pdb=" N LEU c 521 " --> pdb=" O ASP c 517 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N LEU c 522 " --> pdb=" O LEU c 518 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N ILE c 526 " --> pdb=" O LEU c 522 " (cutoff:3.500A) removed outlier: 4.735A pdb=" N ALA c 527 " --> pdb=" O ALA c 523 " (cutoff:3.500A) Proline residue: c 528 - end of helix Processing helix chain 'c' and resid 533 through 546 removed outlier: 3.855A pdb=" N PHE c 545 " --> pdb=" O LEU c 541 " (cutoff:3.500A) Processing helix chain 'c' and resid 573 through 586 removed outlier: 3.859A pdb=" N LYS c 583 " --> pdb=" O GLN c 579 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N ILE c 584 " --> pdb=" O TYR c 580 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N THR c 585 " --> pdb=" O VAL c 581 " (cutoff:3.500A) Proline residue: c 586 - end of helix Processing helix chain 'c' and resid 619 through 625 removed outlier: 3.675A pdb=" N ASP c 625 " --> pdb=" O LEU c 621 " (cutoff:3.500A) Processing helix chain 'c' and resid 638 through 651 removed outlier: 4.226A pdb=" N SER c 643 " --> pdb=" O ASP c 639 " (cutoff:3.500A) removed outlier: 4.468A pdb=" N VAL c 644 " --> pdb=" O SER c 640 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N LEU c 645 " --> pdb=" O THR c 641 " (cutoff:3.500A) Processing helix chain 'c' and resid 687 through 693 removed outlier: 4.181A pdb=" N ASN c 691 " --> pdb=" O PRO c 687 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N ASP c 693 " --> pdb=" O THR c 689 " (cutoff:3.500A) Processing helix chain 'c' and resid 695 through 702 removed outlier: 3.806A pdb=" N PHE c 702 " --> pdb=" O LEU c 698 " (cutoff:3.500A) Processing helix chain 'c' and resid 713 through 730 removed outlier: 4.901A pdb=" N GLU c 730 " --> pdb=" O ASN c 726 " (cutoff:3.500A) Processing helix chain 'c' and resid 745 through 757 removed outlier: 3.579A pdb=" N MET c 749 " --> pdb=" O GLU c 745 " (cutoff:3.500A) Processing helix chain 'c' and resid 763 through 779 removed outlier: 3.560A pdb=" N GLU c 769 " --> pdb=" O ALA c 765 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N ARG c 772 " --> pdb=" O THR c 768 " (cutoff:3.500A) Processing helix chain 'c' and resid 794 through 813 removed outlier: 4.213A pdb=" N LEU c 798 " --> pdb=" O THR c 794 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N GLU c 799 " --> pdb=" O THR c 795 " (cutoff:3.500A) removed outlier: 4.436A pdb=" N LYS c 812 " --> pdb=" O HIS c 808 " (cutoff:3.500A) removed outlier: 5.110A pdb=" N LEU c 813 " --> pdb=" O ALA c 809 " (cutoff:3.500A) Processing helix chain 'c' and resid 818 through 835 removed outlier: 3.502A pdb=" N VAL c 822 " --> pdb=" O GLU c 818 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N ASP c 835 " --> pdb=" O SER c 831 " (cutoff:3.500A) Processing helix chain '5' and resid 21 through 37 removed outlier: 4.634A pdb=" N GLU 5 26 " --> pdb=" O ASP 5 22 " (cutoff:3.500A) Processing helix chain '5' and resid 44 through 57 removed outlier: 3.584A pdb=" N LEU 5 50 " --> pdb=" O TYR 5 46 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N ARG 5 51 " --> pdb=" O ARG 5 47 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N VAL 5 56 " --> pdb=" O ASN 5 52 " (cutoff:3.500A) Processing helix chain '5' and resid 64 through 72 Processing helix chain '5' and resid 73 through 83 removed outlier: 3.561A pdb=" N ASP 5 81 " --> pdb=" O LYS 5 77 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N GLU 5 82 " --> pdb=" O LYS 5 78 " (cutoff:3.500A) Proline residue: 5 83 - end of helix Processing helix chain '5' and resid 84 through 103 Proline residue: 5 88 - end of helix Processing helix chain '5' and resid 350 through 363 removed outlier: 3.823A pdb=" N GLU 5 356 " --> pdb=" O GLU 5 352 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N ASN 5 363 " --> pdb=" O GLN 5 359 " (cutoff:3.500A) Processing helix chain '5' and resid 365 through 374 removed outlier: 3.723A pdb=" N ILE 5 374 " --> pdb=" O LEU 5 370 " (cutoff:3.500A) Processing helix chain '5' and resid 381 through 394 Processing helix chain '5' and resid 421 through 433 removed outlier: 3.829A pdb=" N LEU 5 425 " --> pdb=" O ALA 5 421 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N LEU 5 426 " --> pdb=" O LYS 5 422 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N LYS 5 427 " --> pdb=" O SER 5 423 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N PHE 5 428 " --> pdb=" O GLN 5 424 " (cutoff:3.500A) Processing helix chain '5' and resid 445 through 450 Processing helix chain '5' and resid 467 through 473 removed outlier: 4.270A pdb=" N ASP 5 473 " --> pdb=" O MET 5 469 " (cutoff:3.500A) Processing helix chain '5' and resid 486 through 499 removed outlier: 3.754A pdb=" N VAL 5 491 " --> pdb=" O ASP 5 487 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N ALA 5 492 " --> pdb=" O GLU 5 488 " (cutoff:3.500A) removed outlier: 4.520A pdb=" N ILE 5 493 " --> pdb=" O ASP 5 489 " (cutoff:3.500A) removed outlier: 4.665A pdb=" N HIS 5 494 " --> pdb=" O ARG 5 490 " (cutoff:3.500A) removed outlier: 5.175A pdb=" N GLU 5 495 " --> pdb=" O VAL 5 491 " (cutoff:3.500A) removed outlier: 4.860A pdb=" N ALA 5 496 " --> pdb=" O ALA 5 492 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N GLU 5 498 " --> pdb=" O HIS 5 494 " (cutoff:3.500A) Processing helix chain '5' and resid 535 through 541 removed outlier: 3.516A pdb=" N ASN 5 539 " --> pdb=" O SER 5 535 " (cutoff:3.500A) removed outlier: 5.715A pdb=" N ASP 5 541 " --> pdb=" O GLY 5 537 " (cutoff:3.500A) Processing helix chain '5' and resid 543 through 550 removed outlier: 4.416A pdb=" N ARG 5 549 " --> pdb=" O THR 5 545 " (cutoff:3.500A) removed outlier: 4.247A pdb=" N PHE 5 550 " --> pdb=" O ILE 5 546 " (cutoff:3.500A) Processing helix chain '5' and resid 561 through 578 removed outlier: 3.504A pdb=" N GLY 5 578 " --> pdb=" O ASN 5 574 " (cutoff:3.500A) Processing helix chain '5' and resid 579 through 591 removed outlier: 3.609A pdb=" N MET 5 583 " --> pdb=" O ASN 5 579 " (cutoff:3.500A) removed outlier: 5.179A pdb=" N GLN 5 586 " --> pdb=" O ALA 5 582 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N GLN 5 587 " --> pdb=" O MET 5 583 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N GLY 5 591 " --> pdb=" O GLN 5 587 " (cutoff:3.500A) Processing helix chain '5' and resid 595 through 610 Processing helix chain '5' and resid 615 through 641 removed outlier: 3.545A pdb=" N SER 5 624 " --> pdb=" O GLU 5 620 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N LEU 5 633 " --> pdb=" O ILE 5 629 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N LEU 5 634 " --> pdb=" O ARG 5 630 " (cutoff:3.500A) Processing helix chain '5' and resid 649 through 668 removed outlier: 3.595A pdb=" N LEU 5 653 " --> pdb=" O THR 5 649 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N LEU 5 666 " --> pdb=" O SER 5 662 " (cutoff:3.500A) removed outlier: 4.362A pdb=" N GLU 5 667 " --> pdb=" O LEU 5 663 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N LEU 5 668 " --> pdb=" O ALA 5 664 " (cutoff:3.500A) Processing helix chain '5' and resid 673 through 694 removed outlier: 3.620A pdb=" N GLU 5 679 " --> pdb=" O ARG 5 675 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N MET 5 689 " --> pdb=" O GLN 5 685 " (cutoff:3.500A) removed outlier: 4.744A pdb=" N ASP 5 690 " --> pdb=" O ALA 5 686 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N ALA 5 691 " --> pdb=" O SER 5 687 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N GLN 5 694 " --> pdb=" O ASP 5 690 " (cutoff:3.500A) Processing helix chain '5' and resid 706 through 723 removed outlier: 4.898A pdb=" N ARG 5 712 " --> pdb=" O LEU 5 708 " (cutoff:3.500A) Proline residue: 5 723 - end of helix Processing helix chain '5' and resid 729 through 739 removed outlier: 3.903A pdb=" N PHE 5 737 " --> pdb=" O LEU 5 733 " (cutoff:3.500A) Processing helix chain '5' and resid 746 through 758 removed outlier: 4.058A pdb=" N LYS 5 750 " --> pdb=" O LEU 5 746 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N ALA 5 751 " --> pdb=" O ALA 5 747 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N LEU 5 752 " --> pdb=" O LEU 5 748 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N LYS 5 757 " --> pdb=" O TYR 5 753 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N HIS 5 758 " --> pdb=" O ALA 5 754 " (cutoff:3.500A) Processing helix chain 'd' and resid 21 through 37 removed outlier: 4.633A pdb=" N GLU d 26 " --> pdb=" O ASP d 22 " (cutoff:3.500A) Processing helix chain 'd' and resid 44 through 57 removed outlier: 3.585A pdb=" N LEU d 50 " --> pdb=" O TYR d 46 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N ARG d 51 " --> pdb=" O ARG d 47 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N VAL d 56 " --> pdb=" O ASN d 52 " (cutoff:3.500A) Processing helix chain 'd' and resid 64 through 72 Processing helix chain 'd' and resid 73 through 83 removed outlier: 3.560A pdb=" N ASP d 81 " --> pdb=" O LYS d 77 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N GLU d 82 " --> pdb=" O LYS d 78 " (cutoff:3.500A) Proline residue: d 83 - end of helix Processing helix chain 'd' and resid 84 through 103 Proline residue: d 88 - end of helix Processing helix chain 'd' and resid 350 through 363 removed outlier: 3.823A pdb=" N GLU d 356 " --> pdb=" O GLU d 352 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N ASN d 363 " --> pdb=" O GLN d 359 " (cutoff:3.500A) Processing helix chain 'd' and resid 365 through 374 removed outlier: 3.723A pdb=" N ILE d 374 " --> pdb=" O LEU d 370 " (cutoff:3.500A) Processing helix chain 'd' and resid 381 through 394 Processing helix chain 'd' and resid 421 through 433 removed outlier: 3.829A pdb=" N LEU d 425 " --> pdb=" O ALA d 421 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N LEU d 426 " --> pdb=" O LYS d 422 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N LYS d 427 " --> pdb=" O SER d 423 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N PHE d 428 " --> pdb=" O GLN d 424 " (cutoff:3.500A) Processing helix chain 'd' and resid 445 through 450 Processing helix chain 'd' and resid 467 through 473 removed outlier: 4.271A pdb=" N ASP d 473 " --> pdb=" O MET d 469 " (cutoff:3.500A) Processing helix chain 'd' and resid 486 through 499 removed outlier: 3.754A pdb=" N VAL d 491 " --> pdb=" O ASP d 487 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N ALA d 492 " --> pdb=" O GLU d 488 " (cutoff:3.500A) removed outlier: 4.521A pdb=" N ILE d 493 " --> pdb=" O ASP d 489 " (cutoff:3.500A) removed outlier: 4.665A pdb=" N HIS d 494 " --> pdb=" O ARG d 490 " (cutoff:3.500A) removed outlier: 5.175A pdb=" N GLU d 495 " --> pdb=" O VAL d 491 " (cutoff:3.500A) removed outlier: 4.859A pdb=" N ALA d 496 " --> pdb=" O ALA d 492 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N GLU d 498 " --> pdb=" O HIS d 494 " (cutoff:3.500A) Processing helix chain 'd' and resid 535 through 541 removed outlier: 3.515A pdb=" N ASN d 539 " --> pdb=" O SER d 535 " (cutoff:3.500A) removed outlier: 5.713A pdb=" N ASP d 541 " --> pdb=" O GLY d 537 " (cutoff:3.500A) Processing helix chain 'd' and resid 543 through 550 removed outlier: 4.415A pdb=" N ARG d 549 " --> pdb=" O THR d 545 " (cutoff:3.500A) removed outlier: 4.247A pdb=" N PHE d 550 " --> pdb=" O ILE d 546 " (cutoff:3.500A) Processing helix chain 'd' and resid 561 through 578 removed outlier: 3.505A pdb=" N GLY d 578 " --> pdb=" O ASN d 574 " (cutoff:3.500A) Processing helix chain 'd' and resid 579 through 591 removed outlier: 3.610A pdb=" N MET d 583 " --> pdb=" O ASN d 579 " (cutoff:3.500A) removed outlier: 5.178A pdb=" N GLN d 586 " --> pdb=" O ALA d 582 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N GLN d 587 " --> pdb=" O MET d 583 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N GLY d 591 " --> pdb=" O GLN d 587 " (cutoff:3.500A) Processing helix chain 'd' and resid 595 through 610 Processing helix chain 'd' and resid 615 through 641 removed outlier: 3.547A pdb=" N SER d 624 " --> pdb=" O GLU d 620 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N LEU d 633 " --> pdb=" O ILE d 629 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N LEU d 634 " --> pdb=" O ARG d 630 " (cutoff:3.500A) Processing helix chain 'd' and resid 649 through 668 removed outlier: 3.596A pdb=" N LEU d 653 " --> pdb=" O THR d 649 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N LEU d 666 " --> pdb=" O SER d 662 " (cutoff:3.500A) removed outlier: 4.363A pdb=" N GLU d 667 " --> pdb=" O LEU d 663 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N LEU d 668 " --> pdb=" O ALA d 664 " (cutoff:3.500A) Processing helix chain 'd' and resid 673 through 694 removed outlier: 3.620A pdb=" N GLU d 679 " --> pdb=" O ARG d 675 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N MET d 689 " --> pdb=" O GLN d 685 " (cutoff:3.500A) removed outlier: 4.744A pdb=" N ASP d 690 " --> pdb=" O ALA d 686 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N ALA d 691 " --> pdb=" O SER d 687 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N GLN d 694 " --> pdb=" O ASP d 690 " (cutoff:3.500A) Processing helix chain 'd' and resid 706 through 723 removed outlier: 4.898A pdb=" N ARG d 712 " --> pdb=" O LEU d 708 " (cutoff:3.500A) Proline residue: d 723 - end of helix Processing helix chain 'd' and resid 729 through 739 removed outlier: 3.902A pdb=" N PHE d 737 " --> pdb=" O LEU d 733 " (cutoff:3.500A) Processing helix chain 'd' and resid 746 through 758 removed outlier: 4.058A pdb=" N LYS d 750 " --> pdb=" O LEU d 746 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N ALA d 751 " --> pdb=" O ALA d 747 " (cutoff:3.500A) removed outlier: 4.091A pdb=" N LEU d 752 " --> pdb=" O LEU d 748 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N LYS d 757 " --> pdb=" O TYR d 753 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N HIS d 758 " --> pdb=" O ALA d 754 " (cutoff:3.500A) Processing helix chain '6' and resid 105 through 121 removed outlier: 4.072A pdb=" N GLU 6 109 " --> pdb=" O ASP 6 105 " (cutoff:3.500A) Processing helix chain '6' and resid 134 through 147 Processing helix chain '6' and resid 154 through 163 removed outlier: 3.781A pdb=" N MET 6 160 " --> pdb=" O GLN 6 156 " (cutoff:3.500A) removed outlier: 4.419A pdb=" N ARG 6 161 " --> pdb=" O HIS 6 157 " (cutoff:3.500A) removed outlier: 5.737A pdb=" N GLU 6 162 " --> pdb=" O LEU 6 158 " (cutoff:3.500A) removed outlier: 5.433A pdb=" N ASN 6 163 " --> pdb=" O SER 6 159 " (cutoff:3.500A) Processing helix chain '6' and resid 164 through 174 Processing helix chain '6' and resid 175 through 193 Proline residue: 6 179 - end of helix Processing helix chain '6' and resid 347 through 352 removed outlier: 5.826A pdb=" N ARG 6 352 " --> pdb=" O VAL 6 348 " (cutoff:3.500A) Processing helix chain '6' and resid 364 through 369 Proline residue: 6 369 - end of helix Processing helix chain '6' and resid 406 through 411 removed outlier: 3.990A pdb=" N LEU 6 410 " --> pdb=" O ASP 6 406 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N GLY 6 411 " --> pdb=" O VAL 6 407 " (cutoff:3.500A) No H-bonds generated for 'chain '6' and resid 406 through 411' Processing helix chain '6' and resid 500 through 509 removed outlier: 3.698A pdb=" N SER 6 507 " --> pdb=" O VAL 6 503 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N LEU 6 508 " --> pdb=" O PHE 6 504 " (cutoff:3.500A) removed outlier: 5.965A pdb=" N SER 6 509 " --> pdb=" O LEU 6 505 " (cutoff:3.500A) Processing helix chain '6' and resid 510 through 522 removed outlier: 3.941A pdb=" N ASP 6 522 " --> pdb=" O GLU 6 518 " (cutoff:3.500A) Processing helix chain '6' and resid 524 through 533 removed outlier: 3.806A pdb=" N ARG 6 531 " --> pdb=" O ASP 6 527 " (cutoff:3.500A) Processing helix chain '6' and resid 540 through 553 Processing helix chain '6' and resid 580 through 592 removed outlier: 4.057A pdb=" N PHE 6 584 " --> pdb=" O SER 6 580 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N LEU 6 585 " --> pdb=" O LYS 6 581 " (cutoff:3.500A) Processing helix chain '6' and resid 626 through 632 removed outlier: 3.617A pdb=" N ALA 6 631 " --> pdb=" O ALA 6 627 " (cutoff:3.500A) removed outlier: 4.187A pdb=" N ASP 6 632 " --> pdb=" O LEU 6 628 " (cutoff:3.500A) Processing helix chain '6' and resid 645 through 656 removed outlier: 3.565A pdb=" N ALA 6 651 " --> pdb=" O SER 6 647 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N HIS 6 653 " --> pdb=" O GLN 6 649 " (cutoff:3.500A) removed outlier: 4.582A pdb=" N GLU 6 654 " --> pdb=" O VAL 6 650 " (cutoff:3.500A) removed outlier: 4.071A pdb=" N ALA 6 655 " --> pdb=" O ALA 6 651 " (cutoff:3.500A) Processing helix chain '6' and resid 694 through 699 Processing helix chain '6' and resid 702 through 709 removed outlier: 3.747A pdb=" N ARG 6 708 " --> pdb=" O PRO 6 704 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N PHE 6 709 " --> pdb=" O ILE 6 705 " (cutoff:3.500A) Processing helix chain '6' and resid 720 through 737 removed outlier: 3.588A pdb=" N ASP 6 724 " --> pdb=" O ASN 6 720 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N THR 6 725 " --> pdb=" O GLU 6 721 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N LEU 6 734 " --> pdb=" O HIS 6 730 " (cutoff:3.500A) removed outlier: 5.483A pdb=" N HIS 6 735 " --> pdb=" O ILE 6 731 " (cutoff:3.500A) removed outlier: 5.029A pdb=" N MET 6 736 " --> pdb=" O VAL 6 732 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N LYS 6 737 " --> pdb=" O ASP 6 733 " (cutoff:3.500A) Processing helix chain '6' and resid 747 through 761 removed outlier: 3.885A pdb=" N THR 6 760 " --> pdb=" O LYS 6 756 " (cutoff:3.500A) removed outlier: 4.429A pdb=" N PHE 6 761 " --> pdb=" O TYR 6 757 " (cutoff:3.500A) Processing helix chain '6' and resid 766 through 785 removed outlier: 3.652A pdb=" N ARG 6 770 " --> pdb=" O THR 6 766 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N SER 6 771 " --> pdb=" O LYS 6 767 " (cutoff:3.500A) Processing helix chain '6' and resid 796 through 815 removed outlier: 3.799A pdb=" N LEU 6 800 " --> pdb=" O THR 6 796 " (cutoff:3.500A) Processing helix chain '6' and resid 820 through 835 removed outlier: 3.617A pdb=" N ILE 6 824 " --> pdb=" O THR 6 820 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N SER 6 834 " --> pdb=" O LEU 6 830 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N ILE 6 835 " --> pdb=" O LEU 6 831 " (cutoff:3.500A) Processing helix chain 'e' and resid 105 through 121 removed outlier: 4.070A pdb=" N GLU e 109 " --> pdb=" O ASP e 105 " (cutoff:3.500A) Processing helix chain 'e' and resid 134 through 147 Processing helix chain 'e' and resid 154 through 163 removed outlier: 3.781A pdb=" N MET e 160 " --> pdb=" O GLN e 156 " (cutoff:3.500A) removed outlier: 4.420A pdb=" N ARG e 161 " --> pdb=" O HIS e 157 " (cutoff:3.500A) removed outlier: 5.735A pdb=" N GLU e 162 " --> pdb=" O LEU e 158 " (cutoff:3.500A) removed outlier: 5.433A pdb=" N ASN e 163 " --> pdb=" O SER e 159 " (cutoff:3.500A) Processing helix chain 'e' and resid 164 through 174 Processing helix chain 'e' and resid 175 through 193 Proline residue: e 179 - end of helix Processing helix chain 'e' and resid 347 through 352 removed outlier: 5.827A pdb=" N ARG e 352 " --> pdb=" O VAL e 348 " (cutoff:3.500A) Processing helix chain 'e' and resid 364 through 369 Proline residue: e 369 - end of helix Processing helix chain 'e' and resid 406 through 411 removed outlier: 3.990A pdb=" N LEU e 410 " --> pdb=" O ASP e 406 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N GLY e 411 " --> pdb=" O VAL e 407 " (cutoff:3.500A) No H-bonds generated for 'chain 'e' and resid 406 through 411' Processing helix chain 'e' and resid 500 through 509 removed outlier: 3.698A pdb=" N SER e 507 " --> pdb=" O VAL e 503 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N LEU e 508 " --> pdb=" O PHE e 504 " (cutoff:3.500A) removed outlier: 5.964A pdb=" N SER e 509 " --> pdb=" O LEU e 505 " (cutoff:3.500A) Processing helix chain 'e' and resid 510 through 522 removed outlier: 3.940A pdb=" N ASP e 522 " --> pdb=" O GLU e 518 " (cutoff:3.500A) Processing helix chain 'e' and resid 524 through 533 removed outlier: 3.807A pdb=" N ARG e 531 " --> pdb=" O ASP e 527 " (cutoff:3.500A) Processing helix chain 'e' and resid 540 through 553 Processing helix chain 'e' and resid 580 through 592 removed outlier: 4.058A pdb=" N PHE e 584 " --> pdb=" O SER e 580 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N LEU e 585 " --> pdb=" O LYS e 581 " (cutoff:3.500A) Processing helix chain 'e' and resid 626 through 632 removed outlier: 3.616A pdb=" N ALA e 631 " --> pdb=" O ALA e 627 " (cutoff:3.500A) removed outlier: 4.188A pdb=" N ASP e 632 " --> pdb=" O LEU e 628 " (cutoff:3.500A) Processing helix chain 'e' and resid 645 through 656 removed outlier: 3.563A pdb=" N ALA e 651 " --> pdb=" O SER e 647 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N HIS e 653 " --> pdb=" O GLN e 649 " (cutoff:3.500A) removed outlier: 4.583A pdb=" N GLU e 654 " --> pdb=" O VAL e 650 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N ALA e 655 " --> pdb=" O ALA e 651 " (cutoff:3.500A) Processing helix chain 'e' and resid 694 through 699 Processing helix chain 'e' and resid 702 through 709 removed outlier: 3.746A pdb=" N ARG e 708 " --> pdb=" O PRO e 704 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N PHE e 709 " --> pdb=" O ILE e 705 " (cutoff:3.500A) Processing helix chain 'e' and resid 720 through 737 removed outlier: 3.588A pdb=" N ASP e 724 " --> pdb=" O ASN e 720 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N THR e 725 " --> pdb=" O GLU e 721 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N LEU e 734 " --> pdb=" O HIS e 730 " (cutoff:3.500A) removed outlier: 5.485A pdb=" N HIS e 735 " --> pdb=" O ILE e 731 " (cutoff:3.500A) removed outlier: 5.030A pdb=" N MET e 736 " --> pdb=" O VAL e 732 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N LYS e 737 " --> pdb=" O ASP e 733 " (cutoff:3.500A) Processing helix chain 'e' and resid 747 through 761 removed outlier: 3.885A pdb=" N THR e 760 " --> pdb=" O LYS e 756 " (cutoff:3.500A) removed outlier: 4.429A pdb=" N PHE e 761 " --> pdb=" O TYR e 757 " (cutoff:3.500A) Processing helix chain 'e' and resid 766 through 785 removed outlier: 3.653A pdb=" N ARG e 770 " --> pdb=" O THR e 766 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N SER e 771 " --> pdb=" O LYS e 767 " (cutoff:3.500A) Processing helix chain 'e' and resid 796 through 815 removed outlier: 3.799A pdb=" N LEU e 800 " --> pdb=" O THR e 796 " (cutoff:3.500A) Processing helix chain 'e' and resid 820 through 835 removed outlier: 3.616A pdb=" N ILE e 824 " --> pdb=" O THR e 820 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N SER e 834 " --> pdb=" O LEU e 830 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N ILE e 835 " --> pdb=" O LEU e 831 " (cutoff:3.500A) Processing helix chain '7' and resid 13 through 27 removed outlier: 3.712A pdb=" N LEU 7 17 " --> pdb=" O ASP 7 13 " (cutoff:3.500A) Processing helix chain '7' and resid 61 through 73 removed outlier: 3.707A pdb=" N ALA 7 65 " --> pdb=" O PRO 7 61 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N MET 7 66 " --> pdb=" O LYS 7 62 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N ASN 7 72 " --> pdb=" O GLN 7 68 " (cutoff:3.500A) removed outlier: 4.337A pdb=" N ARG 7 73 " --> pdb=" O LYS 7 69 " (cutoff:3.500A) Processing helix chain '7' and resid 81 through 96 Processing helix chain '7' and resid 101 through 109 Processing helix chain '7' and resid 110 through 125 removed outlier: 3.617A pdb=" N THR 7 114 " --> pdb=" O ALA 7 110 " (cutoff:3.500A) removed outlier: 4.385A pdb=" N GLU 7 115 " --> pdb=" O ASN 7 111 " (cutoff:3.500A) Processing helix chain '7' and resid 137 through 153 removed outlier: 3.799A pdb=" N LEU 7 148 " --> pdb=" O ASN 7 144 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N ARG 7 149 " --> pdb=" O GLN 7 145 " (cutoff:3.500A) Processing helix chain '7' and resid 193 through 199 removed outlier: 4.397A pdb=" N THR 7 197 " --> pdb=" O PRO 7 193 " (cutoff:3.500A) removed outlier: 5.538A pdb=" N ARG 7 199 " --> pdb=" O ASN 7 195 " (cutoff:3.500A) Processing helix chain '7' and resid 208 through 216 Processing helix chain '7' and resid 286 through 291 removed outlier: 4.816A pdb=" N GLN 7 291 " --> pdb=" O GLU 7 287 " (cutoff:3.500A) Processing helix chain '7' and resid 301 through 306 removed outlier: 3.685A pdb=" N SER 7 305 " --> pdb=" O SER 7 301 " (cutoff:3.500A) removed outlier: 5.348A pdb=" N LYS 7 306 " --> pdb=" O THR 7 302 " (cutoff:3.500A) No H-bonds generated for 'chain '7' and resid 301 through 306' Processing helix chain '7' and resid 318 through 323 removed outlier: 3.571A pdb=" N VAL 7 322 " --> pdb=" O LEU 7 318 " (cutoff:3.500A) Proline residue: 7 323 - end of helix No H-bonds generated for 'chain '7' and resid 318 through 323' Processing helix chain '7' and resid 364 through 369 removed outlier: 4.021A pdb=" N ALA 7 368 " --> pdb=" O LYS 7 364 " (cutoff:3.500A) Processing helix chain '7' and resid 394 through 408 removed outlier: 3.558A pdb=" N VAL 7 401 " --> pdb=" O VAL 7 397 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N MET 7 402 " --> pdb=" O GLU 7 398 " (cutoff:3.500A) Processing helix chain '7' and resid 409 through 418 removed outlier: 3.811A pdb=" N ILE 7 418 " --> pdb=" O LEU 7 414 " (cutoff:3.500A) Processing helix chain '7' and resid 425 through 438 removed outlier: 4.607A pdb=" N GLY 7 438 " --> pdb=" O LEU 7 434 " (cutoff:3.500A) Processing helix chain '7' and resid 465 through 478 removed outlier: 3.904A pdb=" N LEU 7 469 " --> pdb=" O ALA 7 465 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N LEU 7 470 " --> pdb=" O LYS 7 466 " (cutoff:3.500A) removed outlier: 4.615A pdb=" N LYS 7 471 " --> pdb=" O SER 7 467 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N LYS 7 475 " --> pdb=" O LYS 7 471 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N ILE 7 476 " --> pdb=" O ALA 7 472 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N SER 7 477 " --> pdb=" O ILE 7 473 " (cutoff:3.500A) Proline residue: 7 478 - end of helix Processing helix chain '7' and resid 511 through 517 removed outlier: 4.995A pdb=" N ASP 7 517 " --> pdb=" O LEU 7 513 " (cutoff:3.500A) Processing helix chain '7' and resid 525 through 530 removed outlier: 3.804A pdb=" N MET 7 529 " --> pdb=" O GLU 7 525 " (cutoff:3.500A) removed outlier: 5.914A pdb=" N ASP 7 530 " --> pdb=" O PHE 7 526 " (cutoff:3.500A) No H-bonds generated for 'chain '7' and resid 525 through 530' Processing helix chain '7' and resid 531 through 543 removed outlier: 3.938A pdb=" N ALA 7 536 " --> pdb=" O SER 7 532 " (cutoff:3.500A) Processing helix chain '7' and resid 579 through 585 removed outlier: 3.584A pdb=" N ASN 7 583 " --> pdb=" O SER 7 579 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N ILE 7 584 " --> pdb=" O PRO 7 580 " (cutoff:3.500A) removed outlier: 4.884A pdb=" N ASN 7 585 " --> pdb=" O LEU 7 581 " (cutoff:3.500A) No H-bonds generated for 'chain '7' and resid 579 through 585' Processing helix chain '7' and resid 587 through 595 removed outlier: 3.771A pdb=" N PHE 7 594 " --> pdb=" O LEU 7 590 " (cutoff:3.500A) removed outlier: 5.564A pdb=" N ASP 7 595 " --> pdb=" O LEU 7 591 " (cutoff:3.500A) Processing helix chain '7' and resid 605 through 623 removed outlier: 3.808A pdb=" N GLU 7 610 " --> pdb=" O ARG 7 606 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N LYS 7 611 " --> pdb=" O ASP 7 607 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N VAL 7 619 " --> pdb=" O HIS 7 615 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N HIS 7 620 " --> pdb=" O VAL 7 616 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N ASN 7 623 " --> pdb=" O VAL 7 619 " (cutoff:3.500A) Processing helix chain '7' and resid 634 through 649 removed outlier: 5.372A pdb=" N ARG 7 649 " --> pdb=" O ALA 7 645 " (cutoff:3.500A) Processing helix chain '7' and resid 653 through 675 removed outlier: 3.654A pdb=" N ASN 7 657 " --> pdb=" O SER 7 653 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ASP 7 658 " --> pdb=" O GLU 7 654 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N TYR 7 659 " --> pdb=" O ALA 7 655 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N VAL 7 660 " --> pdb=" O VAL 7 656 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N VAL 7 661 " --> pdb=" O ASN 7 657 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N GLN 7 662 " --> pdb=" O ASP 7 658 " (cutoff:3.500A) removed outlier: 4.106A pdb=" N ARG 7 673 " --> pdb=" O GLN 7 669 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N MET 7 675 " --> pdb=" O SER 7 671 " (cutoff:3.500A) Processing helix chain '7' and resid 685 through 704 removed outlier: 3.659A pdb=" N LEU 7 689 " --> pdb=" O THR 7 685 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N ALA 7 698 " --> pdb=" O ARG 7 694 " (cutoff:3.500A) removed outlier: 4.318A pdb=" N ARG 7 703 " --> pdb=" O LEU 7 699 " (cutoff:3.500A) Processing helix chain '7' and resid 709 through 727 removed outlier: 3.973A pdb=" N VAL 7 713 " --> pdb=" O ASP 7 709 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N GLU 7 714 " --> pdb=" O ILE 7 710 " (cutoff:3.500A) removed outlier: 4.248A pdb=" N LEU 7 727 " --> pdb=" O SER 7 723 " (cutoff:3.500A) Processing helix chain 'f' and resid 13 through 27 removed outlier: 3.712A pdb=" N LEU f 17 " --> pdb=" O ASP f 13 " (cutoff:3.500A) Processing helix chain 'f' and resid 61 through 73 removed outlier: 3.707A pdb=" N ALA f 65 " --> pdb=" O PRO f 61 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N MET f 66 " --> pdb=" O LYS f 62 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N ASN f 72 " --> pdb=" O GLN f 68 " (cutoff:3.500A) removed outlier: 4.335A pdb=" N ARG f 73 " --> pdb=" O LYS f 69 " (cutoff:3.500A) Processing helix chain 'f' and resid 81 through 96 Processing helix chain 'f' and resid 101 through 109 Processing helix chain 'f' and resid 110 through 125 removed outlier: 3.616A pdb=" N THR f 114 " --> pdb=" O ALA f 110 " (cutoff:3.500A) removed outlier: 4.386A pdb=" N GLU f 115 " --> pdb=" O ASN f 111 " (cutoff:3.500A) Processing helix chain 'f' and resid 137 through 153 removed outlier: 3.799A pdb=" N LEU f 148 " --> pdb=" O ASN f 144 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N ARG f 149 " --> pdb=" O GLN f 145 " (cutoff:3.500A) Processing helix chain 'f' and resid 193 through 199 removed outlier: 4.396A pdb=" N THR f 197 " --> pdb=" O PRO f 193 " (cutoff:3.500A) removed outlier: 5.537A pdb=" N ARG f 199 " --> pdb=" O ASN f 195 " (cutoff:3.500A) Processing helix chain 'f' and resid 208 through 216 Processing helix chain 'f' and resid 286 through 291 removed outlier: 4.815A pdb=" N GLN f 291 " --> pdb=" O GLU f 287 " (cutoff:3.500A) Processing helix chain 'f' and resid 301 through 306 removed outlier: 3.686A pdb=" N SER f 305 " --> pdb=" O SER f 301 " (cutoff:3.500A) removed outlier: 5.349A pdb=" N LYS f 306 " --> pdb=" O THR f 302 " (cutoff:3.500A) No H-bonds generated for 'chain 'f' and resid 301 through 306' Processing helix chain 'f' and resid 318 through 323 removed outlier: 3.571A pdb=" N VAL f 322 " --> pdb=" O LEU f 318 " (cutoff:3.500A) Proline residue: f 323 - end of helix No H-bonds generated for 'chain 'f' and resid 318 through 323' Processing helix chain 'f' and resid 364 through 369 removed outlier: 4.022A pdb=" N ALA f 368 " --> pdb=" O LYS f 364 " (cutoff:3.500A) Processing helix chain 'f' and resid 394 through 408 removed outlier: 3.558A pdb=" N VAL f 401 " --> pdb=" O VAL f 397 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N MET f 402 " --> pdb=" O GLU f 398 " (cutoff:3.500A) Processing helix chain 'f' and resid 409 through 418 removed outlier: 3.810A pdb=" N ILE f 418 " --> pdb=" O LEU f 414 " (cutoff:3.500A) Processing helix chain 'f' and resid 425 through 438 removed outlier: 4.608A pdb=" N GLY f 438 " --> pdb=" O LEU f 434 " (cutoff:3.500A) Processing helix chain 'f' and resid 465 through 478 removed outlier: 3.903A pdb=" N LEU f 469 " --> pdb=" O ALA f 465 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N LEU f 470 " --> pdb=" O LYS f 466 " (cutoff:3.500A) removed outlier: 4.615A pdb=" N LYS f 471 " --> pdb=" O SER f 467 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N LYS f 475 " --> pdb=" O LYS f 471 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N ILE f 476 " --> pdb=" O ALA f 472 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N SER f 477 " --> pdb=" O ILE f 473 " (cutoff:3.500A) Proline residue: f 478 - end of helix Processing helix chain 'f' and resid 511 through 517 removed outlier: 4.994A pdb=" N ASP f 517 " --> pdb=" O LEU f 513 " (cutoff:3.500A) Processing helix chain 'f' and resid 525 through 530 removed outlier: 3.804A pdb=" N MET f 529 " --> pdb=" O GLU f 525 " (cutoff:3.500A) removed outlier: 5.914A pdb=" N ASP f 530 " --> pdb=" O PHE f 526 " (cutoff:3.500A) No H-bonds generated for 'chain 'f' and resid 525 through 530' Processing helix chain 'f' and resid 531 through 543 removed outlier: 3.939A pdb=" N ALA f 536 " --> pdb=" O SER f 532 " (cutoff:3.500A) Processing helix chain 'f' and resid 579 through 585 removed outlier: 3.584A pdb=" N ASN f 583 " --> pdb=" O SER f 579 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N ILE f 584 " --> pdb=" O PRO f 580 " (cutoff:3.500A) removed outlier: 4.884A pdb=" N ASN f 585 " --> pdb=" O LEU f 581 " (cutoff:3.500A) No H-bonds generated for 'chain 'f' and resid 579 through 585' Processing helix chain 'f' and resid 587 through 595 removed outlier: 3.771A pdb=" N PHE f 594 " --> pdb=" O LEU f 590 " (cutoff:3.500A) removed outlier: 5.563A pdb=" N ASP f 595 " --> pdb=" O LEU f 591 " (cutoff:3.500A) Processing helix chain 'f' and resid 605 through 623 removed outlier: 3.808A pdb=" N GLU f 610 " --> pdb=" O ARG f 606 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N LYS f 611 " --> pdb=" O ASP f 607 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N VAL f 619 " --> pdb=" O HIS f 615 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N HIS f 620 " --> pdb=" O VAL f 616 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N ASN f 623 " --> pdb=" O VAL f 619 " (cutoff:3.500A) Processing helix chain 'f' and resid 634 through 649 removed outlier: 5.372A pdb=" N ARG f 649 " --> pdb=" O ALA f 645 " (cutoff:3.500A) Processing helix chain 'f' and resid 653 through 675 removed outlier: 3.652A pdb=" N ASN f 657 " --> pdb=" O SER f 653 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ASP f 658 " --> pdb=" O GLU f 654 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N TYR f 659 " --> pdb=" O ALA f 655 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N VAL f 660 " --> pdb=" O VAL f 656 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N VAL f 661 " --> pdb=" O ASN f 657 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N GLN f 662 " --> pdb=" O ASP f 658 " (cutoff:3.500A) removed outlier: 4.105A pdb=" N ARG f 673 " --> pdb=" O GLN f 669 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N MET f 675 " --> pdb=" O SER f 671 " (cutoff:3.500A) Processing helix chain 'f' and resid 685 through 704 removed outlier: 3.658A pdb=" N LEU f 689 " --> pdb=" O THR f 685 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N ALA f 698 " --> pdb=" O ARG f 694 " (cutoff:3.500A) removed outlier: 4.320A pdb=" N ARG f 703 " --> pdb=" O LEU f 699 " (cutoff:3.500A) Processing helix chain 'f' and resid 709 through 727 removed outlier: 3.972A pdb=" N VAL f 713 " --> pdb=" O ASP f 709 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N GLU f 714 " --> pdb=" O ILE f 710 " (cutoff:3.500A) removed outlier: 4.247A pdb=" N LEU f 727 " --> pdb=" O SER f 723 " (cutoff:3.500A) Processing helix chain 'C' and resid 5 through 14 removed outlier: 3.621A pdb=" N GLY C 13 " --> pdb=" O VAL C 9 " (cutoff:3.500A) removed outlier: 4.272A pdb=" N THR C 14 " --> pdb=" O LEU C 10 " (cutoff:3.500A) Processing helix chain 'C' and resid 47 through 58 removed outlier: 4.663A pdb=" N ILE C 53 " --> pdb=" O TRP C 49 " (cutoff:3.500A) removed outlier: 4.067A pdb=" N ILE C 56 " --> pdb=" O ARG C 52 " (cutoff:3.500A) removed outlier: 6.021A pdb=" N GLY C 58 " --> pdb=" O LEU C 54 " (cutoff:3.500A) Processing helix chain 'C' and resid 81 through 91 Processing helix chain 'C' and resid 96 through 101 removed outlier: 3.701A pdb=" N ILE C 100 " --> pdb=" O ASP C 96 " (cutoff:3.500A) Processing helix chain 'C' and resid 103 through 116 removed outlier: 3.602A pdb=" N SER C 116 " --> pdb=" O ILE C 112 " (cutoff:3.500A) Processing helix chain 'C' and resid 117 through 140 removed outlier: 3.542A pdb=" N ALA C 121 " --> pdb=" O GLU C 117 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N SER C 125 " --> pdb=" O ALA C 121 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N GLU C 126 " --> pdb=" O ASN C 122 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N GLN C 133 " --> pdb=" O LEU C 129 " (cutoff:3.500A) removed outlier: 4.161A pdb=" N GLU C 134 " --> pdb=" O GLN C 130 " (cutoff:3.500A) Processing helix chain 'C' and resid 159 through 169 removed outlier: 3.690A pdb=" N SER C 163 " --> pdb=" O ASN C 159 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N LEU C 167 " --> pdb=" O SER C 163 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N LYS C 168 " --> pdb=" O THR C 164 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N LEU C 169 " --> pdb=" O PHE C 165 " (cutoff:3.500A) Processing helix chain 'C' and resid 170 through 193 removed outlier: 3.931A pdb=" N GLU C 175 " --> pdb=" O GLU C 171 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N ILE C 176 " --> pdb=" O MET C 172 " (cutoff:3.500A) Processing helix chain 'J' and resid 5 through 14 removed outlier: 3.621A pdb=" N GLY J 13 " --> pdb=" O VAL J 9 " (cutoff:3.500A) removed outlier: 4.271A pdb=" N THR J 14 " --> pdb=" O LEU J 10 " (cutoff:3.500A) Processing helix chain 'J' and resid 47 through 58 removed outlier: 4.663A pdb=" N ILE J 53 " --> pdb=" O TRP J 49 " (cutoff:3.500A) removed outlier: 4.067A pdb=" N ILE J 56 " --> pdb=" O ARG J 52 " (cutoff:3.500A) removed outlier: 6.020A pdb=" N GLY J 58 " --> pdb=" O LEU J 54 " (cutoff:3.500A) Processing helix chain 'J' and resid 81 through 91 Processing helix chain 'J' and resid 96 through 101 removed outlier: 3.702A pdb=" N ILE J 100 " --> pdb=" O ASP J 96 " (cutoff:3.500A) Processing helix chain 'J' and resid 103 through 116 removed outlier: 3.603A pdb=" N SER J 116 " --> pdb=" O ILE J 112 " (cutoff:3.500A) Processing helix chain 'J' and resid 117 through 140 removed outlier: 3.542A pdb=" N ALA J 121 " --> pdb=" O GLU J 117 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N SER J 125 " --> pdb=" O ALA J 121 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N GLU J 126 " --> pdb=" O ASN J 122 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N GLN J 133 " --> pdb=" O LEU J 129 " (cutoff:3.500A) removed outlier: 4.162A pdb=" N GLU J 134 " --> pdb=" O GLN J 130 " (cutoff:3.500A) Processing helix chain 'J' and resid 159 through 169 removed outlier: 3.689A pdb=" N SER J 163 " --> pdb=" O ASN J 159 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N LEU J 167 " --> pdb=" O SER J 163 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N LYS J 168 " --> pdb=" O THR J 164 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N LEU J 169 " --> pdb=" O PHE J 165 " (cutoff:3.500A) Processing helix chain 'J' and resid 170 through 193 removed outlier: 3.930A pdb=" N GLU J 175 " --> pdb=" O GLU J 171 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N ILE J 176 " --> pdb=" O MET J 172 " (cutoff:3.500A) Processing helix chain 'D' and resid 55 through 73 removed outlier: 3.549A pdb=" N PHE D 60 " --> pdb=" O PRO D 56 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N CYS D 72 " --> pdb=" O LYS D 68 " (cutoff:3.500A) Processing helix chain 'D' and resid 80 through 113 removed outlier: 3.597A pdb=" N MET D 108 " --> pdb=" O GLY D 104 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N GLN D 109 " --> pdb=" O PHE D 105 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N ASN D 110 " --> pdb=" O LEU D 106 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N ALA D 111 " --> pdb=" O ASP D 107 " (cutoff:3.500A) removed outlier: 4.207A pdb=" N SER D 112 " --> pdb=" O MET D 108 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N ASN D 113 " --> pdb=" O GLN D 109 " (cutoff:3.500A) Processing helix chain 'D' and resid 121 through 155 Proline residue: D 125 - end of helix removed outlier: 3.552A pdb=" N SER D 155 " --> pdb=" O ILE D 151 " (cutoff:3.500A) Processing helix chain 'D' and resid 156 through 165 removed outlier: 5.667A pdb=" N GLU D 165 " --> pdb=" O LEU D 161 " (cutoff:3.500A) Processing helix chain 'D' and resid 170 through 175 Processing helix chain 'D' and resid 176 through 203 removed outlier: 4.046A pdb=" N LEU D 199 " --> pdb=" O ASN D 195 " (cutoff:3.500A) removed outlier: 5.707A pdb=" N LYS D 200 " --> pdb=" O ASP D 196 " (cutoff:3.500A) removed outlier: 6.160A pdb=" N TYR D 201 " --> pdb=" O SER D 197 " (cutoff:3.500A) removed outlier: 4.507A pdb=" N MET D 202 " --> pdb=" O ILE D 198 " (cutoff:3.500A) Proline residue: D 203 - end of helix Processing helix chain 'D' and resid 239 through 244 removed outlier: 3.538A pdb=" N ASP D 243 " --> pdb=" O LYS D 239 " (cutoff:3.500A) Proline residue: D 244 - end of helix No H-bonds generated for 'chain 'D' and resid 239 through 244' Processing helix chain 'D' and resid 278 through 283 removed outlier: 4.108A pdb=" N ILE D 282 " --> pdb=" O ARG D 278 " (cutoff:3.500A) Processing helix chain 'D' and resid 284 through 289 Processing helix chain 'K' and resid 55 through 73 removed outlier: 3.549A pdb=" N PHE K 60 " --> pdb=" O PRO K 56 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N CYS K 72 " --> pdb=" O LYS K 68 " (cutoff:3.500A) Processing helix chain 'K' and resid 80 through 113 removed outlier: 3.598A pdb=" N MET K 108 " --> pdb=" O GLY K 104 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N GLN K 109 " --> pdb=" O PHE K 105 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N ASN K 110 " --> pdb=" O LEU K 106 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N ALA K 111 " --> pdb=" O ASP K 107 " (cutoff:3.500A) removed outlier: 4.207A pdb=" N SER K 112 " --> pdb=" O MET K 108 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N ASN K 113 " --> pdb=" O GLN K 109 " (cutoff:3.500A) Processing helix chain 'K' and resid 121 through 155 Proline residue: K 125 - end of helix removed outlier: 3.552A pdb=" N SER K 155 " --> pdb=" O ILE K 151 " (cutoff:3.500A) Processing helix chain 'K' and resid 156 through 165 removed outlier: 5.667A pdb=" N GLU K 165 " --> pdb=" O LEU K 161 " (cutoff:3.500A) Processing helix chain 'K' and resid 170 through 175 Processing helix chain 'K' and resid 176 through 203 removed outlier: 4.046A pdb=" N LEU K 199 " --> pdb=" O ASN K 195 " (cutoff:3.500A) removed outlier: 5.708A pdb=" N LYS K 200 " --> pdb=" O ASP K 196 " (cutoff:3.500A) removed outlier: 6.160A pdb=" N TYR K 201 " --> pdb=" O SER K 197 " (cutoff:3.500A) removed outlier: 4.507A pdb=" N MET K 202 " --> pdb=" O ILE K 198 " (cutoff:3.500A) Proline residue: K 203 - end of helix Processing helix chain 'K' and resid 239 through 244 removed outlier: 3.541A pdb=" N ASP K 243 " --> pdb=" O LYS K 239 " (cutoff:3.500A) Proline residue: K 244 - end of helix No H-bonds generated for 'chain 'K' and resid 239 through 244' Processing helix chain 'K' and resid 278 through 283 removed outlier: 4.107A pdb=" N ILE K 282 " --> pdb=" O ARG K 278 " (cutoff:3.500A) Processing helix chain 'K' and resid 284 through 289 Processing helix chain 'E' and resid 7 through 19 removed outlier: 3.910A pdb=" N ALA E 11 " --> pdb=" O GLN E 7 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N TYR E 12 " --> pdb=" O PHE E 8 " (cutoff:3.500A) Processing helix chain 'E' and resid 35 through 53 removed outlier: 3.563A pdb=" N LEU E 39 " --> pdb=" O ASN E 35 " (cutoff:3.500A) Processing helix chain 'E' and resid 63 through 75 removed outlier: 3.684A pdb=" N SER E 72 " --> pdb=" O ARG E 68 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N GLN E 73 " --> pdb=" O ARG E 69 " (cutoff:3.500A) removed outlier: 5.581A pdb=" N ASP E 75 " --> pdb=" O TYR E 71 " (cutoff:3.500A) Processing helix chain 'E' and resid 91 through 97 Processing helix chain 'E' and resid 99 through 104 removed outlier: 4.052A pdb=" N VAL E 104 " --> pdb=" O PRO E 100 " (cutoff:3.500A) Processing helix chain 'E' and resid 130 through 135 Processing helix chain 'E' and resid 146 through 151 removed outlier: 4.200A pdb=" N ASP E 150 " --> pdb=" O GLY E 146 " (cutoff:3.500A) Processing helix chain 'E' and resid 152 through 166 removed outlier: 4.398A pdb=" N LYS E 156 " --> pdb=" O LEU E 152 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N GLU E 157 " --> pdb=" O GLY E 153 " (cutoff:3.500A) Processing helix chain 'E' and resid 223 through 243 removed outlier: 4.180A pdb=" N LYS E 227 " --> pdb=" O ARG E 223 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N VAL E 236 " --> pdb=" O GLU E 232 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N TYR E 241 " --> pdb=" O LEU E 237 " (cutoff:3.500A) removed outlier: 4.144A pdb=" N SER E 242 " --> pdb=" O GLU E 238 " (cutoff:3.500A) removed outlier: 5.593A pdb=" N GLN E 243 " --> pdb=" O GLU E 239 " (cutoff:3.500A) Processing helix chain 'E' and resid 250 through 263 removed outlier: 3.561A pdb=" N GLN E 254 " --> pdb=" O SER E 250 " (cutoff:3.500A) Processing helix chain 'E' and resid 266 through 282 removed outlier: 3.567A pdb=" N SER E 279 " --> pdb=" O LEU E 275 " (cutoff:3.500A) removed outlier: 4.376A pdb=" N LEU E 280 " --> pdb=" O GLY E 276 " (cutoff:3.500A) removed outlier: 4.322A pdb=" N ASP E 281 " --> pdb=" O THR E 277 " (cutoff:3.500A) removed outlier: 4.906A pdb=" N ILE E 282 " --> pdb=" O THR E 278 " (cutoff:3.500A) Processing helix chain 'E' and resid 284 through 303 removed outlier: 3.724A pdb=" N TYR E 288 " --> pdb=" O TYR E 284 " (cutoff:3.500A) Proline residue: E 293 - end of helix Processing helix chain 'E' and resid 333 through 341 removed outlier: 3.863A pdb=" N SER E 341 " --> pdb=" O SER E 337 " (cutoff:3.500A) Processing helix chain 'E' and resid 342 through 349 Processing helix chain 'E' and resid 352 through 367 removed outlier: 3.671A pdb=" N LYS E 356 " --> pdb=" O ASN E 352 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N GLY E 367 " --> pdb=" O PHE E 363 " (cutoff:3.500A) Processing helix chain 'E' and resid 369 through 375 removed outlier: 3.702A pdb=" N GLN E 374 " --> pdb=" O LEU E 370 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N GLU E 375 " --> pdb=" O SER E 371 " (cutoff:3.500A) Processing helix chain 'E' and resid 381 through 388 Processing helix chain 'E' and resid 389 through 400 removed outlier: 4.887A pdb=" N ASP E 397 " --> pdb=" O ASP E 393 " (cutoff:3.500A) removed outlier: 5.842A pdb=" N ARG E 398 " --> pdb=" O LYS E 394 " (cutoff:3.500A) removed outlier: 4.458A pdb=" N TYR E 399 " --> pdb=" O ASN E 395 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N GLY E 400 " --> pdb=" O LEU E 396 " (cutoff:3.500A) Processing helix chain 'E' and resid 420 through 434 Processing helix chain 'E' and resid 461 through 485 removed outlier: 4.069A pdb=" N LYS E 465 " --> pdb=" O ASN E 461 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N PHE E 477 " --> pdb=" O TRP E 473 " (cutoff:3.500A) removed outlier: 4.329A pdb=" N TRP E 478 " --> pdb=" O VAL E 474 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N LEU E 479 " --> pdb=" O SER E 475 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ALA E 483 " --> pdb=" O LEU E 479 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N LEU E 484 " --> pdb=" O SER E 480 " (cutoff:3.500A) removed outlier: 4.481A pdb=" N ASP E 485 " --> pdb=" O TRP E 481 " (cutoff:3.500A) Processing helix chain 'E' and resid 488 through 517 removed outlier: 4.112A pdb=" N LEU E 492 " --> pdb=" O LYS E 488 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ALA E 512 " --> pdb=" O ASN E 508 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N LYS E 517 " --> pdb=" O ILE E 513 " (cutoff:3.500A) Processing helix chain 'E' and resid 535 through 541 removed outlier: 4.919A pdb=" N TYR E 539 " --> pdb=" O ASP E 535 " (cutoff:3.500A) removed outlier: 4.296A pdb=" N ARG E 540 " --> pdb=" O LEU E 536 " (cutoff:3.500A) removed outlier: 5.494A pdb=" N ASN E 541 " --> pdb=" O ASP E 537 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 535 through 541' Processing helix chain 'E' and resid 542 through 560 removed outlier: 3.686A pdb=" N GLU E 558 " --> pdb=" O GLU E 554 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N SER E 559 " --> pdb=" O CYS E 555 " (cutoff:3.500A) removed outlier: 5.661A pdb=" N GLU E 560 " --> pdb=" O CYS E 556 " (cutoff:3.500A) Processing helix chain 'E' and resid 593 through 598 removed outlier: 4.576A pdb=" N THR E 597 " --> pdb=" O ASP E 593 " (cutoff:3.500A) removed outlier: 5.585A pdb=" N LYS E 598 " --> pdb=" O THR E 594 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 593 through 598' Processing helix chain 'E' and resid 604 through 616 removed outlier: 3.584A pdb=" N ALA E 608 " --> pdb=" O ASN E 604 " (cutoff:3.500A) Processing helix chain 'E' and resid 633 through 648 removed outlier: 3.554A pdb=" N LEU E 637 " --> pdb=" O ARG E 633 " (cutoff:3.500A) removed outlier: 4.887A pdb=" N SER E 638 " --> pdb=" O ARG E 634 " (cutoff:3.500A) Proline residue: E 639 - end of helix removed outlier: 3.526A pdb=" N GLU E 642 " --> pdb=" O SER E 638 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N GLY E 648 " --> pdb=" O LEU E 644 " (cutoff:3.500A) Processing helix chain 'L' and resid 7 through 19 removed outlier: 3.910A pdb=" N ALA L 11 " --> pdb=" O GLN L 7 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N TYR L 12 " --> pdb=" O PHE L 8 " (cutoff:3.500A) Processing helix chain 'L' and resid 35 through 53 removed outlier: 3.563A pdb=" N LEU L 39 " --> pdb=" O ASN L 35 " (cutoff:3.500A) Processing helix chain 'L' and resid 63 through 75 removed outlier: 3.684A pdb=" N SER L 72 " --> pdb=" O ARG L 68 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N GLN L 73 " --> pdb=" O ARG L 69 " (cutoff:3.500A) removed outlier: 5.582A pdb=" N ASP L 75 " --> pdb=" O TYR L 71 " (cutoff:3.500A) Processing helix chain 'L' and resid 91 through 97 Processing helix chain 'L' and resid 99 through 104 removed outlier: 4.052A pdb=" N VAL L 104 " --> pdb=" O PRO L 100 " (cutoff:3.500A) Processing helix chain 'L' and resid 130 through 135 Processing helix chain 'L' and resid 146 through 151 removed outlier: 4.201A pdb=" N ASP L 150 " --> pdb=" O GLY L 146 " (cutoff:3.500A) Processing helix chain 'L' and resid 152 through 166 removed outlier: 4.400A pdb=" N LYS L 156 " --> pdb=" O LEU L 152 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N GLU L 157 " --> pdb=" O GLY L 153 " (cutoff:3.500A) Processing helix chain 'L' and resid 223 through 243 removed outlier: 4.179A pdb=" N LYS L 227 " --> pdb=" O ARG L 223 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N VAL L 236 " --> pdb=" O GLU L 232 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N TYR L 241 " --> pdb=" O LEU L 237 " (cutoff:3.500A) removed outlier: 4.146A pdb=" N SER L 242 " --> pdb=" O GLU L 238 " (cutoff:3.500A) removed outlier: 5.595A pdb=" N GLN L 243 " --> pdb=" O GLU L 239 " (cutoff:3.500A) Processing helix chain 'L' and resid 250 through 263 removed outlier: 3.562A pdb=" N GLN L 254 " --> pdb=" O SER L 250 " (cutoff:3.500A) Processing helix chain 'L' and resid 266 through 282 removed outlier: 3.567A pdb=" N SER L 279 " --> pdb=" O LEU L 275 " (cutoff:3.500A) removed outlier: 4.375A pdb=" N LEU L 280 " --> pdb=" O GLY L 276 " (cutoff:3.500A) removed outlier: 4.321A pdb=" N ASP L 281 " --> pdb=" O THR L 277 " (cutoff:3.500A) removed outlier: 4.907A pdb=" N ILE L 282 " --> pdb=" O THR L 278 " (cutoff:3.500A) Processing helix chain 'L' and resid 284 through 303 removed outlier: 3.724A pdb=" N TYR L 288 " --> pdb=" O TYR L 284 " (cutoff:3.500A) Proline residue: L 293 - end of helix Processing helix chain 'L' and resid 333 through 341 removed outlier: 3.863A pdb=" N SER L 341 " --> pdb=" O SER L 337 " (cutoff:3.500A) Processing helix chain 'L' and resid 342 through 349 Processing helix chain 'L' and resid 352 through 367 removed outlier: 3.672A pdb=" N LYS L 356 " --> pdb=" O ASN L 352 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N GLY L 367 " --> pdb=" O PHE L 363 " (cutoff:3.500A) Processing helix chain 'L' and resid 369 through 375 removed outlier: 3.703A pdb=" N GLN L 374 " --> pdb=" O LEU L 370 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N GLU L 375 " --> pdb=" O SER L 371 " (cutoff:3.500A) Processing helix chain 'L' and resid 381 through 388 Processing helix chain 'L' and resid 389 through 400 removed outlier: 4.887A pdb=" N ASP L 397 " --> pdb=" O ASP L 393 " (cutoff:3.500A) removed outlier: 5.843A pdb=" N ARG L 398 " --> pdb=" O LYS L 394 " (cutoff:3.500A) removed outlier: 4.458A pdb=" N TYR L 399 " --> pdb=" O ASN L 395 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N GLY L 400 " --> pdb=" O LEU L 396 " (cutoff:3.500A) Processing helix chain 'L' and resid 420 through 434 Processing helix chain 'L' and resid 461 through 485 removed outlier: 4.071A pdb=" N LYS L 465 " --> pdb=" O ASN L 461 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N PHE L 477 " --> pdb=" O TRP L 473 " (cutoff:3.500A) removed outlier: 4.328A pdb=" N TRP L 478 " --> pdb=" O VAL L 474 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N LEU L 479 " --> pdb=" O SER L 475 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N ALA L 483 " --> pdb=" O LEU L 479 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N LEU L 484 " --> pdb=" O SER L 480 " (cutoff:3.500A) removed outlier: 4.482A pdb=" N ASP L 485 " --> pdb=" O TRP L 481 " (cutoff:3.500A) Processing helix chain 'L' and resid 488 through 517 removed outlier: 4.112A pdb=" N LEU L 492 " --> pdb=" O LYS L 488 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ALA L 512 " --> pdb=" O ASN L 508 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N LYS L 517 " --> pdb=" O ILE L 513 " (cutoff:3.500A) Processing helix chain 'L' and resid 535 through 541 removed outlier: 4.919A pdb=" N TYR L 539 " --> pdb=" O ASP L 535 " (cutoff:3.500A) removed outlier: 4.296A pdb=" N ARG L 540 " --> pdb=" O LEU L 536 " (cutoff:3.500A) removed outlier: 5.494A pdb=" N ASN L 541 " --> pdb=" O ASP L 537 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 535 through 541' Processing helix chain 'L' and resid 542 through 560 removed outlier: 3.688A pdb=" N GLU L 558 " --> pdb=" O GLU L 554 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N SER L 559 " --> pdb=" O CYS L 555 " (cutoff:3.500A) removed outlier: 5.661A pdb=" N GLU L 560 " --> pdb=" O CYS L 556 " (cutoff:3.500A) Processing helix chain 'L' and resid 593 through 598 removed outlier: 4.575A pdb=" N THR L 597 " --> pdb=" O ASP L 593 " (cutoff:3.500A) removed outlier: 5.585A pdb=" N LYS L 598 " --> pdb=" O THR L 594 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 593 through 598' Processing helix chain 'L' and resid 604 through 616 removed outlier: 3.583A pdb=" N ALA L 608 " --> pdb=" O ASN L 604 " (cutoff:3.500A) Processing helix chain 'L' and resid 633 through 648 removed outlier: 3.552A pdb=" N LEU L 637 " --> pdb=" O ARG L 633 " (cutoff:3.500A) removed outlier: 4.886A pdb=" N SER L 638 " --> pdb=" O ARG L 634 " (cutoff:3.500A) Proline residue: L 639 - end of helix removed outlier: 3.526A pdb=" N GLU L 642 " --> pdb=" O SER L 638 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N GLY L 648 " --> pdb=" O LEU L 644 " (cutoff:3.500A) Processing helix chain 'F' and resid 13 through 25 removed outlier: 4.060A pdb=" N LEU F 17 " --> pdb=" O GLN F 13 " (cutoff:3.500A) Proline residue: F 19 - end of helix Processing helix chain 'F' and resid 34 through 49 removed outlier: 4.139A pdb=" N GLU F 43 " --> pdb=" O SER F 39 " (cutoff:3.500A) removed outlier: 4.471A pdb=" N PHE F 44 " --> pdb=" O ALA F 40 " (cutoff:3.500A) removed outlier: 4.092A pdb=" N VAL F 45 " --> pdb=" O LEU F 41 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N ASN F 48 " --> pdb=" O PHE F 44 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N ILE F 49 " --> pdb=" O VAL F 45 " (cutoff:3.500A) Processing helix chain 'F' and resid 57 through 73 removed outlier: 3.625A pdb=" N VAL F 69 " --> pdb=" O GLN F 65 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N TRP F 70 " --> pdb=" O PHE F 66 " (cutoff:3.500A) Processing helix chain 'F' and resid 81 through 94 removed outlier: 4.625A pdb=" N LYS F 85 " --> pdb=" O GLN F 81 " (cutoff:3.500A) Processing helix chain 'F' and resid 195 through 200 removed outlier: 3.887A pdb=" N ASN F 199 " --> pdb=" O ASN F 195 " (cutoff:3.500A) Processing helix chain 'F' and resid 210 through 232 removed outlier: 4.245A pdb=" N LYS F 214 " --> pdb=" O ASP F 210 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N VAL F 215 " --> pdb=" O ILE F 211 " (cutoff:3.500A) removed outlier: 5.241A pdb=" N PHE F 218 " --> pdb=" O LYS F 214 " (cutoff:3.500A) removed outlier: 4.903A pdb=" N LEU F 219 " --> pdb=" O VAL F 215 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N ARG F 221 " --> pdb=" O MET F 217 " (cutoff:3.500A) Processing helix chain 'F' and resid 270 through 275 removed outlier: 4.351A pdb=" N LEU F 274 " --> pdb=" O PRO F 270 " (cutoff:3.500A) removed outlier: 4.534A pdb=" N LEU F 275 " --> pdb=" O ILE F 271 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 270 through 275' Processing helix chain 'F' and resid 351 through 360 removed outlier: 3.852A pdb=" N GLU F 357 " --> pdb=" O GLU F 353 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N THR F 358 " --> pdb=" O ILE F 354 " (cutoff:3.500A) Processing helix chain 'F' and resid 379 through 394 removed outlier: 5.519A pdb=" N LEU F 383 " --> pdb=" O LEU F 379 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N LYS F 384 " --> pdb=" O ASP F 380 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N ILE F 385 " --> pdb=" O LYS F 381 " (cutoff:3.500A) removed outlier: 5.244A pdb=" N GLU F 393 " --> pdb=" O LEU F 389 " (cutoff:3.500A) removed outlier: 4.631A pdb=" N LEU F 394 " --> pdb=" O LEU F 390 " (cutoff:3.500A) Processing helix chain 'F' and resid 410 through 428 removed outlier: 3.631A pdb=" N MET F 414 " --> pdb=" O ASP F 410 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N LYS F 423 " --> pdb=" O LYS F 419 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N ASP F 426 " --> pdb=" O GLN F 422 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N ASP F 427 " --> pdb=" O LYS F 423 " (cutoff:3.500A) Proline residue: F 428 - end of helix Processing helix chain 'F' and resid 453 through 473 removed outlier: 4.183A pdb=" N LEU F 465 " --> pdb=" O ASN F 461 " (cutoff:3.500A) removed outlier: 4.274A pdb=" N ALA F 466 " --> pdb=" O PHE F 462 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N THR F 467 " --> pdb=" O ASP F 463 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N ARG F 471 " --> pdb=" O THR F 467 " (cutoff:3.500A) removed outlier: 4.922A pdb=" N PHE F 472 " --> pdb=" O LEU F 468 " (cutoff:3.500A) removed outlier: 5.007A pdb=" N ASP F 473 " --> pdb=" O LEU F 469 " (cutoff:3.500A) Processing helix chain 'F' and resid 474 through 479 Processing helix chain 'F' and resid 490 through 497 removed outlier: 4.083A pdb=" N VAL F 495 " --> pdb=" O TRP F 491 " (cutoff:3.500A) Processing helix chain 'F' and resid 509 through 514 removed outlier: 3.864A pdb=" N THR F 513 " --> pdb=" O PRO F 509 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N LYS F 514 " --> pdb=" O SER F 510 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 509 through 514' Processing helix chain 'F' and resid 515 through 521 removed outlier: 4.939A pdb=" N LYS F 521 " --> pdb=" O ASN F 517 " (cutoff:3.500A) Processing helix chain 'F' and resid 545 through 554 removed outlier: 4.225A pdb=" N ARG F 549 " --> pdb=" O ASP F 545 " (cutoff:3.500A) removed outlier: 4.107A pdb=" N ARG F 554 " --> pdb=" O PHE F 550 " (cutoff:3.500A) Processing helix chain 'F' and resid 594 through 610 removed outlier: 4.754A pdb=" N GLU F 598 " --> pdb=" O GLN F 594 " (cutoff:3.500A) removed outlier: 4.134A pdb=" N THR F 599 " --> pdb=" O LYS F 595 " (cutoff:3.500A) Processing helix chain 'F' and resid 616 through 621 Proline residue: F 621 - end of helix Processing helix chain 'F' and resid 626 through 632 removed outlier: 4.242A pdb=" N LEU F 630 " --> pdb=" O LEU F 626 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N THR F 631 " --> pdb=" O ASP F 627 " (cutoff:3.500A) removed outlier: 5.758A pdb=" N LEU F 632 " --> pdb=" O HIS F 628 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 626 through 632' Processing helix chain 'M' and resid 13 through 25 removed outlier: 4.060A pdb=" N LEU M 17 " --> pdb=" O GLN M 13 " (cutoff:3.500A) Proline residue: M 19 - end of helix Processing helix chain 'M' and resid 34 through 49 removed outlier: 4.139A pdb=" N GLU M 43 " --> pdb=" O SER M 39 " (cutoff:3.500A) removed outlier: 4.472A pdb=" N PHE M 44 " --> pdb=" O ALA M 40 " (cutoff:3.500A) removed outlier: 4.092A pdb=" N VAL M 45 " --> pdb=" O LEU M 41 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N ASN M 48 " --> pdb=" O PHE M 44 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N ILE M 49 " --> pdb=" O VAL M 45 " (cutoff:3.500A) Processing helix chain 'M' and resid 57 through 73 removed outlier: 3.625A pdb=" N VAL M 69 " --> pdb=" O GLN M 65 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N TRP M 70 " --> pdb=" O PHE M 66 " (cutoff:3.500A) Processing helix chain 'M' and resid 81 through 94 removed outlier: 4.626A pdb=" N LYS M 85 " --> pdb=" O GLN M 81 " (cutoff:3.500A) Processing helix chain 'M' and resid 195 through 200 removed outlier: 3.886A pdb=" N ASN M 199 " --> pdb=" O ASN M 195 " (cutoff:3.500A) Processing helix chain 'M' and resid 210 through 232 removed outlier: 4.245A pdb=" N LYS M 214 " --> pdb=" O ASP M 210 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N VAL M 215 " --> pdb=" O ILE M 211 " (cutoff:3.500A) removed outlier: 5.242A pdb=" N PHE M 218 " --> pdb=" O LYS M 214 " (cutoff:3.500A) removed outlier: 4.903A pdb=" N LEU M 219 " --> pdb=" O VAL M 215 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N ARG M 221 " --> pdb=" O MET M 217 " (cutoff:3.500A) Processing helix chain 'M' and resid 270 through 275 removed outlier: 4.351A pdb=" N LEU M 274 " --> pdb=" O PRO M 270 " (cutoff:3.500A) removed outlier: 4.534A pdb=" N LEU M 275 " --> pdb=" O ILE M 271 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 270 through 275' Processing helix chain 'M' and resid 351 through 360 removed outlier: 3.852A pdb=" N GLU M 357 " --> pdb=" O GLU M 353 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N THR M 358 " --> pdb=" O ILE M 354 " (cutoff:3.500A) Processing helix chain 'M' and resid 379 through 394 removed outlier: 5.519A pdb=" N LEU M 383 " --> pdb=" O LEU M 379 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N LYS M 384 " --> pdb=" O ASP M 380 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N ILE M 385 " --> pdb=" O LYS M 381 " (cutoff:3.500A) removed outlier: 5.244A pdb=" N GLU M 393 " --> pdb=" O LEU M 389 " (cutoff:3.500A) removed outlier: 4.631A pdb=" N LEU M 394 " --> pdb=" O LEU M 390 " (cutoff:3.500A) Processing helix chain 'M' and resid 410 through 428 removed outlier: 3.632A pdb=" N MET M 414 " --> pdb=" O ASP M 410 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N LYS M 423 " --> pdb=" O LYS M 419 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N ASP M 426 " --> pdb=" O GLN M 422 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N ASP M 427 " --> pdb=" O LYS M 423 " (cutoff:3.500A) Proline residue: M 428 - end of helix Processing helix chain 'M' and resid 453 through 473 removed outlier: 4.183A pdb=" N LEU M 465 " --> pdb=" O ASN M 461 " (cutoff:3.500A) removed outlier: 4.274A pdb=" N ALA M 466 " --> pdb=" O PHE M 462 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N THR M 467 " --> pdb=" O ASP M 463 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N ARG M 471 " --> pdb=" O THR M 467 " (cutoff:3.500A) removed outlier: 4.922A pdb=" N PHE M 472 " --> pdb=" O LEU M 468 " (cutoff:3.500A) removed outlier: 5.007A pdb=" N ASP M 473 " --> pdb=" O LEU M 469 " (cutoff:3.500A) Processing helix chain 'M' and resid 474 through 479 Processing helix chain 'M' and resid 490 through 497 removed outlier: 4.082A pdb=" N VAL M 495 " --> pdb=" O TRP M 491 " (cutoff:3.500A) Processing helix chain 'M' and resid 509 through 514 removed outlier: 3.867A pdb=" N THR M 513 " --> pdb=" O PRO M 509 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N LYS M 514 " --> pdb=" O SER M 510 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 509 through 514' Processing helix chain 'M' and resid 515 through 521 removed outlier: 4.940A pdb=" N LYS M 521 " --> pdb=" O ASN M 517 " (cutoff:3.500A) Processing helix chain 'M' and resid 545 through 554 removed outlier: 4.224A pdb=" N ARG M 549 " --> pdb=" O ASP M 545 " (cutoff:3.500A) removed outlier: 4.108A pdb=" N ARG M 554 " --> pdb=" O PHE M 550 " (cutoff:3.500A) Processing helix chain 'M' and resid 594 through 610 removed outlier: 4.755A pdb=" N GLU M 598 " --> pdb=" O GLN M 594 " (cutoff:3.500A) removed outlier: 4.134A pdb=" N THR M 599 " --> pdb=" O LYS M 595 " (cutoff:3.500A) Processing helix chain 'M' and resid 616 through 621 Proline residue: M 621 - end of helix Processing helix chain 'M' and resid 626 through 632 removed outlier: 4.243A pdb=" N LEU M 630 " --> pdb=" O LEU M 626 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N THR M 631 " --> pdb=" O ASP M 627 " (cutoff:3.500A) removed outlier: 5.756A pdb=" N LEU M 632 " --> pdb=" O HIS M 628 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 626 through 632' Processing helix chain 'H' and resid 3 through 23 removed outlier: 3.948A pdb=" N LYS H 8 " --> pdb=" O ASP H 4 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N LEU H 9 " --> pdb=" O LEU H 5 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N SER H 23 " --> pdb=" O LEU H 19 " (cutoff:3.500A) Processing helix chain 'H' and resid 33 through 61 removed outlier: 3.842A pdb=" N GLY H 61 " --> pdb=" O GLN H 57 " (cutoff:3.500A) Processing helix chain 'H' and resid 66 through 105 removed outlier: 3.812A pdb=" N CYS H 70 " --> pdb=" O LYS H 66 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N GLN H 71 " --> pdb=" O VAL H 67 " (cutoff:3.500A) removed outlier: 4.700A pdb=" N ASN H 105 " --> pdb=" O ALA H 101 " (cutoff:3.500A) Processing helix chain 'H' and resid 124 through 145 removed outlier: 3.904A pdb=" N GLY H 144 " --> pdb=" O ASP H 140 " (cutoff:3.500A) removed outlier: 5.139A pdb=" N ASP H 145 " --> pdb=" O LEU H 141 " (cutoff:3.500A) Processing helix chain 'H' and resid 192 through 203 removed outlier: 4.089A pdb=" N VAL H 196 " --> pdb=" O ARG H 192 " (cutoff:3.500A) removed outlier: 5.126A pdb=" N ARG H 198 " --> pdb=" O SER H 194 " (cutoff:3.500A) removed outlier: 5.132A pdb=" N LEU H 199 " --> pdb=" O ASP H 195 " (cutoff:3.500A) Processing helix chain 'O' and resid 3 through 23 removed outlier: 3.949A pdb=" N LYS O 8 " --> pdb=" O ASP O 4 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N LEU O 9 " --> pdb=" O LEU O 5 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N SER O 23 " --> pdb=" O LEU O 19 " (cutoff:3.500A) Processing helix chain 'O' and resid 33 through 61 removed outlier: 3.842A pdb=" N GLY O 61 " --> pdb=" O GLN O 57 " (cutoff:3.500A) Processing helix chain 'O' and resid 66 through 105 removed outlier: 3.811A pdb=" N CYS O 70 " --> pdb=" O LYS O 66 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N GLN O 71 " --> pdb=" O VAL O 67 " (cutoff:3.500A) removed outlier: 4.700A pdb=" N ASN O 105 " --> pdb=" O ALA O 101 " (cutoff:3.500A) Processing helix chain 'O' and resid 124 through 145 removed outlier: 3.904A pdb=" N GLY O 144 " --> pdb=" O ASP O 140 " (cutoff:3.500A) removed outlier: 5.138A pdb=" N ASP O 145 " --> pdb=" O LEU O 141 " (cutoff:3.500A) Processing helix chain 'O' and resid 192 through 203 removed outlier: 4.089A pdb=" N VAL O 196 " --> pdb=" O ARG O 192 " (cutoff:3.500A) removed outlier: 5.125A pdb=" N ARG O 198 " --> pdb=" O SER O 194 " (cutoff:3.500A) removed outlier: 5.130A pdb=" N LEU O 199 " --> pdb=" O ASP O 195 " (cutoff:3.500A) Processing helix chain 'I' and resid 12 through 23 removed outlier: 4.254A pdb=" N GLU I 23 " --> pdb=" O ILE I 19 " (cutoff:3.500A) Processing helix chain 'I' and resid 57 through 63 removed outlier: 3.853A pdb=" N MET I 63 " --> pdb=" O ALA I 59 " (cutoff:3.500A) Processing helix chain 'I' and resid 72 through 83 removed outlier: 3.660A pdb=" N GLN I 82 " --> pdb=" O LEU I 78 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N SER I 83 " --> pdb=" O LEU I 79 " (cutoff:3.500A) Processing helix chain 'I' and resid 94 through 109 Proline residue: I 109 - end of helix Processing helix chain 'I' and resid 118 through 130 Processing helix chain 'I' and resid 137 through 161 removed outlier: 3.633A pdb=" N LEU I 141 " --> pdb=" O PRO I 137 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N ILE I 151 " --> pdb=" O ASP I 147 " (cutoff:3.500A) removed outlier: 4.307A pdb=" N LYS I 161 " --> pdb=" O LEU I 157 " (cutoff:3.500A) Processing helix chain 'I' and resid 174 through 200 Proline residue: I 183 - end of helix removed outlier: 3.684A pdb=" N SER I 199 " --> pdb=" O ILE I 195 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N LEU I 200 " --> pdb=" O HIS I 196 " (cutoff:3.500A) Processing helix chain 'P' and resid 12 through 23 removed outlier: 4.254A pdb=" N GLU P 23 " --> pdb=" O ILE P 19 " (cutoff:3.500A) Processing helix chain 'P' and resid 57 through 63 removed outlier: 3.852A pdb=" N MET P 63 " --> pdb=" O ALA P 59 " (cutoff:3.500A) Processing helix chain 'P' and resid 72 through 83 removed outlier: 3.661A pdb=" N GLN P 82 " --> pdb=" O LEU P 78 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N SER P 83 " --> pdb=" O LEU P 79 " (cutoff:3.500A) Processing helix chain 'P' and resid 94 through 109 Proline residue: P 109 - end of helix Processing helix chain 'P' and resid 118 through 130 Processing helix chain 'P' and resid 137 through 161 removed outlier: 3.635A pdb=" N LEU P 141 " --> pdb=" O PRO P 137 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N ILE P 151 " --> pdb=" O ASP P 147 " (cutoff:3.500A) removed outlier: 4.307A pdb=" N LYS P 161 " --> pdb=" O LEU P 157 " (cutoff:3.500A) Processing helix chain 'P' and resid 174 through 200 Proline residue: P 183 - end of helix removed outlier: 3.684A pdb=" N SER P 199 " --> pdb=" O ILE P 195 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N LEU P 200 " --> pdb=" O HIS P 196 " (cutoff:3.500A) Processing helix chain 'N' and resid 1403 through 1414 removed outlier: 3.778A pdb=" N GLU N1412 " --> pdb=" O LEU N1408 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N ASN N1413 " --> pdb=" O GLU N1409 " (cutoff:3.500A) removed outlier: 5.636A pdb=" N CYS N1414 " --> pdb=" O GLU N1410 " (cutoff:3.500A) Processing helix chain 'N' and resid 1432 through 1441 Processing helix chain 'N' and resid 1454 through 1462 removed outlier: 4.392A pdb=" N GLY N1462 " --> pdb=" O GLY N1458 " (cutoff:3.500A) Processing helix chain 'N' and resid 1464 through 1469 removed outlier: 4.710A pdb=" N LEU N1468 " --> pdb=" O GLU N1464 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N SER N1469 " --> pdb=" O MET N1465 " (cutoff:3.500A) No H-bonds generated for 'chain 'N' and resid 1464 through 1469' Processing helix chain 'N' and resid 1596 through 1605 removed outlier: 4.137A pdb=" N ARG N1605 " --> pdb=" O LEU N1601 " (cutoff:3.500A) Processing helix chain 'N' and resid 1606 through 1611 removed outlier: 4.123A pdb=" N MET N1610 " --> pdb=" O LEU N1606 " (cutoff:3.500A) Proline residue: N1611 - end of helix No H-bonds generated for 'chain 'N' and resid 1606 through 1611' Processing helix chain 'N' and resid 1626 through 1657 removed outlier: 4.557A pdb=" N THR N1630 " --> pdb=" O ASN N1626 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N ASN N1637 " --> pdb=" O LYS N1633 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N HIS N1638 " --> pdb=" O LYS N1634 " (cutoff:3.500A) removed outlier: 4.599A pdb=" N SER N1642 " --> pdb=" O HIS N1638 " (cutoff:3.500A) removed outlier: 6.159A pdb=" N GLY N1643 " --> pdb=" O VAL N1639 " (cutoff:3.500A) removed outlier: 5.450A pdb=" N SER N1644 " --> pdb=" O LEU N1640 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N TYR N1655 " --> pdb=" O LYS N1651 " (cutoff:3.500A) Processing helix chain 'N' and resid 1659 through 1664 removed outlier: 5.097A pdb=" N ARG N1664 " --> pdb=" O ILE N1660 " (cutoff:3.500A) Processing helix chain 'N' and resid 1667 through 1684 removed outlier: 5.275A pdb=" N ILE N1671 " --> pdb=" O SER N1667 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N ILE N1672 " --> pdb=" O MET N1668 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N GLU N1683 " --> pdb=" O LYS N1679 " (cutoff:3.500A) removed outlier: 4.141A pdb=" N ASN N1684 " --> pdb=" O LEU N1680 " (cutoff:3.500A) Processing helix chain 'N' and resid 1706 through 1716 removed outlier: 6.066A pdb=" N SER N1716 " --> pdb=" O ILE N1712 " (cutoff:3.500A) Processing helix chain 'N' and resid 1738 through 1747 Processing helix chain 'N' and resid 1784 through 1805 removed outlier: 3.519A pdb=" N LYS N1804 " --> pdb=" O ASP N1800 " (cutoff:3.500A) removed outlier: 4.149A pdb=" N GLU N1805 " --> pdb=" O GLU N1801 " (cutoff:3.500A) Processing helix chain 'N' and resid 1806 through 1819 removed outlier: 4.527A pdb=" N ALA N1817 " --> pdb=" O VAL N1813 " (cutoff:3.500A) removed outlier: 4.580A pdb=" N SER N1818 " --> pdb=" O ASN N1814 " (cutoff:3.500A) Processing helix chain 'N' and resid 1829 through 1855 removed outlier: 4.383A pdb=" N LEU N1854 " --> pdb=" O GLU N1850 " (cutoff:3.500A) removed outlier: 5.318A pdb=" N GLY N1855 " --> pdb=" O PHE N1851 " (cutoff:3.500A) Processing helix chain 'N' and resid 1874 through 1892 removed outlier: 4.066A pdb=" N CYS N1878 " --> pdb=" O SER N1874 " (cutoff:3.500A) removed outlier: 4.578A pdb=" N TYR N1879 " --> pdb=" O PRO N1875 " (cutoff:3.500A) removed outlier: 6.633A pdb=" N ALA N1880 " --> pdb=" O GLU N1876 " (cutoff:3.500A) removed outlier: 5.326A pdb=" N TYR N1881 " --> pdb=" O ASN N1877 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N GLN N1883 " --> pdb=" O TYR N1879 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ASN N1892 " --> pdb=" O ALA N1888 " (cutoff:3.500A) Processing helix chain 'N' and resid 1939 through 1946 removed outlier: 4.523A pdb=" N LYS N1943 " --> pdb=" O TRP N1939 " (cutoff:3.500A) removed outlier: 4.278A pdb=" N PHE N1944 " --> pdb=" O GLN N1940 " (cutoff:3.500A) removed outlier: 4.506A pdb=" N LEU N1945 " --> pdb=" O LEU N1941 " (cutoff:3.500A) removed outlier: 5.595A pdb=" N SER N1946 " --> pdb=" O LYS N1942 " (cutoff:3.500A) No H-bonds generated for 'chain 'N' and resid 1939 through 1946' Processing helix chain 'N' and resid 1947 through 1975 Proline residue: N1951 - end of helix removed outlier: 3.570A pdb=" N ASP N1962 " --> pdb=" O MET N1958 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ASN N1975 " --> pdb=" O TYR N1971 " (cutoff:3.500A) Processing helix chain 'N' and resid 1997 through 2026 removed outlier: 4.202A pdb=" N ASN N2001 " --> pdb=" O GLU N1997 " (cutoff:3.500A) removed outlier: 6.458A pdb=" N GLY N2002 " --> pdb=" O ASN N1998 " (cutoff:3.500A) removed outlier: 6.620A pdb=" N PHE N2003 " --> pdb=" O SER N1999 " (cutoff:3.500A) removed outlier: 6.189A pdb=" N SER N2004 " --> pdb=" O LEU N2000 " (cutoff:3.500A) removed outlier: 7.566A pdb=" N HIS N2005 " --> pdb=" O ASN N2001 " (cutoff:3.500A) removed outlier: 4.714A pdb=" N LEU N2006 " --> pdb=" O GLY N2002 " (cutoff:3.500A) removed outlier: 4.445A pdb=" N PHE N2007 " --> pdb=" O PHE N2003 " (cutoff:3.500A) removed outlier: 5.085A pdb=" N LYS N2009 " --> pdb=" O HIS N2005 " (cutoff:3.500A) Proline residue: N2010 - end of helix Processing helix chain 'N' and resid 2028 through 2036 removed outlier: 3.588A pdb=" N GLU N2032 " --> pdb=" O ASP N2028 " (cutoff:3.500A) removed outlier: 5.246A pdb=" N ALA N2033 " --> pdb=" O PRO N2029 " (cutoff:3.500A) removed outlier: 6.109A pdb=" N ASP N2034 " --> pdb=" O GLN N2030 " (cutoff:3.500A) removed outlier: 4.910A pdb=" N TYR N2035 " --> pdb=" O TYR N2031 " (cutoff:3.500A) removed outlier: 5.020A pdb=" N VAL N2036 " --> pdb=" O GLU N2032 " (cutoff:3.500A) No H-bonds generated for 'chain 'N' and resid 2028 through 2036' Processing helix chain 'N' and resid 2049 through 2064 removed outlier: 3.530A pdb=" N GLU N2053 " --> pdb=" O ASN N2049 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N MET N2062 " --> pdb=" O LEU N2058 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N LEU N2064 " --> pdb=" O HIS N2060 " (cutoff:3.500A) Processing helix chain 'N' and resid 2068 through 2084 removed outlier: 3.792A pdb=" N ILE N2082 " --> pdb=" O GLU N2078 " (cutoff:3.500A) removed outlier: 4.125A pdb=" N PHE N2083 " --> pdb=" O LEU N2079 " (cutoff:3.500A) removed outlier: 4.530A pdb=" N GLU N2084 " --> pdb=" O LEU N2080 " (cutoff:3.500A) Processing helix chain 'N' and resid 2123 through 2129 removed outlier: 3.876A pdb=" N ILE N2127 " --> pdb=" O ALA N2123 " (cutoff:3.500A) removed outlier: 6.818A pdb=" N PHE N2128 " --> pdb=" O PRO N2124 " (cutoff:3.500A) removed outlier: 4.465A pdb=" N SER N2129 " --> pdb=" O GLU N2125 " (cutoff:3.500A) No H-bonds generated for 'chain 'N' and resid 2123 through 2129' Processing helix chain 'N' and resid 2138 through 2160 removed outlier: 3.658A pdb=" N GLN N2160 " --> pdb=" O SER N2156 " (cutoff:3.500A) Processing helix chain 'N' and resid 2190 through 2209 removed outlier: 3.833A pdb=" N ILE N2194 " --> pdb=" O PRO N2190 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N LYS N2202 " --> pdb=" O LEU N2198 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N GLN N2203 " --> pdb=" O ASN N2199 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N TYR N2208 " --> pdb=" O VAL N2204 " (cutoff:3.500A) removed outlier: 4.790A pdb=" N GLY N2209 " --> pdb=" O ALA N2205 " (cutoff:3.500A) Processing helix chain 'N' and resid 2210 through 2220 removed outlier: 3.928A pdb=" N LEU N2220 " --> pdb=" O CYS N2216 " (cutoff:3.500A) Processing helix chain 'N' and resid 1699 through 1704 removed outlier: 6.245A pdb=" N GLN N1702 " --> pdb=" O GLY N1699 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N ASP N1704 " --> pdb=" O ILE N1701 " (cutoff:3.500A) Processing helix chain 'Q' and resid 1403 through 1414 removed outlier: 3.777A pdb=" N GLU Q1412 " --> pdb=" O LEU Q1408 " (cutoff:3.500A) removed outlier: 4.060A pdb=" N ASN Q1413 " --> pdb=" O GLU Q1409 " (cutoff:3.500A) removed outlier: 5.635A pdb=" N CYS Q1414 " --> pdb=" O GLU Q1410 " (cutoff:3.500A) Processing helix chain 'Q' and resid 1432 through 1441 Processing helix chain 'Q' and resid 1454 through 1462 removed outlier: 4.392A pdb=" N GLY Q1462 " --> pdb=" O GLY Q1458 " (cutoff:3.500A) Processing helix chain 'Q' and resid 1464 through 1469 removed outlier: 4.710A pdb=" N LEU Q1468 " --> pdb=" O GLU Q1464 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N SER Q1469 " --> pdb=" O MET Q1465 " (cutoff:3.500A) No H-bonds generated for 'chain 'Q' and resid 1464 through 1469' Processing helix chain 'Q' and resid 1596 through 1605 removed outlier: 4.138A pdb=" N ARG Q1605 " --> pdb=" O LEU Q1601 " (cutoff:3.500A) Processing helix chain 'Q' and resid 1606 through 1611 removed outlier: 4.123A pdb=" N MET Q1610 " --> pdb=" O LEU Q1606 " (cutoff:3.500A) Proline residue: Q1611 - end of helix No H-bonds generated for 'chain 'Q' and resid 1606 through 1611' Processing helix chain 'Q' and resid 1626 through 1657 removed outlier: 4.557A pdb=" N THR Q1630 " --> pdb=" O ASN Q1626 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N ASN Q1637 " --> pdb=" O LYS Q1633 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N HIS Q1638 " --> pdb=" O LYS Q1634 " (cutoff:3.500A) removed outlier: 4.599A pdb=" N SER Q1642 " --> pdb=" O HIS Q1638 " (cutoff:3.500A) removed outlier: 6.160A pdb=" N GLY Q1643 " --> pdb=" O VAL Q1639 " (cutoff:3.500A) removed outlier: 5.450A pdb=" N SER Q1644 " --> pdb=" O LEU Q1640 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N TYR Q1655 " --> pdb=" O LYS Q1651 " (cutoff:3.500A) Processing helix chain 'Q' and resid 1659 through 1664 removed outlier: 5.097A pdb=" N ARG Q1664 " --> pdb=" O ILE Q1660 " (cutoff:3.500A) Processing helix chain 'Q' and resid 1667 through 1684 removed outlier: 5.275A pdb=" N ILE Q1671 " --> pdb=" O SER Q1667 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N ILE Q1672 " --> pdb=" O MET Q1668 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N GLU Q1683 " --> pdb=" O LYS Q1679 " (cutoff:3.500A) removed outlier: 4.142A pdb=" N ASN Q1684 " --> pdb=" O LEU Q1680 " (cutoff:3.500A) Processing helix chain 'Q' and resid 1706 through 1716 removed outlier: 6.066A pdb=" N SER Q1716 " --> pdb=" O ILE Q1712 " (cutoff:3.500A) Processing helix chain 'Q' and resid 1738 through 1747 Processing helix chain 'Q' and resid 1784 through 1805 removed outlier: 3.520A pdb=" N LYS Q1804 " --> pdb=" O ASP Q1800 " (cutoff:3.500A) removed outlier: 4.149A pdb=" N GLU Q1805 " --> pdb=" O GLU Q1801 " (cutoff:3.500A) Processing helix chain 'Q' and resid 1806 through 1819 removed outlier: 4.528A pdb=" N ALA Q1817 " --> pdb=" O VAL Q1813 " (cutoff:3.500A) removed outlier: 4.580A pdb=" N SER Q1818 " --> pdb=" O ASN Q1814 " (cutoff:3.500A) Processing helix chain 'Q' and resid 1829 through 1855 removed outlier: 4.384A pdb=" N LEU Q1854 " --> pdb=" O GLU Q1850 " (cutoff:3.500A) removed outlier: 5.318A pdb=" N GLY Q1855 " --> pdb=" O PHE Q1851 " (cutoff:3.500A) Processing helix chain 'Q' and resid 1874 through 1892 removed outlier: 4.066A pdb=" N CYS Q1878 " --> pdb=" O SER Q1874 " (cutoff:3.500A) removed outlier: 4.579A pdb=" N TYR Q1879 " --> pdb=" O PRO Q1875 " (cutoff:3.500A) removed outlier: 6.635A pdb=" N ALA Q1880 " --> pdb=" O GLU Q1876 " (cutoff:3.500A) removed outlier: 5.326A pdb=" N TYR Q1881 " --> pdb=" O ASN Q1877 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N GLN Q1883 " --> pdb=" O TYR Q1879 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ASN Q1892 " --> pdb=" O ALA Q1888 " (cutoff:3.500A) Processing helix chain 'Q' and resid 1939 through 1946 removed outlier: 4.524A pdb=" N LYS Q1943 " --> pdb=" O TRP Q1939 " (cutoff:3.500A) removed outlier: 4.278A pdb=" N PHE Q1944 " --> pdb=" O GLN Q1940 " (cutoff:3.500A) removed outlier: 4.505A pdb=" N LEU Q1945 " --> pdb=" O LEU Q1941 " (cutoff:3.500A) removed outlier: 5.595A pdb=" N SER Q1946 " --> pdb=" O LYS Q1942 " (cutoff:3.500A) No H-bonds generated for 'chain 'Q' and resid 1939 through 1946' Processing helix chain 'Q' and resid 1947 through 1975 Proline residue: Q1951 - end of helix removed outlier: 3.571A pdb=" N ASP Q1962 " --> pdb=" O MET Q1958 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ASN Q1975 " --> pdb=" O TYR Q1971 " (cutoff:3.500A) Processing helix chain 'Q' and resid 1997 through 2026 removed outlier: 4.203A pdb=" N ASN Q2001 " --> pdb=" O GLU Q1997 " (cutoff:3.500A) removed outlier: 6.456A pdb=" N GLY Q2002 " --> pdb=" O ASN Q1998 " (cutoff:3.500A) removed outlier: 6.620A pdb=" N PHE Q2003 " --> pdb=" O SER Q1999 " (cutoff:3.500A) removed outlier: 6.189A pdb=" N SER Q2004 " --> pdb=" O LEU Q2000 " (cutoff:3.500A) removed outlier: 7.565A pdb=" N HIS Q2005 " --> pdb=" O ASN Q2001 " (cutoff:3.500A) removed outlier: 4.714A pdb=" N LEU Q2006 " --> pdb=" O GLY Q2002 " (cutoff:3.500A) removed outlier: 4.444A pdb=" N PHE Q2007 " --> pdb=" O PHE Q2003 " (cutoff:3.500A) removed outlier: 5.087A pdb=" N LYS Q2009 " --> pdb=" O HIS Q2005 " (cutoff:3.500A) Proline residue: Q2010 - end of helix Processing helix chain 'Q' and resid 2028 through 2036 removed outlier: 3.589A pdb=" N GLU Q2032 " --> pdb=" O ASP Q2028 " (cutoff:3.500A) removed outlier: 5.245A pdb=" N ALA Q2033 " --> pdb=" O PRO Q2029 " (cutoff:3.500A) removed outlier: 6.110A pdb=" N ASP Q2034 " --> pdb=" O GLN Q2030 " (cutoff:3.500A) removed outlier: 4.910A pdb=" N TYR Q2035 " --> pdb=" O TYR Q2031 " (cutoff:3.500A) removed outlier: 5.020A pdb=" N VAL Q2036 " --> pdb=" O GLU Q2032 " (cutoff:3.500A) No H-bonds generated for 'chain 'Q' and resid 2028 through 2036' Processing helix chain 'Q' and resid 2049 through 2064 removed outlier: 3.530A pdb=" N GLU Q2053 " --> pdb=" O ASN Q2049 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N MET Q2062 " --> pdb=" O LEU Q2058 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N LEU Q2064 " --> pdb=" O HIS Q2060 " (cutoff:3.500A) Processing helix chain 'Q' and resid 2068 through 2084 removed outlier: 3.792A pdb=" N ILE Q2082 " --> pdb=" O GLU Q2078 " (cutoff:3.500A) removed outlier: 4.126A pdb=" N PHE Q2083 " --> pdb=" O LEU Q2079 " (cutoff:3.500A) removed outlier: 4.530A pdb=" N GLU Q2084 " --> pdb=" O LEU Q2080 " (cutoff:3.500A) Processing helix chain 'Q' and resid 2123 through 2129 removed outlier: 3.876A pdb=" N ILE Q2127 " --> pdb=" O ALA Q2123 " (cutoff:3.500A) removed outlier: 6.818A pdb=" N PHE Q2128 " --> pdb=" O PRO Q2124 " (cutoff:3.500A) removed outlier: 4.466A pdb=" N SER Q2129 " --> pdb=" O GLU Q2125 " (cutoff:3.500A) No H-bonds generated for 'chain 'Q' and resid 2123 through 2129' Processing helix chain 'Q' and resid 2138 through 2160 removed outlier: 3.658A pdb=" N GLN Q2160 " --> pdb=" O SER Q2156 " (cutoff:3.500A) Processing helix chain 'Q' and resid 2190 through 2209 removed outlier: 3.832A pdb=" N ILE Q2194 " --> pdb=" O PRO Q2190 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N LYS Q2202 " --> pdb=" O LEU Q2198 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N GLN Q2203 " --> pdb=" O ASN Q2199 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N TYR Q2208 " --> pdb=" O VAL Q2204 " (cutoff:3.500A) removed outlier: 4.791A pdb=" N GLY Q2209 " --> pdb=" O ALA Q2205 " (cutoff:3.500A) Processing helix chain 'Q' and resid 2210 through 2220 removed outlier: 3.928A pdb=" N LEU Q2220 " --> pdb=" O CYS Q2216 " (cutoff:3.500A) Processing helix chain 'Q' and resid 1699 through 1704 removed outlier: 6.244A pdb=" N GLN Q1702 " --> pdb=" O GLY Q1699 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N ASP Q1704 " --> pdb=" O ILE Q1701 " (cutoff:3.500A) Processing sheet with id= 1, first strand: chain '2' and resid 240 through 244 Processing sheet with id= 2, first strand: chain '2' and resid 317 through 322 Processing sheet with id= 3, first strand: chain '2' and resid 326 through 330 removed outlier: 4.182A pdb=" N ARG 2 326 " --> pdb=" O THR 2 389 " (cutoff:3.500A) removed outlier: 6.725A pdb=" N ARG 2 387 " --> pdb=" O THR 2 328 " (cutoff:3.500A) removed outlier: 4.441A pdb=" N VAL 2 330 " --> pdb=" O TYR 2 385 " (cutoff:3.500A) removed outlier: 6.606A pdb=" N TYR 2 385 " --> pdb=" O VAL 2 330 " (cutoff:3.500A) removed outlier: 6.148A pdb=" N ARG 2 404 " --> pdb=" O GLU 2 392 " (cutoff:3.500A) removed outlier: 5.331A pdb=" N LEU 2 411 " --> pdb=" O ALA 2 453 " (cutoff:3.500A) Processing sheet with id= 4, first strand: chain '2' and resid 339 through 342 removed outlier: 4.488A pdb=" N PHE 2 339 " --> pdb=" O LEU 2 348 " (cutoff:3.500A) Processing sheet with id= 5, first strand: chain '2' and resid 562 through 567 removed outlier: 5.169A pdb=" N ARG 2 562 " --> pdb=" O LYS 2 601 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N GLY 2 602 " --> pdb=" O ARG 2 643 " (cutoff:3.500A) Processing sheet with id= 6, first strand: chain '2' and resid 578 through 582 Processing sheet with id= 7, first strand: chain '2' and resid 627 through 632 removed outlier: 4.821A pdb=" N GLN 2 627 " --> pdb=" O ALA 2 642 " (cutoff:3.500A) Processing sheet with id= 8, first strand: chain 'a' and resid 240 through 244 Processing sheet with id= 9, first strand: chain 'a' and resid 317 through 322 Processing sheet with id= 10, first strand: chain 'a' and resid 326 through 330 removed outlier: 4.182A pdb=" N ARG a 326 " --> pdb=" O THR a 389 " (cutoff:3.500A) removed outlier: 6.725A pdb=" N ARG a 387 " --> pdb=" O THR a 328 " (cutoff:3.500A) removed outlier: 4.442A pdb=" N VAL a 330 " --> pdb=" O TYR a 385 " (cutoff:3.500A) removed outlier: 6.608A pdb=" N TYR a 385 " --> pdb=" O VAL a 330 " (cutoff:3.500A) removed outlier: 6.149A pdb=" N ARG a 404 " --> pdb=" O GLU a 392 " (cutoff:3.500A) removed outlier: 5.331A pdb=" N LEU a 411 " --> pdb=" O ALA a 453 " (cutoff:3.500A) Processing sheet with id= 11, first strand: chain 'a' and resid 339 through 342 removed outlier: 4.489A pdb=" N PHE a 339 " --> pdb=" O LEU a 348 " (cutoff:3.500A) Processing sheet with id= 12, first strand: chain 'a' and resid 562 through 567 removed outlier: 5.171A pdb=" N ARG a 562 " --> pdb=" O LYS a 601 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N GLY a 602 " --> pdb=" O ARG a 643 " (cutoff:3.500A) Processing sheet with id= 13, first strand: chain 'a' and resid 578 through 582 Processing sheet with id= 14, first strand: chain 'a' and resid 627 through 632 removed outlier: 4.821A pdb=" N GLN a 627 " --> pdb=" O ALA a 642 " (cutoff:3.500A) Processing sheet with id= 15, first strand: chain '3' and resid 94 through 98 removed outlier: 3.557A pdb=" N ILE 3 96 " --> pdb=" O LYS 3 154 " (cutoff:3.500A) Processing sheet with id= 16, first strand: chain '3' and resid 179 through 184 removed outlier: 6.416A pdb=" N ARG 3 291 " --> pdb=" O LEU 3 329 " (cutoff:3.500A) Processing sheet with id= 17, first strand: chain '3' and resid 198 through 203 removed outlier: 4.091A pdb=" N ARG 3 208 " --> pdb=" O ALA 3 203 " (cutoff:3.500A) Processing sheet with id= 18, first strand: chain '3' and resid 253 through 260 removed outlier: 5.755A pdb=" N ARG 3 272 " --> pdb=" O GLU 3 260 " (cutoff:3.500A) Processing sheet with id= 19, first strand: chain '3' and resid 389 through 393 removed outlier: 4.957A pdb=" N VAL 3 389 " --> pdb=" O GLY 3 401 " (cutoff:3.500A) removed outlier: 5.201A pdb=" N GLY 3 401 " --> pdb=" O VAL 3 389 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N LYS 3 391 " --> pdb=" O LEU 3 399 " (cutoff:3.500A) Processing sheet with id= 20, first strand: chain '3' and resid 428 through 433 removed outlier: 5.733A pdb=" N LEU 3 428 " --> pdb=" O ARG 3 467 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N GLY 3 468 " --> pdb=" O ARG 3 509 " (cutoff:3.500A) Processing sheet with id= 21, first strand: chain '3' and resid 446 through 450 removed outlier: 3.997A pdb=" N GLU 3 454 " --> pdb=" O ASP 3 449 " (cutoff:3.500A) Processing sheet with id= 22, first strand: chain 'b' and resid 94 through 98 removed outlier: 3.558A pdb=" N ILE b 96 " --> pdb=" O LYS b 154 " (cutoff:3.500A) Processing sheet with id= 23, first strand: chain 'b' and resid 179 through 184 removed outlier: 6.417A pdb=" N ARG b 291 " --> pdb=" O LEU b 329 " (cutoff:3.500A) Processing sheet with id= 24, first strand: chain 'b' and resid 198 through 203 removed outlier: 4.091A pdb=" N ARG b 208 " --> pdb=" O ALA b 203 " (cutoff:3.500A) Processing sheet with id= 25, first strand: chain 'b' and resid 253 through 260 removed outlier: 5.753A pdb=" N ARG b 272 " --> pdb=" O GLU b 260 " (cutoff:3.500A) Processing sheet with id= 26, first strand: chain 'b' and resid 389 through 393 removed outlier: 4.957A pdb=" N VAL b 389 " --> pdb=" O GLY b 401 " (cutoff:3.500A) removed outlier: 5.200A pdb=" N GLY b 401 " --> pdb=" O VAL b 389 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N LYS b 391 " --> pdb=" O LEU b 399 " (cutoff:3.500A) Processing sheet with id= 27, first strand: chain 'b' and resid 428 through 433 removed outlier: 5.734A pdb=" N LEU b 428 " --> pdb=" O ARG b 467 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N GLY b 468 " --> pdb=" O ARG b 509 " (cutoff:3.500A) Processing sheet with id= 28, first strand: chain 'b' and resid 446 through 450 removed outlier: 3.997A pdb=" N GLU b 454 " --> pdb=" O ASP b 449 " (cutoff:3.500A) Processing sheet with id= 29, first strand: chain '4' and resid 239 through 243 removed outlier: 5.521A pdb=" N LYS 4 302 " --> pdb=" O SER 4 239 " (cutoff:3.500A) removed outlier: 4.482A pdb=" N LEU 4 241 " --> pdb=" O LYS 4 302 " (cutoff:3.500A) removed outlier: 4.184A pdb=" N LEU 4 243 " --> pdb=" O ARG 4 304 " (cutoff:3.500A) Processing sheet with id= 30, first strand: chain '4' and resid 324 through 329 removed outlier: 4.156A pdb=" N LYS 4 324 " --> pdb=" O PHE 4 439 " (cutoff:3.500A) removed outlier: 6.799A pdb=" N THR 4 436 " --> pdb=" O VAL 4 464 " (cutoff:3.500A) removed outlier: 8.187A pdb=" N THR 4 459 " --> pdb=" O SER 4 414 " (cutoff:3.500A) removed outlier: 5.097A pdb=" N SER 4 416 " --> pdb=" O THR 4 459 " (cutoff:3.500A) removed outlier: 5.353A pdb=" N TYR 4 420 " --> pdb=" O VAL 4 463 " (cutoff:3.500A) removed outlier: 5.635A pdb=" N HIS 4 413 " --> pdb=" O GLU 4 401 " (cutoff:3.500A) Processing sheet with id= 31, first strand: chain '4' and resid 344 through 349 removed outlier: 6.393A pdb=" N ALA 4 345 " --> pdb=" O ALA 4 357 " (cutoff:3.500A) removed outlier: 4.556A pdb=" N ALA 4 357 " --> pdb=" O ALA 4 345 " (cutoff:3.500A) removed outlier: 6.953A pdb=" N PHE 4 347 " --> pdb=" O THR 4 355 " (cutoff:3.500A) removed outlier: 4.504A pdb=" N THR 4 355 " --> pdb=" O PHE 4 347 " (cutoff:3.500A) removed outlier: 5.646A pdb=" N CYS 4 349 " --> pdb=" O ASP 4 353 " (cutoff:3.500A) Processing sheet with id= 32, first strand: chain '4' and resid 548 through 552 removed outlier: 5.290A pdb=" N THR 4 548 " --> pdb=" O GLY 4 560 " (cutoff:3.500A) removed outlier: 4.763A pdb=" N GLY 4 560 " --> pdb=" O THR 4 548 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N LYS 4 550 " --> pdb=" O TYR 4 558 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N PHE 4 552 " --> pdb=" O GLY 4 556 " (cutoff:3.500A) removed outlier: 8.437A pdb=" N SER 4 669 " --> pdb=" O GLY 4 560 " (cutoff:3.500A) removed outlier: 6.053A pdb=" N ILE 4 562 " --> pdb=" O SER 4 669 " (cutoff:3.500A) removed outlier: 4.212A pdb=" N ILE 4 671 " --> pdb=" O ILE 4 562 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N VAL 4 628 " --> pdb=" O ARG 4 587 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N VAL 4 589 " --> pdb=" O VAL 4 628 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N THR 4 591 " --> pdb=" O CYS 4 630 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N ASP 4 632 " --> pdb=" O THR 4 591 " (cutoff:3.500A) Processing sheet with id= 33, first strand: chain '4' and resid 603 through 607 removed outlier: 3.861A pdb=" N GLU 4 617 " --> pdb=" O TYR 4 604 " (cutoff:3.500A) Processing sheet with id= 34, first strand: chain '4' and resid 563 through 567 Processing sheet with id= 35, first strand: chain '4' and resid 652 through 657 removed outlier: 7.810A pdb=" N GLN 4 652 " --> pdb=" O ALA 4 667 " (cutoff:3.500A) Processing sheet with id= 36, first strand: chain 'c' and resid 239 through 243 removed outlier: 5.521A pdb=" N LYS c 302 " --> pdb=" O SER c 239 " (cutoff:3.500A) removed outlier: 4.482A pdb=" N LEU c 241 " --> pdb=" O LYS c 302 " (cutoff:3.500A) removed outlier: 4.183A pdb=" N LEU c 243 " --> pdb=" O ARG c 304 " (cutoff:3.500A) Processing sheet with id= 37, first strand: chain 'c' and resid 324 through 329 removed outlier: 4.157A pdb=" N LYS c 324 " --> pdb=" O PHE c 439 " (cutoff:3.500A) removed outlier: 6.800A pdb=" N THR c 436 " --> pdb=" O VAL c 464 " (cutoff:3.500A) removed outlier: 8.187A pdb=" N THR c 459 " --> pdb=" O SER c 414 " (cutoff:3.500A) removed outlier: 5.099A pdb=" N SER c 416 " --> pdb=" O THR c 459 " (cutoff:3.500A) removed outlier: 5.354A pdb=" N TYR c 420 " --> pdb=" O VAL c 463 " (cutoff:3.500A) removed outlier: 5.633A pdb=" N HIS c 413 " --> pdb=" O GLU c 401 " (cutoff:3.500A) Processing sheet with id= 38, first strand: chain 'c' and resid 344 through 349 removed outlier: 6.393A pdb=" N ALA c 345 " --> pdb=" O ALA c 357 " (cutoff:3.500A) removed outlier: 4.556A pdb=" N ALA c 357 " --> pdb=" O ALA c 345 " (cutoff:3.500A) removed outlier: 6.952A pdb=" N PHE c 347 " --> pdb=" O THR c 355 " (cutoff:3.500A) removed outlier: 4.505A pdb=" N THR c 355 " --> pdb=" O PHE c 347 " (cutoff:3.500A) removed outlier: 5.645A pdb=" N CYS c 349 " --> pdb=" O ASP c 353 " (cutoff:3.500A) Processing sheet with id= 39, first strand: chain 'c' and resid 548 through 552 removed outlier: 5.291A pdb=" N THR c 548 " --> pdb=" O GLY c 560 " (cutoff:3.500A) removed outlier: 4.764A pdb=" N GLY c 560 " --> pdb=" O THR c 548 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N LYS c 550 " --> pdb=" O TYR c 558 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N PHE c 552 " --> pdb=" O GLY c 556 " (cutoff:3.500A) removed outlier: 8.437A pdb=" N SER c 669 " --> pdb=" O GLY c 560 " (cutoff:3.500A) removed outlier: 6.052A pdb=" N ILE c 562 " --> pdb=" O SER c 669 " (cutoff:3.500A) removed outlier: 4.211A pdb=" N ILE c 671 " --> pdb=" O ILE c 562 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N VAL c 628 " --> pdb=" O ARG c 587 " (cutoff:3.500A) removed outlier: 4.051A pdb=" N VAL c 589 " --> pdb=" O VAL c 628 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N THR c 591 " --> pdb=" O CYS c 630 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N ASP c 632 " --> pdb=" O THR c 591 " (cutoff:3.500A) Processing sheet with id= 40, first strand: chain 'c' and resid 603 through 607 removed outlier: 3.861A pdb=" N GLU c 617 " --> pdb=" O TYR c 604 " (cutoff:3.500A) Processing sheet with id= 41, first strand: chain 'c' and resid 563 through 567 Processing sheet with id= 42, first strand: chain 'c' and resid 652 through 657 removed outlier: 7.811A pdb=" N GLN c 652 " --> pdb=" O ALA c 667 " (cutoff:3.500A) Processing sheet with id= 43, first strand: chain '5' and resid 59 through 63 Processing sheet with id= 44, first strand: chain '5' and resid 158 through 164 removed outlier: 4.129A pdb=" N LYS 5 158 " --> pdb=" O TYR 5 298 " (cutoff:3.500A) removed outlier: 6.512A pdb=" N VAL 5 295 " --> pdb=" O LEU 5 331 " (cutoff:3.500A) removed outlier: 5.507A pdb=" N ASP 5 279 " --> pdb=" O ILE 5 330 " (cutoff:3.500A) Processing sheet with id= 45, first strand: chain '5' and resid 189 through 193 removed outlier: 4.528A pdb=" N SER 5 180 " --> pdb=" O ILE 5 244 " (cutoff:3.500A) removed outlier: 4.137A pdb=" N ARG 5 184 " --> pdb=" O PRO 5 240 " (cutoff:3.500A) Processing sheet with id= 46, first strand: chain '5' and resid 435 through 440 removed outlier: 5.689A pdb=" N ILE 5 435 " --> pdb=" O GLY 5 474 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N GLY 5 475 " --> pdb=" O ARG 5 516 " (cutoff:3.500A) removed outlier: 6.062A pdb=" N ILE 5 410 " --> pdb=" O THR 5 517 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N VAL 5 519 " --> pdb=" O ILE 5 410 " (cutoff:3.500A) Processing sheet with id= 47, first strand: chain '5' and resid 451 through 457 removed outlier: 4.183A pdb=" N GLU 5 461 " --> pdb=" O ASP 5 456 " (cutoff:3.500A) Processing sheet with id= 48, first strand: chain '5' and resid 760 through 764 removed outlier: 6.554A pdb=" N THR 5 760 " --> pdb=" O SER 5 773 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N SER 5 773 " --> pdb=" O THR 5 760 " (cutoff:3.500A) Processing sheet with id= 49, first strand: chain '5' and resid 292 through 295 Processing sheet with id= 50, first strand: chain 'd' and resid 59 through 63 Processing sheet with id= 51, first strand: chain 'd' and resid 158 through 164 removed outlier: 4.128A pdb=" N LYS d 158 " --> pdb=" O TYR d 298 " (cutoff:3.500A) removed outlier: 6.512A pdb=" N VAL d 295 " --> pdb=" O LEU d 331 " (cutoff:3.500A) removed outlier: 5.507A pdb=" N ASP d 279 " --> pdb=" O ILE d 330 " (cutoff:3.500A) Processing sheet with id= 52, first strand: chain 'd' and resid 189 through 193 removed outlier: 4.528A pdb=" N SER d 180 " --> pdb=" O ILE d 244 " (cutoff:3.500A) removed outlier: 4.136A pdb=" N ARG d 184 " --> pdb=" O PRO d 240 " (cutoff:3.500A) Processing sheet with id= 53, first strand: chain 'd' and resid 435 through 440 removed outlier: 5.691A pdb=" N ILE d 435 " --> pdb=" O GLY d 474 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N GLY d 475 " --> pdb=" O ARG d 516 " (cutoff:3.500A) removed outlier: 6.061A pdb=" N ILE d 410 " --> pdb=" O THR d 517 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N VAL d 519 " --> pdb=" O ILE d 410 " (cutoff:3.500A) Processing sheet with id= 54, first strand: chain 'd' and resid 451 through 457 removed outlier: 4.183A pdb=" N GLU d 461 " --> pdb=" O ASP d 456 " (cutoff:3.500A) Processing sheet with id= 55, first strand: chain 'd' and resid 760 through 764 removed outlier: 6.554A pdb=" N THR d 760 " --> pdb=" O SER d 773 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N SER d 773 " --> pdb=" O THR d 760 " (cutoff:3.500A) Processing sheet with id= 56, first strand: chain 'd' and resid 292 through 295 Processing sheet with id= 57, first strand: chain '6' and resid 149 through 153 Processing sheet with id= 58, first strand: chain '6' and resid 287 through 292 Processing sheet with id= 59, first strand: chain '6' and resid 295 through 298 removed outlier: 4.513A pdb=" N ARG 6 382 " --> pdb=" O ALA 6 456 " (cutoff:3.500A) Processing sheet with id= 60, first strand: chain '6' and resid 308 through 312 removed outlier: 4.257A pdb=" N ALA 6 316 " --> pdb=" O CYS 6 311 " (cutoff:3.500A) Processing sheet with id= 61, first strand: chain '6' and resid 594 through 599 removed outlier: 3.769A pdb=" N ILE 6 635 " --> pdb=" O ARG 6 594 " (cutoff:3.500A) removed outlier: 6.668A pdb=" N ILE 6 569 " --> pdb=" O THR 6 676 " (cutoff:3.500A) removed outlier: 4.229A pdb=" N ILE 6 678 " --> pdb=" O ILE 6 569 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N GLY 6 575 " --> pdb=" O ALA 6 682 " (cutoff:3.500A) Processing sheet with id= 62, first strand: chain '6' and resid 610 through 614 removed outlier: 3.917A pdb=" N ALA 6 611 " --> pdb=" O GLU 6 624 " (cutoff:3.500A) Processing sheet with id= 63, first strand: chain '6' and resid 659 through 665 removed outlier: 4.695A pdb=" N GLN 6 659 " --> pdb=" O ALA 6 674 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N ILE 6 668 " --> pdb=" O LYS 6 665 " (cutoff:3.500A) Processing sheet with id= 64, first strand: chain 'e' and resid 149 through 153 Processing sheet with id= 65, first strand: chain 'e' and resid 287 through 292 Processing sheet with id= 66, first strand: chain 'e' and resid 295 through 298 removed outlier: 4.512A pdb=" N ARG e 382 " --> pdb=" O ALA e 456 " (cutoff:3.500A) Processing sheet with id= 67, first strand: chain 'e' and resid 308 through 312 removed outlier: 4.257A pdb=" N ALA e 316 " --> pdb=" O CYS e 311 " (cutoff:3.500A) Processing sheet with id= 68, first strand: chain 'e' and resid 594 through 599 removed outlier: 3.767A pdb=" N ILE e 635 " --> pdb=" O ARG e 594 " (cutoff:3.500A) removed outlier: 6.668A pdb=" N ILE e 569 " --> pdb=" O THR e 676 " (cutoff:3.500A) removed outlier: 4.230A pdb=" N ILE e 678 " --> pdb=" O ILE e 569 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N GLY e 575 " --> pdb=" O ALA e 682 " (cutoff:3.500A) Processing sheet with id= 69, first strand: chain 'e' and resid 610 through 614 removed outlier: 3.918A pdb=" N ALA e 611 " --> pdb=" O GLU e 624 " (cutoff:3.500A) Processing sheet with id= 70, first strand: chain 'e' and resid 659 through 665 removed outlier: 4.696A pdb=" N GLN e 659 " --> pdb=" O ALA e 674 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N ILE e 668 " --> pdb=" O LYS e 665 " (cutoff:3.500A) Processing sheet with id= 71, first strand: chain '7' and resid 76 through 80 Processing sheet with id= 72, first strand: chain '7' and resid 238 through 242 removed outlier: 3.507A pdb=" N PHE 7 380 " --> pdb=" O THR 7 352 " (cutoff:3.500A) Processing sheet with id= 73, first strand: chain '7' and resid 251 through 255 removed outlier: 5.476A pdb=" N ALA 7 309 " --> pdb=" O GLY 7 337 " (cutoff:3.500A) removed outlier: 6.069A pdb=" N ARG 7 329 " --> pdb=" O GLU 7 317 " (cutoff:3.500A) Processing sheet with id= 74, first strand: chain '7' and resid 257 through 261 Processing sheet with id= 75, first strand: chain '7' and resid 479 through 484 removed outlier: 5.271A pdb=" N ILE 7 454 " --> pdb=" O THR 7 561 " (cutoff:3.500A) Processing sheet with id= 76, first strand: chain 'f' and resid 76 through 80 Processing sheet with id= 77, first strand: chain 'f' and resid 238 through 242 removed outlier: 3.508A pdb=" N PHE f 380 " --> pdb=" O THR f 352 " (cutoff:3.500A) Processing sheet with id= 78, first strand: chain 'f' and resid 251 through 255 removed outlier: 5.475A pdb=" N ALA f 309 " --> pdb=" O GLY f 337 " (cutoff:3.500A) removed outlier: 6.067A pdb=" N ARG f 329 " --> pdb=" O GLU f 317 " (cutoff:3.500A) Processing sheet with id= 79, first strand: chain 'f' and resid 257 through 261 Processing sheet with id= 80, first strand: chain 'f' and resid 479 through 484 removed outlier: 5.271A pdb=" N ILE f 454 " --> pdb=" O THR f 561 " (cutoff:3.500A) Processing sheet with id= 81, first strand: chain 'D' and resid 255 through 261 Processing sheet with id= 82, first strand: chain 'K' and resid 255 through 261 Processing sheet with id= 83, first strand: chain 'E' and resid 56 through 62 removed outlier: 3.594A pdb=" N GLN E 57 " --> pdb=" O LEU E 27 " (cutoff:3.500A) removed outlier: 6.225A pdb=" N ILE E 139 " --> pdb=" O ARG E 118 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N ILE E 120 " --> pdb=" O ILE E 139 " (cutoff:3.500A) Processing sheet with id= 84, first strand: chain 'E' and resid 317 through 320 Processing sheet with id= 85, first strand: chain 'E' and resid 525 through 531 removed outlier: 3.588A pdb=" N ILE E 572 " --> pdb=" O LEU E 530 " (cutoff:3.500A) removed outlier: 6.220A pdb=" N SER E 628 " --> pdb=" O GLY E 583 " (cutoff:3.500A) Processing sheet with id= 86, first strand: chain 'L' and resid 56 through 62 removed outlier: 3.594A pdb=" N GLN L 57 " --> pdb=" O LEU L 27 " (cutoff:3.500A) removed outlier: 6.224A pdb=" N ILE L 139 " --> pdb=" O ARG L 118 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N ILE L 120 " --> pdb=" O ILE L 139 " (cutoff:3.500A) Processing sheet with id= 87, first strand: chain 'L' and resid 317 through 320 Processing sheet with id= 88, first strand: chain 'L' and resid 525 through 531 removed outlier: 3.587A pdb=" N ILE L 572 " --> pdb=" O LEU L 530 " (cutoff:3.500A) removed outlier: 6.221A pdb=" N SER L 628 " --> pdb=" O GLY L 583 " (cutoff:3.500A) Processing sheet with id= 89, first strand: chain 'F' and resid 171 through 174 removed outlier: 3.609A pdb=" N CYS F 642 " --> pdb=" O PHE F 542 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N ASP F 544 " --> pdb=" O CYS F 642 " (cutoff:3.500A) Processing sheet with id= 90, first strand: chain 'F' and resid 180 through 185 removed outlier: 4.897A pdb=" N ARG F 180 " --> pdb=" O VAL F 193 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N GLN F 189 " --> pdb=" O ASN F 184 " (cutoff:3.500A) Processing sheet with id= 91, first strand: chain 'F' and resid 283 through 286 removed outlier: 3.520A pdb=" N GLY F 286 " --> pdb=" O VAL F 326 " (cutoff:3.500A) Processing sheet with id= 92, first strand: chain 'F' and resid 398 through 402 removed outlier: 3.780A pdb=" N LEU F 431 " --> pdb=" O LYS F 398 " (cutoff:3.500A) removed outlier: 5.493A pdb=" N GLN F 435 " --> pdb=" O LEU F 402 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N THR F 480 " --> pdb=" O THR F 430 " (cutoff:3.500A) Processing sheet with id= 93, first strand: chain 'F' and resid 648 through 652 removed outlier: 4.192A pdb=" N PHE F 649 " --> pdb=" O ASN F 660 " (cutoff:3.500A) Processing sheet with id= 94, first strand: chain 'F' and resid 669 through 675 removed outlier: 4.191A pdb=" N ALA F 670 " --> pdb=" O GLU F 686 " (cutoff:3.500A) Processing sheet with id= 95, first strand: chain 'M' and resid 171 through 174 removed outlier: 3.610A pdb=" N CYS M 642 " --> pdb=" O PHE M 542 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N ASP M 544 " --> pdb=" O CYS M 642 " (cutoff:3.500A) Processing sheet with id= 96, first strand: chain 'M' and resid 180 through 185 removed outlier: 4.897A pdb=" N ARG M 180 " --> pdb=" O VAL M 193 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N GLN M 189 " --> pdb=" O ASN M 184 " (cutoff:3.500A) Processing sheet with id= 97, first strand: chain 'M' and resid 283 through 286 removed outlier: 3.520A pdb=" N GLY M 286 " --> pdb=" O VAL M 326 " (cutoff:3.500A) Processing sheet with id= 98, first strand: chain 'M' and resid 398 through 402 removed outlier: 3.779A pdb=" N LEU M 431 " --> pdb=" O LYS M 398 " (cutoff:3.500A) removed outlier: 5.491A pdb=" N GLN M 435 " --> pdb=" O LEU M 402 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N THR M 480 " --> pdb=" O THR M 430 " (cutoff:3.500A) Processing sheet with id= 99, first strand: chain 'M' and resid 648 through 652 removed outlier: 4.192A pdb=" N PHE M 649 " --> pdb=" O ASN M 660 " (cutoff:3.500A) Processing sheet with id=100, first strand: chain 'M' and resid 669 through 675 removed outlier: 4.192A pdb=" N ALA M 670 " --> pdb=" O GLU M 686 " (cutoff:3.500A) Processing sheet with id=101, first strand: chain 'H' and resid 188 through 191 removed outlier: 7.508A pdb=" N TYR H 204 " --> pdb=" O LEU H 168 " (cutoff:3.500A) Processing sheet with id=102, first strand: chain 'O' and resid 188 through 191 removed outlier: 7.508A pdb=" N TYR O 204 " --> pdb=" O LEU O 168 " (cutoff:3.500A) Processing sheet with id=103, first strand: chain 'N' and resid 1321 through 1324 removed outlier: 3.526A pdb=" N VAL N1445 " --> pdb=" O TRP N1322 " (cutoff:3.500A) removed outlier: 6.202A pdb=" N ALA N1443 " --> pdb=" O VAL N1324 " (cutoff:3.500A) Processing sheet with id=104, first strand: chain 'N' and resid 1326 through 1329 removed outlier: 4.082A pdb=" N GLN N1326 " --> pdb=" O PHE N1339 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N PHE N1339 " --> pdb=" O GLN N1326 " (cutoff:3.500A) removed outlier: 4.557A pdb=" N GLY N1334 " --> pdb=" O ILE N1353 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N MET N1359 " --> pdb=" O PHE N1398 " (cutoff:3.500A) Processing sheet with id=105, first strand: chain 'N' and resid 1484 through 1489 removed outlier: 4.048A pdb=" N GLY N1485 " --> pdb=" O LEU N1589 " (cutoff:3.500A) removed outlier: 4.310A pdb=" N SER N1594 " --> pdb=" O LEU N1615 " (cutoff:3.500A) Processing sheet with id=106, first strand: chain 'N' and resid 1724 through 1727 removed outlier: 3.774A pdb=" N LEU N1908 " --> pdb=" O LEU N1920 " (cutoff:3.500A) removed outlier: 6.654A pdb=" N ASN N1916 " --> pdb=" O MET N1912 " (cutoff:3.500A) Processing sheet with id=107, first strand: chain 'N' and resid 1856 through 1859 removed outlier: 6.481A pdb=" N LEU N1867 " --> pdb=" O VAL N1859 " (cutoff:3.500A) removed outlier: 4.555A pdb=" N VAL N1730 " --> pdb=" O THR N1870 " (cutoff:3.500A) removed outlier: 6.991A pdb=" N ASP N1733 " --> pdb=" O LYS N1903 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N ASN N1901 " --> pdb=" O GLY N1735 " (cutoff:3.500A) Processing sheet with id=108, first strand: chain 'N' and resid 2101 through 2104 removed outlier: 6.481A pdb=" N LEU N2101 " --> pdb=" O PHE N2119 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N PHE N2113 " --> pdb=" O CYS N2108 " (cutoff:3.500A) Processing sheet with id=109, first strand: chain 'N' and resid 1358 through 1361 removed outlier: 6.282A pdb=" N TYR N1358 " --> pdb=" O PHE N1427 " (cutoff:3.500A) Processing sheet with id=110, first strand: chain 'N' and resid 1730 through 1733 removed outlier: 3.940A pdb=" N ARG N1904 " --> pdb=" O ASP N1733 " (cutoff:3.500A) Processing sheet with id=111, first strand: chain 'Q' and resid 1321 through 1324 removed outlier: 3.527A pdb=" N VAL Q1445 " --> pdb=" O TRP Q1322 " (cutoff:3.500A) removed outlier: 6.203A pdb=" N ALA Q1443 " --> pdb=" O VAL Q1324 " (cutoff:3.500A) Processing sheet with id=112, first strand: chain 'Q' and resid 1326 through 1329 removed outlier: 4.082A pdb=" N GLN Q1326 " --> pdb=" O PHE Q1339 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N PHE Q1339 " --> pdb=" O GLN Q1326 " (cutoff:3.500A) removed outlier: 4.556A pdb=" N GLY Q1334 " --> pdb=" O ILE Q1353 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N MET Q1359 " --> pdb=" O PHE Q1398 " (cutoff:3.500A) Processing sheet with id=113, first strand: chain 'Q' and resid 1484 through 1489 removed outlier: 4.048A pdb=" N GLY Q1485 " --> pdb=" O LEU Q1589 " (cutoff:3.500A) removed outlier: 4.310A pdb=" N SER Q1594 " --> pdb=" O LEU Q1615 " (cutoff:3.500A) Processing sheet with id=114, first strand: chain 'Q' and resid 1724 through 1727 removed outlier: 3.773A pdb=" N LEU Q1908 " --> pdb=" O LEU Q1920 " (cutoff:3.500A) removed outlier: 6.655A pdb=" N ASN Q1916 " --> pdb=" O MET Q1912 " (cutoff:3.500A) Processing sheet with id=115, first strand: chain 'Q' and resid 1856 through 1859 removed outlier: 6.482A pdb=" N LEU Q1867 " --> pdb=" O VAL Q1859 " (cutoff:3.500A) removed outlier: 4.555A pdb=" N VAL Q1730 " --> pdb=" O THR Q1870 " (cutoff:3.500A) removed outlier: 6.990A pdb=" N ASP Q1733 " --> pdb=" O LYS Q1903 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N ASN Q1901 " --> pdb=" O GLY Q1735 " (cutoff:3.500A) Processing sheet with id=116, first strand: chain 'Q' and resid 2101 through 2104 removed outlier: 6.482A pdb=" N LEU Q2101 " --> pdb=" O PHE Q2119 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N PHE Q2113 " --> pdb=" O CYS Q2108 " (cutoff:3.500A) Processing sheet with id=117, first strand: chain 'Q' and resid 1358 through 1361 removed outlier: 6.282A pdb=" N TYR Q1358 " --> pdb=" O PHE Q1427 " (cutoff:3.500A) Processing sheet with id=118, first strand: chain 'Q' and resid 1730 through 1733 removed outlier: 3.940A pdb=" N ARG Q1904 " --> pdb=" O ASP Q1733 " (cutoff:3.500A) 4408 hydrogen bonds defined for protein. 13086 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 42.65 Time building geometry restraints manager: 33.03 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 17824 1.32 - 1.45: 28239 1.45 - 1.57: 62407 1.57 - 1.70: 264 1.70 - 1.83: 778 Bond restraints: 109512 Sorted by residual: bond pdb=" CA SER 7 467 " pdb=" CB SER 7 467 " ideal model delta sigma weight residual 1.528 1.451 0.077 1.34e-02 5.57e+03 3.32e+01 bond pdb=" CA SER f 467 " pdb=" CB SER f 467 " ideal model delta sigma weight residual 1.528 1.452 0.076 1.34e-02 5.57e+03 3.25e+01 bond pdb=" CA PHE 6 332 " pdb=" C PHE 6 332 " ideal model delta sigma weight residual 1.523 1.463 0.061 1.24e-02 6.50e+03 2.40e+01 bond pdb=" CA PHE e 332 " pdb=" C PHE e 332 " ideal model delta sigma weight residual 1.523 1.469 0.054 1.28e-02 6.10e+03 1.77e+01 bond pdb=" C PHE 6 332 " pdb=" O PHE 6 332 " ideal model delta sigma weight residual 1.235 1.190 0.045 1.22e-02 6.72e+03 1.38e+01 ... (remaining 109507 not shown) Histogram of bond angle deviations from ideal: 98.08 - 106.43: 3481 106.43 - 114.79: 66327 114.79 - 123.15: 72882 123.15 - 131.50: 5736 131.50 - 139.86: 191 Bond angle restraints: 148617 Sorted by residual: angle pdb=" N GLN f 468 " pdb=" CA GLN f 468 " pdb=" C GLN f 468 " ideal model delta sigma weight residual 113.88 100.82 13.06 1.23e+00 6.61e-01 1.13e+02 angle pdb=" N GLN 7 468 " pdb=" CA GLN 7 468 " pdb=" C GLN 7 468 " ideal model delta sigma weight residual 113.88 100.82 13.06 1.23e+00 6.61e-01 1.13e+02 angle pdb=" C CYS e 333 " pdb=" N PRO e 334 " pdb=" CA PRO e 334 " ideal model delta sigma weight residual 119.05 128.06 -9.01 1.11e+00 8.12e-01 6.58e+01 angle pdb=" N PRO 6 334 " pdb=" CA PRO 6 334 " pdb=" C PRO 6 334 " ideal model delta sigma weight residual 112.47 123.97 -11.50 2.06e+00 2.36e-01 3.12e+01 angle pdb=" N LEU 7 469 " pdb=" CA LEU 7 469 " pdb=" C LEU 7 469 " ideal model delta sigma weight residual 111.28 105.21 6.07 1.09e+00 8.42e-01 3.10e+01 ... (remaining 148612 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.85: 65033 34.85 - 69.71: 1786 69.71 - 104.56: 179 104.56 - 139.41: 10 139.41 - 174.26: 2 Dihedral angle restraints: 67010 sinusoidal: 28528 harmonic: 38482 Sorted by residual: dihedral pdb=" O2A ADP 61201 " pdb=" O3A ADP 61201 " pdb=" PA ADP 61201 " pdb=" PB ADP 61201 " ideal model delta sinusoidal sigma weight residual -60.00 76.24 -136.24 1 2.00e+01 2.50e-03 4.13e+01 dihedral pdb=" O2A ADP e1201 " pdb=" O3A ADP e1201 " pdb=" PA ADP e1201 " pdb=" PB ADP e1201 " ideal model delta sinusoidal sigma weight residual -60.00 76.15 -136.15 1 2.00e+01 2.50e-03 4.13e+01 dihedral pdb=" C5' ADP 61201 " pdb=" O5' ADP 61201 " pdb=" PA ADP 61201 " pdb=" O2A ADP 61201 " ideal model delta sinusoidal sigma weight residual -60.00 70.60 -130.60 1 2.00e+01 2.50e-03 3.96e+01 ... (remaining 67007 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.088: 15937 0.088 - 0.175: 1039 0.175 - 0.263: 17 0.263 - 0.350: 8 0.350 - 0.438: 3 Chirality restraints: 17004 Sorted by residual: chirality pdb=" CA PRO 6 334 " pdb=" N PRO 6 334 " pdb=" C PRO 6 334 " pdb=" CB PRO 6 334 " both_signs ideal model delta sigma weight residual False 2.72 2.28 0.44 2.00e-01 2.50e+01 4.80e+00 chirality pdb=" CA GLN f 468 " pdb=" N GLN f 468 " pdb=" C GLN f 468 " pdb=" CB GLN f 468 " both_signs ideal model delta sigma weight residual False 2.51 2.94 -0.43 2.00e-01 2.50e+01 4.72e+00 chirality pdb=" CA GLN 7 468 " pdb=" N GLN 7 468 " pdb=" C GLN 7 468 " pdb=" CB GLN 7 468 " both_signs ideal model delta sigma weight residual False 2.51 2.94 -0.43 2.00e-01 2.50e+01 4.71e+00 ... (remaining 17001 not shown) Planarity restraints: 18640 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA THR 6 331 " 0.026 2.00e-02 2.50e+03 5.29e-02 2.80e+01 pdb=" C THR 6 331 " -0.092 2.00e-02 2.50e+03 pdb=" O THR 6 331 " 0.035 2.00e-02 2.50e+03 pdb=" N PHE 6 332 " 0.031 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR e 331 " -0.023 2.00e-02 2.50e+03 4.65e-02 2.16e+01 pdb=" C THR e 331 " 0.080 2.00e-02 2.50e+03 pdb=" O THR e 331 " -0.030 2.00e-02 2.50e+03 pdb=" N PHE e 332 " -0.027 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ARG f 649 " 0.064 5.00e-02 4.00e+02 9.63e-02 1.48e+01 pdb=" N PRO f 650 " -0.167 5.00e-02 4.00e+02 pdb=" CA PRO f 650 " 0.052 5.00e-02 4.00e+02 pdb=" CD PRO f 650 " 0.051 5.00e-02 4.00e+02 ... (remaining 18637 not shown) Histogram of nonbonded interaction distances: 2.00 - 2.58: 612 2.58 - 3.16: 86000 3.16 - 3.74: 156409 3.74 - 4.32: 216134 4.32 - 4.90: 363883 Nonbonded interactions: 823038 Sorted by model distance: nonbonded pdb=" OG SER 5 423 " pdb="MG MG 51702 " model vdw 1.997 2.170 nonbonded pdb=" OG SER d 423 " pdb="MG MG d1702 " model vdw 1.997 2.170 nonbonded pdb=" OG SER b 416 " pdb="MG MG b1102 " model vdw 2.097 2.170 nonbonded pdb=" OG SER 3 416 " pdb="MG MG 31102 " model vdw 2.098 2.170 nonbonded pdb=" OG1 THR 3 236 " pdb=" OE1 GLU 3 237 " model vdw 2.192 2.440 ... (remaining 823033 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 '2' selection = chain 'a' } ncs_group { reference = chain '3' selection = chain 'b' } ncs_group { reference = chain '4' selection = chain 'c' } ncs_group { reference = chain '5' selection = chain 'd' } ncs_group { reference = chain '6' selection = chain 'e' } ncs_group { reference = chain '7' selection = chain 'f' } ncs_group { reference = (chain 'A' and (resid 1 through 26 or resid 28 through 53)) selection = (chain 'B' and (resid 1 through 26 or resid 28 through 53)) } ncs_group { reference = chain 'C' selection = chain 'J' } ncs_group { reference = chain 'D' selection = chain 'K' } ncs_group { reference = chain 'E' selection = chain 'L' } ncs_group { reference = chain 'F' selection = chain 'M' } ncs_group { reference = chain 'H' selection = chain 'O' } ncs_group { reference = chain 'I' selection = chain 'P' } ncs_group { reference = chain 'N' selection = chain 'Q' } 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=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.570 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.060 Extract box with map and model: 8.340 Check model and map are aligned: 1.220 Set scattering table: 0.740 Process input model: 249.010 Find NCS groups from input model: 8.410 Set up NCS constraints: 1.000 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:2.620 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 271.980 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7582 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 : 0.003 0.092 109512 Z= 0.198 Angle : 0.656 13.058 148617 Z= 0.382 Chirality : 0.043 0.438 17004 Planarity : 0.005 0.096 18640 Dihedral : 15.960 174.263 42014 Min Nonbonded Distance : 1.997 Molprobity Statistics. All-atom Clashscore : 7.26 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.84 % Favored : 96.13 % Rotamer: Outliers : 0.13 % Allowed : 0.17 % Favored : 99.70 % Cbeta Deviations : 0.02 % Peptide Plane: Cis-proline : 0.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.12 (0.07), residues: 12956 helix: 0.99 (0.07), residues: 5216 sheet: -0.04 (0.11), residues: 2092 loop : -1.08 (0.08), residues: 5648 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP F 491 HIS 0.007 0.001 HIS 7 112 PHE 0.021 0.001 PHE M 399 TYR 0.024 0.001 TYR M 183 ARG 0.010 0.000 ARG e 696 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 25912 Ramachandran restraints generated. 12956 Oldfield, 0 Emsley, 12956 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 25912 Ramachandran restraints generated. 12956 Oldfield, 0 Emsley, 12956 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2537 residues out of total 11774 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 2522 time to evaluate : 8.951 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: 2 493 ILE cc_start: 0.8928 (tp) cc_final: 0.8691 (tp) REVERT: 3 261 MET cc_start: 0.8066 (mmm) cc_final: 0.7732 (mmt) REVERT: 4 233 MET cc_start: 0.5715 (mtp) cc_final: 0.5468 (mtp) REVERT: 4 355 THR cc_start: 0.8327 (p) cc_final: 0.8094 (p) REVERT: 4 579 GLN cc_start: 0.7291 (mt0) cc_final: 0.6965 (mt0) REVERT: 5 656 ILE cc_start: 0.8668 (mt) cc_final: 0.8466 (mt) REVERT: 6 156 GLN cc_start: 0.6852 (tt0) cc_final: 0.6641 (tt0) REVERT: 6 269 ASN cc_start: 0.7848 (OUTLIER) cc_final: 0.7445 (t0) REVERT: 6 283 LYS cc_start: 0.8089 (mmtp) cc_final: 0.7539 (mtmm) REVERT: 6 783 ASP cc_start: 0.7567 (m-30) cc_final: 0.7255 (t0) REVERT: 7 92 LYS cc_start: 0.7462 (tppt) cc_final: 0.6647 (tptp) REVERT: 7 466 LYS cc_start: 0.8389 (OUTLIER) cc_final: 0.8031 (tppt) REVERT: 7 470 LEU cc_start: 0.7606 (OUTLIER) cc_final: 0.6982 (mp) REVERT: 7 504 ASP cc_start: 0.6142 (t0) cc_final: 0.5396 (t0) REVERT: D 266 GLU cc_start: 0.7073 (mp0) cc_final: 0.6798 (mp0) REVERT: D 289 ASP cc_start: 0.7345 (t0) cc_final: 0.7097 (t0) REVERT: F 91 MET cc_start: 0.6855 (ptm) cc_final: 0.6465 (ptm) REVERT: F 680 LYS cc_start: 0.7209 (mppt) cc_final: 0.6870 (mptt) REVERT: I 91 GLN cc_start: 0.6929 (mt0) cc_final: 0.6723 (mt0) REVERT: J 130 GLN cc_start: 0.9038 (mm-40) cc_final: 0.8559 (mm-40) REVERT: K 289 ASP cc_start: 0.7598 (t0) cc_final: 0.7247 (t0) REVERT: L 239 GLU cc_start: 0.7033 (tm-30) cc_final: 0.6657 (tm-30) REVERT: L 300 LYS cc_start: 0.8478 (ttmt) cc_final: 0.8163 (ttmm) REVERT: L 525 TYR cc_start: 0.9056 (p90) cc_final: 0.8798 (p90) REVERT: L 536 LEU cc_start: 0.8780 (mm) cc_final: 0.8520 (mt) REVERT: M 382 ASP cc_start: 0.7896 (t0) cc_final: 0.7313 (t0) REVERT: M 423 LYS cc_start: 0.6944 (tttm) cc_final: 0.6681 (mmtt) REVERT: M 459 LYS cc_start: 0.6941 (ttpp) cc_final: 0.6722 (ttpp) REVERT: M 552 ARG cc_start: 0.7825 (ttm110) cc_final: 0.7517 (ttp-110) REVERT: M 554 ARG cc_start: 0.6738 (mtm-85) cc_final: 0.6314 (mtm110) REVERT: M 671 ARG cc_start: 0.7157 (mtm180) cc_final: 0.6918 (mtm180) REVERT: N 1339 PHE cc_start: 0.6930 (m-10) cc_final: 0.6342 (m-80) REVERT: N 1360 LYS cc_start: 0.8128 (tppp) cc_final: 0.7771 (tptt) REVERT: N 1679 LYS cc_start: 0.8253 (mtpp) cc_final: 0.8025 (mtpt) REVERT: N 1722 ASN cc_start: 0.8505 (t0) cc_final: 0.8105 (t0) REVERT: N 1854 LEU cc_start: 0.7854 (mm) cc_final: 0.7618 (mp) REVERT: N 1862 ASP cc_start: 0.7377 (t70) cc_final: 0.6653 (t0) REVERT: N 1872 LYS cc_start: 0.8245 (mmtt) cc_final: 0.8011 (mmmm) REVERT: N 1907 ASP cc_start: 0.7829 (t0) cc_final: 0.7620 (t0) REVERT: N 1962 ASP cc_start: 0.7687 (t0) cc_final: 0.7471 (t0) REVERT: N 1970 SER cc_start: 0.8720 (m) cc_final: 0.8112 (p) REVERT: N 2012 MET cc_start: 0.7829 (mmm) cc_final: 0.7626 (mmm) REVERT: O 8 LYS cc_start: 0.7716 (mtpt) cc_final: 0.7229 (mtpt) REVERT: O 39 ASN cc_start: 0.8486 (m-40) cc_final: 0.8242 (m110) REVERT: O 50 ASN cc_start: 0.7962 (m-40) cc_final: 0.7696 (m-40) REVERT: O 79 MET cc_start: 0.6026 (mtm) cc_final: 0.5785 (mtm) REVERT: O 201 GLN cc_start: 0.7330 (tp40) cc_final: 0.7105 (tp40) REVERT: Q 1360 LYS cc_start: 0.8204 (tppp) cc_final: 0.7903 (tppt) REVERT: Q 1701 ILE cc_start: 0.8565 (tp) cc_final: 0.7860 (tp) REVERT: Q 1854 LEU cc_start: 0.7720 (mm) cc_final: 0.7330 (mp) REVERT: Q 1872 LYS cc_start: 0.7822 (mmtt) cc_final: 0.7602 (mmmm) REVERT: a 186 LEU cc_start: 0.8537 (mm) cc_final: 0.8329 (mt) REVERT: a 457 LYS cc_start: 0.8426 (ttpt) cc_final: 0.8092 (ttpt) REVERT: a 472 ASP cc_start: 0.7881 (t0) cc_final: 0.7659 (t0) REVERT: a 486 LYS cc_start: 0.8732 (tttp) cc_final: 0.8500 (tttp) REVERT: a 783 MET cc_start: 0.7450 (mtt) cc_final: 0.7250 (mtt) REVERT: a 796 GLU cc_start: 0.7504 (mm-30) cc_final: 0.7245 (mm-30) REVERT: b 126 GLU cc_start: 0.6614 (mt-10) cc_final: 0.6372 (mt-10) REVERT: c 233 MET cc_start: 0.5439 (mtp) cc_final: 0.5191 (mtp) REVERT: c 569 ASP cc_start: 0.7405 (m-30) cc_final: 0.7177 (m-30) REVERT: c 579 GLN cc_start: 0.7430 (mt0) cc_final: 0.6981 (mt0) REVERT: c 587 ARG cc_start: 0.7815 (ttp80) cc_final: 0.7398 (ptm-80) REVERT: d 184 ARG cc_start: 0.7300 (mtp85) cc_final: 0.7036 (mtm180) REVERT: d 431 LYS cc_start: 0.8243 (mttm) cc_final: 0.8041 (mttm) REVERT: d 510 THR cc_start: 0.8418 (t) cc_final: 0.8102 (p) REVERT: d 720 ARG cc_start: 0.7646 (ptm160) cc_final: 0.7417 (ptm-80) REVERT: e 188 VAL cc_start: 0.8615 (t) cc_final: 0.8238 (m) REVERT: e 269 ASN cc_start: 0.7790 (OUTLIER) cc_final: 0.7511 (t0) REVERT: e 281 SER cc_start: 0.9105 (p) cc_final: 0.8886 (p) REVERT: f 125 MET cc_start: 0.8497 (tpt) cc_final: 0.6721 (tpp) REVERT: f 373 GLU cc_start: 0.7912 (mt-10) cc_final: 0.7581 (mt-10) REVERT: f 466 LYS cc_start: 0.8716 (OUTLIER) cc_final: 0.8474 (tppt) REVERT: f 506 MET cc_start: 0.7041 (pmm) cc_final: 0.6802 (pmm) REVERT: f 539 GLU cc_start: 0.6768 (tm-30) cc_final: 0.5571 (tm-30) outliers start: 15 outliers final: 4 residues processed: 2532 average time/residue: 0.9817 time to fit residues: 4282.0756 Evaluate side-chains 2138 residues out of total 11774 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 2129 time to evaluate : 9.026 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 6 residue 269 ASN Chi-restraints excluded: chain 6 residue 335 ASN Chi-restraints excluded: chain 7 residue 466 LYS Chi-restraints excluded: chain 7 residue 470 LEU Chi-restraints excluded: chain M residue 687 ILE Chi-restraints excluded: chain e residue 269 ASN Chi-restraints excluded: chain e residue 333 CYS Chi-restraints excluded: chain e residue 338 CYS Chi-restraints excluded: chain f residue 466 LYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1310 random chunks: chunk 1106 optimal weight: 0.0870 chunk 992 optimal weight: 4.9990 chunk 550 optimal weight: 2.9990 chunk 339 optimal weight: 6.9990 chunk 669 optimal weight: 8.9990 chunk 530 optimal weight: 3.9990 chunk 1026 optimal weight: 5.9990 chunk 397 optimal weight: 0.9980 chunk 624 optimal weight: 5.9990 chunk 764 optimal weight: 6.9990 chunk 1189 optimal weight: 10.0000 overall best weight: 2.6164 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 2 238 ASN 2 641 GLN ** 3 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 3 530 HIS 3 531 GLN 3 731 ASN 4 579 GLN 4 646 HIS 5 145 GLN 5 359 GLN 6 139 GLN 6 556 HIS 6 690 ASN 7 332 ASN C 21 GLN D 96 GLN F 52 ASN ** F 435 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 96 GLN L 269 ASN L 296 GLN L 382 HIS L 395 ASN M 52 ASN ** M 435 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 488 ASN N1489 HIS O 202 GLN Q1489 HIS Q1901 ASN a 238 ASN ** b 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** b 530 HIS c 691 ASN ** d 273 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 359 GLN d 636 ASN d 768 GLN e 335 ASN e 409 GLN e 735 HIS ** f 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** f 332 ASN ** f 544 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 37 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7628 moved from start: 0.1168 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 109512 Z= 0.214 Angle : 0.580 13.416 148617 Z= 0.305 Chirality : 0.042 0.187 17004 Planarity : 0.005 0.085 18640 Dihedral : 11.806 172.987 15864 Min Nonbonded Distance : 1.988 Molprobity Statistics. All-atom Clashscore : 7.39 Ramachandran Plot: Outliers : 0.01 % Allowed : 3.88 % Favored : 96.11 % Rotamer: Outliers : 1.69 % Allowed : 8.12 % Favored : 90.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.10 (0.07), residues: 12956 helix: 1.32 (0.07), residues: 5328 sheet: 0.03 (0.11), residues: 2056 loop : -1.14 (0.08), residues: 5572 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP E 481 HIS 0.013 0.001 HIS F 666 PHE 0.026 0.001 PHE f 526 TYR 0.021 0.001 TYR c 519 ARG 0.011 0.000 ARG c 373 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 25912 Ramachandran restraints generated. 12956 Oldfield, 0 Emsley, 12956 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 25912 Ramachandran restraints generated. 12956 Oldfield, 0 Emsley, 12956 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2417 residues out of total 11774 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 199 poor density : 2218 time to evaluate : 9.175 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: 4 233 MET cc_start: 0.5726 (mtp) cc_final: 0.5409 (mtp) REVERT: 4 467 LYS cc_start: 0.7810 (mtmt) cc_final: 0.7468 (mtmm) REVERT: 5 65 MET cc_start: 0.8666 (mtt) cc_final: 0.8237 (mtt) REVERT: 5 157 SER cc_start: 0.8559 (m) cc_final: 0.8043 (t) REVERT: 5 431 LYS cc_start: 0.8221 (mttm) cc_final: 0.7734 (mtpp) REVERT: 6 269 ASN cc_start: 0.7855 (OUTLIER) cc_final: 0.7246 (t0) REVERT: 6 283 LYS cc_start: 0.8028 (mmtp) cc_final: 0.7591 (mtmm) REVERT: 6 527 ASP cc_start: 0.7377 (t0) cc_final: 0.6806 (t0) REVERT: 6 783 ASP cc_start: 0.7567 (m-30) cc_final: 0.7219 (t0) REVERT: 7 92 LYS cc_start: 0.7432 (tppt) cc_final: 0.6700 (tptp) REVERT: 7 199 ARG cc_start: 0.6960 (ptp-110) cc_final: 0.6538 (ptp-110) REVERT: 7 504 ASP cc_start: 0.6140 (t0) cc_final: 0.5482 (t0) REVERT: 7 539 GLU cc_start: 0.6875 (tm-30) cc_final: 0.5550 (tm-30) REVERT: 7 621 MET cc_start: 0.6775 (tpp) cc_final: 0.6528 (tpt) REVERT: C 20 PHE cc_start: 0.7704 (OUTLIER) cc_final: 0.6593 (t80) REVERT: C 193 LYS cc_start: 0.7886 (tptt) cc_final: 0.7571 (tptp) REVERT: D 75 GLU cc_start: 0.7170 (pt0) cc_final: 0.5648 (tt0) REVERT: D 189 ILE cc_start: 0.8767 (mt) cc_final: 0.8539 (tt) REVERT: D 266 GLU cc_start: 0.6984 (mp0) cc_final: 0.6710 (mp0) REVERT: D 289 ASP cc_start: 0.7357 (t0) cc_final: 0.6975 (t0) REVERT: F 91 MET cc_start: 0.6879 (ptm) cc_final: 0.6485 (ptm) REVERT: F 213 ASP cc_start: 0.8292 (m-30) cc_final: 0.8064 (m-30) REVERT: F 468 LEU cc_start: 0.7482 (mp) cc_final: 0.7238 (mp) REVERT: F 552 ARG cc_start: 0.7595 (ttp-110) cc_final: 0.7324 (ttm170) REVERT: I 91 GLN cc_start: 0.6997 (mt0) cc_final: 0.6779 (mt0) REVERT: I 104 TYR cc_start: 0.8647 (t80) cc_final: 0.8337 (t80) REVERT: J 20 PHE cc_start: 0.7940 (OUTLIER) cc_final: 0.6384 (t80) REVERT: K 98 ILE cc_start: 0.8551 (OUTLIER) cc_final: 0.8310 (mp) REVERT: K 256 TYR cc_start: 0.8118 (m-80) cc_final: 0.7650 (m-80) REVERT: K 289 ASP cc_start: 0.7696 (t0) cc_final: 0.7334 (t0) REVERT: L 239 GLU cc_start: 0.7236 (tm-30) cc_final: 0.6821 (tm-30) REVERT: L 525 TYR cc_start: 0.8978 (p90) cc_final: 0.8773 (p90) REVERT: L 536 LEU cc_start: 0.8952 (mm) cc_final: 0.8699 (mt) REVERT: M 333 TYR cc_start: 0.8017 (m-80) cc_final: 0.7086 (m-80) REVERT: M 494 MET cc_start: 0.7593 (tpp) cc_final: 0.7325 (tpp) REVERT: M 552 ARG cc_start: 0.7656 (ttm110) cc_final: 0.7153 (mtm-85) REVERT: M 554 ARG cc_start: 0.6675 (mtm-85) cc_final: 0.6411 (mtm110) REVERT: N 1339 PHE cc_start: 0.6982 (m-10) cc_final: 0.6397 (m-80) REVERT: N 1360 LYS cc_start: 0.7948 (tppp) cc_final: 0.7627 (tptt) REVERT: N 1654 GLN cc_start: 0.7258 (mm-40) cc_final: 0.7009 (mm-40) REVERT: N 1663 LEU cc_start: 0.7661 (tp) cc_final: 0.7433 (tp) REVERT: N 1854 LEU cc_start: 0.7948 (mm) cc_final: 0.7582 (mp) REVERT: N 1862 ASP cc_start: 0.7454 (t70) cc_final: 0.6782 (t0) REVERT: N 1872 LYS cc_start: 0.8277 (mmtt) cc_final: 0.8007 (mmmm) REVERT: N 1896 SER cc_start: 0.8016 (p) cc_final: 0.7412 (m) REVERT: N 1962 ASP cc_start: 0.7740 (t0) cc_final: 0.7512 (t0) REVERT: N 1970 SER cc_start: 0.8764 (m) cc_final: 0.8156 (p) REVERT: N 2012 MET cc_start: 0.7996 (mmm) cc_final: 0.7766 (mmm) REVERT: O 8 LYS cc_start: 0.7972 (mtpt) cc_final: 0.7433 (mttm) REVERT: O 50 ASN cc_start: 0.7956 (m-40) cc_final: 0.7725 (m-40) REVERT: O 51 THR cc_start: 0.8303 (p) cc_final: 0.8085 (p) REVERT: O 201 GLN cc_start: 0.7599 (tp40) cc_final: 0.7275 (tp40) REVERT: O 204 TYR cc_start: 0.8191 (m-80) cc_final: 0.7984 (m-80) REVERT: P 92 TRP cc_start: 0.8783 (p-90) cc_final: 0.8570 (p-90) REVERT: Q 1360 LYS cc_start: 0.8194 (tppp) cc_final: 0.7879 (tppt) REVERT: Q 1384 PRO cc_start: 0.8090 (Cg_exo) cc_final: 0.7884 (Cg_endo) REVERT: Q 1465 MET cc_start: 0.5277 (mmm) cc_final: 0.4038 (mmm) REVERT: Q 1854 LEU cc_start: 0.7835 (mm) cc_final: 0.7560 (mp) REVERT: Q 1862 ASP cc_start: 0.7141 (t70) cc_final: 0.6714 (t70) REVERT: Q 1872 LYS cc_start: 0.7851 (mmtt) cc_final: 0.7566 (mmmm) REVERT: a 486 LYS cc_start: 0.8709 (tttp) cc_final: 0.8494 (tttp) REVERT: a 751 LYS cc_start: 0.7671 (mttt) cc_final: 0.7201 (mmtt) REVERT: a 855 ARG cc_start: 0.6719 (mtm-85) cc_final: 0.6518 (mtp-110) REVERT: b 126 GLU cc_start: 0.6640 (mt-10) cc_final: 0.6365 (mt-10) REVERT: b 202 TYR cc_start: 0.8360 (t80) cc_final: 0.7737 (t80) REVERT: c 233 MET cc_start: 0.5369 (mtp) cc_final: 0.5144 (mtp) REVERT: c 467 LYS cc_start: 0.7806 (mtpt) cc_final: 0.7490 (mtmm) REVERT: d 65 MET cc_start: 0.8610 (mtp) cc_final: 0.8186 (mtt) REVERT: d 85 ASP cc_start: 0.7417 (m-30) cc_final: 0.7084 (m-30) REVERT: d 157 SER cc_start: 0.8660 (m) cc_final: 0.8270 (t) REVERT: d 358 LEU cc_start: 0.7421 (mp) cc_final: 0.7215 (mp) REVERT: d 368 GLU cc_start: 0.7382 (mt-10) cc_final: 0.7094 (mt-10) REVERT: d 720 ARG cc_start: 0.7752 (ptm160) cc_final: 0.7496 (ptm-80) REVERT: e 144 LYS cc_start: 0.7659 (tptp) cc_final: 0.7370 (tptp) REVERT: e 187 ARG cc_start: 0.7639 (mmm-85) cc_final: 0.7329 (ttm-80) REVERT: e 269 ASN cc_start: 0.7873 (OUTLIER) cc_final: 0.7375 (t0) REVERT: e 281 SER cc_start: 0.9146 (p) cc_final: 0.8863 (p) REVERT: e 755 ILE cc_start: 0.8852 (mm) cc_final: 0.8617 (mt) REVERT: f 92 LYS cc_start: 0.7966 (tppt) cc_final: 0.7531 (tptp) REVERT: f 125 MET cc_start: 0.8389 (tpt) cc_final: 0.8178 (tpp) REVERT: f 338 THR cc_start: 0.8662 (p) cc_final: 0.7393 (m) REVERT: f 466 LYS cc_start: 0.8724 (OUTLIER) cc_final: 0.8518 (tppt) outliers start: 199 outliers final: 146 residues processed: 2304 average time/residue: 0.9097 time to fit residues: 3594.8663 Evaluate side-chains 2224 residues out of total 11774 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 152 poor density : 2072 time to evaluate : 8.936 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 245 ASN Chi-restraints excluded: chain 2 residue 251 GLU Chi-restraints excluded: chain 2 residue 292 GLU Chi-restraints excluded: chain 2 residue 302 THR Chi-restraints excluded: chain 2 residue 424 VAL Chi-restraints excluded: chain 2 residue 564 VAL Chi-restraints excluded: chain 2 residue 567 THR Chi-restraints excluded: chain 2 residue 819 SER Chi-restraints excluded: chain 2 residue 860 SER Chi-restraints excluded: chain 3 residue 44 SER Chi-restraints excluded: chain 3 residue 99 SER Chi-restraints excluded: chain 3 residue 112 SER Chi-restraints excluded: chain 3 residue 242 THR Chi-restraints excluded: chain 3 residue 322 LEU Chi-restraints excluded: chain 3 residue 341 MET Chi-restraints excluded: chain 3 residue 346 ASP Chi-restraints excluded: chain 3 residue 448 THR Chi-restraints excluded: chain 3 residue 582 VAL Chi-restraints excluded: chain 3 residue 651 VAL Chi-restraints excluded: chain 3 residue 698 THR Chi-restraints excluded: chain 3 residue 720 THR Chi-restraints excluded: chain 4 residue 375 ASP Chi-restraints excluded: chain 4 residue 535 ASP Chi-restraints excluded: chain 4 residue 646 HIS Chi-restraints excluded: chain 4 residue 709 LEU Chi-restraints excluded: chain 4 residue 767 LYS Chi-restraints excluded: chain 4 residue 802 ILE Chi-restraints excluded: chain 4 residue 813 LEU Chi-restraints excluded: chain 5 residue 153 SER Chi-restraints excluded: chain 5 residue 193 THR Chi-restraints excluded: chain 5 residue 207 LEU Chi-restraints excluded: chain 5 residue 273 ASN Chi-restraints excluded: chain 5 residue 277 THR Chi-restraints excluded: chain 5 residue 426 LEU Chi-restraints excluded: chain 5 residue 453 VAL Chi-restraints excluded: chain 5 residue 675 ARG Chi-restraints excluded: chain 5 residue 727 SER Chi-restraints excluded: chain 6 residue 160 MET Chi-restraints excluded: chain 6 residue 269 ASN Chi-restraints excluded: chain 6 residue 293 THR Chi-restraints excluded: chain 6 residue 337 SER Chi-restraints excluded: chain 6 residue 438 THR Chi-restraints excluded: chain 6 residue 676 THR Chi-restraints excluded: chain 6 residue 807 SER Chi-restraints excluded: chain 7 residue 5 LEU Chi-restraints excluded: chain 7 residue 225 LEU Chi-restraints excluded: chain 7 residue 372 THR Chi-restraints excluded: chain 7 residue 473 ILE Chi-restraints excluded: chain 7 residue 533 ASP Chi-restraints excluded: chain 7 residue 660 VAL Chi-restraints excluded: chain C residue 10 LEU Chi-restraints excluded: chain C residue 20 PHE Chi-restraints excluded: chain C residue 24 ILE Chi-restraints excluded: chain E residue 59 VAL Chi-restraints excluded: chain E residue 82 LEU Chi-restraints excluded: chain E residue 403 ASP Chi-restraints excluded: chain E residue 412 THR Chi-restraints excluded: chain E residue 536 LEU Chi-restraints excluded: chain E residue 638 SER Chi-restraints excluded: chain E residue 645 THR Chi-restraints excluded: chain F residue 86 GLU Chi-restraints excluded: chain F residue 224 LEU Chi-restraints excluded: chain F residue 269 THR Chi-restraints excluded: chain F residue 513 THR Chi-restraints excluded: chain F residue 547 SER Chi-restraints excluded: chain H residue 5 LEU Chi-restraints excluded: chain H residue 43 GLU Chi-restraints excluded: chain H residue 104 ASN Chi-restraints excluded: chain H residue 146 LEU Chi-restraints excluded: chain H residue 147 VAL Chi-restraints excluded: chain I residue 133 ASP Chi-restraints excluded: chain I residue 177 GLU Chi-restraints excluded: chain J residue 20 PHE Chi-restraints excluded: chain J residue 24 ILE Chi-restraints excluded: chain K residue 98 ILE Chi-restraints excluded: chain L residue 59 VAL Chi-restraints excluded: chain L residue 82 LEU Chi-restraints excluded: chain L residue 165 LEU Chi-restraints excluded: chain L residue 310 VAL Chi-restraints excluded: chain L residue 419 ILE Chi-restraints excluded: chain L residue 537 ASP Chi-restraints excluded: chain L residue 638 SER Chi-restraints excluded: chain M residue 86 GLU Chi-restraints excluded: chain M residue 188 MET Chi-restraints excluded: chain M residue 302 SER Chi-restraints excluded: chain M residue 401 ILE Chi-restraints excluded: chain M residue 447 MET Chi-restraints excluded: chain M residue 632 LEU Chi-restraints excluded: chain N residue 1382 SER Chi-restraints excluded: chain N residue 1610 MET Chi-restraints excluded: chain N residue 1736 VAL Chi-restraints excluded: chain N residue 1810 ASP Chi-restraints excluded: chain N residue 1821 GLN Chi-restraints excluded: chain N residue 1848 VAL Chi-restraints excluded: chain N residue 1863 ARG Chi-restraints excluded: chain N residue 1865 GLN Chi-restraints excluded: chain N residue 1882 SER Chi-restraints excluded: chain N residue 1885 MET Chi-restraints excluded: chain N residue 2117 ILE Chi-restraints excluded: chain O residue 5 LEU Chi-restraints excluded: chain O residue 43 GLU Chi-restraints excluded: chain O residue 146 LEU Chi-restraints excluded: chain O residue 147 VAL Chi-restraints excluded: chain P residue 189 MET Chi-restraints excluded: chain Q residue 1426 VAL Chi-restraints excluded: chain Q residue 1736 VAL Chi-restraints excluded: chain Q residue 1810 ASP Chi-restraints excluded: chain Q residue 1848 VAL Chi-restraints excluded: chain Q residue 1936 VAL Chi-restraints excluded: chain Q residue 2115 SER Chi-restraints excluded: chain a residue 202 ASN Chi-restraints excluded: chain a residue 251 GLU Chi-restraints excluded: chain a residue 292 GLU Chi-restraints excluded: chain a residue 381 VAL Chi-restraints excluded: chain a residue 390 LEU Chi-restraints excluded: chain a residue 564 VAL Chi-restraints excluded: chain a residue 567 THR Chi-restraints excluded: chain a residue 819 SER Chi-restraints excluded: chain a residue 860 SER Chi-restraints excluded: chain b residue 44 SER Chi-restraints excluded: chain b residue 91 ILE Chi-restraints excluded: chain b residue 99 SER Chi-restraints excluded: chain b residue 112 SER Chi-restraints excluded: chain b residue 322 LEU Chi-restraints excluded: chain b residue 346 ASP Chi-restraints excluded: chain b residue 437 SER Chi-restraints excluded: chain b residue 448 THR Chi-restraints excluded: chain b residue 486 ILE Chi-restraints excluded: chain b residue 651 VAL Chi-restraints excluded: chain c residue 360 ILE Chi-restraints excluded: chain c residue 468 LYS Chi-restraints excluded: chain c residue 725 THR Chi-restraints excluded: chain c residue 813 LEU Chi-restraints excluded: chain d residue 163 SER Chi-restraints excluded: chain d residue 193 THR Chi-restraints excluded: chain d residue 267 VAL Chi-restraints excluded: chain d residue 273 ASN Chi-restraints excluded: chain d residue 277 THR Chi-restraints excluded: chain d residue 608 LEU Chi-restraints excluded: chain d residue 727 SER Chi-restraints excluded: chain e residue 269 ASN Chi-restraints excluded: chain e residue 409 GLN Chi-restraints excluded: chain e residue 438 THR Chi-restraints excluded: chain e residue 443 LEU Chi-restraints excluded: chain e residue 642 ASP Chi-restraints excluded: chain e residue 676 THR Chi-restraints excluded: chain e residue 807 SER Chi-restraints excluded: chain f residue 372 THR Chi-restraints excluded: chain f residue 466 LYS Chi-restraints excluded: chain f residue 473 ILE Chi-restraints excluded: chain f residue 533 ASP Chi-restraints excluded: chain f residue 689 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1310 random chunks: chunk 661 optimal weight: 4.9990 chunk 369 optimal weight: 20.0000 chunk 990 optimal weight: 0.9990 chunk 810 optimal weight: 10.0000 chunk 328 optimal weight: 3.9990 chunk 1191 optimal weight: 10.0000 chunk 1287 optimal weight: 8.9990 chunk 1061 optimal weight: 30.0000 chunk 1181 optimal weight: 3.9990 chunk 406 optimal weight: 6.9990 chunk 956 optimal weight: 4.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 2 641 GLN 2 703 HIS 3 417 GLN 4 579 GLN 5 499 GLN 6 735 HIS 7 145 GLN 7 543 GLN C 21 GLN E 141 GLN ** F 435 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 146 GLN L 269 ASN L 382 HIS ** M 435 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 488 ASN ** M 522 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N1435 GLN N1662 ASN O 39 ASN b 417 GLN b 532 ASN b 670 GLN b 731 ASN ** d 273 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 499 GLN ** e 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** e 556 HIS e 669 HIS ** f 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 543 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7678 moved from start: 0.1600 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 109512 Z= 0.262 Angle : 0.586 15.147 148617 Z= 0.307 Chirality : 0.043 0.186 17004 Planarity : 0.004 0.063 18640 Dihedral : 11.775 172.864 15852 Min Nonbonded Distance : 1.949 Molprobity Statistics. All-atom Clashscore : 7.25 Ramachandran Plot: Outliers : 0.01 % Allowed : 4.18 % Favored : 95.81 % Rotamer: Outliers : 2.33 % Allowed : 11.61 % Favored : 86.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.11 (0.07), residues: 12956 helix: 1.38 (0.07), residues: 5330 sheet: 0.01 (0.11), residues: 2040 loop : -1.19 (0.08), residues: 5586 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP E 481 HIS 0.026 0.001 HIS 4 646 PHE 0.024 0.002 PHE 5 482 TYR 0.021 0.002 TYR Q1971 ARG 0.020 0.000 ARG 6 137 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 25912 Ramachandran restraints generated. 12956 Oldfield, 0 Emsley, 12956 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 25912 Ramachandran restraints generated. 12956 Oldfield, 0 Emsley, 12956 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2398 residues out of total 11774 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 274 poor density : 2124 time to evaluate : 9.063 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: 2 441 LYS cc_start: 0.7583 (mttt) cc_final: 0.7187 (mttt) REVERT: 2 792 ASP cc_start: 0.7054 (m-30) cc_final: 0.6559 (m-30) REVERT: 3 105 GLU cc_start: 0.7225 (OUTLIER) cc_final: 0.6911 (mp0) REVERT: 3 435 ARG cc_start: 0.7612 (mmm160) cc_final: 0.7344 (mmm160) REVERT: 4 233 MET cc_start: 0.5790 (mtp) cc_final: 0.5469 (mtp) REVERT: 4 467 LYS cc_start: 0.7731 (mtmt) cc_final: 0.7417 (mtmm) REVERT: 4 811 MET cc_start: 0.6662 (tpt) cc_final: 0.5784 (tpp) REVERT: 5 65 MET cc_start: 0.8725 (mtt) cc_final: 0.8317 (mtt) REVERT: 5 157 SER cc_start: 0.8750 (m) cc_final: 0.8289 (t) REVERT: 5 431 LYS cc_start: 0.8217 (mttm) cc_final: 0.7775 (mtpp) REVERT: 5 736 GLU cc_start: 0.7539 (mp0) cc_final: 0.6912 (mp0) REVERT: 5 771 TYR cc_start: 0.8886 (t80) cc_final: 0.8662 (t80) REVERT: 6 143 MET cc_start: 0.7789 (mtm) cc_final: 0.7568 (mtm) REVERT: 6 269 ASN cc_start: 0.7974 (OUTLIER) cc_final: 0.7652 (t0) REVERT: 6 283 LYS cc_start: 0.8160 (mmtp) cc_final: 0.7745 (mtmm) REVERT: 6 527 ASP cc_start: 0.7404 (t0) cc_final: 0.6882 (t0) REVERT: 6 767 LYS cc_start: 0.7139 (mmtp) cc_final: 0.6863 (mmtp) REVERT: 6 783 ASP cc_start: 0.7659 (m-30) cc_final: 0.7308 (t0) REVERT: 7 199 ARG cc_start: 0.7149 (ptp-110) cc_final: 0.6916 (ptp-110) REVERT: 7 427 ASP cc_start: 0.7922 (OUTLIER) cc_final: 0.6611 (m-30) REVERT: 7 504 ASP cc_start: 0.6384 (t0) cc_final: 0.5712 (t0) REVERT: 7 644 TYR cc_start: 0.7314 (t80) cc_final: 0.7093 (t80) REVERT: C 20 PHE cc_start: 0.7847 (OUTLIER) cc_final: 0.6708 (t80) REVERT: C 193 LYS cc_start: 0.7966 (tptt) cc_final: 0.7672 (tptp) REVERT: D 289 ASP cc_start: 0.7348 (t0) cc_final: 0.7020 (t0) REVERT: F 318 HIS cc_start: 0.7358 (OUTLIER) cc_final: 0.6868 (p-80) REVERT: F 468 LEU cc_start: 0.7567 (mp) cc_final: 0.7298 (mp) REVERT: F 552 ARG cc_start: 0.7612 (ttp-110) cc_final: 0.7311 (ttm170) REVERT: H 71 GLN cc_start: 0.6887 (mp10) cc_final: 0.6680 (mp10) REVERT: H 91 ARG cc_start: 0.8282 (ttt-90) cc_final: 0.8078 (ttt90) REVERT: I 104 TYR cc_start: 0.8636 (t80) cc_final: 0.8186 (t80) REVERT: J 20 PHE cc_start: 0.8040 (OUTLIER) cc_final: 0.6556 (t80) REVERT: J 96 ASP cc_start: 0.8475 (t0) cc_final: 0.8230 (t70) REVERT: K 98 ILE cc_start: 0.8551 (OUTLIER) cc_final: 0.8351 (mp) REVERT: K 289 ASP cc_start: 0.7665 (t0) cc_final: 0.7254 (t0) REVERT: L 239 GLU cc_start: 0.7311 (tm-30) cc_final: 0.6974 (tm-30) REVERT: M 333 TYR cc_start: 0.8064 (m-80) cc_final: 0.7166 (m-80) REVERT: M 423 LYS cc_start: 0.7109 (tttm) cc_final: 0.6740 (mptt) REVERT: M 522 ASN cc_start: 0.6892 (m110) cc_final: 0.6542 (m-40) REVERT: M 554 ARG cc_start: 0.6769 (mtm-85) cc_final: 0.6338 (mtm110) REVERT: N 1339 PHE cc_start: 0.7055 (m-10) cc_final: 0.6599 (m-80) REVERT: N 1360 LYS cc_start: 0.7977 (tppp) cc_final: 0.7651 (tptt) REVERT: N 1654 GLN cc_start: 0.7244 (mm-40) cc_final: 0.7022 (mm-40) REVERT: N 1663 LEU cc_start: 0.7640 (tp) cc_final: 0.7418 (tp) REVERT: N 1854 LEU cc_start: 0.7987 (mm) cc_final: 0.7619 (mp) REVERT: N 1862 ASP cc_start: 0.7523 (t70) cc_final: 0.6902 (t70) REVERT: N 1896 SER cc_start: 0.8009 (p) cc_final: 0.7369 (m) REVERT: N 1962 ASP cc_start: 0.7802 (t0) cc_final: 0.7573 (t0) REVERT: N 1970 SER cc_start: 0.8826 (m) cc_final: 0.8197 (p) REVERT: N 2012 MET cc_start: 0.8060 (mmm) cc_final: 0.7796 (mmm) REVERT: O 8 LYS cc_start: 0.8220 (mtpt) cc_final: 0.7636 (mtpt) REVERT: O 39 ASN cc_start: 0.8299 (m-40) cc_final: 0.8058 (m110) REVERT: O 201 GLN cc_start: 0.7549 (tp40) cc_final: 0.7169 (tp40) REVERT: Q 1360 LYS cc_start: 0.8243 (tppp) cc_final: 0.7954 (tppt) REVERT: Q 1439 MET cc_start: 0.5967 (ttm) cc_final: 0.5755 (ttp) REVERT: Q 1854 LEU cc_start: 0.7815 (mm) cc_final: 0.7574 (mp) REVERT: Q 1862 ASP cc_start: 0.7029 (t70) cc_final: 0.6641 (t70) REVERT: Q 1872 LYS cc_start: 0.7900 (mmtt) cc_final: 0.7558 (mmmm) REVERT: Q 2093 GLU cc_start: 0.7059 (mt-10) cc_final: 0.6536 (tt0) REVERT: a 486 LYS cc_start: 0.8743 (tttp) cc_final: 0.8529 (tttp) REVERT: a 656 ARG cc_start: 0.7558 (ttm-80) cc_final: 0.7124 (ttm170) REVERT: a 751 LYS cc_start: 0.7853 (mttt) cc_final: 0.7382 (mtmm) REVERT: a 826 SER cc_start: 0.8776 (t) cc_final: 0.8489 (m) REVERT: b 126 GLU cc_start: 0.6697 (mt-10) cc_final: 0.6383 (mt-10) REVERT: b 202 TYR cc_start: 0.8382 (t80) cc_final: 0.7803 (t80) REVERT: b 491 GLU cc_start: 0.6687 (tp30) cc_final: 0.6384 (tp30) REVERT: c 233 MET cc_start: 0.5413 (mtp) cc_final: 0.5174 (mtp) REVERT: c 467 LYS cc_start: 0.7825 (mtpt) cc_final: 0.7507 (mtmm) REVERT: c 631 ILE cc_start: 0.9098 (mm) cc_final: 0.8735 (mm) REVERT: c 682 TYR cc_start: 0.7788 (t80) cc_final: 0.7525 (t80) REVERT: c 767 LYS cc_start: 0.7551 (OUTLIER) cc_final: 0.7349 (mttt) REVERT: d 65 MET cc_start: 0.8678 (mtp) cc_final: 0.8261 (mtt) REVERT: d 157 SER cc_start: 0.8773 (m) cc_final: 0.8351 (t) REVERT: d 239 ASP cc_start: 0.7667 (p0) cc_final: 0.7307 (p0) REVERT: d 358 LEU cc_start: 0.7573 (mp) cc_final: 0.7335 (mp) REVERT: d 471 LEU cc_start: 0.8727 (mp) cc_final: 0.8437 (mt) REVERT: d 510 THR cc_start: 0.8465 (OUTLIER) cc_final: 0.8233 (p) REVERT: e 187 ARG cc_start: 0.7609 (mmm-85) cc_final: 0.7327 (ttm-80) REVERT: e 269 ASN cc_start: 0.7931 (OUTLIER) cc_final: 0.7436 (t0) REVERT: e 281 SER cc_start: 0.9152 (p) cc_final: 0.8905 (p) REVERT: e 750 GLN cc_start: 0.6442 (mt0) cc_final: 0.6207 (mt0) REVERT: e 755 ILE cc_start: 0.8913 (mm) cc_final: 0.8654 (mt) REVERT: e 829 ASP cc_start: 0.7535 (m-30) cc_final: 0.7148 (m-30) REVERT: f 66 MET cc_start: 0.5505 (OUTLIER) cc_final: 0.4760 (ptm) REVERT: f 92 LYS cc_start: 0.7937 (tppt) cc_final: 0.7513 (tptp) REVERT: f 338 THR cc_start: 0.8641 (p) cc_final: 0.7372 (m) REVERT: f 427 ASP cc_start: 0.7887 (OUTLIER) cc_final: 0.7388 (m-30) REVERT: f 466 LYS cc_start: 0.8819 (OUTLIER) cc_final: 0.8589 (tppt) REVERT: f 621 MET cc_start: 0.7229 (tpp) cc_final: 0.6909 (tpt) outliers start: 274 outliers final: 207 residues processed: 2238 average time/residue: 0.9140 time to fit residues: 3515.6335 Evaluate side-chains 2237 residues out of total 11774 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 220 poor density : 2017 time to evaluate : 9.006 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 186 LEU Chi-restraints excluded: chain 2 residue 226 VAL Chi-restraints excluded: chain 2 residue 241 SER Chi-restraints excluded: chain 2 residue 245 ASN Chi-restraints excluded: chain 2 residue 251 GLU Chi-restraints excluded: chain 2 residue 292 GLU Chi-restraints excluded: chain 2 residue 302 THR Chi-restraints excluded: chain 2 residue 414 LEU Chi-restraints excluded: chain 2 residue 424 VAL Chi-restraints excluded: chain 2 residue 499 SER Chi-restraints excluded: chain 2 residue 564 VAL Chi-restraints excluded: chain 2 residue 567 THR Chi-restraints excluded: chain 2 residue 819 SER Chi-restraints excluded: chain 2 residue 860 SER Chi-restraints excluded: chain 3 residue 44 SER Chi-restraints excluded: chain 3 residue 99 SER Chi-restraints excluded: chain 3 residue 105 GLU Chi-restraints excluded: chain 3 residue 112 SER Chi-restraints excluded: chain 3 residue 135 SER Chi-restraints excluded: chain 3 residue 185 ILE Chi-restraints excluded: chain 3 residue 220 THR Chi-restraints excluded: chain 3 residue 242 THR Chi-restraints excluded: chain 3 residue 322 LEU Chi-restraints excluded: chain 3 residue 346 ASP Chi-restraints excluded: chain 3 residue 448 THR Chi-restraints excluded: chain 3 residue 484 VAL Chi-restraints excluded: chain 3 residue 582 VAL Chi-restraints excluded: chain 3 residue 651 VAL Chi-restraints excluded: chain 3 residue 698 THR Chi-restraints excluded: chain 3 residue 720 THR Chi-restraints excluded: chain 4 residue 292 ASP Chi-restraints excluded: chain 4 residue 320 ASN Chi-restraints excluded: chain 4 residue 355 THR Chi-restraints excluded: chain 4 residue 444 ILE Chi-restraints excluded: chain 4 residue 463 VAL Chi-restraints excluded: chain 4 residue 468 LYS Chi-restraints excluded: chain 4 residue 535 ASP Chi-restraints excluded: chain 4 residue 663 THR Chi-restraints excluded: chain 4 residue 709 LEU Chi-restraints excluded: chain 4 residue 767 LYS Chi-restraints excluded: chain 4 residue 802 ILE Chi-restraints excluded: chain 4 residue 813 LEU Chi-restraints excluded: chain 5 residue 85 ASP Chi-restraints excluded: chain 5 residue 153 SER Chi-restraints excluded: chain 5 residue 193 THR Chi-restraints excluded: chain 5 residue 207 LEU Chi-restraints excluded: chain 5 residue 273 ASN Chi-restraints excluded: chain 5 residue 365 LYS Chi-restraints excluded: chain 5 residue 426 LEU Chi-restraints excluded: chain 5 residue 445 SER Chi-restraints excluded: chain 5 residue 453 VAL Chi-restraints excluded: chain 5 residue 608 LEU Chi-restraints excluded: chain 5 residue 675 ARG Chi-restraints excluded: chain 5 residue 727 SER Chi-restraints excluded: chain 6 residue 150 THR Chi-restraints excluded: chain 6 residue 160 MET Chi-restraints excluded: chain 6 residue 269 ASN Chi-restraints excluded: chain 6 residue 276 ILE Chi-restraints excluded: chain 6 residue 293 THR Chi-restraints excluded: chain 6 residue 438 THR Chi-restraints excluded: chain 6 residue 452 ILE Chi-restraints excluded: chain 6 residue 561 GLU Chi-restraints excluded: chain 6 residue 676 THR Chi-restraints excluded: chain 6 residue 807 SER Chi-restraints excluded: chain 7 residue 5 LEU Chi-restraints excluded: chain 7 residue 225 LEU Chi-restraints excluded: chain 7 residue 372 THR Chi-restraints excluded: chain 7 residue 427 ASP Chi-restraints excluded: chain 7 residue 473 ILE Chi-restraints excluded: chain 7 residue 483 THR Chi-restraints excluded: chain 7 residue 533 ASP Chi-restraints excluded: chain 7 residue 591 LEU Chi-restraints excluded: chain 7 residue 660 VAL Chi-restraints excluded: chain C residue 12 ASP Chi-restraints excluded: chain C residue 20 PHE Chi-restraints excluded: chain C residue 24 ILE Chi-restraints excluded: chain C residue 164 THR Chi-restraints excluded: chain D residue 102 SER Chi-restraints excluded: chain D residue 206 LEU Chi-restraints excluded: chain E residue 82 LEU Chi-restraints excluded: chain E residue 403 ASP Chi-restraints excluded: chain E residue 412 THR Chi-restraints excluded: chain E residue 536 LEU Chi-restraints excluded: chain E residue 607 MET Chi-restraints excluded: chain E residue 636 ASP Chi-restraints excluded: chain E residue 638 SER Chi-restraints excluded: chain E residue 645 THR Chi-restraints excluded: chain F residue 86 GLU Chi-restraints excluded: chain F residue 224 LEU Chi-restraints excluded: chain F residue 269 THR Chi-restraints excluded: chain F residue 318 HIS Chi-restraints excluded: chain F residue 401 ILE Chi-restraints excluded: chain F residue 453 SER Chi-restraints excluded: chain F residue 500 SER Chi-restraints excluded: chain F residue 513 THR Chi-restraints excluded: chain F residue 544 ASP Chi-restraints excluded: chain F residue 547 SER Chi-restraints excluded: chain H residue 1 MET Chi-restraints excluded: chain H residue 5 LEU Chi-restraints excluded: chain H residue 43 GLU Chi-restraints excluded: chain H residue 146 LEU Chi-restraints excluded: chain H residue 147 VAL Chi-restraints excluded: chain I residue 10 THR Chi-restraints excluded: chain I residue 64 VAL Chi-restraints excluded: chain I residue 133 ASP Chi-restraints excluded: chain I residue 177 GLU Chi-restraints excluded: chain J residue 20 PHE Chi-restraints excluded: chain J residue 24 ILE Chi-restraints excluded: chain J residue 164 THR Chi-restraints excluded: chain K residue 98 ILE Chi-restraints excluded: chain L residue 59 VAL Chi-restraints excluded: chain L residue 82 LEU Chi-restraints excluded: chain L residue 165 LEU Chi-restraints excluded: chain L residue 310 VAL Chi-restraints excluded: chain L residue 419 ILE Chi-restraints excluded: chain L residue 537 ASP Chi-restraints excluded: chain L residue 604 ASN Chi-restraints excluded: chain L residue 607 MET Chi-restraints excluded: chain L residue 638 SER Chi-restraints excluded: chain M residue 29 TYR Chi-restraints excluded: chain M residue 86 GLU Chi-restraints excluded: chain M residue 188 MET Chi-restraints excluded: chain M residue 302 SER Chi-restraints excluded: chain M residue 401 ILE Chi-restraints excluded: chain M residue 500 SER Chi-restraints excluded: chain M residue 513 THR Chi-restraints excluded: chain M residue 632 LEU Chi-restraints excluded: chain N residue 1610 MET Chi-restraints excluded: chain N residue 1675 LEU Chi-restraints excluded: chain N residue 1736 VAL Chi-restraints excluded: chain N residue 1810 ASP Chi-restraints excluded: chain N residue 1821 GLN Chi-restraints excluded: chain N residue 1848 VAL Chi-restraints excluded: chain N residue 1863 ARG Chi-restraints excluded: chain N residue 1865 GLN Chi-restraints excluded: chain N residue 1882 SER Chi-restraints excluded: chain N residue 1885 MET Chi-restraints excluded: chain N residue 2036 VAL Chi-restraints excluded: chain N residue 2093 GLU Chi-restraints excluded: chain N residue 2107 LEU Chi-restraints excluded: chain N residue 2117 ILE Chi-restraints excluded: chain N residue 2173 ASP Chi-restraints excluded: chain O residue 16 THR Chi-restraints excluded: chain O residue 43 GLU Chi-restraints excluded: chain O residue 100 MET Chi-restraints excluded: chain O residue 104 ASN Chi-restraints excluded: chain O residue 146 LEU Chi-restraints excluded: chain O residue 147 VAL Chi-restraints excluded: chain P residue 64 VAL Chi-restraints excluded: chain P residue 189 MET Chi-restraints excluded: chain Q residue 1382 SER Chi-restraints excluded: chain Q residue 1426 VAL Chi-restraints excluded: chain Q residue 1736 VAL Chi-restraints excluded: chain Q residue 1848 VAL Chi-restraints excluded: chain Q residue 1865 GLN Chi-restraints excluded: chain Q residue 1936 VAL Chi-restraints excluded: chain Q residue 2115 SER Chi-restraints excluded: chain Q residue 2173 ASP Chi-restraints excluded: chain a residue 202 ASN Chi-restraints excluded: chain a residue 226 VAL Chi-restraints excluded: chain a residue 241 SER Chi-restraints excluded: chain a residue 251 GLU Chi-restraints excluded: chain a residue 292 GLU Chi-restraints excluded: chain a residue 381 VAL Chi-restraints excluded: chain a residue 390 LEU Chi-restraints excluded: chain a residue 564 VAL Chi-restraints excluded: chain a residue 567 THR Chi-restraints excluded: chain a residue 598 LEU Chi-restraints excluded: chain a residue 644 CYS Chi-restraints excluded: chain a residue 819 SER Chi-restraints excluded: chain a residue 860 SER Chi-restraints excluded: chain b residue 44 SER Chi-restraints excluded: chain b residue 91 ILE Chi-restraints excluded: chain b residue 99 SER Chi-restraints excluded: chain b residue 112 SER Chi-restraints excluded: chain b residue 213 ASP Chi-restraints excluded: chain b residue 322 LEU Chi-restraints excluded: chain b residue 346 ASP Chi-restraints excluded: chain b residue 437 SER Chi-restraints excluded: chain b residue 448 THR Chi-restraints excluded: chain b residue 486 ILE Chi-restraints excluded: chain b residue 494 THR Chi-restraints excluded: chain b residue 506 LEU Chi-restraints excluded: chain b residue 553 ILE Chi-restraints excluded: chain b residue 578 GLU Chi-restraints excluded: chain b residue 651 VAL Chi-restraints excluded: chain b residue 723 LYS Chi-restraints excluded: chain c residue 355 THR Chi-restraints excluded: chain c residue 360 ILE Chi-restraints excluded: chain c residue 468 LYS Chi-restraints excluded: chain c residue 767 LYS Chi-restraints excluded: chain c residue 802 ILE Chi-restraints excluded: chain c residue 813 LEU Chi-restraints excluded: chain d residue 85 ASP Chi-restraints excluded: chain d residue 193 THR Chi-restraints excluded: chain d residue 267 VAL Chi-restraints excluded: chain d residue 273 ASN Chi-restraints excluded: chain d residue 277 THR Chi-restraints excluded: chain d residue 510 THR Chi-restraints excluded: chain d residue 608 LEU Chi-restraints excluded: chain d residue 727 SER Chi-restraints excluded: chain e residue 150 THR Chi-restraints excluded: chain e residue 269 ASN Chi-restraints excluded: chain e residue 329 GLU Chi-restraints excluded: chain e residue 438 THR Chi-restraints excluded: chain e residue 642 ASP Chi-restraints excluded: chain e residue 676 THR Chi-restraints excluded: chain e residue 716 LEU Chi-restraints excluded: chain e residue 807 SER Chi-restraints excluded: chain f residue 66 MET Chi-restraints excluded: chain f residue 335 VAL Chi-restraints excluded: chain f residue 372 THR Chi-restraints excluded: chain f residue 427 ASP Chi-restraints excluded: chain f residue 466 LYS Chi-restraints excluded: chain f residue 473 ILE Chi-restraints excluded: chain f residue 483 THR Chi-restraints excluded: chain f residue 533 ASP Chi-restraints excluded: chain f residue 549 SER Chi-restraints excluded: chain f residue 671 SER Chi-restraints excluded: chain f residue 712 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1310 random chunks: chunk 1177 optimal weight: 1.9990 chunk 896 optimal weight: 9.9990 chunk 618 optimal weight: 0.2980 chunk 131 optimal weight: 2.9990 chunk 568 optimal weight: 0.9980 chunk 800 optimal weight: 6.9990 chunk 1196 optimal weight: 6.9990 chunk 1266 optimal weight: 0.9990 chunk 624 optimal weight: 10.0000 chunk 1133 optimal weight: 1.9990 chunk 341 optimal weight: 5.9990 overall best weight: 1.2586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 4 229 GLN 4 646 HIS ** 4 808 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 5 284 ASN 5 587 GLN ** 7 543 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 141 GLN ** F 435 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 435 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 488 ASN N1662 ASN P 146 GLN ** Q1662 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 658 ASN a 703 HIS ** b 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** c 229 GLN ** d 273 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 284 ASN f 90 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7622 moved from start: 0.1770 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.057 109512 Z= 0.147 Angle : 0.522 14.425 148617 Z= 0.273 Chirality : 0.041 0.186 17004 Planarity : 0.004 0.074 18640 Dihedral : 11.605 173.257 15852 Min Nonbonded Distance : 2.012 Molprobity Statistics. All-atom Clashscore : 6.67 Ramachandran Plot: Outliers : 0.01 % Allowed : 3.73 % Favored : 96.26 % Rotamer: Outliers : 2.06 % Allowed : 13.56 % Favored : 84.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.34 (0.07), residues: 12956 helix: 1.62 (0.07), residues: 5328 sheet: 0.07 (0.11), residues: 2108 loop : -1.11 (0.08), residues: 5520 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP Q1688 HIS 0.010 0.001 HIS M 666 PHE 0.026 0.001 PHE L 62 TYR 0.022 0.001 TYR Q1971 ARG 0.007 0.000 ARG 2 209 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 25912 Ramachandran restraints generated. 12956 Oldfield, 0 Emsley, 12956 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 25912 Ramachandran restraints generated. 12956 Oldfield, 0 Emsley, 12956 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2390 residues out of total 11774 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 242 poor density : 2148 time to evaluate : 9.148 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: 2 441 LYS cc_start: 0.7499 (mttt) cc_final: 0.7056 (mttt) REVERT: 2 792 ASP cc_start: 0.7043 (m-30) cc_final: 0.6667 (m-30) REVERT: 3 105 GLU cc_start: 0.7201 (OUTLIER) cc_final: 0.6908 (mp0) REVERT: 4 229 GLN cc_start: 0.7376 (OUTLIER) cc_final: 0.7159 (mt0) REVERT: 4 233 MET cc_start: 0.5756 (mtp) cc_final: 0.5426 (mtp) REVERT: 4 467 LYS cc_start: 0.7693 (mtmt) cc_final: 0.7377 (mtmm) REVERT: 4 538 LYS cc_start: 0.8386 (mmtp) cc_final: 0.8008 (mmtp) REVERT: 4 767 LYS cc_start: 0.7619 (OUTLIER) cc_final: 0.7317 (mttt) REVERT: 4 811 MET cc_start: 0.6437 (tpt) cc_final: 0.4953 (ttm) REVERT: 5 65 MET cc_start: 0.8625 (mtt) cc_final: 0.8239 (mtt) REVERT: 5 239 ASP cc_start: 0.7372 (p0) cc_final: 0.6852 (p0) REVERT: 5 431 LYS cc_start: 0.8161 (mttm) cc_final: 0.7738 (mtpp) REVERT: 5 539 ASN cc_start: 0.8067 (m-40) cc_final: 0.7845 (m-40) REVERT: 5 736 GLU cc_start: 0.7380 (mp0) cc_final: 0.6722 (mp0) REVERT: 5 771 TYR cc_start: 0.8887 (t80) cc_final: 0.8516 (t80) REVERT: 6 269 ASN cc_start: 0.7922 (OUTLIER) cc_final: 0.7318 (t0) REVERT: 6 283 LYS cc_start: 0.8066 (mmtp) cc_final: 0.7659 (mtmm) REVERT: 6 520 VAL cc_start: 0.8452 (t) cc_final: 0.8238 (p) REVERT: 6 527 ASP cc_start: 0.7372 (t0) cc_final: 0.6849 (t0) REVERT: 6 755 ILE cc_start: 0.8748 (mm) cc_final: 0.8418 (mt) REVERT: 6 767 LYS cc_start: 0.7020 (mmtp) cc_final: 0.6752 (mmtp) REVERT: 6 783 ASP cc_start: 0.7572 (m-30) cc_final: 0.7253 (t0) REVERT: 7 199 ARG cc_start: 0.6861 (OUTLIER) cc_final: 0.6643 (ptp-110) REVERT: 7 427 ASP cc_start: 0.7733 (OUTLIER) cc_final: 0.6590 (m-30) REVERT: 7 504 ASP cc_start: 0.6526 (t0) cc_final: 0.5812 (t0) REVERT: C 15 GLU cc_start: 0.7309 (mp0) cc_final: 0.7070 (mp0) REVERT: C 20 PHE cc_start: 0.7756 (OUTLIER) cc_final: 0.6663 (t80) REVERT: D 289 ASP cc_start: 0.7228 (t0) cc_final: 0.6921 (t0) REVERT: E 239 GLU cc_start: 0.7189 (tm-30) cc_final: 0.6955 (tm-30) REVERT: F 22 TYR cc_start: 0.7983 (t80) cc_final: 0.7642 (t80) REVERT: F 91 MET cc_start: 0.6644 (ptm) cc_final: 0.6303 (ptm) REVERT: F 468 LEU cc_start: 0.7560 (mp) cc_final: 0.7268 (mp) REVERT: F 552 ARG cc_start: 0.7503 (ttp-110) cc_final: 0.7250 (ttm170) REVERT: H 71 GLN cc_start: 0.6786 (mp10) cc_final: 0.6433 (mp10) REVERT: H 91 ARG cc_start: 0.8266 (ttt-90) cc_final: 0.7869 (ttt90) REVERT: I 104 TYR cc_start: 0.8591 (t80) cc_final: 0.8076 (t80) REVERT: J 20 PHE cc_start: 0.7928 (OUTLIER) cc_final: 0.6494 (t80) REVERT: K 157 TYR cc_start: 0.8074 (t80) cc_final: 0.7721 (t80) REVERT: K 256 TYR cc_start: 0.8243 (m-80) cc_final: 0.7674 (m-80) REVERT: K 289 ASP cc_start: 0.7594 (t0) cc_final: 0.7245 (t0) REVERT: L 239 GLU cc_start: 0.7223 (tm-30) cc_final: 0.6927 (tm-30) REVERT: M 333 TYR cc_start: 0.7959 (m-80) cc_final: 0.7110 (m-80) REVERT: M 386 ARG cc_start: 0.7339 (mtt90) cc_final: 0.6965 (ttt180) REVERT: M 522 ASN cc_start: 0.6927 (m110) cc_final: 0.6559 (m-40) REVERT: M 554 ARG cc_start: 0.6669 (mtm-85) cc_final: 0.6219 (mtm110) REVERT: M 660 ASN cc_start: 0.7152 (t0) cc_final: 0.6945 (t0) REVERT: M 685 GLU cc_start: 0.6100 (tm-30) cc_final: 0.5474 (tm-30) REVERT: N 1339 PHE cc_start: 0.7130 (m-10) cc_final: 0.6790 (m-10) REVERT: N 1360 LYS cc_start: 0.7912 (tppp) cc_final: 0.7603 (tptt) REVERT: N 1654 GLN cc_start: 0.7260 (mm-40) cc_final: 0.7009 (mm-40) REVERT: N 1713 MET cc_start: 0.8156 (mtp) cc_final: 0.7744 (mtp) REVERT: N 1854 LEU cc_start: 0.7958 (mm) cc_final: 0.7581 (mp) REVERT: N 1862 ASP cc_start: 0.7518 (t70) cc_final: 0.6914 (t70) REVERT: N 1896 SER cc_start: 0.8007 (p) cc_final: 0.7458 (m) REVERT: N 1962 ASP cc_start: 0.7813 (t0) cc_final: 0.7575 (t0) REVERT: N 1970 SER cc_start: 0.8788 (m) cc_final: 0.8172 (p) REVERT: N 2012 MET cc_start: 0.8027 (mmm) cc_final: 0.7800 (mmm) REVERT: O 8 LYS cc_start: 0.8158 (mtpt) cc_final: 0.7650 (mtpt) REVERT: O 39 ASN cc_start: 0.8306 (m-40) cc_final: 0.8021 (m110) REVERT: O 201 GLN cc_start: 0.7526 (tp40) cc_final: 0.7220 (tp40) REVERT: Q 1360 LYS cc_start: 0.8223 (tppp) cc_final: 0.7939 (tppt) REVERT: Q 1854 LEU cc_start: 0.7861 (mm) cc_final: 0.7616 (mp) REVERT: Q 1862 ASP cc_start: 0.6966 (t70) cc_final: 0.6663 (t70) REVERT: Q 1872 LYS cc_start: 0.7903 (mmtt) cc_final: 0.7650 (mmmm) REVERT: Q 2093 GLU cc_start: 0.7073 (mt-10) cc_final: 0.6605 (tt0) REVERT: a 656 ARG cc_start: 0.7502 (ttm-80) cc_final: 0.7297 (ttm110) REVERT: a 751 LYS cc_start: 0.7683 (mttt) cc_final: 0.7300 (mmtt) REVERT: a 754 GLU cc_start: 0.8172 (mp0) cc_final: 0.7965 (mp0) REVERT: a 792 ASP cc_start: 0.7865 (m-30) cc_final: 0.7624 (m-30) REVERT: b 48 TYR cc_start: 0.7804 (t80) cc_final: 0.7567 (t80) REVERT: b 202 TYR cc_start: 0.8339 (t80) cc_final: 0.7767 (t80) REVERT: b 424 ASN cc_start: 0.7700 (OUTLIER) cc_final: 0.7475 (t0) REVERT: c 229 GLN cc_start: 0.7047 (OUTLIER) cc_final: 0.6751 (mt0) REVERT: c 233 MET cc_start: 0.5388 (mtp) cc_final: 0.5165 (mtp) REVERT: c 272 MET cc_start: 0.8289 (mmp) cc_final: 0.8060 (mmp) REVERT: c 467 LYS cc_start: 0.7773 (mtpt) cc_final: 0.7483 (mtmm) REVERT: c 631 ILE cc_start: 0.9069 (mm) cc_final: 0.8767 (mm) REVERT: d 65 MET cc_start: 0.8652 (mtp) cc_final: 0.8191 (mtt) REVERT: d 157 SER cc_start: 0.8754 (m) cc_final: 0.8461 (t) REVERT: d 239 ASP cc_start: 0.7544 (p0) cc_final: 0.7190 (p0) REVERT: d 358 LEU cc_start: 0.7533 (mp) cc_final: 0.7277 (mp) REVERT: d 471 LEU cc_start: 0.8663 (mp) cc_final: 0.8377 (mt) REVERT: e 187 ARG cc_start: 0.7535 (mmm-85) cc_final: 0.7305 (ttm-80) REVERT: e 269 ASN cc_start: 0.7905 (OUTLIER) cc_final: 0.7401 (t0) REVERT: e 281 SER cc_start: 0.9128 (p) cc_final: 0.8885 (p) REVERT: e 755 ILE cc_start: 0.8850 (mm) cc_final: 0.8625 (mt) REVERT: e 829 ASP cc_start: 0.7454 (m-30) cc_final: 0.7093 (m-30) REVERT: f 92 LYS cc_start: 0.7877 (tppt) cc_final: 0.7488 (tptp) REVERT: f 130 LYS cc_start: 0.7976 (ptmt) cc_final: 0.7670 (ptmm) REVERT: f 338 THR cc_start: 0.8565 (p) cc_final: 0.7419 (m) REVERT: f 427 ASP cc_start: 0.7838 (OUTLIER) cc_final: 0.7328 (m-30) REVERT: f 466 LYS cc_start: 0.8865 (OUTLIER) cc_final: 0.8611 (tppt) REVERT: f 621 MET cc_start: 0.7207 (tpp) cc_final: 0.6942 (tpt) outliers start: 242 outliers final: 161 residues processed: 2249 average time/residue: 0.9160 time to fit residues: 3538.1615 Evaluate side-chains 2202 residues out of total 11774 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 174 poor density : 2028 time to evaluate : 9.015 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 186 LEU Chi-restraints excluded: chain 2 residue 245 ASN Chi-restraints excluded: chain 2 residue 262 LYS Chi-restraints excluded: chain 2 residue 292 GLU Chi-restraints excluded: chain 2 residue 414 LEU Chi-restraints excluded: chain 2 residue 424 VAL Chi-restraints excluded: chain 2 residue 486 LYS Chi-restraints excluded: chain 2 residue 499 SER Chi-restraints excluded: chain 2 residue 567 THR Chi-restraints excluded: chain 3 residue 99 SER Chi-restraints excluded: chain 3 residue 105 GLU Chi-restraints excluded: chain 3 residue 112 SER Chi-restraints excluded: chain 3 residue 220 THR Chi-restraints excluded: chain 3 residue 242 THR Chi-restraints excluded: chain 3 residue 346 ASP Chi-restraints excluded: chain 3 residue 424 ASN Chi-restraints excluded: chain 3 residue 582 VAL Chi-restraints excluded: chain 3 residue 698 THR Chi-restraints excluded: chain 4 residue 198 LEU Chi-restraints excluded: chain 4 residue 229 GLN Chi-restraints excluded: chain 4 residue 292 ASP Chi-restraints excluded: chain 4 residue 320 ASN Chi-restraints excluded: chain 4 residue 375 ASP Chi-restraints excluded: chain 4 residue 427 CYS Chi-restraints excluded: chain 4 residue 444 ILE Chi-restraints excluded: chain 4 residue 463 VAL Chi-restraints excluded: chain 4 residue 468 LYS Chi-restraints excluded: chain 4 residue 535 ASP Chi-restraints excluded: chain 4 residue 552 PHE Chi-restraints excluded: chain 4 residue 767 LYS Chi-restraints excluded: chain 4 residue 768 THR Chi-restraints excluded: chain 4 residue 802 ILE Chi-restraints excluded: chain 4 residue 813 LEU Chi-restraints excluded: chain 5 residue 85 ASP Chi-restraints excluded: chain 5 residue 190 THR Chi-restraints excluded: chain 5 residue 207 LEU Chi-restraints excluded: chain 5 residue 273 ASN Chi-restraints excluded: chain 5 residue 365 LYS Chi-restraints excluded: chain 5 residue 426 LEU Chi-restraints excluded: chain 5 residue 445 SER Chi-restraints excluded: chain 5 residue 493 ILE Chi-restraints excluded: chain 5 residue 675 ARG Chi-restraints excluded: chain 5 residue 727 SER Chi-restraints excluded: chain 6 residue 150 THR Chi-restraints excluded: chain 6 residue 160 MET Chi-restraints excluded: chain 6 residue 269 ASN Chi-restraints excluded: chain 6 residue 429 THR Chi-restraints excluded: chain 6 residue 438 THR Chi-restraints excluded: chain 6 residue 532 SER Chi-restraints excluded: chain 6 residue 642 ASP Chi-restraints excluded: chain 6 residue 676 THR Chi-restraints excluded: chain 7 residue 199 ARG Chi-restraints excluded: chain 7 residue 220 ILE Chi-restraints excluded: chain 7 residue 225 LEU Chi-restraints excluded: chain 7 residue 372 THR Chi-restraints excluded: chain 7 residue 427 ASP Chi-restraints excluded: chain 7 residue 473 ILE Chi-restraints excluded: chain 7 residue 483 THR Chi-restraints excluded: chain C residue 10 LEU Chi-restraints excluded: chain C residue 12 ASP Chi-restraints excluded: chain C residue 20 PHE Chi-restraints excluded: chain C residue 24 ILE Chi-restraints excluded: chain C residue 164 THR Chi-restraints excluded: chain D residue 206 LEU Chi-restraints excluded: chain E residue 59 VAL Chi-restraints excluded: chain E residue 82 LEU Chi-restraints excluded: chain E residue 140 ILE Chi-restraints excluded: chain E residue 403 ASP Chi-restraints excluded: chain E residue 536 LEU Chi-restraints excluded: chain E residue 607 MET Chi-restraints excluded: chain E residue 636 ASP Chi-restraints excluded: chain E residue 638 SER Chi-restraints excluded: chain F residue 86 GLU Chi-restraints excluded: chain F residue 224 LEU Chi-restraints excluded: chain F residue 269 THR Chi-restraints excluded: chain F residue 401 ILE Chi-restraints excluded: chain F residue 513 THR Chi-restraints excluded: chain F residue 544 ASP Chi-restraints excluded: chain F residue 547 SER Chi-restraints excluded: chain H residue 5 LEU Chi-restraints excluded: chain H residue 43 GLU Chi-restraints excluded: chain H residue 56 GLU Chi-restraints excluded: chain H residue 104 ASN Chi-restraints excluded: chain H residue 146 LEU Chi-restraints excluded: chain H residue 147 VAL Chi-restraints excluded: chain I residue 64 VAL Chi-restraints excluded: chain I residue 133 ASP Chi-restraints excluded: chain I residue 168 LEU Chi-restraints excluded: chain I residue 177 GLU Chi-restraints excluded: chain J residue 20 PHE Chi-restraints excluded: chain J residue 24 ILE Chi-restraints excluded: chain L residue 82 LEU Chi-restraints excluded: chain L residue 165 LEU Chi-restraints excluded: chain L residue 310 VAL Chi-restraints excluded: chain L residue 387 GLU Chi-restraints excluded: chain L residue 537 ASP Chi-restraints excluded: chain L residue 604 ASN Chi-restraints excluded: chain L residue 607 MET Chi-restraints excluded: chain L residue 638 SER Chi-restraints excluded: chain M residue 29 TYR Chi-restraints excluded: chain M residue 86 GLU Chi-restraints excluded: chain M residue 188 MET Chi-restraints excluded: chain M residue 297 SER Chi-restraints excluded: chain M residue 318 HIS Chi-restraints excluded: chain M residue 401 ILE Chi-restraints excluded: chain M residue 500 SER Chi-restraints excluded: chain M residue 513 THR Chi-restraints excluded: chain M residue 632 LEU Chi-restraints excluded: chain N residue 1736 VAL Chi-restraints excluded: chain N residue 1821 GLN Chi-restraints excluded: chain N residue 1863 ARG Chi-restraints excluded: chain N residue 1865 GLN Chi-restraints excluded: chain N residue 1882 SER Chi-restraints excluded: chain N residue 1885 MET Chi-restraints excluded: chain N residue 2093 GLU Chi-restraints excluded: chain N residue 2107 LEU Chi-restraints excluded: chain N residue 2117 ILE Chi-restraints excluded: chain N residue 2173 ASP Chi-restraints excluded: chain O residue 43 GLU Chi-restraints excluded: chain O residue 56 GLU Chi-restraints excluded: chain O residue 100 MET Chi-restraints excluded: chain O residue 146 LEU Chi-restraints excluded: chain O residue 147 VAL Chi-restraints excluded: chain O residue 164 ASP Chi-restraints excluded: chain P residue 32 THR Chi-restraints excluded: chain P residue 64 VAL Chi-restraints excluded: chain P residue 189 MET Chi-restraints excluded: chain Q residue 1736 VAL Chi-restraints excluded: chain Q residue 1936 VAL Chi-restraints excluded: chain Q residue 2115 SER Chi-restraints excluded: chain Q residue 2173 ASP Chi-restraints excluded: chain a residue 189 VAL Chi-restraints excluded: chain a residue 202 ASN Chi-restraints excluded: chain a residue 292 GLU Chi-restraints excluded: chain a residue 438 LEU Chi-restraints excluded: chain a residue 564 VAL Chi-restraints excluded: chain a residue 567 THR Chi-restraints excluded: chain a residue 644 CYS Chi-restraints excluded: chain b residue 112 SER Chi-restraints excluded: chain b residue 220 THR Chi-restraints excluded: chain b residue 322 LEU Chi-restraints excluded: chain b residue 346 ASP Chi-restraints excluded: chain b residue 424 ASN Chi-restraints excluded: chain b residue 486 ILE Chi-restraints excluded: chain b residue 494 THR Chi-restraints excluded: chain b residue 723 LYS Chi-restraints excluded: chain c residue 198 LEU Chi-restraints excluded: chain c residue 229 GLN Chi-restraints excluded: chain c residue 292 ASP Chi-restraints excluded: chain c residue 360 ILE Chi-restraints excluded: chain c residue 468 LYS Chi-restraints excluded: chain c residue 663 THR Chi-restraints excluded: chain c residue 705 VAL Chi-restraints excluded: chain d residue 267 VAL Chi-restraints excluded: chain d residue 273 ASN Chi-restraints excluded: chain d residue 497 MET Chi-restraints excluded: chain d residue 608 LEU Chi-restraints excluded: chain d residue 727 SER Chi-restraints excluded: chain e residue 144 LYS Chi-restraints excluded: chain e residue 150 THR Chi-restraints excluded: chain e residue 269 ASN Chi-restraints excluded: chain e residue 329 GLU Chi-restraints excluded: chain e residue 438 THR Chi-restraints excluded: chain e residue 642 ASP Chi-restraints excluded: chain e residue 676 THR Chi-restraints excluded: chain e residue 701 MET Chi-restraints excluded: chain e residue 716 LEU Chi-restraints excluded: chain f residue 16 ASN Chi-restraints excluded: chain f residue 372 THR Chi-restraints excluded: chain f residue 427 ASP Chi-restraints excluded: chain f residue 466 LYS Chi-restraints excluded: chain f residue 473 ILE Chi-restraints excluded: chain f residue 671 SER Chi-restraints excluded: chain f residue 712 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1310 random chunks: chunk 1054 optimal weight: 0.6980 chunk 718 optimal weight: 9.9990 chunk 18 optimal weight: 50.0000 chunk 942 optimal weight: 3.9990 chunk 522 optimal weight: 0.1980 chunk 1080 optimal weight: 6.9990 chunk 875 optimal weight: 9.9990 chunk 1 optimal weight: 9.9990 chunk 646 optimal weight: 9.9990 chunk 1136 optimal weight: 3.9990 chunk 319 optimal weight: 0.8980 overall best weight: 1.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 2 641 GLN ** 5 253 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 173 GLN 7 538 HIS ** 7 543 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 13 ASN ** F 435 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 13 ASN M 397 HIS ** M 435 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 488 ASN ** M 667 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N1662 ASN N2023 GLN ** O 202 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q1662 ASN a 658 ASN b 46 GLN ** b 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** b 731 ASN c 188 GLN ** d 273 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 587 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7637 moved from start: 0.1922 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 109512 Z= 0.174 Angle : 0.528 14.392 148617 Z= 0.275 Chirality : 0.041 0.233 17004 Planarity : 0.004 0.081 18640 Dihedral : 11.565 172.932 15852 Min Nonbonded Distance : 1.973 Molprobity Statistics. All-atom Clashscore : 6.87 Ramachandran Plot: Outliers : 0.01 % Allowed : 3.88 % Favored : 96.11 % Rotamer: Outliers : 2.36 % Allowed : 14.70 % Favored : 82.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.38 (0.07), residues: 12956 helix: 1.67 (0.07), residues: 5348 sheet: 0.09 (0.11), residues: 2110 loop : -1.11 (0.08), residues: 5498 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP Q1688 HIS 0.007 0.001 HIS N1434 PHE 0.020 0.001 PHE E 62 TYR 0.029 0.001 TYR c 225 ARG 0.010 0.000 ARG F 386 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 25912 Ramachandran restraints generated. 12956 Oldfield, 0 Emsley, 12956 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 25912 Ramachandran restraints generated. 12956 Oldfield, 0 Emsley, 12956 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2361 residues out of total 11774 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 278 poor density : 2083 time to evaluate : 10.750 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: 2 390 LEU cc_start: 0.8096 (OUTLIER) cc_final: 0.7854 (mp) REVERT: 2 441 LYS cc_start: 0.7512 (mttt) cc_final: 0.7052 (mttt) REVERT: 2 792 ASP cc_start: 0.7070 (m-30) cc_final: 0.6691 (m-30) REVERT: 3 105 GLU cc_start: 0.7191 (OUTLIER) cc_final: 0.6918 (mp0) REVERT: 4 233 MET cc_start: 0.5527 (mtp) cc_final: 0.5269 (mtp) REVERT: 4 538 LYS cc_start: 0.8517 (mmtp) cc_final: 0.8220 (mmtp) REVERT: 4 811 MET cc_start: 0.6472 (tpt) cc_final: 0.5056 (ttm) REVERT: 5 65 MET cc_start: 0.8642 (mtt) cc_final: 0.8243 (mtt) REVERT: 5 239 ASP cc_start: 0.7350 (p0) cc_final: 0.6828 (p0) REVERT: 5 431 LYS cc_start: 0.8169 (mttm) cc_final: 0.7750 (mtpp) REVERT: 5 539 ASN cc_start: 0.8043 (m-40) cc_final: 0.7822 (m-40) REVERT: 6 283 LYS cc_start: 0.8076 (mmtp) cc_final: 0.7677 (mtmm) REVERT: 6 520 VAL cc_start: 0.8448 (t) cc_final: 0.8245 (p) REVERT: 6 527 ASP cc_start: 0.7258 (t0) cc_final: 0.6747 (t0) REVERT: 6 755 ILE cc_start: 0.8797 (mm) cc_final: 0.8452 (mt) REVERT: 6 767 LYS cc_start: 0.7027 (mmtp) cc_final: 0.6762 (mmtp) REVERT: 6 783 ASP cc_start: 0.7586 (m-30) cc_final: 0.7352 (t0) REVERT: 7 121 ILE cc_start: 0.8553 (mm) cc_final: 0.8336 (mt) REVERT: 7 427 ASP cc_start: 0.7729 (OUTLIER) cc_final: 0.6618 (m-30) REVERT: 7 504 ASP cc_start: 0.6546 (t0) cc_final: 0.5806 (t0) REVERT: C 20 PHE cc_start: 0.7841 (OUTLIER) cc_final: 0.6790 (t80) REVERT: C 193 LYS cc_start: 0.7907 (tptt) cc_final: 0.7630 (tptp) REVERT: D 289 ASP cc_start: 0.7250 (t0) cc_final: 0.6914 (t0) REVERT: E 239 GLU cc_start: 0.7249 (tm-30) cc_final: 0.7035 (tm-30) REVERT: F 22 TYR cc_start: 0.7990 (t80) cc_final: 0.7696 (t80) REVERT: F 23 ARG cc_start: 0.6580 (mtm180) cc_final: 0.6215 (mtm-85) REVERT: F 318 HIS cc_start: 0.7275 (OUTLIER) cc_final: 0.6810 (p-80) REVERT: F 468 LEU cc_start: 0.7569 (mp) cc_final: 0.7243 (mp) REVERT: F 472 PHE cc_start: 0.6445 (m-80) cc_final: 0.6221 (m-80) REVERT: F 552 ARG cc_start: 0.7485 (ttp-110) cc_final: 0.7247 (ttm170) REVERT: F 604 LYS cc_start: 0.8196 (tptm) cc_final: 0.7951 (tptm) REVERT: H 71 GLN cc_start: 0.6838 (mp10) cc_final: 0.6434 (mp10) REVERT: I 104 TYR cc_start: 0.8551 (t80) cc_final: 0.8033 (t80) REVERT: J 20 PHE cc_start: 0.7996 (OUTLIER) cc_final: 0.6566 (t80) REVERT: J 122 ASN cc_start: 0.7716 (m110) cc_final: 0.7439 (m-40) REVERT: K 256 TYR cc_start: 0.8248 (m-80) cc_final: 0.7630 (m-80) REVERT: K 289 ASP cc_start: 0.7616 (t0) cc_final: 0.7277 (t0) REVERT: L 239 GLU cc_start: 0.7320 (tm-30) cc_final: 0.7042 (tm-30) REVERT: M 86 GLU cc_start: 0.6438 (OUTLIER) cc_final: 0.6183 (pm20) REVERT: M 333 TYR cc_start: 0.7986 (m-80) cc_final: 0.7171 (m-80) REVERT: M 386 ARG cc_start: 0.7229 (mtt90) cc_final: 0.6886 (ttt180) REVERT: M 554 ARG cc_start: 0.6683 (mtm-85) cc_final: 0.6214 (mtm110) REVERT: M 685 GLU cc_start: 0.6150 (tm-30) cc_final: 0.5561 (tm-30) REVERT: N 1360 LYS cc_start: 0.7924 (tppp) cc_final: 0.7575 (tptt) REVERT: N 1439 MET cc_start: 0.6249 (ttm) cc_final: 0.5920 (ttp) REVERT: N 1654 GLN cc_start: 0.7274 (mm-40) cc_final: 0.7012 (mm-40) REVERT: N 1670 TYR cc_start: 0.8023 (t80) cc_final: 0.7822 (t80) REVERT: N 1713 MET cc_start: 0.8212 (mtp) cc_final: 0.7982 (mtp) REVERT: N 1854 LEU cc_start: 0.7968 (mm) cc_final: 0.7658 (mp) REVERT: N 1862 ASP cc_start: 0.7501 (t70) cc_final: 0.6932 (t70) REVERT: N 1896 SER cc_start: 0.8049 (p) cc_final: 0.7434 (m) REVERT: N 1962 ASP cc_start: 0.7830 (t0) cc_final: 0.7572 (t0) REVERT: N 1970 SER cc_start: 0.8797 (m) cc_final: 0.8171 (p) REVERT: N 2012 MET cc_start: 0.8057 (mmm) cc_final: 0.7791 (mmm) REVERT: O 8 LYS cc_start: 0.8218 (mtpt) cc_final: 0.7679 (mtpt) REVERT: O 39 ASN cc_start: 0.8330 (m-40) cc_final: 0.7964 (m110) REVERT: O 201 GLN cc_start: 0.7506 (tp40) cc_final: 0.7126 (tp40) REVERT: P 63 MET cc_start: 0.7072 (mtt) cc_final: 0.6857 (mtp) REVERT: P 81 GLN cc_start: 0.7911 (tp-100) cc_final: 0.7384 (tt0) REVERT: Q 1360 LYS cc_start: 0.8223 (tppp) cc_final: 0.7928 (tppt) REVERT: Q 1854 LEU cc_start: 0.7819 (mm) cc_final: 0.7590 (mp) REVERT: Q 1862 ASP cc_start: 0.7069 (t70) cc_final: 0.6772 (t70) REVERT: Q 1872 LYS cc_start: 0.7860 (mmtt) cc_final: 0.7482 (mmmm) REVERT: Q 2032 GLU cc_start: 0.6369 (tt0) cc_final: 0.5935 (mt-10) REVERT: Q 2093 GLU cc_start: 0.7072 (mt-10) cc_final: 0.6610 (tt0) REVERT: Q 2144 GLU cc_start: 0.6363 (mm-30) cc_final: 0.5947 (mm-30) REVERT: a 751 LYS cc_start: 0.7758 (mttt) cc_final: 0.7429 (mmmm) REVERT: a 792 ASP cc_start: 0.7873 (m-30) cc_final: 0.7657 (m-30) REVERT: a 826 SER cc_start: 0.8712 (t) cc_final: 0.8415 (m) REVERT: b 48 TYR cc_start: 0.7846 (t80) cc_final: 0.7613 (t80) REVERT: b 202 TYR cc_start: 0.8371 (t80) cc_final: 0.7812 (t80) REVERT: b 424 ASN cc_start: 0.7709 (OUTLIER) cc_final: 0.7486 (t0) REVERT: c 233 MET cc_start: 0.5355 (mtp) cc_final: 0.5152 (mtp) REVERT: c 306 TYR cc_start: 0.6341 (p90) cc_final: 0.6129 (p90) REVERT: c 631 ILE cc_start: 0.9072 (mm) cc_final: 0.8774 (mm) REVERT: d 65 MET cc_start: 0.8579 (mtp) cc_final: 0.8140 (mtt) REVERT: d 239 ASP cc_start: 0.7484 (p0) cc_final: 0.7091 (p0) REVERT: d 358 LEU cc_start: 0.7545 (mp) cc_final: 0.7288 (mp) REVERT: d 471 LEU cc_start: 0.8702 (mp) cc_final: 0.8403 (mt) REVERT: e 187 ARG cc_start: 0.7529 (mmm-85) cc_final: 0.7279 (ttm-80) REVERT: e 269 ASN cc_start: 0.7947 (OUTLIER) cc_final: 0.7427 (t0) REVERT: e 281 SER cc_start: 0.9118 (p) cc_final: 0.8867 (p) REVERT: e 350 ARG cc_start: 0.7404 (ttm-80) cc_final: 0.7010 (mtp-110) REVERT: e 529 LEU cc_start: 0.8786 (OUTLIER) cc_final: 0.8576 (mp) REVERT: e 755 ILE cc_start: 0.8870 (mm) cc_final: 0.8628 (mt) REVERT: e 829 ASP cc_start: 0.7466 (m-30) cc_final: 0.7108 (m-30) REVERT: f 92 LYS cc_start: 0.7834 (tppt) cc_final: 0.7466 (tptp) REVERT: f 130 LYS cc_start: 0.7987 (ptmt) cc_final: 0.7665 (ptmm) REVERT: f 338 THR cc_start: 0.8601 (p) cc_final: 0.7411 (m) REVERT: f 466 LYS cc_start: 0.8837 (OUTLIER) cc_final: 0.8560 (tppt) REVERT: f 621 MET cc_start: 0.7228 (tpp) cc_final: 0.6964 (tpt) outliers start: 278 outliers final: 208 residues processed: 2216 average time/residue: 0.9061 time to fit residues: 3451.9247 Evaluate side-chains 2251 residues out of total 11774 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 219 poor density : 2032 time to evaluate : 8.989 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 186 LEU Chi-restraints excluded: chain 2 residue 226 VAL Chi-restraints excluded: chain 2 residue 241 SER Chi-restraints excluded: chain 2 residue 245 ASN Chi-restraints excluded: chain 2 residue 262 LYS Chi-restraints excluded: chain 2 residue 292 GLU Chi-restraints excluded: chain 2 residue 390 LEU Chi-restraints excluded: chain 2 residue 424 VAL Chi-restraints excluded: chain 2 residue 499 SER Chi-restraints excluded: chain 2 residue 567 THR Chi-restraints excluded: chain 2 residue 819 SER Chi-restraints excluded: chain 2 residue 860 SER Chi-restraints excluded: chain 3 residue 99 SER Chi-restraints excluded: chain 3 residue 105 GLU Chi-restraints excluded: chain 3 residue 112 SER Chi-restraints excluded: chain 3 residue 135 SER Chi-restraints excluded: chain 3 residue 220 THR Chi-restraints excluded: chain 3 residue 242 THR Chi-restraints excluded: chain 3 residue 322 LEU Chi-restraints excluded: chain 3 residue 346 ASP Chi-restraints excluded: chain 3 residue 424 ASN Chi-restraints excluded: chain 3 residue 486 ILE Chi-restraints excluded: chain 3 residue 582 VAL Chi-restraints excluded: chain 3 residue 698 THR Chi-restraints excluded: chain 4 residue 198 LEU Chi-restraints excluded: chain 4 residue 292 ASP Chi-restraints excluded: chain 4 residue 320 ASN Chi-restraints excluded: chain 4 residue 401 GLU Chi-restraints excluded: chain 4 residue 444 ILE Chi-restraints excluded: chain 4 residue 463 VAL Chi-restraints excluded: chain 4 residue 468 LYS Chi-restraints excluded: chain 4 residue 552 PHE Chi-restraints excluded: chain 4 residue 709 LEU Chi-restraints excluded: chain 4 residue 767 LYS Chi-restraints excluded: chain 4 residue 768 THR Chi-restraints excluded: chain 4 residue 802 ILE Chi-restraints excluded: chain 4 residue 813 LEU Chi-restraints excluded: chain 5 residue 85 ASP Chi-restraints excluded: chain 5 residue 193 THR Chi-restraints excluded: chain 5 residue 207 LEU Chi-restraints excluded: chain 5 residue 267 VAL Chi-restraints excluded: chain 5 residue 273 ASN Chi-restraints excluded: chain 5 residue 426 LEU Chi-restraints excluded: chain 5 residue 445 SER Chi-restraints excluded: chain 5 residue 453 VAL Chi-restraints excluded: chain 5 residue 493 ILE Chi-restraints excluded: chain 5 residue 608 LEU Chi-restraints excluded: chain 5 residue 675 ARG Chi-restraints excluded: chain 6 residue 150 THR Chi-restraints excluded: chain 6 residue 160 MET Chi-restraints excluded: chain 6 residue 293 THR Chi-restraints excluded: chain 6 residue 333 CYS Chi-restraints excluded: chain 6 residue 429 THR Chi-restraints excluded: chain 6 residue 438 THR Chi-restraints excluded: chain 6 residue 532 SER Chi-restraints excluded: chain 6 residue 561 GLU Chi-restraints excluded: chain 6 residue 642 ASP Chi-restraints excluded: chain 6 residue 676 THR Chi-restraints excluded: chain 6 residue 702 THR Chi-restraints excluded: chain 7 residue 220 ILE Chi-restraints excluded: chain 7 residue 225 LEU Chi-restraints excluded: chain 7 residue 372 THR Chi-restraints excluded: chain 7 residue 427 ASP Chi-restraints excluded: chain 7 residue 473 ILE Chi-restraints excluded: chain 7 residue 483 THR Chi-restraints excluded: chain 7 residue 533 ASP Chi-restraints excluded: chain 7 residue 591 LEU Chi-restraints excluded: chain C residue 12 ASP Chi-restraints excluded: chain C residue 20 PHE Chi-restraints excluded: chain C residue 24 ILE Chi-restraints excluded: chain D residue 206 LEU Chi-restraints excluded: chain D residue 262 ASP Chi-restraints excluded: chain E residue 59 VAL Chi-restraints excluded: chain E residue 82 LEU Chi-restraints excluded: chain E residue 104 VAL Chi-restraints excluded: chain E residue 403 ASP Chi-restraints excluded: chain E residue 412 THR Chi-restraints excluded: chain E residue 536 LEU Chi-restraints excluded: chain E residue 607 MET Chi-restraints excluded: chain E residue 636 ASP Chi-restraints excluded: chain E residue 638 SER Chi-restraints excluded: chain E residue 645 THR Chi-restraints excluded: chain E residue 646 LEU Chi-restraints excluded: chain F residue 86 GLU Chi-restraints excluded: chain F residue 224 LEU Chi-restraints excluded: chain F residue 269 THR Chi-restraints excluded: chain F residue 318 HIS Chi-restraints excluded: chain F residue 401 ILE Chi-restraints excluded: chain F residue 500 SER Chi-restraints excluded: chain F residue 513 THR Chi-restraints excluded: chain F residue 544 ASP Chi-restraints excluded: chain F residue 547 SER Chi-restraints excluded: chain H residue 5 LEU Chi-restraints excluded: chain H residue 43 GLU Chi-restraints excluded: chain H residue 56 GLU Chi-restraints excluded: chain H residue 104 ASN Chi-restraints excluded: chain H residue 146 LEU Chi-restraints excluded: chain H residue 147 VAL Chi-restraints excluded: chain H residue 164 ASP Chi-restraints excluded: chain I residue 10 THR Chi-restraints excluded: chain I residue 64 VAL Chi-restraints excluded: chain I residue 158 LYS Chi-restraints excluded: chain I residue 168 LEU Chi-restraints excluded: chain I residue 177 GLU Chi-restraints excluded: chain J residue 20 PHE Chi-restraints excluded: chain J residue 24 ILE Chi-restraints excluded: chain J residue 164 THR Chi-restraints excluded: chain L residue 82 LEU Chi-restraints excluded: chain L residue 310 VAL Chi-restraints excluded: chain L residue 419 ILE Chi-restraints excluded: chain L residue 537 ASP Chi-restraints excluded: chain L residue 604 ASN Chi-restraints excluded: chain L residue 607 MET Chi-restraints excluded: chain L residue 624 ASN Chi-restraints excluded: chain L residue 638 SER Chi-restraints excluded: chain M residue 29 TYR Chi-restraints excluded: chain M residue 31 LEU Chi-restraints excluded: chain M residue 86 GLU Chi-restraints excluded: chain M residue 188 MET Chi-restraints excluded: chain M residue 299 GLU Chi-restraints excluded: chain M residue 318 HIS Chi-restraints excluded: chain M residue 401 ILE Chi-restraints excluded: chain M residue 424 LEU Chi-restraints excluded: chain M residue 435 GLN Chi-restraints excluded: chain M residue 500 SER Chi-restraints excluded: chain M residue 513 THR Chi-restraints excluded: chain M residue 632 LEU Chi-restraints excluded: chain N residue 1324 VAL Chi-restraints excluded: chain N residue 1415 THR Chi-restraints excluded: chain N residue 1736 VAL Chi-restraints excluded: chain N residue 1821 GLN Chi-restraints excluded: chain N residue 1863 ARG Chi-restraints excluded: chain N residue 1865 GLN Chi-restraints excluded: chain N residue 1882 SER Chi-restraints excluded: chain N residue 1885 MET Chi-restraints excluded: chain N residue 2093 GLU Chi-restraints excluded: chain N residue 2107 LEU Chi-restraints excluded: chain N residue 2117 ILE Chi-restraints excluded: chain N residue 2173 ASP Chi-restraints excluded: chain O residue 43 GLU Chi-restraints excluded: chain O residue 56 GLU Chi-restraints excluded: chain O residue 146 LEU Chi-restraints excluded: chain O residue 147 VAL Chi-restraints excluded: chain O residue 164 ASP Chi-restraints excluded: chain P residue 32 THR Chi-restraints excluded: chain P residue 64 VAL Chi-restraints excluded: chain P residue 189 MET Chi-restraints excluded: chain Q residue 1415 THR Chi-restraints excluded: chain Q residue 1426 VAL Chi-restraints excluded: chain Q residue 1685 ILE Chi-restraints excluded: chain Q residue 1736 VAL Chi-restraints excluded: chain Q residue 1811 LEU Chi-restraints excluded: chain Q residue 1821 GLN Chi-restraints excluded: chain Q residue 1865 GLN Chi-restraints excluded: chain Q residue 1936 VAL Chi-restraints excluded: chain Q residue 1941 LEU Chi-restraints excluded: chain Q residue 2173 ASP Chi-restraints excluded: chain Q residue 2194 ILE Chi-restraints excluded: chain a residue 189 VAL Chi-restraints excluded: chain a residue 202 ASN Chi-restraints excluded: chain a residue 226 VAL Chi-restraints excluded: chain a residue 251 GLU Chi-restraints excluded: chain a residue 292 GLU Chi-restraints excluded: chain a residue 438 LEU Chi-restraints excluded: chain a residue 536 ASP Chi-restraints excluded: chain a residue 564 VAL Chi-restraints excluded: chain a residue 567 THR Chi-restraints excluded: chain a residue 644 CYS Chi-restraints excluded: chain a residue 819 SER Chi-restraints excluded: chain b residue 99 SER Chi-restraints excluded: chain b residue 112 SER Chi-restraints excluded: chain b residue 220 THR Chi-restraints excluded: chain b residue 240 LYS Chi-restraints excluded: chain b residue 322 LEU Chi-restraints excluded: chain b residue 346 ASP Chi-restraints excluded: chain b residue 424 ASN Chi-restraints excluded: chain b residue 437 SER Chi-restraints excluded: chain b residue 486 ILE Chi-restraints excluded: chain b residue 488 GLU Chi-restraints excluded: chain b residue 682 ASN Chi-restraints excluded: chain b residue 723 LYS Chi-restraints excluded: chain c residue 280 MET Chi-restraints excluded: chain c residue 292 ASP Chi-restraints excluded: chain c residue 355 THR Chi-restraints excluded: chain c residue 360 ILE Chi-restraints excluded: chain c residue 427 CYS Chi-restraints excluded: chain c residue 468 LYS Chi-restraints excluded: chain c residue 552 PHE Chi-restraints excluded: chain c residue 663 THR Chi-restraints excluded: chain c residue 705 VAL Chi-restraints excluded: chain d residue 85 ASP Chi-restraints excluded: chain d residue 190 THR Chi-restraints excluded: chain d residue 267 VAL Chi-restraints excluded: chain d residue 273 ASN Chi-restraints excluded: chain d residue 277 THR Chi-restraints excluded: chain d residue 391 LEU Chi-restraints excluded: chain d residue 402 ASP Chi-restraints excluded: chain d residue 497 MET Chi-restraints excluded: chain d residue 567 SER Chi-restraints excluded: chain d residue 608 LEU Chi-restraints excluded: chain d residue 727 SER Chi-restraints excluded: chain e residue 150 THR Chi-restraints excluded: chain e residue 269 ASN Chi-restraints excluded: chain e residue 329 GLU Chi-restraints excluded: chain e residue 438 THR Chi-restraints excluded: chain e residue 529 LEU Chi-restraints excluded: chain e residue 561 GLU Chi-restraints excluded: chain e residue 642 ASP Chi-restraints excluded: chain e residue 676 THR Chi-restraints excluded: chain e residue 701 MET Chi-restraints excluded: chain e residue 716 LEU Chi-restraints excluded: chain e residue 831 LEU Chi-restraints excluded: chain f residue 335 VAL Chi-restraints excluded: chain f residue 372 THR Chi-restraints excluded: chain f residue 466 LYS Chi-restraints excluded: chain f residue 473 ILE Chi-restraints excluded: chain f residue 549 SER Chi-restraints excluded: chain f residue 671 SER Chi-restraints excluded: chain f residue 712 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1310 random chunks: chunk 426 optimal weight: 5.9990 chunk 1140 optimal weight: 0.4980 chunk 250 optimal weight: 50.0000 chunk 743 optimal weight: 0.7980 chunk 312 optimal weight: 30.0000 chunk 1267 optimal weight: 2.9990 chunk 1052 optimal weight: 3.9990 chunk 586 optimal weight: 3.9990 chunk 105 optimal weight: 0.7980 chunk 419 optimal weight: 4.9990 chunk 665 optimal weight: 9.9990 overall best weight: 1.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 2 641 GLN 4 757 HIS ** 4 808 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 253 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 173 GLN 7 538 HIS ** 7 543 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 435 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 666 HIS H 39 ASN L 141 GLN ** M 435 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 488 ASN M 648 GLN ** M 667 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N1662 ASN a 658 ASN b 201 HIS b 731 ASN ** d 273 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7633 moved from start: 0.2053 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 109512 Z= 0.167 Angle : 0.528 14.125 148617 Z= 0.273 Chirality : 0.041 0.255 17004 Planarity : 0.004 0.085 18640 Dihedral : 11.515 173.021 15850 Min Nonbonded Distance : 1.988 Molprobity Statistics. All-atom Clashscore : 6.71 Ramachandran Plot: Outliers : 0.01 % Allowed : 3.85 % Favored : 96.14 % Rotamer: Outliers : 2.45 % Allowed : 15.27 % Favored : 82.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.44 (0.07), residues: 12956 helix: 1.73 (0.07), residues: 5348 sheet: 0.11 (0.11), residues: 2088 loop : -1.09 (0.08), residues: 5520 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP Q1688 HIS 0.009 0.001 HIS N1434 PHE 0.020 0.001 PHE E 62 TYR 0.023 0.001 TYR b 211 ARG 0.013 0.000 ARG F 386 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 25912 Ramachandran restraints generated. 12956 Oldfield, 0 Emsley, 12956 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 25912 Ramachandran restraints generated. 12956 Oldfield, 0 Emsley, 12956 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2401 residues out of total 11774 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 288 poor density : 2113 time to evaluate : 9.123 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: 2 383 ARG cc_start: 0.7944 (OUTLIER) cc_final: 0.7062 (ptp-170) REVERT: 2 390 LEU cc_start: 0.8067 (OUTLIER) cc_final: 0.7842 (mp) REVERT: 2 441 LYS cc_start: 0.7532 (mttt) cc_final: 0.7092 (mttt) REVERT: 2 792 ASP cc_start: 0.7078 (m-30) cc_final: 0.6692 (m-30) REVERT: 3 105 GLU cc_start: 0.7194 (OUTLIER) cc_final: 0.6915 (mp0) REVERT: 4 233 MET cc_start: 0.5662 (mtp) cc_final: 0.5381 (mtp) REVERT: 4 538 LYS cc_start: 0.8474 (mmtp) cc_final: 0.8212 (mmtp) REVERT: 4 811 MET cc_start: 0.6388 (tpt) cc_final: 0.4947 (ttm) REVERT: 5 239 ASP cc_start: 0.7319 (p0) cc_final: 0.6868 (p0) REVERT: 5 431 LYS cc_start: 0.8132 (mttm) cc_final: 0.7744 (mtpp) REVERT: 6 283 LYS cc_start: 0.8082 (mmtp) cc_final: 0.7675 (mtmm) REVERT: 6 520 VAL cc_start: 0.8446 (t) cc_final: 0.8245 (p) REVERT: 6 527 ASP cc_start: 0.7260 (t0) cc_final: 0.6749 (t0) REVERT: 6 755 ILE cc_start: 0.8792 (mm) cc_final: 0.8457 (mt) REVERT: 6 767 LYS cc_start: 0.7049 (mmtp) cc_final: 0.6783 (mmtp) REVERT: 6 783 ASP cc_start: 0.7566 (m-30) cc_final: 0.7348 (t0) REVERT: 7 121 ILE cc_start: 0.8560 (mm) cc_final: 0.8327 (mt) REVERT: 7 427 ASP cc_start: 0.7825 (OUTLIER) cc_final: 0.6714 (m-30) REVERT: 7 504 ASP cc_start: 0.6606 (t0) cc_final: 0.5859 (t0) REVERT: 7 544 GLN cc_start: 0.7681 (mp10) cc_final: 0.7444 (mp10) REVERT: 7 652 MET cc_start: 0.7104 (mpp) cc_final: 0.6888 (mmt) REVERT: C 20 PHE cc_start: 0.7848 (OUTLIER) cc_final: 0.6730 (t80) REVERT: D 98 ILE cc_start: 0.8287 (OUTLIER) cc_final: 0.7933 (mp) REVERT: D 100 ASN cc_start: 0.7116 (t0) cc_final: 0.6876 (t0) REVERT: D 289 ASP cc_start: 0.7245 (t0) cc_final: 0.6940 (t0) REVERT: E 239 GLU cc_start: 0.7263 (tm-30) cc_final: 0.7053 (tm-30) REVERT: F 22 TYR cc_start: 0.7983 (t80) cc_final: 0.7667 (t80) REVERT: F 231 ARG cc_start: 0.7797 (ttp80) cc_final: 0.6956 (ttp80) REVERT: F 318 HIS cc_start: 0.7396 (OUTLIER) cc_final: 0.7030 (p-80) REVERT: F 386 ARG cc_start: 0.6887 (mtt180) cc_final: 0.6607 (ttt180) REVERT: F 468 LEU cc_start: 0.7588 (OUTLIER) cc_final: 0.7288 (mp) REVERT: F 494 MET cc_start: 0.7817 (tpp) cc_final: 0.7461 (tpp) REVERT: F 552 ARG cc_start: 0.7474 (ttp-110) cc_final: 0.7228 (ttm170) REVERT: F 604 LYS cc_start: 0.8141 (tptm) cc_final: 0.7886 (tptm) REVERT: F 674 GLU cc_start: 0.5948 (tt0) cc_final: 0.5392 (tm-30) REVERT: H 50 ASN cc_start: 0.7558 (m-40) cc_final: 0.7091 (m110) REVERT: H 71 GLN cc_start: 0.6815 (mp10) cc_final: 0.6382 (mp10) REVERT: J 122 ASN cc_start: 0.7690 (m110) cc_final: 0.7398 (m-40) REVERT: J 172 MET cc_start: 0.7842 (ttp) cc_final: 0.7469 (tmm) REVERT: K 289 ASP cc_start: 0.7636 (t0) cc_final: 0.7308 (t0) REVERT: L 239 GLU cc_start: 0.7313 (tm-30) cc_final: 0.7045 (tm-30) REVERT: L 341 SER cc_start: 0.8418 (t) cc_final: 0.8200 (p) REVERT: M 61 LYS cc_start: 0.8144 (mmmm) cc_final: 0.7935 (mmmm) REVERT: M 190 PHE cc_start: 0.8423 (m-80) cc_final: 0.8113 (m-10) REVERT: M 333 TYR cc_start: 0.7965 (m-80) cc_final: 0.7190 (m-80) REVERT: M 386 ARG cc_start: 0.7216 (mtt90) cc_final: 0.6980 (ttt180) REVERT: M 554 ARG cc_start: 0.6662 (mtm-85) cc_final: 0.6155 (mtm110) REVERT: N 1360 LYS cc_start: 0.7903 (tppp) cc_final: 0.7598 (tptt) REVERT: N 1439 MET cc_start: 0.6318 (ttm) cc_final: 0.5997 (ttp) REVERT: N 1654 GLN cc_start: 0.7311 (mm-40) cc_final: 0.7067 (mm-40) REVERT: N 1670 TYR cc_start: 0.8033 (t80) cc_final: 0.7809 (t80) REVERT: N 1713 MET cc_start: 0.8244 (mtp) cc_final: 0.7985 (mtp) REVERT: N 1854 LEU cc_start: 0.8001 (mm) cc_final: 0.7707 (mp) REVERT: N 1862 ASP cc_start: 0.7498 (t70) cc_final: 0.6951 (t70) REVERT: N 1896 SER cc_start: 0.8022 (p) cc_final: 0.7427 (m) REVERT: N 1962 ASP cc_start: 0.7853 (t0) cc_final: 0.7602 (t0) REVERT: N 1970 SER cc_start: 0.8789 (m) cc_final: 0.8168 (p) REVERT: N 2012 MET cc_start: 0.8064 (mmm) cc_final: 0.7788 (mmm) REVERT: O 8 LYS cc_start: 0.8252 (mtpt) cc_final: 0.7680 (mtpt) REVERT: O 39 ASN cc_start: 0.8320 (m-40) cc_final: 0.7942 (m110) REVERT: P 63 MET cc_start: 0.7065 (mtt) cc_final: 0.6851 (mtp) REVERT: P 81 GLN cc_start: 0.7906 (tp-100) cc_final: 0.7373 (tt0) REVERT: Q 1360 LYS cc_start: 0.8185 (tppp) cc_final: 0.7920 (tppt) REVERT: Q 1854 LEU cc_start: 0.7882 (mm) cc_final: 0.7622 (mp) REVERT: Q 1862 ASP cc_start: 0.7072 (t70) cc_final: 0.6795 (t70) REVERT: Q 1872 LYS cc_start: 0.7820 (mmtt) cc_final: 0.7618 (mmmm) REVERT: Q 1903 LYS cc_start: 0.7615 (mttt) cc_final: 0.7030 (mttp) REVERT: Q 2032 GLU cc_start: 0.6330 (tt0) cc_final: 0.5907 (mt-10) REVERT: Q 2093 GLU cc_start: 0.7081 (mt-10) cc_final: 0.6585 (tt0) REVERT: Q 2144 GLU cc_start: 0.6493 (mm-30) cc_final: 0.6117 (mm-30) REVERT: a 383 ARG cc_start: 0.8146 (OUTLIER) cc_final: 0.7212 (ptp-170) REVERT: a 747 ARG cc_start: 0.7196 (mtp85) cc_final: 0.6814 (mtp180) REVERT: a 751 LYS cc_start: 0.7773 (mttt) cc_final: 0.7320 (mtmm) REVERT: a 792 ASP cc_start: 0.7844 (m-30) cc_final: 0.7595 (m-30) REVERT: a 826 SER cc_start: 0.8711 (t) cc_final: 0.8410 (m) REVERT: b 48 TYR cc_start: 0.7864 (t80) cc_final: 0.7630 (t80) REVERT: b 202 TYR cc_start: 0.8392 (t80) cc_final: 0.7888 (t80) REVERT: c 233 MET cc_start: 0.5403 (mtp) cc_final: 0.5177 (mtp) REVERT: c 306 TYR cc_start: 0.6351 (p90) cc_final: 0.6146 (p90) REVERT: c 467 LYS cc_start: 0.7765 (mtmt) cc_final: 0.7489 (mtmm) REVERT: c 576 GLN cc_start: 0.8276 (mm-40) cc_final: 0.7800 (mm-40) REVERT: c 631 ILE cc_start: 0.9074 (mm) cc_final: 0.8779 (mm) REVERT: d 239 ASP cc_start: 0.7498 (p0) cc_final: 0.7087 (p0) REVERT: d 459 THR cc_start: 0.8733 (m) cc_final: 0.8299 (p) REVERT: d 471 LEU cc_start: 0.8728 (mp) cc_final: 0.8427 (mt) REVERT: e 187 ARG cc_start: 0.7531 (mmm-85) cc_final: 0.7269 (ttm-80) REVERT: e 269 ASN cc_start: 0.7986 (OUTLIER) cc_final: 0.7450 (t0) REVERT: e 281 SER cc_start: 0.9100 (p) cc_final: 0.8845 (p) REVERT: e 350 ARG cc_start: 0.7390 (ttm-80) cc_final: 0.6988 (mtp-110) REVERT: e 373 MET cc_start: 0.6570 (OUTLIER) cc_final: 0.6331 (mmp) REVERT: e 529 LEU cc_start: 0.8784 (OUTLIER) cc_final: 0.8573 (mp) REVERT: e 576 ASP cc_start: 0.6483 (OUTLIER) cc_final: 0.5341 (m-30) REVERT: e 755 ILE cc_start: 0.8862 (mm) cc_final: 0.8635 (mt) REVERT: e 829 ASP cc_start: 0.7477 (m-30) cc_final: 0.7105 (m-30) REVERT: f 130 LYS cc_start: 0.7980 (ptmt) cc_final: 0.7670 (ptmm) REVERT: f 338 THR cc_start: 0.8594 (p) cc_final: 0.7388 (m) REVERT: f 466 LYS cc_start: 0.8757 (OUTLIER) cc_final: 0.8484 (tppt) REVERT: f 621 MET cc_start: 0.7263 (tpp) cc_final: 0.7021 (tpt) outliers start: 288 outliers final: 221 residues processed: 2254 average time/residue: 0.8970 time to fit residues: 3475.4291 Evaluate side-chains 2276 residues out of total 11774 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 235 poor density : 2041 time to evaluate : 8.915 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 186 LEU Chi-restraints excluded: chain 2 residue 226 VAL Chi-restraints excluded: chain 2 residue 241 SER Chi-restraints excluded: chain 2 residue 245 ASN Chi-restraints excluded: chain 2 residue 262 LYS Chi-restraints excluded: chain 2 residue 291 SER Chi-restraints excluded: chain 2 residue 292 GLU Chi-restraints excluded: chain 2 residue 302 THR Chi-restraints excluded: chain 2 residue 383 ARG Chi-restraints excluded: chain 2 residue 390 LEU Chi-restraints excluded: chain 2 residue 424 VAL Chi-restraints excluded: chain 2 residue 499 SER Chi-restraints excluded: chain 2 residue 567 THR Chi-restraints excluded: chain 2 residue 751 LYS Chi-restraints excluded: chain 2 residue 819 SER Chi-restraints excluded: chain 2 residue 860 SER Chi-restraints excluded: chain 3 residue 44 SER Chi-restraints excluded: chain 3 residue 99 SER Chi-restraints excluded: chain 3 residue 105 GLU Chi-restraints excluded: chain 3 residue 112 SER Chi-restraints excluded: chain 3 residue 135 SER Chi-restraints excluded: chain 3 residue 220 THR Chi-restraints excluded: chain 3 residue 242 THR Chi-restraints excluded: chain 3 residue 322 LEU Chi-restraints excluded: chain 3 residue 346 ASP Chi-restraints excluded: chain 3 residue 424 ASN Chi-restraints excluded: chain 3 residue 448 THR Chi-restraints excluded: chain 3 residue 582 VAL Chi-restraints excluded: chain 3 residue 698 THR Chi-restraints excluded: chain 4 residue 198 LEU Chi-restraints excluded: chain 4 residue 292 ASP Chi-restraints excluded: chain 4 residue 375 ASP Chi-restraints excluded: chain 4 residue 401 GLU Chi-restraints excluded: chain 4 residue 427 CYS Chi-restraints excluded: chain 4 residue 444 ILE Chi-restraints excluded: chain 4 residue 463 VAL Chi-restraints excluded: chain 4 residue 468 LYS Chi-restraints excluded: chain 4 residue 552 PHE Chi-restraints excluded: chain 4 residue 709 LEU Chi-restraints excluded: chain 4 residue 767 LYS Chi-restraints excluded: chain 4 residue 802 ILE Chi-restraints excluded: chain 4 residue 813 LEU Chi-restraints excluded: chain 5 residue 85 ASP Chi-restraints excluded: chain 5 residue 190 THR Chi-restraints excluded: chain 5 residue 207 LEU Chi-restraints excluded: chain 5 residue 273 ASN Chi-restraints excluded: chain 5 residue 365 LYS Chi-restraints excluded: chain 5 residue 426 LEU Chi-restraints excluded: chain 5 residue 445 SER Chi-restraints excluded: chain 5 residue 493 ILE Chi-restraints excluded: chain 5 residue 608 LEU Chi-restraints excluded: chain 5 residue 675 ARG Chi-restraints excluded: chain 5 residue 727 SER Chi-restraints excluded: chain 6 residue 135 VAL Chi-restraints excluded: chain 6 residue 150 THR Chi-restraints excluded: chain 6 residue 160 MET Chi-restraints excluded: chain 6 residue 293 THR Chi-restraints excluded: chain 6 residue 429 THR Chi-restraints excluded: chain 6 residue 438 THR Chi-restraints excluded: chain 6 residue 449 THR Chi-restraints excluded: chain 6 residue 532 SER Chi-restraints excluded: chain 6 residue 642 ASP Chi-restraints excluded: chain 6 residue 660 THR Chi-restraints excluded: chain 6 residue 676 THR Chi-restraints excluded: chain 6 residue 702 THR Chi-restraints excluded: chain 7 residue 220 ILE Chi-restraints excluded: chain 7 residue 225 LEU Chi-restraints excluded: chain 7 residue 372 THR Chi-restraints excluded: chain 7 residue 427 ASP Chi-restraints excluded: chain 7 residue 473 ILE Chi-restraints excluded: chain 7 residue 483 THR Chi-restraints excluded: chain 7 residue 591 LEU Chi-restraints excluded: chain C residue 12 ASP Chi-restraints excluded: chain C residue 20 PHE Chi-restraints excluded: chain C residue 24 ILE Chi-restraints excluded: chain C residue 164 THR Chi-restraints excluded: chain D residue 98 ILE Chi-restraints excluded: chain D residue 206 LEU Chi-restraints excluded: chain D residue 262 ASP Chi-restraints excluded: chain E residue 1 MET Chi-restraints excluded: chain E residue 59 VAL Chi-restraints excluded: chain E residue 82 LEU Chi-restraints excluded: chain E residue 104 VAL Chi-restraints excluded: chain E residue 140 ILE Chi-restraints excluded: chain E residue 403 ASP Chi-restraints excluded: chain E residue 412 THR Chi-restraints excluded: chain E residue 536 LEU Chi-restraints excluded: chain E residue 607 MET Chi-restraints excluded: chain E residue 636 ASP Chi-restraints excluded: chain E residue 638 SER Chi-restraints excluded: chain E residue 645 THR Chi-restraints excluded: chain F residue 86 GLU Chi-restraints excluded: chain F residue 224 LEU Chi-restraints excluded: chain F residue 269 THR Chi-restraints excluded: chain F residue 318 HIS Chi-restraints excluded: chain F residue 326 VAL Chi-restraints excluded: chain F residue 401 ILE Chi-restraints excluded: chain F residue 439 THR Chi-restraints excluded: chain F residue 468 LEU Chi-restraints excluded: chain F residue 500 SER Chi-restraints excluded: chain F residue 513 THR Chi-restraints excluded: chain F residue 544 ASP Chi-restraints excluded: chain F residue 547 SER Chi-restraints excluded: chain H residue 5 LEU Chi-restraints excluded: chain H residue 43 GLU Chi-restraints excluded: chain H residue 56 GLU Chi-restraints excluded: chain H residue 104 ASN Chi-restraints excluded: chain H residue 133 GLU Chi-restraints excluded: chain H residue 146 LEU Chi-restraints excluded: chain H residue 147 VAL Chi-restraints excluded: chain H residue 165 VAL Chi-restraints excluded: chain I residue 10 THR Chi-restraints excluded: chain I residue 64 VAL Chi-restraints excluded: chain I residue 158 LYS Chi-restraints excluded: chain I residue 168 LEU Chi-restraints excluded: chain I residue 177 GLU Chi-restraints excluded: chain J residue 24 ILE Chi-restraints excluded: chain J residue 164 THR Chi-restraints excluded: chain L residue 82 LEU Chi-restraints excluded: chain L residue 234 GLU Chi-restraints excluded: chain L residue 310 VAL Chi-restraints excluded: chain L residue 419 ILE Chi-restraints excluded: chain L residue 537 ASP Chi-restraints excluded: chain L residue 604 ASN Chi-restraints excluded: chain L residue 607 MET Chi-restraints excluded: chain L residue 624 ASN Chi-restraints excluded: chain L residue 638 SER Chi-restraints excluded: chain M residue 29 TYR Chi-restraints excluded: chain M residue 167 ARG Chi-restraints excluded: chain M residue 188 MET Chi-restraints excluded: chain M residue 299 GLU Chi-restraints excluded: chain M residue 318 HIS Chi-restraints excluded: chain M residue 401 ILE Chi-restraints excluded: chain M residue 424 LEU Chi-restraints excluded: chain M residue 500 SER Chi-restraints excluded: chain M residue 513 THR Chi-restraints excluded: chain M residue 632 LEU Chi-restraints excluded: chain N residue 1324 VAL Chi-restraints excluded: chain N residue 1415 THR Chi-restraints excluded: chain N residue 1736 VAL Chi-restraints excluded: chain N residue 1821 GLN Chi-restraints excluded: chain N residue 1863 ARG Chi-restraints excluded: chain N residue 1865 GLN Chi-restraints excluded: chain N residue 1882 SER Chi-restraints excluded: chain N residue 1885 MET Chi-restraints excluded: chain N residue 2093 GLU Chi-restraints excluded: chain N residue 2107 LEU Chi-restraints excluded: chain N residue 2117 ILE Chi-restraints excluded: chain N residue 2173 ASP Chi-restraints excluded: chain O residue 43 GLU Chi-restraints excluded: chain O residue 56 GLU Chi-restraints excluded: chain O residue 100 MET Chi-restraints excluded: chain O residue 146 LEU Chi-restraints excluded: chain O residue 147 VAL Chi-restraints excluded: chain O residue 164 ASP Chi-restraints excluded: chain P residue 32 THR Chi-restraints excluded: chain P residue 64 VAL Chi-restraints excluded: chain P residue 189 MET Chi-restraints excluded: chain Q residue 1382 SER Chi-restraints excluded: chain Q residue 1415 THR Chi-restraints excluded: chain Q residue 1685 ILE Chi-restraints excluded: chain Q residue 1736 VAL Chi-restraints excluded: chain Q residue 1811 LEU Chi-restraints excluded: chain Q residue 1821 GLN Chi-restraints excluded: chain Q residue 1848 VAL Chi-restraints excluded: chain Q residue 1865 GLN Chi-restraints excluded: chain Q residue 1936 VAL Chi-restraints excluded: chain Q residue 2173 ASP Chi-restraints excluded: chain Q residue 2194 ILE Chi-restraints excluded: chain a residue 189 VAL Chi-restraints excluded: chain a residue 202 ASN Chi-restraints excluded: chain a residue 226 VAL Chi-restraints excluded: chain a residue 241 SER Chi-restraints excluded: chain a residue 251 GLU Chi-restraints excluded: chain a residue 292 GLU Chi-restraints excluded: chain a residue 381 VAL Chi-restraints excluded: chain a residue 383 ARG Chi-restraints excluded: chain a residue 438 LEU Chi-restraints excluded: chain a residue 536 ASP Chi-restraints excluded: chain a residue 564 VAL Chi-restraints excluded: chain a residue 567 THR Chi-restraints excluded: chain a residue 644 CYS Chi-restraints excluded: chain a residue 819 SER Chi-restraints excluded: chain a residue 860 SER Chi-restraints excluded: chain b residue 99 SER Chi-restraints excluded: chain b residue 112 SER Chi-restraints excluded: chain b residue 220 THR Chi-restraints excluded: chain b residue 240 LYS Chi-restraints excluded: chain b residue 322 LEU Chi-restraints excluded: chain b residue 346 ASP Chi-restraints excluded: chain b residue 437 SER Chi-restraints excluded: chain b residue 486 ILE Chi-restraints excluded: chain b residue 488 GLU Chi-restraints excluded: chain b residue 494 THR Chi-restraints excluded: chain b residue 682 ASN Chi-restraints excluded: chain c residue 198 LEU Chi-restraints excluded: chain c residue 280 MET Chi-restraints excluded: chain c residue 292 ASP Chi-restraints excluded: chain c residue 355 THR Chi-restraints excluded: chain c residue 360 ILE Chi-restraints excluded: chain c residue 468 LYS Chi-restraints excluded: chain c residue 552 PHE Chi-restraints excluded: chain c residue 663 THR Chi-restraints excluded: chain c residue 705 VAL Chi-restraints excluded: chain d residue 85 ASP Chi-restraints excluded: chain d residue 190 THR Chi-restraints excluded: chain d residue 267 VAL Chi-restraints excluded: chain d residue 273 ASN Chi-restraints excluded: chain d residue 277 THR Chi-restraints excluded: chain d residue 351 GLU Chi-restraints excluded: chain d residue 391 LEU Chi-restraints excluded: chain d residue 402 ASP Chi-restraints excluded: chain d residue 567 SER Chi-restraints excluded: chain d residue 608 LEU Chi-restraints excluded: chain d residue 727 SER Chi-restraints excluded: chain e residue 150 THR Chi-restraints excluded: chain e residue 269 ASN Chi-restraints excluded: chain e residue 329 GLU Chi-restraints excluded: chain e residue 373 MET Chi-restraints excluded: chain e residue 438 THR Chi-restraints excluded: chain e residue 529 LEU Chi-restraints excluded: chain e residue 576 ASP Chi-restraints excluded: chain e residue 642 ASP Chi-restraints excluded: chain e residue 676 THR Chi-restraints excluded: chain e residue 701 MET Chi-restraints excluded: chain e residue 716 LEU Chi-restraints excluded: chain e residue 831 LEU Chi-restraints excluded: chain f residue 267 TYR Chi-restraints excluded: chain f residue 335 VAL Chi-restraints excluded: chain f residue 372 THR Chi-restraints excluded: chain f residue 466 LYS Chi-restraints excluded: chain f residue 473 ILE Chi-restraints excluded: chain f residue 671 SER Chi-restraints excluded: chain f residue 683 GLN Chi-restraints excluded: chain f residue 712 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1310 random chunks: chunk 1222 optimal weight: 0.4980 chunk 142 optimal weight: 10.0000 chunk 722 optimal weight: 0.8980 chunk 925 optimal weight: 20.0000 chunk 717 optimal weight: 4.9990 chunk 1066 optimal weight: 0.0270 chunk 707 optimal weight: 20.0000 chunk 1262 optimal weight: 9.9990 chunk 790 optimal weight: 10.0000 chunk 769 optimal weight: 10.0000 chunk 582 optimal weight: 9.9990 overall best weight: 3.2842 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 2 282 HIS 2 641 GLN ** 4 808 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 253 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 173 GLN ** 7 543 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 7 622 HIS D 233 ASN E 624 ASN ** F 435 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 39 ASN L 73 GLN ** M 435 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 488 ASN Q1662 ASN a 658 ASN b 731 ASN ** d 273 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 685 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** e 409 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7679 moved from start: 0.2200 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 109512 Z= 0.237 Angle : 0.573 16.996 148617 Z= 0.296 Chirality : 0.042 0.290 17004 Planarity : 0.004 0.088 18640 Dihedral : 11.572 172.932 15850 Min Nonbonded Distance : 1.949 Molprobity Statistics. All-atom Clashscore : 6.98 Ramachandran Plot: Outliers : 0.01 % Allowed : 4.12 % Favored : 95.87 % Rotamer: Outliers : 2.64 % Allowed : 15.96 % Favored : 81.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.33 (0.07), residues: 12956 helix: 1.63 (0.07), residues: 5356 sheet: 0.03 (0.11), residues: 2086 loop : -1.13 (0.08), residues: 5514 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP E 481 HIS 0.008 0.001 HIS N1434 PHE 0.019 0.001 PHE E 62 TYR 0.024 0.001 TYR b 211 ARG 0.011 0.000 ARG F 386 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 25912 Ramachandran restraints generated. 12956 Oldfield, 0 Emsley, 12956 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 25912 Ramachandran restraints generated. 12956 Oldfield, 0 Emsley, 12956 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2382 residues out of total 11774 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 311 poor density : 2071 time to evaluate : 9.332 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: 2 383 ARG cc_start: 0.8005 (OUTLIER) cc_final: 0.7048 (ptp-170) REVERT: 2 390 LEU cc_start: 0.8175 (OUTLIER) cc_final: 0.7927 (mp) REVERT: 2 441 LYS cc_start: 0.7598 (mttt) cc_final: 0.7150 (mttt) REVERT: 2 792 ASP cc_start: 0.7147 (m-30) cc_final: 0.6663 (m-30) REVERT: 3 105 GLU cc_start: 0.7241 (OUTLIER) cc_final: 0.6930 (mp0) REVERT: 3 424 ASN cc_start: 0.7668 (OUTLIER) cc_final: 0.7408 (t0) REVERT: 3 499 LYS cc_start: 0.8019 (tttt) cc_final: 0.7579 (tppt) REVERT: 4 233 MET cc_start: 0.5660 (mtp) cc_final: 0.5381 (mtp) REVERT: 4 538 LYS cc_start: 0.8501 (mmtp) cc_final: 0.8286 (mmtp) REVERT: 4 811 MET cc_start: 0.6536 (tpt) cc_final: 0.6245 (tpp) REVERT: 5 239 ASP cc_start: 0.7323 (p0) cc_final: 0.6875 (p0) REVERT: 5 431 LYS cc_start: 0.8174 (mttm) cc_final: 0.7784 (mtpp) REVERT: 5 732 THR cc_start: 0.8403 (m) cc_final: 0.8103 (p) REVERT: 6 194 PRO cc_start: 0.7807 (Cg_endo) cc_final: 0.7601 (Cg_exo) REVERT: 6 283 LYS cc_start: 0.8150 (mmtp) cc_final: 0.7729 (mtmm) REVERT: 6 520 VAL cc_start: 0.8435 (t) cc_final: 0.8232 (p) REVERT: 6 527 ASP cc_start: 0.7341 (t0) cc_final: 0.6821 (t0) REVERT: 6 755 ILE cc_start: 0.8811 (mm) cc_final: 0.8429 (mt) REVERT: 6 767 LYS cc_start: 0.7263 (mmtp) cc_final: 0.6982 (mmtp) REVERT: 6 783 ASP cc_start: 0.7644 (m-30) cc_final: 0.7402 (t0) REVERT: 7 107 GLN cc_start: 0.6830 (mt0) cc_final: 0.6244 (tt0) REVERT: 7 121 ILE cc_start: 0.8568 (mm) cc_final: 0.8338 (mt) REVERT: 7 427 ASP cc_start: 0.7944 (OUTLIER) cc_final: 0.6714 (m-30) REVERT: 7 504 ASP cc_start: 0.6613 (t0) cc_final: 0.5882 (t0) REVERT: D 98 ILE cc_start: 0.8382 (OUTLIER) cc_final: 0.8027 (mp) REVERT: D 100 ASN cc_start: 0.7259 (t0) cc_final: 0.7008 (t0) REVERT: D 289 ASP cc_start: 0.7305 (t0) cc_final: 0.6969 (t0) REVERT: E 161 LYS cc_start: 0.7578 (OUTLIER) cc_final: 0.7228 (ttpp) REVERT: E 239 GLU cc_start: 0.7302 (tm-30) cc_final: 0.7097 (tm-30) REVERT: F 22 TYR cc_start: 0.8005 (t80) cc_final: 0.7601 (t80) REVERT: F 23 ARG cc_start: 0.6553 (mtm180) cc_final: 0.6179 (mtm-85) REVERT: F 318 HIS cc_start: 0.7485 (OUTLIER) cc_final: 0.7059 (p-80) REVERT: F 468 LEU cc_start: 0.7616 (OUTLIER) cc_final: 0.7323 (mp) REVERT: F 494 MET cc_start: 0.7830 (tpp) cc_final: 0.7422 (tpp) REVERT: F 552 ARG cc_start: 0.7472 (ttp-110) cc_final: 0.7238 (ttm170) REVERT: F 604 LYS cc_start: 0.8245 (tptm) cc_final: 0.7990 (tptm) REVERT: F 669 ARG cc_start: 0.6725 (mmt180) cc_final: 0.6079 (mmp-170) REVERT: F 674 GLU cc_start: 0.5907 (tt0) cc_final: 0.5354 (tm-30) REVERT: H 8 LYS cc_start: 0.7681 (mttm) cc_final: 0.7085 (mmmt) REVERT: H 71 GLN cc_start: 0.6671 (mp10) cc_final: 0.6218 (mp10) REVERT: H 133 GLU cc_start: 0.7345 (OUTLIER) cc_final: 0.6860 (mp0) REVERT: I 81 GLN cc_start: 0.7967 (tp-100) cc_final: 0.7283 (tt0) REVERT: K 256 TYR cc_start: 0.8221 (m-80) cc_final: 0.7595 (m-80) REVERT: K 289 ASP cc_start: 0.7678 (t0) cc_final: 0.7355 (t0) REVERT: L 645 THR cc_start: 0.8547 (m) cc_final: 0.8219 (p) REVERT: M 190 PHE cc_start: 0.8470 (m-80) cc_final: 0.8176 (m-10) REVERT: M 333 TYR cc_start: 0.8000 (m-80) cc_final: 0.7238 (m-80) REVERT: M 554 ARG cc_start: 0.6560 (mtm-85) cc_final: 0.6113 (mtm110) REVERT: M 674 GLU cc_start: 0.6072 (tt0) cc_final: 0.5858 (tt0) REVERT: M 685 GLU cc_start: 0.6253 (tm-30) cc_final: 0.5561 (tm-30) REVERT: N 1439 MET cc_start: 0.6439 (ttm) cc_final: 0.6137 (ttp) REVERT: N 1654 GLN cc_start: 0.7387 (mm-40) cc_final: 0.7156 (mm-40) REVERT: N 1663 LEU cc_start: 0.7679 (tp) cc_final: 0.7428 (tp) REVERT: N 1854 LEU cc_start: 0.8006 (mm) cc_final: 0.7700 (mp) REVERT: N 1862 ASP cc_start: 0.7649 (t70) cc_final: 0.7133 (t70) REVERT: N 1896 SER cc_start: 0.8033 (p) cc_final: 0.7431 (m) REVERT: N 1962 ASP cc_start: 0.7838 (t0) cc_final: 0.7589 (t0) REVERT: N 1970 SER cc_start: 0.8816 (m) cc_final: 0.8197 (p) REVERT: N 2031 TYR cc_start: 0.8400 (m-80) cc_final: 0.7974 (m-80) REVERT: O 8 LYS cc_start: 0.8295 (mtpt) cc_final: 0.7741 (mtpt) REVERT: O 28 ASN cc_start: 0.8587 (p0) cc_final: 0.8236 (p0) REVERT: O 202 GLN cc_start: 0.6782 (mt0) cc_final: 0.6495 (mt0) REVERT: P 63 MET cc_start: 0.7184 (mtt) cc_final: 0.6971 (mtp) REVERT: Q 1360 LYS cc_start: 0.8136 (tppp) cc_final: 0.7833 (tppt) REVERT: Q 1851 PHE cc_start: 0.8200 (OUTLIER) cc_final: 0.7311 (m-80) REVERT: Q 1872 LYS cc_start: 0.7929 (mmtt) cc_final: 0.7525 (mmmm) REVERT: Q 1903 LYS cc_start: 0.7547 (mttt) cc_final: 0.6962 (mttp) REVERT: Q 2032 GLU cc_start: 0.6441 (tt0) cc_final: 0.6005 (mt-10) REVERT: Q 2093 GLU cc_start: 0.7100 (mt-10) cc_final: 0.6591 (tt0) REVERT: Q 2144 GLU cc_start: 0.6454 (mm-30) cc_final: 0.6093 (mm-30) REVERT: a 383 ARG cc_start: 0.8173 (OUTLIER) cc_final: 0.7157 (ptp-170) REVERT: a 747 ARG cc_start: 0.7204 (mtp85) cc_final: 0.6815 (mtp180) REVERT: a 751 LYS cc_start: 0.7844 (mttt) cc_final: 0.7418 (mmmm) REVERT: a 792 ASP cc_start: 0.7840 (m-30) cc_final: 0.7594 (m-30) REVERT: a 826 SER cc_start: 0.8800 (t) cc_final: 0.8488 (m) REVERT: b 48 TYR cc_start: 0.7901 (t80) cc_final: 0.7643 (t80) REVERT: b 126 GLU cc_start: 0.6729 (mt-10) cc_final: 0.6403 (mt-10) REVERT: b 202 TYR cc_start: 0.8414 (t80) cc_final: 0.7894 (t80) REVERT: c 233 MET cc_start: 0.5479 (mtp) cc_final: 0.5251 (mtp) REVERT: c 306 TYR cc_start: 0.6426 (p90) cc_final: 0.6207 (p90) REVERT: c 576 GLN cc_start: 0.8249 (mm-40) cc_final: 0.7821 (mm-40) REVERT: c 631 ILE cc_start: 0.9077 (mm) cc_final: 0.8779 (mm) REVERT: d 239 ASP cc_start: 0.7555 (p0) cc_final: 0.7147 (p0) REVERT: d 471 LEU cc_start: 0.8786 (mp) cc_final: 0.8523 (mt) REVERT: e 144 LYS cc_start: 0.7797 (tptp) cc_final: 0.7587 (tttm) REVERT: e 187 ARG cc_start: 0.7544 (mmm-85) cc_final: 0.7274 (ttm-80) REVERT: e 269 ASN cc_start: 0.8030 (OUTLIER) cc_final: 0.7500 (t0) REVERT: e 281 SER cc_start: 0.9139 (p) cc_final: 0.8896 (p) REVERT: e 350 ARG cc_start: 0.7470 (ttm-80) cc_final: 0.6977 (mtp-110) REVERT: e 576 ASP cc_start: 0.6555 (OUTLIER) cc_final: 0.5505 (m-30) REVERT: e 696 ARG cc_start: 0.5158 (ttp-170) cc_final: 0.4836 (ttp80) REVERT: e 755 ILE cc_start: 0.8907 (mm) cc_final: 0.8657 (mt) REVERT: e 829 ASP cc_start: 0.7477 (m-30) cc_final: 0.7116 (m-30) REVERT: f 130 LYS cc_start: 0.8001 (ptmt) cc_final: 0.7712 (ptmm) REVERT: f 338 THR cc_start: 0.8603 (p) cc_final: 0.7401 (m) outliers start: 311 outliers final: 259 residues processed: 2222 average time/residue: 0.9179 time to fit residues: 3507.5983 Evaluate side-chains 2306 residues out of total 11774 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 273 poor density : 2033 time to evaluate : 9.029 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 186 LEU Chi-restraints excluded: chain 2 residue 241 SER Chi-restraints excluded: chain 2 residue 262 LYS Chi-restraints excluded: chain 2 residue 291 SER Chi-restraints excluded: chain 2 residue 292 GLU Chi-restraints excluded: chain 2 residue 302 THR Chi-restraints excluded: chain 2 residue 383 ARG Chi-restraints excluded: chain 2 residue 390 LEU Chi-restraints excluded: chain 2 residue 424 VAL Chi-restraints excluded: chain 2 residue 499 SER Chi-restraints excluded: chain 2 residue 564 VAL Chi-restraints excluded: chain 2 residue 567 THR Chi-restraints excluded: chain 2 residue 751 LYS Chi-restraints excluded: chain 2 residue 819 SER Chi-restraints excluded: chain 2 residue 860 SER Chi-restraints excluded: chain 3 residue 44 SER Chi-restraints excluded: chain 3 residue 99 SER Chi-restraints excluded: chain 3 residue 105 GLU Chi-restraints excluded: chain 3 residue 112 SER Chi-restraints excluded: chain 3 residue 135 SER Chi-restraints excluded: chain 3 residue 185 ILE Chi-restraints excluded: chain 3 residue 220 THR Chi-restraints excluded: chain 3 residue 242 THR Chi-restraints excluded: chain 3 residue 322 LEU Chi-restraints excluded: chain 3 residue 341 MET Chi-restraints excluded: chain 3 residue 346 ASP Chi-restraints excluded: chain 3 residue 424 ASN Chi-restraints excluded: chain 3 residue 448 THR Chi-restraints excluded: chain 3 residue 553 ILE Chi-restraints excluded: chain 3 residue 582 VAL Chi-restraints excluded: chain 3 residue 697 ILE Chi-restraints excluded: chain 3 residue 698 THR Chi-restraints excluded: chain 4 residue 198 LEU Chi-restraints excluded: chain 4 residue 292 ASP Chi-restraints excluded: chain 4 residue 355 THR Chi-restraints excluded: chain 4 residue 401 GLU Chi-restraints excluded: chain 4 residue 427 CYS Chi-restraints excluded: chain 4 residue 444 ILE Chi-restraints excluded: chain 4 residue 463 VAL Chi-restraints excluded: chain 4 residue 468 LYS Chi-restraints excluded: chain 4 residue 552 PHE Chi-restraints excluded: chain 4 residue 663 THR Chi-restraints excluded: chain 4 residue 709 LEU Chi-restraints excluded: chain 4 residue 723 HIS Chi-restraints excluded: chain 4 residue 767 LYS Chi-restraints excluded: chain 4 residue 768 THR Chi-restraints excluded: chain 4 residue 802 ILE Chi-restraints excluded: chain 4 residue 813 LEU Chi-restraints excluded: chain 5 residue 85 ASP Chi-restraints excluded: chain 5 residue 190 THR Chi-restraints excluded: chain 5 residue 193 THR Chi-restraints excluded: chain 5 residue 207 LEU Chi-restraints excluded: chain 5 residue 267 VAL Chi-restraints excluded: chain 5 residue 273 ASN Chi-restraints excluded: chain 5 residue 365 LYS Chi-restraints excluded: chain 5 residue 417 ASP Chi-restraints excluded: chain 5 residue 426 LEU Chi-restraints excluded: chain 5 residue 445 SER Chi-restraints excluded: chain 5 residue 453 VAL Chi-restraints excluded: chain 5 residue 493 ILE Chi-restraints excluded: chain 5 residue 608 LEU Chi-restraints excluded: chain 5 residue 675 ARG Chi-restraints excluded: chain 5 residue 727 SER Chi-restraints excluded: chain 6 residue 150 THR Chi-restraints excluded: chain 6 residue 160 MET Chi-restraints excluded: chain 6 residue 293 THR Chi-restraints excluded: chain 6 residue 333 CYS Chi-restraints excluded: chain 6 residue 429 THR Chi-restraints excluded: chain 6 residue 438 THR Chi-restraints excluded: chain 6 residue 443 LEU Chi-restraints excluded: chain 6 residue 449 THR Chi-restraints excluded: chain 6 residue 452 ILE Chi-restraints excluded: chain 6 residue 532 SER Chi-restraints excluded: chain 6 residue 642 ASP Chi-restraints excluded: chain 6 residue 660 THR Chi-restraints excluded: chain 6 residue 676 THR Chi-restraints excluded: chain 6 residue 702 THR Chi-restraints excluded: chain 7 residue 220 ILE Chi-restraints excluded: chain 7 residue 225 LEU Chi-restraints excluded: chain 7 residue 300 MET Chi-restraints excluded: chain 7 residue 372 THR Chi-restraints excluded: chain 7 residue 427 ASP Chi-restraints excluded: chain 7 residue 473 ILE Chi-restraints excluded: chain 7 residue 483 THR Chi-restraints excluded: chain 7 residue 546 ILE Chi-restraints excluded: chain 7 residue 591 LEU Chi-restraints excluded: chain C residue 12 ASP Chi-restraints excluded: chain C residue 24 ILE Chi-restraints excluded: chain C residue 164 THR Chi-restraints excluded: chain D residue 98 ILE Chi-restraints excluded: chain D residue 206 LEU Chi-restraints excluded: chain D residue 262 ASP Chi-restraints excluded: chain D residue 269 LEU Chi-restraints excluded: chain E residue 1 MET Chi-restraints excluded: chain E residue 82 LEU Chi-restraints excluded: chain E residue 104 VAL Chi-restraints excluded: chain E residue 140 ILE Chi-restraints excluded: chain E residue 161 LYS Chi-restraints excluded: chain E residue 248 VAL Chi-restraints excluded: chain E residue 403 ASP Chi-restraints excluded: chain E residue 412 THR Chi-restraints excluded: chain E residue 536 LEU Chi-restraints excluded: chain E residue 576 THR Chi-restraints excluded: chain E residue 607 MET Chi-restraints excluded: chain E residue 636 ASP Chi-restraints excluded: chain E residue 638 SER Chi-restraints excluded: chain E residue 645 THR Chi-restraints excluded: chain E residue 646 LEU Chi-restraints excluded: chain F residue 31 LEU Chi-restraints excluded: chain F residue 86 GLU Chi-restraints excluded: chain F residue 170 PHE Chi-restraints excluded: chain F residue 224 LEU Chi-restraints excluded: chain F residue 269 THR Chi-restraints excluded: chain F residue 318 HIS Chi-restraints excluded: chain F residue 326 VAL Chi-restraints excluded: chain F residue 335 VAL Chi-restraints excluded: chain F residue 401 ILE Chi-restraints excluded: chain F residue 439 THR Chi-restraints excluded: chain F residue 468 LEU Chi-restraints excluded: chain F residue 500 SER Chi-restraints excluded: chain F residue 513 THR Chi-restraints excluded: chain F residue 544 ASP Chi-restraints excluded: chain F residue 547 SER Chi-restraints excluded: chain H residue 1 MET Chi-restraints excluded: chain H residue 5 LEU Chi-restraints excluded: chain H residue 43 GLU Chi-restraints excluded: chain H residue 56 GLU Chi-restraints excluded: chain H residue 104 ASN Chi-restraints excluded: chain H residue 132 LYS Chi-restraints excluded: chain H residue 133 GLU Chi-restraints excluded: chain H residue 146 LEU Chi-restraints excluded: chain H residue 147 VAL Chi-restraints excluded: chain H residue 164 ASP Chi-restraints excluded: chain H residue 165 VAL Chi-restraints excluded: chain I residue 10 THR Chi-restraints excluded: chain I residue 64 VAL Chi-restraints excluded: chain I residue 133 ASP Chi-restraints excluded: chain I residue 158 LYS Chi-restraints excluded: chain I residue 168 LEU Chi-restraints excluded: chain I residue 177 GLU Chi-restraints excluded: chain J residue 24 ILE Chi-restraints excluded: chain J residue 164 THR Chi-restraints excluded: chain K residue 262 ASP Chi-restraints excluded: chain L residue 82 LEU Chi-restraints excluded: chain L residue 234 GLU Chi-restraints excluded: chain L residue 310 VAL Chi-restraints excluded: chain L residue 419 ILE Chi-restraints excluded: chain L residue 537 ASP Chi-restraints excluded: chain L residue 604 ASN Chi-restraints excluded: chain L residue 607 MET Chi-restraints excluded: chain L residue 624 ASN Chi-restraints excluded: chain L residue 638 SER Chi-restraints excluded: chain M residue 29 TYR Chi-restraints excluded: chain M residue 31 LEU Chi-restraints excluded: chain M residue 167 ARG Chi-restraints excluded: chain M residue 188 MET Chi-restraints excluded: chain M residue 299 GLU Chi-restraints excluded: chain M residue 302 SER Chi-restraints excluded: chain M residue 318 HIS Chi-restraints excluded: chain M residue 401 ILE Chi-restraints excluded: chain M residue 424 LEU Chi-restraints excluded: chain M residue 500 SER Chi-restraints excluded: chain M residue 513 THR Chi-restraints excluded: chain M residue 632 LEU Chi-restraints excluded: chain N residue 1324 VAL Chi-restraints excluded: chain N residue 1415 THR Chi-restraints excluded: chain N residue 1675 LEU Chi-restraints excluded: chain N residue 1736 VAL Chi-restraints excluded: chain N residue 1821 GLN Chi-restraints excluded: chain N residue 1851 PHE Chi-restraints excluded: chain N residue 1863 ARG Chi-restraints excluded: chain N residue 1865 GLN Chi-restraints excluded: chain N residue 1882 SER Chi-restraints excluded: chain N residue 1885 MET Chi-restraints excluded: chain N residue 2093 GLU Chi-restraints excluded: chain N residue 2107 LEU Chi-restraints excluded: chain N residue 2117 ILE Chi-restraints excluded: chain N residue 2173 ASP Chi-restraints excluded: chain O residue 1 MET Chi-restraints excluded: chain O residue 16 THR Chi-restraints excluded: chain O residue 43 GLU Chi-restraints excluded: chain O residue 56 GLU Chi-restraints excluded: chain O residue 100 MET Chi-restraints excluded: chain O residue 146 LEU Chi-restraints excluded: chain O residue 147 VAL Chi-restraints excluded: chain O residue 164 ASP Chi-restraints excluded: chain P residue 32 THR Chi-restraints excluded: chain P residue 189 MET Chi-restraints excluded: chain Q residue 1382 SER Chi-restraints excluded: chain Q residue 1415 THR Chi-restraints excluded: chain Q residue 1685 ILE Chi-restraints excluded: chain Q residue 1736 VAL Chi-restraints excluded: chain Q residue 1811 LEU Chi-restraints excluded: chain Q residue 1821 GLN Chi-restraints excluded: chain Q residue 1848 VAL Chi-restraints excluded: chain Q residue 1851 PHE Chi-restraints excluded: chain Q residue 1865 GLN Chi-restraints excluded: chain Q residue 1936 VAL Chi-restraints excluded: chain Q residue 1941 LEU Chi-restraints excluded: chain Q residue 2173 ASP Chi-restraints excluded: chain Q residue 2194 ILE Chi-restraints excluded: chain a residue 189 VAL Chi-restraints excluded: chain a residue 202 ASN Chi-restraints excluded: chain a residue 241 SER Chi-restraints excluded: chain a residue 251 GLU Chi-restraints excluded: chain a residue 292 GLU Chi-restraints excluded: chain a residue 383 ARG Chi-restraints excluded: chain a residue 438 LEU Chi-restraints excluded: chain a residue 536 ASP Chi-restraints excluded: chain a residue 564 VAL Chi-restraints excluded: chain a residue 567 THR Chi-restraints excluded: chain a residue 644 CYS Chi-restraints excluded: chain a residue 819 SER Chi-restraints excluded: chain a residue 860 SER Chi-restraints excluded: chain b residue 99 SER Chi-restraints excluded: chain b residue 112 SER Chi-restraints excluded: chain b residue 213 ASP Chi-restraints excluded: chain b residue 220 THR Chi-restraints excluded: chain b residue 240 LYS Chi-restraints excluded: chain b residue 322 LEU Chi-restraints excluded: chain b residue 346 ASP Chi-restraints excluded: chain b residue 424 ASN Chi-restraints excluded: chain b residue 437 SER Chi-restraints excluded: chain b residue 448 THR Chi-restraints excluded: chain b residue 486 ILE Chi-restraints excluded: chain b residue 488 GLU Chi-restraints excluded: chain b residue 494 THR Chi-restraints excluded: chain b residue 682 ASN Chi-restraints excluded: chain b residue 723 LYS Chi-restraints excluded: chain c residue 198 LEU Chi-restraints excluded: chain c residue 280 MET Chi-restraints excluded: chain c residue 292 ASP Chi-restraints excluded: chain c residue 355 THR Chi-restraints excluded: chain c residue 360 ILE Chi-restraints excluded: chain c residue 427 CYS Chi-restraints excluded: chain c residue 468 LYS Chi-restraints excluded: chain c residue 663 THR Chi-restraints excluded: chain c residue 705 VAL Chi-restraints excluded: chain c residue 802 ILE Chi-restraints excluded: chain c residue 822 VAL Chi-restraints excluded: chain d residue 85 ASP Chi-restraints excluded: chain d residue 190 THR Chi-restraints excluded: chain d residue 193 THR Chi-restraints excluded: chain d residue 267 VAL Chi-restraints excluded: chain d residue 273 ASN Chi-restraints excluded: chain d residue 277 THR Chi-restraints excluded: chain d residue 391 LEU Chi-restraints excluded: chain d residue 402 ASP Chi-restraints excluded: chain d residue 567 SER Chi-restraints excluded: chain d residue 608 LEU Chi-restraints excluded: chain d residue 727 SER Chi-restraints excluded: chain e residue 117 GLN Chi-restraints excluded: chain e residue 150 THR Chi-restraints excluded: chain e residue 269 ASN Chi-restraints excluded: chain e residue 409 GLN Chi-restraints excluded: chain e residue 438 THR Chi-restraints excluded: chain e residue 576 ASP Chi-restraints excluded: chain e residue 642 ASP Chi-restraints excluded: chain e residue 652 ILE Chi-restraints excluded: chain e residue 676 THR Chi-restraints excluded: chain e residue 701 MET Chi-restraints excluded: chain e residue 716 LEU Chi-restraints excluded: chain e residue 807 SER Chi-restraints excluded: chain e residue 831 LEU Chi-restraints excluded: chain f residue 267 TYR Chi-restraints excluded: chain f residue 335 VAL Chi-restraints excluded: chain f residue 372 THR Chi-restraints excluded: chain f residue 473 ILE Chi-restraints excluded: chain f residue 483 THR Chi-restraints excluded: chain f residue 533 ASP Chi-restraints excluded: chain f residue 671 SER Chi-restraints excluded: chain f residue 683 GLN Chi-restraints excluded: chain f residue 712 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1310 random chunks: chunk 781 optimal weight: 9.9990 chunk 504 optimal weight: 3.9990 chunk 754 optimal weight: 40.0000 chunk 380 optimal weight: 50.0000 chunk 248 optimal weight: 6.9990 chunk 244 optimal weight: 9.9990 chunk 802 optimal weight: 9.9990 chunk 860 optimal weight: 0.8980 chunk 624 optimal weight: 3.9990 chunk 117 optimal weight: 10.0000 chunk 992 optimal weight: 2.9990 overall best weight: 3.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 2 641 GLN 4 229 GLN ** 4 808 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 253 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 139 GLN 6 173 GLN ** F 435 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 39 ASN M 318 HIS ** M 435 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 488 ASN Q1662 ASN Q2145 HIS a 658 ASN a 665 GLN b 731 ASN c 229 GLN c 691 ASN ** d 273 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 685 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7692 moved from start: 0.2311 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.072 109512 Z= 0.260 Angle : 0.584 14.101 148617 Z= 0.302 Chirality : 0.043 0.295 17004 Planarity : 0.004 0.087 18640 Dihedral : 11.593 173.229 15846 Min Nonbonded Distance : 1.946 Molprobity Statistics. All-atom Clashscore : 7.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.16 % Favored : 95.84 % Rotamer: Outliers : 2.79 % Allowed : 16.23 % Favored : 80.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.23 (0.07), residues: 12956 helix: 1.56 (0.07), residues: 5352 sheet: -0.02 (0.11), residues: 2042 loop : -1.20 (0.08), residues: 5562 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP E 481 HIS 0.010 0.001 HIS N1434 PHE 0.019 0.001 PHE M 399 TYR 0.025 0.001 TYR b 211 ARG 0.011 0.000 ARG F 386 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 25912 Ramachandran restraints generated. 12956 Oldfield, 0 Emsley, 12956 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 25912 Ramachandran restraints generated. 12956 Oldfield, 0 Emsley, 12956 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2385 residues out of total 11774 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 329 poor density : 2056 time to evaluate : 9.114 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: 2 383 ARG cc_start: 0.7895 (OUTLIER) cc_final: 0.6960 (ptp-170) REVERT: 2 390 LEU cc_start: 0.8188 (OUTLIER) cc_final: 0.7942 (mp) REVERT: 2 441 LYS cc_start: 0.7550 (mttt) cc_final: 0.7084 (mttt) REVERT: 2 695 LEU cc_start: 0.8470 (OUTLIER) cc_final: 0.8226 (tt) REVERT: 2 792 ASP cc_start: 0.7179 (m-30) cc_final: 0.6693 (m-30) REVERT: 3 105 GLU cc_start: 0.7289 (OUTLIER) cc_final: 0.6958 (mp0) REVERT: 3 424 ASN cc_start: 0.7628 (OUTLIER) cc_final: 0.7362 (t0) REVERT: 3 499 LYS cc_start: 0.8021 (tttt) cc_final: 0.7581 (tppt) REVERT: 4 233 MET cc_start: 0.5641 (mtp) cc_final: 0.5372 (mtp) REVERT: 4 538 LYS cc_start: 0.8507 (mmtp) cc_final: 0.8293 (mmtp) REVERT: 4 576 GLN cc_start: 0.7718 (mp10) cc_final: 0.7322 (mp10) REVERT: 5 65 MET cc_start: 0.8736 (mtt) cc_final: 0.8320 (mtt) REVERT: 5 239 ASP cc_start: 0.7398 (p0) cc_final: 0.6917 (p0) REVERT: 5 431 LYS cc_start: 0.8211 (mttm) cc_final: 0.7821 (mtpp) REVERT: 6 194 PRO cc_start: 0.7795 (Cg_endo) cc_final: 0.7578 (Cg_exo) REVERT: 6 283 LYS cc_start: 0.8165 (mmtp) cc_final: 0.7737 (mtmm) REVERT: 6 520 VAL cc_start: 0.8408 (t) cc_final: 0.8181 (p) REVERT: 6 527 ASP cc_start: 0.7372 (t0) cc_final: 0.6856 (t0) REVERT: 6 755 ILE cc_start: 0.8820 (mm) cc_final: 0.8434 (mt) REVERT: 6 767 LYS cc_start: 0.7315 (mmtp) cc_final: 0.6985 (mmtp) REVERT: 6 783 ASP cc_start: 0.7652 (m-30) cc_final: 0.7438 (t0) REVERT: 7 107 GLN cc_start: 0.6943 (mt0) cc_final: 0.6336 (tt0) REVERT: 7 121 ILE cc_start: 0.8575 (mm) cc_final: 0.8347 (mt) REVERT: 7 427 ASP cc_start: 0.7915 (OUTLIER) cc_final: 0.6604 (m-30) REVERT: 7 504 ASP cc_start: 0.6606 (t0) cc_final: 0.5749 (t0) REVERT: 7 593 ARG cc_start: 0.6156 (mtt-85) cc_final: 0.5682 (mtt-85) REVERT: C 15 GLU cc_start: 0.7380 (mp0) cc_final: 0.7063 (mp0) REVERT: C 193 LYS cc_start: 0.7945 (tptt) cc_final: 0.7602 (tptp) REVERT: D 98 ILE cc_start: 0.8341 (OUTLIER) cc_final: 0.7960 (mp) REVERT: D 100 ASN cc_start: 0.7080 (t0) cc_final: 0.6835 (t0) REVERT: D 289 ASP cc_start: 0.7334 (t0) cc_final: 0.6996 (t0) REVERT: E 82 LEU cc_start: 0.8693 (OUTLIER) cc_final: 0.8186 (tt) REVERT: E 161 LYS cc_start: 0.7697 (OUTLIER) cc_final: 0.7382 (ttpp) REVERT: E 239 GLU cc_start: 0.7314 (tm-30) cc_final: 0.7021 (tm-30) REVERT: F 22 TYR cc_start: 0.8041 (t80) cc_final: 0.7657 (t80) REVERT: F 318 HIS cc_start: 0.7358 (OUTLIER) cc_final: 0.6836 (p-80) REVERT: F 468 LEU cc_start: 0.7658 (OUTLIER) cc_final: 0.7403 (mp) REVERT: F 494 MET cc_start: 0.7838 (tpp) cc_final: 0.7544 (tpt) REVERT: F 552 ARG cc_start: 0.7488 (ttp-110) cc_final: 0.7230 (ttm170) REVERT: F 604 LYS cc_start: 0.8214 (tptm) cc_final: 0.7935 (tptm) REVERT: F 674 GLU cc_start: 0.5919 (tt0) cc_final: 0.5364 (tm-30) REVERT: H 8 LYS cc_start: 0.7672 (mttm) cc_final: 0.7080 (mmmt) REVERT: H 71 GLN cc_start: 0.6698 (mt0) cc_final: 0.6217 (mp10) REVERT: H 129 GLU cc_start: 0.5935 (OUTLIER) cc_final: 0.4349 (tt0) REVERT: H 133 GLU cc_start: 0.7363 (OUTLIER) cc_final: 0.6947 (mp0) REVERT: I 81 GLN cc_start: 0.7988 (tp-100) cc_final: 0.7293 (tt0) REVERT: J 31 GLU cc_start: 0.5928 (mt-10) cc_final: 0.5680 (mt-10) REVERT: J 172 MET cc_start: 0.7937 (ttp) cc_final: 0.7561 (tmm) REVERT: K 289 ASP cc_start: 0.7653 (t0) cc_final: 0.7382 (t0) REVERT: L 161 LYS cc_start: 0.7679 (OUTLIER) cc_final: 0.7379 (ttpp) REVERT: L 524 ILE cc_start: 0.8819 (OUTLIER) cc_final: 0.8467 (mp) REVERT: M 17 LEU cc_start: 0.8492 (tp) cc_final: 0.8217 (tp) REVERT: M 190 PHE cc_start: 0.8467 (m-80) cc_final: 0.8181 (m-10) REVERT: M 333 TYR cc_start: 0.8013 (m-80) cc_final: 0.7246 (m-80) REVERT: M 554 ARG cc_start: 0.6523 (mtm-85) cc_final: 0.6214 (mtm110) REVERT: M 604 LYS cc_start: 0.8391 (tptp) cc_final: 0.8076 (tptp) REVERT: M 674 GLU cc_start: 0.6048 (tt0) cc_final: 0.5819 (tt0) REVERT: N 1439 MET cc_start: 0.6450 (ttm) cc_final: 0.6148 (ttp) REVERT: N 1713 MET cc_start: 0.8222 (mtp) cc_final: 0.7824 (mtp) REVERT: N 1854 LEU cc_start: 0.8030 (mm) cc_final: 0.7734 (mp) REVERT: N 1862 ASP cc_start: 0.7590 (t70) cc_final: 0.7084 (t70) REVERT: N 1896 SER cc_start: 0.8014 (p) cc_final: 0.7414 (m) REVERT: N 1970 SER cc_start: 0.8827 (m) cc_final: 0.8202 (p) REVERT: N 2031 TYR cc_start: 0.8401 (m-80) cc_final: 0.8090 (m-80) REVERT: O 8 LYS cc_start: 0.8312 (mtpt) cc_final: 0.7751 (mtpt) REVERT: O 28 ASN cc_start: 0.8621 (p0) cc_final: 0.8247 (p0) REVERT: P 63 MET cc_start: 0.7150 (mtt) cc_final: 0.6946 (mtp) REVERT: Q 1360 LYS cc_start: 0.8144 (tppp) cc_final: 0.7834 (tppt) REVERT: Q 1851 PHE cc_start: 0.8252 (OUTLIER) cc_final: 0.7312 (m-80) REVERT: Q 1872 LYS cc_start: 0.7851 (mmtt) cc_final: 0.7503 (mmmm) REVERT: Q 1903 LYS cc_start: 0.7531 (mttt) cc_final: 0.6949 (mttp) REVERT: Q 2032 GLU cc_start: 0.6560 (tt0) cc_final: 0.6118 (mt-10) REVERT: Q 2093 GLU cc_start: 0.7054 (mt-10) cc_final: 0.6519 (tt0) REVERT: a 383 ARG cc_start: 0.8185 (OUTLIER) cc_final: 0.6634 (ptp-170) REVERT: a 751 LYS cc_start: 0.7849 (mttt) cc_final: 0.7438 (mtmm) REVERT: a 792 ASP cc_start: 0.7854 (m-30) cc_final: 0.7598 (m-30) REVERT: a 826 SER cc_start: 0.8819 (t) cc_final: 0.8507 (m) REVERT: b 48 TYR cc_start: 0.7949 (t80) cc_final: 0.7673 (t80) REVERT: b 105 GLU cc_start: 0.7529 (mt-10) cc_final: 0.7260 (mt-10) REVERT: b 202 TYR cc_start: 0.8408 (t80) cc_final: 0.7876 (t80) REVERT: c 233 MET cc_start: 0.5449 (mtp) cc_final: 0.5234 (mtp) REVERT: c 306 TYR cc_start: 0.6417 (p90) cc_final: 0.6216 (p90) REVERT: c 587 ARG cc_start: 0.7850 (ttt180) cc_final: 0.7382 (ptm160) REVERT: c 631 ILE cc_start: 0.9075 (mm) cc_final: 0.8757 (mm) REVERT: c 649 MET cc_start: 0.7021 (mtt) cc_final: 0.6746 (mtt) REVERT: d 239 ASP cc_start: 0.7589 (p0) cc_final: 0.7184 (p0) REVERT: d 471 LEU cc_start: 0.8796 (mp) cc_final: 0.8559 (mt) REVERT: e 187 ARG cc_start: 0.7510 (mmm-85) cc_final: 0.7235 (ttm-80) REVERT: e 281 SER cc_start: 0.9128 (p) cc_final: 0.8888 (p) REVERT: e 350 ARG cc_start: 0.7511 (ttm-80) cc_final: 0.7015 (mtp-110) REVERT: e 576 ASP cc_start: 0.6661 (OUTLIER) cc_final: 0.5516 (m-30) REVERT: e 755 ILE cc_start: 0.8924 (mm) cc_final: 0.8669 (mt) REVERT: e 829 ASP cc_start: 0.7452 (m-30) cc_final: 0.7084 (m-30) REVERT: f 130 LYS cc_start: 0.7992 (ptmt) cc_final: 0.7708 (ptmm) REVERT: f 338 THR cc_start: 0.8598 (p) cc_final: 0.7392 (m) REVERT: f 593 ARG cc_start: 0.6320 (mtt-85) cc_final: 0.5989 (mtp85) outliers start: 329 outliers final: 271 residues processed: 2223 average time/residue: 0.9257 time to fit residues: 3539.5887 Evaluate side-chains 2302 residues out of total 11774 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 289 poor density : 2013 time to evaluate : 8.981 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 186 LEU Chi-restraints excluded: chain 2 residue 241 SER Chi-restraints excluded: chain 2 residue 262 LYS Chi-restraints excluded: chain 2 residue 291 SER Chi-restraints excluded: chain 2 residue 292 GLU Chi-restraints excluded: chain 2 residue 302 THR Chi-restraints excluded: chain 2 residue 383 ARG Chi-restraints excluded: chain 2 residue 390 LEU Chi-restraints excluded: chain 2 residue 424 VAL Chi-restraints excluded: chain 2 residue 473 VAL Chi-restraints excluded: chain 2 residue 499 SER Chi-restraints excluded: chain 2 residue 564 VAL Chi-restraints excluded: chain 2 residue 567 THR Chi-restraints excluded: chain 2 residue 695 LEU Chi-restraints excluded: chain 2 residue 751 LYS Chi-restraints excluded: chain 2 residue 819 SER Chi-restraints excluded: chain 2 residue 860 SER Chi-restraints excluded: chain 3 residue 44 SER Chi-restraints excluded: chain 3 residue 99 SER Chi-restraints excluded: chain 3 residue 105 GLU Chi-restraints excluded: chain 3 residue 112 SER Chi-restraints excluded: chain 3 residue 135 SER Chi-restraints excluded: chain 3 residue 185 ILE Chi-restraints excluded: chain 3 residue 220 THR Chi-restraints excluded: chain 3 residue 242 THR Chi-restraints excluded: chain 3 residue 301 LEU Chi-restraints excluded: chain 3 residue 322 LEU Chi-restraints excluded: chain 3 residue 341 MET Chi-restraints excluded: chain 3 residue 346 ASP Chi-restraints excluded: chain 3 residue 424 ASN Chi-restraints excluded: chain 3 residue 448 THR Chi-restraints excluded: chain 3 residue 505 THR Chi-restraints excluded: chain 3 residue 553 ILE Chi-restraints excluded: chain 3 residue 582 VAL Chi-restraints excluded: chain 3 residue 697 ILE Chi-restraints excluded: chain 3 residue 698 THR Chi-restraints excluded: chain 3 residue 720 THR Chi-restraints excluded: chain 4 residue 198 LEU Chi-restraints excluded: chain 4 residue 292 ASP Chi-restraints excluded: chain 4 residue 401 GLU Chi-restraints excluded: chain 4 residue 427 CYS Chi-restraints excluded: chain 4 residue 444 ILE Chi-restraints excluded: chain 4 residue 468 LYS Chi-restraints excluded: chain 4 residue 663 THR Chi-restraints excluded: chain 4 residue 709 LEU Chi-restraints excluded: chain 4 residue 723 HIS Chi-restraints excluded: chain 4 residue 767 LYS Chi-restraints excluded: chain 4 residue 768 THR Chi-restraints excluded: chain 4 residue 802 ILE Chi-restraints excluded: chain 4 residue 813 LEU Chi-restraints excluded: chain 5 residue 85 ASP Chi-restraints excluded: chain 5 residue 153 SER Chi-restraints excluded: chain 5 residue 190 THR Chi-restraints excluded: chain 5 residue 193 THR Chi-restraints excluded: chain 5 residue 207 LEU Chi-restraints excluded: chain 5 residue 273 ASN Chi-restraints excluded: chain 5 residue 351 GLU Chi-restraints excluded: chain 5 residue 365 LYS Chi-restraints excluded: chain 5 residue 426 LEU Chi-restraints excluded: chain 5 residue 445 SER Chi-restraints excluded: chain 5 residue 453 VAL Chi-restraints excluded: chain 5 residue 493 ILE Chi-restraints excluded: chain 5 residue 510 THR Chi-restraints excluded: chain 5 residue 608 LEU Chi-restraints excluded: chain 5 residue 675 ARG Chi-restraints excluded: chain 5 residue 727 SER Chi-restraints excluded: chain 6 residue 135 VAL Chi-restraints excluded: chain 6 residue 150 THR Chi-restraints excluded: chain 6 residue 160 MET Chi-restraints excluded: chain 6 residue 276 ILE Chi-restraints excluded: chain 6 residue 293 THR Chi-restraints excluded: chain 6 residue 429 THR Chi-restraints excluded: chain 6 residue 438 THR Chi-restraints excluded: chain 6 residue 443 LEU Chi-restraints excluded: chain 6 residue 449 THR Chi-restraints excluded: chain 6 residue 452 ILE Chi-restraints excluded: chain 6 residue 503 VAL Chi-restraints excluded: chain 6 residue 532 SER Chi-restraints excluded: chain 6 residue 642 ASP Chi-restraints excluded: chain 6 residue 660 THR Chi-restraints excluded: chain 6 residue 676 THR Chi-restraints excluded: chain 6 residue 702 THR Chi-restraints excluded: chain 7 residue 5 LEU Chi-restraints excluded: chain 7 residue 220 ILE Chi-restraints excluded: chain 7 residue 225 LEU Chi-restraints excluded: chain 7 residue 300 MET Chi-restraints excluded: chain 7 residue 372 THR Chi-restraints excluded: chain 7 residue 427 ASP Chi-restraints excluded: chain 7 residue 473 ILE Chi-restraints excluded: chain 7 residue 483 THR Chi-restraints excluded: chain 7 residue 546 ILE Chi-restraints excluded: chain 7 residue 591 LEU Chi-restraints excluded: chain 7 residue 671 SER Chi-restraints excluded: chain C residue 12 ASP Chi-restraints excluded: chain C residue 24 ILE Chi-restraints excluded: chain C residue 164 THR Chi-restraints excluded: chain D residue 98 ILE Chi-restraints excluded: chain D residue 206 LEU Chi-restraints excluded: chain D residue 262 ASP Chi-restraints excluded: chain D residue 269 LEU Chi-restraints excluded: chain E residue 82 LEU Chi-restraints excluded: chain E residue 140 ILE Chi-restraints excluded: chain E residue 161 LYS Chi-restraints excluded: chain E residue 403 ASP Chi-restraints excluded: chain E residue 412 THR Chi-restraints excluded: chain E residue 536 LEU Chi-restraints excluded: chain E residue 576 THR Chi-restraints excluded: chain E residue 607 MET Chi-restraints excluded: chain E residue 636 ASP Chi-restraints excluded: chain E residue 638 SER Chi-restraints excluded: chain E residue 645 THR Chi-restraints excluded: chain E residue 646 LEU Chi-restraints excluded: chain F residue 31 LEU Chi-restraints excluded: chain F residue 86 GLU Chi-restraints excluded: chain F residue 224 LEU Chi-restraints excluded: chain F residue 269 THR Chi-restraints excluded: chain F residue 318 HIS Chi-restraints excluded: chain F residue 326 VAL Chi-restraints excluded: chain F residue 335 VAL Chi-restraints excluded: chain F residue 401 ILE Chi-restraints excluded: chain F residue 439 THR Chi-restraints excluded: chain F residue 468 LEU Chi-restraints excluded: chain F residue 500 SER Chi-restraints excluded: chain F residue 513 THR Chi-restraints excluded: chain F residue 544 ASP Chi-restraints excluded: chain F residue 547 SER Chi-restraints excluded: chain H residue 5 LEU Chi-restraints excluded: chain H residue 43 GLU Chi-restraints excluded: chain H residue 56 GLU Chi-restraints excluded: chain H residue 104 ASN Chi-restraints excluded: chain H residue 129 GLU Chi-restraints excluded: chain H residue 133 GLU Chi-restraints excluded: chain H residue 146 LEU Chi-restraints excluded: chain H residue 147 VAL Chi-restraints excluded: chain H residue 164 ASP Chi-restraints excluded: chain H residue 165 VAL Chi-restraints excluded: chain I residue 10 THR Chi-restraints excluded: chain I residue 64 VAL Chi-restraints excluded: chain I residue 133 ASP Chi-restraints excluded: chain I residue 158 LYS Chi-restraints excluded: chain I residue 168 LEU Chi-restraints excluded: chain I residue 177 GLU Chi-restraints excluded: chain J residue 24 ILE Chi-restraints excluded: chain J residue 106 SER Chi-restraints excluded: chain J residue 164 THR Chi-restraints excluded: chain K residue 262 ASP Chi-restraints excluded: chain L residue 59 VAL Chi-restraints excluded: chain L residue 82 LEU Chi-restraints excluded: chain L residue 161 LYS Chi-restraints excluded: chain L residue 234 GLU Chi-restraints excluded: chain L residue 310 VAL Chi-restraints excluded: chain L residue 419 ILE Chi-restraints excluded: chain L residue 524 ILE Chi-restraints excluded: chain L residue 537 ASP Chi-restraints excluded: chain L residue 604 ASN Chi-restraints excluded: chain L residue 607 MET Chi-restraints excluded: chain L residue 624 ASN Chi-restraints excluded: chain L residue 638 SER Chi-restraints excluded: chain M residue 29 TYR Chi-restraints excluded: chain M residue 31 LEU Chi-restraints excluded: chain M residue 86 GLU Chi-restraints excluded: chain M residue 167 ARG Chi-restraints excluded: chain M residue 188 MET Chi-restraints excluded: chain M residue 299 GLU Chi-restraints excluded: chain M residue 302 SER Chi-restraints excluded: chain M residue 401 ILE Chi-restraints excluded: chain M residue 424 LEU Chi-restraints excluded: chain M residue 439 THR Chi-restraints excluded: chain M residue 500 SER Chi-restraints excluded: chain M residue 513 THR Chi-restraints excluded: chain M residue 632 LEU Chi-restraints excluded: chain N residue 1324 VAL Chi-restraints excluded: chain N residue 1415 THR Chi-restraints excluded: chain N residue 1675 LEU Chi-restraints excluded: chain N residue 1736 VAL Chi-restraints excluded: chain N residue 1811 LEU Chi-restraints excluded: chain N residue 1821 GLN Chi-restraints excluded: chain N residue 1851 PHE Chi-restraints excluded: chain N residue 1863 ARG Chi-restraints excluded: chain N residue 1865 GLN Chi-restraints excluded: chain N residue 1882 SER Chi-restraints excluded: chain N residue 1885 MET Chi-restraints excluded: chain N residue 2093 GLU Chi-restraints excluded: chain N residue 2107 LEU Chi-restraints excluded: chain N residue 2117 ILE Chi-restraints excluded: chain N residue 2173 ASP Chi-restraints excluded: chain O residue 1 MET Chi-restraints excluded: chain O residue 16 THR Chi-restraints excluded: chain O residue 43 GLU Chi-restraints excluded: chain O residue 54 LEU Chi-restraints excluded: chain O residue 56 GLU Chi-restraints excluded: chain O residue 100 MET Chi-restraints excluded: chain O residue 146 LEU Chi-restraints excluded: chain O residue 147 VAL Chi-restraints excluded: chain O residue 164 ASP Chi-restraints excluded: chain P residue 32 THR Chi-restraints excluded: chain P residue 62 ASN Chi-restraints excluded: chain P residue 64 VAL Chi-restraints excluded: chain P residue 189 MET Chi-restraints excluded: chain Q residue 1382 SER Chi-restraints excluded: chain Q residue 1415 THR Chi-restraints excluded: chain Q residue 1736 VAL Chi-restraints excluded: chain Q residue 1811 LEU Chi-restraints excluded: chain Q residue 1821 GLN Chi-restraints excluded: chain Q residue 1848 VAL Chi-restraints excluded: chain Q residue 1851 PHE Chi-restraints excluded: chain Q residue 1865 GLN Chi-restraints excluded: chain Q residue 1941 LEU Chi-restraints excluded: chain Q residue 2036 VAL Chi-restraints excluded: chain Q residue 2173 ASP Chi-restraints excluded: chain Q residue 2194 ILE Chi-restraints excluded: chain a residue 189 VAL Chi-restraints excluded: chain a residue 202 ASN Chi-restraints excluded: chain a residue 241 SER Chi-restraints excluded: chain a residue 251 GLU Chi-restraints excluded: chain a residue 292 GLU Chi-restraints excluded: chain a residue 383 ARG Chi-restraints excluded: chain a residue 438 LEU Chi-restraints excluded: chain a residue 536 ASP Chi-restraints excluded: chain a residue 564 VAL Chi-restraints excluded: chain a residue 567 THR Chi-restraints excluded: chain a residue 644 CYS Chi-restraints excluded: chain a residue 819 SER Chi-restraints excluded: chain a residue 860 SER Chi-restraints excluded: chain b residue 44 SER Chi-restraints excluded: chain b residue 91 ILE Chi-restraints excluded: chain b residue 99 SER Chi-restraints excluded: chain b residue 112 SER Chi-restraints excluded: chain b residue 220 THR Chi-restraints excluded: chain b residue 240 LYS Chi-restraints excluded: chain b residue 322 LEU Chi-restraints excluded: chain b residue 346 ASP Chi-restraints excluded: chain b residue 424 ASN Chi-restraints excluded: chain b residue 437 SER Chi-restraints excluded: chain b residue 448 THR Chi-restraints excluded: chain b residue 486 ILE Chi-restraints excluded: chain b residue 488 GLU Chi-restraints excluded: chain b residue 494 THR Chi-restraints excluded: chain b residue 682 ASN Chi-restraints excluded: chain b residue 720 THR Chi-restraints excluded: chain b residue 723 LYS Chi-restraints excluded: chain c residue 198 LEU Chi-restraints excluded: chain c residue 280 MET Chi-restraints excluded: chain c residue 292 ASP Chi-restraints excluded: chain c residue 355 THR Chi-restraints excluded: chain c residue 360 ILE Chi-restraints excluded: chain c residue 427 CYS Chi-restraints excluded: chain c residue 468 LYS Chi-restraints excluded: chain c residue 663 THR Chi-restraints excluded: chain c residue 723 HIS Chi-restraints excluded: chain c residue 802 ILE Chi-restraints excluded: chain c residue 811 MET Chi-restraints excluded: chain c residue 822 VAL Chi-restraints excluded: chain d residue 85 ASP Chi-restraints excluded: chain d residue 163 SER Chi-restraints excluded: chain d residue 190 THR Chi-restraints excluded: chain d residue 193 THR Chi-restraints excluded: chain d residue 267 VAL Chi-restraints excluded: chain d residue 273 ASN Chi-restraints excluded: chain d residue 277 THR Chi-restraints excluded: chain d residue 391 LEU Chi-restraints excluded: chain d residue 402 ASP Chi-restraints excluded: chain d residue 567 SER Chi-restraints excluded: chain d residue 608 LEU Chi-restraints excluded: chain d residue 727 SER Chi-restraints excluded: chain e residue 117 GLN Chi-restraints excluded: chain e residue 150 THR Chi-restraints excluded: chain e residue 438 THR Chi-restraints excluded: chain e residue 532 SER Chi-restraints excluded: chain e residue 576 ASP Chi-restraints excluded: chain e residue 642 ASP Chi-restraints excluded: chain e residue 652 ILE Chi-restraints excluded: chain e residue 676 THR Chi-restraints excluded: chain e residue 701 MET Chi-restraints excluded: chain e residue 716 LEU Chi-restraints excluded: chain e residue 807 SER Chi-restraints excluded: chain e residue 831 LEU Chi-restraints excluded: chain f residue 22 THR Chi-restraints excluded: chain f residue 267 TYR Chi-restraints excluded: chain f residue 335 VAL Chi-restraints excluded: chain f residue 372 THR Chi-restraints excluded: chain f residue 473 ILE Chi-restraints excluded: chain f residue 533 ASP Chi-restraints excluded: chain f residue 546 ILE Chi-restraints excluded: chain f residue 631 THR Chi-restraints excluded: chain f residue 671 SER Chi-restraints excluded: chain f residue 683 GLN Chi-restraints excluded: chain f residue 690 LEU Chi-restraints excluded: chain f residue 712 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1310 random chunks: chunk 1148 optimal weight: 5.9990 chunk 1209 optimal weight: 10.0000 chunk 1103 optimal weight: 9.9990 chunk 1176 optimal weight: 50.0000 chunk 708 optimal weight: 0.5980 chunk 512 optimal weight: 0.9990 chunk 923 optimal weight: 0.0470 chunk 361 optimal weight: 20.0000 chunk 1063 optimal weight: 10.0000 chunk 1112 optimal weight: 9.9990 chunk 1172 optimal weight: 8.9990 overall best weight: 3.3284 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 2 641 GLN 4 757 HIS ** 4 808 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 253 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 139 GLN 6 173 GLN E 26 GLN ** F 435 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 39 ASN L 382 HIS L 476 ASN ** M 435 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 488 ASN ** O 202 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 81 GLN Q1662 ASN a 658 ASN b 731 ASN c 691 ASN ** d 273 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 685 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7689 moved from start: 0.2389 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.083 109512 Z= 0.239 Angle : 0.580 14.080 148617 Z= 0.300 Chirality : 0.042 0.317 17004 Planarity : 0.004 0.087 18640 Dihedral : 11.578 173.367 15844 Min Nonbonded Distance : 1.956 Molprobity Statistics. All-atom Clashscore : 7.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.18 % Favored : 95.82 % Rotamer: Outliers : 2.68 % Allowed : 16.49 % Favored : 80.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.23 (0.07), residues: 12956 helix: 1.57 (0.07), residues: 5354 sheet: -0.02 (0.12), residues: 2028 loop : -1.20 (0.08), residues: 5574 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP Q1688 HIS 0.011 0.001 HIS N1434 PHE 0.021 0.001 PHE M 557 TYR 0.027 0.001 TYR b 211 ARG 0.013 0.000 ARG L 523 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 25912 Ramachandran restraints generated. 12956 Oldfield, 0 Emsley, 12956 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 25912 Ramachandran restraints generated. 12956 Oldfield, 0 Emsley, 12956 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2349 residues out of total 11774 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 316 poor density : 2033 time to evaluate : 9.074 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: 2 383 ARG cc_start: 0.7890 (OUTLIER) cc_final: 0.6990 (ptp-170) REVERT: 2 390 LEU cc_start: 0.8166 (OUTLIER) cc_final: 0.7921 (mp) REVERT: 2 441 LYS cc_start: 0.7620 (mttt) cc_final: 0.7154 (mttt) REVERT: 2 695 LEU cc_start: 0.8459 (OUTLIER) cc_final: 0.8214 (tt) REVERT: 2 792 ASP cc_start: 0.7159 (m-30) cc_final: 0.6718 (m-30) REVERT: 3 105 GLU cc_start: 0.7306 (OUTLIER) cc_final: 0.6983 (mp0) REVERT: 3 424 ASN cc_start: 0.7614 (OUTLIER) cc_final: 0.7356 (t0) REVERT: 3 499 LYS cc_start: 0.8029 (tttt) cc_final: 0.7588 (tppt) REVERT: 4 233 MET cc_start: 0.5615 (mtp) cc_final: 0.5347 (mtp) REVERT: 4 576 GLN cc_start: 0.7728 (mp10) cc_final: 0.7388 (mp10) REVERT: 5 65 MET cc_start: 0.8727 (mtt) cc_final: 0.8310 (mtt) REVERT: 5 239 ASP cc_start: 0.7339 (p0) cc_final: 0.6855 (p0) REVERT: 5 431 LYS cc_start: 0.8208 (mttm) cc_final: 0.7821 (mtpp) REVERT: 6 194 PRO cc_start: 0.7781 (Cg_endo) cc_final: 0.7558 (Cg_exo) REVERT: 6 283 LYS cc_start: 0.8146 (mmtp) cc_final: 0.7732 (mtmm) REVERT: 6 323 GLN cc_start: 0.7939 (OUTLIER) cc_final: 0.7430 (mt0) REVERT: 6 520 VAL cc_start: 0.8404 (t) cc_final: 0.8162 (p) REVERT: 6 527 ASP cc_start: 0.7356 (t0) cc_final: 0.6881 (t0) REVERT: 6 755 ILE cc_start: 0.8812 (mm) cc_final: 0.8433 (mt) REVERT: 6 767 LYS cc_start: 0.7350 (mmtp) cc_final: 0.7007 (mmtp) REVERT: 6 783 ASP cc_start: 0.7669 (m-30) cc_final: 0.7407 (t0) REVERT: 7 107 GLN cc_start: 0.6970 (mt0) cc_final: 0.6373 (tt0) REVERT: 7 121 ILE cc_start: 0.8581 (mm) cc_final: 0.8343 (mt) REVERT: 7 220 ILE cc_start: 0.7888 (OUTLIER) cc_final: 0.7665 (tt) REVERT: 7 427 ASP cc_start: 0.7820 (OUTLIER) cc_final: 0.6549 (m-30) REVERT: 7 504 ASP cc_start: 0.6574 (t0) cc_final: 0.5731 (t0) REVERT: 7 593 ARG cc_start: 0.6122 (mtt-85) cc_final: 0.5615 (mtt-85) REVERT: C 15 GLU cc_start: 0.7347 (mp0) cc_final: 0.7046 (mp0) REVERT: D 98 ILE cc_start: 0.8388 (OUTLIER) cc_final: 0.8007 (mp) REVERT: D 100 ASN cc_start: 0.7056 (t0) cc_final: 0.6830 (t0) REVERT: D 103 MET cc_start: 0.5677 (mmm) cc_final: 0.5330 (mmm) REVERT: D 289 ASP cc_start: 0.7321 (t0) cc_final: 0.6992 (t0) REVERT: E 82 LEU cc_start: 0.8694 (OUTLIER) cc_final: 0.8178 (tt) REVERT: E 161 LYS cc_start: 0.7660 (OUTLIER) cc_final: 0.7347 (ttpp) REVERT: E 239 GLU cc_start: 0.7312 (tm-30) cc_final: 0.7025 (tm-30) REVERT: F 22 TYR cc_start: 0.8038 (t80) cc_final: 0.7648 (t80) REVERT: F 23 ARG cc_start: 0.6540 (mtm180) cc_final: 0.6337 (mtm180) REVERT: F 318 HIS cc_start: 0.7380 (OUTLIER) cc_final: 0.6881 (p-80) REVERT: F 386 ARG cc_start: 0.6876 (ttt180) cc_final: 0.6506 (ttt180) REVERT: F 468 LEU cc_start: 0.7668 (OUTLIER) cc_final: 0.7459 (mp) REVERT: F 552 ARG cc_start: 0.7477 (ttp-110) cc_final: 0.7242 (ttm170) REVERT: F 604 LYS cc_start: 0.8200 (tptm) cc_final: 0.7909 (tptm) REVERT: F 674 GLU cc_start: 0.5970 (tt0) cc_final: 0.5527 (tm-30) REVERT: H 8 LYS cc_start: 0.7690 (mttm) cc_final: 0.7098 (mmmt) REVERT: H 71 GLN cc_start: 0.6619 (mt0) cc_final: 0.6141 (mp10) REVERT: H 129 GLU cc_start: 0.5936 (OUTLIER) cc_final: 0.4358 (tt0) REVERT: H 133 GLU cc_start: 0.7354 (OUTLIER) cc_final: 0.6945 (mp0) REVERT: I 81 GLN cc_start: 0.7973 (tp-100) cc_final: 0.7252 (tt0) REVERT: J 172 MET cc_start: 0.7918 (ttp) cc_final: 0.7554 (tmm) REVERT: K 289 ASP cc_start: 0.7654 (t0) cc_final: 0.7381 (t0) REVERT: L 524 ILE cc_start: 0.8791 (OUTLIER) cc_final: 0.8591 (mp) REVERT: M 17 LEU cc_start: 0.8479 (tp) cc_final: 0.8245 (tp) REVERT: M 20 LEU cc_start: 0.8388 (mm) cc_final: 0.8169 (mm) REVERT: M 190 PHE cc_start: 0.8510 (m-80) cc_final: 0.8208 (m-10) REVERT: M 320 TYR cc_start: 0.8845 (m-10) cc_final: 0.8572 (m-10) REVERT: M 333 TYR cc_start: 0.7995 (m-80) cc_final: 0.7237 (m-80) REVERT: M 604 LYS cc_start: 0.8387 (tptp) cc_final: 0.8132 (tptp) REVERT: M 674 GLU cc_start: 0.6041 (tt0) cc_final: 0.5813 (tt0) REVERT: N 1439 MET cc_start: 0.6434 (ttm) cc_final: 0.6128 (ttp) REVERT: N 1713 MET cc_start: 0.8226 (mtp) cc_final: 0.7815 (mtp) REVERT: N 1854 LEU cc_start: 0.8025 (mm) cc_final: 0.7729 (mp) REVERT: N 1862 ASP cc_start: 0.7558 (t70) cc_final: 0.7068 (t70) REVERT: N 1896 SER cc_start: 0.7998 (p) cc_final: 0.7400 (m) REVERT: N 1970 SER cc_start: 0.8825 (m) cc_final: 0.8204 (p) REVERT: N 2031 TYR cc_start: 0.8357 (m-80) cc_final: 0.8092 (m-80) REVERT: O 8 LYS cc_start: 0.8325 (mtpt) cc_final: 0.7772 (mtpt) REVERT: P 63 MET cc_start: 0.7160 (mtt) cc_final: 0.6956 (mtp) REVERT: Q 1360 LYS cc_start: 0.8119 (tppp) cc_final: 0.7813 (tppt) REVERT: Q 1851 PHE cc_start: 0.8269 (OUTLIER) cc_final: 0.7337 (m-80) REVERT: Q 1872 LYS cc_start: 0.7869 (mmtt) cc_final: 0.7496 (mmmm) REVERT: Q 1903 LYS cc_start: 0.7535 (mttt) cc_final: 0.6965 (mttp) REVERT: Q 2032 GLU cc_start: 0.6556 (tt0) cc_final: 0.6118 (mt-10) REVERT: Q 2093 GLU cc_start: 0.7084 (mt-10) cc_final: 0.6552 (tt0) REVERT: a 383 ARG cc_start: 0.8183 (OUTLIER) cc_final: 0.7226 (ptp-170) REVERT: a 747 ARG cc_start: 0.7350 (mtp85) cc_final: 0.6980 (mtp180) REVERT: a 751 LYS cc_start: 0.7845 (mttt) cc_final: 0.7367 (mtmm) REVERT: a 792 ASP cc_start: 0.7857 (m-30) cc_final: 0.7599 (m-30) REVERT: a 826 SER cc_start: 0.8811 (t) cc_final: 0.8506 (m) REVERT: b 48 TYR cc_start: 0.7952 (t80) cc_final: 0.7675 (t80) REVERT: b 105 GLU cc_start: 0.7625 (mt-10) cc_final: 0.7374 (mt-10) REVERT: b 202 TYR cc_start: 0.8402 (t80) cc_final: 0.7865 (t80) REVERT: c 233 MET cc_start: 0.5470 (mtp) cc_final: 0.5255 (mtp) REVERT: c 272 MET cc_start: 0.8143 (mmp) cc_final: 0.7928 (mmm) REVERT: c 467 LYS cc_start: 0.7684 (mtmt) cc_final: 0.7295 (mtmm) REVERT: c 587 ARG cc_start: 0.7831 (ttt180) cc_final: 0.7368 (ptm160) REVERT: c 631 ILE cc_start: 0.9104 (mm) cc_final: 0.8781 (mm) REVERT: c 649 MET cc_start: 0.7052 (mtt) cc_final: 0.6774 (mtt) REVERT: c 749 MET cc_start: 0.7258 (mmp) cc_final: 0.6930 (mmp) REVERT: d 239 ASP cc_start: 0.7573 (p0) cc_final: 0.7183 (p0) REVERT: d 471 LEU cc_start: 0.8811 (mp) cc_final: 0.8577 (mt) REVERT: e 187 ARG cc_start: 0.7498 (mmm-85) cc_final: 0.7226 (ttm-80) REVERT: e 281 SER cc_start: 0.9133 (p) cc_final: 0.8900 (p) REVERT: e 350 ARG cc_start: 0.7500 (ttm-80) cc_final: 0.7007 (mtp-110) REVERT: e 576 ASP cc_start: 0.6640 (OUTLIER) cc_final: 0.5496 (m-30) REVERT: e 755 ILE cc_start: 0.8920 (mm) cc_final: 0.8667 (mt) REVERT: e 829 ASP cc_start: 0.7444 (m-30) cc_final: 0.7068 (m-30) REVERT: f 130 LYS cc_start: 0.7991 (ptmt) cc_final: 0.7707 (ptmm) REVERT: f 338 THR cc_start: 0.8595 (p) cc_final: 0.7394 (m) REVERT: f 593 ARG cc_start: 0.6289 (mtt-85) cc_final: 0.5953 (mtp85) outliers start: 316 outliers final: 279 residues processed: 2183 average time/residue: 0.9712 time to fit residues: 3663.4040 Evaluate side-chains 2304 residues out of total 11774 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 298 poor density : 2006 time to evaluate : 9.076 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 186 LEU Chi-restraints excluded: chain 2 residue 226 VAL Chi-restraints excluded: chain 2 residue 241 SER Chi-restraints excluded: chain 2 residue 262 LYS Chi-restraints excluded: chain 2 residue 291 SER Chi-restraints excluded: chain 2 residue 292 GLU Chi-restraints excluded: chain 2 residue 302 THR Chi-restraints excluded: chain 2 residue 383 ARG Chi-restraints excluded: chain 2 residue 390 LEU Chi-restraints excluded: chain 2 residue 424 VAL Chi-restraints excluded: chain 2 residue 473 VAL Chi-restraints excluded: chain 2 residue 499 SER Chi-restraints excluded: chain 2 residue 567 THR Chi-restraints excluded: chain 2 residue 695 LEU Chi-restraints excluded: chain 2 residue 751 LYS Chi-restraints excluded: chain 2 residue 819 SER Chi-restraints excluded: chain 2 residue 860 SER Chi-restraints excluded: chain 3 residue 44 SER Chi-restraints excluded: chain 3 residue 99 SER Chi-restraints excluded: chain 3 residue 105 GLU Chi-restraints excluded: chain 3 residue 112 SER Chi-restraints excluded: chain 3 residue 135 SER Chi-restraints excluded: chain 3 residue 185 ILE Chi-restraints excluded: chain 3 residue 220 THR Chi-restraints excluded: chain 3 residue 242 THR Chi-restraints excluded: chain 3 residue 301 LEU Chi-restraints excluded: chain 3 residue 322 LEU Chi-restraints excluded: chain 3 residue 341 MET Chi-restraints excluded: chain 3 residue 346 ASP Chi-restraints excluded: chain 3 residue 424 ASN Chi-restraints excluded: chain 3 residue 448 THR Chi-restraints excluded: chain 3 residue 486 ILE Chi-restraints excluded: chain 3 residue 553 ILE Chi-restraints excluded: chain 3 residue 582 VAL Chi-restraints excluded: chain 3 residue 697 ILE Chi-restraints excluded: chain 3 residue 698 THR Chi-restraints excluded: chain 3 residue 720 THR Chi-restraints excluded: chain 4 residue 198 LEU Chi-restraints excluded: chain 4 residue 292 ASP Chi-restraints excluded: chain 4 residue 401 GLU Chi-restraints excluded: chain 4 residue 427 CYS Chi-restraints excluded: chain 4 residue 444 ILE Chi-restraints excluded: chain 4 residue 468 LYS Chi-restraints excluded: chain 4 residue 663 THR Chi-restraints excluded: chain 4 residue 709 LEU Chi-restraints excluded: chain 4 residue 723 HIS Chi-restraints excluded: chain 4 residue 767 LYS Chi-restraints excluded: chain 4 residue 768 THR Chi-restraints excluded: chain 4 residue 802 ILE Chi-restraints excluded: chain 4 residue 813 LEU Chi-restraints excluded: chain 5 residue 85 ASP Chi-restraints excluded: chain 5 residue 153 SER Chi-restraints excluded: chain 5 residue 190 THR Chi-restraints excluded: chain 5 residue 193 THR Chi-restraints excluded: chain 5 residue 207 LEU Chi-restraints excluded: chain 5 residue 273 ASN Chi-restraints excluded: chain 5 residue 351 GLU Chi-restraints excluded: chain 5 residue 365 LYS Chi-restraints excluded: chain 5 residue 417 ASP Chi-restraints excluded: chain 5 residue 426 LEU Chi-restraints excluded: chain 5 residue 445 SER Chi-restraints excluded: chain 5 residue 453 VAL Chi-restraints excluded: chain 5 residue 493 ILE Chi-restraints excluded: chain 5 residue 608 LEU Chi-restraints excluded: chain 5 residue 636 ASN Chi-restraints excluded: chain 5 residue 675 ARG Chi-restraints excluded: chain 5 residue 727 SER Chi-restraints excluded: chain 6 residue 135 VAL Chi-restraints excluded: chain 6 residue 150 THR Chi-restraints excluded: chain 6 residue 160 MET Chi-restraints excluded: chain 6 residue 276 ILE Chi-restraints excluded: chain 6 residue 293 THR Chi-restraints excluded: chain 6 residue 323 GLN Chi-restraints excluded: chain 6 residue 333 CYS Chi-restraints excluded: chain 6 residue 429 THR Chi-restraints excluded: chain 6 residue 438 THR Chi-restraints excluded: chain 6 residue 449 THR Chi-restraints excluded: chain 6 residue 452 ILE Chi-restraints excluded: chain 6 residue 503 VAL Chi-restraints excluded: chain 6 residue 532 SER Chi-restraints excluded: chain 6 residue 642 ASP Chi-restraints excluded: chain 6 residue 660 THR Chi-restraints excluded: chain 6 residue 676 THR Chi-restraints excluded: chain 6 residue 702 THR Chi-restraints excluded: chain 7 residue 22 THR Chi-restraints excluded: chain 7 residue 220 ILE Chi-restraints excluded: chain 7 residue 225 LEU Chi-restraints excluded: chain 7 residue 300 MET Chi-restraints excluded: chain 7 residue 372 THR Chi-restraints excluded: chain 7 residue 427 ASP Chi-restraints excluded: chain 7 residue 473 ILE Chi-restraints excluded: chain 7 residue 483 THR Chi-restraints excluded: chain 7 residue 546 ILE Chi-restraints excluded: chain 7 residue 591 LEU Chi-restraints excluded: chain 7 residue 671 SER Chi-restraints excluded: chain C residue 12 ASP Chi-restraints excluded: chain C residue 24 ILE Chi-restraints excluded: chain C residue 164 THR Chi-restraints excluded: chain D residue 98 ILE Chi-restraints excluded: chain D residue 206 LEU Chi-restraints excluded: chain D residue 262 ASP Chi-restraints excluded: chain D residue 269 LEU Chi-restraints excluded: chain E residue 82 LEU Chi-restraints excluded: chain E residue 140 ILE Chi-restraints excluded: chain E residue 161 LYS Chi-restraints excluded: chain E residue 403 ASP Chi-restraints excluded: chain E residue 412 THR Chi-restraints excluded: chain E residue 419 ILE Chi-restraints excluded: chain E residue 536 LEU Chi-restraints excluded: chain E residue 576 THR Chi-restraints excluded: chain E residue 607 MET Chi-restraints excluded: chain E residue 636 ASP Chi-restraints excluded: chain E residue 638 SER Chi-restraints excluded: chain E residue 645 THR Chi-restraints excluded: chain E residue 646 LEU Chi-restraints excluded: chain F residue 31 LEU Chi-restraints excluded: chain F residue 86 GLU Chi-restraints excluded: chain F residue 224 LEU Chi-restraints excluded: chain F residue 269 THR Chi-restraints excluded: chain F residue 318 HIS Chi-restraints excluded: chain F residue 326 VAL Chi-restraints excluded: chain F residue 335 VAL Chi-restraints excluded: chain F residue 401 ILE Chi-restraints excluded: chain F residue 439 THR Chi-restraints excluded: chain F residue 468 LEU Chi-restraints excluded: chain F residue 500 SER Chi-restraints excluded: chain F residue 513 THR Chi-restraints excluded: chain F residue 544 ASP Chi-restraints excluded: chain F residue 547 SER Chi-restraints excluded: chain H residue 5 LEU Chi-restraints excluded: chain H residue 43 GLU Chi-restraints excluded: chain H residue 56 GLU Chi-restraints excluded: chain H residue 104 ASN Chi-restraints excluded: chain H residue 129 GLU Chi-restraints excluded: chain H residue 133 GLU Chi-restraints excluded: chain H residue 146 LEU Chi-restraints excluded: chain H residue 147 VAL Chi-restraints excluded: chain H residue 164 ASP Chi-restraints excluded: chain H residue 165 VAL Chi-restraints excluded: chain I residue 10 THR Chi-restraints excluded: chain I residue 64 VAL Chi-restraints excluded: chain I residue 133 ASP Chi-restraints excluded: chain I residue 158 LYS Chi-restraints excluded: chain I residue 168 LEU Chi-restraints excluded: chain I residue 177 GLU Chi-restraints excluded: chain J residue 24 ILE Chi-restraints excluded: chain J residue 106 SER Chi-restraints excluded: chain J residue 164 THR Chi-restraints excluded: chain K residue 262 ASP Chi-restraints excluded: chain L residue 59 VAL Chi-restraints excluded: chain L residue 82 LEU Chi-restraints excluded: chain L residue 161 LYS Chi-restraints excluded: chain L residue 234 GLU Chi-restraints excluded: chain L residue 310 VAL Chi-restraints excluded: chain L residue 419 ILE Chi-restraints excluded: chain L residue 524 ILE Chi-restraints excluded: chain L residue 537 ASP Chi-restraints excluded: chain L residue 604 ASN Chi-restraints excluded: chain L residue 607 MET Chi-restraints excluded: chain L residue 624 ASN Chi-restraints excluded: chain L residue 638 SER Chi-restraints excluded: chain M residue 29 TYR Chi-restraints excluded: chain M residue 31 LEU Chi-restraints excluded: chain M residue 86 GLU Chi-restraints excluded: chain M residue 167 ARG Chi-restraints excluded: chain M residue 188 MET Chi-restraints excluded: chain M residue 299 GLU Chi-restraints excluded: chain M residue 302 SER Chi-restraints excluded: chain M residue 401 ILE Chi-restraints excluded: chain M residue 424 LEU Chi-restraints excluded: chain M residue 439 THR Chi-restraints excluded: chain M residue 500 SER Chi-restraints excluded: chain M residue 513 THR Chi-restraints excluded: chain M residue 632 LEU Chi-restraints excluded: chain N residue 1324 VAL Chi-restraints excluded: chain N residue 1382 SER Chi-restraints excluded: chain N residue 1415 THR Chi-restraints excluded: chain N residue 1675 LEU Chi-restraints excluded: chain N residue 1685 ILE Chi-restraints excluded: chain N residue 1736 VAL Chi-restraints excluded: chain N residue 1811 LEU Chi-restraints excluded: chain N residue 1821 GLN Chi-restraints excluded: chain N residue 1851 PHE Chi-restraints excluded: chain N residue 1863 ARG Chi-restraints excluded: chain N residue 1865 GLN Chi-restraints excluded: chain N residue 1882 SER Chi-restraints excluded: chain N residue 1885 MET Chi-restraints excluded: chain N residue 2093 GLU Chi-restraints excluded: chain N residue 2107 LEU Chi-restraints excluded: chain N residue 2117 ILE Chi-restraints excluded: chain N residue 2173 ASP Chi-restraints excluded: chain O residue 16 THR Chi-restraints excluded: chain O residue 43 GLU Chi-restraints excluded: chain O residue 54 LEU Chi-restraints excluded: chain O residue 56 GLU Chi-restraints excluded: chain O residue 100 MET Chi-restraints excluded: chain O residue 146 LEU Chi-restraints excluded: chain O residue 147 VAL Chi-restraints excluded: chain O residue 164 ASP Chi-restraints excluded: chain P residue 32 THR Chi-restraints excluded: chain P residue 64 VAL Chi-restraints excluded: chain P residue 189 MET Chi-restraints excluded: chain Q residue 1382 SER Chi-restraints excluded: chain Q residue 1415 THR Chi-restraints excluded: chain Q residue 1685 ILE Chi-restraints excluded: chain Q residue 1736 VAL Chi-restraints excluded: chain Q residue 1811 LEU Chi-restraints excluded: chain Q residue 1821 GLN Chi-restraints excluded: chain Q residue 1848 VAL Chi-restraints excluded: chain Q residue 1851 PHE Chi-restraints excluded: chain Q residue 1865 GLN Chi-restraints excluded: chain Q residue 1941 LEU Chi-restraints excluded: chain Q residue 2036 VAL Chi-restraints excluded: chain Q residue 2144 GLU Chi-restraints excluded: chain Q residue 2173 ASP Chi-restraints excluded: chain Q residue 2194 ILE Chi-restraints excluded: chain a residue 189 VAL Chi-restraints excluded: chain a residue 202 ASN Chi-restraints excluded: chain a residue 226 VAL Chi-restraints excluded: chain a residue 241 SER Chi-restraints excluded: chain a residue 251 GLU Chi-restraints excluded: chain a residue 292 GLU Chi-restraints excluded: chain a residue 383 ARG Chi-restraints excluded: chain a residue 438 LEU Chi-restraints excluded: chain a residue 536 ASP Chi-restraints excluded: chain a residue 564 VAL Chi-restraints excluded: chain a residue 567 THR Chi-restraints excluded: chain a residue 644 CYS Chi-restraints excluded: chain a residue 819 SER Chi-restraints excluded: chain a residue 860 SER Chi-restraints excluded: chain b residue 44 SER Chi-restraints excluded: chain b residue 91 ILE Chi-restraints excluded: chain b residue 99 SER Chi-restraints excluded: chain b residue 112 SER Chi-restraints excluded: chain b residue 185 ILE Chi-restraints excluded: chain b residue 213 ASP Chi-restraints excluded: chain b residue 220 THR Chi-restraints excluded: chain b residue 240 LYS Chi-restraints excluded: chain b residue 322 LEU Chi-restraints excluded: chain b residue 346 ASP Chi-restraints excluded: chain b residue 424 ASN Chi-restraints excluded: chain b residue 437 SER Chi-restraints excluded: chain b residue 448 THR Chi-restraints excluded: chain b residue 486 ILE Chi-restraints excluded: chain b residue 488 GLU Chi-restraints excluded: chain b residue 494 THR Chi-restraints excluded: chain b residue 682 ASN Chi-restraints excluded: chain b residue 720 THR Chi-restraints excluded: chain c residue 198 LEU Chi-restraints excluded: chain c residue 280 MET Chi-restraints excluded: chain c residue 292 ASP Chi-restraints excluded: chain c residue 355 THR Chi-restraints excluded: chain c residue 360 ILE Chi-restraints excluded: chain c residue 427 CYS Chi-restraints excluded: chain c residue 468 LYS Chi-restraints excluded: chain c residue 663 THR Chi-restraints excluded: chain c residue 723 HIS Chi-restraints excluded: chain c residue 802 ILE Chi-restraints excluded: chain c residue 811 MET Chi-restraints excluded: chain c residue 822 VAL Chi-restraints excluded: chain d residue 85 ASP Chi-restraints excluded: chain d residue 163 SER Chi-restraints excluded: chain d residue 190 THR Chi-restraints excluded: chain d residue 193 THR Chi-restraints excluded: chain d residue 267 VAL Chi-restraints excluded: chain d residue 273 ASN Chi-restraints excluded: chain d residue 277 THR Chi-restraints excluded: chain d residue 351 GLU Chi-restraints excluded: chain d residue 391 LEU Chi-restraints excluded: chain d residue 402 ASP Chi-restraints excluded: chain d residue 567 SER Chi-restraints excluded: chain d residue 608 LEU Chi-restraints excluded: chain d residue 727 SER Chi-restraints excluded: chain e residue 117 GLN Chi-restraints excluded: chain e residue 150 THR Chi-restraints excluded: chain e residue 438 THR Chi-restraints excluded: chain e residue 532 SER Chi-restraints excluded: chain e residue 576 ASP Chi-restraints excluded: chain e residue 642 ASP Chi-restraints excluded: chain e residue 652 ILE Chi-restraints excluded: chain e residue 676 THR Chi-restraints excluded: chain e residue 701 MET Chi-restraints excluded: chain e residue 716 LEU Chi-restraints excluded: chain e residue 831 LEU Chi-restraints excluded: chain f residue 22 THR Chi-restraints excluded: chain f residue 267 TYR Chi-restraints excluded: chain f residue 335 VAL Chi-restraints excluded: chain f residue 372 THR Chi-restraints excluded: chain f residue 473 ILE Chi-restraints excluded: chain f residue 533 ASP Chi-restraints excluded: chain f residue 544 GLN Chi-restraints excluded: chain f residue 546 ILE Chi-restraints excluded: chain f residue 631 THR Chi-restraints excluded: chain f residue 667 LEU Chi-restraints excluded: chain f residue 671 SER Chi-restraints excluded: chain f residue 683 GLN Chi-restraints excluded: chain f residue 690 LEU Chi-restraints excluded: chain f residue 712 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1310 random chunks: chunk 772 optimal weight: 9.9990 chunk 1244 optimal weight: 8.9990 chunk 759 optimal weight: 30.0000 chunk 590 optimal weight: 7.9990 chunk 864 optimal weight: 40.0000 chunk 1305 optimal weight: 50.0000 chunk 1201 optimal weight: 8.9990 chunk 1039 optimal weight: 2.9990 chunk 107 optimal weight: 0.9990 chunk 802 optimal weight: 6.9990 chunk 637 optimal weight: 9.9990 overall best weight: 5.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 2 641 GLN 4 691 ASN 4 757 HIS ** 4 808 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 253 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 139 GLN 6 173 GLN 7 90 ASN ** F 435 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 39 ASN L 382 HIS L 476 ASN ** M 435 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 488 ASN N1654 GLN N1785 ASN N1835 HIS Q1662 ASN a 658 ASN b 731 ASN c 691 ASN ** d 273 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 543 GLN ** d 685 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** e 264 GLN e 269 ASN f 209 GLN f 622 HIS Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7738 moved from start: 0.2560 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.086 109512 Z= 0.365 Angle : 0.658 14.791 148617 Z= 0.340 Chirality : 0.045 0.322 17004 Planarity : 0.005 0.087 18640 Dihedral : 11.728 173.294 15844 Min Nonbonded Distance : 1.923 Molprobity Statistics. All-atom Clashscore : 7.76 Ramachandran Plot: Outliers : 0.01 % Allowed : 4.84 % Favored : 95.15 % Rotamer: Outliers : 2.68 % Allowed : 16.78 % Favored : 80.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.05 (0.07), residues: 12956 helix: 1.31 (0.07), residues: 5366 sheet: -0.15 (0.11), residues: 2056 loop : -1.33 (0.08), residues: 5534 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP Q1688 HIS 0.010 0.001 HIS Q1434 PHE 0.027 0.002 PHE a 271 TYR 0.029 0.002 TYR b 211 ARG 0.012 0.001 ARG 7 451 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 25912 Ramachandran restraints generated. 12956 Oldfield, 0 Emsley, 12956 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 25912 Ramachandran restraints generated. 12956 Oldfield, 0 Emsley, 12956 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2358 residues out of total 11774 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 315 poor density : 2043 time to evaluate : 9.213 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: 2 383 ARG cc_start: 0.7938 (OUTLIER) cc_final: 0.7009 (ptp-170) REVERT: 2 441 LYS cc_start: 0.7604 (mttt) cc_final: 0.7136 (mttt) REVERT: 2 695 LEU cc_start: 0.8534 (OUTLIER) cc_final: 0.8310 (tt) REVERT: 2 792 ASP cc_start: 0.7243 (m-30) cc_final: 0.6712 (m-30) REVERT: 3 105 GLU cc_start: 0.7378 (OUTLIER) cc_final: 0.7006 (mp0) REVERT: 3 222 THR cc_start: 0.8788 (m) cc_final: 0.8576 (p) REVERT: 3 499 LYS cc_start: 0.8059 (tttt) cc_final: 0.7633 (tppt) REVERT: 4 233 MET cc_start: 0.5571 (mtp) cc_final: 0.5320 (mtp) REVERT: 4 576 GLN cc_start: 0.7687 (mp10) cc_final: 0.7338 (mp10) REVERT: 4 682 TYR cc_start: 0.7260 (t80) cc_final: 0.6959 (t80) REVERT: 5 65 MET cc_start: 0.8802 (mtt) cc_final: 0.8385 (mtt) REVERT: 5 239 ASP cc_start: 0.7460 (p0) cc_final: 0.6988 (p0) REVERT: 5 431 LYS cc_start: 0.8252 (mttm) cc_final: 0.7858 (mtpp) REVERT: 5 512 VAL cc_start: 0.8720 (t) cc_final: 0.8498 (p) REVERT: 6 194 PRO cc_start: 0.7806 (Cg_endo) cc_final: 0.7593 (Cg_exo) REVERT: 6 283 LYS cc_start: 0.8209 (mmtp) cc_final: 0.7781 (mtmm) REVERT: 6 323 GLN cc_start: 0.8017 (OUTLIER) cc_final: 0.7482 (mt0) REVERT: 6 520 VAL cc_start: 0.8397 (t) cc_final: 0.8157 (p) REVERT: 6 527 ASP cc_start: 0.7487 (t0) cc_final: 0.7024 (t0) REVERT: 6 755 ILE cc_start: 0.8855 (mm) cc_final: 0.8473 (mt) REVERT: 6 783 ASP cc_start: 0.7727 (m-30) cc_final: 0.7485 (t0) REVERT: 7 107 GLN cc_start: 0.7077 (mt0) cc_final: 0.6493 (tt0) REVERT: 7 121 ILE cc_start: 0.8582 (mm) cc_final: 0.8336 (mt) REVERT: 7 130 LYS cc_start: 0.7320 (ptmm) cc_final: 0.7111 (ptmm) REVERT: 7 220 ILE cc_start: 0.7928 (OUTLIER) cc_final: 0.7691 (tt) REVERT: 7 427 ASP cc_start: 0.8063 (OUTLIER) cc_final: 0.7264 (m-30) REVERT: 7 504 ASP cc_start: 0.6648 (t0) cc_final: 0.5816 (t0) REVERT: 7 593 ARG cc_start: 0.5955 (mtt-85) cc_final: 0.5408 (mtt-85) REVERT: 7 652 MET cc_start: 0.6895 (mpp) cc_final: 0.6648 (mmt) REVERT: D 98 ILE cc_start: 0.8502 (OUTLIER) cc_final: 0.8107 (mp) REVERT: D 103 MET cc_start: 0.5935 (mmm) cc_final: 0.5505 (mmm) REVERT: D 289 ASP cc_start: 0.7361 (t0) cc_final: 0.7037 (t0) REVERT: E 82 LEU cc_start: 0.8726 (OUTLIER) cc_final: 0.8236 (tt) REVERT: E 161 LYS cc_start: 0.7694 (OUTLIER) cc_final: 0.7375 (ttpp) REVERT: E 239 GLU cc_start: 0.7402 (tm-30) cc_final: 0.7139 (tm-30) REVERT: F 23 ARG cc_start: 0.6583 (mtm180) cc_final: 0.6195 (mtm-85) REVERT: F 281 ASN cc_start: 0.7882 (m-40) cc_final: 0.7623 (m-40) REVERT: F 318 HIS cc_start: 0.7468 (OUTLIER) cc_final: 0.7185 (p-80) REVERT: F 386 ARG cc_start: 0.7022 (ttt180) cc_final: 0.6616 (ttt180) REVERT: F 440 SER cc_start: 0.8501 (t) cc_final: 0.8038 (p) REVERT: F 468 LEU cc_start: 0.7753 (OUTLIER) cc_final: 0.7509 (mp) REVERT: F 552 ARG cc_start: 0.7593 (ttp-110) cc_final: 0.7361 (ttm170) REVERT: F 674 GLU cc_start: 0.5968 (tt0) cc_final: 0.5519 (tm-30) REVERT: H 8 LYS cc_start: 0.7720 (mttm) cc_final: 0.7121 (mmmt) REVERT: H 18 GLN cc_start: 0.7052 (mm110) cc_final: 0.6800 (mt0) REVERT: H 71 GLN cc_start: 0.6881 (mt0) cc_final: 0.6331 (mp10) REVERT: H 129 GLU cc_start: 0.6064 (OUTLIER) cc_final: 0.4483 (tt0) REVERT: H 133 GLU cc_start: 0.7445 (OUTLIER) cc_final: 0.7004 (mp0) REVERT: I 67 ARG cc_start: 0.6604 (mtp85) cc_final: 0.6215 (mtm-85) REVERT: I 81 GLN cc_start: 0.8041 (tp-100) cc_final: 0.7323 (tt0) REVERT: J 172 MET cc_start: 0.8050 (ttp) cc_final: 0.7662 (tmm) REVERT: K 157 TYR cc_start: 0.8386 (t80) cc_final: 0.8137 (t80) REVERT: K 289 ASP cc_start: 0.7675 (t0) cc_final: 0.7361 (t0) REVERT: L 161 LYS cc_start: 0.7703 (OUTLIER) cc_final: 0.7399 (ttpp) REVERT: L 524 ILE cc_start: 0.8839 (mp) cc_final: 0.8638 (mp) REVERT: M 17 LEU cc_start: 0.8486 (tp) cc_final: 0.8261 (tp) REVERT: M 190 PHE cc_start: 0.8561 (m-80) cc_final: 0.8275 (m-10) REVERT: M 333 TYR cc_start: 0.8051 (m-80) cc_final: 0.7209 (m-80) REVERT: M 639 MET cc_start: 0.8792 (ttp) cc_final: 0.8586 (ttp) REVERT: M 674 GLU cc_start: 0.6134 (tt0) cc_final: 0.5878 (tt0) REVERT: N 1439 MET cc_start: 0.6473 (ttm) cc_final: 0.6260 (ttp) REVERT: N 1854 LEU cc_start: 0.7934 (mm) cc_final: 0.7616 (mp) REVERT: N 1862 ASP cc_start: 0.7583 (t70) cc_final: 0.7111 (t70) REVERT: N 1896 SER cc_start: 0.7992 (p) cc_final: 0.7385 (m) REVERT: N 1970 SER cc_start: 0.8850 (m) cc_final: 0.8231 (p) REVERT: O 8 LYS cc_start: 0.8338 (mtpt) cc_final: 0.7806 (mtpt) REVERT: O 42 LYS cc_start: 0.7637 (mttt) cc_final: 0.7299 (mttt) REVERT: O 71 GLN cc_start: 0.7079 (mp10) cc_final: 0.6755 (mp10) REVERT: O 104 ASN cc_start: 0.7440 (t0) cc_final: 0.7170 (t0) REVERT: O 202 GLN cc_start: 0.6755 (mt0) cc_final: 0.6524 (mt0) REVERT: Q 1360 LYS cc_start: 0.8115 (tppp) cc_final: 0.7829 (tppt) REVERT: Q 1851 PHE cc_start: 0.8396 (OUTLIER) cc_final: 0.7238 (m-80) REVERT: Q 1872 LYS cc_start: 0.7873 (mmtt) cc_final: 0.7492 (mmmm) REVERT: Q 1903 LYS cc_start: 0.7533 (mttt) cc_final: 0.6970 (mttp) REVERT: Q 1962 ASP cc_start: 0.7735 (t70) cc_final: 0.7297 (t0) REVERT: Q 2032 GLU cc_start: 0.6757 (tt0) cc_final: 0.6300 (mt-10) REVERT: Q 2093 GLU cc_start: 0.7118 (mt-10) cc_final: 0.6558 (tt0) REVERT: a 383 ARG cc_start: 0.8223 (OUTLIER) cc_final: 0.6685 (ptp-170) REVERT: a 747 ARG cc_start: 0.7363 (mtp85) cc_final: 0.7014 (mtp180) REVERT: a 751 LYS cc_start: 0.8003 (mttt) cc_final: 0.7487 (mtmm) REVERT: a 826 SER cc_start: 0.8847 (t) cc_final: 0.8510 (m) REVERT: b 48 TYR cc_start: 0.7972 (t80) cc_final: 0.7701 (t80) REVERT: b 105 GLU cc_start: 0.7473 (mt-10) cc_final: 0.7232 (mt-10) REVERT: b 202 TYR cc_start: 0.8477 (t80) cc_final: 0.7931 (t80) REVERT: c 233 MET cc_start: 0.5494 (mtp) cc_final: 0.5279 (mtp) REVERT: c 272 MET cc_start: 0.8194 (mmp) cc_final: 0.7993 (mmm) REVERT: c 467 LYS cc_start: 0.7654 (mtmt) cc_final: 0.7336 (mtmm) REVERT: c 576 GLN cc_start: 0.8305 (mm-40) cc_final: 0.7976 (mm-40) REVERT: c 587 ARG cc_start: 0.7874 (ttt180) cc_final: 0.7529 (ptm160) REVERT: c 631 ILE cc_start: 0.9098 (mm) cc_final: 0.8775 (mm) REVERT: c 649 MET cc_start: 0.7149 (mtt) cc_final: 0.6875 (mtt) REVERT: c 749 MET cc_start: 0.7281 (mmp) cc_final: 0.7044 (mmp) REVERT: d 239 ASP cc_start: 0.7627 (p0) cc_final: 0.7227 (p0) REVERT: d 358 LEU cc_start: 0.7613 (mp) cc_final: 0.7267 (mp) REVERT: e 187 ARG cc_start: 0.7524 (mmm-85) cc_final: 0.7231 (ttm-80) REVERT: e 281 SER cc_start: 0.9184 (p) cc_final: 0.8961 (p) REVERT: e 350 ARG cc_start: 0.7542 (ttm-80) cc_final: 0.7052 (mtp-110) REVERT: e 755 ILE cc_start: 0.8985 (mm) cc_final: 0.8711 (mt) REVERT: e 829 ASP cc_start: 0.7474 (m-30) cc_final: 0.7092 (m-30) REVERT: f 130 LYS cc_start: 0.8023 (ptmt) cc_final: 0.7734 (ptmm) REVERT: f 338 THR cc_start: 0.8628 (p) cc_final: 0.7421 (m) REVERT: f 504 ASP cc_start: 0.6803 (t0) cc_final: 0.6009 (t0) REVERT: f 593 ARG cc_start: 0.6273 (mtt-85) cc_final: 0.6038 (mtp85) REVERT: f 697 GLN cc_start: 0.6917 (mm110) cc_final: 0.6715 (mm110) outliers start: 315 outliers final: 274 residues processed: 2195 average time/residue: 1.0087 time to fit residues: 3831.5250 Evaluate side-chains 2301 residues out of total 11774 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 290 poor density : 2011 time to evaluate : 9.096 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 186 LEU Chi-restraints excluded: chain 2 residue 226 VAL Chi-restraints excluded: chain 2 residue 241 SER Chi-restraints excluded: chain 2 residue 262 LYS Chi-restraints excluded: chain 2 residue 291 SER Chi-restraints excluded: chain 2 residue 292 GLU Chi-restraints excluded: chain 2 residue 302 THR Chi-restraints excluded: chain 2 residue 383 ARG Chi-restraints excluded: chain 2 residue 424 VAL Chi-restraints excluded: chain 2 residue 473 VAL Chi-restraints excluded: chain 2 residue 499 SER Chi-restraints excluded: chain 2 residue 564 VAL Chi-restraints excluded: chain 2 residue 567 THR Chi-restraints excluded: chain 2 residue 695 LEU Chi-restraints excluded: chain 2 residue 819 SER Chi-restraints excluded: chain 2 residue 860 SER Chi-restraints excluded: chain 3 residue 44 SER Chi-restraints excluded: chain 3 residue 99 SER Chi-restraints excluded: chain 3 residue 105 GLU Chi-restraints excluded: chain 3 residue 112 SER Chi-restraints excluded: chain 3 residue 135 SER Chi-restraints excluded: chain 3 residue 185 ILE Chi-restraints excluded: chain 3 residue 220 THR Chi-restraints excluded: chain 3 residue 242 THR Chi-restraints excluded: chain 3 residue 301 LEU Chi-restraints excluded: chain 3 residue 322 LEU Chi-restraints excluded: chain 3 residue 341 MET Chi-restraints excluded: chain 3 residue 346 ASP Chi-restraints excluded: chain 3 residue 424 ASN Chi-restraints excluded: chain 3 residue 448 THR Chi-restraints excluded: chain 3 residue 484 VAL Chi-restraints excluded: chain 3 residue 486 ILE Chi-restraints excluded: chain 3 residue 505 THR Chi-restraints excluded: chain 3 residue 553 ILE Chi-restraints excluded: chain 3 residue 582 VAL Chi-restraints excluded: chain 3 residue 697 ILE Chi-restraints excluded: chain 3 residue 698 THR Chi-restraints excluded: chain 3 residue 720 THR Chi-restraints excluded: chain 4 residue 198 LEU Chi-restraints excluded: chain 4 residue 292 ASP Chi-restraints excluded: chain 4 residue 355 THR Chi-restraints excluded: chain 4 residue 401 GLU Chi-restraints excluded: chain 4 residue 427 CYS Chi-restraints excluded: chain 4 residue 444 ILE Chi-restraints excluded: chain 4 residue 468 LYS Chi-restraints excluded: chain 4 residue 663 THR Chi-restraints excluded: chain 4 residue 709 LEU Chi-restraints excluded: chain 4 residue 723 HIS Chi-restraints excluded: chain 4 residue 767 LYS Chi-restraints excluded: chain 4 residue 768 THR Chi-restraints excluded: chain 4 residue 802 ILE Chi-restraints excluded: chain 5 residue 85 ASP Chi-restraints excluded: chain 5 residue 190 THR Chi-restraints excluded: chain 5 residue 193 THR Chi-restraints excluded: chain 5 residue 207 LEU Chi-restraints excluded: chain 5 residue 273 ASN Chi-restraints excluded: chain 5 residue 351 GLU Chi-restraints excluded: chain 5 residue 365 LYS Chi-restraints excluded: chain 5 residue 426 LEU Chi-restraints excluded: chain 5 residue 445 SER Chi-restraints excluded: chain 5 residue 453 VAL Chi-restraints excluded: chain 5 residue 493 ILE Chi-restraints excluded: chain 5 residue 608 LEU Chi-restraints excluded: chain 5 residue 636 ASN Chi-restraints excluded: chain 5 residue 675 ARG Chi-restraints excluded: chain 5 residue 727 SER Chi-restraints excluded: chain 6 residue 135 VAL Chi-restraints excluded: chain 6 residue 150 THR Chi-restraints excluded: chain 6 residue 160 MET Chi-restraints excluded: chain 6 residue 276 ILE Chi-restraints excluded: chain 6 residue 293 THR Chi-restraints excluded: chain 6 residue 323 GLN Chi-restraints excluded: chain 6 residue 429 THR Chi-restraints excluded: chain 6 residue 438 THR Chi-restraints excluded: chain 6 residue 449 THR Chi-restraints excluded: chain 6 residue 452 ILE Chi-restraints excluded: chain 6 residue 503 VAL Chi-restraints excluded: chain 6 residue 532 SER Chi-restraints excluded: chain 6 residue 642 ASP Chi-restraints excluded: chain 6 residue 660 THR Chi-restraints excluded: chain 6 residue 676 THR Chi-restraints excluded: chain 6 residue 702 THR Chi-restraints excluded: chain 7 residue 22 THR Chi-restraints excluded: chain 7 residue 220 ILE Chi-restraints excluded: chain 7 residue 225 LEU Chi-restraints excluded: chain 7 residue 372 THR Chi-restraints excluded: chain 7 residue 427 ASP Chi-restraints excluded: chain 7 residue 473 ILE Chi-restraints excluded: chain 7 residue 483 THR Chi-restraints excluded: chain 7 residue 533 ASP Chi-restraints excluded: chain 7 residue 546 ILE Chi-restraints excluded: chain 7 residue 671 SER Chi-restraints excluded: chain C residue 12 ASP Chi-restraints excluded: chain C residue 24 ILE Chi-restraints excluded: chain C residue 164 THR Chi-restraints excluded: chain D residue 98 ILE Chi-restraints excluded: chain D residue 206 LEU Chi-restraints excluded: chain D residue 262 ASP Chi-restraints excluded: chain D residue 269 LEU Chi-restraints excluded: chain E residue 82 LEU Chi-restraints excluded: chain E residue 140 ILE Chi-restraints excluded: chain E residue 161 LYS Chi-restraints excluded: chain E residue 412 THR Chi-restraints excluded: chain E residue 419 ILE Chi-restraints excluded: chain E residue 536 LEU Chi-restraints excluded: chain E residue 576 THR Chi-restraints excluded: chain E residue 607 MET Chi-restraints excluded: chain E residue 636 ASP Chi-restraints excluded: chain E residue 638 SER Chi-restraints excluded: chain E residue 645 THR Chi-restraints excluded: chain E residue 646 LEU Chi-restraints excluded: chain F residue 31 LEU Chi-restraints excluded: chain F residue 86 GLU Chi-restraints excluded: chain F residue 224 LEU Chi-restraints excluded: chain F residue 269 THR Chi-restraints excluded: chain F residue 318 HIS Chi-restraints excluded: chain F residue 326 VAL Chi-restraints excluded: chain F residue 335 VAL Chi-restraints excluded: chain F residue 401 ILE Chi-restraints excluded: chain F residue 439 THR Chi-restraints excluded: chain F residue 468 LEU Chi-restraints excluded: chain F residue 500 SER Chi-restraints excluded: chain F residue 513 THR Chi-restraints excluded: chain F residue 544 ASP Chi-restraints excluded: chain F residue 547 SER Chi-restraints excluded: chain H residue 5 LEU Chi-restraints excluded: chain H residue 43 GLU Chi-restraints excluded: chain H residue 56 GLU Chi-restraints excluded: chain H residue 104 ASN Chi-restraints excluded: chain H residue 129 GLU Chi-restraints excluded: chain H residue 133 GLU Chi-restraints excluded: chain H residue 146 LEU Chi-restraints excluded: chain H residue 164 ASP Chi-restraints excluded: chain H residue 165 VAL Chi-restraints excluded: chain I residue 10 THR Chi-restraints excluded: chain I residue 64 VAL Chi-restraints excluded: chain I residue 133 ASP Chi-restraints excluded: chain I residue 158 LYS Chi-restraints excluded: chain I residue 168 LEU Chi-restraints excluded: chain I residue 177 GLU Chi-restraints excluded: chain J residue 24 ILE Chi-restraints excluded: chain J residue 106 SER Chi-restraints excluded: chain J residue 164 THR Chi-restraints excluded: chain K residue 262 ASP Chi-restraints excluded: chain L residue 59 VAL Chi-restraints excluded: chain L residue 82 LEU Chi-restraints excluded: chain L residue 161 LYS Chi-restraints excluded: chain L residue 234 GLU Chi-restraints excluded: chain L residue 310 VAL Chi-restraints excluded: chain L residue 419 ILE Chi-restraints excluded: chain L residue 537 ASP Chi-restraints excluded: chain L residue 607 MET Chi-restraints excluded: chain L residue 624 ASN Chi-restraints excluded: chain L residue 638 SER Chi-restraints excluded: chain M residue 29 TYR Chi-restraints excluded: chain M residue 31 LEU Chi-restraints excluded: chain M residue 86 GLU Chi-restraints excluded: chain M residue 167 ARG Chi-restraints excluded: chain M residue 188 MET Chi-restraints excluded: chain M residue 299 GLU Chi-restraints excluded: chain M residue 302 SER Chi-restraints excluded: chain M residue 401 ILE Chi-restraints excluded: chain M residue 424 LEU Chi-restraints excluded: chain M residue 435 GLN Chi-restraints excluded: chain M residue 439 THR Chi-restraints excluded: chain M residue 500 SER Chi-restraints excluded: chain M residue 513 THR Chi-restraints excluded: chain M residue 632 LEU Chi-restraints excluded: chain N residue 1324 VAL Chi-restraints excluded: chain N residue 1382 SER Chi-restraints excluded: chain N residue 1415 THR Chi-restraints excluded: chain N residue 1675 LEU Chi-restraints excluded: chain N residue 1736 VAL Chi-restraints excluded: chain N residue 1811 LEU Chi-restraints excluded: chain N residue 1821 GLN Chi-restraints excluded: chain N residue 1851 PHE Chi-restraints excluded: chain N residue 1865 GLN Chi-restraints excluded: chain N residue 1882 SER Chi-restraints excluded: chain N residue 1885 MET Chi-restraints excluded: chain N residue 2093 GLU Chi-restraints excluded: chain N residue 2107 LEU Chi-restraints excluded: chain N residue 2117 ILE Chi-restraints excluded: chain N residue 2173 ASP Chi-restraints excluded: chain O residue 1 MET Chi-restraints excluded: chain O residue 16 THR Chi-restraints excluded: chain O residue 43 GLU Chi-restraints excluded: chain O residue 54 LEU Chi-restraints excluded: chain O residue 56 GLU Chi-restraints excluded: chain O residue 100 MET Chi-restraints excluded: chain O residue 146 LEU Chi-restraints excluded: chain O residue 147 VAL Chi-restraints excluded: chain O residue 164 ASP Chi-restraints excluded: chain P residue 32 THR Chi-restraints excluded: chain P residue 64 VAL Chi-restraints excluded: chain P residue 189 MET Chi-restraints excluded: chain Q residue 1382 SER Chi-restraints excluded: chain Q residue 1415 THR Chi-restraints excluded: chain Q residue 1610 MET Chi-restraints excluded: chain Q residue 1685 ILE Chi-restraints excluded: chain Q residue 1736 VAL Chi-restraints excluded: chain Q residue 1811 LEU Chi-restraints excluded: chain Q residue 1821 GLN Chi-restraints excluded: chain Q residue 1848 VAL Chi-restraints excluded: chain Q residue 1851 PHE Chi-restraints excluded: chain Q residue 1865 GLN Chi-restraints excluded: chain Q residue 2036 VAL Chi-restraints excluded: chain Q residue 2115 SER Chi-restraints excluded: chain Q residue 2173 ASP Chi-restraints excluded: chain Q residue 2194 ILE Chi-restraints excluded: chain a residue 189 VAL Chi-restraints excluded: chain a residue 202 ASN Chi-restraints excluded: chain a residue 226 VAL Chi-restraints excluded: chain a residue 241 SER Chi-restraints excluded: chain a residue 251 GLU Chi-restraints excluded: chain a residue 292 GLU Chi-restraints excluded: chain a residue 383 ARG Chi-restraints excluded: chain a residue 438 LEU Chi-restraints excluded: chain a residue 473 VAL Chi-restraints excluded: chain a residue 536 ASP Chi-restraints excluded: chain a residue 564 VAL Chi-restraints excluded: chain a residue 567 THR Chi-restraints excluded: chain a residue 644 CYS Chi-restraints excluded: chain a residue 819 SER Chi-restraints excluded: chain a residue 860 SER Chi-restraints excluded: chain b residue 44 SER Chi-restraints excluded: chain b residue 91 ILE Chi-restraints excluded: chain b residue 99 SER Chi-restraints excluded: chain b residue 112 SER Chi-restraints excluded: chain b residue 185 ILE Chi-restraints excluded: chain b residue 213 ASP Chi-restraints excluded: chain b residue 220 THR Chi-restraints excluded: chain b residue 240 LYS Chi-restraints excluded: chain b residue 322 LEU Chi-restraints excluded: chain b residue 346 ASP Chi-restraints excluded: chain b residue 384 MET Chi-restraints excluded: chain b residue 424 ASN Chi-restraints excluded: chain b residue 437 SER Chi-restraints excluded: chain b residue 448 THR Chi-restraints excluded: chain b residue 486 ILE Chi-restraints excluded: chain b residue 488 GLU Chi-restraints excluded: chain b residue 494 THR Chi-restraints excluded: chain b residue 682 ASN Chi-restraints excluded: chain b residue 720 THR Chi-restraints excluded: chain c residue 198 LEU Chi-restraints excluded: chain c residue 292 ASP Chi-restraints excluded: chain c residue 355 THR Chi-restraints excluded: chain c residue 360 ILE Chi-restraints excluded: chain c residue 427 CYS Chi-restraints excluded: chain c residue 468 LYS Chi-restraints excluded: chain c residue 663 THR Chi-restraints excluded: chain c residue 723 HIS Chi-restraints excluded: chain c residue 802 ILE Chi-restraints excluded: chain c residue 811 MET Chi-restraints excluded: chain c residue 822 VAL Chi-restraints excluded: chain d residue 85 ASP Chi-restraints excluded: chain d residue 190 THR Chi-restraints excluded: chain d residue 193 THR Chi-restraints excluded: chain d residue 267 VAL Chi-restraints excluded: chain d residue 277 THR Chi-restraints excluded: chain d residue 351 GLU Chi-restraints excluded: chain d residue 391 LEU Chi-restraints excluded: chain d residue 402 ASP Chi-restraints excluded: chain d residue 567 SER Chi-restraints excluded: chain d residue 579 ASN Chi-restraints excluded: chain d residue 608 LEU Chi-restraints excluded: chain d residue 727 SER Chi-restraints excluded: chain e residue 117 GLN Chi-restraints excluded: chain e residue 150 THR Chi-restraints excluded: chain e residue 384 ASP Chi-restraints excluded: chain e residue 438 THR Chi-restraints excluded: chain e residue 532 SER Chi-restraints excluded: chain e residue 576 ASP Chi-restraints excluded: chain e residue 642 ASP Chi-restraints excluded: chain e residue 652 ILE Chi-restraints excluded: chain e residue 701 MET Chi-restraints excluded: chain e residue 831 LEU Chi-restraints excluded: chain f residue 22 THR Chi-restraints excluded: chain f residue 267 TYR Chi-restraints excluded: chain f residue 335 VAL Chi-restraints excluded: chain f residue 473 ILE Chi-restraints excluded: chain f residue 533 ASP Chi-restraints excluded: chain f residue 544 GLN Chi-restraints excluded: chain f residue 546 ILE Chi-restraints excluded: chain f residue 591 LEU Chi-restraints excluded: chain f residue 631 THR Chi-restraints excluded: chain f residue 667 LEU Chi-restraints excluded: chain f residue 671 SER Chi-restraints excluded: chain f residue 683 GLN Chi-restraints excluded: chain f residue 690 LEU Chi-restraints excluded: chain f residue 712 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1310 random chunks: chunk 825 optimal weight: 10.0000 chunk 1107 optimal weight: 20.0000 chunk 318 optimal weight: 6.9990 chunk 958 optimal weight: 1.9990 chunk 153 optimal weight: 0.7980 chunk 288 optimal weight: 9.9990 chunk 1040 optimal weight: 0.9980 chunk 435 optimal weight: 0.9980 chunk 1068 optimal weight: 0.7980 chunk 131 optimal weight: 30.0000 chunk 191 optimal weight: 0.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 3 688 ASN 4 247 ASN 4 757 HIS ** 4 808 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 253 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 139 GLN 6 173 GLN 6 264 GLN E 269 ASN ** F 435 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 39 ASN L 26 GLN L 269 ASN L 382 HIS L 476 ASN ** M 435 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 488 ASN a 658 ASN c 691 ASN e 269 ASN f 209 GLN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3912 r_free = 0.3912 target = 0.185283 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.139784 restraints weight = 126530.795| |-----------------------------------------------------------------------------| r_work (start): 0.3402 rms_B_bonded: 2.21 r_work: 0.3158 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work (final): 0.3158 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7816 moved from start: 0.2541 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.072 109512 Z= 0.156 Angle : 0.558 13.273 148617 Z= 0.287 Chirality : 0.041 0.333 17004 Planarity : 0.004 0.085 18640 Dihedral : 11.497 174.023 15844 Min Nonbonded Distance : 2.043 Molprobity Statistics. All-atom Clashscore : 7.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.80 % Favored : 96.20 % Rotamer: Outliers : 1.81 % Allowed : 17.88 % Favored : 80.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.35 (0.07), residues: 12956 helix: 1.66 (0.07), residues: 5360 sheet: 0.09 (0.12), residues: 2004 loop : -1.15 (0.08), residues: 5592 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP Q1688 HIS 0.011 0.001 HIS Q1434 PHE 0.019 0.001 PHE Q1828 TYR 0.025 0.001 TYR b 211 ARG 0.012 0.000 ARG L 523 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 45099.21 seconds wall clock time: 775 minutes 50.12 seconds (46550.12 seconds total)